What changed in this filing

/stocks — the workspaceLOADING

Item 9A. Controls and Procedures

2022-02-28 compared with 2021-03-10 · 62 added, 35 removed, 119 unchanged (45% 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, 2021.

This annual report does not include an attestation report of the Company’s registered public accounting firm regarding internal control over financial reporting.

Management’s report was not subject to attestation by the Company’s registered public accounting firm pursuant to rules of the Securities and Exchange Commission that permit the Company to provide only management’s report in this Annual Report on Form 10-K.

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

In designing and evaluating the disclosure controls and procedures and internal control over financial reporting, management recognizes that any 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 and internal control over financial reporting must reflect the fact that there are resource constraints and that management is required to apply judgment in evaluating the benefits of possible controls and procedures relative to their costs.

Changes in internal control over financial reporting

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

Disclosure Regarding Foreign Jurisdictions that Prevent Inspections

Not applicable.

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 to be filed with the SEC in connection with our 2021 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2020.

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.

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

We intend to satisfy the disclosure requirement under Item 5.05 of Form 8-K regarding an amendment to, or waiver from, a provision of this Code of Business Conduct and Ethics by posting such information on our website, at the address and location specified above and, to the extent required by the listing standards of The Nasdaq Global Market, by filing a Current Report on Form 8-K with the SEC, disclosing such information.

We intend to disclose future amendments to certain provisions of the Code of Business Conduct and Ethics, and waivers of the Code of Business Conduct and Ethics granted to executive officers and directors, on our website listed above within four business days following the date of the amendment or waiver.

Executive Compensation

The information required by this item is incorporated by reference from our definitive Proxy Statement to be filed with the SEC in connection with our 2021 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2020.

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.

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.

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.

Exhibits, Financial Statement Schedules

14 unchanged sentences

Form of Indenture

Form of Class A Common Stock Purchase Warrant

Form of Class B Common Stock Purchase Warrant

Form of Warrant

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

Incorporation By Reference

Exhibit Description

Protagonist Therapeutics, Inc.

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.

8 unchanged sentences

Severance Agreement, dated August 1, 2016, by and between the Registrant and David Y.

Employment Offer Letter, dated May 21, 2018, by and between the Registrant and Samuel Saks, M.D.

Research and Collaboration Agreement, dated June 16, 2012, by and among the Registrant, Protagonist Pty.

4 unchanged sentences

and Zealand Pharma A/S.

Incorporation By Reference

Exhibit Description

Protagonist Assumption of Responsibility, dated January 28, 2014, by and between the Registrant and Zealand Pharma A/S.

3 unchanged sentences

and Zealand Pharma A/S.

Exclusive License and Collaboration Agreement, dated May 26, 2017, by and between the Registrant and Janssen Biotech, Inc.

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.

First Amendment to Exclusive License and Collaboration Agreement, by and between Protagonist Therapeutics, Inc.

and Janssen Biotech, Inc., dated May 7, 2019.

Offer Letter, by and between Protagonist Therapeutics Inc.

and Donald Kalkofen, dated May 20, 2019.

Incorporation By Reference

Exhibit Description

Severance Agreement, dated July 19, 2019, by and between Protagonist Therapeutics, Inc.

and Samuel Saks, M.D.

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

3 unchanged sentences

and Donald Kalkofen.

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

and Janssen Biotech, Inc.

Arbitration Resolution Agreement, dated August 4th, 2021, by and among Protagonist Therapeutics, Inc.

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.

List of Subsidiaries

Incorporation By Reference

Exhibit Description

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

7 unchanged sentences

Inline XBRL Taxonomy Extension Schema Document

Incorporation By Reference

Exhibit Description

Inline XBRL Taxonomy Extension Calculation Linkbase Document

2 unchanged sentences

Inline XBRL Taxonomy Extension Presentation Linkbase Document

Cover Page Interactive Data File – the cover page interactive data file does into appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document

Cover Page Interactive Data File – the cover page interactive data file does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document

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

6 unchanged sentences

PROTAGONIST THERAPEUTICS, INC.

March 10, 2021

February 28, 2022

/s/ Dinesh V.

7 unchanged sentences

President, Chief Executive Officer and Director

March 10, 2021

February 28, 2022

(Principal Executive Officer)

1 unchanged sentence

Chief Financial Officer

March 10, 2021

February 28, 2022

(Principal Financial and Accounting Officer)

2 unchanged sentences

Chairman of the Board of Directors

March 10, 2021

February 28, 2022

Selick, Ph.D.

/s/ Bryan Giraudo

March 10, 2021

February 28, 2022

Bryan Giraudo

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

March 10, 2021

February 28, 2022

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

/s/ Sarah O’Dowd

March 10, 2021

February 28, 2022

/s/ William D.

March 10, 2021

February 28, 2022

Williams, M.D., Ph.D.

March 10, 2021

February 28, 2022

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