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. Our lead program is focused on the development of treatments for solid tumors by inhibiting integrin-mediated activation of transforming growth factor-β (TGF-β). 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 six months ended June 30, 2026 are not necessarily indicative of the results to be expected for the year ending December 31, 2026 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, 2025, filed with the SEC on March 11, 2026 (the “2025 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 six months ended June 30, 2026, 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 2025 10-K.

Accounting Pronouncements Not Yet Adopted

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.

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 June 30, 2026 and as of December 31, 2025.

The following tables show the Company’s short-term investments and cash equivalents by significant investment category as of June 30, 2026 and December 31, 2025 (in thousands):

There wereno liabilities measured at fair value on a recurring basis as of June 30, 2026 and December 31, 2025. 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 six months ended June 30, 2026. In addition, there wereno assets or liabilities measured at fair value on a non-recurring basis as of June 30, 2026 and December 31, 2025.

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 $0.2 million and $0.5 million for the three and six months ended June 30, 2026, respectively, and $0.4 million and $0.9 million for the three and six months ended June 30, 2025, respectively.

In the fourth quarter of 2025, the Company committed to a plan to sell certain laboratory equipment that was no longer required following the restructuring of operations initiated May 1, 2025. Management determined that the assets met the criteria for classification as held for sale in accordance with ASC 360, "Property, Plant and Equipment."

The Company intended to divest these assets as part of their strategic realignment of resources, focusing on the development of PLN-101095 and the drug discovery platform. The assets were measured at the lower of their carrying value or fair value less cost to sell, and reclassified to "Property and equipment held for sale" within current assets on the Balance Sheets as of December 31, 2025. Depreciation ceased to be recognized on the assets after the date of their held-for-sale classification.

Laboratory equipment held for sale: (in thousands):

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. As of December 31, 2025, the amount also included accrued severance costs of $2.5 million.

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 (“Oxford”) to borrow a series of term loans up to an aggregate principal amount of $150.0 million. Pursuant to the Amended Loan Agreement, we drew an initial term loan of $30.0 million, inclusive of $10.0 million in principal amount previously outstanding under the initial Oxford Loan Agreement executed in May 2022.

In October 2025, we made a full voluntary prepayment of $32.4 million to extinguish outstanding term loans. Upon prepayment, the term loans, related security interests, and all other obligations, covenants, debts and liabilities under the Amended Loan Agreement were satisfied and discharged in full.

There wasno debt outstandingnor interest expense incurred during the three and six months ended June 30, 2026. Interest expense for the three and six months ended June 30, 2025 was $0.8 million and $1.6 million, respectively.

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 June 30, 2026 and December 31, 2025, the Company was authorized to issue 10,000,000 shares of preferred stock and there wasno outstanding preferred stock as of June 30, 2026 and December 31, 2025.

9. Common Stock

As of June 30, 2026 and December 31, 2025, 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.

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 the Rights Plan 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 Plan, 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 the Rights Plan, dated as of March 12, 2025, 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 Plan) 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 thetenth 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. On March 3, 2026, the Company entered into an Amendment to the Stockholder Rights Agreement to extend the expiration time of the Rights forone year from March 11, 2026 to March 11, 2027, unless the Rights are earlier redeemed, exchanged, or terminated in accordance with the terms and conditions of the Rights Agreement.

The Rights Plan 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 Plan 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 (the “2022 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.

Stock Option Repricing

On April 15, 2026, upon the recommendation of its Compensation Committee, the Board approved an option repricing (the “Repricing”), effective as of April 17, 2026 (the “Effective Date”). The Repricing was undertaken in accordance with, and as permitted by, the Company’s 2015 Plan, 2020 Plan, and 2022 Plan. Pursuant to the Repricing, effective as of the Effective Date, all outstanding vested and unvested options originally granted on or before March 1, 2025 pursuant to the 2015 Plan, the 2020 Plan, or the 2022 Plan that are held by employees as of the Effective Date, including the Company’s executive officers, were repriced to reduce the exercise price to $1.33 per share, the closing price per share of the Company’s common stock on the Effective Date. No other changes were made to the terms and conditions of the eligible stock option awards.

