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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

​

☒ | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |

​

For the quarterly period ended September 30, 2025

OR

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☐ | 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 Number)
incorporation or organization) | ​
5005 McConnell Avenue | ​
Los Angeles, CA | 90066
(Address of principal executive offices) | (Zip Code)

​

Registrant’s telephone number, including area code: (310) 665-2928

Not Applicable

(Former name, former address, and former fiscal year, if changed since last report)

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, $0.01 par value per share | ARMP | NYSE American

​

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 as defined in Rule 12b-2 of the Exchange Act. See the 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 is a shell company (as defined in Rule 12b-2 of the Exchange Act).

Yes ☐ No ☒

The number of shares of the registrant’s Common Stock, par value $0.01 per share, outstanding as of November 4, 2025 was 36,329,842.

​

​

Table of Contents

TABLE OF CONTENTS

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|  | Page
PART I. FINANCIAL INFORMATION |
​ | ​ | ​
Item 1. | Financial Statements (unaudited) | 6
​ | ​ | ​
​ | Condensed Consolidated Balance Sheets | 6
| ​ | ​
| Condensed Consolidated Statements of Operations | 7
| ​ |
​ | Condensed Consolidated Statements of Stockholders’ Deficit | 8
​ | ​ | ​
| Condensed Consolidated Statements of Cash Flows | 10
| ​ |
| Notes to Condensed Consolidated Financial Statements | 11
​ | ​ | ​
Item 2. | Management’s Discussion and Analysis of Financial Condition and Results of Operations | 26
​ | ​ | ​
Item 3. | Quantitative and Qualitative Disclosures About Market Risk | 39
​ | ​ | ​
Item 4. | Controls and Procedures | 39
​ | ​ | ​
PART II. OTHER INFORMATION | 39
Item 1. | Legal Proceedings | 39
Item 1A. | Risk Factors | 39
Item 2. | Unregistered Sales of Equity Securities and Use of Proceeds | 39
Item 3. | Defaults upon Senior Securities | 39
Item 4. | Mine Safety Disclosures | 40
Item 5. | Other Information | 40
Item 6. | Exhibits | 40
SIGNATURES | 42

​

​

​

2

Table of Contents

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q (this “Quarterly 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 Quarterly 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;

| ● | the expected timing of additional clinical trials, including Phase 1b/Phase 2 or registrational clinical trials;

| ● | our research and 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;

| ● | the ability for bacteriophage therapies to disrupt and destroy biofilms and restore sensitivity to antibiotics;

| ● | the potential for bacteriophage technology being uniquely positioned to address the global threat of antibiotic resistance;

| ● | our planned development strategy, presenting data to regulatory agencies and defining planned clinical studies;

| ● | 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 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

Table of Contents

| ● | the content and timing of submissions to and decisions made by the U.S. Food and Drug Administration (the “FDA”) and other regulatory agencies;

| ● | our ability to leverage the experience of our management team and to attract and retain management and other key personnel;

| ● | the capacities and performance of our suppliers, manufacturers, contract research organizations (“CROs”) and other third parties over whom we have limited control;

| ● | our ability to staff and maintain our Los Angeles production facility under fully compliant current Good Manufacturing Practices (“cGMP”);

| ● | the actions of our competitors and success of competing drugs or other therapies that are or may become available;

| ● | our expectations with respect to future growth and investments in our infrastructure, and our ability to effectively manage any such growth;

| ● | the size and potential growth of the markets for any of our product candidates, and our ability to capture share in or impact the size of those markets;

| ● | the benefits of our product candidates;

| ● | the potential market growth and market and industry trends;

| ● | maintaining collaborations with third parties including our partnerships with the Cystic Fibrosis Foundation (the “CFF”) and the U.S. Department of Defense (the “DoD”);

| ● | potential future collaborations with third parties and the potential markets and market opportunities for product candidates;

| ● | our ability to achieve our vision, including improvements through engineering and success of clinical trials;

| ● | our ability to meet anticipated milestones in the development and testing of the relevant product;

| ● | our ability to be a leader in the development of phage-based therapeutics;

| ● | the expected use of proceeds from the $26.2 million DoD award;

| ● | the effects of government regulation and regulatory developments, and our ability and the ability of the third parties with whom we engage to comply with applicable regulatory requirements;

| ● | the accuracy of our estimates regarding future expenses, revenues, capital requirements and need for additional financing;

| ● | our expectations regarding future planned expenditures;

| ● | our ability to achieve and maintain effective internal control over financial reporting in accordance with Section 404 of the Sarbanes-Oxley Act;

| ● | our ability to obtain, maintain and successfully enforce adequate patent and other intellectual property protection of any of our products and product candidates;

4

Table of Contents

| ● | our ability to protect our intellectual property, including pending and issued patents;

| ● | our ability to operate our business without infringing the intellectual property rights of others;

| ● | our ability to advance our clinical development programs;

| ● | the effects of ongoing conflicts between Ukraine and Russia and in the Middle East, potential future bank failures or other geopolitical events;

| ● | the potential economic and regulatory impacts on the biotechnology, pharmaceutical and drug manufacturing industries;

| ● | the effects of artificial intelligence on our business and the industry as a whole; and

| ● | statements of belief and any statement of assumptions underlying any of the foregoing.

In some cases, you can identify these statements by terms such as “anticipate,” “believe,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “project,” “should,” “will,” “would,” or the negative of those terms, and similar expressions. These forward-looking statements reflect our management’s beliefs and views with respect to future events and are based on estimates and assumptions as of the date of this Quarterly Report and are subject to risks and uncertainties. We discuss many of these risks in greater detail in the section hereof entitled “Risk Factors” and in our Annual Report on Form 10-K for the year ended December 31, 2024 (the “2024 Annual Report”). Moreover, we operate in a very competitive and rapidly changing environment. New risks emerge from time to time. It is not possible for our management to predict all risks, nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statements we may make. In addition, statements that “we believe” and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Quarterly Report, and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain. Given these uncertainties, you should not place undue reliance on any of the forward-looking statements included in this Quarterly Report. In addition, this Quarterly Report also contains estimates, projections, and other information concerning our industry, our business, and the markets for our product candidates, as well as data regarding market research, estimates, and forecasts prepared by our management. Information that is based on estimates, forecasts, projections, market research, or similar methodologies is inherently subject to uncertainties and actual events or circumstances may differ materially from events and circumstances reflected in this information. These statements are based upon information available to us as of the date of this Quarterly Report, and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information.

Except as required by law, we assume no obligation to update these forward-looking statements publicly, or to update the reasons actual results could differ materially from those anticipated in any forward-looking statements, whether as a result of new information, future events, or otherwise.

This Quarterly Report includes trademarks and registered trademarks of Armata Pharmaceuticals, Inc. Products or service names of other companies mentioned in this Quarterly Report may be trademarks or registered trademarks of their respective owners.

As used in this Quarterly Report, unless the context requires otherwise, the “Company,” “we,” “us,” and “our” refer to Armata Pharmaceuticals, Inc. and its wholly owned subsidiaries.

​

​

​

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PART I. FINANCIAL INFORMATION

Item 1. FINANCIAL STATEMENTS

Armata Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(unaudited)

(in thousands, except share and per share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, 2025 |  | December 31, 2024
Assets | ​ | ​ | ​ | ​ | ​ | ​
Current assets | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents | ​ | $ | 14,756 | ​ | $ | 9,291
Prepaid expenses and other current assets | ​ |  | 1,415 | ​ |  | 1,273
Other receivables | ​ | ​ | 759 | ​ | ​ | 744
Total current assets | ​ |  | 16,930 | ​ |  | 11,308
Restricted cash | ​ | ​ | 5,390 | ​ | ​ | 5,480
Property and equipment, net | ​ |  | 12,560 | ​ |  | 13,241
Operating lease right-of-use asset | ​ |  | 39,917 | ​ |  | 41,687
In-process research and development | ​ | ​ | 10,256 | ​ | ​ | 10,256
Goodwill | ​ | ​ | 3,490 | ​ | ​ | 3,490
Other assets | ​ |  | 973 | ​ |  | 975
Total assets | ​ | $ | 89,516 | ​ | $ | 86,437
​ | ​ | ​ | ​ | ​ | ​ | ​
Liabilities and stockholders’ deficit | ​ |  |  | ​ |  |
Current liabilities | ​ |  |  | ​ |  |
Accounts payable and accrued liabilities | ​ | $ | 1,999 | ​ | $ | 2,055
Accrued compensation | ​ | ​ | 1,843 | ​ | ​ | 2,280
Convertible Loan, current | ​ | ​ | 48,088 | ​ | ​ | —
Term debt, current | ​ | ​ | 82,992 | ​ | ​ | 38,954
Current portion of operating lease liabilities | ​ | ​ | 4,525 | ​ | ​ | 4,431
Other current liabilities | ​ | ​ | 503 | ​ | ​ | 529
Total current liabilities | ​ |  | 139,950 | ​ |  | 48,249
Convertible Loan, non-current | ​ | ​ | — | ​ | ​ | 32,897
Term debt, non-current | ​ | ​ | 15,240 | ​ | ​ | 22,539
Operating lease liabilities, net of current portion | ​ | ​ | 26,837 | ​ | ​ | 27,694
Deferred tax liability | ​ | ​ | 3,077 | ​ | ​ | 3,077
Total liabilities | ​ |  | 185,104 | ​ |  | 134,456
​ | ​ | ​ | ​ | ​ | ​ | ​
Commitments and contingencies (Note 12) | ​ |  |  | ​ |  |
Stockholders’ deficit | ​ |  |  | ​ |  |
Common Stock, $0.01 par value; 217,000,000 shares authorized; 36,229,842 and 36,183,067 shares issued and outstanding at September 30, 2025 and December 31, 2024, respectively | ​ |  | 362 | ​ |  | 362
Additional paid-in capital | ​ |  | 281,286 | ​ |  | 279,354
Accumulated deficit | ​ |  | (377,236) | ​ |  | (327,735)
Total stockholders’ deficit | ​ |  | (95,588) | ​ |  | (48,019)
Total liabilities and stockholders’ deficit | ​ | $ | 89,516 | ​ | $ | 86,437

​

See accompanying notes to condensed consolidated financial statements.

​

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Armata Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations

(unaudited)

(in thousands, except share and per share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended
​ | ​ | September 30, | ​ | September 30,
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024
Grant and award revenue | ​ | $ | 1,159 | ​ | $ | 2,973 | ​ | $ | 3,819 | ​ | $ | 3,939
Operating expenses | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Research and development | ​ |  | 5,824 | ​ | ​ | 9,485 | ​ |  | 17,647 | ​ | ​ | 25,975
General and administrative | ​ |  | 3,111 | ​ | ​ | 3,244 | ​ |  | 8,983 | ​ | ​ | 9,861
Total operating expenses | ​ | ​ | 8,935 | ​ | ​ | 12,729 | ​ | ​ | 26,630 | ​ | ​ | 35,836
Operating loss | ​ |  | (7,776) | ​ |  | (9,756) | ​ |  | (22,811) | ​ |  | (31,897)
Other income (expense) | ​ |  |  | ​ |  | ​ | ​ |  | ​ | ​ |  |
Interest income | ​ |  | 90 | ​ | ​ | 294 | ​ | ​ | 257 | ​ | ​ | 567
Interest expense | ​ | ​ | (4,346) | ​ | ​ | (2,923) | ​ | ​ | (11,756) | ​ | ​ | (7,462)
Change in fair value of the Convertible Loan | ​ | ​ | (14,643) | ​ | ​ | 6,904 | ​ | ​ | (15,191) | ​ | ​ | 17,276
Total other income (expense), net | ​ |  | (18,899) | ​ |  | 4,275 | ​ |  | (26,690) | ​ |  | 10,381
Net loss | ​ | $ | (26,675) | ​ | $ | (5,481) | ​ | $ | (49,501) | ​ | $ | (21,516)
Per share information: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net loss per share, basic and diluted | ​ | $ | (0.74) | ​ | $ | (0.15) | ​ | $ | (1.37) | ​ | $ | (0.60)
Weighted average shares outstanding, basic and diluted | ​ | ​ | 36,226,285 | ​ | ​ | 36,180,124 | ​ | ​ | 36,201,674 | ​ | ​ | 36,153,388

​

See accompanying notes to condensed consolidated financial statements.

