10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

____________________________________________________

Form 10-Q

____________________________________________________

x Quarterly Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the quarterly period ended: June 30, 2022 or

o Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the transition period from ____________ to ____________

Commission file number: 001-36066

____________________________________________________

PARATEK PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

____________________________________________________

Delaware	33-0960223
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

____________________________________________________

75 Park Plaza

Boston, MA 02116

(617) 807-6600

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive office)

____________________________________________________

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, par value $0.001 per share	PRTK	The Nasdaq Global Market

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes x No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	x	Smaller reporting company	x
Emerging growth company	o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes o No x

As of July 31, 2022, there were 54,862,502 shares of the registrant's common stock, par value $0.001 per share, outstanding.

TABLE OF CONTENTS

		Page
PART I FINANCIAL INFORMATION
Item 1.	Financial Statements (unaudited)	2
	Condensed Consolidated Balance Sheets as of June 30, 2022 and December 31, 2021	2
	Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2022 and 2021	3
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2022 and 2021	4
	Condensed Consolidated Statements of Shareholders’ Equity (Deficit) for the Six Months Ended June 30, 2022 and 2021	5
	Notes to Unaudited Condensed Consolidated Financial Statements	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	31
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	44
Item 4.	Controls and Procedures	44
PART II OTHER INFORMATION
Item 1.	Legal Proceedings	45
Item 1A.	Risk Factors	45
Item 6.	Exhibits	46
SIGNATURES		48

1

PART I – FINANCIAL INFORMATION

Item 1.    Financial Statements

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(in thousands, except for share and par value amounts)

(unaudited)

	June 30, 2022		December 31, 2021
Assets
Current assets
Cash and cash equivalents	$	39,505	$	80,367
Marketable securities	29,886		15,107
Restricted cash	—		125
Accounts receivable, net	28,521		29,438
Inventories	13,083		11,020
Other receivables	3,297		3,679
Prepaid and other current assets	13,476		12,364
Total current assets	127,768		152,100
Long-term restricted cash	125		125
Fixed assets, net	712		794
Goodwill	829		829
Right-of-use assets	1,352		1,757
Long-term inventories	32,662		27,767
Other long-term assets	247		497
Total assets	$	163,695	$	183,869
Liabilities and Stockholders’ Deficit
Current liabilities
Accounts payable	$	2,257	$	5,394
Accrued expenses	25,661		23,446
Other current liabilities	2,182		2,457
Total current liabilities	30,100		31,297
Long-term debt	257,153		254,428
Long-term lease liabilities	854		1,308
Accrued long-term compensation	22,339		21,846
Other liabilities	2,616		2,777
Total liabilities	$	313,062	$	311,656
Stockholders’ deficit
Preferred stock:
Undesignated preferred stock: $0.001 par value, 5,000,000 shares authorized; no shares issued and outstanding	—		—
Common stock, $0.001 par value; 200,000,000 shares authorized; 54,778,638 shares issued and outstanding as of June 30, 2022; and 200,000,000 shares authorized; 51,711,809 shares issued and outstanding as of December 31, 2021	55		52
Additional paid-in capital	753,223		739,053
Accumulated other comprehensive income	(233)		(9)
Accumulated deficit	(902,412)		(866,883)
Total stockholders’ deficit	(149,367)		(127,787)
Total liabilities and stockholders’ deficit	$	163,695	$	183,869

See accompanying notes to unaudited condensed consolidated financial statements.

2

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations and Comprehensive Loss

(in thousands, except share and per share amounts)

(unaudited)

	Three Months Ended June 30,				Six Months Ended June 30,
	2022		2021		2022		2021
Product revenue, net	$	25,082	$	52,803	$	45,000	$	66,009
Government contract service revenue	1,896		2,113		4,068		3,086
Government contract grant revenue	2,082		2,087		4,182		3,701
Collaboration and royalty revenue	577		489		1,248		1,123
Net revenue	$	29,637	$	57,492	$	54,498	$	73,919
Expenses:
Cost of product revenue	4,878		9,778		8,372		12,529
Research and development	7,592		6,519		15,069		12,057
Selling, general and administrative	30,335		27,106		57,937		49,465
Total operating expenses	42,805		43,403		81,378		74,051
Income (loss) from operations	(13,168)		14,089		(26,880)		(132)
Other income and expenses:
Interest income	133		11		240		36
Interest expense	(4,546)		(4,344)		(9,025)		(8,651)
Other gains (losses), net	(38)		(39)		138		118
Net income (loss)	$	(17,619)	$	9,717	$	(35,527)	$	(8,629)
Other comprehensive income (loss)
Unrealized gain (loss) on available-for-sale securities, net of tax	(53)		—		(224)		(4)
Comprehensive income (loss)	$	(17,672)	$	9,717	$	(35,751)	$	(8,633)
Basic and diluted net loss per common share	$	(0.33)	$	0.20	$	(0.67)	$	(0.18)
Weighted average common stock outstanding
Basic	53,023,350		47,122,717		53,310,091		46,894,812
Diluted	53,023,350		48,945,736		53,310,091		46,894,812

See accompanying notes to unaudited condensed consolidated financial statements.

3

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flows

(in thousands)

(unaudited)

	Six Months Ended June 30,
	2022		2021
Operating activities
Net income (loss)	$	(35,527)	$	(8,629)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization and accretion	275		225
Stock-based compensation expense	6,354		6,602
Noncash interest expense	2,725		672
Changes in operating assets and liabilities
Accounts receivable, other receivables, prepaid, and other current assets	187		(46,618)
Inventories	(6,958)		(4,662)
Operating lease right-of-use asset	404		(95)
Accounts payable and accrued expenses	(923)		(525)
Operating lease liability	(455)		158
Other liabilities and other assets	309		(1,852)
Net cash used in operating activities	(33,609)		(54,724)
Investing activities
Purchase of fixed assets	(36)		(379)
Purchase of marketable securities	(15,160)		—
Proceeds from maturities of marketable securities	—		20,000
Net cash (used) provided by investing activities	(15,196)		19,621
Financing activities
Payment of long-term royalty-backed loan agreement debt issuance costs	—		(397)
Proceeds from sale of common stock, net of costs	7,330		4,645
Proceeds from the employee stock purchase plan and stock options	488		355
Net cash (used) provided by financing activities	7,818		4,603
Net (decrease) increase in cash, cash equivalents and restricted cash	(40,987)		(30,500)
Cash, cash equivalents and restricted cash at beginning of period	80,617		106,048
Cash, cash equivalents and restricted cash at end of period	$	39,630	$	75,548
SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION
Cash paid for interest	$	5,739	$	5,865
SUPPLEMENTAL DISCLOSURES OF NONCASH FINANCING ACTIVITIES
Paid in-kind interest included in accrued expenses	$	2,011	$	1,614

See accompanying notes to unaudited condensed consolidated financial statements.

4

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

(in thousands, except share amounts)

(unaudited)

	Common Stock			Additional Paid-in Capital		Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Total Stockholders’ Deficit
	Shares	Amount
Balances at December 31, 2021	51,711,809	$	52	$	739,053	$	(9)	$	(866,883)	$	(127,787)
Exercise of stock options	729	—		6		—		—		6
Issuance of common stock, net of expenses	884,230	1		3,090		—		—		3,091
Vesting of restricted stock unit awards	426,582	—		—		—		—		—
Employee stock purchase plan expense	—	—		36		—		—		36
Unrealized gain (loss) on available-for-sale securities, net of tax	—	—		—		(171)		—		(171)
Stock-based compensation expense	—	—		2,433		—		—		2,433
Net loss	—	—		—		—		(17,910)		(17,910)
Balances at March 31, 2022	53,023,350	$	53	$	744,618	$	(180)	$	(884,793)	$	(140,302)
Issuance of common stock, net of expenses	1,455,156	2		4,237		—		—		4,239
Employee stock purchase plan expense	—	—		29		—		—		29
Issuance of stock under the employee stock purchase plan	300,132	—		483		—		—		483
Unrealized gain (loss) on available-for-sale securities, net of tax	—	—		—		(53)		—		(53)
Stock-based compensation expense	—	—		3,856		—		—		3,856
Net income	—	—		—		—		(17,619)		(17,619)
Balances at June 30, 2022	54,778,638	$	55	$	753,223	$	(233)	$	(902,412)	$	(149,367)

	Common Stock			Additional Paid-in Capital		Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Total Stockholders’ Deficit
	Shares	Amount
Balances at December 31, 2020	46,516,567	$	46	$	705,489	$	4	$	(807,799)	$	(102,260)
Exercise of stock options	961	—		3		—		—		3
Issuance of common stock, net of expenses	—	—		—		—		—		—
Vesting of restricted stock unit awards	389,700	1		(1)		—		—		—
Employee stock purchase plan expense	—	—		27		—		—		27
Unrealized gain (loss) on available-for-sale securities, net of tax	—	—		—		(4)		—		(4)
Stock-based compensation expense	—	—		1,572		—		—		1,572
Net loss	—	—		—		—		(18,346)		(18,346)
Balances at March 31, 2021	46,907,228	$	47	$	707,090	$	—	$	(826,145)	$	(119,008)
Issuance of common stock, net of expenses	649,022	1		4,644		—		—		4,645
Vesting of restricted stock unit awards	376,301	—		—		—		—		—
Employee stock purchase plan expense	—	—		29		—		—		29
Issuance of stock under the employee stock purchase plan	63,920	—		352		—		—		352
Unrealized gain on available-for-sale securities, net of tax	—	—		—		—		—		—
Stock-based compensation expense	—	—		4,974		—		—		4,974
Net income	—	—		—		—		9,717		9,717
Balances at June 30, 2021	47,996,471	$	48	$	717,089	$	—	$	(816,428)	$	(99,291)

5

Paratek Pharmaceuticals, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

(unaudited)

1.    Description of the business

Paratek Pharmaceuticals, Inc., or the Company or Paratek, is a Delaware corporation with its corporate office in Boston, Massachusetts and an office in King of Prussia, Pennsylvania.

The Company is a commercial-stage biopharmaceutical company focused on the development and commercialization of novel life-saving therapies for life-threatening diseases or other public health threats for civilian, government and military use. The Company’s United States, or U.S., Food and Drug Administration, or FDA, approved commercial product, NUZYRA® (omadacycline), is a once-daily oral and intravenous antibiotic for the treatment of adult patients with community-acquired bacterial pneumonia, or CABP, and acute skin and skin structure infections, or ABSSSI, caused by susceptible pathogens. The Company retains worldwide commercial rights to omadacycline, with the exception of the People’s Republic of China, Hong Kong, Macau and Taiwan, where it has entered into a collaboration agreement with Zai Lab (Shanghai) Co., Ltd., or Zai. The National Medical Products Administration, or NMPA, of China approved NUZYRA for the treatment of CABP and ABSSSI in December 2021.

SEYSARA® (sarecycline) is an FDA-approved product with respect to which the Company has exclusively licensed in the U.S. and the People’s Republic of China, or the PRC, Hong Kong and Macau, or the greater China region, certain rights to Almirall, LLC, or Almirall. SEYSARA is currently being marketed by Almirall in the U.S. as a once-daily oral therapy for the treatment of moderate to severe acne vulgaris. With respect to the Company’s technology as it relates to sarecycline, the Company retains development and commercialization rights in all countries other than the U.S. and the greater China region, and in February 2020, the Company exclusively licensed from Almirall certain technology owned or in-licensed by Almirall or its affiliates that is necessary or useful to develop or commercialize sarecycline outside of the U.S. Almirall plans to develop sarecycline for acne in China, with a submission to the NMPA, according to Almirall, expected in 2023.

The Company has incurred significant losses since inception in 1996. The Company has generated an accumulated deficit of $902.4 million through June 30, 2022 and may require substantial additional funding in connection with the Company’s continuing operations to support clinical development and commercialization activities associated with NUZYRA. Based upon the Company’s current operating plan, it anticipates that its cash, cash equivalents and marketable securities of $69.4 million as of June 30, 2022 will enable the Company to fund operating expenses and capital expenditure requirements through at least the next twelve months from the issuance of the financial statements included in this Quarterly Report on Form 10-Q. The Company expects to finance future cash needs primarily through a combination of product sales, royalties, public or private equity offerings, debt or other structured financings, strategic collaborations, grant funding and government funding. The Company is subject to risks common to companies in the biopharmaceutical industry, including, but not limited to, risks of failure of preclinical studies and clinical trials, the need to obtain additional financing to fund the future development of the Company’s product candidates, the need to obtain compliant product from third-party manufacturers, the need to obtain marketing approval for the Company’s product candidates, the need to successfully commercialize and gain market acceptance of product candidates, the risks of manufacturing product with an external supply chain, dependence on key personnel, and compliance with government regulations as well as the risks discussed in the “Risk Factors” section of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021, as filed with the U.S. Securities and Exchange Commission, or the SEC, on March 14, 2022, or the 2021 Form 10-K, and in the Company’s other filings with the SEC.

2.    Summary of Significant Accounting Policies and Basis of Presentation

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or U.S. GAAP, as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB, and pursuant to the rules and regulations of the SEC.

The accompanying condensed consolidated financial statements are unaudited. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements as

6

of and for the year ended December 31, 2021, and, in the opinion of management, reflect all normal recurring adjustments necessary for the fair presentation of the Company’s financial position as of June 30, 2022 and December 31, 2021, results of operations for the three and six month periods ended June 30, 2022 and June 30, 2021, cash flows for the six month periods ended June 30, 2022 and June 30, 2021 and changes in stockholders’ deficit for the three and six month periods ended June 30, 2022 and June 30, 2021.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2022. These unaudited interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements as of and for the year ended December 31, 2021, and notes thereto, which are included in the Company’s 2021 Form 10-K.

Summary of Significant Accounting Policies

As of June 30, 2022, the Company’s significant accounting policies and estimates, which are detailed in the Company’s 2021 Form 10-K, have not changed.

Principles of Consolidation

The accompanying unaudited condensed consolidated financial statements include the results of operations of Paratek Pharmaceuticals, Inc. and its wholly-owned subsidiaries, Paratek Pharma, LLC, Paratek Securities Corporation, Transcept Pharma, Inc., Paratek Ireland Limited, Paratek Royalty Corporation, Paratek Royalty Corporation II, PRTK SPV1 LLC and PRTK SPV2 LLC. All significant intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of the accompanying unaudited condensed consolidated financial statements, in conformity with U.S. GAAP, requires the Company to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses in the Company’s financial statements. On an ongoing basis, the Company evaluates its estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement (as defined below), manufacturing and clinical accruals, useful lives for depreciation and valuation allowances on deferred tax assets. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known by the Company’s management.

Segment and Geographic Information

Operating segments are defined as components of an enterprise engaging in business activities for which discrete financial information is available and regularly reviewed by the chief operating decision maker in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating segment.

Concentration of Credit Risk

Financial instruments that subject the Company to credit risk consist primarily of cash, restricted cash, and accounts receivable. The Company places its cash in an accredited financial institution and this balance is above federally insured amounts. The Company has no off-balance sheet concentrations of credit risk such as foreign currency exchange contracts, option contracts or other hedging arrangements.

7

Accounts receivable as of June 30, 2022 includes $24.4 million due from customers for sales of NUZYRA, net of prompt payment discounts, chargebacks, rebates and certain fees. Accounts receivable as of June 30, 2022 also includes $1.1 million of government contract service revenue earned under contract with the Biomedical Advanced Research and Development Authority, or the BARDA contract, $1.4 million of government contract grant revenue earned under the BARDA contract, and estimated revenue earned of $0.6 million of royalties on SEYSARA sales under the Almirall Collaboration Agreement (as defined below) and XERAVA TM (eravacycline) sales under the Tetraphase License Agreement (as defined below). Refer to Note 7, Government Contract Revenue for further information on the BARDA contract and to Note 8, License and Collaboration Agreements for further information on the Almirall Collaboration Agreement and the Tetraphase License Agreement.

3.    Marketable Securities

The following are summaries of available-for-sale securities as of June 30, 2022 and December 31, 2021 (in thousands):

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
June 30, 2022
U.S. treasury securities	$	30,119	$	—	$	(233)	$	29,886
Total	$	30,119	$	—	$	(233)	$	29,886

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
December 31, 2021
U.S. treasury securities	$	15,116	$	—	$	(9)	$	15,107
Total	$	15,116	$	—	$	(9)	$	15,107

As of June 30, 2022, the Company had securities with a total fair market value of $29.9 million in an unrealized loss position, of which none were in a continuous unrealized loss position for more than twelve months. The Company believes that any unrealized losses associated with the decline in value of its securities is temporary and primarily related to the change in market interest rates since purchase. Therefore, the Company anticipates a full recovery of the amortized cost basis of its securities at maturity.

Securities are evaluated for impairment at the end of each reporting period. The Company did not record any impairment related to its available-for-sale securities during the three and six months ended June 30, 2022.

4.    Cash and Cash Equivalents and Restricted Cash

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the condensed consolidated statement of cash flows that sum to the total of the same such amounts shown in the condensed consolidated statement of cash flows (in thousands):

	June 30, 2022		June 30, 2021
Cash and cash equivalents	$	39,505	$	75,298
Short-term restricted cash	—		125
Long-term restricted cash	125		125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$	39,630	$	75,548

Short-term restricted cash

The Company leases its Boston, Massachusetts office space under a non-cancelable operating lease. In accordance with the lease, the Company had a cash-collateralized irrevocable standby letter of credit in the amount of $0.3 million at December 31, 2021 naming the landlord as beneficiary. The $0.3 million letter of credit was refunded to the Company in April 2022 under the terms of the original lease agreement. The Company executed an amendment to the existing lease agreement in April 2021. In accordance with the amendment, the cash-collateralized irrevocable standby letter of credit

8

was reduced to an insignificant amount and is reclassified as long-term restricted cash as of June 30, 2022. Refer to Note 14, Leases, for further details.

Long-term restricted cash

As of June 30, 2022 and December 31, 2021, long-term restricted cash included the insignificant cash-collateralized irrevocable standby letter of credit described above.

5.    Inventories

The following table presents inventories, net (in thousands):

	June 30, 2022		December 31, 2021
Raw materials	$	903	$	1,082
Work in process	27,351		24,675
Finished goods	17,491		13,030
Total inventories	$	45,745	$	38,787

When recorded, inventory reserves reduce the carrying value of inventories to their net realizable value. The Company reviews inventories on hand at least quarterly and records provisions for estimated excess, slow-moving and obsolete inventory, as well as inventory with a carrying value in excess of net realizable value. No inventory reserves existed as of June 30, 2022 and December 31, 2021.

6.    Net Income (Loss) Per Share

Basic net loss per share is calculated by dividing the net loss by the weighted-average number of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is computed by dividing the net loss by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method or the if-converted method, as applicable. For purposes of this calculation, shares of common stock issuable upon conversion of convertible debt, stock options, restricted stock units, warrants to purchase common stock, and shares issuable under the employee stock purchase plan are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive.

Common equivalent shares result from stock options and restricted stock units, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the employee stock purchase plan (the proceeds of which are then assumed to have been used to repurchase outstanding stock using the treasury stock method). In addition, the assumed proceeds under the treasury stock method include the average unrecognized compensation expense of stock options that are in-the-money. This results in the “assumed” buyback of additional shares, thereby reducing the dilutive impact of stock options. The two-class method is used for outstanding warrants as it is considered to be a participating security, and it is more dilutive than the treasury stock method.

The Company was in a net loss position as of June 30, 2022. The following outstanding shares subject to stock options and RSUs, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the Company’s employee stock purchase plan were antidilutive due to a net loss in the periods presented and, therefore, were excluded from the dilutive securities computation for the three and six months ended June 30, 2022 as indicated below:

9

	Three and Six Months Ended June 30,
	2022
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361
Shares subject to outstanding options to purchase common stock	2,119,588
Unvested restricted stock units	7,213,532
Shares subject to warrants to purchase common stock	426,866
Shares issuable under employee stock purchase plan	159,738
Totals	20,297,085

(1) The number of shares is based on the maximum number of shares issuable on exercise or conversion of the related securities as of June 30, 2022. Such amounts have not been adjusted for the treasury-stock method or weighted-average outstanding calculations as required if the securities were dilutive.

The Company was in a net income position for the three months ended June 30, 2021 and a net loss position for the six months ended June 30, 2021. The following outstanding shares of common stock equivalents were excluded from the computation of net income (loss) per share attributable to common stockholders for the periods presented because including them would have been antidilutive:

	Three Months Ended June 30, 2021	Six Months Ended June 30, 2021
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361	10,377,361
Shares subject to warrants to purchase common stock	469,388	469,388
Shares subject to outstanding options to purchase common stock	1,057,092	2,103,326
Unvested restricted stock units	—	5,917,615
Shares issuable under employee stock purchase plan	—	542,896
Totals	11,903,841	19,410,586

(1) 2,672,999 performance-based RSUs were excluded from the computation of net income (loss) per share as the performance conditions were not satisfied as of June 30, 2021.

Basic and diluted earnings (loss) per common share were determined as follows:

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	Three Months Ended June 30, 2022		Three Months Ended June 30, 2021		Six Months Ended June 30, 2022		Six Months Ended June 30, 2021
Basic
Net income (loss)	$	(17,619)	$	9,717	$	(35,527)	$	(8,629)
Undistributed earnings allocated to warrants	—		(96)		—		—
Net income (loss)	$	(17,619)	$	9,621	$	(35,527)	$	(8,629)
Weighted average common shares outstanding	53,023,350		47,122,717		53,310,091		46,894,812
Basic earnings (loss) per common share	$	(0.33)	$	0.20	$	(0.67)	$	(0.18)
Diluted
Net income (loss)	$	(17,619)	$	9,717	$	(35,527)	$	(8,629)
Undistributed earnings allocated to warrants	—		(96)				—
Net income (loss)	$	(17,619)	$	9,621	$	(35,527)	$	(8,629)
Weighted average common shares outstanding	53,023,350		47,122,717		53,310,091		46,894,812
Effect of dilutive stock options	—		366,793				—
Effect of dilutive restricted stock units	—		1,456,226
Weighted average common shares outstanding assuming dilution	53,023,350		48,945,736		53,310,091		46,894,812
Diluted earnings (loss) per common share	$	(0.33)	$	0.20	$	(0.67)	$	(0.18)

7.    Government Contract Revenue

Biomedical Advanced Research and Development Authority

In December 2019, the Company entered into the original BARDA contract, which is a five-year contract with an option to extend to ten years. The BARDA contract could result in payments to the Company of up to approximately $303.6 million and consists of a five-year base period-of-performance and a total contract period-of-performance (base period plus option exercises) of up to ten years. The BARDA contract supports the development of NUZYRA for the treatment of pulmonary anthrax, FDA post-marketing requirements, or PMRs, associated with the initial NUZYRA approval, and an option for BARDA to procure up to 10,000 treatment courses of NUZYRA for use against potential biothreats. In September 2021, the Company and BARDA modified the original BARDA contract, herein referred to as the amended BARDA contract, to provide additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support a supplemental New Drug Application, or sNDA, to the FDA to include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax, herein referred to as the amended option.

Under the terms of the original BARDA contract, approximately $59.4 million was awarded to the Company by BARDA in December 2019 for the development of NUZYRA for the treatment of pulmonary anthrax and the purchase of an initial 2,500 treatment courses of NUZYRA. As part of this initial $59.4 million award, a $37.9 million procurement of NUZYRA was delivered to and accepted by BARDA in June 2021, and the amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the second quarter of 2021. The Company has been periodically drawing down the remaining $21.5 million of the initial award based on costs incurred during the development program.

Two additional contractual services under the original BARDA contract were initiated by BARDA in March 2020 that awarded the Company approximately $76.8 million for reimbursement of existing FDA PMRs and approximately $20.4 million for reimbursement of manufacturing-related requirements, which the Company has been drawing down based on costs incurred. This additional staged funding is expected to support all FDA PMRs associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study, and support the U.S. onshoring and security requirements of the Companies manufacturing activities for NUZYRA.

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BARDA initiated the amended option in September 2021 that awarded the Company additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support an sNDA that will include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax for approximately $31.6 million.

The remaining government options under the amended BARDA contract include a maximum of approximately $115.4 million to provide for three additional purchases of NUZYRA anthrax treatment courses, each of which may be exercised at BARDA’s discretion upon achievement of development milestones related to the anthrax treatment development program. The amended BARDA contract formalized the triggers for BARDA’s option to purchase the second NUZYRA procurement upon BARDA's receipt of positive top-line data from our pilot efficacy treatment study of inhalation anthrax in rabbits, which we anticipate will be available as early as the end of 2022. The third procurement will be triggered by BARDA's receipt of positive top-line data in PEP and treatment of inhalation anthrax from a combination of pilot and pivotal efficacy studies in animal models, which the Company anticipates will be available in 2024. The fourth procurement will be triggered by the Company’s receipt of sNDA approval from the FDA for treatment of inhalation anthrax, which is anticipated to follow the third procurement by approximately 18-24 months.

The BARDA contract contains a number of terms and conditions that are customary for government contracts of this nature, including provisions giving the government the right to terminate the contract at any time for its convenience.

The Company evaluated the BARDA contract under ASC, Topic 606, Revenue from Contracts with Customers, or ASC 606, and concluded that a portion of the arrangement represents a transaction with a customer. The Company identified five material promises under the BARDA contract: (i) research and development services performed for the treatment of pulmonary anthrax, (ii) the procurement of 2,500 treatment courses of NUZYRA, (iii) an option for services performed for the supplemental late-stage development of NUZYRA for treatment and prophylaxis of pulmonary anthrax, (iv) an option for services related to U.S. manufacturing onshoring and security requirements, which includes shelf-life stability extension work and regulatory activities that will benefit the manufacturing processes that support NUZYRA for the treatment of pulmonary anthrax, and (v) options to procure up to three tranches of up to 2,500 anthrax treatment courses of NUZYRA each.

In December 2019, the Company determined material promises (i) and (ii) above were performance obligations since they were distinct within the context of the contract as the services are separately identifiable from other promises within the arrangement. The Company also determined that for (i) and (ii) the transaction price included within the BARDA contract was equivalent to the standalone selling price of the services and the cost of the procurement.

The Company evaluated the material promises that contained option rights ((iii), (iv), and (v) above). The Company determined that (iii) and (iv) were not offered at a discount that is incremental to the range of discounts typically given for these goods and services, and therefore do not represent material rights. As such, options for additional services in (iii) and (iv) were not considered performance obligations at the outset of the arrangement. The Company also evaluated the future procurement option rights (v) and determined that those option rights represent a material right. As such, the optional additional NUZYRA procurements in (v) were considered performance obligations at the outset of the arrangement. The Company concluded that three performance obligations existed at the outset of the BARDA contract.

As the BARDA contract is partially within the scope of ASC 606 and partially within the scope of other guidance, the Company applied the guidance of ASC 606 to initially measure the parts of the contract to which ASC 606 is applicable. The total transaction price of the parts of the BARDA contract that existed at the outset of the contract that fall under ASC 606 was determined to be $63.6 million, inclusive of $4.2 million in variable consideration and was allocated to each of the three performance obligations based on the performance obligation’s estimated relative stand-alone selling prices. As of June 30, 2022, the Company reevaluated the variable consideration of $4.2 million that is included in the transaction price and determined that the variable consideration should not be constrained as it is not probable that a significant reversal in the amount of the cumulative revenue recognized will occur in a future period. The transaction price was allocated as follows: $21.5 million to research and development services performed for the treatment of pulmonary anthrax in (i), which will be classified as government contract service revenue when recognized, $37.9 million to the procurement of 2,500 treatment courses of NUZYRA in (ii), which was classified as product revenue when recognized, and a total of $4.2 million to the options to procure up to three 2,500 treatment courses of NUZYRA in (v), which will be included within product revenue when recognized upon exercise and transfer of control of related treatment courses. The Company estimated the stand-alone selling price of the research and development services performed for the treatment of pulmonary anthrax based on the Company’s projected cost of providing the services plus an applicable profit margin commensurate with observable market data for similar services. The Company estimated the stand-alone selling price of

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the procurement of 2,500 treatment courses of NUZYRA based on historical pricing of the Company’s commercial products to similar customers. The Company estimated the stand-alone selling price of the future procurement options based on the discount that the customer would obtain when exercising the option, adjusted for any discount that the customer could receive without entering into the contract, and the likelihood that the option will be exercised.

The Company’s performance obligations are either satisfied over time as work progresses or at a point in time.

The Company concluded that research and development services performed for the treatment of pulmonary anthrax in (i) would be recognized as government contract service revenue over time as the performance obligation is satisfied. Costs incurred represent work performed, which corresponds with, and thereby best depicts, the transfer of control to the customer. Types of contract costs include labor, material, and third-party services.

The product procurement performance obligations ((ii) and, if any optional additional procurements are exercised from (v) above), generate revenue at a point in time, upon transfer of control of the product. As such, the related revenue for these performance obligations is recognized at a point in time as product revenue within the Company’s consolidated statement of operations. As of December 31, 2021, the product procurement performance obligation (ii) was completed and $37.9 million of product revenue was earned and recognized due to the delivery and acceptance of the first procurement under the BARDA contract.

In April 2020, BARDA exercised its option to obtain manufacturing-related services under material promise (iv) and the Company is treating these services as a separate $20.4 million contract for accounting purposes since manufacturing-related services were determined at the contract outset to be optional services that did not represent a material right. The Company’s manufacturing-related services are satisfied over time as work progresses.

In September 2021, BARDA exercised the amended option under the amended BARDA contract, to fund an FDA Animal Rule development program to support an sNDA for the treatment of and the PEP against pulmonary anthrax. The Company is treating these services as a separate $31.6 million contract for accounting purposes since the completion of a late-stage development program was determined at the contract outset to be optional services that did not represent a material right. The additional services added as part of the amended option were distinct and the increased transaction price is reflective of the entity’s standalone selling prices of the additional promised services. The Company’s late-stage development program obligations are satisfied over time as work progresses. Research and development services performed under the amended option will be recognized as government contract service revenue over time as the performance obligation is satisfied.

The Company recognized $4.1 million and $3.1 million of government contract service revenue under the BARDA contract during the six months ended June 30, 2022 and June 30, 2021, respectively. The Company recognized $1.9 million and $2.1 million of government contract service revenue under the BARDA contract during the three months ended June 30, 2022 and June 30, 2021, respectively.

As of June 30, 2022, the aggregate amount of transaction price allocated to remaining performance obligations, excluding unexercised contract options, was $63.7 million. The Company expects to recognize this amount as revenue over the next three to six years.

The Company concluded that BARDA’s reimbursement for existing FDA PMRs associated with the initial NUZYRA approval was not within the scope of ASC 606 as BARDA is not receiving services as the Company’s customer. The Company estimated the consideration to be allocated to government contract grant revenue based on the consideration under the BARDA contract in excess of the estimated standalone selling prices for components of the BARDA contract accounted for under ASC 606. The Company recognizes the allocated consideration for BARDA’s reimbursement of existing FDA PMRs associated with the initial NUZYRA approval of $72.6 million as government contract grant revenue as the related reimbursable expenses are incurred.

The Company recognized $4.2 million and $3.7 million of government contract grant revenue under the BARDA contract during the six months ended June 30, 2022 and June 30, 2021, respectively. The Company recognized $2.1 million and $2.1 million of government contract grant revenue under the BARDA contract during the three months ended June 30, 2022 and June 30, 2021, respectively.

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Contract Balances

Contract assets (i.e., unbilled accounts receivable) and/or contract liabilities (i.e., customer advances and deposits) may exist at the end of each reporting period under the BARDA contract. When amounts are received prior to performance obligations being satisfied, the amounts allocated to those performance obligations are reflected as contract liabilities on the consolidated balance sheets, as deferred revenue, until the performance obligations are satisfied.

As of June 30, 2022, $0.9 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet. As of December 31, 2021, $0.8 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet.

As of June 30, 2022 and December 31, 2021, $1.1 million and $0.8 million, respectively of deferred revenue was recorded and is a component of other current liabilities on the Company’s condensed consolidated balance sheet.

