Organization and Nature of the Business

3 Months Ended

Mar. 31, 2025

Organization and Nature of the Business

Organization and Nature of the Business

1. Organization and Nature of the Business

Organization and Business

Alumis Inc. (the “Company”) is a clinical stage biopharmaceutical company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines for autoimmune disorders. The Company leverages its proprietary precision data analytics platform, biological insights, and a team of experts with deep experience in precision medicine drug discovery, development, and immunology, to create medicines that significantly improve the lives of patients by replacing broad immunosuppression with targeted therapies.

The Company was founded on January 29, 2021, as a Delaware corporation under the name FL2021-001, Inc. FL2021-001, Inc.’s name was changed to Esker Therapeutics, Inc. on March 8, 2021, and to Alumis Inc. on January 6, 2022. The Company is headquartered in South San Francisco, California. As of March 31, 2025, the Company had one wholly owned subsidiary, Arrow Merger Sub, Inc. (“Merger Sub”), incorporated in January 2025.

Reverse Stock Split

On June 19, 2024, the board of directors approved, and on June 20, 2024, the Company effected, a reverse stock split of the shares of the Company’s outstanding common stock at a ratio of 1-for-4.675 (the “Reverse Stock Split”). The number of authorized shares and par value per share were not adjusted as a result of the Reverse Stock Split. All references to shares, options to purchase common stock, share amounts, per share amounts, and related information contained in the unaudited condensed consolidated financial statements have been retrospectively adjusted to reflect the effect of the Reverse Stock Split for all periods presented. The shares of common stock underlying outstanding stock options and other equity instruments were proportionately reduced and the respective exercise prices, if applicable, were proportionately increased in accordance with the terms of the agreements governing such securities. In addition, the conversion ratios for each series of the Company’s redeemable convertible preferred stock, which were automatically convertible into shares of common stock upon the closing of the Company’s initial public offering (the “IPO”) of common stock, were proportionally adjusted.

IPO and Concurrent Private Placement

On July 1, 2024, the Company completed its IPO, pursuant to which it issued and sold 13,125,000 shares of its common stock at $16.00 price per share to the public. Net proceeds from the IPO were $193.3 million, after deducting underwriting discounts and commissions and other offering costs totaling $16.7 million. On July 17, 2024, an existing investor and a holder of more than 5% of the Company’s capital stock, purchased an additional 2,500,000 shares of the Company’s common stock at the IPO price per share for total gross and net proceeds of $40.0 million in a private placement transaction (the “Concurrent Private Placement”).

Immediately prior to the closing of the IPO on July 1, 2024, all of the shares of the Company’s redeemable convertible preferred stock then outstanding converted into 28,855,656 shares of Class A common stock and 7,184,908 shares of Class B common stock at a 1-for-4.675 conversion ratio (the “Preferred Stock Conversion”). All outstanding Class A common stock shares and all outstanding Class B common stock shares were redesignated immediately thereafter into the same number of shares of voting common stock and non-voting common stock, respectively. Unless the context otherwise requires a different meaning, all references to “common stock” in these notes refers to the Company’s voting common stock and non-voting common stock combined.

Merger Agreement

On February 6, 2025, the Company entered into an Agreement and Plan of Merger and, on April 20, 2025, the Company entered into an Amendment to Agreement and Plan of Merger (collectively the “Merger Agreement”) with ACELYRIN, Inc., a Delaware corporation (“ACELYRIN”), and Merger Sub, a Delaware corporation and a direct wholly owned subsidiary of the Company. Under the terms of the Merger Agreement, Merger Sub will merge with and into ACELYRIN, with ACELYRIN continuing as a direct wholly owned subsidiary of the Company (the “Merger”). The Merger Agreement was approved by the disinterested directors on the Company’s board of directors and the board of directors of ACELYRIN and is subject to stockholder approval by the stockholders of each company and satisfaction or waiver of other closing conditions. The Merger is anticipated to qualify as a tax-free reorganization for U.S. federal income tax purposes.

Subject to the terms and conditions of the Merger Agreement, and at the effective time of the Merger (the “Effective Time”), the Company will (i) issue shares of its common stock in exchange for ACELYRIN issued and outstanding common stock shares (the number of shares of the Company’s common stock issued in exchange for each share of ACELYRIN common stock, the “Exchange Ratio”) and will pay cash for any fractional shares, (ii) assume options of ACELYRIN option holders with an exercise price of $18.00 or less outstanding and unexercised immediately prior to the Effective Time, which will be exercisable in the Company’s common stock, (iii) assume restricted stock units (“RSUs”) outstanding and unvested immediately prior to the Effective Time, and (iv) assume performance RSUs outstanding and unvested immediately prior to the Effective Time, which will be convertible into the Company’s RSUs awards subject only to a service vesting condition.

