PLIANT THERAPEUTICS, INC.

Notes to Condensed Financial Statements

1. Organization and Description of Business

Pliant Therapeutics, Inc. (the “Company” or “Pliant” or “we” or “our” or “us”) is a clinical-stage biopharmaceutical company focused on discovering and developing integrin-based therapeutics. The Company is located in South San Francisco, California, and was incorporated in the state of Delaware in June 2015.

Bexotegrast in Idiopathic Pulmonary Fibrosis (IPF)

In March 2025, we announced that we were discontinuing the BEACON-IPF Phase 2b trial following a prespecified data review and recommendation by the trial’s independent Data Safety Monitoring Board (“DSMB”), as well as a secondary review and recommendation by an outside expert panel, due to an imbalance in safety events between the treatment and placebo groups. In June 2025, we announced that we were discontinuing the development of bexotegrast in IPF as the results of BEACON-IPF demonstrated an unfavorable risk-benefit profile.

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited interim condensed financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and follow the requirements of the Securities and Exchange Commission (“SEC”), for interim financial reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by U.S. GAAP have been condensed or omitted, and accordingly the unaudited interim condensed financial statements do not include all of the information and notes required by U.S. GAAP for complete financial statements. These unaudited interim condensed financial statements have been prepared on the same basis as our annual financial statements and, in the opinion of management, reflect all adjustments (consisting only of normal recurring adjustments) that are necessary for a fair presentation of the Company's financial information. The results of operations for the three and nine months ended September 30, 2025 are not necessarily indicative of the results to be expected for the year ending December 31, 2025 or for any other interim period or for any other future year.

The financial information included herein should be read in conjunction with the audited financial statements and related notes in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, filed with the SEC on March 3, 2025 (the “2024 10-K”).

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, and expenses as well as the disclosure of contingent assets and liabilities as of and during the reporting period. The Company bases its estimates and assumptions on historical experience when available and on various factors that it believes to be reasonable under the circumstances. Significant estimates and assumptions reflected in these financial statements include, but are not limited to, stock-based compensation expense, operating lease right-of-use (“ROU”) assets and liabilities, accruals and prepayments for research and development costs, income taxes and uncertain tax positions. The Company assesses estimates on an ongoing basis, however, actual results could materially differ from those estimates.

Significant Accounting Policies

There have been no significant changes to the accounting policies during the three and nine months ended September 30, 2025, as compared to the significant accounting policies described in Note 2 of the "Notes to the Financial Statements" in the Company's audited financial statements included in its 2024 10-K.

Accounting Pronouncements Not Yet Adopted

In December 2023, the Financial Accounting Standards Board (“FASB”) issued ASU 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures. ASU 2023-09 requires disclosure of additional categories of information about federal, state and foreign income taxes in the rate reconciliation table and more details about the reconciling items in some categories if items meet a quantitative threshold. The ASU requires entities to disclose income taxes paid, net of refunds, disaggregated by federal (national), state and foreign taxes for annual periods and to disaggregate the information by jurisdiction based on a quantitative threshold. ASU 2023-09 is effective for fiscal years beginning after December 15, 2024 on a prospective basis and retrospective application is permitted. The Company is currently evaluating the impact of this standard on its disclosures and will adopt the ASU for its Annual Report on Form 10-K for the year ended December 31, 2025.

In November 2024, the FASB issued ASU 2024-03 “Disaggregation of Income Statement Expenses,” which aims to improve the disclosures about a public business entity’s expenses and address requests from investors for more detailed information about the types of expenses in commonly presented expense captions. The guidance is effective for the Company's annual periods beginning in 2027 and interim periods beginning in the first quarter of fiscal year 2028. The Company will first apply this guidance, on an annual basis for the year ending December 31, 2025. While this ASU will expand our income tax disclosures, it is not expected to have a material impact on our consolidated financial statements.