8.    License and Collaboration Agreements

Tetraphase Pharmaceuticals, Inc.

On March 18, 2019, Paratek and Tetraphase Pharmaceuticals, Inc., or Tetraphase, which is now a subsidiary of La Jolla Pharmaceutical Company, entered into a License Agreement, or the Tetraphase License Agreement. Under the terms of the Tetraphase License Agreement, Paratek granted to Tetraphase a non-exclusive, worldwide, royalty-bearing license, with the right to grant sublicenses, under certain Paratek patents, to develop, make, have, use, import, offer for sale and sell the licensed product, or XERAVA, a drug for the treatment of complicated, intra-abdominal infections caused by bacteria that was approved by the FDA in August 2018.

The terms of the Tetraphase License Agreement provide for Tetraphase to pay Paratek royalties at a low single digit percent on net product revenues of the licensed product sold in the U.S. Tetraphase’s obligation to pay royalties with respect to the licensed product shall be retroactive to the date of the first commercial sale of the licensed product in the U.S., which occurred in February 2019. Tetraphase is currently selling XERAVA in the U.S.

The Tetraphase License Agreement will continue until the expiration of and payment by Tetraphase of all its payment obligations, which is when there are no longer any valid claims of the licensed Paratek patents that would be infringed, in the absence of a license, by a manufacture, use, or sales of the licensed product. The principal licensed patent under the Tetraphase License Agreement is expected to expire in October 2023.

In accordance with the Company’s revenue recognition policy, the Company recognized an insignificant amount of royalty revenue during the three and six months ended June 30, 2022 under the Tetraphase License Agreement.

Zai Lab (Shanghai) Co., Ltd.

On April 21, 2017, Paratek Bermuda Ltd., a former wholly-owned subsidiary of Paratek Pharmaceuticals, Inc., and Zai Lab (Shanghai) Co., Ltd., or Zai, entered into a License and Collaboration Agreement, or the Zai Collaboration Agreement. On December 18, 2019 Paratek Bermuda Ltd. assigned its rights under the Agreement to Paratek Pharmaceuticals, Inc. Under the terms of the Zai Collaboration Agreement, Paratek granted Zai an exclusive license to develop, manufacture and commercialize omadacycline, or the licensed product, in the People’s Republic of China, Hong Kong, Macau and Taiwan, or the Zai territory, for all human therapeutic and preventative uses other than biodefense. Zai is responsible for the development, manufacturing and commercialization of the licensed product in the Zai territory, at its sole cost with certain assistance from Paratek.

Under the terms of the Zai Collaboration Agreement, Paratek earned an upfront cash payment of $7.5 million in April 2017, $5.0 million upon approval by the FDA of a NDA submission in the CABP indication in October 2018 and $3.0 million upon submission of the first regulatory approval application for a licensed product in the People’s Republic of China in December 2019, and a $6.0 million milestone payment upon regulatory approval for a licensed product in the People’s Republic of China on December 16, 2021. Paratek is eligible to receive up to $40.5 million in potential future commercial milestone payments. The terms of the Zai Collaboration Agreement also provide for Zai to pay Paratek tiered royalties at a low double digit to mid-teen percent on net sales of the licensed product in the Zai territory.

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The Zai Collaboration Agreement will continue, on a region-by-region basis, until the expiration of and payment by Zai of all Zai’s payment obligations, which is until the later of: (i) the abandonment, expiry or final determination of invalidity of the last valid claim within the Paratek patents that covers the licensed product in the region in the Zai territory in the manner that Zai or its affiliates or sublicensees exploit the licensed product or intend for the licensed product to be exploited; or (ii) 2032, the eleventh anniversary of the first commercial sale of such licensed product in such region.

The Company evaluated the Zai Collaboration Agreement under ASC 606. The Company determined that there were six material promises under the Zai Collaboration Agreement: (i) an exclusive license to develop, manufacture and commercialize omadacycline in the Zai territory, (ii) the initial technology transfer (iii) a transfer of certain materials and materials know-how, (iv) optional manufacturing services, (v) optional regulatory support and (vi) optional commercialization support. The Company determined that the exclusive license and initial technology transfer were not distinct from one another, as the license has limited value without the transfer of the Company’s technology, which will allow Zai to develop the manufacturing process and commercialize omadacycline in the Zai territory in the timeline anticipated under the agreement. Without the technology transfer, Zai would incur additional costs to recreate the Company’s know-how. Therefore, the license and initial technology transfer are combined as a single performance obligation. The transfer of materials is a single distinct performance obligation. The Company evaluated the option rights for manufacturing services, regulatory support and commercialization support to determine whether they represent or include material rights to Zai and concluded that the options were not issued at a discount, and therefore do not represent material rights. As such, they are not considered performance obligations at the outset of the arrangement.

Based on these assessments, the Company determined that two performance obligations existed at the outset of the Zai Collaboration Agreement: (i) the exclusive license combined with the initial technology transfer and (ii) the transfer of certain materials. The Company has recognized $21.5 million in milestone revenue, as described above, under the Zai Collaboration Agreement as of June 30, 2022. As the performance obligation to deliver the license was satisfied in 2017 and research and development services completed by December 2021, all milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. Therefore, the $6.0 million milestone payment upon regulatory approval of NUZYRA in the People’s Republic of China was recognized in December 2021.

There was no deferred revenue as of June 30, 2022 and December 31, 2021 under the Zai Collaboration Agreement.

Almirall, LLC

In July 2007, the Company and Warner Chilcott Company, Inc. (which became a part of Allergan plc, or Allergan), entered into a collaborative research and license agreement under which the Company granted Allergan an exclusive license to research, develop, manufacture and commercialize tetracycline products for use in the U.S. for the treatment of acne and rosacea. In September 2018, Allergan assigned to Almirall its rights under the collaboration agreement, or the Almirall Collaboration Agreement. Since Allergan did not exercise its development option with respect to the treatment of rosacea prior to initiation of a Phase 3 trial for the product, the license grant to Allergan, which was assigned to Almirall, converted to a non-exclusive license for the treatment of rosacea as of December 2014.

Under the terms of the Almirall Collaboration Agreement, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize tetracycline compounds that are specified in the agreement for the treatment of acne. The Company has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compounds in the U.S. for the treatment of acne, and Almirall has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compound included as part of the agreement for any use other than as provided in the Almirall Collaboration Agreement.

In February 2020, the Company finalized a license agreement with Almirall granting the Company exclusive rights to develop, manufacture and commercialize sarecycline outside of the U.S., including rights of reference to Almirall’s clinical data thus formalizing the Company’s rights to develop, manufacture and commercialize sarecycline in the rest of the world. In connection with that license, the Company then exclusively licensed Almirall pursuant to the Almirall China License Agreement, the rights to develop, manufacture and commercialize sarecycline in the greater China region. Almirall currently holds a nonexclusive license to develop and commercialize sarecycline for the treatment of rosacea in the U.S., and in the U.S., Paratek cannot grant rights on back-up compounds, lead candidate(s), or products licensed to Almirall for rosacea.

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The Almirall Collaboration Agreement contains two performance obligations: (i) an exclusive license to research, develop and commercialize tetracycline products for use in the U.S. for the treatment of acne and rosacea and (ii) research and development services. The performance obligation to deliver the license was satisfied upon execution of the Almirall Collaboration Agreement in July 2007. All research and development services were completed by December 2010. The options provided to Almirall for additional development services do not provide Almirall with a material right as these services will not be provided at a significant or incremental discount. As such, the option services are not performance obligations. As the performance obligation to deliver the license was satisfied in 2007 and research and development services were completed by December 2010, all subsequent milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. The Company recognized all Almirall milestones in prior years. There are no milestones left to be recognized under the Almirall Collaboration Agreement.

Almirall is also obligated to pay the Company tiered royalties, ranging from the mid-single digits to the low double digits, based on net sales of tetracycline compounds developed under the Almirall Collaboration Agreement, with a standard royalty reduction post patent expiration for such product for the remainder of the royalty term.

Royalty payments are recognized when the sales occur. During the six months ended June 30, 2022 and June 30, 2021, the Company recognized $0.9 million and $1.0 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. During the three months ended June 30, 2022 and June 30, 2021, the Company recognized $0.4 million and $0.5 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. Royalty revenue recognized for sales of SEYSARA in the U.S. is estimated using third-party data and an approximation of discounts and allowances to calculate net product sales, to which the Company then applies the applicable royalty percentage specified in the Almirall Collaboration Agreement. Differences between actual and estimated royalty revenues are adjusted for in the period in which they become known, which is expected to be the following quarter.

In February 2020, we entered into (i) an ex-U.S. license agreement with Almirall, or the Ex-U.S. License, under which Almirall granted to us an exclusive license in and to certain technology owned or in-licensed by Almirall or its affiliates in order to research, develop, manufacture and commercialize sarecycline for the treatment of acne in all countries other than the U.S. and (ii) a license agreement with Almirall that is specific to China, or the China License, under which we granted to Almirall an exclusive license in and to certain technology owned or in-licensed by us or our affiliates in order to research, develop and commercialize sarecycline for the treatment of acne in the greater China region.

Under the terms of the China License, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize sarecycline for the treatment of acne, including requirements to (i) file an Investigational New Drug Application (or analogous foreign submission) for sarecycline for the treatment of acne in the greater China region in calendar year 2020, (ii) receive regulatory approval for sarecycline for the treatment of acne in the greater China region within seven years following such submission and (iii) commercialize sarecycline for the treatment of acne in the greater China region within eighteen months after obtaining regulatory approval. If Almirall does not satisfy the diligence requirements set forth in subclauses ii or iii above, we may terminate the China License.

In connection with the Ex-U.S. License, the Company pays Almirall, on a country-by-country and product-by-product basis, (i) for eight years following the first commercial sale of a sarecycline product in a country, a royalty in the middle-single digits on its or its affiliates’ nets sales of sarecycline products outside of the U.S., subject to certain standard reductions, and (ii) for fifteen years following the first commercial sale of a sarecycline product in a country, a percentage of the consideration (e.g., milestones, royalties) we receive from sublicensees in connection with developing and commercializing sarecycline outside of the U.S., which ranges from one-fifth to one-half of such consideration, subject to certain standard reductions. In connection with the China License, for fifteen years following the first commercial sale of a sarecycline product in China, Almirall pays the Company a royalty in the high-single digits on their, their affiliates’ or their sublicensees’ net sales of sarecycline products in the greater China region, subject to certain standard reductions.

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Tufts University

In February 1997, the Company and Tufts University, or Tufts, entered into a license agreement under which the Company acquired an exclusive license to certain patent applications and other intellectual property of Tufts related to the drug resistance field to develop and commercialize products for the treatment or prevention of bacterial or microbial diseases or medical conditions in humans or animals or for agriculture. The Company subsequently entered into eleven amendments to that agreement, collectively the Tufts License Agreement, to include patent applications filed after the effective date of the original license agreement, to exclusively license additional technology from Tufts, to expand the field of the agreement to include disinfectant applications, and to change the royalty rate and percentage of sublicense income paid by the Company to Tufts under sublicense agreements with specified sublicensees. The Company is obligated under the Tufts License Agreement to provide Tufts with annual diligence reports and a business plan and to meet certain other diligence milestones. The Company has the right to grant sublicenses of the licensed rights to third parties, which will be subject to the prior approval of Tufts unless the proposed sublicensee meets a certain net worth or market capitalization threshold. The Company is primarily responsible for the preparation, filing, prosecution and maintenance of all patent applications and patents covering the intellectual property licensed under the Tufts License Agreement at its sole expense. The Company has the first right, but not the obligation, to enforce the licensed intellectual property against infringement by third parties.

The Company issued Tufts 1,024 shares of the Company’s common stock on the date of execution of the original license agreement, and the Company was required to make certain payments of up to $0.3 million to Tufts upon the achievement by products developed under the agreement of specified development and regulatory approval milestones. The Company made a payment of $50,000 to Tufts for achieving the first milestone following commencement of the Phase 3 clinical trial for omadacycline and a payment of $100,000 to Tufts for achieving the second milestone following its first marketing application submitted in the U.S. The third, and final, payment of $150,000 became due upon FDA approval of omadacycline in October 2018. The Company is also obligated to pay Tufts a minimum royalty payment in the amount of $25,000 per year. In addition, the Company is obligated to pay Tufts royalties based on gross sales of products, as defined in the agreement, ranging in the low single digits depending on the applicable field of use for such product sale. If the Company enters into a sublicense under the agreement, based on the applicable field of use for such product, the Company will be obligated to pay Tufts (i) a percentage, ranging from 10% to 14% (ten percent to fourteen percent) for compounds other than omadacycline, and a percentage in the single digits for the compound omadacycline, of that portion of any sublicense issue fees or maintenance fees received by the Company that are reasonably attributable to the sublicense of the rights granted to the Company under the Tufts License Agreement and (ii) the lesser of (a) a percentage, ranging from the low tens to the high twenties based on the applicable field of use for such product, of the royalty payments made to the Company by the sublicensee or (b) the amount of royalty payments that would have been paid by the Company to Tufts if it had sold the product.

Unless terminated earlier, the Tufts License Agreement will expire at the same time as the last-to-expire patent in the patent rights licensed to the Company under the agreement and after any such expiration the Company will continue to have an exclusive, fully-paid-up license to such intellectual property licensed from Tufts. Tufts has the right to terminate the agreement upon 30 days’ notice should the Company fail to make a material payment under the Tufts License Agreement or commit a material breach of the agreement and not cure such failure or breach within such 30-day period, or if, after the Company has started to commercialize a product under the Tufts License Agreement, the Company ceases to carry on its business for a period of 90 consecutive days. The Company has the right to terminate the Tufts License Agreement at any time upon 180 days’ notice. Tufts has the right to convert the Company’s exclusive license to a non-exclusive license if the Company does not commercialize a product licensed under the agreement within a specified time period.

During the six months ended June 30, 2022 and June 30, 2021, the Company incurred $0.7 million and $1.0 million of royalty expense, respectively, under the Tufts License Agreement. During the three months ended June 30, 2022 and June 30, 2021, the Company incurred $0.4 million and $0.8 million of royalty expense, respectively, under the Tufts License Agreement.

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Past Collaborations

Novartis International Pharmaceutical Ltd.

In September 2009, the Company and Novartis International Pharmaceutical Ltd., or Novartis, which merged into Novartis Pharma AG, a wholly owned subsidiary of Novartis AG, entered into a Collaborative Development, Manufacture and Commercialization License Agreement, or the Novartis Agreement, which provided Novartis with a global, exclusive patent and technology license for the development, manufacturing and marketing of omadacycline. The Novartis Agreement was terminated by Novartis without cause in June 2011 and the termination was effective 60 days later. The Company and Novartis subsequently entered in a letter agreement in January 2012, or the Novartis Letter Agreement, as amended, pursuant to which we reconciled shared development costs and expenses and granted Novartis a right of first negotiation with respect to commercialization rights of omadacycline following approval of omadacycline from the FDA, European Medicines Agency, or EMA, or any regulatory agency, but only to the extent the Company had not previously granted such commercialization rights related to omadacycline to another third-party as of any such approval. The Company also agreed to pay Novartis a 0.25% royalty, to be paid from net sales received by the Company in any country following the launch of omadacycline in that country and continuing until the later of expiration of the last active valid patent claim covering such product in the country of sale and 10 years from the date of first commercial sale in such country. The first royalty payment became payable as of March 31, 2019. The amended Novartis Letter Agreement resulted in a long-term liability in the amount of $2.6 million and $2.8 million as of June 30, 2022 and December 31, 2021, respectively, included within “Other Liabilities” on the Company’s consolidated balance sheet. In addition, short-term liabilities of $0.4 million included within “Other Current Liabilities” on our consolidated balance sheets as of June 30, 2022 and December 31, 2021 represent the portion of royalty payments due to Novartis within twelve months of each balance sheet date. There are no other payment obligations to Novartis under the Novartis Agreement or the amended Novartis Letter Agreement.

For additional information related to these agreements, as well as the Company’s other significant collaborative agreements, please read Note 6, License and Collaboration Agreements, to the consolidated financial statements included within the Company’s 2021 Form 10-K.

9.    Capital Stock

On June 9, 2021, the Company’s shareholders approved an amendment to the Company’s Amended and Restated Certificate of Incorporation to increase the number of authorized shares of common stock of the Company to 200,000,000 shares from 100,000,000 shares. Subsequent to such approval, on June 10, 2021, the Company filed the Certificate of Amendment to its Amended and Restated Certificate of Incorporation with the Delaware Secretary of State, giving effect to the authorized share increase.

On May 17, 2021, the Company entered into an At-the-Market Sales Agreement, or the Sales Agreement, with BTIG, LLC, or BTIG, under which it may offer and sell its common stock having aggregate sales proceeds of up to $50.0 million from time to time through BTIG as its sales agent. Sales of the Company’s common stock through BTIG, if any, will be made by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415(a)(4) under the Securities Act of 1933, as amended, including without limitation sales made directly on the Nasdaq Global Market or any other existing trading market for its common stock. BTIG will use commercially reasonable efforts to sell the Company’s common stock from time to time, based upon instructions from the Company (including any price, time or size limits or other customary parameters or conditions the Company may impose). The Company will pay BTIG a commission of 3% of the gross sales proceeds of any common stock sold through BTIG under the Sales Agreement. The Company has also provided BTIG with customary indemnification rights.

The Company is not obligated to make any sales of common stock under the Sales Agreement. The offering of shares of the Company’s common stock pursuant to the Sales Agreement will terminate upon the earlier of (i) the sale of all common stock subject to the Sales Agreement, or (ii) termination of the Sales Agreement in accordance with its terms.

The Company sold 2,339 shares of common stock pursuant to the Sales Agreement for $7.3 million in proceeds, after deducting an insignificant amount of commissions, during the six months ended June 30, 2022. As of July 31, 2022, $23.3 million remains available for sale under the Sales Agreement.

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On May 11, 2020, the Company filed a registration statement on Form S-3 with the SEC, as amended on June 19, 2020, and declared effective on July 9, 2020, to sell certain of its securities in an aggregate amount of up to $250.0 million. As of July 31, 2022, $223.3 million remains available on this shelf registration statement, with $23.3 million reserved for potential sales under the Sales Agreement.

10.    Accrued Expenses

Accrued expenses consist of the following (in thousands):

	June 30,		December 31,
	2022		2021
Accrued sales allowances	$	8,771	$	7,012
Accrued compensation	6,180		8,935
Accrued interest	2,389		2,365
Accrued commercial	2,372		1,654
Accrued inventory	2,446		307
Accrued contract research	1,151		1,019
Accrued professional fees	907		781
Accrued manufacturing	714		670
Accrued other	440		361
Accrued legal costs	291		342
Total	$	25,661	$	23,446

11.    Fair Value Measurements

Financial instruments, including cash, cash equivalents, restricted cash, money market funds, U.S. treasury securities, accounts receivable, accounts payable, and accrued expenses are carried on the condensed consolidated financial statements at amounts that approximate fair value. The fair value of the Company’s long-term debt is determined using current applicable rates for similar instruments as of the balance sheet date. The fair value of the Company’s debt (including the Notes as defined in Note 13, Long-Term Debt), is $225.8 million as of June 30, 2022 and $238.3 million as of December 31, 2021. The fair value of the Company’s debt was determined using Level 2 inputs. Fair values are based on assumptions concerning the amount and timing of estimated future cash flows and assumed discount rates, reflecting varying degrees of perceived risk.

The following table presents information about the Company’s financial assets and liabilities that have been measured at fair value as of December 31, 2021 and indicate the fair value hierarchy of the valuation inputs utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities or other inputs that are observable market data. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability (in thousands):

Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		June 30, 2022
Assets:
U.S. treasury securities	$	29,886	$	—	$	—	$	29,886
Total Assets	$	29,886	$	—	$	—	$	29,886

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Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		December 31, 2021
Assets:
U.S. treasury securities	$	15,107	$	—	$	—	$	15,107
Total Assets	$	15,107	$	—	$	—	$	15,107

12.    Stock-Based and Incentive Compensation

Stock-based Compensation

The following table presents stock-based compensation expense included in the Company’s condensed consolidated statements of operations and comprehensive income (loss) (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2022		2021		2022		2021
Research and development expense	$	515	$	793	$	692	$	1,116
Selling, general and administrative expense	3,371		4,210		5,662		5,486
Total stock-based compensation expense	$	3,886	$	5,003	$	6,354	$	6,602

Stock-based compensation expense is estimated as of the grant date based on the fair value of the award and is recognized as expense over the requisite service period, which generally represents the vesting period. The Company estimates the fair value of its stock options using the Black-Scholes option-pricing model. The weighted-average assumptions used to determine the fair value of the stock option grants is as follows:

	Six Months Ended June 30,
	2022		2021
Volatility	62.2	%	63.2	%
Risk-free interest rate	2.3	%	0.7	%
Expected dividend yield	0.0	%	0.0	%
Expected life of options (in years)	5.9		5.9

Stock Plan Activity

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Equity Incentive Plan, or the 2015 Plan, which was approved by Company stockholders at the annual meeting of shareholders held on June 9, 2015. As of June 30, 2022, there are 326,818 shares available for future issuance under the 2015 Plan.

The Company recognizes the stock-based compensation expense of awards subject to performance-based vesting conditions over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance using the accelerated attribution method. A change in the requisite service period that does not change the estimate of the total stock-based compensation expense (i.e., it does not affect the grant-date fair value or quantity of awards to be recognized) is recognized prospectively over the remaining requisite service period.

During the six months ended June 30, 2022, the Company’s Board of Directors granted 103,860 stock options and 2,737,840 RSUs to directors, executives, and employees of the Company under the 2015 Plan. The stock option awards are subject to time-based vesting over a period of one to four years. The RSU awards granted to executives in March 2022 are subject to time-based vesting, with 1/3 of the shares vesting on December 10, 2022, and an additional 1/3 of the shares vesting on the succeeding two anniversaries of such date. The RSU awards granted to non-executive employees of the Company during March 2022 are subject to time-based vesting, with 1/3 of the shares vesting on February 16, 2023, and an additional 1/3 of the shares vesting on the succeeding two anniversaries of such date.

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The March 2022 grants also included performance-based RSU, or PRSU, awards to certain executives and employees of the Company, which will vest as follows: (a) 35/55 on certain net product revenue achievements, (b) 10/55 upon BARDA's purchase of the second NUZYRA procurement, and (c) 10/55 on certain business achievements. Since the Company believes it is probable that milestone (a) and (b) above will be achieved, the Company recognized $0.8 million of stock-based compensation expense for the performance condition during the six months ended June 30, 2022 using the accelerated attribution method.

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Inducement Plan, or the 2015 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 360,000 shares of common stock solely for the grant of inducement stock options to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. The Company has not made any grants under the 2015 Inducement Plan since December 31, 2015. Although the Company does not currently anticipate the issuance of additional grants under the 2015 Inducement Plan, as of June 30, 2022, 341,500 shares remain available for grant under that plan, as well as any shares underlying outstanding stock options that may become available for grant pursuant to the plan’s terms. It is therefore possible that the Company may, based on the business and recruiting needs of the Company, issue additional stock options under the 2015 Inducement Plan.

In June 2017, the Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2017 Inducement Plan, or the 2017 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 550,000 shares of common stock solely for the grant of inducement stock options and RSU awards to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. In October 2018 and March 2022, the Company’s Board of Directors approved the reserve of an additional 500,000 shares and 750,000 shares, respectively, for the 2017 Inducement Plan, for a total of 1,800,000 shares reserved for issuance under it. During the six months ended June 30, 2022, the Company’s Board of Directors granted 83,800 stock options and 223,300 RSUs to employees of the Company under the 2017 Inducement Plan. The stock option awards are subject to time-based vesting over a period of one to four years. The RSU awards are generally subject to time-based vesting, with 100% of the shares of common stock subject to the RSU award vesting three years from the grant date. As of June 30, 2022, 813,604 shares remain available for grant under the 2017 Inducement Plan, as well as any shares underlying awards that may become available for grant pursuant to the plan’s terms.

Stock Options

A summary of stock option activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Exercise Price		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2021	2,051,484	$	10.92	5.12	$	303
Granted	187,660	$	2.94
Exercised	(1,646)	$	3.58
Cancelled or forfeited	(117,910)	$	12.94
Outstanding at June 30, 2022	2,119,588	$	10.10	4.96	$	—
Exercisable at June 30, 2022	1,756,972	$	11.30	4.12	$	—

The total intrinsic value of stock options exercised was insignificant for the six months ended June 30, 2022.

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Restricted Stock Units

A summary of RSU activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Grant Date Fair Value
Unvested balance at December 31, 2021	4,920,063	$	5.82
Granted	2,961,140	3.09
Released	(432,982)	6.13
Forfeited	(234,689)	5.40
Unvested balance at June 30, 2022	7,213,532	$	4.69

Total unrecognized stock-based compensation expense for all stock-based awards was $19.1 million as of June 30, 2022. This amount will be recognized over a weighted-average period of 1.62 years.

2009 Employee Stock Purchase Plan

In June 2009, at the annual meeting of stockholders, the stockholders of the Company approved the 2009 Employee Stock Purchase Plan, or the 2009 ESPP. As of June 30, 2022, 36,539 shares were available for issuance under the 2009 ESPP. Since the merger involving privately-held Paratek Pharmaceuticals, Inc. and Transcept Pharmaceuticals, Inc., the Company has not made the 2009 ESPP available to employees.

2018 Employee Stock Purchase Plan

The Company’s Board of Directors adopted, and in June 2018 Company’s stockholders approved, the Paratek Pharmaceuticals, Inc. 2018 Employee Stock Purchase Plan, or the 2018 ESPP. The 2018 ESPP was amended in October 2018 to change the commencement dates of the offering periods. The maximum aggregate number of shares of the Company’s common stock that may be purchased under the 2018 ESPP is 943,294 shares, or the ESPP Share Pool, subject to adjustment as provided for in the 2018 ESPP. The ESPP Share Pool represented 3% of the total number of shares of our common stock outstanding as of March 31, 2018. The 2018 ESPP allows eligible employees to purchase shares during certain offering periods, which will be 6 -month periods commencing June 1 and ending November 30 and commencing December 1 and ending May 31 of each year. The first offering under the 2018 ESPP was December 1, 2018. As of June 30, 2022, 123,199 shares remained available for issuance under the 2018 ESPP. During the six months ended June 30, 2022, the Company recognized an insignificant amount of stock-based compensation expense related to the 2018 ESPP.

Revenue Performance Incentive Plan

On October 4, 2018, the Company adopted the Revenue Performance Incentive Plan, or the Plan, to grant performance-based cash incentive awards to key employees and consultants of the Company. The Plan provides for an incentive pool of up to $50.0 million, plus accrued interest during the period between the awards’ vesting date and payment dates. Each participant will be allocated a percentage of the incentive pool.

The incentive pool will be divided into two equal tranches with the first tranche vesting upon the Company’s achievement of cumulative net product revenues over $300.0 million by December 31, 2025, or Tranche 1, and the second tranche vesting upon the Company’s achievement of cumulative product revenues over $600.0 million by December 31, 2026, or Tranche 2. Participants will vest annually in each tranche of their awards in four equal installments on December 31, 2019, December 31, 2020, December 31, 2021, and December 31, 2022, subject to their continued employment with the Company through the applicable vesting date. If a participant’s employment terminates prior to December 31, 2022 due to death or disability, the participant will automatically vest in an additional 25% of each tranche of his or her award. Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant who has remained in continuous employment with the Company through December 31, 2022 will be 100% vested in the applicable tranche. In the event of a change of control of the Company prior to December 31, 2026, participants whose employment has terminated prior to such date will be eligible for payouts under the Plan based on the

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then-vested portion of their awards, and participants who have remained employed through the change of control will be deemed to have time vested in full in each tranche of their awards.

Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant’s payout in respect of the applicable tranche of his or her award will equal (a) the participant’s then-vested percentage, multiplied by (b) $25 million, multiplied by (c) the participant’s individual percentage allocation of the incentive pool.

If a change of control occurs prior to December 31, 2026, and the Tranche 1 milestone was not achieved prior to the change of control, the Tranche 1 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 50% and (2) the cumulative product revenues as of the change of control, divided by $300.0 million. If a change of control occurs prior to December 31, 2026, and the Tranche 2 milestone was not achieved prior to the change of control, the Tranche 2 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 30% and (2) the cumulative product revenues as of the change of control, divided by $600.0 million. A participant’s payout in respect of each tranche of his or her award in a change of control will equal (1) the participant’s then-vested percentage of such tranche, multiplied by (2) the percentage of that tranche’s milestone that has been achieved or is deemed to have been achieved, multiplied by (3)$25.0 million, multiplied by (4) the participant’s individual percentage allocation of the incentive pool.

Amounts that become payable upon achievement of the Tranche 1 milestone will be paid in a lump-sum in the first quarter of 2026 and amounts that become payable upon achievement of the Tranche 2 milestone will be paid in a lump-sum in the first quarter of 2027. In the event of a change of control, any portion of the incentive pool that is earned, but unpaid, or deemed earned in connection with the change of control will be paid at the time of the change of control.

If a change of control occurs prior to the achievement of either or both of the Tranche 1 and Tranche 2 milestones, the awards will remain outstanding and the remaining unpaid portion of the incentive pool applicable to the Tranche 1 or Tranche 2 milestone, as applicable, will be paid following the achievement of either such milestone at the time or times the awards would otherwise be paid out. Any successor in interest to the Company upon or following a change of control will be required to assume all obligations under the Plan.

Awards may be paid out in cash or in a combination of cash and registered securities of equal value (based on the Company’s 20-day trailing average closing common stock price), with the portion paid in registered securities not to exceed 50% of the aggregate payment amount with respect to each tranche; provided, however, that any amounts that are immediately payable on closing with respect to an award in connection with a change in control will be paid in cash.

The Company recognizes the compensation cost over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance. The performance condition under the first tranche of the Plan was deemed probable during 2021. $0.5 million of compensation expense was recognized during the six months ended June 30, 2022. No such compensation expense was recognized during the six months ended June 30, 2021. Compensation cost of $22.3 million and $21.8 million is included in accrued long-term compensation in the Company’s consolidated balance sheet as of June 30, 2022 and December 31, 2021, respectively.

13.    Long-Term Debt

R-Bridge Loan Agreement

On December 31, 2020, or the Closing Date, the Company, through its wholly-owned subsidiary PRTK SPV2 LLC, a Delaware limited liability company, or the Subsidiary, entered into a royalty and revenue interest-backed loan agreement, or the R-Bridge Loan Agreement, with an affiliate of R-Bridge Healthcare Investment Advisory, Ltd., or the R-Bridge Lender. Pursuant to the terms of the R-Bridge Loan Agreement, the Subsidiary borrowed a $60.0 million term loan, secured by, and repaid with proceeds from, (i) royalties from the Zai Collaboration Agreement, and such royalties, or the Royalty Interest, and (ii) a revenue interest based on the Company’s U.S. sales of NUZYRA in an initial amount of two and a half percent (2.5%), which amount may adjust under certain circumstances up to five percent (5%), of the Company’s net U.S. sales, subject to an annual cap of $10.0 million, which may adjust under certain circumstances to $12.0 million, or the Revenue Interest.

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Under the R-Bridge Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 7.0%, increasing to an annual rate of 10% during the continuance of any event of default. Payments of the obligations outstanding under the R-Bridge Loan Agreement are made quarterly out of the Royalty Interest payments and Revenue Interest payments received by the Subsidiary during such quarter, or the Collection Amount. On each payment date, after payment of certain expenses, the Collection Amount shall be applied first to accrued interest, with any excess up to $15.0 million per annum applied to repay principal until the balance is fully repaid, and any shortfalls being capitalized and added to the principal balance of the loan. Amounts in excess of the $15.0 million annual cap shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement. Following repayment in full of the loan, the first $15.0 million per annum in Collection Amount shall be paid to the Company and any amounts in excess shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement.