Outstanding shares, options, RSUs and performance RSUs will be exchanged at the Exchange Ratio of 0.4814-for-one. ACELYRIN’s outstanding and unexercised options with exercise prices more than $18.00 will be cancelled. Exercise prices for the assumed options will be determined as the product of the original exercise prices multiplied by the reciprocal of the Exchange Ratio. Converted ACELYRIN options and RSUs will continue to vest in accordance with their original terms. Performance RSUs will be deemed to have 100% satisfied their performance conditions and will vest in three equal installments on May 15 of calendar years 2025, 2026 and 2027, unless the closing of the Merger occurs after May 15, 2025, in which case the converted performance RSUs will vest in two equal installments on May 15 of calendar years 2026 and 2027, subject to the holder of the converted performance RSUs remaining in service with Alumis or any of its subsidiaries on such date.

Consummation of the Merger is subject to certain closing conditions, including the absence of any law or judgment that restrains, enjoins or otherwise prohibits consummation of the Merger, the effectiveness of a registration statement on Form S-4 filed with the Securities and Exchange Commission (the “SEC”) by the Company, adoption of the Merger Agreement by the holders of a majority of the outstanding ACELYRIN Shares at ACELYRIN’s stockholders’ meeting, and approval of the share issuance by the holders of a majority of votes of the Company’s common stock cast at the Company’s stockholders’ meeting.

The Merger Agreement contains certain termination rights for both the Company and ACELYRIN, including the right of either party to terminate the Merger Agreement if the transactions have not been consummated prior to July 7, 2025. The Company or ACELYRIN will pay a termination fee of $10.0 million or $10.0 million, respectively, under certain circumstances, including termination to accept and enter into a definitive agreement with respect to a superior proposal. Immediately following the Merger, the Company’s pre-Merger equityholders are expected to collectively own approximately 52% of the shares of the combined company and the pre-Merger equityholders of ACELYRIN as of immediately prior to the Merger are expected to collectively own approximately 48% of the combined company, in each case, calculated on a fully diluted basis as of January 31, 2025.

The Merger will be accounted for as a business combination under the provisions of the Accounting Standards Codification (“ASC”) Topic 805, Business Combinations, with the Company being treated as the accounting acquirer. This determination is primarily based on a number of factors expected at the closing of the Merger, including: (i) which entity

is issuing its equity interests, (ii) the expectation that, following the Effective Time, the holders of shares of the Company’s common stock will hold, in the aggregate, more than 50% of the issued and outstanding shares of the Company’s common stock immediately following the Effective Time, (iii) the intended corporate governance structure of the Company following the Effective Time, (iv) the intended senior management of the Company following the Effective Time, and (v) the terms of the share exchange. Net assets acquired will be recognized at their fair value at the closing of the Merger. Goodwill will be calculated as a difference between the purchase consideration and the fair value of net assets acquired.

The Merger is expected to close in the second quarter of 2025. The Company recognized Merger transaction costs of approximately $7.7 million in general and administrative expenses in the condensed consolidated statement of operations and comprehensive loss for the three months ended March 31, 2025.

Liquidity and Going Concern

The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the three months ended March 31, 2025 and 2024, the Company incurred net losses of $99.0 million and $49.8 million, respectively. Cash used in operating activities was $80.4 million and $44.3 million for the three months ended March 31, 2025 and 2024, respectively. As of March 31, 2025, the Company had an accumulated deficit of $757.5 million.

The Company has historically financed its operations primarily through issuance of common stock, including in its IPO and Concurrent Private Placement, the issuance of redeemable convertible preferred stock and convertible promissory notes in private placements and, most recently, an upfront payment related to its collaboration and license agreement. The Company expects to continue to incur substantial losses for the foreseeable future, and its ability to achieve and sustain profitability will depend on the successful development, approval, and commercialization of any product candidates it may develop, and on the achievement of sufficient revenue to support its cost structure. The Company may never achieve profitability and, unless and until it does, it will need to continue to raise additional capital. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and marketable securities of $208.7 million as of March 31, 2025, will not be sufficient to meet its operating and capital requirements for at least 12 months from the date of issuance of these unaudited condensed consolidated financial statements and there is substantial doubt about the Company’s ability to continue as a going concern.

If the Merger closes, the Company’s liquidity would improve. However, as of the date of the issuance of these unaudited condensed consolidated financial statements, the Merger has not been completed and there can be no assurance that it will be consummated.

The Company will need to raise significant additional capital to fund ongoing research and development activities and maintain future operations. The Company’s management plans to monitor expenses and may raise additional capital through a combination of public and private equity, debt financings, strategic alliances and licensing arrangements. The Company’s ability to access capital when needed is not assured and, if capital is not available to the Company when, and in the amounts, needed, on the terms which are favorable, the Company could be required to delay, scale back, or abandon some or all of its planned development programs and other operations, which could materially harm the Company’s business, financial condition and results of operations.

The accompanying unaudited condensed consolidated financial statements have been prepared assuming that the Company will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. The accompanying unaudited condensed consolidated financial statements do not reflect any adjustments relating to the recoverability and reclassifications of assets and liabilities that might be necessary if the Company is unable to continue as a going concern.