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Stock-Based Compensation
 9 Months Ended
Sep. 30, 2024
Share-Based Payment Arrangement [Abstract]  
Stock-Based Compensation Stock-Based Compensation
2015 Equity Incentive Plan
In March 2015, the Company adopted the 2015 Equity Incentive Plan (“2015 Plan”), administered by the board of directors, and provides for the Company to sell or issue share of Common Stock or restricted Common Stock, or to grant incentive stock options or nonqualified stock options for the purchase of Common Stock, to employees, members of the board of directors and consultants of the Company. The Company granted options under the 2015 Plan until April 2016 when it was terminated as to future awards, although it continues to govern the terms of options that remain outstanding under the 2015 Plan.
As of September 30, 2024, a total of 952 shares of Common Stock are subject to options outstanding under the 2015 Plan and will become available under the 2016 Equity Incentive Plan (“2016 Plan”) to the extent the options are forfeited or lapse unexercised.
2016 Equity Incentive Plan
The 2016 Plan became effective in April 2016 and serves as the successor to the 2015 Plan. Under the 2016 Plan, the Company may grant stock options, stock appreciation rights, restricted stock awards, restricted stock units, performance awards, and stock bonuses. The 2016 Plan, as amended, provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each year for the remaining term of the plan equal to (a) 5.0% of the number of issued and outstanding shares of Common Stock (including such shares issuable pursuant to the exercise or conversion, as applicable, of any outstanding pre-funded warrants and nonvoting convertible preferred stock) on December 31 of the immediately preceding year, or (b) a lesser amount as approved by the board each year (the “Evergreen Provision”). As a result of the Evergreen Provision, on January 1, 2024 and 2023, an additional 3,023,650 and 104,561 shares, respectively, became available for issuance under the 2016 Plan.
As of September 30, 2024, the 2016 Plan had 7,228,113 shares available for future issuance, of which 3,247,677 shares were subject to outstanding option awards.
2018 Equity Inducement Plan
The 2018 Equity Inducement Plan (“2018 Plan”) became effective in February 2018.
During the third quarter of 2024, the Company amended the 2018 Plan to increase the number of shares of Common Stock reserved for issuance by 1,000,000. After this amendment and as of September 30, 2024, the 2018 Plan had 6,999,445 shares available for future issuance, of which 5,624,067 shares were subject to outstanding option awards and restricted unit awards.
Service-based awards granted under the 2018 Plan, 2016 Plan, and 2015 Plan generally vest over four years and expire after ten years, although awards have been granted with vesting terms less than four years. Under the 2016 Plan and 2018 Plan, the Company may grant stock-based awards with service conditions (“service-based” awards), performance conditions (“performance-based” awards), and market conditions (“market-based” awards).
Spyre 2023 Equity Incentive Plan
On June 22, 2023, in connection with the Asset Acquisition, the Company assumed the Amended and Restated Spyre 2023 Equity Incentive Plan and its outstanding and unexercised stock options, which were
converted to options to purchase 2,734 shares of Common Stock. The acquisition-date fair value of these grants will be recognized as an expense on a pro-rata basis over the vesting period.
The following table summarizes the Company’s stock awards granted under all equity incentive and inducement plans for each of the periods indicated:
Three Months Ended September 30,Nine Months Ended September 30,
2024202320242023
GrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair Value
Stock options425,500$25.74 1,044,667$14.50 1,857,853$28.40 3,867,366$9.65 
Parapyre Option Obligation
As of September 30, 2024, the pro-rated estimated fair value of the options to be granted on December 31, 2024 related to the Parapyre Option Obligation, was approximately $13.0 million. For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. As of September 30, 2024, the unamortized expense related to the Parapyre Option Obligation was $4.4 million.
2016 Employee Stock Purchase Plan
Under the Company’s 2016 Employee Stock Purchase Plan (“2016 ESPP”), the Company issued and sold 14,053 and 16,383 shares during the three and nine months ended September 30, 2024, respectively, and sold 704 and 2,496 shares during the three and nine months ended September 30, 2023, respectively. The aggregate cash proceeds were not material for all periods.
Stock-based Compensation Expense
Total stock-based compensation expense recognized from the Company’s equity incentive plans, 2018 Plan, 2016 ESPP and Parapyre Option Obligation during the periods presented was as follows (in thousands):
Three Months Ended
September 30,		Nine Months Ended
September 30,
2024202320242023
Research and development (1)
$8,555 $2,965 $18,863 $4,136 
General and administrative4,545 1,820 16,754 4,269 
Total stock-based compensation expense (2)
$13,100 $4,785 $35,617 $8,405 
(1) For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation.
(2) Of the total $13.1 million and $35.6 million of stock-based compensation expense for the three and nine months ended September 30, 2024, $0.1 million and $3.6 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the respective period. Of the total $4.8 million and $8.4 million of stock-based compensation expense for the three and nine months ended September 30, 2023, $0.8 million and $4.2 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the period.

The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchasable under the 2016 ESPP during the periods presented:
Three Months Ended
September 30,		Nine Months Ended
September 30,
2024202320242023
Stock Options Granted
Expected term (in years)6.086.086.026.04
Expected volatility105%101%105%111%
Risk-free interest4.13%4.28%4.03%4.07%
Dividend yield————
 
2016 ESPP
Expected term (in years)0.500.500.500.49
Expected volatility71%222%83%181%
Risk-free interest5.02%5.29%5.15%4.99%
Dividend yield————