What changed in this filing

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Item 9A. Controls and Procedures

2023-03-15 compared with 2022-02-28 · 36 added, 71 removed, 110 unchanged (49% of the section changed)

7 unchanged sentences

Based on its evaluation under the criteria set forth in Internal Control-Integrated Framework , our management concluded that our internal control over financial reporting was effective as of December 31, 2022.

Our independent registered public accounting firm, Ernst & Young LLP, has audited the effectiveness of our internal control over financial reporting as of December 31, 2021 as stated in their attestation report which is included herein.

Limitations on Effectiveness of Controls and Procedures and Internal Control over Financial Reporting

3 unchanged sentences

There have been no changes in our internal control over financial reporting that occurred during our most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Report of Independent Registered Public Accounting Firm

To the Stockholders and the Board of Directors of Protagonist Therapeutics, Inc.

Opinion on Internal Control over Financial Reporting

We have audited Protagonist Therapeutics, Inc.’s internal control over financial reporting as of December 31, 2021, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria).

In our opinion, Protagonist Therapeutics, Inc.

(the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2021, based on the COSO criteria.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2021 and 2020, the related consolidated statements of operations, comprehensive loss, stockholders’ equity and cash flows for each of the two years in the period ended December 31, 2021, and the related notes, and our report dated February 28, 2022 expressed an unqualified opinion thereon.

Basis for Opinion

The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s annual report on internal control over financial reporting.

Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit.

We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S.

federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB.

Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects.

Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances.

We believe that our audit provides a reasonable basis for our opinion.

Definition and Limitations of Internal Control Over Financial Reporting

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles.

A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company;

(2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company;

and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements.

Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

/s/ Ernst & Young LLP

Redwood City, California

February 28, 2022

Other Information

2 unchanged sentences

Directors, Executive Officers, and Corporate Governance

Except as set forth below, the information required by this item is incorporated by reference from our definitive Proxy Statement, under the headings “Proposal 1 – Election of Directors,” “Executive Officers,” “Director Compensation – Equity Compensation Plan Information” and, if applicable, “Delinquent Section 16(a) Reports,” to be filed with the SEC in connection with our 2022 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2021.

We have adopted a Code of Business Conduct and Ethics that applies to all directors, officers and employees, including our principal executive officer and principal financial officer.

Except as set forth below, the information required by this item is incorporated herein by reference to information in our definitive proxy statement relating to our 2023 Annual Meeting of Stockholders, which we expect to be filed with the SEC within 120 days of the end of our fiscal year ended December 31, 2022 (the “Proxy Statement”), including under the headings “Election of Directors,” “Executive Officers,” “Information Regarding Committees of the Board of Directors” and, if applicable, “Delinquent Section 16(a) Reports.”

We have adopted a Code of Business Conduct and Ethics that applies to all directors, officers and employees, including our principal executive, principal financial and principal accounting officers, or persons performing similar functions.

The Code of Business Conduct and Ethics is posted on our website at www.protagonist-inc.com.

1 unchanged sentence

Executive Compensation

The information required by this item is incorporated by reference from our definitive Proxy Statement, under the headings “Information Regarding the Committees of the Board of Directors – Compensation Committee,” “– Compensation Committee Interlocks and Insider Participation” and “Executive Compensation,” to be filed with the SEC in connection with our 2022 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2021.

The information required by this item is incorporated herein by reference to information in our Proxy Statement under the headings “Information Regarding Committees of the Board of Directors – Compensation Committee,” “– Compensation Committee Interlocks and Insider Participation” and “Executive Compensation.”

Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

The information required by this item is incorporated by reference from our definitive Proxy Statement, under the heading “Security Ownership of Certain Beneficial Owners and Management,” to be filed with the SEC in connection with our 2022 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2021.

The information required by this item is incorporated herein by reference to information in our Proxy Statement under the heading “Security Ownership of Certain Beneficial Owners and Management” and “Director Compensation – Equity Compensation Plan Information.”