​

​

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Armata Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

Three and Nine Months Ended September 30, 2025 and 2024

(unaudited)

(in thousands, except share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Stockholders’ Deficit
​ | ​ | Common Stock | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Additional | ​ | ​ | ​ | Total
​ | ​ | ​ | ​ | ​ | ​ | ​ | Paid-in | ​ | Accumulated | ​ | Stockholders’
​ |  | Shares |  | Amount |  | Capital |  | Deficit |  | Deficit
Balances, June 30, 2024 |  | 36,155,992 | ​ | $ | 362 | ​ | $ | 278,391 | ​ | $ | (324,854) | ​ | $ | (46,101)
Issuance of Common Stock upon release of restricted stock units, net of tax withholdings | ​ | 27,075 | ​ | ​ | — | ​ | ​ | (61) | ​ | ​ | — | ​ | ​ | (61)
Stock-based compensation expense |  | — | ​ | ​ | — | ​ | ​ | 670 | ​ | ​ | — | ​ | ​ | 670
Net loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (5,481) | ​ | ​ | (5,481)
Balances, September 30, 2024 |  | 36,183,067 | ​ | $ | 362 | ​ | $ | 279,000 | ​ | $ | (330,335) | ​ | $ | (50,973)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Stockholders’ Deficit
​ | ​ | Common Stock | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Additional | ​ | ​ | ​ | Total
​ | ​ | ​ | ​ | ​ | ​ | ​ | Paid-in | ​ | Accumulated | ​ | Stockholders’
​ |  | Shares |  | Amount |  | Capital |  | Deficit |  | Deficit
Balances, June 30, 2025 |  | 36,193,479 | ​ | $ | 362 | ​ | $ | 280,696 | ​ | $ | (350,561) | ​ | $ | (69,503)
Issuance of Common Stock upon release of restricted stock units, net of tax withholdings | ​ | 36,363 | ​ | ​ | — | ​ | ​ | (32) | ​ | ​ | — | ​ | ​ | (32)
Stock-based compensation expense |  | — | ​ | ​ | — | ​ | ​ | 622 | ​ | ​ | — | ​ | ​ | 622
Net loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (26,675) | ​ | ​ | (26,675)
Balances, September 30, 2025 |  | 36,229,842 | ​ | $ | 362 | ​ | $ | 281,286 | ​ | $ | (377,236) | ​ | $ | (95,588)

​

​

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​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Stockholders’ Deficit
​ | ​ | Common Stock | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Additional | ​ | ​ | ​ | Total
​ | ​ | ​ | ​ | ​ | ​ | ​ | Paid-in | ​ | Accumulated | ​ | Stockholders’
​ |  | Shares |  | Amount |  | Capital |  | Deficit |  | Deficit
Balances, December 31, 2023 |  | 36,122,932 | ​ | $ | 361 | ​ | $ | 276,393 | ​ | $ | (308,819) | ​ | $ | (32,065)
Exercise of stock options | ​ | 37,282 | ​ | ​ | 1 | ​ | ​ | 129 | ​ | ​ | — | ​ | ​ | 130
Withholdings for taxes related to net share settlement of equity awards | ​ | (4,222) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Issuance of Common Stock upon release of restricted stock units, net of tax withholdings | ​ | 27,075 | ​ | ​ | — | ​ | ​ | (61) | ​ | ​ | — | ​ | ​ | (61)
Stock-based compensation expense |  | — | ​ | ​ | — | ​ | ​ | 2,539 | ​ | ​ | — | ​ |  | 2,539
Net loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (21,516) | ​ |  | (21,516)
Balances, September 30, 2024 |  | 36,183,067 | ​ | $ | 362 | ​ | $ | 279,000 | ​ | $ | (330,335) | ​ | $ | (50,973)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Stockholders’ Deficit
​ | ​ | Common Stock | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Additional | ​ | ​ | ​ | Total
​ | ​ | ​ | ​ | ​ | ​ | ​ | Paid-in | ​ | Accumulated | ​ | Stockholders’
​ | ​ | Shares |  | Amount |  | Capital |  | Deficit |  | Deficit
Balances, December 31, 2024 |  | 36,183,067 | ​ | $ | 362 | ​ | $ | 279,354 | ​ | $ | (327,735) | ​ | $ | (48,019)
Issuance of Common Stock upon release of restricted stock units, net of tax withholdings | ​ | 46,775 | ​ | ​ | — | ​ | ​ | (46) | ​ | ​ | ​ | ​ | ​ | (46)
Stock-based compensation expense | ​ | — | ​ | ​ | — | ​ | ​ | 1,978 | ​ | ​ | — | ​ | ​ | 1,978
Net loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (49,501) | ​ | ​ | (49,501)
Balances, September 30, 2025 |  | 36,229,842 | ​ | $ | 362 | ​ | $ | 281,286 | ​ | $ | (377,236) | ​ | $ | (95,588)

​

See accompanying notes to condensed consolidated financial statements.

​

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Armata Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flows

(unaudited)

(in thousands)

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ |  | 2025 |  | 2024
Operating activities: | ​ | ​ | ​ | ​ | ​ | ​
Net loss | ​ | $ | (49,501) | ​ | $ | (21,516)
Adjustments required to reconcile net loss to net cash used in operating activities: | ​ | ​ | ​ | ​ | ​ | ​
Depreciation expense | ​ |  | 1,113 | ​ |  | 945
Stock-based compensation expense | ​ | ​ | 1,978 | ​ | ​ | 2,539
Change in fair value of the Convertible Loan | ​ | ​ | 15,191 | ​ | ​ | (17,276)
Non-cash interest expense | ​ | ​ | 11,739 | ​ | ​ | 7,483
Change in right-of-use asset | ​ | ​ | 1,770 | ​ | ​ | 1,489
Changes in operating assets and liabilities: | ​ |  | ​ | ​ |  | ​
Prepaid expenses and other assets | ​ |  | (155) | ​ |  | 2,095
Accounts payable and accrued liabilities | ​ |  | (24) | ​ |  | (2,031)
Accrued compensation | ​ | ​ | (437) | ​ | ​ | 812
Operating lease liability | ​ | ​ | (763) | ​ | ​ | (4,164)
Net cash used in operating activities | ​ |  | (19,089) | ​ |  | (29,624)
Investing activities: | ​ |  |  | ​ |  |
Purchases of property and equipment | ​ | ​ | (490) | ​ | ​ | (1,956)
Net cash used in investing activities | ​ |  | (490) | ​ |  | (1,956)
Financing activities: | ​ |  |  | ​ |  |
Proceeds from issuance of term debt, net of issuance costs | ​ | ​ | 25,000 | ​ | ​ | 34,889
Payments for taxes related to net share settlement of equity awards | ​ | ​ | (46) | ​ | ​ | (61)
Proceeds from exercise of stock options | ​ | ​ | — | ​ | ​ | 130
Net cash provided by financing activities | ​ |  | 24,954 | ​ |  | 34,958
Net increase in cash, cash equivalents and restricted cash | ​ |  | 5,375 | ​ |  | 3,378
Cash, cash equivalents and restricted cash, beginning of period | ​ |  | 14,771 | ​ |  | 19,243
Cash, cash equivalents and restricted cash, end of period | ​ | $ | 20,146 | ​ | $ | 22,621
Supplemental disclosure of cash flow information: | ​ |  |  | ​ |  |
Right-of-use asset obtained by assuming operating lease liabilities | ​ | $ | — | ​ | $ | 977
Property and equipment included in accounts payable and accrued liabilities | ​ | ​ | 31 | ​ | ​ | 263

​

Reconciliation of cash, cash equivalents and restricted cash to the consolidated balance sheets:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | 2025 |  | 2024
Cash and cash equivalents | ​ | $ | 14,756 | ​ | $ | 17,141
Restricted cash | ​ | ​ | 5,390 | ​ | ​ | 5,480
Cash, cash equivalents and restricted cash | ​ | $ | 20,146 | ​ | $ | 22,621

​

See accompanying notes to condensed consolidated financial statements.

​

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Armata Pharmaceuticals, Inc.

Notes to Condensed Consolidated Financial Statements

(Unaudited)

1. Organization and Description of the Business

Armata Pharmaceuticals, Inc. (“Armata”) together with its subsidiaries (the “Company”), is a clinical-stage biotechnology company focused on the development of pathogen-specific bacteriophage therapeutics for the treatment of antibiotic-resistant and difficult-to-treat bacterial infections using its proprietary bacteriophage-based technology.

Armata’s common stock, par value $0.01 per share (the “Common Stock”) is traded on the New York Stock Exchange (the “NYSE”) American exchange under the ticker symbol “ARMP.”

2. Liquidity and Going Concern

The Company has incurred significant operating losses since inception and has primarily relied on equity, debt, grant, and award financing to fund its operations. As of September 30, 2025, the Company had an accumulated deficit of $377.2 million. The Company expects to continue to incur substantial losses, and its transition to profitability will depend on the successful development, approval and commercialization of product candidates and on the achievement of sufficient revenues to support its cost structure. The Company may never achieve profitability, and unless and until then, the Company will need to continue to raise additional capital. The existing cash and cash equivalents of $14.8 million as of September 30, 2025 will not be sufficient to fund its operations for the next 12 months from the date of these condensed consolidated financial statements. These circumstances raise substantial doubt about the Company’s ability to continue as a going concern.

The Company has prepared its condensed consolidated financial statements on a going concern basis, which assumes that the Company will realize its assets and satisfy its liabilities in the normal course of business. The accompanying condensed consolidated financial statements do not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classifications of liabilities that may result from the outcome of the uncertainty concerning the Company’s ability to continue as a going concern.

Recent Financing:

August 2025 Credit Agreement

On August 11, 2025, the Company entered into a credit and security agreement (the “August 2025 Credit Agreement”) for a loan in the aggregate amount of $15.0 million (the “August 2025 Loan”) with Innoviva Strategic Opportunities LLC, a wholly owned subsidiary of Innoviva, Inc. (NASDAQ: INVA), the Company’s principal stockholder and a related party (collectively, “Innoviva”). The August 2025 Loan bears interest at an annual rate of 14.0% and matures on January 11, 2029. Principal and accrued interest are payable at maturity. Repayment of the August 2025 Loan is guaranteed by the Company’s domestic subsidiaries, and the loan is secured by substantially all of the assets of the Company and the subsidiary guarantors.

March 2025 Credit Agreement

On March 12, 2025, the Company entered into a credit and security agreement (the “March 2025 Credit Agreement”) for a loan in an aggregate amount of $10.0 million (the “March 2025 Loan”) with Innoviva. The March 2025 Loan bears interest at an annual rate of 14.0% and matures on March 12, 2026. Principal and accrued interest are payable at maturity. Repayment of the March 2025 Loan is guaranteed by the Company’s domestic subsidiaries, and the loan is secured by substantially all of the assets of the Company and the subsidiary guarantors.

​

Concurrently with the execution of the March 2025 Credit Agreement, the Company entered into amendments to (i) its existing convertible loan (the “Convertible Loan”) and secured credit and security agreement, dated January 10, 2023, with Innoviva (the “Convertible Credit Agreement”), (ii) its existing secured term loan facility (the “2023 Loan”) and

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credit and security agreement, dated July 10, 2023, with Innoviva (the “2023 Credit Agreement”) and (iii) its existing secured term loan facility (the “2024 Loan”) and credit and security agreement, dated March 4, 2024, with Innoviva (the “2024 Credit Agreement”), which, among other things, extended the maturity date of each loan to March 12, 2026.

​

2024 Credit Agreement

On March 4, 2024, the Company entered into the 2024 Credit Agreement for the 2024 Loan in an aggregate amount of $35.0 million. The 2024 Loan bears interest at an annual rate of 14.0% and matures on March 12, 2026. Principal and accrued interest are payable at maturity. Repayment of the 2024 Loan is guaranteed by the Company’s domestic subsidiaries, and the loan is secured by substantially all of the assets of the Company and the subsidiary guarantors. Concurrently with the execution of the 2024 Credit Agreement, the Company amended certain provisions of the Convertible Loan and Convertible Credit Agreement and the 2023 Loan and 2023 Credit Agreement to, among other things, conform certain terms relating to permitted indebtedness and permitted liens.

​

The Company plans to raise additional capital through equity offerings, debt financings, or other capital sources, including potential collaborations, licenses and other similar arrangements. While the Company believes this plan to raise additional funds will alleviate the conditions that raise substantial doubt about the Company’s ability to continue as a going concern, these plans are not entirely within its control and cannot be assessed as being probable of occurring. The Company’s ability to raise additional capital may be adversely impacted by potential worsening global economic conditions and the recent disruptions to, and volatility in, financial markets in the United States and worldwide. The Company may not be able to secure additional financing in a timely manner or on favorable terms, if at all. Furthermore, if the Company issues equity securities to raise additional funds, its existing stockholders may experience dilution, and the new equity securities may have rights, preferences and privileges senior to those of the Company’s existing stockholders. If the Company raises additional funds through collaboration, licensing or other similar arrangements, it may be necessary to relinquish valuable rights to its potential products on terms that are not favorable to the Company. If the Company is unable to raise capital when needed or on attractive terms, it would be forced to delay, reduce or eliminate its research and development programs or other operations. If any of these events occur, the Company’s ability to achieve the development and commercialization goals would be adversely affected.

3. Significant Accounting Policies

Basis of Presentation

The condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany accounts and transactions have been eliminated.

The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited financial statements and accompanying notes thereto as of and for the year ended December 31, 2024 included in the Company’s Form 10-K, filed with the U.S. Securities and Exchange Commission (the “SEC”) on March 21, 2025. The information as of December 31, 2024 included in the condensed consolidated balance sheets was derived from the Company’s audited financial statements. The accompanying unaudited condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and the requirements of the SEC for interim reporting. In the opinion of management, the accompanying condensed consolidated financial statements include all adjustments that are of a normal and recurring nature and that are necessary for the fair presentation of the Company’s financial position and the results of its operations and cash flows for the periods presented. Interim results are not necessarily indicative of results for the full year or any future period.

Any reference in the condensed consolidated financial statements to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”).

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Significant Accounting Policies

The significant accounting policies used in preparation of the condensed consolidated financial statements for the three and nine months ended September 30, 2025 and 2024 are consistent with those discussed in Note 3 to the consolidated financial statements included in the Company’s Form 10-K for the year ended December 31, 2024, filed with the SEC on March 21, 2025.

Use of Estimates

The preparation of condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the reported amounts of expenses during the reporting period. On an ongoing basis, the Company evaluates estimates and assumptions, including but not limited to those related to the fair value of the Convertible Loan, stock-based compensation expense, accruals for research and development costs, the valuation of deferred tax assets, impairment of goodwill and intangible assets and impairment of long-lived assets. Management bases its estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from those estimates.

Concentration of Credit Risks and Certain Other Risks

Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents and restricted cash. As of September 30, 2025, cash equivalents and restricted cash were invested primarily in money market funds through highly rated financial institutions in accordance with the Company’s investment policy, to a concentration limit per issuer or sector.

Other receivables represent amounts due from the Medical Technology Enterprise Consortium (“MTEC”) (Note 13, “Grants and Awards”).

Recent Accounting Pronouncements Not Yet Adopted

In November 2024, the FASB issued Accounting Standards Update 2024-03 Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses. The guidance in ASU 2024-03 requires public business entities to disclose in the notes to the financial statements, among other things, specific information about certain costs and expenses including purchases of inventory; employee compensation; and depreciation, amortization and depletion expenses for each caption on the income statement where such expenses are included. ASU 2024-03 is effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027. Early adoption is permitted, and the amendments may be applied prospectively to reporting periods after the effective date or retrospectively to all periods presented in the financial statements. The Company is currently evaluating the provisions of this guidance and assessing the potential impact on the Company’s consolidated financial statement disclosures.

​

4. Fair Value Measurements

The Company utilizes valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible. The Company determines fair value based on assumptions that market participants would use in pricing an asset or liability in the principal or most advantageous market. When considering

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market participant assumptions in fair value measurements, the following fair value hierarchy distinguishes between observable and unobservable inputs, which are categorized in one of the following three levels:

●Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical assets or liabilities at the measurement date.
●Level 2: Inputs (other than quoted prices included in Level 1) that are either directly or indirectly observable for the asset or liability. These include quoted prices for similar assets or liabilities in active markets and quoted prices for identical or similar assets or liabilities in markets that are not active.
●Level 3: Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The financial assets and liabilities measured and recognized at fair value were as follows as of September 30, 2025 and December 31, 2024 (in thousands):

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | September 30, 2025
​ | ​ | Total | ​ | ​ | Level 1 | ​ | ​ | Level 2 | ​ | ​ | Level 3
Investments in money market fund – financial assets, included in cash and cash equivalents | $ | 12,119 | ​ | $ | 12,119 | ​ | $ | — | ​ | $ | —
Convertible Loan– financial liabilities | ​ | 48,088 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 48,088

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | December 31, 2024
​ | ​ | Total | ​ | ​ | Level 1 | ​ | ​ | Level 2 | ​ | ​ | Level 3
Investments in money market fund – financial assets, included in cash and cash equivalents | $ | 4,955 | ​ | $ | 4,955 | ​ | $ | — | ​ | $ | —
Convertible Loan– financial liabilities | ​ | 32,897 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 32,897

​

The Company’s Convertible Loan (Note 7, “Convertible Loan”) is measured at fair value at inception and remeasured at each measurement period, with changes in fair value recorded as other income (expense) in the condensed consolidated statement of operations. The Company estimates the fair value of its Convertible Loan using a weighted probability model of various debt settlement scenarios during its term discounted to the reporting date. Conversion option scenarios are valued using option pricing models with assumptions and estimates such as volatility, expected term and risk-free interest rates. Level 3 fair value inputs include probability and timing of various settlement scenarios and selection of comparable companies.

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The Company estimated the fair value of its Convertible Loan using the following inputs as of September 30, 2025 and December 31, 2024:

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025 | ​ | ​ | December 31, 2024
Discount rate | ​ | 18.59% | ​ | ​ | 15.67%-28.28%
Probabilities of settlement scenarios | ​ | 0%-65% | ​ | ​ | 0%-75%
Volatility | ​ | 93.50% | ​ | ​ | 83.30%-111.60%
Expected term (in years) | ​ | 0.30-0.50 | ​ | ​ | 0.10-1.20
Risk-free rate | ​ | 3.79%-3.94% | ​ | ​ | 4.08%-5.33%

​

The following table presents a summary of the changes in the fair value of its Convertible Loan for the nine months ended September 30, 2025 and 2024 (in thousands):

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | ​ | 2024
Convertible Loan at the beginning of the period | $ | 32,897 | ​ | $ | 58,633
Change in fair value | ​ | 15,191 | ​ |  | (17,276)
Convertible Loan at the end of the period | $ | 48,088 | ​ | $ | 41,357

​

​

​

5. Net Loss per Share

The computation of basic EPS is based on the weighted-average number of the Company’s Common Stock outstanding. The computation of diluted EPS is based on the weighted-average number of the Company’s Common Stock outstanding and potential dilutive common stock. Diluted EPS is computed using the treasury stock method, which reflects the potential dilution that would occur if securities or other contracts to issue Common Stock were exercised or converted to the Company’s Common Stock. The Company’s Common Stock options, warrants, and unvested restricted stock units were not included in dilutive EPS for the periods presented as their impact would be antidilutive.

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024 | ​
Numerator: |  | ​ |  |  | ​ |  |  | ​ |  |  | ​ |  |
Net loss attributable to common stockholders, basic and diluted | ​ | $ | (26,675) | ​ | $ | (5,481) | ​ | $ | (49,501) | ​ | $ | (21,516) | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Denominator: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Weighted average common shares outstanding, basic and diluted | ​ |  | 36,226,285 | ​ |  | 36,180,124 | ​ |  | 36,201,674 | ​ |  | 36,153,388 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net loss per share, basic and diluted | ​ | $ | (0.74) | ​ | $ | (0.15) | ​ | $ | (1.37) | ​ | $ | (0.60) | ​

​

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The following outstanding securities as of September 30, 2025 and December 31, 2024 have been excluded from the computation of dilutive weighted-average shares outstanding, as they would have been anti-dilutive:

​

​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, 2025 |  | December 31, 2024 |
Outstanding stock options |  | 5,012,648 |  | 3,755,965 | ​
Unvested restricted stock units | ​ | 152,500 | ​ | 220,000 | ​
Shares issuable upon the conversion of the Convertible Loan (1) | ​ | 24,096,491 | ​ | — | ​
Outstanding warrants | ​ | 10,655,047 | ​ | 19,365,847 | ​
Total |  | 39,916,686 |  | 23,341,812 |

​

(1) The Company determined the number of shares issuable upon the conversion of the Convertible Loan as of September 30, 2025, based on the Convertible Loan principal amount of $30.0 million, accrued and unpaid interest of $6.6 million, calculated at an annual interest rate of 8%, converted at $1.52 per share.

​

6. Balance Sheet Details

Property and Equipment, net

Property and equipment as of September 30, 2025 and December 31, 2024 consisted of the following (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, 2025 |  | December 31, 2024
Laboratory equipment | ​ | $ | 21,728 | ​ | $ | 21,316
Furniture and fixtures | ​ | ​ | 851 | ​ | ​ | 831
Office and computer equipment | ​ |  | 438 | ​ |  | 438
Leasehold improvements | ​ |  | 3,802 | ​ |  | 3,802
Total | ​ | ​ | 26,819 | ​ | ​ | 26,387
Less: accumulated depreciation | ​ |  | (14,259) | ​ |  | (13,146)
Property and equipment, net | ​ | $ | 12,560 | ​ | $ | 13,241

​

Depreciation expense totaled $0.4 million and $0.3 million for the three months ended September 30, 2025 and 2024, respectively, and $1.1 million and $0.9 million for the nine months ended September 30, 2025 and 2024, respectively. Property and equipment not yet in use was $8.2 million and $8.3 million as of September 30, 2025 and December 31, 2024, respectively, and is included in the laboratory equipment in the table above. These assets are not depreciated until they are placed in service.

Accounts payable and accrued liabilities

Accounts payable and accrued liabilities as of September 30, 2025 and December 31, 2024 consisted of the following (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025 |  | December 31, 2024
Accounts payable | ​ | $ | 1,280 | ​ | $ | 766
Accrued clinical trial expenses | ​ | ​ | 137 | ​ | ​ | 828
Other accrued expenses | ​ | ​ | 582 | ​ | ​ | 461
​ | ​ | $ | 1,999 | ​ | $ | 2,055

​

​

7. Convertible Loan

On January 10, 2023, the Company received the Convertible Loan in the aggregate amount of $30.0 million from Innoviva pursuant to the Convertible Credit Agreement. The Convertible Loan bears interest at a rate of 8.0% per annum and was scheduled to mature on January 10, 2024. The Convertible Credit Agreement was amended on July 10, 2023, in connection with the Company’s entry into the 2023 Credit Agreement to, among other changes, extend the maturity of the Convertible Loan to January 10, 2025. Subsequently, on November 12, 2024, the Company executed another

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amendment to the Convertible Credit Agreement, which, among other things, extended the Convertible Credit Agreement maturity date to January 10, 2026. Then, on March 12, 2025, the Company executed a subsequent amendment to the Convertible Credit Agreement which, among other things, extended the Convertible Loan maturity date to March 12, 2026.

The Convertible Loan principal and accrued interest are payable at maturity. Repayment of the Convertible Loan is guaranteed by the Company’s domestic subsidiaries and foreign material subsidiaries, and the Convertible Loan is secured by substantially all of the assets of the Company and the subsidiary guarantors.

The Convertible Credit Agreement provides that if there is a financing from new investors of at least $30.0 million (a “Qualified Financing”), the outstanding principal amount of and all accrued and unpaid interest on the Convertible Loan shall be converted into shares of the Company’s Common Stock, at a price per share equal to a 15.0% discount to the lowest price per share for Common Stock paid by investors in such Qualified Financing. The Convertible Credit Agreement also required the Company to file a registration statement for the resale of all securities issued to the lender in connection with any conversion under the Convertible Credit Agreement, which the Company originally filed on February 13, 2023 and which was declared effective by the SEC on April 6, 2023. The Convertible Credit Agreement also confers upon the lender the option to convert any outstanding Convertible Loan amount, including all accrued and unpaid interest thereon, at the lender’s option, into shares of Common Stock at a price per share equal to the greater of book value or market value per share of Common Stock on the date immediately preceding the effective date of the Convertible Credit Agreement, which was $1.52 (as may be appropriately adjusted for any stock split, combination or similar act).

The Company evaluated authoritative guidance for accounting for the Convertible Loan and concluded that the Convertible Loan should be accounted for at fair value under ASC 480, Distinguishing Liabilities from Equity, due to the fact that the Convertible Loan will predominately be settled with the Company’s Common Stock. Consequently, the Company recorded the Convertible Loan in its entirety at fair value on its consolidated balance sheet, with changes in fair value recorded as other income (expenses) in the consolidated statements of operations during each reporting period.

On November 12, 2024, the Company amended the terms of the Convertible Credit Agreement and 2023 Credit Agreement, to, among other changes, extend the maturity of both loans to January 10, 2026. The Company concluded that the amendments were a combined transaction and an extinguishment for accounting purposes. The Company estimated fair value of the combined transaction, the 2023 Loan and the Convertible Loan, before and after modification and calculated an extinguishment gain of $2.2 million, which was recognized as other income (expense) in the consolidated statement of operations for the year ended December 31, 2024. After this amendment, the Company continued to account for the Convertible Loan at fair value on its consolidated balance sheet, with changes in fair value recorded as other income (expense) in the consolidated statements of operations during each reporting period. The Company recognized $31.4 million as the change in fair value of the Convertible Loan for the year ended December 31, 2024.

On March 12, 2025, the Company amended the terms of the Convertible Credit Agreement, the 2023 Credit Agreement and the 2024 Credit Agreement, to, among other changes, extend the maturity of the loans to March 12, 2026. The Company concluded that the amendments were a combined transaction and a modification for accounting purposes. After this amendment, the Company continued to account for the Convertible Loan at fair value on its consolidated balance sheet, with changes in fair value recorded as other income (expense) in the consolidated statements of operations during each reporting period.

The Company recognized a loss of $14.6 million and a gain of $6.9 million as the change in fair value of the Convertible Loan for the three months ended September 30, 2025 and 2024, and a loss of $15.2 million and a gain of $17.3 million for the nine months ended September 30, 2025 and 2024, respectively.

8. Term Debt

The 2023 Credit Agreement, 2024 Credit Agreement, March 2025 Credit Agreement, and August 2025 Credit Agreement each contains customary affirmative and negative covenants and representations and warranties, including

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financial reporting obligations and certain limitations on indebtedness, liens, investments, distributions (including dividends), collateral, investments, mergers or acquisitions and fundamental corporate changes. Each of the 2023 Credit Agreement, the 2024 Credit Agreement, March 2025 Credit Agreement, and August 2025 Credit Agreement also includes customary events of default, including payment defaults, breaches of provisions under the loan documents, certain losses or impairment of collateral and related security interests, the occurrence of certain events that could reasonably be expected to have a “material adverse effect” as set forth therein, certain bankruptcy or insolvency events, and a material deviation from the Company’s operating budget. In addition, each of the credit agreements include customary mandatory prepayment provisions that require the Company to apply specified proceeds received by the Company to prepay outstanding borrowings under the respective credit facilities. Mandatory prepayment events are triggered upon the receipt of proceeds from asset sales or other dispositions, casualty or condemnation events, the incurrence of indebtedness not otherwise permitted under the agreements, or the issuance of certain equity interests.

On July 10, 2023, the Company entered into the 2023 Credit Agreement. The 2023 Credit Agreement provides for the 2023 Loan, a secured term loan facility in an aggregate amount of $25.0 million at an interest rate of 14.0% per annum, and was scheduled to mature on January 10, 2025. Principal and accrued interest are payable at maturity. Repayment of the 2023 Loan is guaranteed by the Company’s domestic subsidiaries, and the 2023 Loan is secured by substantially all of the assets of the Company and the subsidiary guarantors.

On March 4, 2024, the Company entered into the 2024 Credit Agreement for the 2024 Loan in an aggregate amount of $35.0 million. The 2024 Loan bears interest at an annual rate of 14.0% and was scheduled to mature on June 4, 2025. On March 12, 2025, the Company executed an amendment to the 2024 Credit Agreement which, among other things, extended the 2024 Loan maturity date to March 12, 2026. Principal and accrued interest are payable at maturity.

Repayment of the 2024 Loan is guaranteed by the Company’s domestic subsidiaries, and the 2024 Loan is secured by substantially all of the assets of the Company and the subsidiary guarantors. The 2024 Loan was initially recognized at cash proceeds of $35.0 million net of debt issuance costs of $0.1 million, and subsequently is recognized at the amortized cost. Debt issuance costs are amortized using the effective interest method to interest expense over the term of the 2024 Loan. The 2024 Loan’s annual effective interest rate was 12.68% and 14.25% as of September 30, 2025 and 2024, respectively.

On November 12, 2024, the Company executed an amendment to the 2023 Credit Agreement, which, among other things, extended the 2023 Loan maturity date to January 10, 2026. On March 12, 2025, the Company executed a subsequent amendment to the 2023 Credit Agreement which, among other things, extended the 2023 Loan maturity date to March 12, 2026. The 2023 Loan was initially recognized at fair value of $21.2 million and subsequently recognized at the amortized cost net of debt issuance costs and debt discount of $3.8 million. Debt issuance costs are amortized using the effective interest method to interest expense over the term of the 2023 Loan. The 2023 Loan’s annual effective interest rate was 41.64% and 27.31% as of September 30, 2025 and 2024, respectively.

On March 12, 2025, the Company entered into the March 2025 Credit Agreement for the March 2025 Loan in an aggregate amount of $10.0 million. The March 2025 Loan bears interest at an annual rate of 14.0% and matures on March 12, 2026. Principal and accrued interest are payable at maturity. Repayment of the March 2025 Loan is guaranteed by the Company’s domestic subsidiaries, and the loan is secured by substantially all of the assets of the Company and the subsidiary guarantors. The March 2025 Loan was initially recognized at cash proceeds of $10.0 million and subsequently is recognized at the amortized cost. The March 2025 Loan’s annual effective interest rate was 14.19% as of September 30, 2025.