Prior to the eighth (8th) anniversary of the Closing Date, the R-Bridge Loan Agreement will automatically terminate once the Subsidiary has paid to the R-Bridge Lender, in the form of regularly scheduled payments or as a voluntary prepayment, a capped amount of $114.0 million, less principal, interest and certain fee payments through the date of such prepayment, or the Capped Amount. From and after the eighth (8th) anniversary of the Closing Date, the Revenue Interest can be terminated by payment of the Capped Amount, but the Royalty Interest payments shall continue until maturity of the R-Bridge Loan Agreement on December 31, 2032, at which time, the outstanding principal amount of the loan, if any, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash by the Subsidiary.

The Company’s subsidiary, PRTK SPV1 LLC, a Delaware limited liability company and owner of the Subsidiary’s capital stock, has entered into a Pledge and Security Agreement in favor of the R-Bridge Lender, pursuant to which the Subsidiary’s obligations under the R-Bridge Loan Agreement are secured by PRTK SPV1 LLC’s pledge of all of the Subsidiary’s capital stock.

The R-Bridge Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The R-Bridge Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Zai Collaboration Agreement; and permitting any additional liens on the collateral provided to the R-Bridge Lender under the R-Bridge Loan Agreement. As of June 30, 2022, the Company was in compliance with all covenants under the R-Bridge Loan Agreement.

An ancillary agreement executed by the Company and the Subsidiary in respect of the Revenue Interest, contains negative covenants applicable to the Company, including restrictions on the sale or transfer of our assets related to NUZYRA and giving rise to the Revenue Interest, each subject to the exceptions set forth therein.

The R-Bridge Loan Agreement contains customary defined events of default, upon which any outstanding principal, unpaid interest, and other obligations of the Subsidiary, shall be immediately due and payable by the Subsidiary. These include: failure to pay any principal or interest when due; failure to pay the Capped Amount when due following a non-qualified change of control of the Company, any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured breach of our representations, warranties or covenants under an ancillary agreement executed by the Company and the Subsidiary in respect of the Royalty Interest; any termination of the Zai Collaboration Agreement; and certain bankruptcy or insolvency events. No events of default had occurred under the R-Bridge Loan Agreement through June 30, 2022.

The Company raised approximately $58.3 million in net proceeds in connection with the R-Bridge Loan Agreement, comprised of the $60.0 million term loan funded at execution, net of $1.1 million in lender fees accounted for as debt discount and $0.6 million in direct and incremental third-party expenses accounted for as debt issuance costs. The net proceeds of the term loan, together with cash on hand, was used to prepay in full all obligations outstanding under our loan arrangement with Hercules Capital, Inc.

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The accounting for the R-Bridge Loan Agreement requires the Company to make certain estimates and assumptions, particularly about future royalties under the Zai Collaboration Agreement and sales of NUZYRA in the U.S. Such estimates and assumptions are utilized in determining the expected repayment term, amortization period of the debt discount and issuance costs, accretion of interest expense and classification between current and long-term portions of amounts outstanding. The Company amortizes the debt discount and issuance costs to interest expense over the expected term of the arrangement using the interest method based on projected cash flows. Similarly, the Company classifies as current debt for the R-Bridge Loan Agreement, amounts that are expected to be repaid during the succeeding twelve months after the reporting period end. However, the repayment of amounts due under the R-Bridge Loan Agreement is variable because the cash flows to be utilized for periodic payments is a function of amounts received by the Company with respect to the Royalty Interest and the Revenue Interest. Accordingly, the estimates of the magnitude and timing of amounts to be available for debt service are subject to significant variability and thus, subject to significant uncertainty. Therefore, these estimates and assumptions are likely to change, which may result in future adjustments to the portion of the debt that is classified as a current liability, the amortization of debt discount and issuance costs and the accretion of interest expense.

The amount of principal to be repaid in each of the five succeeding years is not fixed and determinable.

Other amounts that may become due and payable under the R-Bridge Loan Agreement, including amounts shared between the parties with respect to cash flows received in excess of pre-defined thresholds, are recognized as additional interest expense when they become probable and estimable.

The following table summarizes the impact of the R-Bridge Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	62,025	$	61,256
Unamortized debt discount and issuance costs	(1,326)		(1,443)
Carrying value	$	60,699	$	59,813

During the six months ended June 30, 2022, $0.8 million of paid-in-kind interest was capitalized and added to the principal balance of the loan, which represents the shortfall between the interest owed and the Collection Amount.

The Company recognized interest expense of $1.1 million and $2.2 million, and an insignificant amount of amortization expense on the debt issuance costs, on the R-Bridge Loan Agreement for the three and six months ended June 30, 2022, respectively.

Convertible Senior Subordinated Notes

On April 18, 2018, the Company entered into a Purchase Agreement, or the Purchase Agreement, with several initial purchasers, or the Initial Purchasers, for whom Merrill Lynch, Pierce, Fenner & Smith Incorporated and Leerink Partners LLC acted as representatives, relating to the sale of $135.0 million aggregate principal amount of 4.75% Convertible Senior Subordinated Notes due 2024, or the Notes, to the Initial Purchasers. The Company also granted the Initial Purchasers an option to purchase up to an additional $25.0 million aggregate principal amount of Notes, which was exercised in full on April 20, 2018.

The Purchase Agreement includes customary representations, warranties and covenants. Under the terms of the Purchase Agreement, the Company agreed to indemnify the Initial Purchasers against certain liabilities.

In addition, J. Wood Capital Advisors LLC, the Company’s financial advisor, purchased $5.0 million aggregate principal amount of Notes in a separate, concurrent private placement on the same terms as other investors.

The Notes were issued by the Company on April 23, 2018, pursuant to an Indenture, dated as of such date, or the Indenture, between the Company and U.S. Bank National Association, as trustee, or the Trustee. The Notes bear cash interest at the annual rate of 4.75%, payable on November 1 and May 1 of each year, beginning on November 1, 2018, and mature on May 1, 2024 unless earlier repurchased, redeemed or converted. The Company will settle conversions of the Notes through delivery of shares of common stock of the Company, in accordance with the terms of the Indenture. The

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initial conversion rate for the Notes is 62.8931 shares of common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the Notes, which is equal to an initial conversion price of approximately $15.90 per share, representing a conversion premium of approximately 20% above the closing price of the common stock of $13.25 per share on April 18, 2018.

Holders of the Notes may convert all or any portion of their Notes, in multiples of $1,000 principal amount, at their option at any time prior to the close of business on the second scheduled trading day immediately preceding the stated maturity date.

The Company may redeem for cash all or part of the Notes, at its option, on or after May 6, 2021, if the last reported sale price of the Company’s common stock has been at least 130% of the conversion price then in effect for at least 20 20 trading days (whether or not consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption at a redemption price equal to 100% of the principal amount of the Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date.

If the Company experiences a fundamental change, as described in the Indenture, prior to the maturity date of the Notes, holders of the Notes will, subject to specified conditions, have the right, at their option, to require the Company to repurchase for cash all or a portion of their Notes at a repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date. In addition, following certain corporate events that occur prior to the maturity date of the Notes and following a notice of redemption of the Notes, the Company will increase the conversion rate for a holder who elects to convert its Notes in connection with such corporate event or redemption.

The Indenture provides for customary events of default. In the case of an event of default with respect to the Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the Notes under the Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes may declare the principal amount of the Notes to be immediately due and payable.

After deducting costs incurred of $6.0 million, the Company raised net proceeds from the issuance of long-term convertible debt of $159.0 million in April 2018. All costs were deferred and are being amortized over the life of the Notes at an effective interest rate of 5.47% and recorded as additional interest expense.

The Company has evaluated the Indenture for derivatives pursuant to ASC 815, Derivatives and Hedging, or ASC 815, and identified an embedded derivative that requires bifurcation as the feature is not clearly and closely related to the host instrument. The embedded derivative is a default provision, which could require additional interest payments. The Company determined in the prior year that the fair value of this embedded derivative was nominal.

The Company evaluated the conversion feature and determined it was not within the scope of ASC 815 and therefore is not required to be accounted for separately. The Company concluded that the embedded conversion option is not subject to separate accounting pursuant to either the cash conversion guidance or the beneficial conversion feature guidance. Under the general conversion guidance in ASC 470, Debt, all of the proceeds received from the Notes was recorded as a liability on the condensed consolidated balance sheet.

The following table summarizes the impact of the Notes on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt	$	165,000	$	165,000
Unamortized debt issuance costs	(2,048)		(2,572)
Carrying value	$	162,952	$	162,428

The Company recognized coupon interest expense of $2.0 million and $3.9 million, and amortization expense on the debt issuance costs of $0.3 million and $0.5 million, on the Notes for the three and six months ended June 30, 2022, respectively.

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Royalty-Backed Loan Agreement

On February 25, 2019, the Company, through its wholly-owned subsidiary Paratek Royalty Corporation, or the Subsidiary, entered into the Royalty-Backed Loan Agreement with HCRP. Pursuant to the terms of the Royalty-Backed Loan Agreement, upon the satisfaction of the conditions precedent set forth therein, the Subsidiary borrowed a $32.5 million loan, which was secured by, and will be repaid based upon, royalties from the Almirall Collaboration Agreement. On May 1, 2019, the Company received $27.8 million, net of $0.5 million lender discount, $0.2 million in lender expenses incurred, and $4.0 million that was deposited into an interest reserve account. The Company also paid $1.2 million in other lender fees related to the Royalty-Backed Loan Agreement.

Under the Royalty-Backed Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 12.0%. Payments of interest under the Royalty-Backed Loan Agreement are made quarterly out of the Almirall Collaboration Agreement royalty payments received since the immediately preceding payment date. On each interest payment date, any royalty payments in excess of accrued interest on the loan will be used to repay the principal of the loan until the balance is fully repaid and any royalty shortfalls will be capitalized and added to the principal balance of the loan. In addition, the Subsidiary made up-front payments to HCRP of (i) a 1.5% fee and (ii) up to $300,000 for HCRP’s expenses. The Royalty-Backed Loan Agreement matures on May 1, 2029, at which time, if not earlier repaid in full, the outstanding principal amount of the loan, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash. The Company has entered into a Pledge and Security Agreement in favor of HCRP, pursuant to which the Subsidiary’s obligations under the Royalty-Backed Loan Agreement are secured by a pledge of all of the Company’s holdings of the Subsidiary’s capital stock.

The Royalty-Backed Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The Royalty-Backed Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Almirall Collaboration Agreement; and permitting any additional liens on the collateral provided to HCRP under the Royalty-Backed Loan Agreement.

The Royalty-Backed Loan Agreement contains customary defined events of default, upon which any outstanding principal and unpaid interest shall be immediately due and payable. These include: failure to pay any principal or interest when due; any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured cross default under a material contract; any uncured breach of the Company’s representations, warranties or covenants under its Contribution and Servicing Agreement with the Subsidiary; any termination of the Almirall Collaboration Agreement; and certain bankruptcy or insolvency events.

The following table summarizes the impact of the Royalty-Backed Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	35,101	$	33,860
Unamortized debt issuance costs	(1,599)		(1,673)
Carrying value	$	33,502	$	32,187

During the six months ended June 30, 2022, $1.2 million of paid-in-kind interest was capitalized and added to the principal balance of the loan, which represents the shortfall between the interest owed, and the Almirall Collaboration Agreement royalty payments received.

The Company recognized interest expense of $1.0 million and $2.0 million and an insignificant amount of amortization expense on the debt issuance costs on the Royalty-Backed Loan Agreement for the three and six months ended June 30, 2022, respectively.

Debt issuance costs are presented on the consolidated balance sheet as a direct deduction from the related debt liability rather than capitalized as an asset in accordance with ASU No. 2015-03, Interest - Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs.

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Long-term debt on the Company’s consolidated balance sheets at June 30, 2022 and December 31, 2021 includes the carrying value of the R-Bridge Loan Agreement, the Notes and the Royalty-Backed Loan Agreement.

14.    Leases

Operating Leases

The Company leases its Boston, Massachusetts and King of Prussia, Pennsylvania office spaces under non-cancelable operating leases expiring in 2023 and 2024, respectively.

The Company executed an amendment to the existing lease agreement on its Boston office space in April 2021. The amended lease agreement released 8,104 rentable square feet of office space and extends the lease term for the remaining 4,153 rentable square feet of office space through August 2023 for an additional commitment of $0.4 million. In accordance with the amendment, the Company will be refunded the insignificant security deposit paid in July 2016.

The Company executed an amended lease agreement on its King of Prussia office space in October 2016. The amended lease agreement is for 19,708 rentable square feet of office space and the Company took control of this office space during the first quarter of 2017. The total lease commitment is over a seven-year and seven-month lease term. The amended lease agreement contains rent escalation and a partial rent abatement period, which is accounted for as rent expense under the straight-line method.

The Company has also identified an embedded lease in its manufacturing and services agreement with CIPAN – Companhia Industrial Produtora de Antibióticos, or CIPAN, which was later amended and restated in April 2018, and further amended and restated in February 2019, December 2019, July 2020, and December 2020. For additional details relating to these agreements, refer to Note 18, Commitments and Contingencies of the 2021 Form 10-K.

The total operating lease liability is presented on the Company’s condensed consolidated balance sheet based on maturity dates. $0.7 million of the total operating leases liabilities is classified under “other current liabilities” for the portion due within twelve months of June 30, 2022, and $0.7 million is classified under “long-term lease liability”.

15.    Income Taxes

The Company recorded no provision for income taxes for the three or six months ended June 30, 2022 and June 30, 2021.

Deferred tax assets and deferred tax liabilities are recognized based on temporary differences between the financial reporting and tax bases of assets and liabilities using statutory rates. Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets, which are comprised principally of net operating loss carryforwards and research and development credits. Under the applicable accounting standards, management has considered the Company’s history of losses and concluded that it is more likely than not that the Company will not recognize the benefits of federal and state deferred tax assets. Accordingly, a full valuation allowance has been established against the Company’s otherwise recognizable net deferred tax assets.

16.    Product Revenue

To date, the Company’s only source of product revenue has been from NUZYRA product sales beginning in February 2019 when NUZYRA was launched in the U.S. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories (in thousands):

	Chargebacks, discounts and fees		Government and other rebates		Returns		Patient assistance		Total
Balance at December 31, 2021	$	1,006	$	5,198	$	469	$	339	$	7,012
Provision related to current period sales	3,472		10,256		595		538		14,861
Adjustment related to prior period sales	(32)		(38)		(373)		—		(443)
Credit or payments made during the period	(3,101)		(8,451)		(624)		(483)		(12,659)
Balance at June 30, 2022	$	1,345	$	6,965	$	67	$	394	$	8,771

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17.    Commitments and Contingencies

In the ordinary course of business, the Company is from time to time involved in lawsuits, claims, investigations, proceedings, and threats of litigation relating to intellectual property, commercial arrangements, employment and other matters. While the outcome of these proceedings and claims cannot be predicted with certainty, as of June 30, 2022, the Company was not party to any legal or arbitration proceedings that may have, or have had in the recent past, significant effects on the Company’s financial position. No governmental proceedings are pending or, to the Company’s knowledge, contemplated against the Company. The Company is not a party to any material proceedings in which any director, member of executive management or affiliate of the Company is either a party adverse to the Company or the Company’s subsidiaries or has a material interest adverse to the Company or the Company’s subsidiaries.

In July 2021, the Company entered into a supply agreement with CARBOGEN AMCIS AG, or Carbogen, that provides for the terms and conditions under which Carbogen will manufacture and supply to the Company the active pharmaceutical ingredient for the Company’s omadacycline product in bulk quantities, or the Carbogen Product. Under this agreement, the Company is responsible for the cost and supply of crude omadacycline that Carbogen requires to manufacture the Carbogen Product and perform related services. The Company is obligated to initially pay Carbogen an amount in the high six-digit U.S. dollar range per batch of Carbogen Product that the Company orders, and the price may be adjusted in accordance with the terms of the agreement. The Company may also request that Carbogen perform certain services related to the Carbogen Product, for which the Company will pay reasonable compensation to Carbogen.

The agreement will remain in effect for a fixed initial term. If neither party has provided notice of its intent to terminate the agreement prior to the end of the initial term, then the Agreement will automatically be extended for a fixed period of time. The agreement may be terminated under certain circumstances, including by either party delivering notice of termination following the initial term, or by either party due to a material uncured breach by the other party or the other party’s insolvency.

In November 2016, the Company entered into a manufacturing and services agreement, or MSA, with CIPAN, which was later amended and restated in April 2018, and further amended in February 2019, December 2019, July 2020, December 2020, and January 2022, collectively, the CIPAN Agreements. The CIPAN Agreements provide the terms and conditions under which CIPAN will manufacture and supply to the Company increased quantities of minocycline starting material and crude omadacycline, or the CIPAN Products, for purification into omadacycline and, subsequently, for use in the Company’s products that contain omadacycline tosylate as the active pharmaceutical ingredient.

Additionally, the CIPAN Agreements included an investment by the Company in a new facility area to increase the manufacturing capacity for production of crude omadacycline. The Company was required to make advance payments to CIPAN upon completion of certain milestones within the CIPAN Agreements.

The term of the CIPAN Agreements will continue throughout the term that the Company receives benefit from the new facility area. The Company may renew the CIPAN Agreements for additional periods and can terminate the CIPAN Agreements at any time by delivery, within a certain time period, of prior written notice to CIPAN. Following the first renewal term, CIPAN may terminate the MSA in its entirety by delivery, within a certain time period, of prior written notice to the Company.

Under the CIPAN Agreements, the Company will purchase product in batches from CIPAN in quantities to be set forth on purchase orders submitted to CIPAN, within a certain time period, prior to the requested date of delivery. The Company will provide CIPAN with a rolling forecast with a best estimate of the quantities that will be ordered each month. Upon execution of the CIPAN Agreements, the Company determined that the CIPAN Agreements contain an embedded lease because the Company has the right to direct the use of the facility and related equipment therein. Further, the Company determined that it did not control the facility or related equipment during construction and, thus, the lease did not fall in the scope of “build-to-suit” accounting. The lease commenced during the fourth quarter of 2020, the point at which the new facility area and the related equipment was available for use by the Company.

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18.    Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption.

In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, or ASU 2016-13. The FASB subsequently issued amendments to ASU 2016-13, which have the same effective date and transition date of January 1, 2023. These standards require that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, these standards now require allowances to be recorded instead of reducing the amortized cost of the investment. These standards limit the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases. Based on the composition of our investment portfolio, accounts receivable and other financial assets, current market conditions and historical credit loss activity, the adoption of these standards is not expected to have a material effect on the Company’s consolidated balance sheet, consolidated statements of operation and comprehensive loss and related disclosures.

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Item 2.    Management’s Discussion and Analysis of Financial Condition and Results of Operations

You should read the following discussion and analysis of our financial condition and results of operations in conjunction with our unaudited condensed consolidated financial statements and related notes included in Part I, Item 1 of this Quarterly Report on Form 10-Q. All references to “Paratek,” “we,” “us,” “our” or the “Company” in this Quarterly Report on Form 10-Q mean Paratek Pharmaceuticals, Inc. and our subsidiaries.

This discussion contains certain forward-looking statements that involve risks and uncertainties. We make such forward-looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. Forward-looking statements are identified by words such as “believe,” “will,” “may,” “estimate,” “continue,” “anticipate,” “intend,” “should,” “plan,” “expect,” “predict,” “could,” “potential,” “potentially” or the negative of these terms or similar expressions. You should read these statements carefully because they discuss future expectations, contain projections of future results of operations or financial condition, or state other “forward- looking” information. These statements relate to our future plans, objectives, expectations, intentions and financial performance and the assumptions that underlie these statements. These forward-looking statements are subject to certain risks and uncertainties that could cause actual results to differ materially from those anticipated in the forward-looking statements. Factors that might cause such a difference include, but are not limited to, those discussed in the “Risk Factors” section of our Annual Report on Form 10-K for the year ended December 31, 2021, as filed with the U.S. Securities and Exchange Commission, or the SEC, on March 14, 2022, or the 2021 Form 10-K. Forward-looking statements are based on our management’s beliefs and assumptions and on information currently available to our management. These statements, like all statements in this report, speak only as of their date, and except as required by law, we undertake no obligation to update or revise these statements in light of future developments. We caution investors that our business and financial performance are subject to substantial risks and uncertainties.

Company Overview

We are a commercial-stage biopharmaceutical company focused on the development and commercialization of novel life-saving therapies for life-threatening diseases or other public health threats for civilian, government and military use. Our United States, or U.S., Food and Drug Administration, or FDA, approved commercial product, NUZYRA® (omadacycline) is a once-daily oral and intravenous antibiotic for the treatment of adult patients with community-acquired bacterial pneumonia, or CABP, and acute skin and skin structure infections, or ABSSSI, caused by susceptible pathogens. We retain worldwide commercial rights to omadacycline, with the exception in the People’s Republic of China, Hong Kong, Macau and Taiwan, where we have entered into a collaboration agreement with Zai Lab (Shanghai) Co., Ltd., or Zai. The National Medical Products Administration, or NMPA, of China approved NUZYRA for the treatment of CABP and ABSSSI in December 2021. 

SEYSARA® (sarecycline) is an FDA-approved product with respect to which we have exclusively licensed in the U.S. and the People’s Republic of China, Hong Kong and Macau, or the greater China region, certain rights to Almirall, LLC, or Almirall. SEYSARA is currently being marketed by Almirall in the U.S. as a once-daily oral therapy for the treatment of moderate to severe acne vulgaris. With respect to our technology as it relates to sarecycline, we retain development and commercialization rights in all countries other than the U.S. and the greater China region, and in February 2020, we exclusively licensed from Almirall certain technology owned or in-licensed by Almirall or its affiliates that is necessary or useful to develop or commercialize sarecycline outside of the U.S. Almirall plans to develop sarecycline for acne in China, with a submission to the China National Medical Products Administration, or NMPA, according to Almirall, expected in 2023.

We believe that NUZYRA has the potential to become the primary choice of physicians for use as a once-daily broad-spectrum monotherapy oral and IV antibiotic for ABSSSI, CABP and other serious community-acquired bacterial infections where resistance is of concern. NUZYRA is used in the emergency room, hospital, and community care settings. We have designed NUZYRA to provide potential advantages over existing antibiotics, including activity against resistant bacteria, broad-spectrum antibacterial activity, oral and IV formulations with once-daily dosing, no dosing adjustments for patients on concomitant medications and a generally safe and well-tolerated profile. NUZYRA also has the potential to be used as a once-daily oral and IV antibiotic for the treatment of NTM and pulmonary anthrax, where it could be suitable for both the treatment and post-exposure prophylaxis as a priority medical countermeasure.

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In December 2019, we entered into the original BARDA contract, which is a five-year contract with an option to extend to ten years. The BARDA contract could result in payments to the Company of up to approximately $303.6 million and consists of a five-year base period-of-performance and a total contract period-of-performance (base period plus option exercises) of up to ten years. The original BARDA contract supports the development of NUZYRA for the treatment of pulmonary anthrax, FDA post-marketing requirements, or PMRs, associated with the initial NUZYRA approval, and an option for BARDA to procure up to 10,000 treatment courses of NUZYRA for use against potential biothreats. In September 2021, we and BARDA modified the original BARDA contract, herein referred to as the amended BARDA contract, to provide additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support a supplemental New Drug Application, or sNDA, to the FDA to include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax, herein referred to as the amended option.

Under the terms of the original BARDA contract, approximately $59.4 million was awarded to us by BARDA in December 2019 for the development of NUZYRA for the treatment of pulmonary anthrax and the purchase of an initial 2,500 treatment courses of NUZYRA. As part of this initial $59.4 million award, the $37.9 million procurement of NUZYRA was delivered to and accepted by BARDA in June 2021, and the amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the second quarter of 2021. The Company has been periodically invoicing against the remaining $21.5 million of the initial award based on costs incurred during the development program.

Two additional contractual services under the original BARDA contract were initiated by BARDA in March 2020 that awarded us approximately $76.8 million for reimbursement of existing FDA Post-Marketing Requirements, PMRs, and approximately $20.4 million for reimbursement of manufacturing-related requirements, which the Company has been invoicing against based on costs incurred. This additional funding is projected to support all FDA PMRs associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study, and support the U.S. onshoring and security requirements of our manufacturing activities for NUZYRA.

BARDA initiated the amended option in September 2021 that awarded us additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support an sNDA that will include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax for approximately $31.6 million.

The remaining contractual options under the original and amended BARDA contract include a maximum of approximately $115.4 million to provide for three additional purchases of NUZYRA anthrax treatment courses, each of which will be exercised at BARDA’s discretion upon achievement of development milestones related to the anthrax treatment development program. The amended BARDA contract formalized the triggers for BARDA’s option to purchase the second NUZYRA procurement upon BARDA's receipt of positive top-line data from our pilot efficacy treatment study of inhalation anthrax in rabbits, which we anticipate will be available as early as the end of 2022. The third procurement will be triggered by BARDA's receipt of positive top-line data in PEP and treatment of inhalation anthrax from a combination of pilot and pivotal efficacy studies in animal models, which the Company anticipates will be available in 2024. The fourth procurement will be triggered by the Company’s receipt of sNDA approval from the FDA for treatment of inhalation anthrax, which is anticipated to follow the third procurement by approximately 18 to 24 months.

We have made significant progress in the pulmonary anthrax development program under the amended BARDA contract. Several omadacycline PK studies have been completed in rabbits and in non-human primates to derive the doses to be tested in upcoming pilot OMC efficacy (dose range finding) studies for the treatment of inhalation anthrax. The first oral omadacycline PK study in non-human primates was also completed marking the initiation of the development program for the post exposure prophylaxis indication. In addition, we have evaluated minimum inhibitory concentrations, or MICs, of omadacycline against more than 130 anthrax strains. Omadacycline continued to demonstrate potent MICs and is considered effective against all anthrax isolates that were tested. The collection of isolates included a strain resistant to doxycycline and a strain resistant to ciprofloxacin. Omadacycline activity was not impacted by either of these resistant strains.

Together with BARDA, we also continue to advance our efforts to onshore the manufacturing of NUZYRA to the U.S. We have completed the knowledge transfer and development stage of our manufacturing process for the active pharmaceutical ingredient, or API, of omadacycline to our U.S. onshoring partners and are currently in the engineering stage of the initiative. We have completed knowledge transfer and the initiation of the process development work for production of vials. Our goal is to have U.S. based commercial supply production of tablets by the end of 2022.

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Additionally, NUZYRA was added to the Center for Disease Control and Prevention's updated report, "Antimicrobial Treatment and Prophylaxis of Plague: Recommendations for Naturally Acquired Infections and Bioterrorism Response" in July 2021. NUZYRA was added as an alternative agent for the treatment, pre-exposure prophylaxis, and postexposure prophylaxis of primary bubonic and pharyngeal plague infections in adults 18 years of age and over.

We also continue to pursue a number of other life-cycle opportunities for NUZYRA. In May 2021, the FDA approved our supplemental new drug application, or sNDA, for the oral-only loading dose regimen for patients diagnosed with CABP, based upon the results of a study that demonstrated an oral-only loading dose regimen has a comparable PK profile to the approved IV loading dose regimen in patients with CABP that was established in the Phase 3 CABP registration study.

We have discussed trial designs and potential registration pathways with the FDA to determine the efficacy and safety of omadacycline in patients afflicted with non-tuberculous mycobacteria abscessus, or NTM abscessus, which are environmental organisms that can be found in soil, dust, and water, including natural and municipal water sources. Infection occurs when a person is exposed to NTM organisms. NTM abscessus can form difficult-to-eliminate biofilms, which are collections of microorganisms that stick to each other, and adhere to surfaces in moist environments. Although severe infection can affect the lymph nodes, skin, soft tissues, bones, and joints, the vast majority of NTM abscessus infection cases are pulmonary. The diagnosis of NTM abscessus infection is often delayed due to the constellation of non-specific symptoms and a lack of disease state awareness by clinicians.

NTM abscessus is a rare and orphan disease with no FDA-approved therapies, which we estimate has a potential $1.0 billion addressable market in the U.S. This opportunity has broadened based upon the demonstration of potent in vitro activity in a dynamic hollow fiber model of NUZYRA against mycobacterium avium complex, or MAC, a significantly larger segment of NTM pulmonary disease. In August 2021, FDA granted orphan drug designation for NUZYRA for the treatment of infections caused by NTM. This orphan drug designation includes NTM pulmonary disease caused by both NTM abscessus as well as MAC.

To date, we have devoted a substantial amount of our resources to research and development efforts, including conducting clinical trials for omadacycline, protecting our intellectual property and providing selling, general and administrative support for these operations. We began generating revenue from product sales in February 2019; as such, we have historically financed our operations primarily through sales of our common stock, debt financings, strategic collaborations, and grant funding.

We have incurred significant losses since our inception in 1996. Our accumulated deficit at June 30, 2022 was $902.4 million and our net loss for the six months ended June 30, 2022 was $17.6 million. A substantial amount of our net losses resulted from costs incurred in connection with our research and development programs and selling, general and administrative costs associated with our operations. The net losses and negative operating cash flows incurred to date, together with expected future losses, have had, and likely will continue to have, an adverse effect on our stockholders’ deficit and working capital. The amount of future net losses will depend, in part, on the rate of future growth of our expenses and our ability to generate offsetting revenue. We expect to continue to incur significant expenses and operating losses for the next several years.

While our BARDA contract is expected to significantly strengthen our cash position, unless we can generate a sufficient amount of revenue from our commercial products, we may need to raise additional capital in order to support and accelerate the commercialization of omadacycline and to advance the development of our other indications for omadacycline, such as NTM, or other product candidates. If we cannot generate a sufficient amount of product or royalty revenue to finance our cash requirements, we expect to finance our future cash needs primarily through a combination of public or private equity offerings, debt or other structured financings, strategic collaborations, grant funding and government funding. We may be unable to raise capital when needed or on attractive terms, which would force us to delay, limit, reduce or terminate our development programs or commercialization efforts. We will need to generate significant revenue to achieve and sustain profitability, and we may never be able to do so.

Business Update Regarding COVID-19

The COVID-19 pandemic continues to present a substantial public health and economic challenge around the world and is continuing to affect our employees, health care institutions, patients, communities and business operations, as well as the U.S. economy and financial markets. The COVID-19 related restrictions on in-person promotional access to health care

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institutions and the overall impact of COVID-19 restrictions on the health care and hospital environments continue to ebb and flow and could limit the full potential of NUZYRA’s growth. The length of time and full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations and financial condition will depend on future developments that are highly uncertain and cannot be accurately predicted, including the duration, spread and severity of the outbreak, new information that may emerge concerning COVID-19, any resurgence of COVID-19 cases, including as a result of variant strains of the underlying virus, the actions taken to contain the virus or treat its impact, the availability and efficacy of vaccines against COVID-19 and the economic impact on local, regional, national and international markets.

To date, we and our partners have been able to continue to supply our products to our patients worldwide and currently do not anticipate any interruptions in supply for the foreseeable future. We continue to assess the potential impact of the COVID-19 pandemic on our three on-going clinical studies, our BARDA anthrax development program, as well as on our business and operations, including our sales, expenses, supply chain and other clinical studies. Our office-based employees have been permitted to work from home since early March 2020 and have now adopted a hybrid approach with in-person business meetings and collaboration. Our customer-facing personnel are operating through a hybrid model of both virtual and in-person engagement in a manner compliant with guidance issued by the Centers for Disease Control and Prevention and other state and local mandates, with in-person engagement increasing during severe periods of the pandemic in the U.S.

Our third-party contract manufacturing partners continue to operate their manufacturing facilities at or near normal levels. While we currently do not anticipate any interruptions in our supply chain, it is possible that the COVID-19 pandemic and response efforts may have an impact in the future on our and/or our third-party suppliers’ and contract manufacturing partners' ability to manufacture our products or the products of our partners. During the first half of the year, our technical service, quality assurance and collaboration teams began to travel for the first time in the pandemic to our third party contract manufacturing partners in Europe, after being largely prevented during the COVID-19 pandemic.

