aTYR PHARMA INC 10-Q

Item 5. Other Information 10b5-1 Trading Arrangements During the quarter ended June 30, 2026, no director or officer (as defined in Exchange Act Rule 16a-1(f)) adopted or terminated any "Rule 10b5-1 trading arrangement" or "non-Rule 10b5-1 trading arrangement" as those terms are defined in Item 408 of Regulation S-K. Costs Associated with Exit or Disposal Activities On August 7, 2026, our board of directors approved the implementation of a corporate restructuring and program prioritization plan (the Restructuring Plan) to streamline our operations and conserve capital prior to the potential initiation of the Planned Phase 3 Study. In connection with the Restructuring Plan, we committed to a reduction in our total workforce by approximately 60% to 20 full-time employees, and we estimate that the Restructuring Plan will reduce annualized operating expenses by approximately $13 million, beginning in the fourth quarter of 2026. We began notifying affected employees on August 7, 2026 and expect the Restructuring Plan to be substantially completed in the second half of 2026. We estimate that we will record charges of approximately $4.2 million for employee severance, employee health benefit obligations and other related termination benefits. Severance payments are expected to be paid in full between August 2026 and September 2027, and we expect to incur the charges in the third quarter of 2026. The charges that we expect to incur in connection with, or as a result of, the Restructuring Plan, are subject to a number of assumptions, and actual results may differ materially. We may also incur other charges or cash expenditures not currently contemplated due to events that may occur as a result of, or associated with, the Restructuring Plan. Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers. Chief Financial Officer and General Counsel Separation and Consulting Agreements On August 7, 2026, in connection with the Restructuring Plan, our board of directors approved the separation of employment of Jill M. Broadfoot as our Chief Financial Officer and Nancy E. Denyes as our General Counsel, expected to be effective September 30, 2026 (the actual date of such separation of employment, the Transition Date). We have offered Ms. Broadfoot and Ms. Denyes 63 Separation Agreements in connection with the separation of their employment (the Separation Agreements). Additionally, in connection with the transition support that Ms. Broadfoot and Ms. Denyes have agreed to provide, we, Ms. Broadfoot and Ms. Denyes will enter into Consulting Agreements expected to take effect October 1, 2026 (the Consulting Agreements). The Separation Agreements generally provide that, subject to Ms. Broadfoot’s and Ms. Denyes's execution of a general release and waiver of claims, we will provide Ms. Broadfoot and Ms. Denyes the following severance benefits in connection with the separation of their employment, consistent with our Executive Severance and Change in Control Policy (the Policy): we will pay Ms. Broadfoot and Ms. Denyes twelve months of their base salary, less taxes and withholdings, in installments over the twelve-month period following the Transition Date, we will reimburse Ms. Broadfoot’s and Ms. Denyes's premiums to continue healthcare coverage under COBRA for up to twelve months, and each of Ms. Broadfoot and Ms. Denyes will be entitled to acceleration of the time-based vesting provision of outstanding stock options for an additional twelve months following the date of separation. The Consulting Agreements generally provide that Ms. Broadfoot and Ms. Denyes will provide consulting assistance and transition support to us for up to twelve months following the Transition Date, or September 30, 2027, which may be extended upon mutual agreement by us, on the one hand, and Ms. Broadfoot or Ms. Denyes, on the other. The respective Consulting Agreement may be terminated by either us, Ms. Broadfoot or Ms. Denyes, as applicable, upon 15 days’ notice to the other party. We will pay Ms. Broadfoot and Ms. Denyes an hourly rate for the services they provide under the Consulting Agreements. Additionally, our board of directors approved extending the post-termination exercise periods of Ms. Broadfoot’s and Ms. Denyes's vested and outstanding stock options granted by us until three months following termination of their services under the Consulting Agreements. Receipt of the foregoing benefits are contingent upon Ms. Broadfoot and Ms. Denyes satisfying certain customary conditions as required by their respective Separation Agreement. The foregoing description of the Separation Agreements and the Consulting Agreements are only a summary of the terms thereof, do not purport to be complete and are each subject to, and qualified in their entirety by the complete text of the Separation Agreements and the Consulting Agreements, which we anticipate filing with our Quarterly Report on Form 10-Q for the three months ending September 30, 2026. Appointment of new Chief Financial Officer On August 7, 2026, our board of directors appointed Brandon Yaras, our Vice President, Finance, to succeed Ms. Broadfoot as our Chief Financial Officer and designated him as our “principal financial officer” and “principal accounting officer,” each within the meaning of Rule 16a-1(f) under the Exchange Act, all effective as of October 1, 2026. Mr. Yaras, age 40, has served as our Vice President, Finance since May 2022. Mr. Yaras has nearly 20 years of corporate finance and accounting experience, having overseen internal and external SEC reporting, forecasting and valuation, Sarbanes-Oxley compliance, payroll and equity administration and accounts payable. Prior to joining aTyr, from 2014 to 2022, he served as Director of Finance and Accounting for Arrowhead Pharmaceuticals, Inc., where he oversaw similar finance and accounting operations as well as procurement. Prior to that, he was Manager of Financial Planning and Analysis for Tutor Perini Corporation from 2009 to 2014. He began his career in the assurance practice at Deloitte & Touche LLP (Deloitte) and was an Audit Senior prior to leaving Deloitte. Mr. Yaras holds a B.A. in business economics with a minor in accounting from the University of California, Los Angeles and is a certified public accountant. There are no understandings or arrangements between Mr. Yaras and any other person pursuant to which he was appointed as our Chief Financial Officer, and