On March 12, 2025, concurrently with the execution of the March 2025 Credit Agreement, the Company entered into amendments to (i) the Convertible Loan and Convertible Credit Agreement, (ii) the 2023 Loan and 2023 Credit Agreement, and (iii) the 2024 Loan and 2024 Credit Agreement, which, among other things, extended the maturity date of the Convertible Loan, 2023 Loan and 2024 Loan, respectively, to March 12, 2026.

On August 11, 2025, the Company entered into the August 2025 Credit Agreement for the August 2025 Loan in an aggregate amount of $15.0 million. The August 2025 Loan bears interest at an annual rate of 14.0% and matures on January 11, 2029. Principal and accrued interest are payable at maturity. Repayment of the August 2025 Loan is

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guaranteed by the Company’s domestic subsidiaries, and the loan is secured by substantially all of the assets of the Company and the subsidiary guarantors. The August 2025 Loan was initially recognized at cash proceeds of $15.0 million and subsequently is recognized at the amortized cost. The August 2025 Loan’s annual effective interest rate was 12.27% as of September 30, 2025.

9. Stockholders’ Deficit

Warrants

As of September 30, 2025, outstanding warrants to purchase shares of the Company’s Common Stock were as follows:

​

​ | ​ | ​ | ​ | ​ | ​
Shares |  | Exercise Price |  | Expiration Date
1,867,912 | ​ | $ | 3.25 | ​ | January 26, 2026
4,285,935 | ​ | $ | 3.25 | ​ | March 16, 2026
1,807,396 | ​ | $ | 5.00 | ​ | February 8, 2027
2,692,604 | ​ | $ | 5.00 | ​ | March 30, 2027
1,200 | ​ | $ | 1,680.00 | ​ | None
10,655,047 | ​ |  |  | ​ |

​

Shares Reserved for Future Issuance

As of September 30, 2025, the Company had reserved shares of its Common Stock for future issuance as follows:

​

​ | ​ | ​
​ |  | September 30, 2025
Stock options outstanding | ​ | 5,012,648
Unvested restricted stock units | ​ | 152,500
Shares issuable under the Employee Stock Purchase Plan | ​ | 11,890
Shares available for future grants under the 2016 Plan | ​ | 2,169,950
Shares issuable upon the conversion of the Convertible Loan | ​ | 24,096,491
Warrants outstanding | ​ | 10,655,047
Total shares reserved | ​ | 42,098,526

​

​

10. Equity Incentive Plans

Stock Award Plans

The Company maintains a 2016 Equity Incentive Plan (the “2016 Plan”), which provides for the issuance of incentive share awards in the form of non-qualified and incentive stock options, stock appreciation rights, restricted stock awards, restricted stock unit awards and performance-based stock awards. As of September 30, 2025, there were 2,169,950 shares available for issuance under the 2016 Plan.

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Stock option transactions during the nine months ended September 30, 2025 are presented below:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Weighted | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | Average | ​ | ​ | ​
​ | ​ | ​ | ​ | Weighted | ​ | Remaining | ​ | ​ | ​
​ | ​ | ​ | ​ | Average | ​ | Contractual | ​ | Aggregate
​ | ​ | ​ | ​ | Exercise | ​ | Term | ​ | Intrinsic
​ |  | Shares |  | Price |  | (Years) |  | Value (in thousands)
Outstanding at December 31, 2024 |  | 3,755,965 | ​ | $ | 3.74 |  | 7.5 | ​ | $ | 4
Granted |  | 1,596,058 | ​ | $ | 2.04 |  | ​ |  | $ | —
Exercised | ​ | — | ​ | $ | — | ​ | ​ | ​ | $ | —
Forfeited/Cancelled/Expired |  | (339,375) | ​ | $ | 3.37 |  | ​ |  | $ | 9
Outstanding at September 30, 2025 |  | 5,012,648 | ​ | $ | 3.23 |  | 7.5 | ​ | $ | 1,617
Vested and expected to vest at September 30, 2025 |  | 5,012,648 | ​ | $ | 3.23 |  | 7.5 | ​ | $ | 1,617
Exercisable at September 30, 2025 |  | 2,496,564 | ​ | $ | 3.89 |  | 6.1 | ​ | $ | 122

​

The aggregate intrinsic value of options at September 30, 2025 is based on the Company’s closing stock price on that date of $2.98 per share.

Restricted stock unit awards transactions during the nine months ended September 30, 2025 are presented below:

​

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | Weighted Avg
​ | ​ | ​ | ​ | Grant Date
​ |  | Shares |  | Fair Value
Outstanding at December 31, 2024 | ​ | 220,000 | ​ | $ | 2.73
Granted | ​ | — | ​ | $ | —
Vested | ​ | (67,500) | ​ | $ | 2.65
Cancelled | ​ | — | ​ | $ | —
Outstanding at September 30, 2025 | ​ | 152,500 | ​ | $ | 2.73

​

Share-based Compensation

The Company estimates the fair value of stock options with performance and service conditions using the Black-Scholes valuation model (“Black-Scholes”). Compensation expense related to stock options granted is measured at the grant date based on the estimated fair value of the award and is recognized on the accelerated attribution method over the requisite service period.

The assumptions used in the Black-Scholes model during the nine months ended September 30, 2025 and 2024 are presented below. There were no stock options granted during the three months ended September 30, 2025 and 2024.

​

​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ |  | 2025 |  | 2024
Risk-free interest rate | ​ | 4.22%-4.28% | ​ | 4.24%-4.25%
Expected volatility | ​ | 99.6%-101.4% | ​ | 89.4%-92.5%
Expected term (in years) | ​ | 5.5-7.0 | ​ | 5.1-7.0
Expected dividend yield | ​ | 0% | ​ | 0%

​

The table below summarizes the total share-based compensation expense included in the Company’s condensed consolidated statements of operations for the periods presented (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30,
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024
Research and development | ​ | $ | 246 | ​ | $ | 323 | ​ | $ | 733 | ​ | $ | 698
General and administrative | ​ |  | 376 | ​ |  | 347 | ​ |  | 1,245 | ​ |  | 1,841
Total stock-based compensation | ​ | $ | 622 | ​ | $ | 670 | ​ | $ | 1,978 | ​ | $ | 2,539

​

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As of September 30, 2025, there was $2.7 million of total unrecognized compensation expense related to unvested stock options and restricted stock units, which the Company expects to recognize over the weighted average remaining period of approximately 1.8 years.

11. Income Taxes

The Company did no t record a provision or benefit for income taxes during the three and nine months ended September 30, 2025 and 2024. The Company expects to generate net taxable losses and continues to maintain a full valuation allowance against all of its deferred tax assets.

On July 4, 2025, the One Big Beautiful Bill Act (the “OBBBA”) was enacted in the United States. The OBBBA includes significant provisions, such as the permanent extension of certain expiring provisions of the Tax Cuts and Jobs Act, modifications to the international tax framework and the restoration of favorable tax treatment for certain business provisions. The legislation has multiple effective dates, with certain provisions effective in 2025 and others implemented through 2027. While the Company continues to assess the potential impact of the OBBBA, due to its full valuation allowance, it expects that the legislation will likely not have a material impact on its consolidated financial statements.

12. Commitments and Contingencies

Operating Leases

The Company leases office and research and development space under a non-cancelable operating lease in Marina del Rey, California, with the lease term running through December 31, 2031. Annual base rent is from $1.9 million and increases by 3% annually and will be $2.5 million by the end of the lease term. The Company also maintains an irrevocable letter of credit in connection with this lease, which had a balance of $0.2 million as of September 30, 2025 and which is reduced 20% annually through the end of the lease term.

​

On October 28, 2021, the Company entered into a lease for office and research and development space under a non-cancellable lease in Los Angeles, California (the “2021 Lease”). The 2021 Lease payment start date was May 1, 2022 and the total lease term is for 16 years and runs through 2038. Monthly rent for 2022 and 2023 was fully or partially abated while the lessor and the Company completed planned tenant improvements to the facility. The Company was responsible for construction costs over the tenant improvement allowance of $7.2 million. The construction was completed as of December 31, 2024, and the Company received the full allowance. Out-of-pocket expenses to be incurred by the Company are considered noncash lease payments, and included in the lease liability and right-of-use asset.

In connection with the execution of the 2021 Lease, the Company delivered an irrevocable standby letter of credit in the amount of $5.0 million to the landlord in 2022.

Future minimum annual lease payments under the Company’s non-cancelable operating leases as of September 30, 2025 are as follows (in thousands):

​

​ | ​ | ​ | ​
​ |  | Operating
​ | ​ | Leases
2025 (remaining three months) | ​ | $ | 862
2026 | ​ | ​ | 5,293
2027 | ​ | ​ | 5,452
2028 | ​ | ​ | 5,616
2029 | ​ | ​ | 5,784
Thereafter | ​ | ​ | 37,995
Total minimum lease payments | ​ | ​ | 61,002
Less: amount representing interest | ​ | ​ | (29,640)
Present value of operating lease obligations | ​ | ​ | 31,362
Less: current portion | ​ | ​ | (4,525)
Noncurrent operating lease obligations | ​ | $ | 26,837

​

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Operating lease expenses were $2.0 million for each of the three months ended September 30, 2025 and 2024, and $6.0 million and $6.3 million for the nine months ended September 30, 2025 and 2024, respectively. Variable costs related to operating expenses and taxes, which are recognized as incurred, were $0.4 million for each of the three months ended September 30, 2025 and 2024, and $1.2 million and $1.4 million for the nine months ended September 30, 2025 and 2024, respectively.

The following table summarizes supplemental cash flow information related to the Company’s operating leases for the nine months ended September 30, 2025 and 2024 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | ​ | 2025 |  | 2024
Cash paid for amounts included in the measurement of lease liabilities: | ​ | ​ | ​ | ​ | ​ | ​
Operating cash flows from operating leases | ​ | $ | 3,855 | ​ | $ | 2,006

​

The following table summarizes the weighted-average remaining lease term and weighted-average discount rate related to the Company’s operating leases as of September 30, 2025 and December 31, 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | September 30, 2025 | ​ | ​ | December 31, 2024
Weighted-average remaining lease term, years | ​ | ​ | 11.05 | ​ | ​ | 11.74
Weighted-average discount rate, % | ​ | ​ | 14.0 | ​ | ​ | 13.9

​

Legal Proceedings

From time to time, the Company may be involved in disputes, including litigation, relating to claims arising out of operations in the normal course of business. Any of these claims could subject the Company to costly legal expenses and, while management generally believes that there is adequate insurance to cover many different types of liabilities, the Company’s insurance carriers may deny coverage or policy limits may be inadequate to fully satisfy any damage awards or settlements. If this were to happen, the payment of any such awards could have a material adverse effect on the Company’s consolidated results of operations and financial position. Additionally, any such claims, whether or not successful, could damage the Company’s reputation and business. The Company is currently not a party to any legal proceedings, the adverse outcome of which, in management’s opinion, individually or in the aggregate, would have a material adverse effect on our consolidated results of operations or financial position.

13. Grants and Awards

MTEC Award

On June 15, 2020, the Company entered into an agreement (the “MTEC Agreement”) with MTEC, pursuant to which the Company received a $15.0 million award and entered into a multi-year program administered by the DoD through MTEC and managed by the Naval Medical Research Command (“NMRC”) – Naval Advanced Medical Development (“NAMD”) with funding from the Defense Health Agency and Joint Warfighter Medical Research Program. On September 29, 2022, the MTEC Agreement was modified to increase the total award by $1.3 million to $16.3 million and extend the term into the third quarter of 2024. On July 29, 2024, the MTEC Agreement was modified to increase the total award by $5.3 million to $21.6 million and extend the term into the third quarter of 2025. On April 29, 2025, the Company received $4.65 million of additional non-dilutive award funding through MTEC, thereby increasing the total MTEC award to $26.2 million, and the MTEC Agreement was modified to extend the term to September 30, 2025. On July 2, 2025, the MTEC Agreement was modified to extend the term to March 31, 2026. This award has been used to partially fund the Phase 1b/2a, randomized, double-blind, placebo-controlled, dose escalation clinical study to assess the safety, tolerability and efficacy of the Company’s therapeutic phage-based candidate, AP-SA02, for the treatment of complicated S. aureus bacteremia (“SAB”) infections and to support activities required for an end-of-Phase 2 meeting with the FDA. The MTEC Agreement specifies that the award will be paid to the Company over the term of the award through a cost reimbursable model, based on agreed upon cost share percentages, and the money received is not refundable to MTEC.

Upon license or commercialization of intellectual property developed with the funding from the MTEC Agreement, additional fees will be due to MTEC. The Company will elect whether to (a) pay a fixed royalty amount, which is

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subject to a cap based upon total funding received, or (b) pay an additional assessment fee, which would also be subject to a cap based upon a percentage of total funding received.

The MTEC Agreement is effective through March 31, 2026 and may be terminated, in whole or in part, upon 30 calendar days’ prior written notice from the Company to MTEC. In addition, MTEC has the right to terminate the MTEC Agreement upon material breach by the Company.

The Company determined that the MTEC Agreement is not in the scope of ASC 808 or ASC 606. Applying ASC 606 by analogy the Company recognizes proceeds received under the MTEC Agreement as grant and award revenue in the statement of operations when related costs are incurred. The Company recognized $1.2 million and $3.0 million in grant and award revenue from the MTEC Agreement during the three months ended September 30, 2025 and 2024, respectively, and $3.8 million and $3.9 million during the nine months ended September 30, 2025 and 2024, respectively. As of September 30, 2025 and December 31, 2024, the Company had $0.7 million as awards receivable from MTEC.

CFF Therapeutics Development Award

On March 13, 2020, the Company entered into an award agreement (the “Award Agreement”) with the CFF, pursuant to which the Company received a Therapeutics Development Award of up to $5.0 million (the “CFF Award”). The CFF Award was used to fund a portion of the Company’s Phase 1b/2a clinical trial of the Pseudomonas aeruginosa (“P. aeruginosa”) phage candidate, AP-PA02, as a treatment for Pseudomonas airway infections in people with cystic fibrosis (“CF”).