3. Financial Instruments

The Company’s short-term investments consist of U.S. Treasury securities, U.S. Government agency securities and highly rated, investment-grade corporate debt securities with original maturities beyond three months at the date of purchase. The Company has classified and accounted for its short-term investments as available-for-sale securities as the Company may sell these securities at any time for reasons including, but not limited to, managing liquidity, credit risk, duration and asset allocation and such investments represent cash available for current operations. As a result, short-term investments may include securities with maturities beyond twelve months that are classified within current assets in the condensed balance sheets. The Company’s short-term investments classified as available-for-sale are carried at fair market value with unrealized gains or losses recognized in the statements of operations and comprehensive loss.

The Company’s cash equivalent Money Market Funds are classified as Level 1 in the fair value hierarchy because they are valued using quoted active market prices. The fair value of the Company’s U.S. Treasury securities, U.S. Government agency securities and corporate debt securities are classified as Level 2 because they are valued using observable inputs to quoted market prices other than Level 1 prices, benchmark yields, reported trades, broker/dealer quotes or alternative pricing sources with reasonable levels of price transparency and include U.S. Government agency securities, U.S. Treasury securities and corporate debt securities.

There wereno assets or liabilities recorded at fair value to the condensed balance sheets using Level 3 inputs as of September 30, 2025 and as of December 31, 2024.

The following tables show the Company’s short-term investments and cash equivalents by significant investment category as of September 30, 2025 and December 31, 2024 (in thousands):

There wereno liabilities measured at fair value on a recurring basis as of September 30, 2025 and December 31, 2024. The Company evaluates transfers between levels at the end of each reporting period and there have been no transfers between fair value measurement levels during the nine months ended September 30, 2025. In addition, there wereno assets or liabilities measured at fair value on a non-recurring basis as of September 30, 2025 and December 31, 2024.

The Company records interest income, accretion income and amortization expense on short-term investments to interest and other income (expense), net in its condensed statement of operations and comprehensive loss.

4. Property and Equipment, net

Property and equipment, net consisted of the following (in thousands):

Depreciation expense was $0.4 million and $1.3 million for the three and nine months ended September 30, 2025, respectively, and $0.5 million and $1.7 million for the three and nine months ended September 30, 2024, respectively.

5. Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consisted of the following (in thousands):

6. Accrued Liabilities

Accrued liabilities consisted of the following (in thousands):

Accrued compensation and benefits consist primarily of accrued bonuses and accrued vacation.

7. Long-term Debt

In March 2024 we entered into an Amended and Restated Loan and Security Agreement (the "Amended Loan Agreement") with Oxford Finance LLC (the “Lender” or “Oxford”) and drew an additional Term Loan (as defined below) of $20.0 million. While the Amended Loan Agreement upsized our existing Term Loan facility to a total size of $150.0 million aggregate principal amount (the "Term Loans"), the availability of additional Term Loans is contingent upon the continued development of bexotegrast in IPF, and therefore, we do not expect to have access to additional borrowing under the Amended Loan Agreement. See Note 7 of the "Notes to the Financial Statements" in the Company's audited financial statements included in the 2024 10-K for more information.

The principal amount outstanding under the Term Loans will accrue interest at a floating per annum rate equal to (i) the greater of (a) 1-month term Chicago Mercantile Exchange (“CME”) Term Secured Overnight Financing Rate (“SOFR”) on the last business day of the month that immediately precedes the month in which the interest will accrue and (b) three and one-half percent (3.50%) plus (ii) five and one-quarter percent (5.25%), subject to an agreed upon floor of 8.75%. Beginning on July 1, 2028, the Company is required to repay the Term Loans in consecutive equal monthly payments of principal, together with applicable interest, in arrears. Interest on the Term Loans is paid on a monthly basis. All unpaid principal and accrued and unpaid interest with respect to each Term Loan will be due and payable in full on March 1, 2029. Accrued interest as of September 30, 2025 and December 31, 2024 is included in other accrued liabilities.