Business Update Regarding Geo-Political Events

Russia’s invasion of Ukraine has caused us to suspend enrollment in both countries for a post-marketing required clinical study for adult patients with CABP. The cost of this trial is being reimbursed under our BARDA contract. Identification and preparation of alternative countries and sites is ongoing and will delay the study completion and could result in significant additional costs.

Additionally, Russia’s invasion of Ukraine has affected manufacturing and supply chains abroad. Although we have not been materially impacted by these disruptions to date, it could impact our ability to timely obtain materials, supplies or medical equipment to conduct our research and development or manufacturing work.

For additional information on the various risks posed by the COVID-19 pandemic and geo-political events, refer to Item 3. Quantitative and Qualitative Disclosures About Market Risk and Item 1A. Risk Factors included in the 2021 Form 10-K.

Financial Operations Overview

Product Revenue, Net

Product revenue, net, is recognized when earned on sales of NUZYRA, which was approved by the FDA in October 2018 and launched in the U.S. in February 2019. NUZYRA is sold principally to a limited number of specialty distributors and specialty pharmacy providers in the U.S. These customers subsequently resell our product to health care providers or dispense the product to patients. In addition to distribution agreements with customers, we enter into arrangements with health care providers and payers that provide for government mandated and/or privately negotiated rebates, chargebacks and discounts with respect to the purchase of our product. Product revenue is recognized net of reserves for all variable consideration, including rebates, chargebacks, discounts and product returns.

Under the terms of the BARDA contract, BARDA can procure up to 10,000 anthrax treatment courses of NUZYRA. As of June 30, 2022, an initial 2,500 treatment courses of NUZYRA were purchased by BARDA. The product procurement performance obligations generate revenue at a point in time, which is upon transfer of control of the product. As such, the related revenue for these performance obligations is recognized at a point in time as product revenue within our consolidated statement of operations. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

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Government Contract Service Revenue

Government contract service revenue is recognized when earned under our BARDA contract and represents the reimbursement by BARDA of costs incurred by us for work performed to develop NUZYRA for the treatment of pulmonary anthrax and for the U.S. onshoring of NUZYRA manufacturing plus a small fixed administrative fee. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

Government Contract Grant Revenue

The allocated consideration of government contract grant revenue is recognized when earned under our BARDA contract and represents the reimbursement by BARDA of costs incurred by us for FDA post-marketing requirements, or PMRs, associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

Collaboration and Royalty Revenue

Collaboration and royalty revenue are recognized when revenue earned under our collaboration and license agreements. Refer to Note 8, License and Collaboration Agreements to the interim condensed consolidated financial statements included in this report for further discussion of the collaboration agreements and the related revenue recognition.

Cost of Product Revenue

Cost of product revenue represents the cost of the product itself, labor and overhead, and any reserve for excess or obsolete inventory, as well as stability studies, and inventory scrap. Cost of product revenue also represents royalties owed on net sales of NUZYRA.

Research and Development Expense

Research and development expenses consisted primarily of costs directly incurred by us for the development of our product candidates, which include:

•expenses incurred under agreements with clinical research organizations, or CROs, and investigative sites that conduct our clinical trials;

•the cost of acquiring and manufacturing preclinical and clinical study materials and developing manufacturing processes;

•direct employee-related expenses, including salaries, benefits, travel and stock-based compensation expense of our research and development personnel;

•allocated facilities, depreciation, and other expenses, which include rent and maintenance of facilities, insurance and other supplies; and

•costs associated with preclinical activities and regulatory compliance.

Research and development expenses also include gross reimbursable costs incurred related to research and development services performed for the treatment of pulmonary anthrax, services performed for U.S. manufacturing onshoring and security requirements, and services performed for FDA PMRs under the BARDA contract.

Research and development costs are expensed as incurred. Costs for certain development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and our clinical sites.

We cannot determine with certainty the duration and completion costs of the current or future clinical trials of our product candidates or if, when, or to what extent we will generate revenues from the commercialization and sale of any of

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our products or product candidates for which we or any partner obtain regulatory approval, such as NUZYRA and SEYSARA. Aside from the FDA approval of NUZYRA and SEYSARA in the U.S., we or our partners may never succeed in achieving regulatory approval for any of our other product candidates. The duration, costs and timing of clinical trials and development of our product candidates depend on a variety of factors, including:

•the scope, rate of progress, and expense of our ongoing, as well as any additional, clinical trials and other research and development activities;

•future clinical trial results;

•potential changes in government regulation; and

•the timing and receipt of any regulatory approvals.

A change in the outcome of any of these variables with respect to the development of a product candidate could mean a significant change in the costs and timing associated with the development of that therapeutic candidate. For example, if the FDA, or another regulatory authority, were to require us to conduct clinical trials beyond those that we currently anticipate will be required for the completion of the clinical development of product candidates, or if we experience significant delays in the enrollment in any clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

We manage certain activities, such as clinical trial operations, manufacture of clinical trial material, and preclinical animal toxicology studies, through third-party contract organizations. The only costs we track by each product candidate are external costs such as services provided to us by CROs, manufacturing of preclinical and clinical drug product, and other outsourced research and development expenses. We do not assign or allocate to individual development programs internal costs such as salaries and benefits, facilities costs, lab supplies and the costs of preclinical research and studies. Our research and development expenses for omadacycline and other projects during the three and six months ended June 30, 2022 and 2021 are as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(in thousands)	2022		2021		2022		2021
Omadacycline costs	$	4,986	$	4,100	$	10,067	$	6,973
Other research and development costs	2,606		2,419		5,002		5,084
Total	$	7,592	$	6,519	$	15,069	$	12,057

Selling, General and Administrative Expense

Selling, general and administrative expenses consist principally of compensation costs for our sales force, commercial support personnel, and medical affairs professionals, as well as personnel in executive and other administrative functions. Other selling, general and administrative expenses include marketing, trade, and other commercial costs and distribution fees for the sale of NUZYRA and professional fees for legal, consulting and accounting services.

Interest Income

Interest income represents interest earned on our money market funds and marketable securities.

Interest Expense

Interest expense represents interest incurred on the R-Bridge Loan Agreement, the Notes, and the Royalty-Backed Loan Agreement (each as defined in Note 13, Long-Term Debt to the interim condensed consolidated financial statements), as well as the adjustment of our marketable securities to amortized cost.

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Results of Operations

Comparison of the three months ended June 30, 2022 and 2021

	Three Months Ended June 30,
(in thousands)	2022		2021		$ Change
Product revenue, net	$	25,082	$	52,803	$	(27,721)
Government contract service revenue	1,896		2,113		(217)
Government contract grant revenue	2,082		2,087		(5)
Collaboration and royalty revenue	577		489		88
Net revenue	$	29,637	$	57,492	$	(27,855)
Expenses:
Cost of product revenue	4,878		9,778		(4,900)
Research and development	7,592		6,519		1,073
Selling, general and administrative	30,335		27,106		3,229
Total operating expenses	42,805		43,403		(598)
Income (loss) from operations	(13,168)		14,089		(27,257)
Other income and expenses:
Interest income	133		11		122
Interest expense	(4,546)		(4,344)		(202)
Other gains (losses), net	(38)		(39)		1
Net income (loss)	$	(17,619)	$	9,717	$	(27,336)

Product Revenue, Net

Net product revenue recognized on sales of NUZYRA in the U.S. was $25.1 million and $52.8 million for the three months ended June 30, 2022 and June 30, 2021, respectively. The decrease in net product revenue is primarily the result of the delivery and acceptance of the first procurement under the BARDA contract of $37.9 million during the three months ended June 30, 2021, partially offset by an increase in sales volume due to higher customer demand during the three months ended June 30, 2022.

Government Contract Service Revenue

Government contract service revenue earned under our BARDA contract was $1.9 million and $2.1 million for the three months ended June 30, 2022 and June 30, 2021, respectively. The slight decrease in government contract service revenue is primarily due to the timing of activities for the U.S. onshoring of NUZYRA manufacturing and additional work completed under the anthrax development program.

Government Contract Grant Revenue

Government contract grant revenue earned under our BARDA contract was $2.1 million for both the three months ended June 30, 2022 and June 30, 2021 and represents the ongoing costs incurred to support existing FDA PMRs.

Collaboration and Royalty Revenue

Collaboration and royalty revenue was $0.6 million for three months ended June 30, 2022, which increased slightly from $0.5 million for the three months ended June 30, 2021 as a result of royalty revenue earned on initial sales of NUZYRA in China. Royalty revenue recognized for sales of SEYSARA in the U.S. was estimated using third-party data and an approximation of discounts and allowances to calculate net product sales, to which we then applied the applicable royalty percentage specified in the Almirall Collaboration Agreement. Differences between actual and estimated royalty revenue will be adjusted in the period in which they become known, which is expected to be the following quarter.

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Cost of Product Revenue

Cost of product revenue was $4.9 million for the three months ended June 30, 2022, compared to $9.8 million for the three months ended June 30, 2021. The $4.9 million decrease is primarily the result of the delivery and acceptance of the first procurement under the BARDA contract during the three months ended June 30, 2021, partially offset by increases in NUZYRA product sales and royalties owed on net sales of NUZYRA during the three months ended June 30, 2022. Based on our policy to expense costs associated with the manufacture of our products prior to regulatory approval, certain of the costs of NUZYRA units recognized as revenue during the three months ended June 30, 2022 and June 30, 2021 were expensed prior to FDA approval in October 2018, and therefore are not included in cost of product revenue during the period. We expect cost of product revenue to increase in absolute dollars as product revenue increases.

Research and Development Expense

Research and development expenses were $7.6 million for the three months ended June 30, 2022, compared to $6.5 million for the three months ended June 30, 2021. The $1.1 million increase in research and development expenses was primarily the result of costs incurred for analytical testing as well as for other non-clinical studies.

We anticipate an increase in research and development expenses in future periods as we continue development of NUZYRA for the treatment of and PEP against pulmonary anthrax, continue the work on our FDA PMRs, and continue the onshoring of our manufacturing process, the majority of which is reimbursable under the BARDA contract. We will also incur additional spend as we continue exploring pathways for NTM indications.

Selling, General and Administrative Expense

Selling, general and administrative expenses were $30.3 million for the three months ended June 30, 2022, compared to $27.1 million for the three months ended June 30, 2021. The $3.2 million increase is primarily the result of an increase in compensation expense and costs incurred for the NUZYRA community expansion.

We anticipate an increase in selling, general and administrative expenses in support of our expansion into the community setting and other commercial activities, as well as the continued costs of operating as a public company. These increases will likely include costs for travel, in-person training events and sales meetings, the hiring of additional personnel, executing marketing and promotional programs, and engaging consultants, legal and other professional fees, and other operating expenses.

Other Income and Expenses

Interest expense for the three months ended June 30, 2022 represents interest incurred on the Notes of $2.2 million, the R-Bridge Loan Agreement of $1.2 million, the Royalty-Backed Loan Agreement of $1.1 million, and insignificant interest expense related to our money market funds and marketable securities. Interest income for the three months ended June 30, 2022 represents interest earned on our money market funds and marketable securities.

Interest expense for the three months ended June 30, 2021 represents interest incurred on the Notes of $2.2 million, the R-Bridge Loan Agreement of $1.1 million, and the Royalty-Backed Loan Agreement of $1.0 million. Interest income for the three months ended June 30, 2021 represents interest earned on our money market funds and marketable securities.

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Comparison of the Six Months Ended June 30, 2022 and 2021

	Six Months Ended June 30,
(in thousands)	2022		2021		$ Change
Product revenue, net	$	45,000	$	66,009	$	(21,009)
Government contract service revenue	4,068		3,086		982
Government contract grant revenue	4,182		3,701		481
Collaboration and royalty revenue	1,248		1,123		125
Net revenue	$	54,498	$	73,919	$	(19,421)
Expenses:
Cost of product revenue	8,372		12,529		(4,100)
Research and development	15,069		12,057		3,012
Selling, general and administrative	57,937		49,465		8,400
Total operating expenses	81,378		74,051		7,327
Income (loss) from operations	(26,880)		(132)		(26,748)
Other income and expenses:
Interest income	240		36		204
Interest expense	(9,025)		(8,651)		(374)
Other gains (losses), net	138		118		20
Net income (loss)	$	(35,527)	$	(8,629)	$	(26,898)

Product Revenue, Net

Net product revenue recognized on sales of NUZYRA in the U.S. was $45.0 million and $66.0 million for the six months ended June 30, 2022 and June 30, 2021, respectively. The decrease in net product revenue is primarily the result of the delivery and acceptance of the first procurement under the BARDA contract of $37.9 million during the six months ended June 30, 2021, partially offset by an increase in sales volume due to higher customer demand during the six months ended June 30, 2022.

Government Contract Service Revenue

Government contract service revenue earned under our BARDA contract was $4.1 million and $3.1 million for the six months ended June 30, 2022 and June 30, 2021, respectively. The increase in government contract service revenue is primarily the result of activities for the U.S. onshoring of NUZYRA manufacturing and additional work completed under the anthrax development program.

Government Contract Grant Revenue

Government contract grant revenue earned under our BARDA contract was $4.2 million and $3.7 million during the six months ended June 30, 2022 and June 30, 2021, respectively. The increase in government contract service revenue is primarily the result of increased costs incurred to support existing FDA PMRs.

Collaboration and Royalty Revenue

Collaboration and royalty revenue was $1.2 million for the six months ended June 30, 2022, which increased slightly from $1.1 million for the six months ended June 30, 2021 as a result of royalty revenue earned on initial sales of NUZYRA in China. Royalty revenue recognized for sales of SEYSARA in the U.S. was estimated using third-party data and an approximation of discounts and allowances to calculate net product sales, to which we then applied the applicable royalty percentage specified in the Almirall Collaboration Agreement. Differences between actual and estimated royalty revenue will be adjusted in the period in which they become known, which is expected to be the following quarter.

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Cost of Product Revenue

Cost of product revenue was $8.4 million for the six months ended June 30, 2022, compared to $12.5 million for the six months ended June 30, 2021. The $4.1 million decrease is primarily the result of the delivery and acceptance of the first procurement under the BARDA contract of $37.9 million during the six months ended June 30, 2021, partially offset by an increase in sales volume due to higher customer demand during the six months ended June 30, 2022. Based on our policy to expense costs associated with the manufacture of our products prior to regulatory approval, certain of the costs of NUZYRA units recognized as revenue during the six months ended June 30, 2022 and six months ended June 30, 2021were expensed prior to FDA approval in October 2018, and therefore are not included in cost of product revenue during the period. We expect cost of product revenue to increase in absolute dollars as product revenue increases.

Research and Development Expense

Research and development expenses were $15.1 million for the six months ended June 30, 2022, compared to $12.1 million for the six months ended June 30, 2021. The $3.0 million increase in research and development expenses was primarily due to costs for activities reimbursed under the BARDA contract, analytical testing, and other non-clinical studies.

We anticipate an increase in research and development expenses in future periods as we continue development of NUZYRA for the treatment of and PEP against pulmonary anthrax, continue the work on our FDA PMRs, and continue the onshoring of our manufacturing process, the majority of which is reimbursable under the BARDA contract. We will also incur additional spend as we continue exploring pathways for NTM indications.

Selling, General and Administrative Expense

Selling, general and administrative expenses were $57.9 million for the six months ended June 30, 2022, compared to $49.5 million for the six months ended June 30, 2021. The $8.4 million increase is primarily the result of an increase in compensation expense and costs incurred for the NUZYRA community expansion.

We anticipate an increase in selling, general and administrative expenses in support of our expansion into the community setting and other commercial activities, as well as the continued costs of operating as a public company. These increases will likely include costs for travel, in-person training events and sales meetings, the hiring of additional personnel, executing marketing and promotional programs, and engaging consultants, legal and other professional fees, and other operating expenses.

Other Income and Expenses

Interest expense for the six months ended June 30, 2022 represents interest incurred on the Notes of $4.4 million, the R-Bridge Loan Agreement of $2.3 million, the Royalty-Backed Loan Agreement of $2.1 million, and insignificant interest expense related to our money market funds and marketable securities. Interest income for the six months ended June 30, 2022 represents interest earned on our money market funds and marketable securities.

Interest expense for the six months ended June 30, 2021 represents interest incurred on the Notes of $4.4 million, the R-Bridge Loan Agreement of $2.2 million, and the Royalty-Backed Loan Agreement of $2.0 million. Interest income for the six months ended June 30, 2021represents interest earned on our money market funds and marketable securities.

Liquidity and Capital Resources

On May 11, 2020, we filed a registration statement on Form S-3 with the SEC, as amended on June 19, 2020 and declared effective on July 9, 2020, to sell certain of our securities in an aggregate amount of up to $250.0 million. As of July 31, 2022, $223.3 million remains available on this shelf registration statement, with $23.3 million reserved for potential sales under our Sales Agreement (as defined below).On May 17, 2021, we entered into an At-the-Market Sales Agreement, or the Sales Agreement, with BTIG, LLC, or BTIG, under which we may offer and sell our common stock having aggregate sales proceeds of up to $50.0 million from time to time through BTIG as our sales agent. Sales of our common stock through BTIG, if any, will be made by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415(a)(4) under the Securities Act of 1933, as amended, including without limitation sales made directly on the Nasdaq Global Market or any other existing trading market for its common stock. BTIG will use commercially reasonable efforts to sell our common stock from time to time, based upon instructions (including any price,

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time or size limits or other customary parameters or conditions we may impose). We will pay BTIG a commission of 3% of the gross sales proceeds of any common stock sold through BTIG under the Sales Agreement. During six months ended June 30, 2022, we sold 2,339 shares of our common stock pursuant to the Sales Agreement for $7.3 million in proceeds, after deducting an insignificant amount of commissions. As of July 31, 2022, $23.3 million remains available for sale under the Sales Agreement.

We have used and we intend to continue to use the net proceeds from the above offerings of our common stock and the Notes, as well as other current and retired long-term debt agreements, together with our existing capital resources and future NUZYRA product sales, government contract revenue and royalty revenue, to fund our ongoing company operations, including clinical studies of omadacycline, NUZYRA commercial operations, and for working capital and other general corporate purposes. Refer to Note 13, Long-Term Debt, for further details on our loan agreements, which include the R-Bridge Loan Agreement, the Notes, and the Royalty-Backed Loan Agreement.

As of June 30, 2022, we had cash, cash equivalents and marketable securities of $69.4 million.

The following table summarizes our cash provided by and used in operating, investing and financing activities:

	Six Months Ended June 30,
(in thousands)	2022		2021
Net cash used in operating activities	$	(33,609)	$	(54,724)
Net cash (used) provided by investing activities	$	(15,196)	$	19,621
Net cash (used) provided by financing activities	$	7,818	$	4,603

Operating Activities

Net cash used in operating activities was $33.6 million for the six months ended June 30, 2022, compared to $54.7 million for the six months ended June 30, 2021. The change in net cash used in operating activities primarily consists of our net losses adjusted for non-cash items and changes in components of operating assets and liabilities as follows:

–for the six months ended June 30, 2022, a net loss of $35.5 million was adjusted for non-cash items, including stock-based compensation expense of $6.4 million, non-cash interest expense of $2.7 million, and a net increase of $7.4 million due to changes in operating assets and liabilities. The significant items in the change in operating assets and liabilities include a net increase in accounts payable and accrued expenses, inventories, and other liabilities and other assets of $8.0 million, offset by a decrease in accounts receivable, other receivables, prepaid, and other current assets of $0.2 million.

–for the six months ended June 30, 2021, a net loss of $8.6 million was adjusted for non-cash items including stock-based compensation expense of $6.6 million and non-cash interest expense of $0.7 million and a net decrease of $53.6 million due to changes in operating assets and liabilities. The significant items in the change in operating assets and liabilities include an increase in accounts receivable, other receivables, prepaid, and other current assets of $46.6 million, an increase in inventories of $4.7 million, an increase in other liabilities and other assets of $1.9 million and an increase in accounts payable and accrued expenses of $0.5 million.

Investing Activities

Net cash used by investing activities during the six months ended June 30, 2022 consists of $15.2 million in purchases of marketable securities.

Net cash provided by investing activities during the six months ended June 30, 2021 consists of $20.0 million in proceeds from maturities of marketable securities, offset by $0.3 million in purchases of fixed assets.

Financing Activities

Net cash provided by financing activities during the six months ended June 30, 2022 consists of $7.3 million in net proceeds raised through the sale of shares of our common stock under the Sales Agreement and $0.5 million in proceeds received from the ESPP.

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Net cash provided by financing activities during the six months ended June 30, 2021 consists of $4.6 million in net proceeds raised through the sale of shares of our common stock under the Sales Agreement and $0.4 million in net proceeds raised through the 2018 ESPP, offset by $0.4 million in payments of debt issuance costs under the R-Bridge Loan Agreement.

Future Funding Requirements

We began generating revenue from product sales when we launched NUZYRA in the U.S. in February 2019. We also began earning royalties on net sales of SEYSARA in the U.S. when Almirall launched the product in January 2019 and on net sales of NUZYRA in the greater China region when Zai launched the product in December 2021. Our future funding requirements will depend on our ability to generate continued revenue from sales of NUZYRA, and our partners, Almirall and Zai's, ability to generate continued revenue from sales of SEYSARA and NUZYRA, respectively. We do not expect to generate any other revenue unless and until our SEYSARA greater China region partner, Almirall, obtains regulatory approval of and commercializes its respective product in the greater China region. We will require substantial additional funding to meet FDA PMRs for NUZYRA, which we expect to continue to be funded through the BARDA contract. Additional resources will also be needed to support and accelerate the commercialization of NUZYRA, fund the development of omadacycline in other indications, including NTM, and to advance the development of potential other product candidates, and such funding may not be available on favorable terms or at all. BARDA’s procurements of NUZYRA will also be an important component to satisfying future funding requirements.

We expect to continue to incur significant expenditures and operating losses for the next few years as we:

•conduct additional clinical trials of omadacycline;

•seek regulatory approvals for additional indications for omadacycline, such as omadacycline for the treatment of NTM;

•continue to augment our sales, marketing and distribution infrastructure to commercialize NUZYRA and increase our manufacturing capacity and capabilities to satisfy demand;

•add personnel to support our planned commercialization efforts;

•build product inventory; and

•service and pay down our debt.

Based upon our current operating plan, we anticipate that our existing cash, cash equivalents and marketable securities of $69.4 million as of June 30, 2022 will extend our cash runway through the end of 2023 with a pathway to cash flow break even.

We have based this estimate on assumptions that may prove to be wrong, and we could use our available capital resources sooner than we currently expect. Because of the numerous risks and uncertainties associated with the development and commercialization of our pharmaceutical products, especially given the constraints on in-person promotion of NUZYRA and reduced access to prescribers due to restrictions in access to hospitals during the COVID-19 pandemic, and the unknown extent to which we will maintain existing or enter into new collaborations with third parties to participate in the development and commercialization of our product and product candidates, we are unable to estimate with certainty the amounts of increased capital outlays and operating expenditures that we will require to fund our continuing operations, including for our clinical development programs and commercialization efforts for NUZYRA. Our future capital requirements will depend on many factors, including:

•the progress of clinical development of omadacycline in additional indications, including NTM and pulmonary anthrax;

•the costs and timing of commercialization activities for NUZYRA;

•product revenue received from commercial sales of NUZYRA;

•royalty revenue received from commercial sales of SEYSARA by Almirall;

•timing and amount of actual reimbursements and NUZYRA purchases under the BARDA contract;

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•the ability of Zai to develop, manufacture and commercialize omadacycline in the Zai territory;

•the number and characteristics of other product candidates that we may pursue;

•the scope, progress, timing, cost and results of research, preclinical development and clinical trials;

•the costs, timing and outcome of seeking, obtaining, maintaining and expanding FDA and non-U.S. regulatory approvals;

•the costs associated with manufacturing and maintaining high quality sales, marketing and distribution capabilities;

•the number and characteristics of other product candidates that we may pursue;

•our ability to maintain, expand and defend the scope of our intellectual property portfolio, including the amount and timing of any payments we may be required to make in connection with the licensing, filing, defense and enforcement of any patents or other intellectual property rights;

•our need and ability to hire additional management, scientific, commercial, operations and medical personnel;

•the effect of competing products that may limit market penetration of our products;

•our need to implement additional internal systems and infrastructure, including financial and reporting systems;

•resources required to develop and implement policies and processes to promote ongoing compliance with applicable healthcare laws and regulations;

•costs required to ensure that our and our partners’ business arrangements with third parties comply with applicable healthcare laws and regulations;

•the economic and other terms, timing and success of our existing collaboration and licensing arrangements and any collaboration, licensing or other arrangements into which we may enter in the future, including the timing of receipt of any milestone or royalty payments under such arrangements; and

•the effect of the COVID-19 pandemic on the economy generally and on our business and operations specifically, including our sales of NUZYRA, sales by our collaboration partners with respect to which we are entitled to royalties, our third-party manufacturers and supply chain, our research and development efforts, our clinical trials and our employees.

Until we can generate a sufficient amount of product and royalty revenue to finance our cash requirements, if ever, we expect to finance our future cash needs primarily through a combination of public or private equity offerings, debt or other structured financings, strategic collaborations, grant funding and government funding. We do not have any committed external sources of funds other than the rights under the BARDA contract and the rights to contingent milestone payments and/or royalties under the Almirall Collaboration Agreement, the Almirall China License, the Tetraphase License Agreement and the Zai Collaboration Agreement, which are terminable by Almirall, Tetraphase and Zai, respectively, upon prior written notice. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of our stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect stockholders’ rights. Future debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Additionally, future equity or debt financing may be difficult to obtain on favorable terms, if at all, complicated by the increased volatility within the global financial markets as a result of the COVID-19 pandemic. If we raise additional funds through marketing and distribution arrangements or other collaborations, strategic alliances or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, NUZYRA, sarecycline, future revenue streams, research programs, product candidates or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings when needed, we may be required to delay, limit, reduce or terminate our product development or commercialization efforts or grant rights to develop and market NUZYRA, sarecycline or our other product candidates that we may otherwise prefer to develop and market ourselves.

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Critical Accounting Policies and Estimates

Our management’s discussion and analysis of our financial condition and results of operations are based on our financial statements, which have been prepared in accordance with generally accepted accounting principles of the United States of America. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses and the disclosure of contingent liabilities in our financial statements. On an ongoing basis, we evaluate our estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, accrued sales allowances, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement, manufacturing and clinical accruals, useful lives for depreciation and amortization of long-lived assets and valuation allowances on deferred tax assets. Actual results could differ from those estimates.

Recent Accounting Pronouncements

Refer to Note 18, Recent Accounting Pronouncements, to our Condensed Consolidated Financial Statements in this Quarterly Report on Form 10-Q.

Item 3.    Quantitative and Qualitative Disclosures about Market Risks

Our cash and cash equivalents balance as of June 30, 2022 consisted solely of cash and cash equivalents. Our primary exposure to market risk is interest income sensitivity, which is affected by changes in the general level of interest rates, including interest rate changes resulting from the impact of the COVID-19 pandemic. However, a sudden change in market interest rates would not be expected to have a material impact on the fair market value of our cash and cash equivalents balance. Accordingly, we would not expect our operating results or cash flows to be affected to any significant degree by the effect of a sudden change in market interest rates on our cash and cash equivalents balance.

We engage CROs and contract manufacturers on a global scale. We may be subject to fluctuations in foreign currency rates in connection with certain of these agreements. We currently do not hedge any such foreign currency exchange rate risk. Transactions denominated in currencies other than U.S. dollars are recorded based on exchange rates at the time such transactions arise and were less than 5.0% of total liabilities as of June 30, 2022.

Item 4.    Controls and Procedures

Management’s Evaluation of our Disclosure Controls and Procedures

We maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Securities Exchange Act of 1934, as amended, is (1) recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms and (2) accumulated and communicated to our management, including our principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure.

As of June 30, 2022, our management, with the participation of our principal executive officer and principal financial officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended). Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Our principal executive officer and principal financial officer have concluded based upon the evaluation described above that, as of June 30, 2022, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting

During the three months ended June 30, 2022, there have been no changes in our internal control over financial reporting, as such term is defined in Rules 13a-15(f) and 15(d)-15(f) promulgated under the Securities Exchange Act of 1934, as amended, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II – OTHER INFORMATION

Item 1.    Legal Proceedings

Information in response to this Item is incorporated herein by reference from Note 17, Commitments and Contingencies, to our Condensed Consolidated Financial Statements in this Quarterly Report on Form 10-Q.

Item 1A.    Risk Factors

There have been no material changes from the risk factors set forth in our 2021 Form 10-K.

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Item 6.    Exhibits

EXHIBIT INDEX

		Incorporated by Reference
Exhibit No.	Exhibit Description	Schedule/ Form	File Number	Exhibit	Filing Date
3.1	Amended and Restated Certificate of Incorporation.	Form 8-K	001-36066	3.1	October 31, 2014
3.2	Certificate of Amendment of Amended and Restated Certificate of Incorporation.	Form 8-K	001-36066	3.2	October 31, 2014
3.3	Certificate of Elimination of Series A Junior Participating Preferred Stock	Form 8-K	001-36066	3.1	July 24, 2015
3.4	Certificate of Amendment to the Amended and Restated Certificate of Incorporation.	Form 10-Q	001-36066	3.4	August 9, 2021
3.5	Amended and Restated Bylaws.	Form 8-K	001-36066	3.1	April 16, 2015
4.1	Specimen Common Stock Certificate.	Form S-3	333-201458	4.2	January 12, 2015
4.2	Form of Warrant Agreement issued to Hercules Capital, Inc.	Form 8-K	001-36066	4.1	June 29, 2017
4.3	Warrant Agreement issued to Hercules Capital, Inc.	Form 10-Q	001-36066	4.5	August 2, 2018
4.4	Warrant Agreement, dated as of August 5, 2020 issued to Hercules Capital, Inc.	Form 10-Q	001-36066	4.9	August 10, 2020
31.1*	Certification of the Company’s Chief Executive Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities and Exchange Act of 1934, as amended, pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2*	Certification of the Company’s Principal Financial Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities and Exchange Act of 1934, as amended, pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1*	Certification of the Company’s Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2*	Certification of the Company’s Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS*	Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.
101.SCH*	Inline XBRL Taxonomy Extension Schema Document.

46

		Incorporated by Reference
Exhibit No.	Exhibit Description	Schedule/ Form	File Number	Exhibit	Filing Date
101.CAL*	Inline XBRL Taxonomy Extension Calculation Linkbase Document.
101.DEF*	Inline XBRL Taxonomy Extension Definition Linkbase Document.
101.LAB*	Inline XBRL Taxonomy Extension Labels Linkbase Document.
101.PRE*	Inline XBRL Taxonomy Extension Presentation Linkbase Document.
104*	Cover Page Interactive Data File (embedded within the Inline XBRL document)

_____________________________________

47

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized, on the 3rd day of August 2022.

Paratek Pharmaceuticals, Inc.
By:	/s/ Evan Loh M.D.
	Evan Loh M.D.
	Chief Executive Officer (Principal Executive Officer)
By:	/s/ Sarah Higgins
	Sarah Higgins
	Vice President, Finance (Principal Financial and Accounting Officer)

48

EX-31.1

Exhibit 31.1

CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO

SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, Evan Loh, certify that:

1.I have reviewed this Form 10-Q of Paratek Pharmaceuticals, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b)Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision; to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c)Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d)Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a)All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b)Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

/s/ EVAN LOH, M.D.

Evan Loh, M.D.