​

The first payment under the Award Agreement, in the amount of $1.0 million, became due upon signing the Award Agreement and was received in April 2020. The remainder of the CFF Award was payable to the Company incrementally in installments upon the achievement of certain milestones related to the development program and progress of the Phase 1b/2a clinical trial of AP-PA02, as set forth in the Award Agreement. The total amount of the CFF Award was recognized through December 2023 and no additional payments are expected.

​

If the Company ceases to use commercially reasonable efforts directed to the development of AP-PA02, or any other Product (as defined in the Award Agreement), for a period of 360 days (an “Interruption”) and fails to resume the development of the Product after receiving from CFF notice of an Interruption, then the Company must either repay the amount of the CFF Award actually received by the Company, plus interest, or grant to CFF (1) an exclusive (even as to the Company), worldwide, perpetual, sublicensable license under technology developed under the Award Agreement that covers the Product for use in treating infections in CF patients (the “CF Field”), and (2) a non-exclusive, worldwide, perpetual, sublicensable license under certain background intellectual property covering the Product, to the extent necessary to commercialize the Product in the CF Field.

Upon commercialization by the Company of any Product, the Company will owe a fixed royalty amount to CFF, which is to be paid in installments determined, in part, based on commercial sales volumes of the Product. The Company will be obligated to make an additional fixed royalty payment upon achieving specified sales milestones. The Company may also be obligated to make a payment to CFF if the Company transfers, sells or licenses the Product in the CF Field, or if the Company enters into a change of control transaction.

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The term of the Award Agreement commenced on March 10, 2020 and expires on the earlier of the date on which the Company has paid CFF all of the fixed royalty payments set forth therein, the effective date of any license granted to CFF following an Interruption, or upon earlier termination of the Award Agreement. Either CFF or the Company may terminate the Award Agreement for cause, which includes the Company’s material failure to achieve certain development milestones. The Company’s payment obligations survive the termination of the Award Agreement.

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The Company concluded that the CFF Award is in the scope of ASC 808. Accordingly, as discussed in Note 3, “Significant Accounting Policies” of its 2024 Annual Report, the Company recognizes the award upon achievement of certain milestones as credits to research and development expenses. No credits to research and development expenses were recognized during the three and nine months ended September 30, 2025 and 2024, related to the CFF Award. In

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addition, the Company concluded under the guidance in ASC 730 that it does not have an obligation to repay funds received once related research and development expenses are incurred.

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14. Segment Reporting

The Company operates and manages its business as one reportable operating segment, which is the business of developing pathogen-specific bacteriophage therapeutics for the treatment of antibiotic-resistant and difficult-to-treat acute and chronic bacterial infections using its proprietary bacteriophage-based technology. The determination of a single business segment is consistent with the consolidated financial information regularly provided to the Company’s chief operating decision maker (“CODM”). The Company’s CODM is its Chief Executive Officer, who reviews financial information on an aggregate basis for purposes of assessing performance, making operating decisions, allocating resources and evaluating financial performance. The Company maintains 99.5% of its $12.6 million property and equipment, net within the United States.

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The following table includes certain segment information for the periods presented (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | 2024 | ​ | 2025 | ​ | 2024
Grant and award revenue | ​ | $ | 1,159 | ​ | $ | 2,973 | ​ | $ | 3,819 | ​ | $ | 3,939
Operating expenses | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Research and development expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
AP-PA02: Non-Cystic Fibrosis Bronchiectasis | ​ | ​ | 190 | ​ | ​ | 1,858 | ​ | ​ | (98) | ​ | ​ | 5,459
AP-PA02: Cystic Fibrosis | ​ | ​ | - | ​ | ​ | - | ​ | ​ | 25 | ​ | ​ | 235
AP-SA02: Bacteremia | ​ | ​ | 404 | ​ | ​ | 1,618 | ​ | ​ | 2,067 | ​ | ​ | 2,752
AP-SA02: Prosthetic Joint Infection | ​ | ​ | - | ​ | ​ | - | ​ | ​ | 2 | ​ | ​ | 8
Expenses not allocated by projects* | ​ | ​ | 545 | ​ | ​ | 726 | ​ | ​ | 1,657 | ​ | ​ | 1,903
Total external research and development expenses | ​ | ​ | 1,139 | ​ | ​ | 4,202 | ​ | ​ | 3,653 | ​ | ​ | 10,357
Research and development personnel expenses | ​ | ​ | 2,287 | ​ | ​ | 2,874 | ​ | ​ | 6,893 | ​ | ​ | 8,296
Other research and development expenses | ​ | ​ | 2,398 | ​ | ​ | 2,409 | ​ | ​ | 7,101 | ​ | ​ | 7,322
Total research and development expenses | ​ | ​ | 5,824 | ​ | ​ | 9,485 | ​ | ​ | 17,647 | ​ | ​ | 25,975
General and administrative expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
General and administrative personnel expenses | ​ | ​ | 1,141 | ​ | ​ | 1,273 | ​ | ​ | 3,733 | ​ | ​ | 3,778
Other general and administrative expenses | ​ | ​ | 1,970 | ​ | ​ | 1,971 | ​ | ​ | 5,250 | ​ | ​ | 6,083
Total general and administrative expenses | ​ | ​ | 3,111 | ​ | ​ | 3,244 | ​ | ​ | 8,983 | ​ | ​ | 9,861
Total operating expenses | ​ | ​ | 8,935 | ​ | ​ | 12,729 | ​ | ​ | 26,630 | ​ | ​ | 35,836
Operating loss | ​ | ​ | (7,776) | ​ | ​ | (9,756) | ​ | ​ | (22,811) | ​ | ​ | (31,897)
Other income (expense), net | ​ | ​ | (18,899) | ​ | ​ | 4,275 | ​ | ​ | (26,690) | ​ | ​ | 10,381
Net loss | ​ | $ | (26,675) | ​ | $ | (5,481) | ​ | $ | (49,501) | ​ | $ | (21,516)

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Item 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements and related notes included in this Quarterly Report, and our audited financial statements and notes thereto as of and for the year ended December 31, 2024 included in our Annual Report on Form 10-K filed on March 21, 2025 with the U.S. Securities and Exchange Commission (the “SEC”).

Our common stock, par value $0.01 per share (the “Common Stock”) is traded on the NYSE American exchange under the symbol “ARMP.” We are headquartered in Los Angeles, California, and we have a research and development facility (the “McConnell Facility”) to support advancing phage products from discovery to the clinic. The facility is also equipped with approximately 10,000 square feet of licensed current good manufacturing practice (“cGMP”) drug manufacturing suites enabling the production, testing and release of clinical trial material.

Statements contained in this Quarterly Report that are not statements of historical fact are forward-looking statements within the meaning of the U.S. Private Securities Litigation Reform Act of 1995. Such forward-looking statements include, without limitation, statements concerning product development plans, commercialization of our products, the expected market opportunity for our products, the use of bacteriophages and synthetic phages to kill bacterial pathogens, having resources sufficient to fund our operations into the first quarter of 2026, future funding sources, general and administrative expenses, clinical trial and other research and development expenses, costs of manufacturing, costs relating to our intellectual property, capital expenditures, the expected benefits of our targeted phage therapies strategy, the potential market for our products, tax credits and carry-forwards, and litigation-related matters. Words such as “believe,” “anticipate,” “plan,” “expect,” “intend,” “will,” “goal,” “potential” and similar expressions are intended to identify forward-looking statements, though not all forward-looking statements necessarily contain these identifying words. These statements are subject to risks and uncertainties. Our actual results could differ materially from those anticipated in these forward-looking statements as a result of various factors, including those set forth under Item 1A, “Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2024, filed on March 21, 2025 with the SEC, and under Item 1A, “Risk Factors” and elsewhere in this Quarterly Report. These forward-looking statements speak only as of the date on which they were made, and we undertake no obligation to update any forward-looking statements.

Overview

We are a clinical-stage biotechnology company focused on the development of high-purity, pathogen-specific bacteriophage therapeutics for the treatment of antibiotic-resistant and difficult-to-treat bacterial infections using our proprietary bacteriophage-based technology. We have completed three Phase 2 clinical trials to date. We see bacteriophages as a potentially safer and effective alternative to antibiotics and an essential response to the growing bacterial resistance to current classes of antibiotics. Bacteriophages or “phages” have a powerful and highly differentiated mechanism of action that enables binding to and killing of specific targeted bacteria while uniquely preserving the normal human microbiome or “healthy bacteria”. This is in direct contrast to traditional broad-spectrum antibiotics which can alter the human microbiome increasing susceptibility to opportunistic pathogens, such as Clostridium difficile. We believe that phages represent a promising means to effectively treat bacterial infections as an alternative to broad-spectrum antibiotics, especially for patients with bacterial infections resistant to current standard of care therapies, including the multidrug-resistant or “superbug” strains of bacteria. We are a leading developer of clinical-stage phage therapeutics of high purity, and believe we are uniquely positioned to address the growing worldwide threat of antibiotic-resistant bacterial infections.

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We are combining our proprietary approach and expertise in identifying, characterizing and developing both naturally occurring and engineered (synthetic) bacteriophages with our proprietary phage-specific host-engineered cGMP manufacturing capabilities to advance a target pipeline of high-quality bacteriophage product candidates for late-stage clinical development. Our optimized manufacturing processes significantly increase phage titers and improve production efficiency with the goal of ensuring commercial viability.

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We remain committed to our mission to evaluate phage-based therapeutics in randomized controlled clinical trials that evaluate safety and efficacy required to support potential regulatory approval and commercialization of our phage products as alternatives to traditional antibiotics, providing a potential method of treating patients suffering from drug-resistant and difficult-to-treat bacterial infections. To date, we have completed three critical Phase 2 trials, utilizing two distinct phage cocktails against two different bacterial pathogens with the potential to treat chronic pulmonary disease complicated by bacterial infection, as well as acute systemic bacterial infection. In October 2025, we announced positive results from our Phase 2a diSArm study evaluating our intravenous bacteriophage cocktail candidate AP-SA02 for the treatment of complicated SAB, which demonstrated statistically significant improvement in clinical response rates and favorable tolerability. We believe these results support advancing AP-SA02 into a pivotal Phase 3 trial. We continue to advance our two lead candidates, referred to as AP-PA02 and AP-SA02, to address both chronic and acute bacterial infections.

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Pseudomonas aeruginosa Phage Product Candidate, AP-PA02

Clinical Development of AP-PA02 in Cystic Fibrosis: Completed Phase 1b/2a Study

​

Our first phage candidate, inhaled AP-PA02, is focused primarily on the treatment of chronic pulmonary infections due to Pseudomonas aeruginosa (“P. aeruginosa”). On October 14, 2020, we received the approval to proceed from the U.S. Food and Drug Administration (the “FDA”) for our Investigational New Drug (“IND”) application for AP-PA02. In the first quarter of 2023, we announced positive topline results from the completed “SWARM-P.a.” study – a Phase 1b/2a, multicenter, double-blind, randomized, placebo-controlled, single ascending dose and multiple ascending dose clinical trial to evaluate the safety and tolerability of inhaled AP-PA02 in subjects with cystic fibrosis (“CF”) and chronic pulmonary P. aeruginosa infection. Data indicate that AP-PA02 was well-tolerated with a treatment emergent adverse event profile similar to placebo. Pharmacokinetics findings confirm that AP-PA02 can be effectively delivered to the lungs through nebulization with minimal systemic exposure, with single ascending doses and multiple ascending doses resulting in a proportional increase in exposure as measured in induced sputum. AP-PA02 exposures were generally consistent across subjects. Additionally, bacterial levels of P. aeruginosa in the sputum measured at several timepoints suggest improvement in bacterial load reduction for subjects treated with AP-PA02 at the end of treatment as compared to placebo after ten days of dosing. In addition, a correlation was seen between increasing phage dose (higher AP-PA02 exposures) and reduction in the bacterial load, supporting the biologic plausibility of a bacterial specific mechanism of action and creating the opportunity for phage as a therapeutic alternative to inhaled antibiotics. This study was supported by the CFF, which granted us a Therapeutics Development Award of $5.0 million. We received the full award’s amount, including the final payment of $0.3 million, in January 2024. Following the promising Phase 1b/2a results of favorable safety and tolerability profile and plausible mechanism of action, an additional confirmatory Phase 2 trial was initiated in non-cystic fibrosis bronchiectasis (“NCFB”) patients with similar chronic pulmonary disease with infections due to P. aeruginosa.

Clinical Development of AP-PA02 in Non-Cystic Fibrosis Bronchiectasis: Completed Phase 2 Study

​

On February 22, 2022, Armata announced that it had received from the FDA the approval to proceed for our IND application for AP-PA02, in a second indication, NCFB. On December 19, 2024, Armata announced encouraging results from the completed “Tailwind” study – a Phase 2 multicenter, double-blind, randomized, placebo-controlled study to evaluate the safety, phage kinetics, and efficacy of inhaled AP-PA02 in subjects with NCFB and chronic pulmonary P. aeruginosa infection. Data indicated that inhaled AP-PA02 provides a durable reduction of P. aeruginosa in the lung, with a favorable safety and tolerability profile. The Tailwind study was conducted in two cohorts running in parallel: subjects in one cohort (cohort A) received inhaled AP-PA02 as monotherapy, while subjects in another cohort (cohort B) received inhaled AP-PA02 in combination with inhaled anti-pseudomonal antibiotic treatment. Subjects in both cohorts were dosed at home by nebulization with study drug administered every 12 hours for 10 days and were followed for approximately four weeks after receiving their last dose of study drug. The primary efficacy endpoint was the reduction in P. aeruginosa colony forming units (“CFUs”) in lung sputum at one week following completion of dosing (day 17) compared to baseline. Per the statistical analysis plan, efficacy analysis of each independent cohort showed no significant difference between subjects treated with AP-PA02 and placebo due to small numbers of subjects in each cohort. Notably, a post-hoc intent-to-treat analysis (n=33 active and n=15 placebo; all subjects from both cohorts) demonstrated a statistically significant reduction of P. aeruginosa CFUs in the lung at day 17 (AP-PA02 vs. placebo;

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P=0.05). The reduction in P. aeruginosa CFUs persisted two weeks following completion of dosing with AP-PA02 when compared with placebo at day 24 (AP-PA02 vs. placebo; P=0.015). Additionally, paired analysis of P. aeruginosa CFU density at baseline compared to day 10 (P=0.03), day 11 (P=0.01), day 17 (P=0.003) and day 24 (P=0.018) was significant in the AP-PA02-treated cohort. We believe the data suggest that AP-PA02 alone is as effective as the combination therapy of phage and antibiotics in reducing P. aeruginosa CFUs in the lung. Additionally, approximately one-third of subjects treated with phage monotherapy exhibited at least a 2-log CFU reduction in P. aeruginosa compared to no reduction in placebo treated subjects. Safety data indicate that inhaled AP-PA02 was well-tolerated with treatment-emergent adverse events mild and self-limiting. There was one possibly related serious adverse event that was linked to an acute pulmonary event requiring hospitalization that was responsive to antibiotics. We believe the safety and tolerability of AP-PA02 offers a promising profile for treating chronically infected NCFB patients.