there are no actual or proposed transactions between us and Mr. Yaras or any related person that would require disclosure under Item 404(a) of Regulation S-K. Mr. Yaras has no family relationship with any of our directors or executive officers. In connection with Mr. Yaras's appointment, we entered into an at-will employment offer letter with Mr. Yaras, dated August 7, 2026 and effective as of October 1, 2026 (the Employment Offer Letter), pursuant to which Mr. Yaras would become employed as the Chief Financial Officer of our company. Pursuant to the Employment Offer Letter, Mr. Yaras's annual base salary will be $350,000. Mr. Yaras is also eligible for a discretionary bonus target of up to 40% of his base salary based upon certain performance achievement goals. Pursuant to the Employment Offer Letter, Mr. Yaras will continue to be eligible to participate in our annual equity incentive award grants and will be granted an option to purchase 410,000 shares of our common stock (the Option) under our 2015 Stock Option and Incentive Plan, as amended, and subject to the terms and conditions set forth in the applicable notice of the award, with an exercise price equal to the closing price per share of our common stock as reported on the Nasdaq Capital Market on October 1, 2026. The Option is a non-qualified stock option and the shares subject to the Option will vest over a period of four years in equal monthly installments, subject to Mr. Yaras's continued employment on the applicable vesting date. We will also enter into our standard form of indemnification agreement with Mr. Yaras. In addition, Mr. Yaras is eligible to participate in the Policy as in effect from time to time. The purpose of the Policy is to 64 provide certain of our senior management employees with compensation and benefits in the event of a termination of employment without Cause or for Good Reason (as such terms are defined in the Policy). The post-termination compensation and benefits under the Policy include (i) acceleration of time-based vesting provisions of outstanding equity awards that would have vested within 12 months of the termination, (ii) severance in a lump sum in the amount of 12 months of base salary, and (iii) monthly payment of the employer portion of group health care benefits under COBRA for up to 12 months after termination. In addition, if the termination occurs within two months prior to or one year after the closing of a Sale Event (as defined in the Policy), then, in lieu of the benefits described above, the post-termination compensation and benefits under the Policy include (i) full acceleration of time-based vesting provisions of all outstanding equity awards, (ii) severance in a lump sum in the amount of 12 months of base salary, (iii) payment of the bonus target for the calendar year in which the termination occurred, and (iv) monthly payment of the employer portion of group health care benefits under COBRA for up to 12 months after termination. In each case, receipt of any compensation or benefits under the Policy is subject to Mr. Yaras’s execution of a severance agreement and release of claims. The foregoing description of the Employment Offer Letter is only a summary of the terms thereof, does not purport to be complete and is subject to, and qualified in its entirety by, the full text of the Employment Offer Letter, which is attached hereto as Exhibit 10.2 and incorporated into this Item 5 under the heading “Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers—Appointment of new Chief Financial Officer” by reference. The foregoing description of the Policy is only a summary of the terms thereof, does not purport to be complete and is subject to, and qualified in its entirety by the full text of the Policy, which we filed as Exhibit 10.16 to our Annual Report on Form 10-K for the year ended December 31, 2015, filed with the SEC on March 30, 2016, and which was most recently described in our definitive proxy statement on Schedule 14A, filed with the SEC on March 26, 2026, and is incorporated into this Item 5 under the heading “Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers” by reference. 65 Item 6. Exhibits Index to Exhibits Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 3.1 Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.1 November 14, 2022 3.2 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 June 28, 2019 3.3 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.3 May 12, 2020 3.4 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 4, 2021 3.5 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 April 29, 2022 3.6 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 19, 2023 3.7 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.7 May 15, 2026 3.8 Amended and Restated Bylaws of the Registrant 10-Q 333-203272 3.6 November 14, 2022 4.1 Specimen Common Stock Certificate S-1/A 333-203272 4.1 April 27, 2015 10.1 aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended 10-Q 001-37378 10.1 May 15, 2026 10.2 Employment Offer Letter by and between the Registrant and Brandon Yaras, dated August 7, 2026 — — — Filed herewith 10.3 Termination Agreement dated July 30, 2026, entered between aTyr Pharma, Inc. and Kyorin Pharmaceutical Co., Ltd. 8-K 001-37378 99.1 July 31, 2026 31.1 Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 31.2 Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 32.1# Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 32.2# Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 66 Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 101.INS Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document — — — Filed herewith 101.SCH Inline XBRL Taxonomy Extension Schema with Embedded Linkbase Document — — — Filed herewith 104 Cover Page Interactive Data File (embedded within the Inline XBRL document) — — — Filed herewith # The information in Exhibits 32.1 and 32.2 shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act (including this Quarterly Report), unless the Registrant specifically incorporates the foregoing information into those documents by reference. 67 SIGNAT URES 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. aTyr Pharma, Inc. Date: August 7, 2026 By: /s/ Sanjay S. Shukla Sanjay S. Shukla, M.D., M.S. President, Chief Executive Officer and Director (Principal Executive Officer) By: /s/ Jill M. Broadfoot Jill M. Broadfoot Chief Financial Officer (Principal Financial and Accounting Officer) 68