The Company will be required to make a final payment of 5.50% of the original principal amount of the Term Loans that were drawn, payable at maturity or upon any earlier acceleration or prepayment of the Term Loans. The Company may prepay the Term Loans in whole or in part, subject to a prepayment fee equal to (i) if prepaid on or before the first anniversary date of the funding date of such Term Loan,3.00% of the principal amount of the applicable Term Loan prepaid, (ii) if prepaid after the first anniversary and on or before the second anniversary of the funding date of such Term Loan,2.00% of the principal amount of the applicable Term Loan prepaid, and (iii) if prepaid after the second anniversary and on or before the third anniversary of the funding date of such Term Loan prepaid,1.00% of the principal amount of the applicable Term Loan prepaid.

The Amended Loan Agreement contains representations and warranties, affirmative, and negative covenants, and events of default that are customary for loans of this type. The occurrence of an event of default could result in the acceleration of the obligations under the Amended Loan Agreement, termination of the Term Loan commitments and the right by the Lender to foreclose on the collateral securing the obligations. During the existence of an event of default, the Term Loans would accrue interest at a rate per annum equal to 5.00% above the otherwise applicable interest rate.

The estimated fair value of the Term Loans as of September 30, 2025 was measured using Level 3 inputs and approximates the carrying value recorded to the balance sheet. The effective interest rate for the Term Loan is 10.61% for the three and nine months ended September 30, 2025 and 11.57% and 11.72% for the three and nine months ended September 30, 2024, respectively. Interest expense during the three and nine months ended September 30, 2025 was $0.8 million and $2.4 million, respectively and during the three and nine months ended September 30, 2024 was $0.9 million and $2.2 million, respectively. On October 14, 2025, we completed a voluntary prepayment of our Amended Loan Agreement with Oxford disclosed in Footnote 19, Subsequent Events.

Future maturities of debt as of September 30, 2025 are as follows (in thousands):

8. Preferred Stock

Under the Company’s Amended and Restated Certificate of Incorporation, the Company is authorized to issuetwo classes of shares: preferred stock and common stock. The preferred stock may be issued in series, and the Company’s board of directors is authorized to determine the rights, preferences, and terms of each series. These rights, preferences and terms could include dividend rights, conversion rights, voting rights, terms of redemptions, liquidation preferences and sinking fund terms. As of September 30, 2025 and December 31, 2024, the Company was authorized to issue 10,000,000 shares of preferred stock and there wasno outstanding preferred stock as of September 30, 2025 and December 31, 2024.

9. Common Stock

As of September 30, 2025 and December 31, 2024, the Company was authorized to issue 300,000,000 shares of common stock at a par value of $0.0001 per share. The Common Stock has the following rights and privileges:

Voting

The holders of shares of common stock are entitled toone vote for each share of common stock held at any meeting of stockholders and at the time of any written action in lieu of a meeting.

Dividends

The holders of shares of common stock are entitled to receive dividends, when declared by the Company’s board of directors. Cash dividends may not be declared or paid to holders of shares of common stock until all unpaid dividends on preferred stock have been paid in accordance with their terms. No dividends have been declared or paid by the Company since its inception. The terms of the Amended Loan Agreement restrict our ability to declare and pay dividends.

Liquidation

Subject to the preferential rights of holders of preferred stock then outstanding, the holders of shares of common stock are entitled to share ratably in the Company’s remaining assets available for distribution to its stockholders in the event of any voluntary or involuntary liquidation, dissolution or winding up of the Company.