Results from the Phase 2 Tailwind study demonstrate the potential of Armata’s high-purity phage cocktail, AP-PA02, as a new monotherapy treatment alternative for chronic pulmonary disease caused by P. aeruginosa infection, including drug-resistant bacteria, and indicate the potential for phage therapy to reduce reliance on chronic antibiotic use. The Phase 2 Tailwind study represents the second successful clinical trial for AP-PA02, Armata’s lead pulmonary candidate, which was first evaluated in people with cystic fibrosis in the Phase 1b/2a SWARM-P.a. trial that completed in 2023. We believe the learnings on dose-schedule regimens gained from the two completed Phase 2 studies position us to define a safe and promising biologic correlation for a Phase 3 definitive trial to evaluate inhaled AP-PA02 as an alternative to antibiotics in chronic pulmonary P. aeruginosa infection.

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Contingent upon securing sufficient additional funding, we may at the appropriate time in the future resume clinical development of AP-PA02 for NCFB, which may include the execution of a definitive Phase 3 clinical trial. We are also actively exploring potential strategic partnerships as a means to further advance this important program.

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Additional Clinical Indications for AP-PA02

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The current Pseudomonas phage cocktail formulated for inhalation (AP-PA02) is prepared with the same high potency and purity of our injectable phage cocktail for S. aureus (AP-SA02). Based on the AP-SA02 clinical findings, we are exploring the potential development of our Pseudomonas phage cocktail for acute ventilator-associated pneumonia and severe infections due to multidrug-resistant P. aeruginosa.

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Staphylococcus aureus Phage Product Candidate, AP-SA02

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Clinical Development of AP-SA02 in Bacteremia: Completed Phase 1b/2a Study

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In parallel to developing novel phage therapeutics that target chronic bacterial infections, we have an acute bacterial infection clinical development plan focused on Staphylococcus aureus (“S. aureus”) bacteremia, a difficult-to-treat and often life-threatening human infection that can result in high morbidity and mortality and for which bacterial resistance to antibiotics is growing.

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We believe a key advantage of our phage manufacturing expertise is the purity profiles of our phage products, including AP-SA02, our phage product candidate for S. aureus; this has enabled us to pursue treatment of complicated S. aureus bacteremia, where repetitive intravenous (“IV”) dosing is required. On November 17, 2021, we announced that we had received approval from the FDA to proceed with our IND application for AP-SA02.

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On May 19, 2025, we announced positive topline data from the Phase 1b/2a diSArm study of intravenously administered AP-SA02 in complicated S. aureus bacteremia. The diSArm study (NCT05184764) was a Phase 1b/2a, multicenter, randomized, double-blind, placebo-controlled, multiple ascending dose escalation study of the safety, tolerability, and efficacy of intravenous AP-SA02 in addition to best available antibiotic therapy (“BAT”) compared to BAT alone (placebo) for the treatment of adults with complicated SAB. All doses of AP-SA02 were dosed intravenously every six hours for five days. The primary clinical efficacy endpoint for the Phase 2a portion of the diSArm study was clinical outcome (responder rate) in subjects with complicated bacteremia, measured at (i) Test of Cure (“TOC”) for AP-SA02, defined as one week following the end of IV treatment with AP-SA02 (day 12), (ii) TOC for BAT, defined as one week following the end of IV BAT, and (iii) end of study (“EOS”), defined as four weeks following the end of IV BAT.

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Clinical outcome was evaluated by both the blinded site investigators and a blinded Clinical Efficacy Adjudication Committee (the “CEAC”) in the intent-to-treat (“ITT”) population.

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Safety and efficacy were assessed in the ITT population, which included all subjects (n=50) who received at least one dose of AP-SA02 or placebo. The Phase 2a study enrolled and dosed 42 patients, with 29 randomized to AP-SA02 in addition to BAT and 13 to placebo (BAT alone). Methicillin-resistant S. aureus (“MRSA”) was the causative pathogen in ~38% of both the AP-SA02 and placebo groups.

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AP-SA02 was well-tolerated with no serious adverse events related to the study drug. Two subjects had adverse events that were possibly related to the study drug: one with transient liver enzyme elevation and one with hypersensitivity that resolved with discontinuation of vancomycin.

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A statistically significant increase in clinical response rate was observed at TOC for AP-SA02 (day 12) in AP-SA02 treated subjects (88%; 21/24) versus placebo (58%; 7/12) (p = 0.047) as assessed by blinded site investigators, and 83% (20/24) in the AP-SA02 group versus 58% (7/12) in the placebo group as assessed by the blinded CEAC. At TOC for BAT and at EOS, 100% of the AP-SA02 treated subjects had clinically responded (p = 0.017) versus 25% of placebo subjects considered non-responsive due to either relapse or treatment failure, consistent with the non-responder rate reported in the literature for recent phase 3 trials. Of note, the clinical response with AP-SA02 occurred regardless of whether subjects were infected with methicillin-sensitive S. aureus (“MSSA”) or MRSA. All subjects infected with MRSA and treated with AP-SA02 and BAT cleared their infection by TOC for BAT with no evidence of relapse through EOS, as compared to the relapse rate of BAT alone as noted above. Supporting the investigator assessment, clinical outcome was assessed by the CEAC, who agreed that subjects who received placebo had a 22% and 25% non-responder rate at TOC with BAT and at EOS, respectively, while 100% of the subjects who received AP-SA02 clinically responded (p = 0.025: TOC BAT; p = 0.020: EOS).

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Additionally, patients treated with AP-SA02 showed trends toward rapid normalization of key predictors of mortality and complications in SAB including C-reactive protein and interleukin-10, shorter time to negative blood culture, quicker time to resolution of signs and symptoms at the infection site, shorter intensive care unit and hospital utilization.

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Defined and reproducible laboratory derived stable genomic variants present in AP-SA02 drug product may provide an immediate advantage, enabling rapid, strain-specific response to each patient’s S. aureus isolate. These characterized variants can expand from as little as 2% to dominance when infecting certain patient isolates in vitro, highlighting that these variants are favored for their enhanced ability to infect those clinical strains and the importance of integrating this diversity into Armata’s phage cocktail from the outset. This inherent flexibility may be central to achieving optimal therapeutic efficacy in the clinic.

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Conclusions:

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| • | AP-SA02, combined with BAT, had a higher and earlier cure rate compared to placebo in patients with complicated SAB at day 12 as assessed by both blinded site investigators and independent adjudicators.

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| • | No patients who received AP-SA02 demonstrated non-response or relapse at one week post-BAT or at EOS, as assessed by both blinded site investigators and the independent adjudication committee, compared with approximately 25% non-response or relapse in the placebo group.

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| • | AP-SA02 appears safe with clinical efficacy against both MRSA and MSSA and trends toward earlier resolution and shorter hospitalization, with no evidence of relapse four weeks post-therapy.

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| • | We previously demonstrated the persistence of AP-SA02 in the IV space on multiple days one hour post IV push. These trial results support AP-SA02 homing to different sites of infection, presumably penetrating biofilms, and infecting and lysing the target S. aureus bacteria, independent of both antibiotic resistance patterns and site of infection.

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| • | Defined phage variants in AP-SA02 drug product ensure an intrinsic adaptive mechanism — a flexibility that may be key to achieving effective phage therapy from patient to patient.

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| • | We believe that these results strongly support advancement into a pivotal Phase 3 trial that Armata plans to initiate in 2026, subject to review and feedback from the FDA. We are engaged with the FDA regarding a potential superiority trial design.

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On October 22, 2025, we highlighted the positive results from our Phase 2a diSArm clinical study of AP-SA02 in an oral presentation at IDWeek 2025TM. The abstract, titled, “A Phase 2a Randomized, Double-Blind, Controlled Trial of the Efficacy and Safety of an Intravenous (IV) Bacteriophage Cocktail (AP-SA02) vs. Placebo in Combination with Best Available Antibiotic Therapy (BAT) in Patients with Complicated Staphylococcus aureus Bacteremia,” was accepted as a late-breaking abstract for oral presentation, and was presented by Dr. Loren G. Miller, M.D., M.P.H., Professor of Medicine, David Geffen School of Medicine at UCLA, Chief, Division of Infectious Diseases at Harbor-UCLA Medical Center and the Lundquist Institute.

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The results from our Phase 1b/2a diSArm study are an important step forward in our effort to confirm the potent antimicrobial activity of phage therapy and the completion of the study represents a significant milestone in the development of AP-SA02, moving us one step closer to introducing an effective new treatment option to patients suffering from complicated SAB. This is the first clear evidence in a randomized controlled trial of the efficacy of phage against a serious systemic pathogen that is responsible for significant morbidity and mortality in the United States.

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Findings from the Phase 1b/2a study, including the favorable safety and tolerability profile of AP-SA02, inform the design of a larger definitive efficacy study to demonstrate superiority of AP-SA02 in treating complicated SAB, and form the basis for an end-of-Phase-2 meeting with the FDA which the Company plans to hold in the second half of 2025. Subject to review and feedback from the FDA, we are committed to developing a superiority pivotal trial focused on phage as an alternative to broad-spectrum antibiotics and/or antibiotic sparing to decrease the utilization of broad-spectrum antibiotics and their detrimental impact on the normal human microbiome.

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On June 15, 2020, we entered into an agreement (the “MTEC Agreement”) with the Medical Technology Enterprise Consortium (“MTEC”), pursuant to which we received a $15.0 million award and entered into a multi-year program administered by the U.S Department of Defense through MTEC and managed by the Naval Medical Research Command (“NMRC”) – Naval Advanced Medical Development (“NAMD”) with funding from the Defense Health Agency and Joint Warfighter Medical Research Program. This award has been used to partially fund the Phase 1b/2a, multicenter, randomized, double-blind, placebo-controlled dose escalation study to assess the safety, tolerability and efficacy of our phage-based candidate, AP-SA02, for the treatment of adults with S. aureus (the “diSArm” study) and to support activities required for an end-of-Phase 2 meeting with the FDA. On September 29, 2022, the MTEC Agreement was modified to increase the total award by $1.3 million to $16.3 million and extend the term into the second half of 2024. On July 29, 2024, the MTEC Agreement was modified to increase the total award by $5.3 million to $21.6 million and extend the term into the third quarter of 2025. On April 29, 2025, we received $4.65 million of additional non-dilutive award funding through MTEC, thereby increasing the total MTEC award to $26.2 million, and the MTEC Agreement was modified to extend the term to September 30, 2025. On July 2, 2025, the MTEC Agreement was modified to extend the term to March 31, 2026.

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Additional Clinical Indications for AP-SA02

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On August 1, 2022, we announced FDA approval to proceed with our IND application for AP-SA02 in a second indication, prosthetic joint infections (“PJI”) with S. aureus. We had planned to initiate a Phase 1b/2a trial; however, in light of the growing concerns of both PJI and wound infections, we are considering revising the protocol to include both indications. Driven by data from the bacteremia study, and with sufficient funding, we may in the future initiate a Phase 1b/2a trial to assess the safety and tolerability of intravenous and intra-articular AP-SA02 as an adjunct to standard of care antibiotics in adults undergoing treatment of periprosthetic joint infections and/or wound infections caused by S. aureus.

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The following chart summarizes the status of our phage product candidate development programs and partners.

We have incurred net losses since our inception and our operations to date have been primarily limited to research and development and raising capital. As of September 30, 2025, we had an accumulated deficit of $377.2 million. We currently expect to use our existing cash and cash equivalents for the focused research and development of our current product candidates and for working capital and other general corporate purposes. We anticipate that a substantial portion of our capital resources and efforts in the foreseeable future will be focused on completing the development of and seeking to obtain regulatory approval for our product candidates. We do not expect to generate product revenue unless and until we successfully complete development and obtain marketing approval for at least one of our product candidates. We may also use a portion of our existing cash and cash equivalents for the potential acquisition of, or investment in, product candidates, technologies, formulations or companies that complement our business, although we have no current understandings, commitments or agreements to do so.

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Our existing cash and cash equivalents of $14.8 million as of September 30, 2025 will not be sufficient to enable us to complete all necessary development of any potential product candidates and fund our operations for the next 12 months from the date the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q are issued. These circumstances raise substantial doubt about the Company’s ability to continue as a going concern. Accordingly, we will be required to obtain further funding through one or more other public or private equity offerings, debt financings, collaboration, strategic financing, grants or government contract awards, licensing arrangements or other sources. Our ability to raise additional capital may be adversely impacted by potential worsening global economic conditions and potential disruptions to, and volatility in, financial markets in the United States and worldwide. Adequate additional funding may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed or on acceptable terms, we may be required to defer, reduce or eliminate significant planned expenditures, restructure, curtail or eliminate some or all of our development programs or other operations, dispose of assets, enter into arrangements that may require us to relinquish rights to certain of our product candidates, technologies or potential markets, file for bankruptcy or cease operations altogether. Any of these events could have a material adverse effect on our business, financial condition and results of operations and result in a loss of investment by our stockholders.

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Recent Events

August 2025 Credit Agreement

On August 11, 2025, we entered into a credit and security agreement (the “August 2025 Credit Agreement”) for a loan in the aggregate amount of $15.0 million (the “August 2025 Loan”) with Innoviva. The August 2025 Loan bears interest at an annual rate of 14.0% and matures on January 11, 2029. Principal and accrued interest are payable at maturity. Repayment of the August 2025 Loan is guaranteed by our domestic subsidiaries, and the loan is secured by substantially all of our assets and the subsidiary guarantors.

