Biomea Fusion, Inc.

Note 1. Organization

Organization

Biomea Fusion, Inc., (the Company), was established in the state of Delaware in August 2017 as Biomea Fusion, LLC. In December 2020, all outstanding membership interests in Biomea Fusion, LLC were converted into equity interests in the Company. The capitalization information included in these unaudited condensed financial statements is consistently presented as if it is that of Biomea Fusion, Inc., even during the prior period when investors held their equity interests in Biomea Fusion, LLC.

The Company is a clinical-stage diabetes and obesity medicines company dedicated to discovering and developing novel small molecules to treat and improve the lives of patients with diabetes, obesity and metabolic disorders. Since its inception in 2017, the Company has built its proprietary FUSIONTM System platform to design and develop a pipeline of novel covalent product candidates.

Basis of Presentation

The accompanying unaudited condensed financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America (GAAP) and applicable rules and regulations of the Securities and Exchange Commission (SEC) regarding interim financial reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP have been condensed or omitted, and accordingly the balance sheet as of December 31, 2024 has been derived from the audited financial statements at that date but does not include all of the information required by GAAP for complete financial statements. These unaudited condensed financial statements have been prepared on the same basis as the Company’s annual financial statements and, in the opinion of management, reflect all adjustments, consisting only of normal recurring adjustments which are necessary for a fair statement of the Company’s financial information. The unaudited interim results of operations for the three and six months ended June 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 accompanying unaudited condensed financial statements should be read in conjunction with the audited financial statements and the related notes thereto for the year ended December 31, 2024, included in the Company’s Annual Report on Form 10-K filed with the SEC on March 31, 2025.

Liquidity and Capital Resources

The Company has incurred net operating losses and negative cash flows from operations since its inception and had an accumulated deficit of $437.3 million at June 30, 2025. As of June 30, 2025, the Company had cash, cash equivalents, and restricted cash of $56.6 million. Management believes that the existing financial resources are not sufficient to continue operating activities for at least one year past the issuance date of these unaudited condensed financial statements. The Company’s ability to continue as a going concern will require the Company to raise additional capital to fund the Company's operations through public or private equity offerings, debt financings, collaborations and licensing arrangements or other sources. There can be no assurance that additional financing will be available to the Company or that such financing, if available, will be available on terms acceptable to the Company. Accordingly, there is substantial doubt about the Company’s ability to continue as a going concern.

The Company has historically financed its operations primarily through the sale of common stock and the issuance of unsecured promissory notes. To date, none of the Company’s product candidates have been approved for commercial sale, and the Company has not generated any revenue since inception. Management expects operating losses to continue and increase for the foreseeable future, as the Company continues clinical development activities for its lead product candidate and advances the preclinical and clinical development of other product candidates. The Company’s prospects are subject to risks, expenses and uncertainties frequently encountered by companies in the biotechnology industry as discussed below. There can be no assurance that in the event the Company requires additional financing, such financing will be available on terms which are favorable or at all. Failure to generate sufficient cash flows from operations, raise additional capital or reduce certain discretionary spending would have a material adverse effect on the Company’s ability to achieve its intended business objectives.

Note 2. Summary of Significant Accounting Policies

There have been no significant changes to the significant accounting policies during the six months ended June 30, 2025, as compared to those included in the Company’s Annual Report on Form 10-K filed with the SEC on March 31, 2025, except as described below.

Warrant Liability

The Company accounts for its warrants in accordance with ASC 815, Derivatives and Hedging - Contracts in Entity's Own Equity, as either liabilities or as equity instruments depending on the specific terms of the warrant agreement. The common warrants issued in connection with the June 2025 underwritten public offering (see Note 5) are classified as liabilities and are recorded at fair value. The warrants are subject to re-measurement at each settlement date and at each balance sheet date and any change in fair value is recognized in Interest and Other income, net in the condensed statements of operations and comprehensive loss. The Company estimates the fair value of the warranty liability using a Black-Scholes pricing model. The Company is required to make assumptions and estimates in determining an appropriate expected term, risk-free interest rate, volatility factor, dividend yield, and the fair value of common stock. Any significant adjustments to the unobservable inputs would have a direct impact on the fair value of the warrant liability.

Recent Accounting Pronouncements - Not Yet Adopted

In December 2023, the Financial Accounting Standard Board (FASB) issued Accounting Standards Update (ASU) 2023-09, “Income Taxes - Improvements to Income Tax Disclosures” requiring, on annual basis, enhancements and further transparency to certain income tax disclosures, most notably the tax rate reconciliation and income taxes paid. This ASU 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 the adoption of this standard on the Company’s financial statements and related disclosures.