Chief Executive Officer

August 3, 2022

EX-31.2

Exhibit 31.2

CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER PURSUANT TO

SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, Sarah Higgins, certify that:

1.I have reviewed this Form 10-Q of Paratek Pharmaceuticals, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b)Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision; to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c)Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d)Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a)All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b)Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

/s/ SARAH HIGGINS

Sarah Higgins

Principal Financial Officer

August 3, 2022

EX-32.1

Exhibit 32.1

CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

Pursuant to the requirement set forth in Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C. §1350), Evan Loh, M.D., Chief Executive Officer of Paratek Pharmaceuticals, Inc. (the “Company”), hereby certifies that, to the best of his knowledge:

1.The Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2022 (the “Quarterly Report”), to which this Certification is attached as Exhibit 32.1 fully complies with the requirements of Section 13(a) or Section 15(d), of the Exchange Act; and

2.The information contained in the Quarterly Report fairly presents, in all material respects, the financial condition and results of operations the Company.

In Witness Whereof, the undersigned has set his hand hereto as of the 3rd day of August, 2022.

/s/ EVAN LOH, M.D.

Evan Loh, M.D.

Chief Executive Officer

This certification accompanies the Form 10-Q to which it relates, is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Paratek Pharmaceuticals, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended (whether made before or after the date of the Form 10-Q), irrespective of any general incorporation language contained in such filing.

EX-32.2

Exhibit 32.2

CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

Pursuant to the requirement set forth in Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C. §1350), Sarah Higgins, Principal Financial Officer of Paratek Pharmaceuticals, Inc. (the “Company”), hereby certifies that, to the best of her knowledge:

1.The Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2022 (the “Quarterly Report”), to which this Certification is attached as Exhibit 32.2 fully complies with the requirements of Section 13(a) or Section 15(d) of the Exchange Act; and

2.The information contained in the Quarterly Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

In Witness Whereof, the undersigned has set her hand hereto as of the 3rd day of August, 2022.

/s/ SARAH HIGGINS

Sarah Higgins

Principal Financial Officer

This certification accompanies the Form 10-Q to which it relates, is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Paratek Pharmaceuticals, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended (whether made before or after the date of the Form 10-Q), irrespective of any general incorporation language contained in such filing.

XML

Cover Page - shares	6 Months Ended
	Jun. 30, 2022	Jul. 31, 2022
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 2022
Document Transition Report	false
Entity File Number	001-36066
Entity Registrant Name	PARATEK PHARMACEUTICALS, INC.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	33-0960223
Entity Address, Address Line One	75 Park Plaza
Entity Address, City or Town	Boston
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02116
City Area Code	617
Local Phone Number	807-6600
Title of 12(b) Security	Common Stock, par value $0.001 per share
Trading Symbol	PRTK
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		54,862,502
Entity Central Index Key	0001178711
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2022
Document Fiscal Period Focus	Q2
Amendment Flag	false

XML

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Current assets
Cash and cash equivalents	$ 39,505	$ 80,367
Marketable securities	29,886	15,107
Restricted cash	0	125
Accounts receivable, net	28,521	29,438
Inventories	13,083	11,020
Other receivables	3,297	3,679
Prepaid and other current assets	13,476	12,364
Total current assets	127,768	152,100
Long-term restricted cash	125	125
Fixed assets, net	712	794
Goodwill	829	829
Right-of-use assets	1,352	1,757
Long-term inventories	32,662	27,767
Other long-term assets	247	497
Total assets	163,695	183,869
Current liabilities
Accounts payable	2,257	5,394
Accrued expenses	25,661	23,446
Other current liabilities	2,182	2,457
Total current liabilities	30,100	31,297
Long-term debt	257,153	254,428
Long-term lease liabilities	854	1,308
Accrued long-term compensation	22,339	21,846
Other liabilities	2,616	2,777
Total liabilities	313,062	311,656
Stockholders’ deficit
Undesignated preferred stock: $0.001 par value, 5,000,000 shares authorized; no shares issued and outstanding	0	0
Common stock, $0.001 par value; 200,000,000 shares authorized; 54,778,638 shares issued and outstanding as of June 30, 2022; and 200,000,000 shares authorized; 51,711,809 shares issued and outstanding as of December 31, 2021	55	52
Additional paid-in capital	753,223	739,053
Accumulated other comprehensive income	(233)	(9)
Accumulated deficit	(902,412)	(866,883)
Total stockholders’ deficit	(149,367)	(127,787)
Total liabilities and stockholders’ deficit	$ 163,695	$ 183,869

XML

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2022	Dec. 31, 2021
Statement of Financial Position [Abstract]
Undesignated preferred stock, par value (in USD per share)	$ 0.001	$ 0.001
Undesignated preferred stock, shares authorized	5,000,000	5,000,000
Undesignated preferred stock, shares issued	0	0
Undesignated preferred stock, shares outstanding	0	0
Common stock, par value (in USD per share)	$ 0.001	$ 0.001
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	54,778,638	51,711,809
Common stock, shares outstanding	54,778,638	51,711,809

XML

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021	Jun. 30, 2022	Jun. 30, 2021
Net revenue	$ 29,637	$ 57,492	$ 54,498	$ 73,919
Expenses:
Cost of product revenue	4,878	9,778	8,372	12,529
Research and development	7,592	6,519	15,069	12,057
Selling, general and administrative	30,335	27,106	57,937	49,465
Total operating expenses	42,805	43,403	81,378	74,051
Income (loss) from operations	(13,168)	14,089	(26,880)	(132)
Other income and expenses:
Interest income	133	11	240	36
Interest expense	(4,546)	(4,344)	(9,025)	(8,651)
Other gains (losses), net	(38)	(39)	138	118
Net income (loss)	(17,619)	9,717	(35,527)	(8,629)
Other comprehensive income (loss)
Unrealized gain (loss) on available-for-sale securities, net of tax	(53)	0	(224)	(4)
Comprehensive income (loss)	$ (17,672)	$ 9,717	$ (35,751)	$ (8,633)
Earnings per share, diluted (in USD per share)	$ (0.33)	$ 0.20	$ (0.67)	$ (0.18)
Earnings per share, basic (in USD per share)	$ (0.33)	$ 0.20	$ (0.67)	$ (0.18)
Weighted average common stock outstanding
Weighted average number of shares outstanding, basic	53,023,350	47,122,717	53,310,091	46,894,812
Weighted average number of shares outstanding, diluted	53,023,350	48,945,736	53,310,091	46,894,812
Product revenue, net
Net revenue	$ 25,082	$ 52,803	$ 45,000	$ 66,009
Government contract service revenue
Net revenue	1,896	2,113	4,068	3,086
Government contract grant revenue
Net revenue	2,082	2,087	4,182	3,701
Collaboration and royalty revenue
Net revenue	$ 577	$ 489	$ 1,248	$ 1,123

XML

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021
Operating activities
Net income (loss)	$ (35,527)	$ (8,629)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization and accretion	275	225
Stock-based compensation expense	6,354	6,602
Noncash interest expense	2,725	672
Changes in operating assets and liabilities
Accounts receivable, other receivables, prepaid, and other current assets	187	(46,618)
Inventories	(6,958)	(4,662)
Operating lease right-of-use asset	404	(95)
Accounts payable and accrued expenses	(923)	(525)
Operating lease liability	(455)	158
Other liabilities and other assets	309	(1,852)
Net cash used in operating activities	(33,609)	(54,724)
Investing activities
Purchase of fixed assets	(36)	(379)
Purchase of marketable securities	(15,160)	0
Proceeds from maturities of marketable securities	0	20,000
Net cash (used) provided by investing activities	(15,196)	19,621
Financing activities
Payment of long-term royalty-backed loan agreement debt issuance costs	0	(397)
Proceeds from sale of common stock, net of costs	7,330	4,645
Proceeds from the employee stock purchase plan and stock options	488	355
Net cash (used) provided by financing activities	7,818	4,603
Net (decrease) increase in cash, cash equivalents and restricted cash	(40,987)	(30,500)
Cash, cash equivalents and restricted cash at beginning of period	80,617	106,048
Cash, cash equivalents and restricted cash at end of period	39,630	75,548
SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION
Cash paid for interest	5,739	5,865
SUPPLEMENTAL DISCLOSURES OF NONCASH FINANCING ACTIVITIES
Paid in-kind interest included in accrued expenses	$ 2,011	$ 1,614

XML

Condensed Consolidated Statements of Stockholders' Deficit (unaudited) - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Beginning balance (in shares) at Dec. 31, 2020		46,516,567
Beginning balance at Dec. 31, 2020	$ (102,260)	$ 46	$ 705,489	$ 4	$ (807,799)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options (in shares)		961
Exercise of stock options	3		3
Issuance of common stock, net of expenses	0
Vesting of restricted stock unit awards (in shares)		389,700
Vesting of restricted stock unit awards	0	$ 1	(1)
Employee stock purchase plan expense	27		27
Unrealized gain (loss) on available-for-sale securities, net of tax	(4)			(4)
Stock-based compensation expense	1,572		1,572
Net loss	(18,346)				(18,346)
Ending balance (in shares) at Mar. 31, 2021		46,907,228
Ending balance at Mar. 31, 2021	(119,008)	$ 47	707,090	0	(826,145)
Beginning balance (in shares) at Dec. 31, 2020		46,516,567
Beginning balance at Dec. 31, 2020	(102,260)	$ 46	705,489	4	(807,799)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Unrealized gain (loss) on available-for-sale securities, net of tax	(4)
Net loss	(8,629)
Ending balance (in shares) at Jun. 30, 2021		47,996,471
Ending balance at Jun. 30, 2021	(99,291)	$ 48	717,089	0	(816,428)
Beginning balance (in shares) at Mar. 31, 2021		46,907,228
Beginning balance at Mar. 31, 2021	(119,008)	$ 47	707,090	0	(826,145)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock, net of expenses (in shares)		649,022
Issuance of common stock, net of expenses	4,645	$ 1	4,644
Vesting of restricted stock unit awards (in shares)		376,301
Vesting of restricted stock unit awards	0
Employee stock purchase plan expense	29		29
Issuance of stock under the employee stock purchase plan (in shares)		63,920
Issuance of stock under the employee stock purchase plan	352		352
Unrealized gain (loss) on available-for-sale securities, net of tax	0
Stock-based compensation expense	4,974		4,974
Net loss	9,717				9,717
Ending balance (in shares) at Jun. 30, 2021		47,996,471
Ending balance at Jun. 30, 2021	(99,291)	$ 48	717,089	0	(816,428)
Beginning balance (in shares) at Dec. 31, 2021		51,711,809
Beginning balance at Dec. 31, 2021	(127,787)	$ 52	739,053	(9)	(866,883)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options (in shares)		729
Exercise of stock options	6		6
Issuance of common stock, net of expenses (in shares)		884,230
Issuance of common stock, net of expenses	3,091	$ 1	3,090
Vesting of restricted stock unit awards (in shares)		426,582
Vesting of restricted stock unit awards	0
Employee stock purchase plan expense	36		36
Unrealized gain (loss) on available-for-sale securities, net of tax	(171)			(171)
Stock-based compensation expense	2,433		2,433
Net loss	(17,910)				(17,910)
Ending balance (in shares) at Mar. 31, 2022		53,023,350
Ending balance at Mar. 31, 2022	(140,302)	$ 53	744,618	(180)	(884,793)
Beginning balance (in shares) at Dec. 31, 2021		51,711,809
Beginning balance at Dec. 31, 2021	$ (127,787)	$ 52	739,053	(9)	(866,883)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options (in shares)	1,646
Unrealized gain (loss) on available-for-sale securities, net of tax	$ (224)
Net loss	(35,527)
Ending balance (in shares) at Jun. 30, 2022		54,778,638
Ending balance at Jun. 30, 2022	(149,367)	$ 55	753,223	(233)	(902,412)
Beginning balance (in shares) at Mar. 31, 2022		53,023,350
Beginning balance at Mar. 31, 2022	(140,302)	$ 53	744,618	(180)	(884,793)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock, net of expenses (in shares)		1,455,156
Issuance of common stock, net of expenses	4,239	$ 2	4,237
Employee stock purchase plan expense	29		29
Issuance of stock under the employee stock purchase plan (in shares)		300,132
Issuance of stock under the employee stock purchase plan	483		483
Unrealized gain (loss) on available-for-sale securities, net of tax	(53)			(53)
Stock-based compensation expense	3,856		3,856
Net loss	(17,619)				(17,619)
Ending balance (in shares) at Jun. 30, 2022		54,778,638
Ending balance at Jun. 30, 2022	$ (149,367)	$ 55	$ 753,223	$ (233)	$ (902,412)

XML

Description of the Business

6 Months Ended

Jun. 30, 2022

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Description of the business

Description of the business

Paratek Pharmaceuticals, Inc., or the Company or Paratek, is a Delaware corporation with its corporate office in Boston, Massachusetts and an office in King of Prussia, Pennsylvania.

The Company is a commercial-stage biopharmaceutical company focused on the development and commercialization of novel life-saving therapies for life-threatening diseases or other public health threats for civilian, government and military use. The Company’s United States, or U.S., Food and Drug Administration, or FDA, approved commercial product, NUZYRA® (omadacycline), is a once-daily oral and intravenous antibiotic for the treatment of adult patients with community-acquired bacterial pneumonia, or CABP, and acute skin and skin structure infections, or ABSSSI, caused by susceptible pathogens. The Company retains worldwide commercial rights to omadacycline, with the exception of the People’s Republic of China, Hong Kong, Macau and Taiwan, where it has entered into a collaboration agreement with Zai Lab (Shanghai) Co., Ltd., or Zai. The National Medical Products Administration, or NMPA, of China approved NUZYRA for the treatment of CABP and ABSSSI in December 2021.

SEYSARA® (sarecycline) is an FDA-approved product with respect to which the Company has exclusively licensed in the U.S. and the People’s Republic of China, or the PRC, Hong Kong and Macau, or the greater China region, certain rights to Almirall, LLC, or Almirall. SEYSARA is currently being marketed by Almirall in the U.S. as a once-daily oral therapy for the treatment of moderate to severe acne vulgaris. With respect to the Company’s technology as it relates to sarecycline, the Company retains development and commercialization rights in all countries other than the U.S. and the greater China region, and in February 2020, the Company exclusively licensed from Almirall certain technology owned or in-licensed by Almirall or its affiliates that is necessary or useful to develop or commercialize sarecycline outside of the U.S. Almirall plans to develop sarecycline for acne in China, with a submission to the NMPA, according to Almirall, expected in 2023.

The Company has incurred significant losses since inception in 1996. The Company has generated an accumulated deficit of $902.4 million through June 30, 2022 and may require substantial additional funding in connection with the Company’s continuing operations to support clinical development and commercialization activities associated with NUZYRA. Based upon the Company’s current operating plan, it anticipates that its cash, cash equivalents and marketable securities of $69.4 million as of June 30, 2022 will enable the Company to fund operating expenses and capital expenditure requirements through at least the next twelve months from the issuance of the financial statements included in this Quarterly Report on Form 10-Q. The Company expects to finance future cash needs primarily through a combination of product sales, royalties, public or private equity offerings, debt or other structured financings, strategic collaborations, grant funding and government funding. The Company is subject to risks common to companies in the biopharmaceutical industry, including, but not limited to, risks of failure of preclinical studies and clinical trials, the need to obtain additional financing to fund the future development of the Company’s product candidates, the need to obtain compliant product from third-party manufacturers, the need to obtain marketing approval for the Company’s product candidates, the need to successfully commercialize and gain market acceptance of product candidates, the risks of manufacturing product with an external supply chain, dependence on key personnel, and compliance with government regulations as well as the risks discussed in the “Risk Factors” section of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021, as filed with the U.S. Securities and Exchange Commission, or the SEC, on March 14, 2022, or the 2021 Form 10-K, and in the Company’s other filings with the SEC.

XML

Summary of Significant Accounting Policies and Basis of Presentation

6 Months Ended

Jun. 30, 2022

Accounting Policies [Abstract]

Summary of Significant Accounting Policies and Basis of Presentation

Summary of Significant Accounting Policies and Basis of Presentation

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or U.S. GAAP, as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB, and pursuant to the rules and regulations of the SEC.

The accompanying condensed consolidated financial statements are unaudited. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements as

of and for the year ended December 31, 2021, and, in the opinion of management, reflect all normal recurring adjustments necessary for the fair presentation of the Company’s financial position as of June 30, 2022 and December 31, 2021, results of operations for the three and six month periods ended June 30, 2022 and June 30, 2021, cash flows for the six month periods ended June 30, 2022 and June 30, 2021 and changes in stockholders’ deficit for the three and six month periods ended June 30, 2022 and June 30, 2021.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2022. These unaudited interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements as of and for the year ended December 31, 2021, and notes thereto, which are included in the Company’s 2021 Form 10-K.

Summary of Significant Accounting Policies

As of June 30, 2022, the Company’s significant accounting policies and estimates, which are detailed in the Company’s 2021 Form 10-K, have not changed.

Principles of Consolidation

The accompanying unaudited condensed consolidated financial statements include the results of operations of Paratek Pharmaceuticals, Inc. and its wholly-owned subsidiaries, Paratek Pharma, LLC, Paratek Securities Corporation, Transcept Pharma, Inc., Paratek Ireland Limited, Paratek Royalty Corporation, Paratek Royalty Corporation II, PRTK SPV1 LLC and PRTK SPV2 LLC. All significant intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of the accompanying unaudited condensed consolidated financial statements, in conformity with U.S. GAAP, requires the Company to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses in the Company’s financial statements. On an ongoing basis, the Company evaluates its estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement (as defined below), manufacturing and clinical accruals, useful lives for depreciation and valuation allowances on deferred tax assets. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known by the Company’s management.

Segment and Geographic Information

Operating segments are defined as components of an enterprise engaging in business activities for which discrete financial information is available and regularly reviewed by the chief operating decision maker in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating segment.

Concentration of Credit Risk

Financial instruments that subject the Company to credit risk consist primarily of cash, restricted cash, and accounts receivable. The Company places its cash in an accredited financial institution and this balance is above federally insured amounts. The Company has no off-balance sheet concentrations of credit risk such as foreign currency exchange contracts, option contracts or other hedging arrangements.

Accounts receivable as of June 30, 2022 includes $24.4 million due from customers for sales of NUZYRA, net of prompt payment discounts, chargebacks, rebates and certain fees. Accounts receivable as of June 30, 2022 also includes $1.1 million of government contract service revenue earned under contract with the Biomedical Advanced Research and Development Authority, or the BARDA contract, $1.4 million of government contract grant revenue earned under the BARDA contract, and estimated revenue earned of $0.6 million of royalties on SEYSARA sales under the Almirall Collaboration Agreement (as defined below) and XERAVA TM (eravacycline) sales under the Tetraphase License Agreement (as defined below). Refer to Note 7, Government Contract Revenue for further information on the BARDA contract and to Note 8, License and Collaboration Agreements for further information on the Almirall Collaboration Agreement and the Tetraphase License Agreement.

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Marketable Securities

6 Months Ended

Jun. 30, 2022

Marketable Securities [Abstract]

Marketable Securities

Marketable Securities

The following are summaries of available-for-sale securities as of June 30, 2022 and December 31, 2021 (in thousands):

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
June 30, 2022
U.S. treasury securities	$	30,119	$	—	$	(233)	$	29,886
Total	$	30,119	$	—	$	(233)	$	29,886

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
December 31, 2021
U.S. treasury securities	$	15,116	$	—	$	(9)	$	15,107
Total	$	15,116	$	—	$	(9)	$	15,107

As of June 30, 2022, the Company had securities with a total fair market value of $29.9 million in an unrealized loss position, of which none were in a continuous unrealized loss position for more than twelve months. The Company believes that any unrealized losses associated with the decline in value of its securities is temporary and primarily related to the change in market interest rates since purchase. Therefore, the Company anticipates a full recovery of the amortized cost basis of its securities at maturity.

Securities are evaluated for impairment at the end of each reporting period. The Company did not record any impairment related to its available-for-sale securities during the three and six months ended June 30, 2022.

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Cash and Cash Equivalents and Restricted Cash

6 Months Ended

Jun. 30, 2022

Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents [Abstract]

Cash and cash equivalents and restricted cash

Cash and Cash Equivalents and Restricted Cash

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the condensed consolidated statement of cash flows that sum to the total of the same such amounts shown in the condensed consolidated statement of cash flows (in thousands):

	June 30, 2022		June 30, 2021
Cash and cash equivalents	$	39,505	$	75,298
Short-term restricted cash	—		125
Long-term restricted cash	125		125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$	39,630	$	75,548

Short-term restricted cash

The Company leases its Boston, Massachusetts office space under a non-cancelable operating lease. In accordance with the lease, the Company had a cash-collateralized irrevocable standby letter of credit in the amount of $0.3 million at December 31, 2021 naming the landlord as beneficiary. The $0.3 million letter of credit was refunded to the Company in April 2022 under the terms of the original lease agreement. The Company executed an amendment to the existing lease agreement in April 2021. In accordance with the amendment, the cash-collateralized irrevocable standby letter of credit

was reduced to an insignificant amount and is reclassified as long-term restricted cash as of June 30, 2022. Refer to Note 14, Leases, for further details.

Long-term restricted cash

As of June 30, 2022 and December 31, 2021, long-term restricted cash included the insignificant cash-collateralized irrevocable standby letter of credit described above.

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Inventories

6 Months Ended

Jun. 30, 2022

Inventory Disclosure [Abstract]

Inventories

Inventories

The following table presents inventories, net (in thousands):

	June 30, 2022		December 31, 2021
Raw materials	$	903	$	1,082
Work in process	27,351		24,675
Finished goods	17,491		13,030
Total inventories	$	45,745	$	38,787

When recorded, inventory reserves reduce the carrying value of inventories to their net realizable value. The Company reviews inventories on hand at least quarterly and records provisions for estimated excess, slow-moving and obsolete inventory, as well as inventory with a carrying value in excess of net realizable value. No inventory reserves existed as of June 30, 2022 and December 31, 2021.

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Net Income (Loss) Per Share

6 Months Ended

Jun. 30, 2022

Earnings Per Share [Abstract]

Net Income (Loss) Per Share

Net Income (Loss) Per Share

Basic net loss per share is calculated by dividing the net loss by the weighted-average number of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is computed by dividing the net loss by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method or the if-converted method, as applicable. For purposes of this calculation, shares of common stock issuable upon conversion of convertible debt, stock options, restricted stock units, warrants to purchase common stock, and shares issuable under the employee stock purchase plan are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive.

Common equivalent shares result from stock options and restricted stock units, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the employee stock purchase plan (the proceeds of which are then assumed to have been used to repurchase outstanding stock using the treasury stock method). In addition, the assumed proceeds under the treasury stock method include the average unrecognized compensation expense of stock options that are in-the-money. This results in the “assumed” buyback of additional shares, thereby reducing the dilutive impact of stock options. The two-class method is used for outstanding warrants as it is considered to be a participating security, and it is more dilutive than the treasury stock method.

The Company was in a net loss position as of June 30, 2022. The following outstanding shares subject to stock options and RSUs, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the Company’s employee stock purchase plan were antidilutive due to a net loss in the periods presented and, therefore, were excluded from the dilutive securities computation for the three and six months ended June 30, 2022 as indicated below:

	Three and Six Months Ended June 30,
	2022
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361
Shares subject to outstanding options to purchase common stock	2,119,588
Unvested restricted stock units	7,213,532
Shares subject to warrants to purchase common stock	426,866
Shares issuable under employee stock purchase plan	159,738
Totals	20,297,085

(1) The number of shares is based on the maximum number of shares issuable on exercise or conversion of the related securities as of June 30, 2022. Such amounts have not been adjusted for the treasury-stock method or weighted-average outstanding calculations as required if the securities were dilutive.

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Government Contract Revenue

6 Months Ended

Jun. 30, 2022

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Government Contract Revenue

Government Contract Revenue

Biomedical Advanced Research and Development Authority

In December 2019, the Company entered into the original BARDA contract, which is a five-year contract with an option to extend to ten years. The BARDA contract could result in payments to the Company of up to approximately $303.6 million and consists of a five-year base period-of-performance and a total contract period-of-performance (base period plus option exercises) of up to ten years. The BARDA contract supports the development of NUZYRA for the treatment of pulmonary anthrax, FDA post-marketing requirements, or PMRs, associated with the initial NUZYRA approval, and an option for BARDA to procure up to 10,000 treatment courses of NUZYRA for use against potential biothreats. In September 2021, the Company and BARDA modified the original BARDA contract, herein referred to as the amended BARDA contract, to provide additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support a supplemental New Drug Application, or sNDA, to the FDA to include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax, herein referred to as the amended option.

Under the terms of the original BARDA contract, approximately $59.4 million was awarded to the Company by BARDA in December 2019 for the development of NUZYRA for the treatment of pulmonary anthrax and the purchase of an initial 2,500 treatment courses of NUZYRA. As part of this initial $59.4 million award, a $37.9 million procurement of NUZYRA was delivered to and accepted by BARDA in June 2021, and the amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the second quarter of 2021. The Company has been periodically drawing down the remaining $21.5 million of the initial award based on costs incurred during the development program.

Two additional contractual services under the original BARDA contract were initiated by BARDA in March 2020 that awarded the Company approximately $76.8 million for reimbursement of existing FDA PMRs and approximately $20.4 million for reimbursement of manufacturing-related requirements, which the Company has been drawing down based on costs incurred. This additional staged funding is expected to support all FDA PMRs associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study, and support the U.S. onshoring and security requirements of the Companies manufacturing activities for NUZYRA.

BARDA initiated the amended option in September 2021 that awarded the Company additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support an sNDA that will include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax for approximately $31.6 million.

The remaining government options under the amended BARDA contract include a maximum of approximately $115.4 million to provide for three additional purchases of NUZYRA anthrax treatment courses, each of which may be exercised at BARDA’s discretion upon achievement of development milestones related to the anthrax treatment development program. The amended BARDA contract formalized the triggers for BARDA’s option to purchase the second NUZYRA procurement upon BARDA's receipt of positive top-line data from our pilot efficacy treatment study of inhalation anthrax in rabbits, which we anticipate will be available as early as the end of 2022. The third procurement will be triggered by BARDA's receipt of positive top-line data in PEP and treatment of inhalation anthrax from a combination of pilot and pivotal efficacy studies in animal models, which the Company anticipates will be available in 2024. The fourth procurement will be triggered by the Company’s receipt of sNDA approval from the FDA for treatment of inhalation anthrax, which is anticipated to follow the third procurement by approximately 18-24 months.

The BARDA contract contains a number of terms and conditions that are customary for government contracts of this nature, including provisions giving the government the right to terminate the contract at any time for its convenience.

The Company evaluated the BARDA contract under ASC, Topic 606, Revenue from Contracts with Customers, or ASC 606, and concluded that a portion of the arrangement represents a transaction with a customer. The Company identified five material promises under the BARDA contract: (i) research and development services performed for the treatment of pulmonary anthrax, (ii) the procurement of 2,500 treatment courses of NUZYRA, (iii) an option for services performed for the supplemental late-stage development of NUZYRA for treatment and prophylaxis of pulmonary anthrax, (iv) an option for services related to U.S. manufacturing onshoring and security requirements, which includes shelf-life stability extension work and regulatory activities that will benefit the manufacturing processes that support NUZYRA for the treatment of pulmonary anthrax, and (v) options to procure up to three tranches of up to 2,500 anthrax treatment courses of NUZYRA each.

In December 2019, the Company determined material promises (i) and (ii) above were performance obligations since they were distinct within the context of the contract as the services are separately identifiable from other promises within the arrangement. The Company also determined that for (i) and (ii) the transaction price included within the BARDA contract was equivalent to the standalone selling price of the services and the cost of the procurement.

The Company evaluated the material promises that contained option rights ((iii), (iv), and (v) above). The Company determined that (iii) and (iv) were not offered at a discount that is incremental to the range of discounts typically given for these goods and services, and therefore do not represent material rights. As such, options for additional services in (iii) and (iv) were not considered performance obligations at the outset of the arrangement. The Company also evaluated the future procurement option rights (v) and determined that those option rights represent a material right. As such, the optional additional NUZYRA procurements in (v) were considered performance obligations at the outset of the arrangement. The Company concluded that three performance obligations existed at the outset of the BARDA contract.

As the BARDA contract is partially within the scope of ASC 606 and partially within the scope of other guidance, the Company applied the guidance of ASC 606 to initially measure the parts of the contract to which ASC 606 is applicable. The total transaction price of the parts of the BARDA contract that existed at the outset of the contract that fall under ASC 606 was determined to be $63.6 million, inclusive of $4.2 million in variable consideration and was allocated to each of the three performance obligations based on the performance obligation’s estimated relative stand-alone selling prices. As of June 30, 2022, the Company reevaluated the variable consideration of $4.2 million that is included in the transaction price and determined that the variable consideration should not be constrained as it is not probable that a significant reversal in the amount of the cumulative revenue recognized will occur in a future period. The transaction price was allocated as follows: $21.5 million to research and development services performed for the treatment of pulmonary anthrax in (i), which will be classified as government contract service revenue when recognized, $37.9 million to the procurement of 2,500 treatment courses of NUZYRA in (ii), which was classified as product revenue when recognized, and a total of $4.2 million to the options to procure up to three 2,500 treatment courses of NUZYRA in (v), which will be included within product revenue when recognized upon exercise and transfer of control of related treatment courses. The Company estimated the stand-alone selling price of the research and development services performed for the treatment of pulmonary anthrax based on the Company’s projected cost of providing the services plus an applicable profit margin commensurate with observable market data for similar services. The Company estimated the stand-alone selling price of

the procurement of 2,500 treatment courses of NUZYRA based on historical pricing of the Company’s commercial products to similar customers. The Company estimated the stand-alone selling price of the future procurement options based on the discount that the customer would obtain when exercising the option, adjusted for any discount that the customer could receive without entering into the contract, and the likelihood that the option will be exercised.

The Company’s performance obligations are either satisfied over time as work progresses or at a point in time.

The Company concluded that research and development services performed for the treatment of pulmonary anthrax in (i) would be recognized as government contract service revenue over time as the performance obligation is satisfied. Costs incurred represent work performed, which corresponds with, and thereby best depicts, the transfer of control to the customer. Types of contract costs include labor, material, and third-party services.

The product procurement performance obligations ((ii) and, if any optional additional procurements are exercised from (v) above), generate revenue at a point in time, upon transfer of control of the product. As such, the related revenue for these performance obligations is recognized at a point in time as product revenue within the Company’s consolidated statement of operations. As of December 31, 2021, the product procurement performance obligation (ii) was completed and $37.9 million of product revenue was earned and recognized due to the delivery and acceptance of the first procurement under the BARDA contract.

In April 2020, BARDA exercised its option to obtain manufacturing-related services under material promise (iv) and the Company is treating these services as a separate $20.4 million contract for accounting purposes since manufacturing-related services were determined at the contract outset to be optional services that did not represent a material right. The Company’s manufacturing-related services are satisfied over time as work progresses.

In September 2021, BARDA exercised the amended option under the amended BARDA contract, to fund an FDA Animal Rule development program to support an sNDA for the treatment of and the PEP against pulmonary anthrax. The Company is treating these services as a separate $31.6 million contract for accounting purposes since the completion of a late-stage development program was determined at the contract outset to be optional services that did not represent a material right. The additional services added as part of the amended option were distinct and the increased transaction price is reflective of the entity’s standalone selling prices of the additional promised services. The Company’s late-stage development program obligations are satisfied over time as work progresses. Research and development services performed under the amended option will be recognized as government contract service revenue over time as the performance obligation is satisfied.

The Company recognized $4.1 million and $3.1 million of government contract service revenue under the BARDA contract during the six months ended June 30, 2022 and June 30, 2021, respectively. The Company recognized $1.9 million and $2.1 million of government contract service revenue under the BARDA contract during the three months ended June 30, 2022 and June 30, 2021, respectively.

As of June 30, 2022, the aggregate amount of transaction price allocated to remaining performance obligations, excluding unexercised contract options, was $63.7 million. The Company expects to recognize this amount as revenue over the next three to six years.