MTEC Agreement Modification

On July 2, 2025, the MTEC Agreement was modified to extend the term to March 31, 2026. We will continue to recognize additional grant and award revenue until the full amount of the amended award is utilized.

Results of Operations

Comparison of three and nine months ended September 30, 2025 and 2024 (in thousands):

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Change
​ |  | 2025 |  | 2024 |  | Amount |  | %
Grant and award revenue | ​ | $ | 1,159 | ​ | $ | 2,973 | ​ | $ | (1,814) | ​ | ​ | (61.0%)
Operating expenses | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Research and development | ​ |  | 5,824 | ​ | ​ | 9,485 | ​ |  | (3,661) | ​ | ​ | (38.6%)
General and administrative | ​ |  | 3,111 | ​ | ​ | 3,244 | ​ |  | (133) | ​ | ​ | (4.1%)
Total operating expenses | ​ | ​ | 8,935 | ​ | ​ | 12,729 | ​ | ​ | (3,794) | ​ | ​ | (29.8%)
Operating loss | ​ |  | (7,776) | ​ |  | (9,756) | ​ |  | 1,980 | ​ |  | (20.3%)
Other income (expense) | ​ |  |  | ​ |  |  | ​ |  |  | ​ |  |
Interest income | ​ | ​ | 90 | ​ | ​ | 294 | ​ |  | (204) | ​ |  | (69.4%)
Interest expense | ​ | ​ | (4,346) | ​ | ​ | (2,923) | ​ | ​ | (1,423) | ​ | ​ | 48.7%
Change in fair value of the Convertible Loan | ​ | ​ | (14,643) | ​ | ​ | 6,904 | ​ | ​ | (21,547) | ​ | ​ | (312.1%)
Total other income (expense), net | ​ |  | (18,899) | ​ |  | 4,275 | ​ |  | (23,174) | ​ |  | (542.1%)
Net loss | ​ | $ | (26,675) | ​ | $ | (5,481) | ​ | $ | (21,194) | ​ |  | 386.7%

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30, | ​ | Change
​ |  | 2025 |  | 2024 |  | Amount |  | %
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Grant and award revenue | ​ | $ | 3,819 | ​ | $ | 3,939 | ​ | $ | (120) | ​ | ​ | (3.0%)
Operating expenses | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Research and development | ​ |  | 17,647 | ​ | ​ | 25,975 | ​ |  | (8,328) | ​ | ​ | (32.1%)
General and administrative | ​ |  | 8,983 | ​ | ​ | 9,861 | ​ |  | (878) | ​ | ​ | (8.9%)
Total operating expenses | ​ | ​ | 26,630 | ​ | ​ | 35,836 | ​ | ​ | (9,206) | ​ | ​ | (25.7%)
Operating loss | ​ |  | (22,811) | ​ |  | (31,897) | ​ |  | 9,086 | ​ |  | (28.5%)
Other income (expense) | ​ |  |  | ​ |  |  | ​ |  |  | ​ |  |
Interest income | ​ | ​ | 257 | ​ | ​ | 567 | ​ |  | (310) | ​ |  | (54.7%)
Interest expense | ​ | ​ | (11,756) | ​ | ​ | (7,462) | ​ | ​ | (4,294) | ​ | ​ | 57.5%
Change in fair value of the Convertible Loan | ​ | ​ | (15,191) | ​ | ​ | 17,276 | ​ | ​ | (32,467) | ​ | ​ | (187.9%)
Total other income (expense), net | ​ |  | (26,690) | ​ |  | 10,381 | ​ |  | (37,071) | ​ |  | (357.1%)
Net loss | ​ | $ | (49,501) | ​ | $ | (21,516) | ​ | $ | (27,985) | ​ |  | 130.1%

​

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Grant and Award Revenue

We recognized $1.2 million and $3.0 million of grant and award revenue during the three months ended September 30, 2025 and 2024, respectively, which represents MTEC’s share of the costs incurred for our AP-SA02 program for the treatment of SAB.

​

We recognized $3.8 million and $3.9 million of grant and award revenue during the nine months ended September 30, 2025 and 2024, respectively, which represents MTEC’s share of the costs incurred for our AP-SA02 program for the treatment of SAB.

​

Research and Development

The following table summarizes our research and development expenses for the three and nine months ended September 30, 2025 and 2024 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Change
​ |  | 2025 |  | 2024 |  | Amount |  | %
External costs: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Clinical trials | ​ | $ | 531 | ​ | $ | 3,244 | ​ | $ | (2,713) | ​ | ​ | (83.6%)
Other research and development costs, including laboratory materials and supplies | ​ | ​ | 608 | ​ | ​ | 958 | ​ | ​ | (350) | ​ | ​ | (36.5%)
Total external costs | ​ |  | 1,139 | ​ | ​ | 4,202 | ​ |  | (3,063) | ​ | ​ | (72.9%)
Internal costs: | ​ |  | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ | ​ | ​
Personnel-related costs | ​ | ​ | 2,287 | ​ | ​ | 2,874 | ​ | ​ | (587) | ​ | ​ | (20.4%)
Facilities and overhead costs | ​ |  | 2,398 | ​ |  | 2,409 | ​ |  | (11) | ​ |  | (0.5%)
Total research and development expense: | ​ | $ | 5,824 | ​ | $ | 9,485 | ​ | $ | (3,661) | ​ |  | (38.6%)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30, | ​ | Change
​ |  | 2025 |  | 2024 |  | Amount |  | %
External costs: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Clinical trial expenses | ​ | $ | 1,794 | ​ | $ | 7,623 | ​ | $ | (5,829) | ​ | ​ | (76.5%)
Other research and development costs, including consulting, laboratory supplies and other | ​ | ​ | 1,859 | ​ | ​ | 2,734 | ​ | ​ | (875) | ​ | ​ | (32.0%)
Total external costs | ​ |  | 3,653 | ​ | ​ | 10,357 | ​ |  | (6,704) | ​ | ​ | (64.7%)
Internal costs: | ​ |  | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ | ​ | ​
Personnel-related costs | ​ | ​ | 6,893 | ​ | ​ | 8,296 | ​ | ​ | (1,403) | ​ | ​ | (16.9%)
Facilities and overhead costs | ​ |  | 7,101 | ​ |  | 7,322 | ​ |  | (221) | ​ |  | (3.0%)
Total research and development expense: | ​ | $ | 17,647 | ​ | $ | 25,975 | ​ | $ | (8,328) | ​ |  | (32.1%)

​

Research and development expenses decreased by $3.7 million, from $9.5 million for the three months ended September 30, 2024 to $5.8 million for the three months ended September 30, 2025.

Research and development expenses decreased by $8.3 million, from $26.0 million for the nine months ended September 30, 2024 to $17.7 million for the nine months ended September 30, 2025.

Clinical trial costs decreased by $2.7 million, from $3.2 million for the three months ended September 30, 2024, to $0.5 million for the three months ended September 30, 2025. The decrease is primarily attributable to a $1.6 million decrease in AP-PA02 NCFB trial costs and a $1.1 million decrease in SA study costs.

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Clinical trial costs decreased by $5.8 million, from $7.6 million for the nine months ended September 30, 2024, to $1.8 million for the nine months ended September 30, 2025. The decrease is primarily attributable to a $5.2 million decrease in AP-PA02 NCFB trial costs, a $0.4 decrease in SA study costs, and a $0.2 million decrease in the CF study.

Other external research and development costs decreased by $0.4 million from $1.0 million for the three months ended September 30, 2024 to $0.6 million for the three months ended September 30, 2025. The decrease was primarily due to a decrease of $0.3 million in consulting expenses and a decrease of $0.1 million in other costs related to the AP-PA02 NCFB and SA studies nearing completion.

Other external research and development costs decreased by $0.8 million from $2.7 million for the nine months ended September 30, 2024 to $1.9 million for the nine months ended September 30, 2025. The decrease was primarily due to a decrease of $0.8 million in consulting expenses.

Our expenses by product and by project for the three and nine months ended September 30, 2025 and 2024 were as follows (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30,
​ | ​ | ​ | 2025 |  | 2024
Product | Project name | ​ | ​ | ​ | ​
AP-PA02 | Non-Cystic Fibrosis Bronchiectasis | ​ | $ | 190 | ​ | $ | 1,858
AP-SA02 | Bacteremia | ​ | ​ | 404 | ​ | ​ | 1,618
​ | Expenses not allocated by projects* | ​ | ​ | 545 | ​ | ​ | 726
​ | Total external costs | ​ | $ | 1,139 | ​ | $ | 4,202

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | ​ | 2025 |  | 2024
Product | Project name | ​ | ​ | ​ | ​
AP-PA02 | Non-Cystic Fibrosis Bronchiectasis | ​ | $ | (98) | ​ | $ | 5,459
AP-PA02 | Cystic Fibrosis | ​ | ​ | 25 | ​ | ​ | 235
AP-SA02 | Bacteremia | ​ | ​ | 2,067 | ​ | ​ | 2,752
AP-SA02 | Prosthetic Joint Infection | ​ | ​ | 2 | ​ | ​ | 8
​ | Expenses not allocated by projects* | ​ | ​ | 1,657 | ​ | ​ | 1,903
​ | Total external costs | ​ | $ | 3,653 | ​ | $ | 10,357

​

​

* Expenses not allocated by projects include consultants, laboratory supplies and outsourced services expenses.

Personnel-related costs, including employee payroll and related expenses, decreased by $0.6 million, from $2.9 million for the three months ended September 30, 2024 to $2.3 million for the three months ended September 30, 2025. This decrease was mainly driven by a $0.6 million decrease in incentive compensation, salaries and wages, vacation and insurance due to a reduction in personnel.

Personnel-related costs, including employee payroll and related expenses, decreased by $1.4 million, from $8.3 million for the nine months ended September 30, 2024 to $6.9 million for the nine months ended September 30, 2025. This decrease was mainly driven by a $1.6 million decrease in incentive compensation, salaries and wages, vacation and insurance due to a reduction in personnel as we maximize efficiency for product development. This decrease was partially offset by a $0.2 million increase in stock-based compensation expense and employee training expenses.

Facilities and overhead costs remained consistent at $2.4 million for the three months ended September 30, 2024 and for the three months ended September 30, 2025.

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Facilities and overhead costs decreased by $0.2 million, from $7.3 million for the nine months ended September 30, 2024 to $7.1 million for the nine months ended September 30, 2025 mainly due to a decrease of $0.3 million in lease expense partially offset by a $0.1 million increase in depreciation and other variable facility costs.

General and Administrative

General and administrative expenses were $3.1 million and $3.2 million for the three months ended September 30, 2025 and 2024, respectively. The decrease of $0.1 million is primarily related to a decrease in personnel-related costs.

General and administrative expenses were $8.9 million and $9.9 million for the nine months ended September 30, 2025 and 2024, respectively. The decrease of $1.0 million is primarily related to a decrease of $1.0 million in consulting fees as we continue to streamline and increase in-house expertise and a decrease of $0.6 million in stock-based compensation expense, partially offset by an increase of $0.6 million in personnel-related costs other than stock-based compensation expense.

Interest Income

Interest income for the three months ended September 30, 2025 and 2024 was $0.1 million and $0.3 million, respectively, and related to interest earned on our money market fund investments.

Interest income for the nine months ended September 30, 2025 and 2024 was $0.3 million and $0.6 million, respectively, and related to interest earned on our money market fund investments.

Interest Expense

We recognized interest expense of $4.3 million and $2.9 million for the three months ended September 30, 2025 and 2024 respectively. The increase is primarily related to increased debt balances as compared to the prior year period. Interest expense related to the interest expenses and the amortization of debt discount and issuance costs for the 2023 Loan, 2024 Loan, March 2025 Loan, and August 2025 Loan. Stated interest is accrued and is payable at the maturity of the 2023 Loan, 2024 Loan and March 2025 Loan in March 2026, and the August 2025 Loan in January 2029.

We recognized interest expense of $11.8 million and $7.5 million for the nine months ended September 30, 2025 and 2024 respectively. The increase is primarily related to increased debt balances as compared to the prior year period. Interest expense related to the interest expenses and the amortization of debt discount and issuance costs for the 2023 Loan, 2024 Loan, March 2025 Loan and August 2025 Loan. Stated interest is accrued and is payable at the maturity of the 2023 Loan, 2024 Loan and March 2025 Loan in March 2026, and the August 2025 Loan in January 2029.

Change in Fair Value of the Convertible Loan

We recognized a loss of $14.6 million and gain of $6.9 million on the change in the fair value of the Convertible Loan for the three months ended September 30, 2025 and 2024, respectively.

We recognized a loss of $15.2 million and a gain of $17.3 million on the change in the fair value of the Convertible Loan for the nine months ended September 30, 2025 and 2024, respectively.

The Convertible Loan received from Innoviva in January 2023 and amended in July 2023, November 2024, and March 2025 is accounted for at fair value using a weighted probability of various settlement scenarios of the Convertible Loan during its term discounted to each reporting date. Conversion option scenarios are valued using an option pricing model with significant assumptions and estimates such as volatility, expected term and risk-free interest rates.

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Liquidity, Capital Resources and Financial Condition

We have incurred net losses since our inception and have negative operating cash flows. Our cash and cash equivalents of $14.8 million as of September 30, 2025 will not be sufficient to fund our operations for the next 12 months from the date of issuance of our condensed consolidated financial statements for the nine months ended September 30, 2025. We plan to control our expenses and to raise additional capital through a combination of public and private equity, debt financing, strategic alliances, and grant and award arrangements. These circumstances raise substantial doubt about our ability to continue as a going concern. While management believes this plan to raise additional funds will alleviate the conditions that raise substantial doubt, these plans are not entirely within our control and cannot be assessed as being probable of occurring. We may not be able to secure additional financing in a timely manner or on favorable terms, if at all.