Shares reserved for future issuance

10. Stockholder Rights Agreement

On March 12, 2025, the Company's board of directors adopted a stockholder rights agreement and declared a dividend ofone right (each, a “Right”) for each outstanding share of our common stock to stockholders of record at the close of business on March 25, 2025. Each Right entitles its holder, subject to the terms of the Rights Agreement (as defined below), to purchase from the Company one one-thousandth of a share of Series A Junior Participating Preferred Stock, par value $0.0001 per share, of the Company at an exercise price of $12.64 per Right, subject to adjustment. The description and terms of the Rights are set forth in a Rights Agreement, dated as of March 12, 2025 (the “Rights Agreement”), by and between the Company and Computershare Trust Company, N.A., a federally chartered trust company, as rights agent. Subject to certain exceptions, Rights become exercisable and trade separately from our common stock only upon the earlier of (i) the close of business on thetenth business day following the public announcement of an Acquiring Person (as defined in the Rights Agreement) beneficially owning 20%, when referring to a passive investor, and 10%, when referring to a person that is not a passive investor, or more of our common stock, and (ii) the close of business on the tenth business day after the commencement of a tender offer or exchange offer that, if consummated, would result in a person or group becoming an Acquiring Person. The Rights will expire on March 11, 2026, unless such Rights are earlier redeemed, exchanged or terminated, as provided in the Rights Agreement.

The Rights Agreement is intended to reduce the likelihood that any entity, person or group is able to gain control of the Company through open market accumulation without paying all stockholders an appropriate control premium or providing the board of directors sufficient opportunity to make informed judgments and take actions that are in the best interests of the Company and all stockholders. The Rights Agreement is not intended to interfere with any merger or other business combination approved by the board of directors.

11. Equity Incentive Plans and Stock-Based Compensation

In 2015, the Company's board of directors adopted the 2015 Equity Incentive Plan, as amended in 2018, 2019 and 2020 (the “2015 Plan”), which provided for the grant of incentive stock options, nonqualified stock options or other awards including stock appreciation rights and restricted stock awards to the Company’s employees, officers, directors, advisors, and consultants. In May 2020, the board of directors adopted the 2020 Stock Option and Incentive Plan (the “2020 Plan”) and suspended the 2015 Plan. Awards outstanding under either the 2015 Plan or 2020 Plan that are cancelled, expire or otherwise terminated subsequent to May 2020 will become available for issuance as common stock under the 2020 Plan. Additionally, the 2020 Plan is subject to automatic increases on January 1 of each year beginning January 1, 2021. The number of shares added each January 1 will be equal to the lesser of: (i)5% of the outstanding shares on the immediately preceding December 31 or (ii) such amount as determined by the compensation committee of the board of directors.

The 2020 Plan provides for the grant of incentive stock options, nonqualified stock options or other awards including stock appreciation rights, restricted stock awards and restricted stock units to the Company’s employees, officers, directors, advisors and consultants.

In 2022, the board of directors adopted the 2022 Inducement Plan (“Inducement Plan”), under which the Company may grant nonqualified stock options or other awards including stock appreciation rights and restricted stock awards.

Options under the 2020 Plan and Inducement Plan may be granted for periods of up to 10 years and at prices no less than the market price of the Company’s common stock on the date of grant, provided, however, that the exercise price of an incentive stock option granted to a 10% shareholder shall not be less than 110% of the fair value of the shares on the date of grant and the option is not exercisable after the expiration offive years from the date of grant.

Incentive Stock Options and Nonqualified Stock Options

Stock options issued under either the 2015 Plan, the 2020 Plan or the Inducement Plan generally vest over four years and expireten years from the date of grant. Certain options provide for accelerated vesting if there is a change in control, as defined in the respective plans.

The Company used Black-Scholes option pricing model to estimate stock-based compensation expense for stock option awards with the following assumptions:

A summary of option activity under the 2015 Plan and the 2020 Plan is as follows:

As of September 30, 2025, there were $28.4 million of unrecognized compensation costs that are expected to be recognized over the weighted-average period of 2.4 years related to stock options. Aggregate intrinsic value represents the difference between the fair value of the underlying common stock and the exercise price as of September 30, 2025.

Restricted Stock Units

The service-based condition for restricted stock units (“RSUs”) is generally satisfied over three years.

As of September 30, 2025, the Company had $9.5 million of unrecognized stock-based compensation expense related to outstanding RSUs expected to be recognized over a weighted-average period of 1.7 years.

Performance-Based Restricted Stock Units

Performance-based restricted stock units (“PSUs”) were granted in 2022 and vested upon the achievement of market and performance conditions. Market conditions include the Company's total shareholder return (“TSR”) relative to the Nasdaq

Biotechnology Index over the term of the award ending on June 30, 2024. Additionally, the number of shares of common stock issuable upon vesting ranged from 0% to 200% of the PSUs based on achievement of certain targets.

The fair value of the TSR PSUs were derived from a Monte Carlo simulation model that used the following key assumptions:

The measurement period for the PSUs associated with TSR concluded on the last trading day of the second quarter 2024 and in July 2024, upon certification of the TSR results by the compensation committee of the board of directors, the award recipients vested in a total of 155,292 shares of common stock, representing 55% achievement. Such 155,292 shares of common stock were issued to award recipients as of September 30, 2024. There were no outstanding PSUs as of September 30, 2025.

2020 Employee Stock Purchase Plan

In June 2020, the Company adopted the Company's 2020 Employee Stock Purchase Plan (the “2020 ESPP”). The 2020 ESPP provides that the number of shares reserved and available for issuance will automatically increase on January 1 of each calendar year, beginning January 1, 2021, by the least of (1)1.0% of the total number of shares of common stock outstanding on December 31 of the preceding calendar year, (2)700,000 shares or (3) such lesser amount as determined by the administrator of the 2020 ESPP, which is the compensation committee of the board of directors of the Company.

Under the 2020 ESPP, eligible employees may purchase shares of our common stock through payroll deductions that cannot exceed 15% of each employee’s salary. The 2020 ESPP provides for asix-month offering period. At the end of the purchase period, eligible employees are permitted to purchase shares of common stock at the lower of 85% of the fair market value at the beginning of the offering period or 85% of the fair market value at the end of the purchase period, subject to tax limitations on the total value of the purchase. The 2020 ESPP is considered a compensatory plan, and the Company recorded $0.1 million and $0.2 million in stock-based compensation expense for the three and nine months ended September 30, 2025, respectively, and $0.1 million and $0.4 million for the three and nine months ended September 30, 2024, respectively. During the three and nine months ended September 30, 2025,61,231 and 211,218 shares of common stock were issued respectively under the 2020 ESPP with 1,692,136 shares remaining available for issuance under the 2020 ESPP. The Company used Black-Scholes option pricing model to estimate stock-based compensation expense for the 2020 ESPP with the following assumptions:

Stock-Based Compensation Expense

The following table presents the components and classification of stock-based compensation expense for the Company’s stock-based awards for the three and nine months ended September 30, 2025 and 2024 (in thousands):

12. Income Taxes

For the three and nine months ended September 30, 2025 and 2024, the Company didnot record an income tax provision. The Company will continue to maintain a 100% valuation allowance on total deferred tax assets. The Company believes it is more likely than not that the related deferred tax asset will not be realized. As a result, the Company’s effective tax rate will remain at 0% because there are no estimated or discrete items that would impact the tax provision.

On July 4, 2025, the One Big Beautiful Bill Act, or OBBBA, was enacted in the United States, which includes significant changes to federal tax law and other regulatory provisions that may impact the Company. Based on the Company's assessment to date, the provisions of the OBBBA are not expected to have a material impact on the Company's effective tax rate or cash flow in the current fiscal year due to the Company's position on its deferred tax assets. The Company will continue to monitor developments and assess any future impacts as the implementation of regulations are finalized.

13. Segments

The Company operates and manages its business asone reportable and operating segment, which is the business of developing and commercializing novel therapies for patients. The Company’s chief executive officer, who is the chief operating decision maker (“CODM”), reviews financial information on an aggregate basis for allocating and evaluating financial performance. The Company defines its segments based on the way in which internally reported financial information is regularly reviewed by the CODM to analyze financial performance, make decisions, and allocate resources. The CODM assesses performance for the segment and decides how to allocate resources based on net loss which is also reported on the Statement of Operations and Comprehensive Loss as consolidated net loss.

All long-lived assets are maintained in the United States of America.

Our CODM is regularly provided with more detailed expense information than what is included in our Statement of Operations and Comprehensive Loss. The table below shows a reconciliation of the Company’s net loss, including the significant expense categories regularly provided to and reviewed by the CODM, as computed under U.S. GAAP to the Company’s total net loss in the statements of operations (in thousands).