The Company concluded that BARDA’s reimbursement for existing FDA PMRs associated with the initial NUZYRA approval was not within the scope of ASC 606 as BARDA is not receiving services as the Company’s customer. The Company estimated the consideration to be allocated to government contract grant revenue based on the consideration under the BARDA contract in excess of the estimated standalone selling prices for components of the BARDA contract accounted for under ASC 606. The Company recognizes the allocated consideration for BARDA’s reimbursement of existing FDA PMRs associated with the initial NUZYRA approval of $72.6 million as government contract grant revenue as the related reimbursable expenses are incurred.

The Company recognized $4.2 million and $3.7 million of government contract grant revenue under the BARDA contract during the six months ended June 30, 2022 and June 30, 2021, respectively. The Company recognized $2.1 million and $2.1 million of government contract grant revenue under the BARDA contract during the three months ended June 30, 2022 and June 30, 2021, respectively.

Contract Balances

Contract assets (i.e., unbilled accounts receivable) and/or contract liabilities (i.e., customer advances and deposits) may exist at the end of each reporting period under the BARDA contract. When amounts are received prior to performance obligations being satisfied, the amounts allocated to those performance obligations are reflected as contract liabilities on the consolidated balance sheets, as deferred revenue, until the performance obligations are satisfied.

As of June 30, 2022, $0.9 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet. As of December 31, 2021, $0.8 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet.

As of June 30, 2022 and December 31, 2021, $1.1 million and $0.8 million, respectively of deferred revenue was recorded and is a component of other current liabilities on the Company’s condensed consolidated balance sheet.

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License and Collaboration Agreements

6 Months Ended

Jun. 30, 2022

Revenue from Contract with Customer [Abstract]

License and Collaboration Agreements

License and Collaboration Agreements

Tetraphase Pharmaceuticals, Inc.

On March 18, 2019, Paratek and Tetraphase Pharmaceuticals, Inc., or Tetraphase, which is now a subsidiary of La Jolla Pharmaceutical Company, entered into a License Agreement, or the Tetraphase License Agreement. Under the terms of the Tetraphase License Agreement, Paratek granted to Tetraphase a non-exclusive, worldwide, royalty-bearing license, with the right to grant sublicenses, under certain Paratek patents, to develop, make, have, use, import, offer for sale and sell the licensed product, or XERAVA, a drug for the treatment of complicated, intra-abdominal infections caused by bacteria that was approved by the FDA in August 2018.

The terms of the Tetraphase License Agreement provide for Tetraphase to pay Paratek royalties at a low single digit percent on net product revenues of the licensed product sold in the U.S. Tetraphase’s obligation to pay royalties with respect to the licensed product shall be retroactive to the date of the first commercial sale of the licensed product in the U.S., which occurred in February 2019. Tetraphase is currently selling XERAVA in the U.S.

The Tetraphase License Agreement will continue until the expiration of and payment by Tetraphase of all its payment obligations, which is when there are no longer any valid claims of the licensed Paratek patents that would be infringed, in the absence of a license, by a manufacture, use, or sales of the licensed product. The principal licensed patent under the Tetraphase License Agreement is expected to expire in October 2023.

In accordance with the Company’s revenue recognition policy, the Company recognized an insignificant amount of royalty revenue during the three and six months ended June 30, 2022 under the Tetraphase License Agreement.

Zai Lab (Shanghai) Co., Ltd.

On April 21, 2017, Paratek Bermuda Ltd., a former wholly-owned subsidiary of Paratek Pharmaceuticals, Inc., and Zai Lab (Shanghai) Co., Ltd., or Zai, entered into a License and Collaboration Agreement, or the Zai Collaboration Agreement. On December 18, 2019 Paratek Bermuda Ltd. assigned its rights under the Agreement to Paratek Pharmaceuticals, Inc. Under the terms of the Zai Collaboration Agreement, Paratek granted Zai an exclusive license to develop, manufacture and commercialize omadacycline, or the licensed product, in the People’s Republic of China, Hong Kong, Macau and Taiwan, or the Zai territory, for all human therapeutic and preventative uses other than biodefense. Zai is responsible for the development, manufacturing and commercialization of the licensed product in the Zai territory, at its sole cost with certain assistance from Paratek.

Under the terms of the Zai Collaboration Agreement, Paratek earned an upfront cash payment of $7.5 million in April 2017, $5.0 million upon approval by the FDA of a NDA submission in the CABP indication in October 2018 and $3.0 million upon submission of the first regulatory approval application for a licensed product in the People’s Republic of China in December 2019, and a $6.0 million milestone payment upon regulatory approval for a licensed product in the People’s Republic of China on December 16, 2021. Paratek is eligible to receive up to $40.5 million in potential future commercial milestone payments. The terms of the Zai Collaboration Agreement also provide for Zai to pay Paratek tiered royalties at a low double digit to mid-teen percent on net sales of the licensed product in the Zai territory.

The Zai Collaboration Agreement will continue, on a region-by-region basis, until the expiration of and payment by Zai of all Zai’s payment obligations, which is until the later of: (i) the abandonment, expiry or final determination of invalidity of the last valid claim within the Paratek patents that covers the licensed product in the region in the Zai territory in the manner that Zai or its affiliates or sublicensees exploit the licensed product or intend for the licensed product to be exploited; or (ii) 2032, the eleventh anniversary of the first commercial sale of such licensed product in such region.

The Company evaluated the Zai Collaboration Agreement under ASC 606. The Company determined that there were six material promises under the Zai Collaboration Agreement: (i) an exclusive license to develop, manufacture and commercialize omadacycline in the Zai territory, (ii) the initial technology transfer (iii) a transfer of certain materials and materials know-how, (iv) optional manufacturing services, (v) optional regulatory support and (vi) optional commercialization support. The Company determined that the exclusive license and initial technology transfer were not distinct from one another, as the license has limited value without the transfer of the Company’s technology, which will allow Zai to develop the manufacturing process and commercialize omadacycline in the Zai territory in the timeline anticipated under the agreement. Without the technology transfer, Zai would incur additional costs to recreate the Company’s know-how. Therefore, the license and initial technology transfer are combined as a single performance obligation. The transfer of materials is a single distinct performance obligation. The Company evaluated the option rights for manufacturing services, regulatory support and commercialization support to determine whether they represent or include material rights to Zai and concluded that the options were not issued at a discount, and therefore do not represent material rights. As such, they are not considered performance obligations at the outset of the arrangement.

Based on these assessments, the Company determined that two performance obligations existed at the outset of the Zai Collaboration Agreement: (i) the exclusive license combined with the initial technology transfer and (ii) the transfer of certain materials. The Company has recognized $21.5 million in milestone revenue, as described above, under the Zai Collaboration Agreement as of June 30, 2022. As the performance obligation to deliver the license was satisfied in 2017 and research and development services completed by December 2021, all milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. Therefore, the $6.0 million milestone payment upon regulatory approval of NUZYRA in the People’s Republic of China was recognized in December 2021.

There was no deferred revenue as of June 30, 2022 and December 31, 2021 under the Zai Collaboration Agreement.

Almirall, LLC

In July 2007, the Company and Warner Chilcott Company, Inc. (which became a part of Allergan plc, or Allergan), entered into a collaborative research and license agreement under which the Company granted Allergan an exclusive license to research, develop, manufacture and commercialize tetracycline products for use in the U.S. for the treatment of acne and rosacea. In September 2018, Allergan assigned to Almirall its rights under the collaboration agreement, or the Almirall Collaboration Agreement. Since Allergan did not exercise its development option with respect to the treatment of rosacea prior to initiation of a Phase 3 trial for the product, the license grant to Allergan, which was assigned to Almirall, converted to a non-exclusive license for the treatment of rosacea as of December 2014.

Under the terms of the Almirall Collaboration Agreement, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize tetracycline compounds that are specified in the agreement for the treatment of acne. The Company has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compounds in the U.S. for the treatment of acne, and Almirall has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compound included as part of the agreement for any use other than as provided in the Almirall Collaboration Agreement.

In February 2020, the Company finalized a license agreement with Almirall granting the Company exclusive rights to develop, manufacture and commercialize sarecycline outside of the U.S., including rights of reference to Almirall’s clinical data thus formalizing the Company’s rights to develop, manufacture and commercialize sarecycline in the rest of the world. In connection with that license, the Company then exclusively licensed Almirall pursuant to the Almirall China License Agreement, the rights to develop, manufacture and commercialize sarecycline in the greater China region. Almirall currently holds a nonexclusive license to develop and commercialize sarecycline for the treatment of rosacea in the U.S., and in the U.S., Paratek cannot grant rights on back-up compounds, lead candidate(s), or products licensed to Almirall for rosacea.

The Almirall Collaboration Agreement contains two performance obligations: (i) an exclusive license to research, develop and commercialize tetracycline products for use in the U.S. for the treatment of acne and rosacea and (ii) research and development services. The performance obligation to deliver the license was satisfied upon execution of the Almirall Collaboration Agreement in July 2007. All research and development services were completed by December 2010. The options provided to Almirall for additional development services do not provide Almirall with a material right as these services will not be provided at a significant or incremental discount. As such, the option services are not performance obligations. As the performance obligation to deliver the license was satisfied in 2007 and research and development services were completed by December 2010, all subsequent milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. The Company recognized all Almirall milestones in prior years. There are no milestones left to be recognized under the Almirall Collaboration Agreement.

Almirall is also obligated to pay the Company tiered royalties, ranging from the mid-single digits to the low double digits, based on net sales of tetracycline compounds developed under the Almirall Collaboration Agreement, with a standard royalty reduction post patent expiration for such product for the remainder of the royalty term.

Royalty payments are recognized when the sales occur. During the six months ended June 30, 2022 and June 30, 2021, the Company recognized $0.9 million and $1.0 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. During the three months ended June 30, 2022 and June 30, 2021, the Company recognized $0.4 million and $0.5 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. Royalty revenue recognized for sales of SEYSARA in the U.S. is estimated using third-party data and an approximation of discounts and allowances to calculate net product sales, to which the Company then applies the applicable royalty percentage specified in the Almirall Collaboration Agreement. Differences between actual and estimated royalty revenues are adjusted for in the period in which they become known, which is expected to be the following quarter.

In February 2020, we entered into (i) an ex-U.S. license agreement with Almirall, or the Ex-U.S. License, under which Almirall granted to us an exclusive license in and to certain technology owned or in-licensed by Almirall or its affiliates in order to research, develop, manufacture and commercialize sarecycline for the treatment of acne in all countries other than the U.S. and (ii) a license agreement with Almirall that is specific to China, or the China License, under which we granted to Almirall an exclusive license in and to certain technology owned or in-licensed by us or our affiliates in order to research, develop and commercialize sarecycline for the treatment of acne in the greater China region.

Under the terms of the China License, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize sarecycline for the treatment of acne, including requirements to (i) file an Investigational New Drug Application (or analogous foreign submission) for sarecycline for the treatment of acne in the greater China region in calendar year 2020, (ii) receive regulatory approval for sarecycline for the treatment of acne in the greater China region within seven years following such submission and (iii) commercialize sarecycline for the treatment of acne in the greater China region within eighteen months after obtaining regulatory approval. If Almirall does not satisfy the diligence requirements set forth in subclauses ii or iii above, we may terminate the China License.

In connection with the Ex-U.S. License, the Company pays Almirall, on a country-by-country and product-by-product basis, (i) for eight years following the first commercial sale of a sarecycline product in a country, a royalty in the middle-single digits on its or its affiliates’ nets sales of sarecycline products outside of the U.S., subject to certain standard reductions, and (ii) for fifteen years following the first commercial sale of a sarecycline product in a country, a percentage of the consideration (e.g., milestones, royalties) we receive from sublicensees in connection with developing and commercializing sarecycline outside of the U.S., which ranges from one-fifth to one-half of such consideration, subject to certain standard reductions. In connection with the China License, for fifteen years following the first commercial sale of a sarecycline product in China, Almirall pays the Company a royalty in the high-single digits on their, their affiliates’ or their sublicensees’ net sales of sarecycline products in the greater China region, subject to certain standard reductions.

Tufts University

In February 1997, the Company and Tufts University, or Tufts, entered into a license agreement under which the Company acquired an exclusive license to certain patent applications and other intellectual property of Tufts related to the drug resistance field to develop and commercialize products for the treatment or prevention of bacterial or microbial diseases or medical conditions in humans or animals or for agriculture. The Company subsequently entered into eleven amendments to that agreement, collectively the Tufts License Agreement, to include patent applications filed after the effective date of the original license agreement, to exclusively license additional technology from Tufts, to expand the field of the agreement to include disinfectant applications, and to change the royalty rate and percentage of sublicense income paid by the Company to Tufts under sublicense agreements with specified sublicensees. The Company is obligated under the Tufts License Agreement to provide Tufts with annual diligence reports and a business plan and to meet certain other diligence milestones. The Company has the right to grant sublicenses of the licensed rights to third parties, which will be subject to the prior approval of Tufts unless the proposed sublicensee meets a certain net worth or market capitalization threshold. The Company is primarily responsible for the preparation, filing, prosecution and maintenance of all patent applications and patents covering the intellectual property licensed under the Tufts License Agreement at its sole expense. The Company has the first right, but not the obligation, to enforce the licensed intellectual property against infringement by third parties.

The Company issued Tufts 1,024 shares of the Company’s common stock on the date of execution of the original license agreement, and the Company was required to make certain payments of up to $0.3 million to Tufts upon the achievement by products developed under the agreement of specified development and regulatory approval milestones. The Company made a payment of $50,000 to Tufts for achieving the first milestone following commencement of the Phase 3 clinical trial for omadacycline and a payment of $100,000 to Tufts for achieving the second milestone following its first marketing application submitted in the U.S. The third, and final, payment of $150,000 became due upon FDA approval of omadacycline in October 2018. The Company is also obligated to pay Tufts a minimum royalty payment in the amount of $25,000 per year. In addition, the Company is obligated to pay Tufts royalties based on gross sales of products, as defined in the agreement, ranging in the low single digits depending on the applicable field of use for such product sale. If the Company enters into a sublicense under the agreement, based on the applicable field of use for such product, the Company will be obligated to pay Tufts (i) a percentage, ranging from 10% to 14% (ten percent to fourteen percent) for compounds other than omadacycline, and a percentage in the single digits for the compound omadacycline, of that portion of any sublicense issue fees or maintenance fees received by the Company that are reasonably attributable to the sublicense of the rights granted to the Company under the Tufts License Agreement and (ii) the lesser of (a) a percentage, ranging from the low tens to the high twenties based on the applicable field of use for such product, of the royalty payments made to the Company by the sublicensee or (b) the amount of royalty payments that would have been paid by the Company to Tufts if it had sold the product.

Unless terminated earlier, the Tufts License Agreement will expire at the same time as the last-to-expire patent in the patent rights licensed to the Company under the agreement and after any such expiration the Company will continue to have an exclusive, fully-paid-up license to such intellectual property licensed from Tufts. Tufts has the right to terminate the agreement upon 30 days’ notice should the Company fail to make a material payment under the Tufts License Agreement or commit a material breach of the agreement and not cure such failure or breach within such 30-day period, or if, after the Company has started to commercialize a product under the Tufts License Agreement, the Company ceases to carry on its business for a period of 90 consecutive days. The Company has the right to terminate the Tufts License Agreement at any time upon 180 days’ notice. Tufts has the right to convert the Company’s exclusive license to a non-exclusive license if the Company does not commercialize a product licensed under the agreement within a specified time period.

During the six months ended June 30, 2022 and June 30, 2021, the Company incurred $0.7 million and $1.0 million of royalty expense, respectively, under the Tufts License Agreement. During the three months ended June 30, 2022 and June 30, 2021, the Company incurred $0.4 million and $0.8 million of royalty expense, respectively, under the Tufts License Agreement.

Past Collaborations

Novartis International Pharmaceutical Ltd.

In September 2009, the Company and Novartis International Pharmaceutical Ltd., or Novartis, which merged into Novartis Pharma AG, a wholly owned subsidiary of Novartis AG, entered into a Collaborative Development, Manufacture and Commercialization License Agreement, or the Novartis Agreement, which provided Novartis with a global, exclusive patent and technology license for the development, manufacturing and marketing of omadacycline. The Novartis Agreement was terminated by Novartis without cause in June 2011 and the termination was effective 60 days later. The Company and Novartis subsequently entered in a letter agreement in January 2012, or the Novartis Letter Agreement, as amended, pursuant to which we reconciled shared development costs and expenses and granted Novartis a right of first negotiation with respect to commercialization rights of omadacycline following approval of omadacycline from the FDA, European Medicines Agency, or EMA, or any regulatory agency, but only to the extent the Company had not previously granted such commercialization rights related to omadacycline to another third-party as of any such approval. The Company also agreed to pay Novartis a 0.25% royalty, to be paid from net sales received by the Company in any country following the launch of omadacycline in that country and continuing until the later of expiration of the last active valid patent claim covering such product in the country of sale and 10 years from the date of first commercial sale in such country. The first royalty payment became payable as of March 31, 2019. The amended Novartis Letter Agreement resulted in a long-term liability in the amount of $2.6 million and $2.8 million as of June 30, 2022 and December 31, 2021, respectively, included within “Other Liabilities” on the Company’s consolidated balance sheet. In addition, short-term liabilities of $0.4 million included within “Other Current Liabilities” on our consolidated balance sheets as of June 30, 2022 and December 31, 2021 represent the portion of royalty payments due to Novartis within twelve months of each balance sheet date. There are no other payment obligations to Novartis under the Novartis Agreement or the amended Novartis Letter Agreement.

For additional information related to these agreements, as well as the Company’s other significant collaborative agreements, please read Note 6, License and Collaboration Agreements, to the consolidated financial statements included within the Company’s 2021 Form 10-K.

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Capital Stock

6 Months Ended

Jun. 30, 2022

Equity [Abstract]

Capital Stock

Capital Stock

On June 9, 2021, the Company’s shareholders approved an amendment to the Company’s Amended and Restated Certificate of Incorporation to increase the number of authorized shares of common stock of the Company to 200,000,000 shares from 100,000,000 shares. Subsequent to such approval, on June 10, 2021, the Company filed the Certificate of Amendment to its Amended and Restated Certificate of Incorporation with the Delaware Secretary of State, giving effect to the authorized share increase.

On May 17, 2021, the Company entered into an At-the-Market Sales Agreement, or the Sales Agreement, with BTIG, LLC, or BTIG, under which it may offer and sell its common stock having aggregate sales proceeds of up to $50.0 million from time to time through BTIG as its sales agent. Sales of the Company’s common stock through BTIG, if any, will be made by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415(a)(4) under the Securities Act of 1933, as amended, including without limitation sales made directly on the Nasdaq Global Market or any other existing trading market for its common stock. BTIG will use commercially reasonable efforts to sell the Company’s common stock from time to time, based upon instructions from the Company (including any price, time or size limits or other customary parameters or conditions the Company may impose). The Company will pay BTIG a commission of 3% of the gross sales proceeds of any common stock sold through BTIG under the Sales Agreement. The Company has also provided BTIG with customary indemnification rights.

The Company is not obligated to make any sales of common stock under the Sales Agreement. The offering of shares of the Company’s common stock pursuant to the Sales Agreement will terminate upon the earlier of (i) the sale of all common stock subject to the Sales Agreement, or (ii) termination of the Sales Agreement in accordance with its terms.

The Company sold 2,339 shares of common stock pursuant to the Sales Agreement for $7.3 million in proceeds, after deducting an insignificant amount of commissions, during the six months ended June 30, 2022. As of July 31, 2022, $23.3 million remains available for sale under the Sales Agreement.

On May 11, 2020, the Company filed a registration statement on Form S-3 with the SEC, as amended on June 19, 2020, and declared effective on July 9, 2020, to sell certain of its securities in an aggregate amount of up to $250.0 million. As of July 31, 2022, $223.3 million remains available on this shelf registration statement, with $23.3 million reserved for potential sales under the Sales Agreement.

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Accrued Expenses

6 Months Ended

Jun. 30, 2022

Payables and Accruals [Abstract]

Accounts Expenses

Accrued Expenses

Accrued expenses consist of the following (in thousands):

	June 30,		December 31,
	2022		2021
Accrued sales allowances	$	8,771	$	7,012
Accrued compensation	6,180		8,935
Accrued interest	2,389		2,365
Accrued commercial	2,372		1,654
Accrued inventory	2,446		307
Accrued contract research	1,151		1,019
Accrued professional fees	907		781
Accrued manufacturing	714		670
Accrued other	440		361
Accrued legal costs	291		342
Total	$	25,661	$	23,446

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Fair Value Measurements

6 Months Ended

Jun. 30, 2022

Fair Value Disclosures [Abstract]

Fair Value Measurements

Fair Value Measurements

Financial instruments, including cash, cash equivalents, restricted cash, money market funds, U.S. treasury securities, accounts receivable, accounts payable, and accrued expenses are carried on the condensed consolidated financial statements at amounts that approximate fair value. The fair value of the Company’s long-term debt is determined using current applicable rates for similar instruments as of the balance sheet date. The fair value of the Company’s debt (including the Notes as defined in Note 13, Long-Term Debt), is $225.8 million as of June 30, 2022 and $238.3 million as of December 31, 2021. The fair value of the Company’s debt was determined using Level 2 inputs. Fair values are based on assumptions concerning the amount and timing of estimated future cash flows and assumed discount rates, reflecting varying degrees of perceived risk.

The following table presents information about the Company’s financial assets and liabilities that have been measured at fair value as of December 31, 2021 and indicate the fair value hierarchy of the valuation inputs utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities or other inputs that are observable market data. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability (in thousands):

Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		June 30, 2022
Assets:
U.S. treasury securities	$	29,886	$	—	$	—	$	29,886
Total Assets	$	29,886	$	—	$	—	$	29,886

Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		December 31, 2021
Assets:
U.S. treasury securities	$	15,107	$	—	$	—	$	15,107
Total Assets	$	15,107	$	—	$	—	$	15,107

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Stock-Based and Incentive Compensation

6 Months Ended

Jun. 30, 2022

Share-based Payment Arrangement [Abstract]

Stock-Based and Incentive Compensation

Stock-Based and Incentive Compensation

Stock-based Compensation

The following table presents stock-based compensation expense included in the Company’s condensed consolidated statements of operations and comprehensive income (loss) (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2022		2021		2022		2021
Research and development expense	$	515	$	793	$	692	$	1,116
Selling, general and administrative expense	3,371		4,210		5,662		5,486
Total stock-based compensation expense	$	3,886	$	5,003	$	6,354	$	6,602

Stock-based compensation expense is estimated as of the grant date based on the fair value of the award and is recognized as expense over the requisite service period, which generally represents the vesting period. The Company estimates the fair value of its stock options using the Black-Scholes option-pricing model. The weighted-average assumptions used to determine the fair value of the stock option grants is as follows:

	Six Months Ended June 30,
	2022		2021
Volatility	62.2	%	63.2	%
Risk-free interest rate	2.3	%	0.7	%
Expected dividend yield	0.0	%	0.0	%
Expected life of options (in years)	5.9		5.9

Stock Plan Activity

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Equity Incentive Plan, or the 2015 Plan, which was approved by Company stockholders at the annual meeting of shareholders held on June 9, 2015. As of June 30, 2022, there are 326,818 shares available for future issuance under the 2015 Plan.

The Company recognizes the stock-based compensation expense of awards subject to performance-based vesting conditions over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance using the accelerated attribution method. A change in the requisite service period that does not change the estimate of the total stock-based compensation expense (i.e., it does not affect the grant-date fair value or quantity of awards to be recognized) is recognized prospectively over the remaining requisite service period.

During the six months ended June 30, 2022, the Company’s Board of Directors granted 103,860 stock options and 2,737,840 RSUs to directors, executives, and employees of the Company under the 2015 Plan. The stock option awards are subject to time-based vesting over a period of one to four years. The RSU awards granted to executives in March 2022 are subject to time-based vesting, with 1/3 of the shares vesting on December 10, 2022, and an additional 1/3 of the shares vesting on the succeeding two anniversaries of such date. The RSU awards granted to non-executive employees of the Company during March 2022 are subject to time-based vesting, with 1/3 of the shares vesting on February 16, 2023, and an additional 1/3 of the shares vesting on the succeeding two anniversaries of such date.

The March 2022 grants also included performance-based RSU, or PRSU, awards to certain executives and employees of the Company, which will vest as follows: (a) 35/55 on certain net product revenue achievements, (b) 10/55 upon BARDA's purchase of the second NUZYRA procurement, and (c) 10/55 on certain business achievements. Since the Company believes it is probable that milestone (a) and (b) above will be achieved, the Company recognized $0.8 million of stock-based compensation expense for the performance condition during the six months ended June 30, 2022 using the accelerated attribution method.

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Inducement Plan, or the 2015 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 360,000 shares of common stock solely for the grant of inducement stock options to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. The Company has not made any grants under the 2015 Inducement Plan since December 31, 2015. Although the Company does not currently anticipate the issuance of additional grants under the 2015 Inducement Plan, as of June 30, 2022, 341,500 shares remain available for grant under that plan, as well as any shares underlying outstanding stock options that may become available for grant pursuant to the plan’s terms. It is therefore possible that the Company may, based on the business and recruiting needs of the Company, issue additional stock options under the 2015 Inducement Plan.

In June 2017, the Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2017 Inducement Plan, or the 2017 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 550,000 shares of common stock solely for the grant of inducement stock options and RSU awards to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. In October 2018 and March 2022, the Company’s Board of Directors approved the reserve of an additional 500,000 shares and 750,000 shares, respectively, for the 2017 Inducement Plan, for a total of 1,800,000 shares reserved for issuance under it. During the six months ended June 30, 2022, the Company’s Board of Directors granted 83,800 stock options and 223,300 RSUs to employees of the Company under the 2017 Inducement Plan. The stock option awards are subject to time-based vesting over a period of one to four years. The RSU awards are generally subject to time-based vesting, with 100% of the shares of common stock subject to the RSU award vesting three years from the grant date. As of June 30, 2022, 813,604 shares remain available for grant under the 2017 Inducement Plan, as well as any shares underlying awards that may become available for grant pursuant to the plan’s terms.

Stock Options

A summary of stock option activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Exercise Price		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2021	2,051,484	$	10.92	5.12	$	303
Granted	187,660	$	2.94
Exercised	(1,646)	$	3.58
Cancelled or forfeited	(117,910)	$	12.94
Outstanding at June 30, 2022	2,119,588	$	10.10	4.96	$	—
Exercisable at June 30, 2022	1,756,972	$	11.30	4.12	$	—

The total intrinsic value of stock options exercised was insignificant for the six months ended June 30, 2022.

Restricted Stock Units

A summary of RSU activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Grant Date Fair Value
Unvested balance at December 31, 2021	4,920,063	$	5.82
Granted	2,961,140	3.09
Released	(432,982)	6.13
Forfeited	(234,689)	5.40
Unvested balance at June 30, 2022	7,213,532	$	4.69

Total unrecognized stock-based compensation expense for all stock-based awards was $19.1 million as of June 30, 2022. This amount will be recognized over a weighted-average period of 1.62 years.

2009 Employee Stock Purchase Plan

In June 2009, at the annual meeting of stockholders, the stockholders of the Company approved the 2009 Employee Stock Purchase Plan, or the 2009 ESPP. As of June 30, 2022, 36,539 shares were available for issuance under the 2009 ESPP. Since the merger involving privately-held Paratek Pharmaceuticals, Inc. and Transcept Pharmaceuticals, Inc., the Company has not made the 2009 ESPP available to employees.

2018 Employee Stock Purchase Plan

The Company’s Board of Directors adopted, and in June 2018 Company’s stockholders approved, the Paratek Pharmaceuticals, Inc. 2018 Employee Stock Purchase Plan, or the 2018 ESPP. The 2018 ESPP was amended in October 2018 to change the commencement dates of the offering periods. The maximum aggregate number of shares of the Company’s common stock that may be purchased under the 2018 ESPP is 943,294 shares, or the ESPP Share Pool, subject to adjustment as provided for in the 2018 ESPP. The ESPP Share Pool represented 3% of the total number of shares of our common stock outstanding as of March 31, 2018. The 2018 ESPP allows eligible employees to purchase shares during certain offering periods, which will be 6 -month periods commencing June 1 and ending November 30 and commencing December 1 and ending May 31 of each year. The first offering under the 2018 ESPP was December 1, 2018. As of June 30, 2022, 123,199 shares remained available for issuance under the 2018 ESPP. During the six months ended June 30, 2022, the Company recognized an insignificant amount of stock-based compensation expense related to the 2018 ESPP.

Revenue Performance Incentive Plan

On October 4, 2018, the Company adopted the Revenue Performance Incentive Plan, or the Plan, to grant performance-based cash incentive awards to key employees and consultants of the Company. The Plan provides for an incentive pool of up to $50.0 million, plus accrued interest during the period between the awards’ vesting date and payment dates. Each participant will be allocated a percentage of the incentive pool.

The incentive pool will be divided into two equal tranches with the first tranche vesting upon the Company’s achievement of cumulative net product revenues over $300.0 million by December 31, 2025, or Tranche 1, and the second tranche vesting upon the Company’s achievement of cumulative product revenues over $600.0 million by December 31, 2026, or Tranche 2. Participants will vest annually in each tranche of their awards in four equal installments on December 31, 2019, December 31, 2020, December 31, 2021, and December 31, 2022, subject to their continued employment with the Company through the applicable vesting date. If a participant’s employment terminates prior to December 31, 2022 due to death or disability, the participant will automatically vest in an additional 25% of each tranche of his or her award. Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant who has remained in continuous employment with the Company through December 31, 2022 will be 100% vested in the applicable tranche. In the event of a change of control of the Company prior to December 31, 2026, participants whose employment has terminated prior to such date will be eligible for payouts under the Plan based on the

then-vested portion of their awards, and participants who have remained employed through the change of control will be deemed to have time vested in full in each tranche of their awards.

Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant’s payout in respect of the applicable tranche of his or her award will equal (a) the participant’s then-vested percentage, multiplied by (b) $25 million, multiplied by (c) the participant’s individual percentage allocation of the incentive pool.

If a change of control occurs prior to December 31, 2026, and the Tranche 1 milestone was not achieved prior to the change of control, the Tranche 1 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 50% and (2) the cumulative product revenues as of the change of control, divided by $300.0 million. If a change of control occurs prior to December 31, 2026, and the Tranche 2 milestone was not achieved prior to the change of control, the Tranche 2 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 30% and (2) the cumulative product revenues as of the change of control, divided by $600.0 million. A participant’s payout in respect of each tranche of his or her award in a change of control will equal (1) the participant’s then-vested percentage of such tranche, multiplied by (2) the percentage of that tranche’s milestone that has been achieved or is deemed to have been achieved, multiplied by (3)$25.0 million, multiplied by (4) the participant’s individual percentage allocation of the incentive pool.

Amounts that become payable upon achievement of the Tranche 1 milestone will be paid in a lump-sum in the first quarter of 2026 and amounts that become payable upon achievement of the Tranche 2 milestone will be paid in a lump-sum in the first quarter of 2027. In the event of a change of control, any portion of the incentive pool that is earned, but unpaid, or deemed earned in connection with the change of control will be paid at the time of the change of control.

If a change of control occurs prior to the achievement of either or both of the Tranche 1 and Tranche 2 milestones, the awards will remain outstanding and the remaining unpaid portion of the incentive pool applicable to the Tranche 1 or Tranche 2 milestone, as applicable, will be paid following the achievement of either such milestone at the time or times the awards would otherwise be paid out. Any successor in interest to the Company upon or following a change of control will be required to assume all obligations under the Plan.

Awards may be paid out in cash or in a combination of cash and registered securities of equal value (based on the Company’s 20-day trailing average closing common stock price), with the portion paid in registered securities not to exceed 50% of the aggregate payment amount with respect to each tranche; provided, however, that any amounts that are immediately payable on closing with respect to an award in connection with a change in control will be paid in cash.