In November 2024, the FASB issued ASU 2024-03, Income Statement-Reporting Comprehensive Income-Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses (ASU 2024-03), which requires disaggregated information about certain income statement expense line items on an annual and interim basis. ASU 2024-03 is effective for annual periods beginning after December 15, 2026 and interim reporting periods within annual reporting periods beginning after December 15, 2027. Early adoption is permitted and can be applied prospectively or retrospectively. The Company is evaluating the impact of the adoption of this standard on the Company’s financial statements and related disclosures.

Note 3. Fair Value Measurement

The Company measures and reports certain financial instruments as assets and liabilities at fair value on a recurring basis. The following tables set forth the fair value of the Company’s financial assets, which consist of cash equivalents and marketable securities measured and recognized at fair value (in thousands):

The Company evaluates transfers between levels at the end of each reporting period. There wereno transfers between Levels 1,2 and

3 during thethree and six months ended June 30, 2025 and 2024. As of June 30, 2025 and December 31, 2024, there wereno financial instruments classified as Level 2. There have beenno realized or unrealized gains or losses recognized for the periods presented.

There wereno investments as of June 30, 2025 and December 31, 2024, as such, no allowance for credit losses has been recognized as of June 30, 2025. During the three and six months ended June 30, 2025 and 2024, the Company didnot recognize any impairment losses related to investments.

The warrant liability in the table above consisted of the fair value of the Common Warrants (see Note 5) and was based on significant inputs not observable in the market, which represents a Level 3 measurement within the fair value hierarchy.

The following table provides a full roll forward of the aggregate fair value of the warrant liability categorized within Level 3 inputs:

Note 4. Balance Sheet Components

Prepaid Expenses and Other Current Assets

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

In September 2022, the Company entered into athirty-month sublease agreement for office space located at 900 Middlefield Road, 4th Floor, Redwood City, California, which commenced in January 2023 and expired in July 2025. In connection with the sublease, the Company made a security deposit of $2.1 million which is included in other current assets on the balance sheet at June 30, 2025.

Property and Equipment, Net

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

Depreciation expense for the three and six months ended June 30, 2025 was$0.5 million and$0.9 million, respectively. Depreciation expense for the three and six months ended June 30, 2024 was$0.4 million and$0.8 million, respectively.

Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

Note 5. Capital Structure

Common Stock

The Company’s amended and restated certificate of incorporation authorizes the Company to issue up to 300,000,000 shares of common stock with a par value of $0.0001 per share and 10,000,000 shares of preferred stock with a par value of $0.0001 per share.

Common stockholders are entitled to dividends when and if declared by the Company’s Board of Directors and after any preferred share dividends are fully paid. The holder of each share of common stock is entitled to one vote. As of June 30, 2025, no dividends have been declared.

Public Offerings

In April 2023, pursuant to a registration statement on Form S-3, the Company issued and sold 5,750,000 shares of common stock at a public offering price of $30.00 per share in an underwritten public offering. The net proceeds to the Company from the offering were approximately $161.8 million, after deducting underwriting discounts and commissions and offering costs of approximately $11.0 million.

In June 2025, the Company completed an underwritten public offering transaction in which it issued and sold 19,450,000 shares of common stock at an offering price of $2.00 per share and, to a certain investor in lieu of common stock, pre-funded warrants to purchase up to 550,000 shares of common stock at an offering price of $1.9999 per share and accompanying common warrants to purchase up to 23,000,000 shares of common stock at a per share exercise price of $2.50. The net proceeds to the Company from the offering were approximately $37.2 million, after deducting underwriting discounts and commissions and offering costs of approximately $2.8 million. The Company concluded that the common warrants do not meet the equity contract scope exception. The liability associated with the common warrants is recorded as warrant liability in the condensed balance sheet as of June 30, 2025.

The valuation of the common warrants is adjusted to fair value (Level 3) at each subsequent balance sheet date until the common warrants are settled or expired. To this date, due primarily to fluctuations in the Company's common stock price between the issuance date and June 30, 2025, the warrant liability was revaluated at $21.8 million as of June 30, 2025. The change in fair value of $0.2 million has been recorded as other income.

The Company calculated the fair value of common warrants using the Black-Scholes option pricing model with the following inputs:

Common Stock Warrants

As of June 30, 2025, the following warrants and pre-funded warrants to purchase shares of the Company's common stock were issued and outstanding:

There wereno warrants exercised during the three and six months ended June 30, 2025.

ATM Offering Agreement with Piper Sandler & Co.

On November 25, 2022, the Company entered into an equity distribution agreement (the 2022 ATM Agreement) with Piper Sandler & Co., as sales agent (the Sales Agent), with respect to an ATM offering program (the 2022 ATM Offering Program). Pursuant to the prospectus supplement relating to the Offering (as defined below), dated as of November 25, 2022 (the Prospectus Supplement), the Company may offer and sell, from time to time in its sole discretion, shares of its common stock, par value $0.0001 per share (the Common Stock), having an aggregate offering price of up to $100 million (the Shares) through the Sales Agent (the Offering).

The Offering was registered under the Securities Act of 1933, as amended (the Securities Act), pursuant to our shelf registration statement on Form S-3 (Registration Statement No. 333-267884), as previously filed with the SEC and declared effective on October 14, 2022. The Company filed a prospectus supplement, dated November 25, 2022, with the SEC that provides for the sale of shares of common stock having an aggregate offering price of up to $100 million in connection with the 2022 ATM Offering Program.

The 2022 ATM Agreement contains customary representations, warranties and agreements by us, and customary indemnification and contribution rights and obligations of the parties. The Company agreed to pay the sales agent a placement fee of up to 3.0% of the aggregate gross proceeds from the sale. The Company also agreed to reimburse the sales agent for certain specified expenses in connection with entering into the 2022 ATM Agreement.

During the six months ended June 30, 2025, the Company has received aggregate proceeds from its 2022 ATM Offering Program of$4.9 million, net of commissions and offering costs, pursuant to the issuance of 2,271,122 shares of its common stock.

Note 6. Stock-Based Compensation

Effective January 1, 2025, the number of shares of common stock available under the 2021 Incentive Award Plan (the 2021 Plan) increased by 1,815,535 shares pursuant to the evergreen provision. As of June 30, 2025,5,197,494 shares of common stock remained available for issuance under the 2021 Plan.

Effective January 1, 2025, the number of shares of common stock available under the 2021 Employee Stock Purchase Plan (the ESPP) increased by 363,107 shares pursuant to the evergreen provision of the ESPP. As of June 30, 2025,850,949 shares of common stock remained available for issuance under the ESPP.

As of June 30, 2025,1,839,250 shares of common stock remained available for issuance under the 2023 Inducement Equity Plan as adopted in November 2023.

Stock-Based Compensation Expense

Total stock-based compensation expense related to the Company’s equity incentive plans and ESPP was recorded in the statements of operations and allocated as follows (in thousands):

As of June 30, 2025, there was$15.4 million of total unrecognized stock-based compensation expense which is expected to be recognized over a weighted-average period of 1.6 years.

Stock Options

The following table summarizes stock option activity:

Note 7. Commitments and Contingencies

Legal Proceedings

The Company, from time to time, may be party to litigation arising in the ordinary course of business. The Company records a liability for such matters when it is probable that future losses will be incurred and that such losses can be reasonably estimated. Significant judgment by the Company is required to determine both probability and the estimated amount. Management is currently not aware of any legal matters that could have a material adverse effect on the Company's financial position, results of operations or cash flows.

Indemnification

The Company enters into standard indemnification agreements in the ordinary course of business. Pursuant to these arrangements, the Company indemnifies, holds harmless and agrees to reimburse the indemnified parties for losses suffered or incurred by the indemnified party, in connection with any trade secret, copyright, patent or other intellectual property infringement claim by any third party with respect to its technology. The term of these indemnification agreements is generally perpetual any time after the execution of the agreement. The maximum potential amount of future payments the Company could be required to make under these arrangements is not determinable. The Company has never incurred costs to defend lawsuits or settle claims related to these indemnification agreements. As a result, the Company believes the fair value of these agreements is not material.

The Company has also entered into indemnification agreements with its directors and officers that may require the Company to indemnify its directors and officers against liabilities that may arise by reason of their status or service as directors or officers to the fullest extent permitted by Delaware corporate law. The Company currently has directors’ and officers’ insurance.

Note 8. Net Loss Per Share

Basic and diluted net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding for the period. For periods in which the Company generated a net loss, the Company does not include the potential impact of dilutive securities in diluted net loss per share, as the impact of these items is anti-dilutive.

The following equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented:

Note 9. Segment Reporting

The Company operates and manages its business asone reportable and operating segment, which is the business of developing small molecule drugs to treat patients with metabolic diseases. The Company’s interim chief executive officer, who is the chief operating decision maker, reviews financial information on an aggregate basis for allocating resources and evaluating financial performance. All long-lived assets are maintained in, and all losses are attributable to, the United States of America.

The following table presents reportable segment profit and loss, including significant expense categories, attributable to our reportable segment for the periods indicated:

Reconciliation of segment loss from operations to net loss:

Note 10. Subsequent Events

On July 15, 2025, in connection with the completed underwritten public offering, the underwriters partially exercised their over-allotment option to purchase an additional 1,381,262 shares of common stockat an offering price of $2.00 per share. The gross proceeds from the offering pursuant to the over-allotment option were approximately $2.8 million, before deducting underwriting discounts and commissions and offering expenses.