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Stock-Based Compensation
 6 Months Ended
Jun. 30, 2025
Share-Based Payment Arrangement [Abstract]  
Stock-Based Compensation Stock-Based Compensation
2016 Equity Incentive Plan
The Company's 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, 2025 and 2024, an additional 3,814,905 and 3,023,650 shares, respectively, became available for issuance under the 2016 Plan.
As of June 30, 2025, the 2016 Plan had 10,911,455 shares available for future issuance, of which 4,932,059 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 second quarter of 2025, the Company amended the 2018 Plan to increase the number of shares of common stock reserved for issuance by 750,000. After this amendment and as of June 30, 2025, the 2018 Plan had 7,606,811 shares available for future issuance, of which 6,508,168 shares were subject to outstanding option awards and restricted unit awards.
Service-based awards granted under the 2018 Plan and 2016 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, performance conditions, and market conditions.
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 (the "2023 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. As of June 30, 2025, none of the stock options under the 2023 Plan remained outstanding.
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 June 30,Six Months Ended June 30,
2025202420252024
GrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair ValueGrantsWeighted Average Grant Date Fair Value
Stock options427,800$15.29 387,695$36.42 2,325,717$20.32 1,432,353$29.19 
Parapyre Option Obligation
As of December 31, 2024, the Company settled its obligations under the Parapyre Option Obligation by issuing Parapyre 848,184 warrants to purchase the Company's common stock at an exercise price of $23.28. As of June 30, 2025, a total of 1,532,591 warrants with a weighted-average exercise price of $22.49 had been issued to Parapyre under the Parapyre Option Obligation. As of June 30, 2025 none of the warrants issued under the Parapyre Option Obligation have been exercised and all remain outstanding.
For the three and six months ended June 30, 2024, $1.5 million and $6.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. There are no ongoing obligations under the Parapyre Option Obligation as of June 30, 2025.
2016 Employee Stock Purchase Plan
Under the Company’s 2016 Employee Stock Purchase Plan (“2016 ESPP”), the Company issued and sold 16,877 and 2,330 shares during the six months ended June 30, 2025 and 2024, respectively. There were no shares issued and sold during the three months ended June 30, 2025 and 2024. The aggregate cash proceeds were nil for the three months ended June 30, 2025 and 2024, and were $0.3 million and de minimis for the six months ended June 30, 2025 and 2024, respectively.
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
June 30,		Six Months Ended
June 30,
2025202420252024
Research and development (1)
$4,100 $3,451 $7,612 $10,308 
General and administrative5,278 5,231 10,625 12,209 
Total stock-based compensation expense (2)
$9,378 $8,682 $18,237 $22,517 
(1) For the three and six months ended June 30, 2024, $1.5 million and $6.9 million, respectively was recognized as stock compensation expense related to the Parapyre Option Obligation.
(2) Of the total $8.7 million and $22.5 million of stock-based compensation expense for the three and six months ended June 30, 2024, respectively, $0.7 million and $3.8 million is related to legacy Aeglea employees and directors who had been terminated as of the end of the period, respectively.

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 purchased under the 2016 ESPP during the periods presented:
Three Months Ended
June 30,		Six Months Ended
June 30,
2025202420252024
Stock Options Granted
Expected term (in years)5.745.925.976.00
Expected volatility74%104%76%105%
Risk-free interest4.02%4.35%4.38%4.01%
Dividend yield————
 
2016 ESPP
Expected term (in years)——0.500.50
Expected volatility——69%98%
Risk-free interest——4.23%5.31%
Dividend yield————