The Company recognizes the compensation cost over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance. The performance condition under the first tranche of the Plan was deemed probable during 2021. $0.5 million of compensation expense was recognized during the six months ended June 30, 2022. No such compensation expense was recognized during the six months ended June 30, 2021. Compensation cost of $22.3 million and $21.8 million is included in accrued long-term compensation in the Company’s consolidated balance sheet as of June 30, 2022 and December 31, 2021, respectively.

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Long-Term Debt

6 Months Ended

Jun. 30, 2022

Debt Disclosure [Abstract]

Long-Term Debt

Long-Term Debt

R-Bridge Loan Agreement

On December 31, 2020, or the Closing Date, the Company, through its wholly-owned subsidiary PRTK SPV2 LLC, a Delaware limited liability company, or the Subsidiary, entered into a royalty and revenue interest-backed loan agreement, or the R-Bridge Loan Agreement, with an affiliate of R-Bridge Healthcare Investment Advisory, Ltd., or the R-Bridge Lender. Pursuant to the terms of the R-Bridge Loan Agreement, the Subsidiary borrowed a $60.0 million term loan, secured by, and repaid with proceeds from, (i) royalties from the Zai Collaboration Agreement, and such royalties, or the Royalty Interest, and (ii) a revenue interest based on the Company’s U.S. sales of NUZYRA in an initial amount of two and a half percent (2.5%), which amount may adjust under certain circumstances up to five percent (5%), of the Company’s net U.S. sales, subject to an annual cap of $10.0 million, which may adjust under certain circumstances to $12.0 million, or the Revenue Interest.

Under the R-Bridge Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 7.0%, increasing to an annual rate of 10% during the continuance of any event of default. Payments of the obligations outstanding under the R-Bridge Loan Agreement are made quarterly out of the Royalty Interest payments and Revenue Interest payments received by the Subsidiary during such quarter, or the Collection Amount. On each payment date, after payment of certain expenses, the Collection Amount shall be applied first to accrued interest, with any excess up to $15.0 million per annum applied to repay principal until the balance is fully repaid, and any shortfalls being capitalized and added to the principal balance of the loan. Amounts in excess of the $15.0 million annual cap shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement. Following repayment in full of the loan, the first $15.0 million per annum in Collection Amount shall be paid to the Company and any amounts in excess shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement.

Prior to the eighth (8th) anniversary of the Closing Date, the R-Bridge Loan Agreement will automatically terminate once the Subsidiary has paid to the R-Bridge Lender, in the form of regularly scheduled payments or as a voluntary prepayment, a capped amount of $114.0 million, less principal, interest and certain fee payments through the date of such prepayment, or the Capped Amount. From and after the eighth (8th) anniversary of the Closing Date, the Revenue Interest can be terminated by payment of the Capped Amount, but the Royalty Interest payments shall continue until maturity of the R-Bridge Loan Agreement on December 31, 2032, at which time, the outstanding principal amount of the loan, if any, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash by the Subsidiary.

The Company’s subsidiary, PRTK SPV1 LLC, a Delaware limited liability company and owner of the Subsidiary’s capital stock, has entered into a Pledge and Security Agreement in favor of the R-Bridge Lender, pursuant to which the Subsidiary’s obligations under the R-Bridge Loan Agreement are secured by PRTK SPV1 LLC’s pledge of all of the Subsidiary’s capital stock.

The R-Bridge Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The R-Bridge Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Zai Collaboration Agreement; and permitting any additional liens on the collateral provided to the R-Bridge Lender under the R-Bridge Loan Agreement. As of June 30, 2022, the Company was in compliance with all covenants under the R-Bridge Loan Agreement.

An ancillary agreement executed by the Company and the Subsidiary in respect of the Revenue Interest, contains negative covenants applicable to the Company, including restrictions on the sale or transfer of our assets related to NUZYRA and giving rise to the Revenue Interest, each subject to the exceptions set forth therein.

The R-Bridge Loan Agreement contains customary defined events of default, upon which any outstanding principal, unpaid interest, and other obligations of the Subsidiary, shall be immediately due and payable by the Subsidiary. These include: failure to pay any principal or interest when due; failure to pay the Capped Amount when due following a non-qualified change of control of the Company, any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured breach of our representations, warranties or covenants under an ancillary agreement executed by the Company and the Subsidiary in respect of the Royalty Interest; any termination of the Zai Collaboration Agreement; and certain bankruptcy or insolvency events. No events of default had occurred under the R-Bridge Loan Agreement through June 30, 2022.

The Company raised approximately $58.3 million in net proceeds in connection with the R-Bridge Loan Agreement, comprised of the $60.0 million term loan funded at execution, net of $1.1 million in lender fees accounted for as debt discount and $0.6 million in direct and incremental third-party expenses accounted for as debt issuance costs. The net proceeds of the term loan, together with cash on hand, was used to prepay in full all obligations outstanding under our loan arrangement with Hercules Capital, Inc.

The accounting for the R-Bridge Loan Agreement requires the Company to make certain estimates and assumptions, particularly about future royalties under the Zai Collaboration Agreement and sales of NUZYRA in the U.S. Such estimates and assumptions are utilized in determining the expected repayment term, amortization period of the debt discount and issuance costs, accretion of interest expense and classification between current and long-term portions of amounts outstanding. The Company amortizes the debt discount and issuance costs to interest expense over the expected term of the arrangement using the interest method based on projected cash flows. Similarly, the Company classifies as current debt for the R-Bridge Loan Agreement, amounts that are expected to be repaid during the succeeding twelve months after the reporting period end. However, the repayment of amounts due under the R-Bridge Loan Agreement is variable because the cash flows to be utilized for periodic payments is a function of amounts received by the Company with respect to the Royalty Interest and the Revenue Interest. Accordingly, the estimates of the magnitude and timing of amounts to be available for debt service are subject to significant variability and thus, subject to significant uncertainty. Therefore, these estimates and assumptions are likely to change, which may result in future adjustments to the portion of the debt that is classified as a current liability, the amortization of debt discount and issuance costs and the accretion of interest expense.

The amount of principal to be repaid in each of the five succeeding years is not fixed and determinable.

Other amounts that may become due and payable under the R-Bridge Loan Agreement, including amounts shared between the parties with respect to cash flows received in excess of pre-defined thresholds, are recognized as additional interest expense when they become probable and estimable.

The following table summarizes the impact of the R-Bridge Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	62,025	$	61,256
Unamortized debt discount and issuance costs	(1,326)		(1,443)
Carrying value	$	60,699	$	59,813

During the six months ended June 30, 2022, $0.8 million of paid-in-kind interest was capitalized and added to the principal balance of the loan, which represents the shortfall between the interest owed and the Collection Amount.

The Company recognized interest expense of $1.1 million and $2.2 million, and an insignificant amount of amortization expense on the debt issuance costs, on the R-Bridge Loan Agreement for the three and six months ended June 30, 2022, respectively.

Convertible Senior Subordinated Notes

On April 18, 2018, the Company entered into a Purchase Agreement, or the Purchase Agreement, with several initial purchasers, or the Initial Purchasers, for whom Merrill Lynch, Pierce, Fenner & Smith Incorporated and Leerink Partners LLC acted as representatives, relating to the sale of $135.0 million aggregate principal amount of 4.75% Convertible Senior Subordinated Notes due 2024, or the Notes, to the Initial Purchasers. The Company also granted the Initial Purchasers an option to purchase up to an additional $25.0 million aggregate principal amount of Notes, which was exercised in full on April 20, 2018.

The Purchase Agreement includes customary representations, warranties and covenants. Under the terms of the Purchase Agreement, the Company agreed to indemnify the Initial Purchasers against certain liabilities.

In addition, J. Wood Capital Advisors LLC, the Company’s financial advisor, purchased $5.0 million aggregate principal amount of Notes in a separate, concurrent private placement on the same terms as other investors.

The Notes were issued by the Company on April 23, 2018, pursuant to an Indenture, dated as of such date, or the Indenture, between the Company and U.S. Bank National Association, as trustee, or the Trustee. The Notes bear cash interest at the annual rate of 4.75%, payable on November 1 and May 1 of each year, beginning on November 1, 2018, and mature on May 1, 2024 unless earlier repurchased, redeemed or converted. The Company will settle conversions of the Notes through delivery of shares of common stock of the Company, in accordance with the terms of the Indenture. The

initial conversion rate for the Notes is 62.8931 shares of common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the Notes, which is equal to an initial conversion price of approximately $15.90 per share, representing a conversion premium of approximately 20% above the closing price of the common stock of $13.25 per share on April 18, 2018.

Holders of the Notes may convert all or any portion of their Notes, in multiples of $1,000 principal amount, at their option at any time prior to the close of business on the second scheduled trading day immediately preceding the stated maturity date.

The Company may redeem for cash all or part of the Notes, at its option, on or after May 6, 2021, if the last reported sale price of the Company’s common stock has been at least 130% of the conversion price then in effect for at least 20 20 trading days (whether or not consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption at a redemption price equal to 100% of the principal amount of the Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date.

If the Company experiences a fundamental change, as described in the Indenture, prior to the maturity date of the Notes, holders of the Notes will, subject to specified conditions, have the right, at their option, to require the Company to repurchase for cash all or a portion of their Notes at a repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date. In addition, following certain corporate events that occur prior to the maturity date of the Notes and following a notice of redemption of the Notes, the Company will increase the conversion rate for a holder who elects to convert its Notes in connection with such corporate event or redemption.

The Indenture provides for customary events of default. In the case of an event of default with respect to the Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the Notes under the Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes may declare the principal amount of the Notes to be immediately due and payable.

After deducting costs incurred of $6.0 million, the Company raised net proceeds from the issuance of long-term convertible debt of $159.0 million in April 2018. All costs were deferred and are being amortized over the life of the Notes at an effective interest rate of 5.47% and recorded as additional interest expense.

The Company has evaluated the Indenture for derivatives pursuant to ASC 815, Derivatives and Hedging, or ASC 815, and identified an embedded derivative that requires bifurcation as the feature is not clearly and closely related to the host instrument. The embedded derivative is a default provision, which could require additional interest payments. The Company determined in the prior year that the fair value of this embedded derivative was nominal.

The Company evaluated the conversion feature and determined it was not within the scope of ASC 815 and therefore is not required to be accounted for separately. The Company concluded that the embedded conversion option is not subject to separate accounting pursuant to either the cash conversion guidance or the beneficial conversion feature guidance. Under the general conversion guidance in ASC 470, Debt, all of the proceeds received from the Notes was recorded as a liability on the condensed consolidated balance sheet.

The following table summarizes the impact of the Notes on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt	$	165,000	$	165,000
Unamortized debt issuance costs	(2,048)		(2,572)
Carrying value	$	162,952	$	162,428

The Company recognized coupon interest expense of $2.0 million and $3.9 million, and amortization expense on the debt issuance costs of $0.3 million and $0.5 million, on the Notes for the three and six months ended June 30, 2022, respectively.

Royalty-Backed Loan Agreement

On February 25, 2019, the Company, through its wholly-owned subsidiary Paratek Royalty Corporation, or the Subsidiary, entered into the Royalty-Backed Loan Agreement with HCRP. Pursuant to the terms of the Royalty-Backed Loan Agreement, upon the satisfaction of the conditions precedent set forth therein, the Subsidiary borrowed a $32.5 million loan, which was secured by, and will be repaid based upon, royalties from the Almirall Collaboration Agreement. On May 1, 2019, the Company received $27.8 million, net of $0.5 million lender discount, $0.2 million in lender expenses incurred, and $4.0 million that was deposited into an interest reserve account. The Company also paid $1.2 million in other lender fees related to the Royalty-Backed Loan Agreement.

Under the Royalty-Backed Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 12.0%. Payments of interest under the Royalty-Backed Loan Agreement are made quarterly out of the Almirall Collaboration Agreement royalty payments received since the immediately preceding payment date. On each interest payment date, any royalty payments in excess of accrued interest on the loan will be used to repay the principal of the loan until the balance is fully repaid and any royalty shortfalls will be capitalized and added to the principal balance of the loan. In addition, the Subsidiary made up-front payments to HCRP of (i) a 1.5% fee and (ii) up to $300,000 for HCRP’s expenses. The Royalty-Backed Loan Agreement matures on May 1, 2029, at which time, if not earlier repaid in full, the outstanding principal amount of the loan, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash. The Company has entered into a Pledge and Security Agreement in favor of HCRP, pursuant to which the Subsidiary’s obligations under the Royalty-Backed Loan Agreement are secured by a pledge of all of the Company’s holdings of the Subsidiary’s capital stock.

The Royalty-Backed Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The Royalty-Backed Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Almirall Collaboration Agreement; and permitting any additional liens on the collateral provided to HCRP under the Royalty-Backed Loan Agreement.

The Royalty-Backed Loan Agreement contains customary defined events of default, upon which any outstanding principal and unpaid interest shall be immediately due and payable. These include: failure to pay any principal or interest when due; any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured cross default under a material contract; any uncured breach of the Company’s representations, warranties or covenants under its Contribution and Servicing Agreement with the Subsidiary; any termination of the Almirall Collaboration Agreement; and certain bankruptcy or insolvency events.

The following table summarizes the impact of the Royalty-Backed Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	35,101	$	33,860
Unamortized debt issuance costs	(1,599)		(1,673)
Carrying value	$	33,502	$	32,187

During the six months ended June 30, 2022, $1.2 million of paid-in-kind interest was capitalized and added to the principal balance of the loan, which represents the shortfall between the interest owed, and the Almirall Collaboration Agreement royalty payments received.

The Company recognized interest expense of $1.0 million and $2.0 million and an insignificant amount of amortization expense on the debt issuance costs on the Royalty-Backed Loan Agreement for the three and six months ended June 30, 2022, respectively.

Debt issuance costs are presented on the consolidated balance sheet as a direct deduction from the related debt liability rather than capitalized as an asset in accordance with ASU No. 2015-03, Interest - Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs.

Long-term debt on the Company’s consolidated balance sheets at June 30, 2022 and December 31, 2021 includes the carrying value of the R-Bridge Loan Agreement, the Notes and the Royalty-Backed Loan Agreement.

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Leases

6 Months Ended

Jun. 30, 2022

Leases [Abstract]

Leases

Leases

Operating Leases

The Company leases its Boston, Massachusetts and King of Prussia, Pennsylvania office spaces under non-cancelable operating leases expiring in 2023 and 2024, respectively.

The Company executed an amendment to the existing lease agreement on its Boston office space in April 2021. The amended lease agreement released 8,104 rentable square feet of office space and extends the lease term for the remaining 4,153 rentable square feet of office space through August 2023 for an additional commitment of $0.4 million. In accordance with the amendment, the Company will be refunded the insignificant security deposit paid in July 2016.

The Company executed an amended lease agreement on its King of Prussia office space in October 2016. The amended lease agreement is for 19,708 rentable square feet of office space and the Company took control of this office space during the first quarter of 2017. The total lease commitment is over a seven-year and seven-month lease term. The amended lease agreement contains rent escalation and a partial rent abatement period, which is accounted for as rent expense under the straight-line method.

The Company has also identified an embedded lease in its manufacturing and services agreement with CIPAN – Companhia Industrial Produtora de Antibióticos, or CIPAN, which was later amended and restated in April 2018, and further amended and restated in February 2019, December 2019, July 2020, and December 2020. For additional details relating to these agreements, refer to Note 18, Commitments and Contingencies of the 2021 Form 10-K.

The total operating lease liability is presented on the Company’s condensed consolidated balance sheet based on maturity dates. $0.7 million of the total operating leases liabilities is classified under “other current liabilities” for the portion due within twelve months of June 30, 2022, and $0.7 million is classified under “long-term lease liability”.

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Income Taxes

6 Months Ended

Jun. 30, 2022

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

The Company recorded no provision for income taxes for the three or six months ended June 30, 2022 and June 30, 2021.

Deferred tax assets and deferred tax liabilities are recognized based on temporary differences between the financial reporting and tax bases of assets and liabilities using statutory rates. Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets, which are comprised principally of net operating loss carryforwards and research and development credits. Under the applicable accounting standards, management has considered the Company’s history of losses and concluded that it is more likely than not that the Company will not recognize the benefits of federal and state deferred tax assets. Accordingly, a full valuation allowance has been established against the Company’s otherwise recognizable net deferred tax assets.

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Product Revenue

6 Months Ended

Jun. 30, 2022

Revenue from Contract with Customer [Abstract]

Product Revenue

Product Revenue

To date, the Company’s only source of product revenue has been from NUZYRA product sales beginning in February 2019 when NUZYRA was launched in the U.S. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories (in thousands):

	Chargebacks, discounts and fees		Government and other rebates		Returns		Patient assistance		Total
Balance at December 31, 2021	$	1,006	$	5,198	$	469	$	339	$	7,012
Provision related to current period sales	3,472		10,256		595		538		14,861
Adjustment related to prior period sales	(32)		(38)		(373)		—		(443)
Credit or payments made during the period	(3,101)		(8,451)		(624)		(483)		(12,659)
Balance at June 30, 2022	$	1,345	$	6,965	$	67	$	394	$	8,771

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Commitments and Contingencies

6 Months Ended

Jun. 30, 2022

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

In the ordinary course of business, the Company is from time to time involved in lawsuits, claims, investigations, proceedings, and threats of litigation relating to intellectual property, commercial arrangements, employment and other matters. While the outcome of these proceedings and claims cannot be predicted with certainty, as of June 30, 2022, the Company was not party to any legal or arbitration proceedings that may have, or have had in the recent past, significant effects on the Company’s financial position. No governmental proceedings are pending or, to the Company’s knowledge, contemplated against the Company. The Company is not a party to any material proceedings in which any director, member of executive management or affiliate of the Company is either a party adverse to the Company or the Company’s subsidiaries or has a material interest adverse to the Company or the Company’s subsidiaries.

In July 2021, the Company entered into a supply agreement with CARBOGEN AMCIS AG, or Carbogen, that provides for the terms and conditions under which Carbogen will manufacture and supply to the Company the active pharmaceutical ingredient for the Company’s omadacycline product in bulk quantities, or the Carbogen Product. Under this agreement, the Company is responsible for the cost and supply of crude omadacycline that Carbogen requires to manufacture the Carbogen Product and perform related services. The Company is obligated to initially pay Carbogen an amount in the high six-digit U.S. dollar range per batch of Carbogen Product that the Company orders, and the price may be adjusted in accordance with the terms of the agreement. The Company may also request that Carbogen perform certain services related to the Carbogen Product, for which the Company will pay reasonable compensation to Carbogen.

The agreement will remain in effect for a fixed initial term. If neither party has provided notice of its intent to terminate the agreement prior to the end of the initial term, then the Agreement will automatically be extended for a fixed period of time. The agreement may be terminated under certain circumstances, including by either party delivering notice of termination following the initial term, or by either party due to a material uncured breach by the other party or the other party’s insolvency.

In November 2016, the Company entered into a manufacturing and services agreement, or MSA, with CIPAN, which was later amended and restated in April 2018, and further amended in February 2019, December 2019, July 2020, December 2020, and January 2022, collectively, the CIPAN Agreements. The CIPAN Agreements provide the terms and conditions under which CIPAN will manufacture and supply to the Company increased quantities of minocycline starting material and crude omadacycline, or the CIPAN Products, for purification into omadacycline and, subsequently, for use in the Company’s products that contain omadacycline tosylate as the active pharmaceutical ingredient.

Additionally, the CIPAN Agreements included an investment by the Company in a new facility area to increase the manufacturing capacity for production of crude omadacycline. The Company was required to make advance payments to CIPAN upon completion of certain milestones within the CIPAN Agreements.

The term of the CIPAN Agreements will continue throughout the term that the Company receives benefit from the new facility area. The Company may renew the CIPAN Agreements for additional periods and can terminate the CIPAN Agreements at any time by delivery, within a certain time period, of prior written notice to CIPAN. Following the first renewal term, CIPAN may terminate the MSA in its entirety by delivery, within a certain time period, of prior written notice to the Company.

Under the CIPAN Agreements, the Company will purchase product in batches from CIPAN in quantities to be set forth on purchase orders submitted to CIPAN, within a certain time period, prior to the requested date of delivery. The Company will provide CIPAN with a rolling forecast with a best estimate of the quantities that will be ordered each month. Upon execution of the CIPAN Agreements, the Company determined that the CIPAN Agreements contain an embedded lease because the Company has the right to direct the use of the facility and related equipment therein. Further, the Company determined that it did not control the facility or related equipment during construction and, thus, the lease did not fall in the scope of “build-to-suit” accounting. The lease commenced during the fourth quarter of 2020, the point at which the new facility area and the related equipment was available for use by the Company.

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Recent Accounting Pronouncements

6 Months Ended

Jun. 30, 2022

Accounting Changes and Error Corrections [Abstract]

Recent Accounting Pronouncements

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption.

In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, or ASU 2016-13. The FASB subsequently issued amendments to ASU 2016-13, which have the same effective date and transition date of January 1, 2023. These standards require that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, these standards now require allowances to be recorded instead of reducing the amortized cost of the investment. These standards limit the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases. Based on the composition of our investment portfolio, accounts receivable and other financial assets, current market conditions and historical credit loss activity, the adoption of these standards is not expected to have a material effect on the Company’s consolidated balance sheet, consolidated statements of operation and comprehensive loss and related disclosures.

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Summary of Significant Accounting Policies and Basis of Presentation (Policies)

6 Months Ended

Jun. 30, 2022

Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or U.S. GAAP, as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB, and pursuant to the rules and regulations of the SEC.

The accompanying condensed consolidated financial statements are unaudited. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements as

of and for the year ended December 31, 2021, and, in the opinion of management, reflect all normal recurring adjustments necessary for the fair presentation of the Company’s financial position as of June 30, 2022 and December 31, 2021, results of operations for the three and six month periods ended June 30, 2022 and June 30, 2021, cash flows for the six month periods ended June 30, 2022 and June 30, 2021 and changes in stockholders’ deficit for the three and six month periods ended June 30, 2022 and June 30, 2021.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2022. These unaudited interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements as of and for the year ended December 31, 2021, and notes thereto, which are included in the Company’s 2021 Form 10-K.

Summary of Significant Accounting Policies

Summary of Significant Accounting PoliciesAs of June 30, 2022, the Company’s significant accounting policies and estimates, which are detailed in the Company’s 2021 Form 10-K, have not changed.

Principles of Consolidation

Principles of Consolidation

The accompanying unaudited condensed consolidated financial statements include the results of operations of Paratek Pharmaceuticals, Inc. and its wholly-owned subsidiaries, Paratek Pharma, LLC, Paratek Securities Corporation, Transcept Pharma, Inc., Paratek Ireland Limited, Paratek Royalty Corporation, Paratek Royalty Corporation II, PRTK SPV1 LLC and PRTK SPV2 LLC. All significant intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

Use of Estimates

The preparation of the accompanying unaudited condensed consolidated financial statements, in conformity with U.S. GAAP, requires the Company to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses in the Company’s financial statements. On an ongoing basis, the Company evaluates its estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement (as defined below), manufacturing and clinical accruals, useful lives for depreciation and valuation allowances on deferred tax assets. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known by the Company’s management.

Segment and Geographic Information

Segment and Geographic Information

Operating segments are defined as components of an enterprise engaging in business activities for which discrete financial information is available and regularly reviewed by the chief operating decision maker in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating segment.

Concentration of Credit Risk

Concentration of Credit Risk

Financial instruments that subject the Company to credit risk consist primarily of cash, restricted cash, and accounts receivable. The Company places its cash in an accredited financial institution and this balance is above federally insured amounts. The Company has no off-balance sheet concentrations of credit risk such as foreign currency exchange contracts, option contracts or other hedging arrangements.

Accounts receivable as of June 30, 2022 includes $24.4 million due from customers for sales of NUZYRA, net of prompt payment discounts, chargebacks, rebates and certain fees. Accounts receivable as of June 30, 2022 also includes $1.1 million of government contract service revenue earned under contract with the Biomedical Advanced Research and Development Authority, or the BARDA contract, $1.4 million of government contract grant revenue earned under the BARDA contract, and estimated revenue earned of $0.6 million of royalties on SEYSARA sales under the Almirall Collaboration Agreement (as defined below) and XERAVA TM (eravacycline) sales under the Tetraphase License Agreement (as defined below). Refer to Note 7, Government Contract Revenue for further information on the BARDA contract and to Note 8, License and Collaboration Agreements for further information on the Almirall Collaboration Agreement and the Tetraphase License Agreement.

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption.

In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, or ASU 2016-13. The FASB subsequently issued amendments to ASU 2016-13, which have the same effective date and transition date of January 1, 2023. These standards require that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, these standards now require allowances to be recorded instead of reducing the amortized cost of the investment. These standards limit the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases. Based on the composition of our investment portfolio, accounts receivable and other financial assets, current market conditions and historical credit loss activity, the adoption of these standards is not expected to have a material effect on the Company’s consolidated balance sheet, consolidated statements of operation and comprehensive loss and related disclosures.

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Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2022

Marketable Securities [Abstract]

Marketable Securities

The following are summaries of available-for-sale securities as of June 30, 2022 and December 31, 2021 (in thousands):

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
June 30, 2022
U.S. treasury securities	$	30,119	$	—	$	(233)	$	29,886
Total	$	30,119	$	—	$	(233)	$	29,886

	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
December 31, 2021
U.S. treasury securities	$	15,116	$	—	$	(9)	$	15,107
Total	$	15,116	$	—	$	(9)	$	15,107

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Cash and Cash Equivalents and Restricted Cash (Tables)

6 Months Ended

Jun. 30, 2022

Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents [Abstract]

Cash, cash equivalents and investments

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the condensed consolidated statement of cash flows that sum to the total of the same such amounts shown in the condensed consolidated statement of cash flows (in thousands):

	June 30, 2022		June 30, 2021
Cash and cash equivalents	$	39,505	$	75,298
Short-term restricted cash	—		125
Long-term restricted cash	125		125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$	39,630	$	75,548

Restrictions on cash and cash equivalents

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the condensed consolidated statement of cash flows that sum to the total of the same such amounts shown in the condensed consolidated statement of cash flows (in thousands):

	June 30, 2022		June 30, 2021
Cash and cash equivalents	$	39,505	$	75,298
Short-term restricted cash	—		125
Long-term restricted cash	125		125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$	39,630	$	75,548

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Inventories (Tables)

6 Months Ended

Jun. 30, 2022

Inventory Disclosure [Abstract]

Schedule of Inventories

The following table presents inventories, net (in thousands):

	June 30, 2022		December 31, 2021
Raw materials	$	903	$	1,082
Work in process	27,351		24,675
Finished goods	17,491		13,030
Total inventories	$	45,745	$	38,787

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Net Income (Loss) Per Share (Tables)

6 Months Ended

Jun. 30, 2022

Earnings Per Share [Abstract]

Antidilutive Shares Excluded from Computation of Diluted Net Income (Loss) Per Share

The following outstanding shares subject to stock options and RSUs, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the Company’s employee stock purchase plan were antidilutive due to a net loss in the periods presented and, therefore, were excluded from the dilutive securities computation for the three and six months ended June 30, 2022 as indicated below:

	Three and Six Months Ended June 30,
	2022
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361
Shares subject to outstanding options to purchase common stock	2,119,588
Unvested restricted stock units	7,213,532
Shares subject to warrants to purchase common stock	426,866
Shares issuable under employee stock purchase plan	159,738
Totals	20,297,085

(1) The number of shares is based on the maximum number of shares issuable on exercise or conversion of the related securities as of June 30, 2022. Such amounts have not been adjusted for the treasury-stock method or weighted-average outstanding calculations as required if the securities were dilutive.

The following outstanding shares of common stock equivalents were excluded from the computation of net income (loss) per share attributable to common stockholders for the periods presented because including them would have been antidilutive:

	Three Months Ended June 30, 2021	Six Months Ended June 30, 2021
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361	10,377,361
Shares subject to warrants to purchase common stock	469,388	469,388
Shares subject to outstanding options to purchase common stock	1,057,092	2,103,326
Unvested restricted stock units	—	5,917,615
Shares issuable under employee stock purchase plan	—	542,896
Totals	11,903,841	19,410,586

(1) 2,672,999 performance-based RSUs were excluded from the computation of net income (loss) per share as the performance conditions were not satisfied as of June 30, 2021.