Certain Relationships and Related Transactions, and Director Independence

The information required by this item is incorporated by reference from our definitive Proxy Statement, under the headings “Transactions with Related Persons and Indemnification” and “Information Regarding the Board of Directors and Corporate Governance – Independence of the Board of Directors,” to be filed with the SEC in connection with our 2022 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 20, 2021.

Principal Accounting Fees and Services

The information required by this item is incorporated by reference from our definitive Proxy Statement, under the heading “Proposal 2 – Ratification of Selection of Independent Registered Public Accounting Firm,” to be filed with the SEC in connection with our 2022 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2021.

The information required by this item is incorporated herein by reference to information in our Proxy Statement under the headings “Transactions with Related Persons and Indemnification” and “Information Regarding the Board of Directors and Corporate Governance – Independence of the Board of Directors.”

Principal Accountant Fees and Services

The information required by this item is incorporated by reference to information in our Proxy Statement under the heading “Ratification of Selection of Independent Registered Public Accounting Firm.”

Exhibits, Financial Statement Schedules

11 unchanged sentences

Specimen stock certificate evidencing the shares of common stock

Third Amended and Restated Investor Rights Agreement, by and among Protagonist Therapeutics, Inc.

and the stockholders named therein, dated July 31, 2016.

Form of Indenture

Form of Common Stock Warrant

Form of Preferred Stock Warrant

Form of Debt Securities Warrant

Description of Protagonist Therapeutics, Inc.’s Securities Registered Pursuant to Section 12 of the Exchange Act

1 unchanged sentence

2007 Stock Option and Incentive Plan, as amended and restated, and form of option agreement, exercise notice, joinder, and adoption agreement thereunder.

Incorporation By Reference

Exhibit Description

Protagonist Therapeutics, Inc.

3 unchanged sentences

Form of Indemnity Agreement for Directors and Officers.

Amended and Restated Protagonist Therapeutics, Inc.

2018 Inducement Plan, form of stock option grant notice, form of option agreement, form of restricted stock unit grant notice and form of restricted stock unit agreement.

Protagonist Therapeutics, Inc.

Amended and Restated 2018 Inducement Plan, and forms of stock option grant notice, option agreement, restricted stock unit grant notice and restricted stock unit agreement thereunder.

Lease, dated March 6, 2017, by and between the Registrant and BMR-Pacific Research Center LP.

3 unchanged sentences

and Zealand Pharma A/S.

Incorporation By Reference

Exhibit Description

Contract Extension Letter of Agreement, dated June 1, 2013, by and among the Registrant, Protagonist Pty.

7 unchanged sentences

and Zealand Pharma A/S.

Incorporation By Reference

Exhibit Description

Registration Rights Agreement, dated August 8, 2018, by and between the Registrant and certain parties identified on the signature pages thereto

5 unchanged sentences

and Suneel Gupta, Ph.D.

Offer Letter, by and between Protagonist Therapeutics Inc.

and Donald Kalkofen, dated May 20, 2019.

Credit and Security Agreement, dated October 30, 2019, by and between Protagonist Therapeutics, Inc., MidCap Financial, and Silicon Valley Bank.

Open Market Sale Agreement SM , dated November 27, 2019, by and between Protagonist Therapeutics, Inc.

Incorporation By Reference

Exhibit Description

Open Market Sale Agreement SM , dated August 5, 2022, by and between Protagonist Therapeutics, Inc.

and Jefferies LLC.

Severance Agreement, dated August 4, 2020, by and between Protagonist Therapeutics, Inc.

and Donald Kalkofen.

Second Amendment, dated July 2, 2021, to Lease, dated March 6, 2017, by and between Protagonist Therapeutics, Inc., as Tenant, and BMR-Pacific Research Center, LP as Landlord.

Amended and Restated License and Collaboration Agreement, dated July 27, 2021, by and between Protagonist Therapeutics, Inc.