On August 11, 2025, we entered into the August 2025 Credit Agreement for a loan in the aggregate amount of $15.0 million. The August 2025 Loan bears interest at an annual rate of 14.0% and matures on January 11, 2029. Principal and accrued interest are payable at maturity. Repayment of the August 2025 Loan is guaranteed by our domestic subsidiaries, and the loan is secured by substantially all of our assets and the subsidiary guarantors.

On March 12, 2025, we entered into the March 2025 Credit Agreement for the March 2025 Loan in an aggregate amount of $10.0 million. The March 2025 Loan bears interest at an annual rate of 14.0% and matures on March 12, 2026. Principal and accrued interest are payable at maturity. Repayment of the March 2025 Loan is guaranteed by our domestic subsidiaries, and the loan is secured by substantially all of our assets and the subsidiary guarantors. Concurrently with the execution of the March 2025 Credit Agreement, we entered into amendments to (i) the Convertible Loan and Convertible Credit Agreement, (ii) the 2023 Loan and 2023 Credit Agreement, and (iii) the 2024 Loan and 2024 Credit Agreement, which, among other things, extended the maturity date of the Convertible Loan, 2023 Loan and 2024 Loan, respectively, to March 12, 2026.

On July 29, 2024, we amended the MTEC Agreement and increased the amount of the award by $5.3 million to a total of $21.6 million. We will recognize grant and award revenue from the third quarter of 2024 until the full amount of the amended award is utilized.

On April 29, 2025, we received $4.65 million of additional non-dilutive award funding through MTEC, thereby increasing the total MTEC award to $26.2 million, and the MTEC Agreement was modified to extend the term to September 30, 2025. On July 2, 2025, the MTEC Agreement was modified to extend the term to March 31, 2026. We will continue to recognize additional grant and award revenue until the full amount of the amended award is utilized.

Future Capital Requirements

We will need to raise additional capital in the future to continue to fund our operations. Our future funding requirements will depend on many factors, including:

| ● | the costs and timing of our research and development activities;

​

| ● | the progress and cost of our clinical trials and other research and development activities;

​

| ● | manufacturing costs associated with our targeted phage therapies strategy and other research and development activities;

​

| ● | the costs and timing of seeking regulatory approvals;

​

| ● | the costs of filing, prosecuting and enforcing any patent applications, claims, patents and other intellectual property rights; and

​

| ● | the costs of potential lawsuits involving us or our product candidates.

​

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We may seek to raise capital through a variety of sources, including:

| ● | the public equity market;

| ● | private equity or debt financings;

| ● | collaborative arrangements;

| ● | government grants or awards; or

| ● | strategic financing.

Any additional fundraising efforts may divert our management team from their day-to-day activities, which may adversely affect our ability to develop and commercialize our product candidates. Our ability to raise additional funds will depend, in part, on the success of our product development activities, including our targeted phage therapies strategy and any clinical trials we initiate, regulatory events, our ability to identify and enter into in-licensing or other strategic arrangements, and other events or conditions that may affect our value or prospects, as well as factors related to financial, economic and market conditions, many of which are beyond our control. We cannot be certain that sufficient funds will be available to us when required or on acceptable terms. If we are unable to secure additional funds on a timely basis or on acceptable terms, we may be required to defer, reduce or eliminate significant planned expenditures, restructure, curtail or eliminate some or all of our development programs or other operations, dispose of technology or assets, pursue an acquisition of our company by a third party at a price that may result in a loss on investment for our stockholders, enter into arrangements that may require us to relinquish rights to certain of our product candidates, technologies or potential markets, file for bankruptcy or cease operations altogether. Any of these events could have a material adverse effect on our business, financial condition and results of operations, increase the risk of insolvency and loss of investment by our stockholders. To the extent that additional capital is raised through the sale of equity or convertible loan securities, the issuance of such securities could result in dilution to our existing stockholders. Our ability to raise additional capital may be adversely impacted by potential worsening global economic conditions and the recent disruptions to, and volatility in, financial markets in the United States and worldwide.

Cash Flows

The following table summarizes our sources and uses of cash for the periods presented (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | Nine Months Ended September 30, | ​
​ | 2025 |  | 2024 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​
Net cash used in operating activities | $ | (19,089) | ​ | $ | (29,624) | ​
Net cash used in investing activities | ​ | (490) | ​ | ​ | (1,956) | ​
Net cash provided by financing activities | ​ | 24,954 | ​ | ​ | 34,958 | ​
Net increase in cash, cash equivalents and restricted cash | $ | 5,375 | ​ | $ | 3,378 | ​

​

Cash Flows Used in Operating Activities

Net cash used in operating activities was $19.1 million and $29.6 million for the nine months ended September 30, 2025 and 2024, respectively.

Cash used in operating activities in the nine months ended September 30, 2025 was primarily due to our net loss for the period of $49.5 million, adjusted by non-cash items of $31.8 million and a decrease of $1.4 million in our net operating assets and liabilities. The non-cash items consist of $15.2 million related to a loss from change in fair value of the Convertible Loan, $11.7 million of non-cash interest expense on the 2023 Loan, 2024 Loan, March 2025 Loan, and August 2025 Loan, $2.0 million related to stock-based compensation expense, $1.1 million related to depreciation expense and $1.8 million related to change in right-of-use asset. The decrease in our net operating assets and liabilities

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was primarily due to a decrease of $0.4 million in accrued compensation, a decrease of $0.8 million in the operating lease liability, and an increase of $0.2 million in prepaid expenses and other assets.

Cash used in operating activities in the nine months ended September 30, 2024 was primarily due to our net loss for the period of $21.5 million, adjusted by non-cash items of $4.8 million and a decrease of $3.3 million in our net operating assets and liabilities. The non-cash items consist of $17.3 million related to a gain from change in fair value of convertible debt, $7.5 million of non-cash interest expense on the 2023 Loan and the 2024 Loan, $2.5 million related to stock-based compensation expense, $1.5 million related to change in right-of-use asset and $0.9 million related to depreciation expense. The decrease in our net operating assets and liabilities was primarily due to a decrease of $4.2 million in operating lease liability related to lease payments and payments for the construction of office and laboratory and manufacturing space at our new leased facility in Los Angeles, CA, a decrease of $2.0 million in accounts payable and accrued liabilities, an increase of $0.8 million in accrued compensation, and a decrease of $2.1 million in prepaid expenses and other current assets.

Cash Flows Used in I nvesting Activities

Net cash used in investing activities was $0.5 million and $2.0 million for the nine months ended September 30, 2025 and 2024, respectively, which is attributable to purchases of laboratory and manufacturing equipment for the new office, laboratory and manufacturing space at our leased facility in Los Angeles, California.

Cash Flows from Financing Activities

Cash provided by financing activities for the nine months ended September 30, 2025 was $25.0 million, which consisted primarily of proceeds from issuance of term debt.

Cash provided by financing activities for the nine months ended September 30, 2024 was $34.9 million, which consisted primarily of proceeds from issuance of term debt, net of issuance costs of less than $0.1 million, and proceeds from exercise of stock options of $0.1 million.

Off-Balance Sheet Arrangements

As of September 30, 2025, we did not have off-balance sheet arrangements.

Critical Accounting Policies and Estimates

Management’s discussion and analysis of financial condition and results of operations are based upon our condensed consolidated financial statements, which have been prepared in accordance with U.S. GAAP. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. On an ongoing basis, we evaluate estimates and assumptions, including but not limited to those related to convertible debt, stock-based compensation expense, accruals for research and development costs, lease assets and liabilities, the valuation of deferred tax assets, valuation of uncertain income tax positions, impairment of goodwill and intangible assets and impairment of long-lived assets. We base our estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

Refer to Note 3 to the consolidated financial statements and critical accounting policies and estimated included in our Form 10-K filed with the SEC on March 21, 2025. There were no material changes to our critical accounting policies from December 31, 2024.

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Item 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

We are a smaller reporting company as defined by Rule 12b-2 of the Securities Exchange Act of 1934, as amended, or the Exchange Act, and are not required to provide the information required under this item.

Item 4. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Under the supervision of our Chief Executive Officer (“CEO”) and Senior Vice President, Finance and Principal Financial Officer (“PFO”), we evaluated the effectiveness of our disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) of the Securities Exchange Act (the “Exchange Act”) as of September 30, 2025. Based on that evaluation, our CEO and PFO have concluded that our disclosure controls and procedures were effective as of September 30, 2025 to ensure that information required to be disclosed by us in the reports we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including our CEO and PFO, as appropriate to allow timely discussion regarding required disclosures.

In designing and evaluating our disclosure controls and procedures, management recognizes that any disclosure controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives. In addition, the design of disclosure controls and procedures must reflect the fact that there are resource constraints and that management is required to apply its judgment in evaluating the benefits of possible controls and procedures relative to their costs.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting (as defined by Rules 13a-15(d) and 15d-15(d) of the Exchange Act) that occurred during the nine months ended September 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1. LEGAL PROCEEDINGS

From time to time, we are a party to certain litigation that is either judged to be not material or that arises in the ordinary course of business. We intend to vigorously defend our interests in these matters. We expect that the resolution of these matters will not have a material adverse effect on our business, financial condition or results of operations. However, due to the uncertainties inherent in litigation, no assurance can be given as to the outcome of these proceedings.

Item 1A. RISK FACTORS

Our business is subject to a number of risks, including those identified in Item 1A of Part I of our 2024 Form 10-K. There have been no material changes to the risk factors described in our 2024 Form 10-K.

Item 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

None.

Item 3. DEFAULTS UPON SENIOR SECURITIES

None.

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Item 4. MINE SAFETY DISCLOSURES

Not applicable.

Item 5. OTHER INFORMATION

Insider Trading Arrangements

During the three months ended September 30, 2025, none of the Company’s directors or officers (as defined in Rule 16a-1(f) of the Exchange Act) adopted or terminated a “Rule 10b5-1 trading arrangement,” and none of the Company’s directors or officers (as defined in Rule 16a-1(f) of the Exchange Act) adopted or terminated a “non-Rule 10b5-1 trading arrangement” (as such terms are defined in Item 408 of Regulation S-K of the Securities Act of 1933, as amended).

Item 6. EXHIBITS

​

Number |  | Description
3.1 | ​ | Amended and Restated Articles of Incorporation of the Company, as amended (incorporated by reference to Exhibit 3.1 to the Company’s Quarterly Report on Form 10-Q, filed with the SEC on November 16, 2015).
​ | ​ | ​
3.2 | ​ | Articles of Amendment to Amended and Restated Articles of Incorporation of the Company (incorporated by reference to Exhibit 3.1 to the registrant’s Current Report on Form 8-K (File No. 001-37544), filed with the SEC on April 24, 2017).
​ | ​ | ​
3.3 | ​ | Statement of Correction to Articles of Amendment to Amended and Restated Articles of Incorporation of the Company (incorporated by reference to Exhibit 3.2 to the Company’s Quarterly Report on Form 10-Q, filed on November 8, 2018).
​ | ​ | ​
3.4 | ​ | Articles of Amendment to Amended and Restated Articles of Incorporation of the registrant (incorporated by reference to Exhibit 3.1 to the Current Report on Form 8-K, filed with the SEC on December 18, 2018).
​ | ​ | ​
3.5 | ​ | Articles of Amendment to Amended and Restated Articles of Incorporation of the registrant (incorporated by reference to Exhibit 3.1 to the Current Report on Form 8-K, filed with the SEC on May 10, 2019).
​ | ​ | ​
3.6 | ​ | Articles of Amendment to Amended and Restated Articles of Incorporation of the registrant (incorporated by reference to Exhibit 3.1 to the Current Report on Form 8-K, filed with the SEC on December 11, 2019).
​ | ​ | ​
3.7 | ​ | Articles of Amendment to Articles of Incorporation of the Company (effective March 26, 2020) (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed with the SEC on March 30, 2020).
​ | ​ | ​
3.8 | ​ | Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit 3.5 to the Company’s Quarterly Report on Form 10-Q, filed with the SEC on August 14, 2019).
​ | ​ | ​
3.9 | ​ | Amendment to Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit 3.2 to the Company’s Current Report on Form 8-K, filed with the SEC on December 11, 2019).
​ | ​ | ​
3.10 | ​ | Amendment to Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed with the SEC on February 26, 2020).
​ | ​ | ​
4.1 | ​ | Reference is made to Exhibits 3.1 through 3.10.
​ | ​ | ​
10.1 | ​ | Credit and Security Agreement, dated August 11, 2025 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, filed with the SEC on August 12, 2025).
​ | ​ | ​

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31.1 | ​ | Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a).
​ | ​ | ​
31.2 |  | Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a).
​ | ​ | ​
32.1† |  | Certification of Principal Executive Officer Required by Rule 13a-14(b) or Rule 15d-14(b) and 18 U.S.C. 1350.
​ | ​ | ​
32.2† |  | Certification of Principal Financial Officer Required by Rule 13a-14(b) or Rule 15d-14(b) and 18 U.S.C. 1350.
​ | ​ | ​
101.INS |  | Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.
​ | ​ | ​
101.SCH |  | Inline XBRL Taxonomy Extension Schema Document.
​ | ​ | ​
101.CAL |  | Inline XBRL Taxonomy Extension Calculation Linkbase Document.
​ | ​ | ​
101.DEF |  | Inline XBRL Taxonomy Extension Definition Linkbase Document.
​ | ​ | ​
101.PRE |  | Inline XBRL Taxonomy Extension Presentation Linkbase Document.
​ | ​ | ​
101.LAB |  | Inline XBRL Taxonomy Extension Label Linkbase Document.
​ | ​ | ​
104 | ​ | Cover Page Interactive Data File Cover Page Interactive Data File (embedded within the Inline XBRL document)

​

† | The certifications furnished in Exhibits 32.1 and 32.2 hereto are deemed not “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall they be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

​

​

​

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

​

|  | ​ | ​
| ARMATA PHARMACEUTICALS, INC. ​
Date: November 12, 2025 |  | By | /s/ Deborah L. Birx
|  | ​ | Name: Deborah L. Birx, M.D.
|  | ​ | Title: Chief Executive Officer
|  | ​ | (Principal Executive Officer)
​ | ​ | ​ | ​
​ | ​ | By | /s/ David House
​ | ​ | ​ | Name: David House
​ | ​ | ​ | Title: Senior Vice President, Finance and Principal Financial Officer
​ | ​ | ​ | (Principal Financial Officer)

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