Schedule of Earnings Per Share, Basic and Diluted

Basic and diluted earnings (loss) per common share were determined as follows:

	Three Months Ended June 30, 2022		Three Months Ended June 30, 2021		Six Months Ended June 30, 2022		Six Months Ended June 30, 2021
Basic
Net income (loss)	$	(17,619)	$	9,717	$	(35,527)	$	(8,629)
Undistributed earnings allocated to warrants	—		(96)		—		—
Net income (loss)	$	(17,619)	$	9,621	$	(35,527)	$	(8,629)
Weighted average common shares outstanding	53,023,350		47,122,717		53,310,091		46,894,812
Basic earnings (loss) per common share	$	(0.33)	$	0.20	$	(0.67)	$	(0.18)
Diluted
Net income (loss)	$	(17,619)	$	9,717	$	(35,527)	$	(8,629)
Undistributed earnings allocated to warrants	—		(96)				—
Net income (loss)	$	(17,619)	$	9,621	$	(35,527)	$	(8,629)
Weighted average common shares outstanding	53,023,350		47,122,717		53,310,091		46,894,812
Effect of dilutive stock options	—		366,793				—
Effect of dilutive restricted stock units	—		1,456,226
Weighted average common shares outstanding assuming dilution	53,023,350		48,945,736		53,310,091		46,894,812
Diluted earnings (loss) per common share	$	(0.33)	$	0.20	$	(0.67)	$	(0.18)

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Accrued Expenses (Tables)

6 Months Ended

Jun. 30, 2022

Payables and Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consist of the following (in thousands):

	June 30,		December 31,
	2022		2021
Accrued sales allowances	$	8,771	$	7,012
Accrued compensation	6,180		8,935
Accrued interest	2,389		2,365
Accrued commercial	2,372		1,654
Accrued inventory	2,446		307
Accrued contract research	1,151		1,019
Accrued professional fees	907		781
Accrued manufacturing	714		670
Accrued other	440		361
Accrued legal costs	291		342
Total	$	25,661	$	23,446

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Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2022

Fair Value Disclosures [Abstract]

Schedule of Financial Assets and Liabilities Measured at Fair Value

Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability (in thousands):

Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		June 30, 2022
Assets:
U.S. treasury securities	$	29,886	$	—	$	—	$	29,886
Total Assets	$	29,886	$	—	$	—	$	29,886

Description	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		December 31, 2021
Assets:
U.S. treasury securities	$	15,107	$	—	$	—	$	15,107
Total Assets	$	15,107	$	—	$	—	$	15,107

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Stock-Based and Incentive Compensation (Tables)

6 Months Ended

Jun. 30, 2022

Share-based Payment Arrangement [Abstract]

Summary of Stock-Based Compensation Expense Included in Company's Condensed Consolidated Statements of Operations and Comprehensive Income (Loss)

The following table presents stock-based compensation expense included in the Company’s condensed consolidated statements of operations and comprehensive income (loss) (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2022		2021		2022		2021
Research and development expense	$	515	$	793	$	692	$	1,116
Selling, general and administrative expense	3,371		4,210		5,662		5,486
Total stock-based compensation expense	$	3,886	$	5,003	$	6,354	$	6,602

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions

The weighted-average assumptions used to determine the fair value of the stock option grants is as follows:

	Six Months Ended June 30,
	2022		2021
Volatility	62.2	%	63.2	%
Risk-free interest rate	2.3	%	0.7	%
Expected dividend yield	0.0	%	0.0	%
Expected life of options (in years)	5.9		5.9

Schedule of Share-based Compensation, Stock Options, Activity

A summary of stock option activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Exercise Price		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2021	2,051,484	$	10.92	5.12	$	303
Granted	187,660	$	2.94
Exercised	(1,646)	$	3.58
Cancelled or forfeited	(117,910)	$	12.94
Outstanding at June 30, 2022	2,119,588	$	10.10	4.96	$	—
Exercisable at June 30, 2022	1,756,972	$	11.30	4.12	$	—

Schedule of Share-based Compensation, Restricted Stock Unit, Activity

A summary of RSU activity for the six months ended June 30, 2022 is as follows:

	Number of Shares	Weighted Average Grant Date Fair Value
Unvested balance at December 31, 2021	4,920,063	$	5.82
Granted	2,961,140	3.09
Released	(432,982)	6.13
Forfeited	(234,689)	5.40
Unvested balance at June 30, 2022	7,213,532	$	4.69

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Long-Term Debt (Tables)

6 Months Ended

Jun. 30, 2022

Debt Disclosure [Abstract]

Summary of Debt

The following table summarizes the impact of the R-Bridge Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	62,025	$	61,256
Unamortized debt discount and issuance costs	(1,326)		(1,443)
Carrying value	$	60,699	$	59,813

The following table summarizes the impact of the Notes on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt	$	165,000	$	165,000
Unamortized debt issuance costs	(2,048)		(2,572)
Carrying value	$	162,952	$	162,428

The following table summarizes the impact of the Royalty-Backed Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2022 and December 31, 2021 (in thousands):

	June 30, 2022		December 31, 2021
Principal debt including paid-in-kind interest	$	35,101	$	33,860
Unamortized debt issuance costs	(1,599)		(1,673)
Carrying value	$	33,502	$	32,187

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Product Revenue (Tables)

6 Months Ended

Jun. 30, 2022

Revenue from Contract with Customer [Abstract]

Schedule of Product Revenue Allowance and Reserve Categories

The following table summarizes balances and activity in each of the product revenue allowance and reserve categories (in thousands):

	Chargebacks, discounts and fees		Government and other rebates		Returns		Patient assistance		Total
Balance at December 31, 2021	$	1,006	$	5,198	$	469	$	339	$	7,012
Provision related to current period sales	3,472		10,256		595		538		14,861
Adjustment related to prior period sales	(32)		(38)		(373)		—		(443)
Credit or payments made during the period	(3,101)		(8,451)		(624)		(483)		(12,659)
Balance at June 30, 2022	$	1,345	$	6,965	$	67	$	394	$	8,771

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Description of the Business - Narrative (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Accumulated deficit	$ (902,412)	$ (866,883)
Cash, cash equivalents, and marketable securities	$ 69,400

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Summary of Significant Accounting Policies and Basis of Presentation - Narrative (Detail)	6 Months Ended
	Jun. 30, 2022 USD ($) Segment	Dec. 31, 2021 USD ($)
Accounting Policies [Line Items]
Number of operating segments | Segment	1
Off-balance sheet concentration of credit risk	$ 0
Accounts receivable, net	28,521,000	$ 29,438,000
Almirall
Accounting Policies [Line Items]
Accounts receivable, net	600,000
Tetraphase License Agreement
Accounting Policies [Line Items]
Accounts receivable, net	600,000
NUZYRA
Accounting Policies [Line Items]
Accounts receivable, net	24,400,000
BARDA Contract | Government contract service revenue
Accounting Policies [Line Items]
Accounts receivable, net	1,100,000
BARDA Contract | Government contract grant revenue
Accounting Policies [Line Items]
Accounts receivable, net	$ 1,400,000

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Marketable Securities - Summary of Available for Sale Securities (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Schedule Of Available For Sale Securities [Line Items]
Cost	$ 30,119	$ 15,116
Gains	0	0
Losses	(233)	(9)
Value	29,886	15,107
U.S. treasury securities
Schedule Of Available For Sale Securities [Line Items]
Cost	30,119	15,116
Gains	0	0
Losses	(233)	(9)
Value	$ 29,886	$ 15,107

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Marketable Securities - Narrative (Details) $ in Millions	Jun. 30, 2022 USD ($)
U.S. treasury securities
Schedule Of Available For Sale Securities [Line Items]
Total fair market value of marketable securities	$ 29.9

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Cash and Cash Equivalents and Restricted Cash - Summary of Reconciliation of Cash, Cash Equivalents, and Restricted Cash Reported Within Condensed Consolidated Statement of Cash Flows (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021	Jun. 30, 2021	Dec. 31, 2020
Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents [Abstract]
Cash and cash equivalents	$ 39,505	$ 80,367	$ 75,298
Short-term restricted cash	0	125	125
Long-term restricted cash	125	125	125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$ 39,630	$ 80,617	$ 75,548	$ 106,048

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Cash and Cash Equivalents and Restricted Cash - Narrative (Detail) $ in Millions	Dec. 31, 2021 USD ($)
Standby Letters of Credit
Cash And Cash Equivalents [Line Items]
Cash collateralized letter of credit	$ 0.3

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Inventories - Schedule of Inventories (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Inventory Disclosure [Abstract]
Raw materials	$ 903	$ 1,082
Work in process	27,351	24,675
Finished goods	17,491	13,030
Total inventories	$ 45,745	$ 38,787

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Inventories - Narrative (Detail) - USD ($)	6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021
Inventory Disclosure [Abstract]
Inventory reserves	$ 0	$ 0

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Net Income (Loss) Per Share - Antidilutive Shares Excluded from Computation of Diluted Net Income (Loss) Per Share (Detail) - shares	3 Months Ended	6 Months Ended
	Jun. 30, 2021	Jun. 30, 2022	Jun. 30, 2021
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	11,903,841	20,297,085	19,410,586
Common stock issuable under outstanding convertible notes
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	10,377,361	10,377,361	10,377,361
Shares subject to outstanding options to purchase common stock
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	1,057,092	2,119,588	2,103,326
Unvested restricted stock units
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	0	7,213,532	5,917,615
Shares subject to warrants to purchase common stock
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	469,388	426,866	469,388
Shares issuable under employee stock purchase plan
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	0	159,738	542,896
PRSUs
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Total (in shares)	2,672,999		2,672,999

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Net Income (Loss) Per Share - Schedule of Earnings Per Share, Basic and Diluted (Details) - USD ($)	3 Months Ended				6 Months Ended
	Jun. 30, 2022	Mar. 31, 2022	Jun. 30, 2021	Mar. 31, 2021	Jun. 30, 2022	Jun. 30, 2021
Basic
Net income (loss)	$ (17,619,000)	$ (17,910,000)	$ 9,717,000	$ (18,346,000)	$ (35,527,000)	$ (8,629,000)
Undistributed earnings allocated to warrants	0		(96,000)		0	0
Net income (loss)	$ (17,619,000)		$ 9,621,000		$ (35,527,000)	$ (8,629,000)
Weighted average common shares outstanding (in shares)	53,023,350		47,122,717		53,310,091	46,894,812
Basic earnings (loss) per common share (in USD per share)	$ (0.33)		$ 0.20		$ (0.67)	$ (0.18)
Diluted
Undistributed earnings allocated to warrants	$ 0		$ (96,000)			$ 0
Net income (loss)	$ (17,619,000)		$ 9,621,000		$ (35,527,000)	$ (8,629,000)
Weighted average common shares outstanding assuming dilution (in shares)	53,023,350		48,945,736		53,310,091	46,894,812
Diluted earnings (loss) per common share (in USD per share)	$ (0.33)		$ 0.20		$ (0.67)	$ (0.18)
Shares subject to outstanding options to purchase common stock
Diluted
Effect on dilutive shares (in shares)	$ 0		$ 366,793			$ 0
Restricted stock units
Diluted
Effect on dilutive shares (in shares)	$ 0		$ 1,456,226

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Government Contract Revenue - Narrative (Detail) $ in Thousands	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2022 USD ($) course	Jun. 30, 2021 USD ($)	Jun. 30, 2022 USD ($) course	Jun. 30, 2021 USD ($)	Dec. 31, 2021 USD ($)	Sep. 30, 2021 USD ($)	Apr. 30, 2020 USD ($)
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Milestone payment recognized as revenue	$ 29,637	$ 57,492	$ 54,498	$ 73,919
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date: 2022-07-01
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Remaining performance obligations	$ 63,700		$ 63,700
Maximum | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date: 2022-07-01
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Remaining performance obligations, expected recognize period	6 years		6 years
Minimum | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date: 2022-07-01
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Remaining performance obligations, expected recognize period	3 years		3 years
Government contract service revenue
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Milestone payment recognized as revenue	$ 1,896	2,113	$ 4,068	3,086
Product Revenue, Net
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Milestone payment recognized as revenue	25,082	52,803	45,000	66,009
Government contract grant revenue
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Milestone payment recognized as revenue	2,082	2,087	$ 4,182	3,701
BARDA Contract
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Contract term			5 years
Option to extend term			10 years
Maximum payment receivable in contract	303,600		$ 303,600
Term of base period of performance			5 years
Maximum number of years in contract period of performance			10 years
Maximum number of treatment courses procured | course			10,000
Initial award based on costs drawing down			$ 21,500
Potential additional staged funding for reimbursement of existing FDA PMR commitments	76,800		76,800			$ 31,600
Potential additional staged funding for reimbursement of manufacturing-related requirements	20,400		$ 20,400
Post-marketing bacterial surveillance study, period			5 years
Revenue performance obligations allocated transaction price			$ 63,600
Product revenue recognized					$ 37,900
Manufacturing-related requirements exercised						$ 31,600	$ 20,400
BARDA Contract | Accounts Receivable, Net
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Unbilled accounts receivable	900		900		$ 800
BARDA Contract | Other Current Liabilities
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Deferred revenue	1,100	800	1,100	800
BARDA Contract | NUZYRA
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Initial funding for development of NUZYRA	$ 59,400		$ 59,400
Maximum number of treatment courses of drug product | course	2,500		2,500
Funding amount to procure ZUZYRA			$ 37,900
Funding for three additional purchases	$ 115,400		$ 115,400
Maximum number of anthrax treatment courses procure options | course			2,500
Revenue performance obligations allocated transaction price			$ 4,200
BARDA Contract | NUZYRA | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
FDA approval period			24 months
BARDA Contract | NUZYRA | Minimum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
FDA approval period			18 months
BARDA Contract | Government contract service revenue
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Revenue performance obligations allocated transaction price			$ 21,500
Milestone payment recognized as revenue	1,900	2,100	4,100	3,100
BARDA Contract | Product Revenue, Net
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Revenue performance obligations allocated transaction price			37,900
BARDA Contract | Government contract grant revenue
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Milestone payment recognized as revenue	$ 2,100	$ 2,100	4,200	$ 3,700
Allocated consideration for reimbursement of existing FDA PMR requirements related to reimbursable expenses			$ 72,600

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License and Collaboration Agreements - Narrative (Detail)	1 Months Ended			3 Months Ended		6 Months Ended
	Oct. 31, 2018 USD ($)	Apr. 30, 2017 USD ($)	Feb. 28, 1997 shares	Jun. 30, 2022 USD ($) promise	Jun. 30, 2021 USD ($)	Jun. 30, 2022 USD ($) promise Obligation	Jun. 30, 2021 USD ($)	Dec. 31, 2021 USD ($)	Dec. 16, 2021 USD ($)	Dec. 31, 2019 USD ($)
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Material promises | promise				6		6
Milestone payment recognized as revenue				$ 29,637,000	$ 57,492,000	$ 54,498,000	$ 73,919,000
Other Current Liabilities
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Short-term liability				400,000		$ 400,000		$ 400,000
Almirall
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Number of performance obligations | Obligation						2
Milestone payment recognized as revenue				400,000	500,000	$ 900,000	1,000,000
Tufts
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Shares issued in connection with license agreement shares | shares			1,024
Milestone payments maximum amount						300,000
First milestone payment following phase 3 clinical trail for omadacycline						50,000
Second milestone payment amount following marketing application submission						100,000
Final milestone payment FDA approval of omadacycline	$ 150,000
Minimum royalty payment per year				25,000		25,000
Royalty expense				400,000	$ 800,000	$ 700,000	$ 1,000,000
Maximum | Tufts
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Sublicensing fees (in percent)						14.00%
Minimum | Tufts
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Sublicensing fees (in percent)						10.00%
Zai Lab (Shanghai) Co., Ltd.
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Number of performance obligations | Obligation						2
Revenue recognition milestone revenue						$ 21,500,000
Milestone payment recognized as revenue						6,000,000
Deferred revenue				0		0		0
Zai Lab (Shanghai) Co., Ltd. | Paratek Bermuda Ltd
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Upfront cash payment		$ 7,500,000
Upfront cash payment due upon new drug applications acceptance	$ 5,000,000
Upfront cash payment due upon submission of first regulatory approval application for a licensed product										$ 3,000,000
Upfront cash payment due upon regulatory approval for a licensed product									$ 6,000,000
Zai Lab (Shanghai) Co., Ltd. | Paratek Bermuda Ltd | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Potential future commercial milestone payment				40,500,000		$ 40,500,000
Novartis
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Advance notice to terminate collaboration agreement						60 days
Percentage of royalty on net sales						0.25%
Patent licensing arrangement paid support period						10 years
Novartis | Other Long Term Liabilities
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Long-term liability				$ 2,600,000		$ 2,600,000		$ 2,800,000

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Capital Stock - Additional Information (Detail) - USD ($) $ in Thousands		6 Months Ended
	May 17, 2021	Jun. 30, 2022	Jun. 30, 2021	Jul. 31, 2022	Dec. 31, 2021	Jun. 09, 2021	May 11, 2020
Class Of Stock [Line Items]
Common stock, shares authorized		200,000,000			200,000,000	100,000,000
Proceeds from issuance of common stock		$ 7,330	$ 4,645
At-the-Market Sales Agreement | BTIG
Class Of Stock [Line Items]
Percentage of proceeds payable as compensation to underwriter	3.00%
Number of common stock shares sold		2,339,000
Proceeds from issuance of common stock		$ 7,300
At-the-Market Sales Agreement | BTIG | Subsequent Event
Class Of Stock [Line Items]
Common stock for sale				$ 23,300
At-the-Market Sales Agreement | Maximum | BTIG
Class Of Stock [Line Items]
Common stock for sale	$ 50,000
Amended and Restated Certificate of Incorporation
Class Of Stock [Line Items]
Common stock, shares authorized						200,000,000
Shelf Registration | Subsequent Event
Class Of Stock [Line Items]
Common stock for sale				23,300
Common stock value, available for future issuance				$ 223,300
Shelf Registration | Initial Public Offering | Maximum
Class Of Stock [Line Items]
Common stock, aggregate amount authorized							$ 250,000

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Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Payables and Accruals [Abstract]
Accrued sales allowances	$ 8,771	$ 7,012
Accrued compensation	6,180	8,935
Accrued interest	2,389	2,365
Accrued commercial	2,372	1,654
Accrued inventory	2,446	307
Accrued contract research	1,151	1,019
Accrued professional fees	907	781
Accrued manufacturing	714	670
Accrued other	440	361
Accrued legal costs	291	342
Total	$ 25,661	$ 23,446

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Fair Value Measurements - Narrative (Detail) - USD ($) $ in Millions	Jun. 30, 2022	Dec. 31, 2021
Fair Value Disclosures [Abstract]
Carrying value of debt	$ 225.8	$ 238.3

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Fair Value Measurements - Schedule of Financial Assets and Liabilities Measured at Fair Value (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021
Assets:
U.S. treasury securities	$ 29,886	$ 15,107
Total Assets	29,886	15,107
U.S. treasury securities
Assets:
U.S. treasury securities	29,886	15,107
Quoted Prices in Active Markets (Level 1)
Assets:
Total Assets	29,886	15,107
Quoted Prices in Active Markets (Level 1) | U.S. treasury securities
Assets:
U.S. treasury securities	29,886	15,107
Significant Other Observable Inputs (Level 2)
Assets:
Total Assets	0	0
Significant Other Observable Inputs (Level 2) | U.S. treasury securities
Assets:
U.S. treasury securities	0	0
Significant Unobservable Inputs (Level 3)
Assets:
Total Assets	0	0
Significant Unobservable Inputs (Level 3) | U.S. treasury securities
Assets:
U.S. treasury securities	$ 0	$ 0

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Stock-Based and Incentive Compensation - Summary of Stock-Based Compensation Expense Included in Company's Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) (Detail) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021	Jun. 30, 2022	Jun. 30, 2021
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 3,886	$ 5,003	$ 6,354	$ 6,602
Research and development expense
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	515	793	692	1,116
Selling, general and administrative expense
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 3,371	$ 4,210	$ 5,662	$ 5,486

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Stock-Based and Incentive Compensation - Schedule of Share-based Payment Award, Stock Options, Weighted-Average Valuation Assumptions (Detail) - Employee Stock Option	6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Volatility (in percent)	62.20%	63.20%
Risk-free interest rate	2.30%	0.70%
Expected dividend yield (in percent)	0.00%	0.00%
Expected life of options (in years)	5 years 10 months 24 days	5 years 10 months 24 days

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Stock-Based and Incentive Compensation - Narrative (Detail)								3 Months Ended		6 Months Ended		12 Months Ended
	Feb. 16, 2025	Dec. 10, 2024	Feb. 16, 2024	Dec. 10, 2023	Feb. 16, 2023	Dec. 10, 2022	Mar. 31, 2018	Jun. 30, 2022 USD ($) Tranche shares	Jun. 30, 2021 USD ($)	Jun. 30, 2022 USD ($) Tranche Installment d shares	Jun. 30, 2021 USD ($)	Dec. 31, 2021 USD ($)	Mar. 31, 2022 shares	Oct. 31, 2018 shares	Oct. 04, 2018 USD ($)	Jun. 30, 2018 shares	Jun. 30, 2017 shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted under plan (in options)										187,660
Share-based compensation arrangement by share-based payment award, purchase period							6 months
Total stock-based compensation expense | $								$ 3,886,000	$ 5,003,000	$ 6,354,000	$ 6,602,000
2009 Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant								36,539		36,539
Shares subject to outstanding options to purchase common stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock shares, authorized																943,294
Number of shares available for grant								123,199		123,199
Percentage of total number of shares of common stock outstanding							3.00%
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation cost related to unvested share-based arrangements | $								$ 19,100,000		$ 19,100,000
Weighted average compensation cost recognition period (in years)										1 year 7 months 13 days
PRSUs
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense | $										$ 800,000
2015 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance								326,818		326,818
2015 Plan | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted under plan (in options)										103,860
2015 Plan | RSU
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted under plan (in RSUs)										2,737,840
2015 Plan | RSU | Tranche One | Forecast
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio						0.333
2015 Plan | RSU | Tranche One | Forecast | Non-Executive Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Additional Vesting ratio					0.333
2015 Plan | RSU | Tranche Two | Forecast
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio				0.333
2015 Plan | RSU | Tranche Two | Forecast | Non-Executive Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Additional Vesting ratio			0.333
2015 Plan | RSU | Tranche Three | Forecast
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio		0.333
2015 Plan | RSU | Tranche Three | Forecast | Non-Executive Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio	0.333
2015 Plan | PRSUs | Tranche One | March 2021
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio										0.6
2015 Plan | PRSUs | Tranche Two | March 2021
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio										0.182
2015 Plan | PRSUs | Tranche Three | March 2021
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting ratio										0.182
2015 Plan | Minimum | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Time-based vesting period (in years)										1 year
2015 Plan | Maximum | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Time-based vesting period (in years)										4 years
2015 Inducement Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock shares, authorized								341,500		341,500
2015 Inducement Plan | New Employee
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options reserved for future issuance (in options)								360,000		360,000
2015 Inducement Plan | Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Time-based vesting period (in years)										1 year
2017 Inducement Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock shares, authorized								813,604		813,604
2017 Inducement Plan | Employees Entering into Employment Or Returning to Employment
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options reserved for future issuance (in options)								1,800,000		1,800,000
2017 Inducement Plan | Tranche One | Employees Entering into Employment Or Returning to Employment
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options reserved for future issuance (in options)																	550,000
2017 Inducement Plan | Tranche Two | Employees Entering into Employment Or Returning to Employment
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options reserved for future issuance (in options)														500,000
2017 Inducement Plan | Tranche Three | Employees Entering into Employment Or Returning to Employment
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options reserved for future issuance (in options)													750,000
2017 Inducement Plan | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted under plan (in options)										83,800
2017 Inducement Plan | RSU
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted under plan (in RSUs)										223,300
Time-based vesting period (in years)										3 years
Vesting percentage										100.00%
2017 Inducement Plan | Minimum | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Time-based vesting period (in years)										1 year
2017 Inducement Plan | Maximum | Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Time-based vesting period (in years)										4 years
Revenue Performance Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting percentage										100.00%
Number of tranches | Tranche								2		2
Percentage of additional performance-based cash incentive awards										25.00%
Revenue incentive plan, payout multiplier | $										$ 25,000,000
Number of trailing days | d										20
Percentage of cash and registered securities of aggregate payment										50.00%
Total stock-based compensation expense | $										$ 22,300,000	$ 0	$ 21,800,000
Revenue Performance Incentive Plan | Tranche One
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense | $										$ 500,000
Revenue Performance Incentive Plan | Tranche 1 Milestone
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of equal installments | Installment										4
Percentage of milestone deemed to be achieved if milestone not achieved prior to change of control										50.00%
Base amount for dividing cumulative product revenue if milestone not achieved prior to change of control | $										$ 300,000,000
Revenue incentive plan, payout multiplier | $										$ 25,000,000
Revenue Performance Incentive Plan | Tranche 2 Milestone
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of equal installments | Installment										4
Percentage of milestone deemed to be achieved if milestone not achieved prior to change of control										30.00%
Base amount for dividing cumulative product revenue if milestone not achieved prior to change of control | $										$ 600,000,000
Revenue incentive plan, payout multiplier | $										25,000,000
Revenue Performance Incentive Plan | Minimum | Tranche 1 Milestone
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Cumulative net product revenues | $										300,000,000
Revenue Performance Incentive Plan | Minimum | Tranche 2 Milestone
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Cumulative net product revenues | $										$ 600,000,000
Revenue Performance Incentive Plan | Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Incentive pool amount plus accrued interest | $															$ 50,000,000

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Stock-Based and Incentive Compensation - Schedule of Share-based Compensation, Stock Options, Activity (Detail) - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2022	Dec. 31, 2021
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Number of Shares Outstanding, Beginning Balances	2,051,484
Number of Shares Outstanding, Granted	187,660
Number of Shares Outstanding, Exercised	(1,646)
Number of Shares Outstanding, Cancelled or forfeited	(117,910)
Number of Shares Outstanding, Ending Balances	2,119,588	2,051,484
Number of Shares Outstanding, Exercisable	1,756,972
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest [Abstract]
Weighted Average Exercise Price, Beginning Balances (in USD per share)	$ 10.92
Weighted Average Exercise Price, Granted (in USD per share)	2.94
Weighted Average Exercise Price, Exercised (in USD per share)	3.58
Weighted Average Exercise Price, Cancelled or forfeited (in USD per share)	12.94
Weighted Average Exercise Price, Ending Balances (in USD per share)	10.10	$ 10.92
Weighted Average Exercise Price, Exercisable (in USD per share)	$ 11.30
Share-based Compensation Arrangement by Share-based Payment Award, Options, Weighted-Average Remaining Contractual Term (in Years)
Options Outstanding, Weighted-Average Remaining Contractual Term (in Years)	4 years 11 months 15 days	5 years 1 month 13 days
Options Exercisable, Weighted-Average Remaining Contractual Term (in Years)	4 years 1 month 13 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Aggregate Intrinsic Value
Options Outstanding, Aggregate Intrinsic Value, beginning balance	$ 303
Options Outstanding, Aggregate Intrinsic Value, ending balance	0	$ 303
Options Exercisable, Aggregate Intrinsic Value	$ 0

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Stock-Based and Incentive Compensation - Schedule of Share-based Compensation, Restricted Stock Unit, Activity (Detail) - Restricted stock units	6 Months Ended
	Jun. 30, 2022 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Unvested Number of Shares, Beginning Balance | shares	4,920,063
Number of Shares, Granted | shares	2,961,140
Number of Shares, Released | shares	(432,982)
Number of Shares, Forfeited | shares	(234,689)
Unvested Number of Shares, Ending Balance | shares	7,213,532
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Unvested Weighted Average Grant Date Fair Value, Beginning Balance (in USD per share) | $ / shares	$ 5.82
Weighted Average Grant Date Fair Value, Granted (in USD per share) | $ / shares	3.09
Weighted Average Grant Date Fair Value, Released (in USD per share) | $ / shares	6.13
Weighted Average Grant Date Fair Value, Forfeited (in USD per share) | $ / shares	5.40
Unvested Weighted Average Grant Date Fair Value, Ending Balance (in USD per share) | $ / shares	$ 4.69

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Long-Term Debt - Narrative (Detail)					1 Months Ended	3 Months Ended	6 Months Ended
	May 06, 2021 d	May 01, 2019 USD ($)	Feb. 25, 2019 USD ($)	Apr. 23, 2018 $ / shares	Apr. 30, 2018 USD ($)	Jun. 30, 2022 USD ($)	Jun. 30, 2022 USD ($)	Jun. 30, 2021 USD ($)	Dec. 31, 2021 USD ($)	Apr. 18, 2018 USD ($) $ / shares
Debt Instrument [Line Items]
Direct and incremental third-party expenses accounted for as debt issuance costs							$ 0	$ 397,000
Paid-in-kind interest							2,725,000	$ 672,000
4.75% Convertible Senior Subordinated Notes due 2024
Debt Instrument [Line Items]
Term loan funded at execution						$ 165,000,000	$ 165,000,000		$ 165,000,000
Debt Instrument, Frequency of Periodic Payment (in years)							five
Principal amount outstanding										$ 135,000,000
Debt instrument, interest rate				4.75%						4.75%
Additional principal amount outstanding										$ 25,000,000
Debt instrument conversion (in USD per share) | $ / shares				$ 15.90
Debt instrument conversion premium (in percent)				20.00%
Closing price of the common stock (in USD per share) | $ / shares										$ 13.25
Percentage of common stock price	130.00%
Debt instrument, convertible, threshold trading days | d	20
Debt instrument, convertible, threshold consecutive trading days | d	30
Percentage of debt instrument redemption price	100.00%
Debt instrument, debt default, minimum percentage of aggregate principal amount due				25.00%
Costs incurred on issuance of debt					$ 6,000,000	$ 2,048,000	$ 2,048,000		2,572,000
Net proceeds from issuance of long-term convertible debt					$ 159,000,000
Loan interest rate						5.47%	5.47%
Debt instrument initial conversion rate				0.063
4.75% Convertible Senior Subordinated Notes due 2024 | J. Wood Capital Advisors LLC
Debt Instrument [Line Items]
Principal amount outstanding										$ 5,000,000
R-Bridge Loan Agreement
Debt Instrument [Line Items]
Line of credit facility, borrowing capacity						$ 60,000,000	$ 60,000,000
Percentage of Initial sale on NUZYRA						2.50%	2.50%
Maximum percentage of net sales adjust under certain circumstances						5.00%	5.00%
Sales annual cap						$ 10,000,000	$ 10,000,000
Sales annual cap adjust under certain circumstances						$ 12,000,000	$ 12,000,000
Interest rate of annual rate						7.00%	7.00%
Annual interest rate on event of default						10.00%	10.00%
Accrued interest up to excess of principal payment							$ 15,000,000
Collection amount in excess of annual cap shared between parties							15,000,000
Excess of initial collection amount shared between parties							15,000,000
Loan capped amount						$ 114,000,000	114,000,000
Event of default occurred amount						0	0
Net proceeds							58,300,000
Term loan funded at execution						60,000,000	60,000,000
Lender fees accounted for as debt discount							1,100,000
Direct and incremental third-party expenses accounted for as debt issuance costs							600,000
Costs incurred on issuance of debt						1,326,000	1,326,000		1,443,000
Interest expense						2,000,000	3,900,000
Paid-in-kind interest						300,000	500,000
R-Bridge Loan Agreement | 4.75% Convertible Senior Subordinated Notes due 2024
Debt Instrument [Line Items]
Amortization expense on debt issuance costs							800,000
Coupon interest expense						1,100,000	2,200,000
Royalty Backed Loan Agreement
Debt Instrument [Line Items]
Costs incurred on issuance of debt						1,599,000	1,599,000		$ 1,673,000
Paid-in-kind interest							1,200,000
Royalty Backed Loan Agreement | Healthcare Royalty Partners III, L.P
Debt Instrument [Line Items]
Line of credit facility, borrowing capacity			$ 32,500,000
Interest rate of annual rate			12.00%
Interest expense						$ 1,000,000	$ 2,000,000
Proceeds from lines of credit		$ 27,800,000
Line of credit net of lender discount		500,000
Line of credit lender expenses		200,000
Line of credit deposits into interest reserve account		4,000,000
Repayment of other lender fees		$ 1,200,000
Line of credit facility, fee (in percent)			1.50%
Royalty Backed Loan Agreement | Healthcare Royalty Partners III, L.P | Maximum
Debt Instrument [Line Items]
Line of credit facility, periodic payment			$ 300,000

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Long-Term Debt - Summary of Debt (Detail) - USD ($) $ in Thousands	Jun. 30, 2022	Dec. 31, 2021	Apr. 30, 2018
4.75% Convertible Senior Subordinated Notes due 2024
Debt Instrument [Line Items]
Principal debt	$ 165,000	$ 165,000
Unamortized debt discount and issuance costs	(2,048)	(2,572)	$ (6,000)
Carrying value	162,952	162,428
R-Bridge Loan Agreement
Debt Instrument [Line Items]
Principal debt	60,000
Principal debt including paid-in-kind interest	62,025	61,256
Unamortized debt discount and issuance costs	(1,326)	(1,443)
Carrying value	60,699	59,813
Royalty Backed Loan Agreement
Debt Instrument [Line Items]
Principal debt including paid-in-kind interest	35,101	33,860
Unamortized debt discount and issuance costs	(1,599)	(1,673)
Carrying value	$ 33,502	$ 32,187

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Leases - Additional Information (Detail) $ in Thousands	Jun. 30, 2022 USD ($)	Dec. 31, 2021 USD ($)	Apr. 30, 2021 USD ($) ft²	Oct. 31, 2016 ft²
Leases [Line Items]
Long-term lease liabilities	$ 854	$ 1,308
Other Current Liabilities
Leases [Line Items]
Operating lease, liability, current	700
Long-Term Lease Liability
Leases [Line Items]
Long-term lease liabilities	$ 700
Boston
Leases [Line Items]
Lease agreement, released rented office space | ft²			8,104
Lease agreement, remaining rented office space | ft²			4,153
Operating lease, additional commitment			$ 400
King of Prussia
Leases [Line Items]
Area of leased space | ft²				19,708
Term of lease commitment				7 years 7 months

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Income Taxes - Additional Information (Detail) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2022	Jun. 30, 2021	Jun. 30, 2022	Jun. 30, 2021
Income Tax Disclosure [Abstract]
Provision for income taxes	$ 0	$ 0	$ 0	$ 0

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Product Revenue - Summary of Product Revenue Allowance and Reserve Categories (Detail) $ in Thousands	6 Months Ended
	Jun. 30, 2022 USD ($)
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at December 31, 2021	$ 7,012
Provision related to current period sales	14,861
Adjustment related to prior period sales	(443)
Credit or payments made during the period	(12,659)
Balance at June 30, 2022	8,771
Chargebacks, discounts and fees
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at December 31, 2021	1,006
Provision related to current period sales	3,472
Adjustment related to prior period sales	(32)
Credit or payments made during the period	(3,101)
Balance at June 30, 2022	1,345
Government and other rebates
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at December 31, 2021	5,198
Provision related to current period sales	10,256
Adjustment related to prior period sales	(38)
Credit or payments made during the period	(8,451)
Balance at June 30, 2022	6,965
Returns
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at December 31, 2021	469
Provision related to current period sales	595
Adjustment related to prior period sales	(373)
Credit or payments made during the period	(624)
Balance at June 30, 2022	67
Patient assistance
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at December 31, 2021	339
Provision related to current period sales	538
Adjustment related to prior period sales	0
Credit or payments made during the period	(483)
Balance at June 30, 2022	$ 394