2 unchanged sentences

and Zealand Pharma, A/S.

Second Amendment to Lease, dated August 10, 2021, by and between Protagonist Therapeutics, Inc., as Tenant, and BMR-Pacific Research Center, LP as Landlord.

Employment Offer Letter, by and between Protagonist Therapeutics Inc.

and Asif Ali, dated March 25, 2022.

Offer Letter, by and between Protagonist Therapeutics Inc.

and Arturo Molina, M.D., Ph.D., dated November 1, 2022.

Severance Agreement, by and between Protagonist Therapeutics Inc.

and Arturo Molina, M.D., Ph.D., dated November 7, 2022.

List of Subsidiaries

Incorporation By Reference

Exhibit Description

Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm

Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm

Consent of Independent Registered Public Accounting Firm

Power of Attorney (included in signature page of this Form 10-K)

1 unchanged sentence

Certification of Chief 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

Incorporation By Reference

Exhibit Description

Certification of Chief Executive Officer and Chief Financial Officer, as required by Rule 13a-14(b) or Rule 15d-14(b) and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C.

8 unchanged sentences

+ Indicates management contract or compensatory plan, contract or agreement.

† Confidential treatment has been granted for a portion of this exhibit.

† Certain identified information has been omitted by means of marking such information with asterisks in reliance on Item 601(b)(10)(iv) of Regulation S-K because it is both (i) not material and (ii) the type that the registrant treats as private or confidential.

* This certification attached as Exhibit 32.1 that accompanies this Annual Report on Form 10-K is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Protagonist Therapeutics, Inc.

under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of the Form 10-K, irrespective of any general incorporation language contained in such filing.

# Portions of this exhibit (indicated by hashtag) have been omitted as the registrant has determined that (i) the omitted information is not material and (ii) the omitted information would likely cause competitive harm to the registrant if publicly disclosed.

Form 10-K Summary

1 unchanged sentence

PROTAGONIST THERAPEUTICS, INC.

February 28, 2022

March 15, 2023

/s/ Dinesh V.

3 unchanged sentences

KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Dinesh V.

Patel and Don Kalkofen, and each of them, his true and lawful attorneys-in-fact, with full power of substitution, for him in any and all capacities, to sign any and all amendments to this Annual Report on Form 10-K, and to file the same, with exhibits thereto and other documents in connection therewith with the Securities and Exchange Commission, hereby ratifying and confirming all that said attorneys-in-fact or any of them or their substitute or substitutes may lawfully do or cause to be done by virtue thereof.

Patel and Asif Ali, and each of them, his true and lawful attorneys-in-fact, with full power of substitution, for him in any and all capacities, to sign any and all amendments to this Annual Report on Form 10-K, and to file the same, with exhibits thereto and other documents in connection therewith with the Securities and Exchange Commission, hereby ratifying and confirming all that said attorneys-in-fact or any of them or their 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 in the capacities and on the dates indicated:

1 unchanged sentence

President, Chief Executive Officer and Director

February 28, 2022

March 15, 2023

(Principal Executive Officer)

/s/ Don Kalkofen

Chief Financial Officer

February 28, 2022

Executive Vice President, Chief Financial Officer

March 15, 2023

(Principal Financial and Accounting Officer)

2 unchanged sentences

Chairman of the Board of Directors

February 28, 2022

March 15, 2023

Selick, Ph.D.

/s/ Bryan Giraudo

February 28, 2022

March 15, 2023

Bryan Giraudo

/s/ Sarah Noonberg, M.D., Ph.D.

February 28, 2022

March 15, 2023

Sarah Noonberg, M.D., Ph.D.

/s/ Sarah O’Dowd

February 28, 2022

March 15, 2023

/s/ William D.

February 28, 2022

March 15, 2023

Williams, M.D., Ph.D.

February 28, 2022

March 15, 2023

Williams, M.D., Ph.D.

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