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Item 9A. Controls and Procedures

2025-02-27 compared with 2024-02-28 · 60 added, 31 removed, 151 unchanged (38% of the section changed)

11 unchanged sentences

We reviewed the results of management’s assessment with our Audit Committee.

Our internal control over financial reporting as of December 31, 2023 has been audited by BDO USA, P.C., an independent registered public accounting firm, as stated in their report which is included in Item 8 of this Annual Report.

Inherent Limitations on Effectiveness of Controls

13 unchanged sentences

The information required by this item is incorporated by reference from the information that will be set forth in the 2025 Proxy Statement.

The Company has adopted an insider trading policy which governs transactions in our securities by the Company and its directors, officers, employees, and consultants, and is reasonably designed to promote compliance with insider trading laws, rules and regulations, as well as listing standards, applicable to the Company.

A copy of our insider trading policy is filed with this Annual Report on Form 10-K as Exhibit 19.1.

EXECUTIVE COMPENSATION

19 unchanged sentences

3.3 Certificate of Amendment to the Amended and Restated Certificate of Incorporation of Codexis, Inc., filed with the Secretary of the State of the State of Delaware on June 14, 2023 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

3.4 Amended and Restated Bylaws of Codexis, Inc.

effective as of February 8 , 2024 (incorporated by reference to Exhibit 3.

1 to the Company’s Current Report on Form 8-K , filed on February 9, 2024 ).

3.4 Second A mended and Restated Bylaws of Codexis, Inc.

effective as of November 7 , 2024 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on November 12 , 2024).

4.1 Reference is made to Exhibits 3.1 through 3.4.

2 unchanged sentences

(incorporated by reference to Exhibit 4.1 to the Company’s Current Report on Form 8-K, filed on February 13, 2024).

Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934.

10.1A* Lease Agreement by and between the Company and Metropolitan Life Insurance Company dated as of February 1, 2004.

Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934 (incorporated by reference to Exhibit 4.

4 to the Company’s Annual Report on Form 10-K for the year ended December 31, 202 3 , filed on February 28, 202 4 ).

10.1A* Lease Agreement by and between the Company and Metropolitan Life Insurance Company comm e ncing as of February 1, 2004.

10.1B* Amendment to Lease Agreement by and between the Company and Metropolitan Life Insurance Company dated as of June 1, 2004.

5 unchanged sentences

10.1H Seventh Amendment to Lease by and between the Company and Metropolitan Life Insurance Company dated as of October 11, 2016 (incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2016, filed on November 8, 2016).

10.1I*** Eighth Amendment to Lease, dated as of February 8, 2019, by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2019, filed on May 8, 2019).

Eighth Amendment to Lease, dated as of February 8, 2019, by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2019, filed on May 8, 2019).

10.1J*** Ninth Amendment to Lease, dated as of December 4, 202 4 , by and between the Company and Metropolitan Life Insurance Company.

10.2+* Codexis, Inc.

24 unchanged sentences

2023 Employee Stock Purchase Plan (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

Amendment to the Codexis, Inc.

2023 Employee Stock Purchase Plan.

(incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 20 2 4 , filed on October 31, 2024 ).

Form of Indemnification Agreement between the Company and each of its directors, officers and certain employees (incorporated by reference to Exhibit 10.4 to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

3 unchanged sentences

Employment Agreement by and between the Company and Ross Taylor effective as of August 4, 2019 (incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed on November 6, 2019).

Transition and Separation Agreement by and between the Company and Ross Taylor, dated as of February 3, 2023 (incorporated by reference to Exhibit 10.

8B to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Transition and Separation Agreement by and between the Company and Ross Taylor, dated as of February 3, 2023 (incorporated by reference to Exhibit 10.8B to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Employment Agreement by and between the Company and John Nicols effective as of May 28, 2012 (incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2012, filed on August 9, 2012).

3 unchanged sentences

Transition and Separation Agreement by and between the Company and John Nicols, dated as of July 18, 2022 (incorporated by reference to Exhibit 10.1 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

Acquisition Agre ement by and among the Company, Societé des Produits Nestlé S.A., formerly known as Nestec Ltd.

Acquisition Agreement by and among the Company, Societé des Produits Nestlé S.A., formerly known as Nestec Ltd.

( “ Nestlé Health Science ” ), effective as of December 26, 2023.

(incorporated by reference to Exhibit 10.

11 to the Company’s Annual Report on Form 10-K for the year ended December 31, 20 23 , filed on February 28, 2024 ).

Lease Agreement by and between the Company and ARE-SAN FRANCISCO NO.

4 unchanged sentences

and ARE-San Francisco No.

63, LLC dated as of September 6, 2023 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2023, filed on November 3, 2023).

63, LLC dated as of September 6, 2023 (incorporated by reference to Exhibit 10.

2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2023, filed on November 3, 2023).

Employment Agreement by and between the Company and Stephen Dilly dated as of August 9, 2022 (incorporated by reference to Exhibit 10.2 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

1 unchanged sentence

Change in Control Severance Agreement by and between the Company and Kevin Norrett dated September 12, 2022 (incorporated by reference to Exhibit 10.4 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

Offer Letter by and between the Company and Margaret Fitzgerald dated as of October 5, 2022 (incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Change in Control Severance Agreement by and between the Company and Margaret Fitzgerald dated October 10, 2022 (incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Offer Letter by and between the Company and Sriram Ryali dated as of December 30, 2023 (incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Change in Control Severance Agreement by and between the Company and Sriram Ryali dated January 27, 2023 (incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

10.17 Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP.