In order to exercise the repriced options at the $1.33 per share exercise price, employees are required to remain in service with the Company through the Retention Period, which begins on the Effective Date and ends on the earliest of the following: (i) the 18-month anniversary following the Effective Date if the employee is a member of the Company’s executive leadership team, or the 12-month anniversary following the Effective Date for all other employees; (ii) the consummation of a Corporate Transaction (as defined by the 2015 Plan); (iii) the consummation of a Sale Event (as defined by the 2020 Plan and 2022 Plan); and (iv) the employee’s (a) termination by the Company without cause (as defined in the Eligible Participant’s applicable severance plan) or due to a reduction in force, (b) death or termination due to disability, or (c) if the employee is a Vice President or above, resignation from service for good reason (as defined in the Eligible Participant’s applicable severance plan).

The repriced options will be subject to the original exercise price that was in effect immediately prior to the Effective Date if the employee (i) is terminated by the Company for cause (as defined in the Eligible Participant’s applicable severance plan); (ii) resigns from the Company prior to the end of the applicable Retention Period, except for good reason (as defined in the Eligible Participant’s applicable severance plan) if the employee is a Vice President or above; or (iii) elects to exercise the repriced options prior to the end of the applicable Retention Period.

Total incremental expense for the repriced options is $2.0 million which is expected to be recognized over a weighted-average period of 1.37 years.

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.

Excluding the effect of the repriced options, 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, 2020 Plan and 2022 Plan is as follows:

As of June 30, 2026, there was $18.6 million of unrecognized compensation costs, inclusive of the incremental cost of repriced options, that are expected to be recognized over a weighted-average period of 2.23 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 June 30, 2026.

Restricted Stock Units

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

As of June 30, 2026, the Company had $3.6 million of unrecognized stock-based compensation expense related to outstanding RSUs expected to be recognized over a weighted-average period of 1.66 years.

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 $27.5 thousand in stock-based compensation expense for the six months ended June 30, 2026 and $118.2 thousand for the six months ended June 30, 2025. During the six months ended June 30, 2026,65,652 shares of common stock were issued, under the 2020 ESPP with 1,626,484 shares remaining available for issuance as of June 30, 2026. 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 six months ended June 30, 2026 and 2025 (in thousands):

12. Income Taxes

For the three and six months ended June 30, 2026 and 2025, 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.

The One Big Beautiful Bill Act (“OBBBA”), enacted on July 4, 2025, introduced Internal Revenue Code (“IRC”) Section 174A, which permits the full expensing of domestic research and experimental (“R&E”) expenditures incurred in taxable years beginning after December 31, 2024. For domestic R&E expenditures incurred prior to January 1, 2025, the Company has elected to continue amortizing the remaining balances over their existing five-year periods as permitted by Rev. Proc. 2025-28.

For the three and six months ended June 30, 2026, the full expensing of current domestic R&E costs resulted in an increase in net operating loss carryforwards. However, because the Company maintains a full valuation allowance against its deferred tax assets, these changes had no impact on the effective tax rate.

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. Following our decision to discontinue development of bexotegrast, we re-prioritized development of programs formerly included in "other segment items" below. Beginning in the first quarter of 2026, significant segment expense includes the reprioritized pipeline within "Program expense - clinical trial and third-party contracting costs". Prior period amounts have been reclassified to conform to current year presentation.

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 reflecting the changes made by the Company's reprioritized pipeline, 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 not directly associated with active, prioritized 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 $36.6 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 June 30, 2026.

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 June 30, 2026 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 six months ended June 30, 2026 and 2025. Lease expenses for each of the three and six months ended June 30, 2026 and 2025 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 $0.1 million and $0.5 million for the three and six months ended June 30, 2026, respectively, and $0.3 million and $1.0 million for three and six months ended June 30, 2025 respectively.

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 restructuring plan was completed in the third quarter of 2025 and amounted to $3.8 million.

In December 2025, we initiated an additional restructuring plan totaling $2.5 million. The restructuring plan was completed on December 15, 2025 and the entire cost, consisting of severance and a benefits continuation payment was accrued within Accrued Compensation and Benefits as of December 31, 2025 and settled in cash during the three months ended March 31, 2026.