Armata Pharmaceuticals : Annual Report Package for the 2025 Annual Meeting

About this update from Armata Pharmaceuticals, Inc.

Dear Fellow Shareholders, Thank you for the opportunity to share Armata Pharmaceutical, Inc.'s ("Armata" or the "Company") progress since last year's Annual Shareholder Meeting. Since that time, we have been acutely focused on the critical development of our two clinical-stage phage product candidates, which we believe have the potential to help address the growing global health crisis of bacterial antimicrobial resistance. Our first candidate is a multi-phage cocktail (AP-PA02) that we are developing as an inhaled treatment for chronic pulmonary Pseudomonas aeruginosa infection in people with cystic fibrosis and non-cystic fibrosis bronchiectasis ("NCFB"). Our second candidate, also a multi-phage cocktail (AP-SA02), is being developed to treat Staphylococcus aureus bacteremia, an acute clinical indication for which antibiotic resistance continues to be a growing problem. We believe this dual approach of treating both chronic and acute infections allows us to address the broadest range of unmet patient needs while also generating sustained long-term value for the Company. The positive results of studies that we have completed to date support the initiation of pivotal trials-the next critical step for Armata as we work to advance the clinical development of these novel pathogen-specific therapeutics towards registration and commercialization. We have achieved significant progress towards these goals across three crucial areas: With the completion of our new research and development and manufacturing facility in Los Angeles, we now expect to be able to fully commercialize in the United States by utilizing our state-of-the-art capabilities in developing and manufacturing phage therapeutics, including our proprietary processes, validated release assays, high-throughput semi-automated fill and finish, storage and shipment of drug product. All of our active pharmaceutical ingredients are sourced in the United States with no offsite manufacturing. In parallel, we have significantly improved the efficiency of all aspects of our production, increasing phage titers while maintaining high purity of drug product. Additionally, we have increased shelf life at 4  C. We accelerated patient enrollment in our two parallel Phase 2 clinical trials. Our NCFB Pseudomonas trial ("Tail wind ") completed enrollment in the second half of 2024, which was ahead of plan, and we released promising topline results in December of 2024. Tail wind was the second patient population for AP-PA02, which was first evaluated in patients with cystic fibrosis in the Phase 1b/2a SWARM- P.a. trial that successfully concluded in 2023. We also accelerated enrollment in our Staphylococcus bacteremia trial ("DiSArm"), announcing full enrollment in November 2024, with the last patient visit having taken place in January 2025. During the execution of the trial, we were able to dose escalate to 5e10 PFU every six hours (2E11 PFU every 24 hours) for five days without clinically significant adverse events. In parallel with dose escalation, the evolution of two distinct blinded subsets of subjects receiving phage has been observed. One subset, comprising approximately half of the treated group, has evidence of persistence of detectable phage in the blood consistent with in vivo phage amplification. This suggests that, despite the best available antibiotic treatment for greater than five days, reservoirs of active Staphylococcus aureus bacteria remained that our phages targeted, infected and killed before recirculating in the intravascular space. As of now, we anticipate database lock and receipt of topline data in the next few weeks, where we can explore the two aforementioned subsets in an unblinded manner. Topline results are also expected to inform the optimal dose of AP-SA02 to be evaluated in the larger definitive efficacy study. Our research and development team has completed the engineering of both the Pseudomonas and Staphylococcus production hosts, resulting in higher titers and maintaining high purity. We believe this positions us well for the execution of future pivotal trials. We believe our advanced process development capabilities ensure that we are a leader in the field in phage purity, allowing us to dose escalate in both inhaled and intravenous routes of administration. Finally, we are happy to report that we completed all prespecified actions outlined in last year's proxy letter on time or ahead of plan. In parallel, our leadership team is focused on managing costs and ensuring that our resources are focused on efficient clinical trial execution backed by rigorous core science. I am personally proud to be part of the highly committed team at Armata. Our continued strong progress is the result of the passion and dedication of each employee to achieve our mission of meeting the global challenge of antibiotic resistance by developing high-impact, best-in-class phage therapeutics for all patients in need. Despite these uncertain times, we remain laser focused on demonstrating the important role that phages can have in combatting serious bacterial infections in the blood stream and lungs. I speak for the entire Armata team when I say that I am optimistic about what the future holds for the Company. I would like to thank you, our shareholders, for continuing to support our efforts and sharing in our lofty goals. Sincerely, Deborah Birx, M.D. Chief Executive Officer UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 or TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number 001-37544 ARMATA PHARMACEUTICALS, INC. (Exact name of registrant as specified in its charter) Washington 91-1549568 (State or other jurisdiction of (I.R.S. Employer Identification No.) incorporation and organization) 5005 McConnell Avenue Los Angeles, CA 90066 (Address of principal executive offices, including zip code) (310) 665-2928 (Registrant's telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: Title of each class Trading Symbol(s) Name of each exchange on which registered Common Stock, par value $0.01 per share ARMP NYSE American Securities registered pursuant to Section 12(g) of the Act: None. Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes ☐ No ☒ Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Exchange Act. Yes ☐ No ☒ Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company or an emerging growth company. See definitions of "large accelerated filer," "accelerated filer," "smaller reporting company" and "emerging growth company" in Rule 12b-2 of the Exchange Act. Large accelerated filer ☐ Accelerated filer ☐ Non-accelerated filer ☒ Smaller reporting company ☒ Emerging growth company ☐ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management's assessment of the effectiveness of its internal control over financial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its audit report. ☐ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect the correction of an error to previously issued financial statements. ☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant's executive officers during the relevant recovery period pursuant to §240.10D-1(b). ☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒ As of June 30, 2024, the aggregate market value of voting stock held by non-affiliates of the Registrant, based on the closing price of the common stock on June 28, 2024 (the last business day of the Registrant's most recently completed second quarter) as quoted on the NYSE American, was approximately $30.3 million. As of February 28, 2025, 36,183,067 shares of the Registrant's common stock were outstanding. Document Incorporated by Reference Portions of the registrant's Definitive Proxy Statement relating to the 2025 Annual Meeting of Stockholders, which will be filed with the Securities and Exchange Commission within 120 days after the end of the registrant's fiscal year ended December 31, 2024, are incorporated by reference into Part III of this Annual Report on Form 10-K. TABLE OF CONTENTS ARMATA PHARMACEUTICALS, INC. PART I Page No. Item 1. Business 6 Item 1A. Risk Factors 40 Item 1B. Unresolved Staff Comments 62 Item 1C. Cybersecurity 62 Item 2. Properties 63 Item 3. Legal Proceedings 63 Item 4. Mine Safety Disclosures 64 PART II Item 5. Market for Registrant's Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities 64 Item 6. Reserved 64 Item 7. Management's Discussion and Analysis of Financial Condition and Results of Operations 64 Item 7A. Quantitative and Qualitative Disclosures About Market Risk 75 Item 8. Financial Statements and Supplementary Data 75 Item 9. Changes In and Disagreements With Accountants on Accounting and Financial Disclosure 103 Item 9A. Controls and Procedures 103 Item 9B. Other Information 104 Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections 105 PART III Item 10. Directors, Executive Officers and Corporate Governance 106 Item 11. Executive Compensation 106 Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters 106 Item 13. Certain Relationships and Related Transactions and Director Independence 106 Item 14. Principal Accountant Fees and Services 106 PART IV Item 15. Exhibits and Financial Statement Schedules 107 Item 16. Form 10-K Summary 112 Signatures and Power of Attorney 113 2 SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS This Annual Report on Form 10-K (this "Annual Report") and certain information incorporated herein by reference contain forward-looking statements, which are provided under the "safe harbor" protection of the Private Securities Litigation Reform Act of 1995. These statements relate to future events, results or to our future financial performance and involve known and unknown risks, uncertainties and other factors which may cause our actual results, performance or events to be materially different from any future results, performance or events expressed or implied by the forward-looking statements. Forward-looking statements in this Annual Report include, but are not limited to, statements regarding: our estimates regarding anticipated operating losses, capital requirements and needs for additional funds; our ability to raise additional capital when needed and to continue as a going concern; our ability to manufacture, or otherwise secure the manufacture of, sufficient amounts of our product candidates for our preclinical studies and clinical trials; our clinical development plans, including planned clinical trials; our research and development plans, including our clinical development plans; our ability to select combinations of phages to formulate our product candidates; our development of bacteriophage-based therapies; the potential use of bacteriophages to treat bacterial infections; the potential future of antibiotic resistance; our ability for bacteriophage therapies to disrupt and destroy biofilms and restore sensitivity to antibiotics; our planned development strategy, presenting data to regulatory agencies and defining planned clinical studies; the expected timing of additional clinical trials, including Phase 1b/Phase 2 or registrational clinical trials; our ability to manufacture and secure sufficient quantities of our product candidates for clinical trials; the drug product candidates to be supplied by us for clinical trials; the potential for bacteriophage technology being uniquely positioned to address the global threat of antibiotic resistance; the safety and efficacy of our product candidates; our anticipated regulatory pathways for our product candidates; the activities to be performed by specific parties in connection with clinical trials; our ability to successfully complete preclinical and clinical development of, and obtain regulatory approval of our product candidates and commercialize any approved products on our expected timeframes or at all; our pursuit of additional indications; 3

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