Other segment items include total stock-based compensation and research and development costs related to other pipeline programs and other non-program costs (excluding employee-related expenses).

14. Commitments and Contingencies

Purchase Commitments

The Company has contractual arrangements with research and development organizations and suppliers; however, these contracts are generally cancellable on 30 days’ notice and the obligations under these contracts are largely based on services performed.

15. Leases

On September 28, 2023, the Company entered into a lease agreement with HCP BTC, LLC, a Delaware limited liability company (“the Landlord”) for premises consisting of approximately 100,904 square feet of office and laboratory space located at Oyster Point Blvd, South San Francisco, California (the “Oyster Point Lease”), which is being used as a single unified Company headquarters. The lease term of approximately seven years started in the second quarter of 2024 when the Landlord substantially completed tenant improvements and may be extended for a period ofeight years at the then prevailing market rates for a comparable property. Future lease payments are approximately $39.3 million which represent the non-cancellable periods of the lease. We excluded extension options that are not reasonably certain to be exercised from our lease terms. Our lease payments consist primarily of fixed rental payments for the right to use the underlying leased assets over the lease term. Our lease agreement provides us the right to sublet the premises, subject to approval by the Landlord. Additionally, the Company provided a letter of credit to the Landlord in the amount of $1.4 million in connection with the Oyster Point Lease, which is classified as restricted cash as of September 30, 2025.

Though the Oyster Point Lease is accounted for as a single contract, the office space was occupied in March 2024 while the laboratory space was occupied in June 2024. Accordingly, the Company measured and allocated consideration to each lease component. Upon commencement of each lease component the Company recognized an aggregate right-of-use asset ("ROU") and lease liability of $23.7 million and $6.1 million during the quarters ended March 31, 2024 and June 30, 2024, respectively.

The undiscounted future non-cancellable lease payments of the Company's operating lease liability as of September 30, 2025 were as follows (in thousands):

The weighted-average remaining lease terms and discount rates related to the Company's operating leases were as follows:

Variable lease costs comprise primarily of the Company's proportionate share of operating expenses, property taxes, and insurance. Short-term lease expense and variable lease payments recorded in operating expenses were immaterial for the three and nine months ended September 30, 2025 and 2024. Lease expenses for each of the three and nine months ended September 30, 2025 and 2024 are as follows (in thousands):

16. Defined Contribution Plan

The Company sponsors a defined contribution plan under Section 401(k) of the Internal Revenue Code covering substantially all full-time U.S. employees. Employee contributions are voluntary and are determined on an individual basis subject to the maximum allowable under federal tax regulations. The Company made contributions to the plan of $0.2 million and $1.2 million for the three and nine months ended September 30, 2025 and $0.3 million and $1.1 million for the three and nine months ended September 30, 2024.

17. Net Loss Per Share Attributable to Common Stockholders

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share attributable to common stockholders for the periods presented, because including them would have been antidilutive:

18. Restructuring of Operations

On May 1, 2025, we announced a reduction in workforce that impacted approximately 45% of our then-current employees. The current restructuring plan was completed in the third quarter and amounted to $3.8 million. For the three and nine months ended September 30, 2025, we made cash payments of $0.6 million and $3.8 million, respectively. For the three and nine months ended September 30, 2025, one-time termination benefits totaling $0.1 million and $2.8 million was recorded to research and development expenses and $0 and $1.0 million was recorded to general and administrative expenses, respectively.

19. Subsequent Events

On October 14, 2025, we completed a voluntary prepayment of our Amended Loan Agreement with Oxford for $32.4 million, representing all outstanding principal, accrued and unpaid interest, fees, costs and expenses. Upon prepayment, all obligations, covenants, debts and liabilities under the Amended Loan Agreement were satisfied and discharged in full, and the Amended Loan Agreement and all other documents entered into in connection with the Amended Loan Agreement were terminated.