, e ffective as of February 13, 2024

23.1 Consent of BDO USA, P.C., independent registered public accounting firm.

Offer Letter by and between the Company and Sriram Ryali dated as of December 30, 2023 (incorporated by reference to Exhibit 10.

2 3A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Change in Control Severance Agreement by and between the Company and Sriram Ryali dated January 27, 2023 (incorporated by reference to Exhibit 10.

23B to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Separation and Consulting Agreement by and between the Company and Sriram Ryali dated October 16, 2024 .

Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP., effective as of February 13, 2024 (incorporated by reference to Exhibit 10.17 to the Company's Annual Report on Form 10-K for the year ended December 31, 2023, filed on February 28, 2024).

First Amendment to the Loan and Security Agreement , dated May 1, 2024, by and between the Company and Innovatus Life Sciences Fund I, LP .

(incorporated by reference to Exhibit 10.

1 to the Company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2024 , filed on A u gust 8, 2024 ).

Second Amendment to the Loan and Security Agreement, dated December 20 , 2024, by and between the Company and Innovatus Life Sciences Fund I, LP.

Codexis, Inc.

2024 Inducement Plan (incorporated by reference to Exhibit 4.1 to the Company's Registration Statement on Form S-8 (File No.

333-281429) filed with the SEC on August 9, 2024).

Offer Letter by and between the Company and Georgia Erbez, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

3 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024 , filed on October 31 , 2024).

Change in Control Severance Agreement by and between the Company and Georgia Erbez, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

4 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

Offer Letter by and between the Company and Alison Moore, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

5 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

Change in Control Severance Agreement by and between the Company and Alison Moore, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

6 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

19.1 C odexis Insider Trading P olicy effective as of May 9, 2024

23.1 Consent of KPMG LLP , independent registered public accounting firm.

Consent of BDO USA, P.C.

, independent registered public accounting firm.

24.1 Power of Attorney (see signature page to this Annual Report on Form 10-K).

2 unchanged sentences

32.1** Certification of Principal Executive Officer and Principal Financial Officer Required Under Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended, and 18 U.S.C.

C odexis, Inc.

Clawback Policy effective August 24, 2023

Codexis, Inc.

Clawback Policy effective as of August 24, 2023

101 The following materials from Registrant’s Annual Report on Form 10-K for the fiscal year ended December 31, 2024 formatted in Inline Extensible Business Reporting Language (iXBRL) includes:

7 unchanged sentences

+ Indicates a management contract or compensatory plan or arrangement.

† Confidential treatment has been granted for certain information contained in this exhibit.

Such information has been omitted and filed separately with the Securities and Exchange Commission.

* Filed as exhibits to the registrant’s Registration Statement on Form S-1 (File No.

8 unchanged sentences

/s/ Stephen Dilly

President and Chief Executive Officer

Chairman of the Board of Directors, President, and Chief Executive Officer

(Principal Executive Officer)

POWER OF ATTORNEY

Each person whose individual signature appears below hereby authorizes and appoints Stephen Dilly, Sriram Ryali and Margaret Fitzgerald, and each of them, with full power of substitution and resubstitution and full power to act without the other, as his or her true and lawful attorney-in-fact and agent to act in his or her name, place and stead and to execute in the name and on behalf of each person, individually and in each capacity stated below, and to file any and all amendments to this annual report on Form 10-K and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing, ratifying and confirming all that said attorneys-in-fact and agents or any of them or their or his substitute or substitutes may lawfully do or cause to be done by virtue thereof.

Each person whose individual signature appears below hereby authorizes and appoints Stephen Dilly and Georgia Erbez, and each of them, with full power of substitution and resubstitution and full power to act without the other, as his or her true and lawful attorney-in-fact and agent to act in his or her name, place and stead and to execute in the name and on behalf of each person, individually and in each capacity stated below, and to file any and all amendments to this annual report on Form 10-K and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing, ratifying and confirming all that said attorneys-in-fact and agents or any of them or their or his substitute or substitutes may lawfully do or cause to be done by virtue thereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

SIGNATURE TITLE DATE

/s/ Stephen Dilly President, Chief Executive Officer and Director (Principal Executive Officer) Date:

/s/ Stephen Dilly Chairman of the Board of Directors, President, and Chief Executive Officer (Principal Executive Officer)

February 27, 2025

Stephen Dilly

/s/ Sriram Ryali Chief Financial Officer (Principal Financial and Accounting Officer) Date:

/s/ Georgia Erbez Chief Financial Officer (Principal Financial and Accounting Officer) Date:

February 27, 2025

Dorgan Chairman of the Board of Directors Date:

Georgia Erbez

/s/ Raymond De Vré Director Date:

February 27, 2025

/s/ Jennifer Aaker Director Date:

Raymond De Vré

Dorgan Director Date:

February 27, 2025

Jennifer Aaker

/s/ Esther Martinborough Director Date:

1 unchanged sentence

Esther Martinborough

/s/ Alison Moore Director Date:

February 28, 2024

Stewart Parker Director Date:

1 unchanged sentence

Stewart Parker

/s/ Christos Richards Director Date:

February 27, 2025

Christos Richards

/s/ Rahul Singhvi Director Date:

7 unchanged sentences

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures