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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION
Washington,

WASHINGTON, D.C. 20549

SCHEDULE 14A

Proxy Statement Pursuant to Section 14(a) of

the Securities Exchange Act of 1934 (Amendment
(Amendment
No.           )

Filed by the Registrant ☒
Filed by a Party other than the Registrant ☐
Check the appropriate box:

Preliminary Proxy Statement

Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))

Definitive Proxy Statement

Definitive Additional Materials

Soliciting Material under §240.14a-12
PROTAGONIST THERAPEUTICS, INC.
(Name of Registrant as Specified In Its Charter)
(Name of Person(s) Filing Proxy Statement, if other than The Registrant)
Payment of Filing Fee (Check all boxes that apply):

No fee required.

Fee paid previously with preliminary materials.

Fee computed on table in exhibit required by Item 25(b) per Exchange Act Rules 14a-6(i)(1) and 0-11.


Filed by the Registrantý

Filed by a Party other than the Registranto

Check the appropriate box:

o


Preliminary Proxy Statement

o


Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))

ý


Definitive Proxy Statement

o


Definitive Additional Materials

o


Soliciting Material under §240.14a-12


[MISSING IMAGE: lg_protagonist-pn.jpg]
PROTAGONIST THERAPEUTICS, INC.

(Name of Registrant as Specified In Its Charter)


(Name of Person(s) Filing Proxy Statement, if other than the Registrant)

Payment of Filing Fee (Check the appropriate box):

ý


No fee required.

o


Fee computed on table below per Exchange Act Rules 14a-6(i)(1) and 0-11.
(1)Title of each class of securities to which transaction applies:
(2)Aggregate number of securities to which transaction applies:
(3)Per unit price or other underlying value of transaction computed pursuant to Exchange Act Rule 0-11 (set forth the amount on which the filing fee is calculated and state how it was determined):
(4)Proposed maximum aggregate value of transaction:
(5)Total fee paid:

o


Fee paid previously with preliminary materials.

o


Check box if any part of the fee is offset as provided by Exchange Act Rule 0-11(a)(2) and identify the filing for which the offsetting fee was paid previously. Identify the previous filing by registration statement number, or the Form or Schedule and the date of its filing.



(1)


Amount Previously Paid:
(2)Form, Schedule or Registration Statement No.:
(3)Filing Party:
(4)Date Filed:

LOGO

7707 Gateway Blvd., Suite 140

Newark, CACalifornia 94560

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS


To Be Held On May 29, 2018

June 20, 2024

Dear Stockholder:

You are cordially invited to attend the 2024 Annual Meeting of Stockholders (the "Annual Meeting"“Annual Meeting”) of Protagonist Therapeutics, Inc., a Delaware corporation (the "Company"“Company”). The meeting will be held exclusively online via live audio webcast at www.virtualshareholdermeeting.com/PTGX2024on Tuesday, May 29, 2018Thursday, June 20, 2024 at 11:10:00 a.m. local time at Pacific Research Center, Conference Center, 7677 Gateway Blvd., Newark, CA 94560Time for the following purposes:

1.

To elect the Company's Board of Directors three Class II director nominees Chaitan Khosla, Ph.D., William D. Waddill and Lewis T. "Rusty" Williams, M.D., Ph.D., tonamed in the Board of DirectorsProxy Statement to hold office until the 20212027 Annual Meeting of Stockholders.

Stockholders and until their successors are duly elected and qualified.
2.

To approve, on an advisory basis, the compensation of the Company’s named executive officers.
3.
To ratify the selection by the Audit Committee of the Board of Directors of PricewaterhouseCoopersErnst & Young LLP as the Company’s independent registered public accounting firm of the Company for its fiscal year ending December 31, 2018.

3.
2024.
4.
To approve an amendment to the Company’s Certificate of Incorporation to increase the number of authorized shares of our common stock from 90,000,000 to 180,000,000.
5.
To conduct any other business that may be properly brought before the meeting.

meeting or any adjournment or postponement thereof.

These items of business are more fully described in the Proxy Statement accompanying this Notice.

The Annual Meeting will be held virtually this year. Online check-in will begin at 9:45 a.m. Pacific Time and you should allow ample time for the check-in procedures. You will not be able to attend the Annual Meeting in person.
The record date for the Annual Meeting is April 9, 2018.24, 2024. Only stockholders of record at the close of business on that date may vote at the meeting or any adjournment or postponement thereof.

To participate in the meeting, you must have your 16-digit control number shown on your Notice of Internet Availability of Proxy Materials or on the instructions that accompanied your proxy materials.

Instructions for accessing the virtual Annual Meeting are provided in the Proxy Statement. In the event of a technical malfunction or other situation that the meeting chair determines may affect the ability of the Annual Meeting to satisfy the requirements for a meeting of stockholders to be held by means of remote communication under the Delaware General Corporation Law, or that otherwise makes it advisable to adjourn the Annual Meeting, the meeting chair or secretary will convene the meeting at 11:00 a.m. Pacific Time on the date specified above and at the Company’s address specified above solely for the purpose of adjourning the meeting to reconvene at a date, time and physical or virtual location announced by the meeting chair or secretary. Under either of the foregoing circumstances, we will post information regarding the announcement on the Investors page of the Company’s website at www.protagonist-inc.com.
By Order of the Board of Directors,

/s/ Dinesh V. Patel, Ph.D.
/s/ Dinesh V. Patel

Dinesh V. Patel, Ph.D.
Dinesh V. Patel, Ph.D.
President and Chief Executive Officer

Newark, California

April 18, 2018

You are cordially invited to attend the meeting in person. 26, 2024

Whether or not you expect to attendparticipate in the meeting,virtual Annual Meeting, please complete, date, sign and return the proxy mailed to you, or vote over the telephone or the internet as instructed in these materials, as promptly as possible in order to ensure your representation at the meeting. A return envelope (which is postage prepaid if mailed in the United States) has been provided for your convenience. EvenAnnual Meeting. You may vote online or, if you have votedrequested printed copies of the proxy materials, by telephone or by using the proxy you may still vote in person if you attendcard or voting instruction form provided with the meeting. Please note, however, that if your shares are held of record by a broker, bank or other nominee and you wish to vote at the meeting, you must obtain aprinted proxy issued in your name from that record holder.


LOGO

materials.




[MISSING IMAGE: lg_protagonist-pn.jpg]
7707 Gateway Blvd., Suite 140

Newark, CACalifornia 94560

PROXY STATEMENT

FOR THE 20182024 ANNUAL MEETING OF STOCKHOLDERS

Tuesday, May 29, 2018

Thursday, June 20, 2024
QUESTIONS AND ANSWERS ABOUT THESE PROXY MATERIALS AND VOTING

Why did I receive a notice regarding theof internet availability of proxy materials on the internet?

materials?

Pursuant to rules adopted by the Securities and Exchange Commission (the "SEC"“SEC”), we have elected to provide access to our proxy materials over the internet. Accordingly, we have sent you a Notice of Internet Availability of Proxy Materials (the "Notice"“Notice”) because the Board of Directors (the “Board”) of Protagonist Therapeutics, Inc. (sometimes referred to as the "Company"“Company” or "Protagonist"“Protagonist”) is soliciting your proxy to vote at the 20182024 Annual Meeting of Stockholders (the “Annual Meeting”), including at any adjournments or postponements of the meeting. All stockholdersStockholders will have the ability to access the proxy materials on the website referred to in the Notice or may request to receive a printed set of the proxy materials.materials to be sent to them free of charge. Instructions on how to access the proxy materials over the internet or to request a printed copy may be found in the Notice.

We intend to mail the Notice on or about April 18, 201826, 2024 to all stockholders of record entitled to vote at the annual meeting.

Annual Meeting.

Will I receive any other proxy materials by mail?

We may send you a proxy card, along with a second Notice, on or after April 28, 2018.

May 6, 2024.

How do I attend and participate in the Annual Meeting?

The meetingAnnual Meeting will be held virtually via live audio webcast at www.virtualshareholdermeeting.com/PTGX2024on Tuesday, May 29, 2018Thursday, June 20, 2024 at 11:10:00 a.m. local time at Pacific Research Center, Conference Center, 7677 Gateway Blvd., Newark, CA 94560. DirectionsTime. You will not be able to attend the Annual Meeting may be foundin person. Stockholders of record as of the close of business on the record date are entitled to participate in and vote at the Annual Meeting. To participate in the "Events & Presentations" sectionAnnual Meeting, including to vote and ask questions, stockholders of record should go to the Company'smeeting website at www.protagonist-inc.com.listed above, enter the 16-digit control number found on your proxy card or Notice, and follow the instructions on the website. Information on how to vote in persononline at the Annual Meeting is discussed below.

Online check-in will begin at 9:45 a.m. Pacific Time and stockholders should allow ample time for the check-in procedures. If your shares are held in the name of your broker, bank or other nominee (sometimes referred to as shares held in “street name”) and your voting instruction form or Notice indicates that you may vote those shares through www.proxyvote.com, then you may access, participate in and vote at the Annual Meeting with the 16-digit access code indicated on that voting instruction form or Notice. Otherwise, stockholders who hold their shares in street name should contact their bank, broker or other nominee (preferably at least five days before the Annual Meeting) and obtain a “legal proxy” in order to be able to attend, participate in or vote at the Annual Meeting.

Conducting the Annual Meeting virtually increases the opportunity for all stockholders to participate and communicate their views to a much wider audience. The virtual meeting is designed to provide the same rights and advantages of a physical meeting. Stockholders will be able to submit questions online during the meeting, providing our stockholders with the opportunity for meaningful engagement with the Company. Questions must comply with the meeting rules of conduct, which will be posted on the virtual meeting website.

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We will endeavor to answer as many stockholder-submitted questions as time permits that comply with the Annual Meeting rules of conduct. We reserve the right to edit profanity or other inappropriate language and to exclude questions regarding topics that are not pertinent to meeting matters or Company business. If we receive substantially similar questions, we may group such questions together and provide a single response to avoid repetition.
Who can vote at the Annual Meeting?

Only stockholders of record at the close of business on April 9, 201824, 2024 (the “Record Date”) will be entitled to vote at the Annual Meeting. On this record date,the Record Date, there were 21,183,71958,643,133 shares of common stock outstanding and entitled to vote.

Stockholder of Record: Shares Registeredrecord: shares registered in Your Name

your name

If on April 9, 2018the Record Date, your shares were registered directly in your name with Protagonist'sthe Company’s transfer agent, American Stock Transfer &Equiniti Trust Company, LLC, then you are a stockholder of record. As a stockholder of record, you may vote in persononline at the meetingAnnual Meeting or vote by proxy. Whether or not you plan to attend the meeting,Annual Meeting, we urge you to fill outvote and returnsubmit your proxy in advance of the enclosed proxy cardAnnual Meeting. For information on how to ensure your vote is counted.

prior to the Annual Meeting, see “How do I vote?”

Beneficial Owner: Shares Registeredowner: shares registered in the Namename of a Brokerbroker or Bank

bank

If on April 9, 2018,the Record Date, your shares were held, not in your name, but rather in an account at a brokerage firm, bank, dealer or other similar organization, then you are the beneficial owner of shares held in "street name"“street name” and the Notice is being forwarded to you by that organization. The organization holding your account is considered to be the stockholder of record for purposes of voting at the Annual Meeting. As a beneficial owner, you have the right to direct your broker or other agent regarding how to vote the shares in your account. You are also invited to attend the Annual Meeting. However, since you are not the stockholder of record, you may not vote your shares in person at the meeting unless you request and obtain a valid proxy from your broker or other agent.

Meeting virtually via live webcast.

What am I voting on?

There are twofour matters scheduled for a vote:


Proposal No. 1—1 — To elect the three Class II director nominees named herein to our Board of Directors to hold office until the 2021 annual meeting2027 Annual Meeting of stockholders and until their successors are duly elected and qualified, subject to their earlier resignation or removal; and

Stockholders;

Proposal No. 2—2 — To approve, on an advisory basis, the compensation of the Company’s named executive officers;

Proposal No. 3 — To ratify the selection by the Audit Committee of the Board of Directors of PricewaterhouseCoopersErnst & Young LLP as the Company’s independent registered public accounting firmauditor for 2024; and

Proposal No. 4 — To approve an amendment to the Company’s Certificate of Incorporation to increase the Company for its fiscal year ending December 31, 2018.

Asnumber of authorized shares of our common stock from 90,000,000 to 180,000,000.

How does the date of this proxy statement, we are not aware of any other mattersBoard recommend that will be presented for consideration at the Annual Meeting.

I vote?

The Board recommends that you vote your shares “FOR ALL” director nominees in Proposal No. 1 and “FOR” Proposals Nos. 2, 3 and 4.
What if another matter is properly brought before the meeting?

The Board knows of no other matters that will be presented for consideration at the Annual Meeting. If any other matters are properly brought before the meeting, it is the intention of the persons named in the accompanying proxy to vote on those matters in accordance with their best judgment.

How do I vote?

You may either vote "For" all the nominees

With respect to the Boardelection of directors, you may vote “FOR ALL” the Class II director nominees or you may "Withhold"WITHHOLD ALL” or withhold your vote for anya specific nominee you specify. ForWith respect to: (i) the

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ratification of the selection by the Audit Committee of the Board of PricewaterhouseCoopersErnst & Young LLP as the Company’s independent registered public accounting firmauditor for 2024, (ii) the advisory approval of executive compensation and (iii) the approval of the Company foramendment to the fiscal year ending December 31, 2018,Company’s Certificate of Incorporation to increase the number of authorized shares of common stock, you may vote "For"FOR,” “AGAINST or "Against" or abstain from voting.

The procedures for voting are fairly simple:

ABSTAIN.”

Stockholder of Record: Shares Registeredrecord: shares registered in Your Name

your name

If you are a stockholder of record, you may vote in person atonline during the live webcast of the Annual Meeting, vote by proxy over the telephone, vote by proxy through the internet or, if you request paper copies of the proxy materials, vote by proxy usingover the telephone or by mailing a proxy card that you may request or that we may elect to deliver at a later time.card. Whether or not you plan to attend the meeting online, we urge you to vote by proxy to ensure your vote is counted. You may still attend the meeting and vote in persononline even if you have already voted by proxy.


To vote online at the Annual Meeting, you must be present via live webcast. To vote live during the meeting, please visit www.virtualshareholdermeeting.com/PTGX2024 and have available the 16-digit control number included in person, comeyour Notice.

To vote through the internet prior to the Annual Meeting, and wego to www.proxyvote.com to complete an electronic proxy card. You will givebe asked to provide certain information from the Notice. Your internet vote must be received by 11:59 p.m. Eastern Time on June 19, 2024 to be counted.

If you a ballot when you arrive.

Torequested paper copies of the proxy materials, to vote using the proxy card, simply complete, sign and date the proxy card that may be delivered and return it promptly in the envelope provided. If you return yourYour signed proxy card tomust be received by us before the Annual Meeting we will vote your shares asto be counted.

If you direct.

Torequested paper copies of the proxy materials, to vote over the telephone prior to the Annual Meeting, dial toll-free 1-800-690-6903 using a touch-tone phone and follow the recorded instructions. You will be asked to provide the company number and control

      numbercertain information from the Notice. Your telephone vote must be received by 11:59 p.m., Eastern Time on May 28, 2018June 19, 2024 to be counted.

    To vote through the internet, go to www.proxyvote.com to complete an electronic proxy card. You will be asked to provide the company number and control number from the Notice. Your internet vote must be received by 11:59 p.m., Eastern Time on May 28, 2018 to be counted.

Beneficial Owner: Shares Registeredowner: shares registered in the Namename of Brokera broker or Bank

bank

If you are a beneficial owner of shares registered in the name of your broker, bank or other agent, you should have received Notice containing voting instructions from that organization rather than from Protagonist. Simply follow the voting instructions in the Notice to ensure that your vote is counted. To vote in person at the Annual Meeting, you must obtain a valid proxy fromYou may direct your broker, bank or other agent. Followagent how to vote in advance of the Annual Meeting by following the instructions from your brokerthey provide, or bank included with these proxy materials or contact your broker or bank to request a proxy form.

Internet proxy votingyou may be provided to allow you to vote your shares online with procedures designed to ensureduring the authenticityvirtual Annual Meeting (see “How do I attend and correctness of your proxy vote instructions. However, please be aware that you must bear any costs associated with your internet access, such as usage charges from internet access providers and telephone companies.

participate in the Annual Meeting?” above).

How many votes do I have?

On each matter to be voted upon, you have one vote for each share of common stock you own as of April 9, 2018.

the Record Date.

What happens if I do not vote?

Stockholder of Record: Shares Registeredrecord: shares registered in Your Name

your name

If you are a stockholder of record and do not vote by completing your proxy card, by telephone, through the internet or in persononline at the Annual Meeting, your shares will not be voted.

voted and will not be counted towards the quorum requirement.

Beneficial Owner: Shares Registeredowner: shares registered in the Namename of Brokera broker or Bank

bank

If you are a beneficial owner of shares registered in the name of your broker, bank or other nominee (sometimes referred to as shares held in "street name"),“street name” and you do not provide the broker or other nominee that holds your shares with voting instructions, the question of whether your broker or nominee will still be able to vote your shares depends on whether the particular proposal is a "routine"“routine” matter. Brokers and other nominees can use their discretion to vote "uninstructed"“uninstructed” shares with respect to matters that are considered to be "routine,"“routine” but not with respect to "non-routine"“non-routine” matters. "Non-routine" matters are matters that may substantially affect the rights or privileges of stockholders, such as mergers, stockholder proposals, elections of directors (even if not contested), executive compensation, and certain corporate governance proposals, even if management-supported. Proposal 1Whether a proposal is considered "non-routine"routine or non-routine is subject to stock exchange rules and Proposal 2final determination by the stock exchange. Even with respect to

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routine matters, some brokers are choosing not to exercise discretionary voting authority. As a result, we urge you to direct your broker, bank or other nominee how to vote your shares on all proposals to ensure that your vote is considered "routine."

counted.

What if I am a stockholder of record and return a proxy card or otherwise vote but do not make specific choices?

If you are a stockholder of record and return a signed and dated proxy card or otherwise vote without marking voting selections, your shares will be voted as applicable:

    "For"in accordance with the election of three Class II nominees for director; and

    "For" the ratification of PricewaterhouseCoopers LLP as the independent registered public accounting firmrecommendations of the Company for its fiscal year ending December 31, 2018.

Board. If any other matter is properly presented at the Annual Meeting, your proxyholder (one of the individuals named on your proxy card) will vote your shares using his or her best judgment.

Who is paying for this proxy solicitation?

We will pay for the entire cost of soliciting proxies. In addition to these proxy materials, our directors, officers and employees may also solicit proxies in person, by telephone or by other means of communication. Directors and employeescommunication, but will not be paid any additional compensation for soliciting proxies. We may also reimburse brokerage firms, banks and other agents for the cost of forwarding proxy materials to beneficial owners.

What does it mean if I receive more than one Notice?

If you receive more than one Notice, your shares may be registered in more than one name or in different accounts. Please follow the voting instructions on the Noticescast your vote with respect to each set of proxy materials that you receive to ensure that all of your shares are voted.

Can I change my vote after submitting my proxy?

Stockholder of Record: Shares Registeredrecord: shares registered in Your Name

Yes. your name

You can revoke your proxy at any time before the final vote at the meeting. If you are the record holder of your shares, you may revoke your proxy in any one of the following ways:


You may submit another properly completed proxy card with a later date.


You may grant a subsequent proxy by telephone or through the internet.


You may send a timely written notice that you are revoking your proxy to Protagonist'sProtagonist’s Corporate Secretary at 7707 Gateway Blvd., Suite 140, Newark, CACalifornia 94560.


You may attend the Annual Meeting and vote online by visiting www.virtualshareholdermeeting.com/PTGX2024. To attend the meeting, you will need the 16-digit control number included in person.your Notice or on the instructions that accompanied your proxy materials. Simply attending the meeting will not, by itself, revoke your proxy.

Your most current proxy card or telephone or internet proxylast submitted vote is the one that iswill be counted.

Beneficial Owner: Shares Registeredowner: shares registered in the Namename of Brokera broker or Bank

bank

If your shares are held by your broker, bank or bank as aother nominee, or agent, you should follow the instructions provided by your broker, bank or bank.

other nominee with respect to changing your vote.

When are stockholder proposals and director nominations due for next year'syear’s Annual Meeting?

To

Pursuant to Rule 14a-8 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), to be considered for inclusion in next year'syear’s proxy materials, your proposal must be submitted in writing by December 19, 2018, to Protagonist'sour Corporate Secretary at 7707 Gateway Blvd., Suite 140, Newark, CA 94560. If you wish to submitthe address set forth on the first page of this Proxy Statement. Such proposals must be received by us as of the close of business (6:00 p.m. Pacific Time) on December 27, 2024 and must comply with the requirements of Rule 14a-8. The submission of a stockholder proposal (including a director nomination) at the meetingdoes not guarantee that is not toit will be included in next year'sthe proxy materials,statement.

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As set forth in our Amended and Restated Bylaws (the “Bylaws”), if you intend to make a nomination for director election or present a proposal for other business (other than pursuant to Rule 14a-8 of the Exchange Act) at the 2025 Annual Meeting of Stockholders, you must provide the information specified informationin our Bylaws in writing to our corporateCorporate Secretary at the address above no earlier than January 29, 2019February 20, 2025 and no later than February 28, 2019;the close of business (6:00 p.m. Pacific Time) on March 22, 2025; provided, however, that if our 20192025 Annual Meeting of Stockholders is held before April 29, 2019,May 21, 2025 or after June 28, 2019,July 20, 2025, notice by the stockholder to be timely must be received no earlier than the close of business on the 120th day prior to such Annual Meetingannual meeting and not later than the close of business on the later of the 90th day prior to such Annual Meetingannual meeting or the tenth (1010th) day following the day on which public announcement of the date of such meeting is first made. Any such director nomination or stockholder proposal must be a proper matter for stockholder action and must comply with the terms and conditions set forth in our Bylaws. If you fail to meet these deadlines or fail to satisfy the requirements of Rule 14a-4 of the Exchange Act, we may exercise discretionary voting authority under proxies we solicit to vote on any such proposal as we determine appropriate. In addition to satisfying the deadlines and other requirements in the advance notice provisions of our Bylaws, if you intend to solicit proxies in support of nominees submitted under these advance notice provisions for the 2025 Annual Meeting of Stockholders, you must provide the notice required under Rule 14a-19 of the Exchange Act to our Corporate Secretary in writing not later than the close of business (6:00 p.m. Pacific Time) on April 21, 2025. You are also advised to review our Amended and Restated Bylaws, which contain additional requirements about the advance notice of stockholder proposalsdirector nominations and director nominations.

proposal for other business (other than pursuant to Rule 14a-8 of the Exchange Act). We reserve the right to reject, rule out of order or take other appropriate action with respect to any nomination or proposal that does not comply with these and other applicable requirements.

Who will count the votes?

How are votes counted?

Votes will be counted by Broadridge Financial Solutions, the inspector of election appointed for the meeting, who will separately count, (i) for the proposal to elect directors, votes "For," "Withhold" and broker non-votes; and (ii) with respect to Proposal 2 and any other proposals, votes "For" and "Against," abstentions and, if applicable, broker non-votes. Abstentions will be counted towards the vote total for Proposal 2 and will have the same effect as "Against" votes. Broker non-votes have no effect and will not be counted towards the vote total for any proposal.

meeting.

What are "broker non-votes"?

“broker non-votes?”

As discussed above, when a beneficial owner of shares held in "street name"“street name” does not give instructions to the broker or other nominee holding the shares as to how to vote, the broker or other nominee cannot vote those shares on matters deemed to be "non-routine," the broker or nominee cannot vote the shares.“non-routine.” These unvoted shares are counted as "brokerconsidered “broker non-votes."


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How many votes are needed to approve each proposal?

The following table summarizes the minimum vote needed to approve each proposal and the effect of abstentions and broker non-votes.

non-votes, if any.
Proposal
Number
Description
Proposal
Number
Proposal DescriptionVote Required for ApprovalEffect of
Abstentions
Effect of AbstentionsEffect of
Broker

Non-Votes,
If Any
1Election of DirectorsClass II director nomineesNominees receivingFOR” votes from the most "For" votes; withheldplurality of votes will have no effect.cast on the matterUnder plurality voting, there are no abstentions.abstentions; votes that are withheld will have no effect on the matterNone

2


Ratification
Advisory approval of the selectioncompensation of PricewaterhouseCoopers LLP as the Company's independent registered public accounting firm for fiscal year ending December 31, 2018our named executive officers

"For"
FOR votes from the holders of a majority of shares present in person or represented by proxyduring the meeting and entitled to vote on the matter.matter

Against

Against

None
3Ratification of the selection of Ernst & Young LLP as the Company’s independent auditor for 2024FOR” votes from the majority of shares present or represented during the meeting and entitled to vote on the matterAgainstNone
4Approval of an amendment to our Certificate of Incorporation to increase the number of authorized shares of common stockFOR” votes from the majority of votes cast on the matterNoneNone

What is the quorum requirement?

A quorum of stockholders is necessary to hold a validtransact business at the meeting. A quorum will be present if stockholders holding a majority of the outstanding shares entitled to vote are present at the meeting in persononline or represented by proxy. On the record date, there were 21,183,719 shares outstanding and entitled to vote. Thus, the holders of 10,591,860 shares must be present in person or represented by proxy at the meeting to have a quorum.

Your shares will be counted towards the quorum only if you submit a valid proxy (or one is submitted on your behalf by your broker, bank or other nominee) or if you vote in persononline at the meeting. Abstentions and broker non-votes, if any, will be counted towards the quorum requirement. If there is no quorum, the chairperson of the meeting chair or the holders of a majority of shares present at the meeting in persononline or represented by proxy may adjourn the meeting to another time or date.

How can I find out the results of the voting at the Annual Meeting?

Preliminary voting results will be announced at the Annual Meeting. In addition, final voting results will be published in a Current Report on Form 8-K that we expect to file within four business days after the Annual Meeting. If final voting results are not available
Important Notice Regarding the Availability of Proxy Materials for the 2024 Annual Meeting of Stockholders to us in time to file a CurrentBe Held on June 20, 2024. The Proxy Statement and Annual Report on Form 8-K10-K for the
year ended December 31, 2023 are available at
www.proxyvote.com.

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LEGAL MATTERS
Forward-Looking Statements.   The Proxy Statement may contain “forward-looking statements” within four business days after the meeting, we intendmeaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, which statements are subject to file a Currentsubstantial risks and uncertainties and are based on estimates and assumptions. All statements other than statements of historical fact included in the Proxy Statement are forward-looking statements, including statements about the Company’s Board, corporate governance practices, executive compensation program, equity compensation utilization and environmental, social and governance (“ESG”) initiatives. In some cases, you can identify forward-looking statements by terms such as “may,” “might,” “will,” “objective,” “intend,” “should,” “could,” “can,” “would,” “expect,” “believe,” “design,” “estimate,” “predict,” “potential,” “plan” or the negative of these terms, and similar expressions intended to identify forward-looking statements. These statements involve known and unknown risks, uncertainties and other factors that could cause our actual results to differ materially from the forward-looking statements expressed or implied in the Proxy Statement. Such risks, uncertainties and other factors include those identified in the Company’s Annual Report on Form 8-K10-K for the year ended December 31, 2023 filed with the SEC and other subsequent documents we file with the SEC. The Company expressly disclaims any obligation to publish preliminary resultsupdate or alter any statements whether as a result of new information, future events or otherwise, except as required by law.
Website References.   Website references throughout this document are inactive textual references and within four business days afterprovided for convenience only, and the final results are known to us, file an additional Current Report on Form 8-K to publish the final results.

What proxy materials are availablecontent on the internet?

The annual report to stockholdersreferenced websites is available at www.proxyvote.com.

not incorporated herein by reference and does not constitute a part of the Proxy Statement.

Use of Trademarks.   Protagonist Therapeutics is the trademark of Protagonist Therapeutics, Inc. Other names and brands may be claimed as the property of others.



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PROPOSAL 1

ELECTION OF DIRECTORS

Protagonist'sCLASS II DIRECTOR NOMINEES

Protagonist’s Board is divided into three classes. Each class consists as nearly as possible, of approximately one-third of the total number of directors, and each class hasis elected for a three-year term. Vacancies on the Board may be filled only by persons elected by a majority of the remaining directors. A director elected by the Board to fill a vacancy in a class, including vacancies created by an increase in the number of directors, shall serve for the remainder of the full term of that class and until the director'sdirector’s successor is duly elected and qualified.

The Board presently hascurrently consists of seven members. There are three directors in the class whose termThe terms of office expires in 2018. Each nominee is recommended for election by theof our three Class II directors expire at this Annual Meeting. The Nominating and Corporate Governance Committee has recommended Sarah A. O’Dowd, William D. Waddill and Lewis T. “Rusty” Williams, M.D., Ph.D. for election to the Board at this Annual Meeting. Each of these nominees is currently a director of the Board. Dr. KhoslaCompany and Mr. Waddill werewas previously elected by stockholders at the stockholders, and Dr. Williams joined the Board in June 2017.2021 Annual Meeting of Stockholders. If elected at the Annual Meeting, each of these nomineesthe three Class II directors would serve until the 20212027 Annual Meeting of Stockholders and until his successor hastheir respective successors have been duly elected and qualified, or, if sooner,earlier, until the director'stheir death, resignation or removal. It is the Company'sCompany’s policy to encourage the directors and director nominees for director to attend Annual Meetings of Stockholders. Six of our directors then-serving on the Board attended the 2023 Annual Meeting.

Meeting of Stockholders.

Directors are elected by a plurality of the votes of the holders of shares present in person or represented by proxy and entitled to vote on the election of directors.cast. Accordingly, the three nominees receiving the highest number of affirmative votes will be elected. Shares represented by executed proxies will be voted, if authority to do so is not withheld, for the election of the three nominees named below. If any nominee becomes unavailable for election as a result of an unexpected occurrence,or unable to serve, shares that would have been voted for that nominee will instead be voted for the election of a substitute nominee proposed by Protagonist.the Board or the Board may decrease its size. Each person nominated for election has agreed to serve if elected. The Company'sCompany’s management has no reason to believe that any nominee will be unable to serve.

The brief biographies below include information, as of the date of this proxy statement,Proxy Statement, regarding the specific and particular experience,experiences, qualifications, attributes or skills of each nominee for director. In addition, following the biographies of the nominees are the biographies of Class Idirector and Class III directors containing information regarding each director continuing in office that caused the Nominating and Corporate Governance Committee and the Board to determine that the applicable nominee or director should serve onas a member of the Board.

CLASS II DIRECTOR NOMINEES FOR ELECTION TO CLASS II FOR A THREE-YEAR TERMTERMS EXPIRING AT THE 20212027 ANNUAL MEETING

Chaitan Khosla, Ph.D.

Dr. Khosla, 53,

Sarah A. O’Dowd
Ms. O’Dowd, 74, has served as a member of the Board since October 2014. Dr. Khosla was the scientific founder andAugust 2020. Ms. O’Dowd is a member of the Boardboard of Directorsdirectors of Alvine Pharmaceuticals from 2005 until 2016. Prior to Alvine Pharmaceuticals, Dr. Khosla foundedIchor Holdings, Ltd. (Nasdaq: ICHR), a leader in the design, engineering and wasmanufacturing of critical fluid delivery subsystems and components for semiconductor capital equipment, and is a director of Kosan Biosciences,the Independent Institute, a non-profit, non-partisan, public policy research and communications organization. Until her retirement in March 2020, she was Senior Vice President and Chief Legal Officer at Lam Research Corporation (Nasdaq: LRCX), an S&P 500 technology company. For 11 years at Lam, she served as Chief Legal Officer and Secretary. From 2009 to 2012 she also served as Group Vice President of Human Resources at Lam. From February 2007 to September 2008, she served as Vice President of FibroGen, Inc. (Nasdaq: FGEN), a biopharmaceutical company. Ms. O’Dowd received a J.D. from 1995 until it was acquired by BristolMyers SquibbStanford Law School, an M.A. in 2008. Dr. Khosla has been a Professor of Chemical Engineering and Chemistry atCommunications from Stanford University since 2001 and has been a faculty member since 1992. Since 2013, he has served as the founding Director of Stanford ChEM-H. Dr. Khosla is an elected member of the American Academy of Arts & Sciences and the National Academy of Engineering. He is the recipient of several awards, including the 1999 Alan T. Waterman award by the National Science Foundation, the 1999 Eli Lilly AwardA.B. in biological chemistry and the 2000 ACS Award in Pure Chemistry. Dr. Khosla is the author of over 300 publications and is an inventor on over 75 issued U.S. patents. Dr. Khosla received a Ph.D.Mathematics from the California Institute of Technology.Immaculata College. The Company believes that Dr. Khosla is qualified to serve on the Board because of hisher executive business experience as a founder, consultant and director of biotechnology companies and his expertisewell as her experience in the biotechnology field.

field and at public companies, Ms. O’Dowd is well positioned to make valuable contributions and provide valuable guidance to the Board.

William D. Waddill

Mr. Waddill, 61,67, has served as a member of the Board since July 2016. From April 2014 to December 2016, Mr. Waddill served as Senior Vice President and Chief Financial Officer, Treasurer and Secretary of Calithera Biosciences, Inc. (OTCMKTS: CALA), a biotechnology company. From October 2007 to March 2014, Mr. Waddillhe served as Senior Vice President and Chief Financial Officer of OncoMed Pharmaceuticals,

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Inc., a biopharmaceutical company. From October 2006 to September 2007, Mr. Waddill served as the Senior Vice President, Chief Financial Officer of Ilypsa, Inc., a biotechnology company that was acquired in 2007 by Amgen, Inc. From February 2000 to September 2006, Mr. Waddillhe served as a Principal at Square One Finance, a financial consulting business. From December 1996 to February 2000, Mr. Waddill served as Senior Director of Finance and Administration at Exelixis, Inc., a biotechnology company. He has served as a director of Arrowhead Pharmaceuticals, Inc. (Nasdaq: ARWR), a publicly-heldbiopharmaceutical company, since January 2018.2018, Annexon, Inc. (Nasdaq: ANNX), a biopharmaceutical company, since August 2021 and Turnstone Biologics Corp. (Nasdaq: TSBX), a biotechnology company, since April 2024. Mr. Waddill received a B.S. in Accounting from the University of Illinois, Chicago, and a certification as a public accountant, which is currently inactive, after working at PricewaterhouseCoopers LLP and Deloitte LLP. The Company believes that Mr. Waddill is qualified to serve on the Board because of his financial expertise and extensive experience in the biotechnology field.

Lewis T. "Rusty"“Rusty” Williams, M.D., Ph.D.

Dr. Williams, 68,74, has served as a member of the Board since June 2017. Dr. Williams has served as Executive Chairman of Ten30 Bio, a biotechnology start-up company, since April 2024. He previously served as Chairman and Chief Executive Officer of Walking Fish Therapeutics, a biotechnology start-up company, from February 2019 to March 2024. Dr. Williams has also served as a venture partner of Quan Capital, LLP, a healthcare-focused venture capital firm, since October 2018. He founded and has served as a director of Five Prime Therapeutics, Inc., a former public biotechnology company sinceacquired by Amgen, Inc., from January 2002 until January 2020, and served as its President and Chief Executive Officer from April 2011 to December 2017. Previously, Dr. Williams spent seven years at Chiron Corporation, ("Chiron"), a biopharmaceutical company now known as Novartis Vaccines and Diagnostics, Inc., where he served most recently as its Chief Scientific Officer. He also served on Chiron'sChiron’s board of directors from 1999 to 2001. Prior to joining Chiron, Dr. Williams was a professor of medicine at the University of California, San Francisco, and served as Director of the University'sUniversity’s Cardiovascular Research Institution and Daiichi Research Center. Dr. Williams also has served on the faculties of Harvard Medical School and Massachusetts General Hospital and co-founded COR Therapeutics, Inc., a biotechnology company focused on cardiovascular disease. He is a member of the National Academy of Sciences and a fellow of the American Academy of Arts and Sciences. Dr. Williams was previously a member of the board of directors of Neoleukin Therapeutics, Inc. (formerly, Nasdaq: NLTX), COR Therapeutics, Inc., and Beckman Coulter, Inc., each of which was a public company during his service as a director. Dr. Williams received a B.S. from Rice University and an M.D. and a Ph.D. from Duke University. The Company believes that Dr. Williams'Williams’ extensive experience in drug discovery and development, his executive experience with several pharmaceutical companies and his service as a director of other publicly-tradedpublicly traded healthcare companies have provided him the qualifications, skills and financial expertise to serve on the Board.


THE BOARD OF DIRECTORS RECOMMENDS
A
VOTE IN FAVOR OF EACH NAMED NOMINEE.

“FOR ALL” THE CLASS II DIRECTOR NOMINEES.

In addition to the three Class II director nominees, for director, Protagonist has four other directors who will continue in office after the Annual Meeting, with terms expiring in 20192025 and 2020. The following includes a brief biography of each director composing the remainder of the Board with terms expiring as shown, with each biography including information regarding the experience, qualifications, attributes or skills that caused the Nominating and Corporate Governance Committee and the Board to determine that the applicable director should serve as a member of the Board.

2026, respectively.

CLASS III DIRECTORS CONTINUING IN OFFICE UNTIL THE 20192025 ANNUAL MEETING

Armen B. Shanafelt,

Harold E. Selick, Ph.D.

Dr. Shanafelt, 59,Selick, 69, has served as a member of the Board since January 2010. Since April 2009, Dr. Shanafelt was venture partner, then a general partner, of Lilly Ventures, a venture capital firm. Previous to joining Lilly Ventures, Dr. Shanafelt was one of several Chief Scientific Officer(s) at Eli Lilly and Company, a pharmaceutical research company, specifically responsible for the generation of the early biotherapeutic pipeline which spanned the therapeutic areas of oncology, metabolic disease, autoimmunity, and neuroscience. Dr. Shanafelt received his B.S. in Chemistry and Physics from Pacific Lutheran University, and his Ph.D. in Chemistry from the University of California, Berkeley. He completed his postdoctoral work at DNAX Research Institute, where he studied the structure-function relationships of cytokines and their receptors. Dr. Shanafelt also serves as a director for Aeglea Biotherapeutics, Inc. and Aileron Therapeutics Inc., both clinical stage publicly-traded biopharmaceutical companies, as well as a director of three privately-held biotechnology companies. The Company believes Dr. Shanafelt is qualified to serve on the Board because of his experience in the pharmaceutical and biotechnology businesses, including his expertise with respect to the generation of early biotherapeutic pipelines and his investment experience while a partner with Lilly Ventures.

Harold E. Selick, Ph.D.

Dr. Selick, 63, has served on the Board since February 2009. Dr. Selick hasis currently Chief Executive Officer and board member of Hinge Bio, Inc., a private biotechnology company focused on developing therapeutics for patients living with cancer. He previously served as Vice Chancellor of Business Development, Innovation and Partnerships at the University of California, San Francisco, sincefrom April 2017.2017 to December 2022. Dr. Selick was a Venture Partner at Mission Bay Capital, a venture capital firm, from 2018 until his resignation at the end of 2022. Previously, he was the Chief Executive Officer of Threshold Pharmaceuticals, Inc., a biotechnology company, from June 2002 until the company’s merger with Molecular Templates Inc. in April 2017. From June 2002 until July 2007, Dr. Selick was also a Venture Partner of Sofinnova Ventures, Inc., a venture capital firm. From January 1999 to April 2002, he was Chief Executive Officer of Camitro Corporation, a biotechnology company.company, which was acquired two years after its founding. From 1992 to 1999, he was at Affymax Research Institute, the drug discovery technology development center


9


for Glaxo Wellcome plc, most recently as Vice President of Research. Prior to working at Affymax he held scientific positions at Protein Design Labs, Inc. and Anergen, Inc. Dr. Selick serves as Lead Director of PDL, a public company, and Chairman of the board of directors of Molecular Templates, Inc. (Nasdaq: MTEM), a publicbiopharmaceutical company. Dr. Selick previously served as Lead Director and then Chairman of PDL BioPharma, Inc., a biopharmaceutical company, from 2009 to December 2019, and served as Chairman of the board of directors of Threshold Pharmaceuticals, Inc., a public company, until it merged with Molecular Templates Inc. in April 2017. Dr. Selick received hisa B.A. in Biophysics and a Ph.D. in Biology from the University of Pennsylvania and was a Damon Runyon-Walter Winchell Cancer Fund Fellow and an American Cancer Society Senior Fellow at the University of California, San Francisco. The Company believes that because of his broad experience in building and running both private and public companies and serving on the boards of directors of a variety of biotechnology companies, Dr. Selick is well positioned to provide guidance and insight to the Board and management team.

CLASS I DIRECTORS CONTINUING IN OFFICE UNTIL THE 2020 ANNUAL MEETING

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

Dr. Noonberg, 50,

Bryan Giraudo
Mr. Giraudo, 48, has served as a member of the Board since December 2017. Dr. NoonbergMay 2018. Mr. Giraudo has served as the Chief MedicalFinancial Officer of Prothena Corporation plcGossamer Bio, Inc. (Nasdaq: GOSS), a biotechnology company, since May 2018 and as Chief Operating Officer of Gossamer Bio since September 2021. He has completed nearly $1.0 billion in financings for Gossamer Bio since inception, from May 2017 to March 2018.Series B financing through its initial public offering and additional debt and equity financings. Prior to joining Prothena, she servedGossamer Bio, Mr. Giraudo was a Senior Managing Director at Leerink Partners from 20152009 to 2017 as Group Vice President and Head of Global Clinical Development at BioMarin Pharmaceuticals Inc.,April 2018, where shehe was responsible for development strategytheir western North America and execution acrossAsia Pacific biotechnology and medical technology banking practice. Before joining Leerink, he was a diverse clinical portfolio. From 2007 to 2015, Dr. Noonberg held several positions at Medivation, Inc., where, as Senior Vice President of Early DevelopmentManaging Director with Merrill Lynch and Vice President of Clinical Development, she led programs across all phases of development, including enzalutamide (XTANDI) for the treatment of chemotherapy-naïve metastatic prostate cancer. She also held several clinical positions between 2004Co.’s Global Healthcare Investment Banking Group. Mr. Giraudo joined Merrill Lynch in 1997. As a banker, he completed over 200 corporate finance, corporate partnership and 2007 at Chiron Corporation, where she led the clinical development


of compounds in infectious disease and pulmonary indications. Dr. Noonberg earned her M.D. at the University of California, San Francisco, her Ph.D. in Bioengineering at the University of California, Berkeley, and her B.S. at Dartmouth College. Dr. Noonberg is a board-certified internist and completed her residency at Johns Hopkins Hospital. Since 2002, shestrategic advisory transactions. Mr. Giraudo has been an active part-time hospitalist, working as an attending physician treating a broad rangemember of inpatient and critical care patients.the board of directors of Valerio Therapeutics, S.A. (EPA: ALVIO) (formerly, Onxeo SA (EPA: ALONX)), a biotechnology company, since November 2021. He received a B.A. from Georgetown University. The Company believes thatMr. Giraudo is qualified to serve on the Board because of her executive businesshis extensive experience as well as her extensive medical knowledgein the investment banking field, financial expertise and expertise, Dr. Noonberg is well positioned to make valuable contributions and provide valuable guidance toexperience in the Board.

biotechnology field.

CLASS I DIRECTORS CONTINUING IN OFFICE UNTIL THE 2026 ANNUAL MEETING
Dinesh V. Patel, Ph.D.

Dr. Patel, 61,67, has served as a member of the Board and as the Company'sCompany’s President and Chief Executive Officer since December 2008. Dr. Patel has more than 3038 years of executive, entrepreneurial and scientific experience spanning the pharmaceutical, biotechnology and biopharmaceutical industries. Prior to joining Protagonist, Dr. Patelhe served from 2006 to 2008 as the President and Chief Executive Officer of Arête Therapeutics, a privately held company focused on the development of novel drugs for metabolic syndrome. Prior to that, heDr. Patel was the President, and Chief Executive Officer and co-founder of Miikana Therapeutics, an oncology-based company, from 2003 until it was acquired by Entremed (later renamed CASI Pharmaceuticals) in 2005. Prior to Miikana, Dr. Patelhe held positions of increasing responsibility at Versicor, a biotechnology company (later renamed Vicuron and which was acquired by Pfizer in 2015)Vicuron), from 1996 to 2003, most recently as Senior Vice President of Drug Discovery and Licensing. Vicuron’s research and development efforts led to two marketed drugs, anidulafungin (Eraxis®), and Dalbavancin (Dalvance®), and the Company was acquired by Pfizer in 2005 in a $1.9 billion cash transaction. Prior to Vicuron, Dr. Patel was a director of chemistry at the combinatorial chemistry company Affymax, from 1993 to 1996. Dr. PatelHe was also a medicinal chemist at BristolMyersBristol Myers Squibb (NYSE: BMY) from 1985 to 1993. Dr. Patel received hisa Ph.D. in Chemistry from Rutgers University, New Jersey and hisa B.S. in Industrial Chemistry from S. P. University, Vallabh Vidyanagar, India. The Company believes that because of his expertise, extensive knowledge of the Company and experience as an executive officer of biotechnology companies, Dr. Patel is able to make valuable contributions to the Board.


Daniel N. Swisher, Jr.
Mr. Swisher, age 61, has served as a member of the Board since October 2023. Mr. Swisher served as a Strategic Advisor to Jazz Pharmaceuticals plc (Nasdaq: JAZZ), a biopharmaceutical company, from September 2023 to March 2024. He previously served as the President of Jazz Pharmaceuticals from January 2018 to September 2023, and also as its Chief Operating Officer from January 2018 until May 2021

10


and from November 2022 until September 2023. Prior to Jazz Pharmaceuticals, he served in various roles at Sunesis Pharmaceuticals, Inc., a biopharmaceutical company, from 2001 to December 2017, including as its Chief Executive Officer and a member of its board of directors from 2003 to December 2017, and President from 2005 through December 2017. Prior to that, Mr. Swisher held a range of senior management roles, including serving as Senior Vice President of Sales and Marketing at ALZA Corporation, a pharmaceutical and medical systems company that merged with Johnson & Johnson, from 1992 to 2001. Mr. Swisher has served as a director of Cerus Corporation (Nasdaq: CERS), a biopharmaceutical company, since June 2011 and as chairman of the board of directors since October 2013. Mr. Swisher has also served as a director of Corcept Therapeutics Incorporated (Nasdaq: CORT), a pharmaceutical company, since June 2015. Mr. Swisher received a B.A. from Yale University and an M.B.A. from the Stanford Graduate School of Business. The Company believes that Mr. Swisher’s senior leadership and business experience leading biopharmaceutical companies makes him a qualified and valuable member of the Board.
INFORMATION REGARDING THE BOARD OF DIRECTORS AND
CORPORATE GOVERNANCE

INDEPENDENCE OF THE BOARD OF DIRECTORS

As required under the Nasdaq Stock Market ("Nasdaq"(“Nasdaq”) listing standards, a majority of the members of a listed company's Boardcompany’s board must qualify as "independent,"“independent,” as affirmatively determined by the Board.board. The Board consults with the Company'sCompany’s counsel to ensureso that the Board'sBoard’s determinations are consistent with relevant securities and other laws and regulations regarding the definition of "independent,"“independent,” including those set forth in pertinentunder the listing standards of Nasdaq, as in effect from time to time.

Consistent with these considerations, after a review of all relevant identified transactions or relationships between each director, or any of his or her family members, and the Company, its senior management and its independent auditors, the Board has affirmatively determined that the following six directors are independent directors within the meaning of the applicable Nasdaq listing standards: Dr. Khosla, Dr. Noonberg,Mr. Giraudo, Ms. O’Dowd, Dr. Selick, Dr. Shanafelt,Mr. Swisher, Mr. Waddill and Dr. Williams. Dr. Sarah Noonberg, who served on the Board until the 2023 Annual Meeting of Stockholders, was also deemed to be an independent director within the meaning of the applicable Nasdaq listing standards during the period she served on the Board. In making this determination, the Board found that none of these directors or nominees for director had a material or other disqualifying relationship with the Company.Company that would interfere with the exercise of independent judgment in carrying out the responsibilities of a director. Dr. Patel is not considered independent because he is an executive officer of the Company.

In making those independence determinations, the Board took into account certain relationships and transactions that occurred in the ordinary course of business between the Company and entities with which some of its directors are or have been affiliated.


BOARD LEADERSHIP STRUCTURE

The Board has an independent Chairperson of the Board (“Chairperson”), Dr. Selick, who has authority, among other things, to call and preside over meetings of the Board, meetings, including meetings of the independent directors, to set meeting agendas and to determine materials to be distributed to the Board. Accordingly, the Chairperson of the Board ("Chairperson") has substantial ability to shape the work of the Board of Directors.Board. The Company believes that separation of the positions of Chairperson and Chief Executive Officer reinforces the independence of the Board in its oversight of the business and affairs of the Company. In addition, the Company believes that having an independent Chairperson creates an environment that is more conducive to objective evaluation and oversight of management'smanagement’s performance, increasingincreases management accountability and improvingimproves the ability of the Board to monitor whether management'sconfirm that management’s actions are in the best interests of the Company and its stockholders. As a result, the Company believes that having an independent Chairperson can enhance the effectiveness of the Board as a whole.

The Board believes that its programs for overseeing risk, as described below, would be effective under a variety of leadership frameworks. Accordingly, the Board’s risk oversight function did not significantly impact its selection of the current leadership structure.
ROLE OF THE BOARD IN RISK OVERSIGHT

The Board has responsibility for the oversight of the Company'sCompany’s risk management processes and, either as a whole or through its committees, regularly discusses with management the Company'sCompany’s major risk exposures, their potential impact on the Company'sCompany’s business and the steps taken to manage them. The risk

11


oversight process includes receiving regular reports from Board committees and members of senior management to enable the Board to understand the company'sCompany’s risk identification, risk management and risk mitigation strategies with respect to areas of potential material risk, including operations, finance, legal, regulatory, strategic and reputational risk. The Audit Committee reviews information regarding liquidity and operations and oversees the Company'sCompany’s management of financial risks. Periodically, the Audit Committee reviews the Company'sCompany’s policies with respect to risk assessment, risk management, loss prevention and regulatory compliance. Oversight by the Audit Committee includes direct communicationcommunications with the Company'sCompany’s external auditors, and discussions with management regarding significant risk exposures and the actions management has taken to limit, monitor or controlmitigate such exposures. The Compensation Committee is responsible for assessing whether any of the Company'sCompany’s compensation policies or programs has the potential to encourage excessive risk taking. The Nominating and Corporate Governance Committee manages risks associated with the independence of the Board, corporate disclosure practices and potential conflicts of interest. While each committee is responsible for evaluating certain risks and overseeing the management of such risks, the entire Board is regularly informed through committee reports about such risks. Matters of significant strategic risk, such as regarding cybersecurity and information technology matters, are considered by the Board as a whole.

MEETINGS OF THE BOARD OF DIRECTORS

The Board met foursix times during the last fiscal year. Each Board member attended 75% or more of the aggregate number of meetings of the Board and of the committees on which he or she served held during the portion of the last fiscal year for which he or she was a director or committee member.

As required under applicable Nasdaq listing standards, in fiscal 2017, the Company's

The independent directors met four timeshave the opportunity to meet in regularly scheduled executive sessions without management present at which onlyevery regular Board meeting and at such other times as may be determined by the Chairperson. The purpose of these executive sessions is to encourage and enhance communication among independent directors were present.directors. Dr. Selick, the Chairperson, of the Board presides over the executive sessions.


INFORMATION REGARDING COMMITTEES OF THE BOARD OF DIRECTORS

The Board has three standing committees: an Audit Committee, a Compensation Committee and a Nominating and Corporate Governance Committee. The following table provides current membership and meeting information for fiscal 20172023 for each of the Board committees:

NameAuditCompensationNominating
and Corporate
Governance
Bryan GiraudoXX*
Sarah A. O’DowdX
Dinesh V. Patel, Ph.D.
Harold E. Selick, Ph.D.X*X
Daniel N. Swisher, Jr.(1)
X
William D. WaddillX*X
Lewis T. Williams, M.D., Ph.D.X
Total meetings in fiscal 2023541
Name
 Audit Compensation Nominating and
Corporate
Governance
 

Chaitan Khosla, Ph.D. 

              X 

Sarah B. Noonberg, M.D., Ph.D. 

  X(1)            

Dinesh V. Patel, Ph.D. 

                   

Harold E. Selick, Ph.D. 

        X* X 

Armen B. Shanafelt, Ph.D. 

  X        X*

William D. Waddill

  X* X       

Lewis T. Williams, M.D., Ph.D. 

        X(2)      

Total meetings in fiscal 2017

  4  4  3 

*
*
Committee Chairperson
(1)
Dr. Noonberg
Mr. Swisher was appointed to serve as a member of the Audit Committee on December 12, 2017.
(2)
Dr. Williams was appointed to serve as a member of the Compensation Committee on December 12, 2017.
in March 2024.

Below is a description of each committee of the Board.

Each of the committees has authority to engage legal counsel or other experts or consultants, as it deems appropriate to carry out its responsibilities.responsibilities, has the opportunity to meet regularly in executive session and regularly reports its activities to the full Board. The Board has determined that each member of each committee meets the applicable Nasdaq and SEC rules and regulations regarding "independence"“independence” for service on such committee (and, in the case of Compensation Committee members, qualifies as a “non-employee director” as defined in Rule 16b-3 under the Exchange Act) and each member is free of any relationship that would impair his or her individual exercise of independent judgment with regard to the Company.

The Board


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has adopted written charters for each committee that are available to stockholders in the “Governance” section of the Company’s website at www.protagonist-inc.com. Below is a description of each committee of the Board.
Audit Committee

The Audit Committee was established byoversees the Board in accordance with Section 3(a)(58)(A) of the Securities Exchange Act of 1934, as amended (the "Exchange Act"), to oversee the Company'sCompany’s corporate accounting and financial reporting processes and audits of its financial statements. For this purpose, the Audit Committee performs several functions. The Audit Committee evaluates the performance of and assesses the qualifications of the independent auditors;auditor; determines and approves the engagement of the independent auditors;auditor; determines whether to retain or terminate the existing independent auditorsauditor or to appoint and engage a new independent auditors;auditor; reviews and approves the retention of the independent auditorsauditor to perform any proposed permissible non-audit services; monitors the rotation of partners of the independent auditorsauditor on the Company'sCompany’s audit engagement team as required by law; reviews and approves or rejects transactions between the Company and any related persons; confers with management and the independent auditorsauditor regarding the effectiveness of internal control over financial reporting; establishes procedures, as required under applicable law, for the receipt, retention and treatment of complaints received by the Company regarding accounting, internal accounting controls or auditing matters and the confidential and anonymous submission by employees of concerns regarding questionable accounting or auditing matters; and meets to review the Company'sCompany’s annual audited financial statements and quarterly financial statements with management and the independent auditor, including a review of the Company'sCompany’s disclosures under "Management's“Management’s Discussion and Analysis of Financial Condition and Results of Operations."


The Audit Committee is composed of three directors: Mr. Waddill, Dr. Shanafelt and Dr. Noonberg. The Audit Committee met four times during the fiscal year. The Board has adopted a written Audit Committee charter that is available to stockholders in the "Corporate Governance" section of the Company's website at www.protagonist-inc.com.

The Board reviews the Nasdaq listing standards definition of independence for Audit Committee members on an annual basis and has determined that all members of the Company's Audit Committee are independent (as independence is currently defined in Rule 5605(c)(2)(A)(i) and (ii) of the Nasdaq listing standards).

The Board has also determined that Mr. Waddill qualifies as an "audit“audit committee financial expert," as defined in applicable SEC rules. The Board made a qualitative assessment of Mr. Waddill'sWaddill’s level of knowledge and experience based on a number of factors, including his formal education and experience as a chief financial officer for public reporting companies. In addition to our Audit Committee, Dr. ShanafeltThe Board has also serves ondetermined that all members of the Audit Committee of Aeglea Biotherapeutics, Inc. The Board has determined that this simultaneous service does not impair Dr. Shanafelt's ability to effectively serve on our Audit Committee.

are “financially literate” under Nasdaq listing rules.

Report of the Audit Committee of the Board of Directors

The Audit Committee has reviewed and discussed the audited financial statements for the fiscal year ended December 31, 20172023 with management of the Company.Company and with Ernst & Young LLP, the Company’s independent registered public accounting firm. The Audit Committee has discussed with the Company's independent registered public accounting firm, PricewaterhouseCoopersErnst & Young LLP the matters required to be discussed by Auditing Standard No. 1301,Communications with Audit Committees, as adopted bythe applicable requirements of the Public Company Accounting Oversight Board ("PCAOB"(“PCAOB”). and the SEC. The Audit Committee has also received the written disclosures and the letter from PricewaterhouseCoopersErnst & Young LLP required by applicable requirements of the PCAOB regarding the independent accountants'accountant’s communications with the audit committeeAudit Committee concerning independence and has discussed with PricewaterhouseCoopersErnst & Young LLP the accounting firm'sfirm’s independence. Based on the foregoing, the Audit Committee has recommended to the Board that the audited financial statements be included in the Company'sCompany’s Annual Report on Form 10-K for the fiscal year ended December 31, 2017.

Mr. William D. Waddill
Dr. Armen B. Shanafelt
Dr. Sarah B. Noonberg

The material in this2023 for filing with the SEC.

This report is not "soliciting material," is not deemed "filed" withprovided by the Commission and is not to be incorporated by reference in anyfollowing directors who served on the Audit Committee through the filing of the Company underCompany’s Annual Report on Form 10-K for the Securities Act or the Exchange Act, whether made before or after the date hereof and irrespective of any general incorporation language in any such filing.

fiscal year ended December 31, 2023:

William D. Waddill (Chairperson)
Bryan Giraudo
Compensation Committee

The Compensation Committee is composed of three directors: Dr. Selick, Mr. Waddill and Dr. Williams. All members of the Company's Compensation Committee are independent (as independence is currently defined in Rule 5605(d)(2) of the Nasdaq listing standards and regulations of the SEC), and are "non-employee directors" as defined in Rule 16b-3 promulgated under the Exchange Act. The Compensation Committee met four times during the fiscal year. The Board has adopted a written Compensation Committee charter that is available to stockholders in the "Corporate Governance" section of the Company's website at www.protagonist-inc.com.


The Compensation Committee of the Board acts on behalf of the Board to review, adopt and oversee the Company'sCompany’s compensation strategy, policies, plans and programs, including:


determining the compensation and other terms of employment of the chief executive officerChief Executive Officer and the other executive officers and reviewing and approving corporate performance goals and objectives relevant to such compensation;


reviewing and recommending to the full Board the compensation of the Company'sCompany’s directors;


evaluating and administering the equity incentive plans, compensation plans and similar programs advisable for us, as well as reviewing and recommending to the Board the adoption, modification or termination of the Company'sCompany’s plans and programs;


13



establishing policies with respect to equity compensation arrangements;

and
administration of the Company's equity compensation plans, pension and profit-sharing plans, deferred compensation plans and other similar plan and programs; and


conducting an annual assessment of the performance of the Compensation Committee and its members, and the adequacy of its charter.

In addition, once the Company ceases to be an "emerging growth company" as defined in the Jumpstart Our Business Startups Act of 2012, the Compensation Committee will review with management the Company's Compensation Discussion and Analysis and consider whether to recommend that it be included in Proxy Statements and other filings.

Compensation Committee Processes and Procedures

Typically, the Compensation Committee meets as often as its members deem necessary or appropriate. The agenda for each meeting is usually developed by the Chairperson of the Compensation Committee, in consultation with the Company's Chief Executive Officer. The Compensation Committee meets regularly in executive session. However, from

From time to time, various members of management and other employees as well as outside advisors or consultants may be invited by the Compensation Committee to make presentations, to provide financial or other background information or advice or to otherwise participate in Compensation Committee meetings. TheHowever, the Chief Executive Officer (or any other executive officer) may not participate in, or be present during, any deliberations or determinations of the Compensation Committee regarding his compensation or individual performance objectives. The charter of the Compensation Committee grants the Compensation Committee full access to all books, records, facilities and personnel of the Company. In addition, under the charter, the Compensation Committee has the authority to obtain, at the expense of the Company, advice and assistance from compensation consultants and internal and external legal, accounting or other advisors and other external resources that the Compensation Committee considers necessary or appropriate in the performance of its duties. The Compensation Committee has direct responsibility for the oversight of the work of any consultants or advisers engaged for the purpose of advising the Committee.committee. In particular, the Compensation Committee has the sole authority to retain, in its sole discretion, compensation consultants to assist in its evaluation of executive and director compensation, including the authority to approve the consultant'sconsultant’s reasonable fees and other retention terms. Under the charter, the Compensation Committee may select, or receive advice from, a compensation consultant, legal counsel or other advisoradviser to the compensation committee, other than in-house legal counsel and certain other types of advisors,advisers, only after taking into consideration six factors prescribed bythat bear upon the adviser’s independence under the SEC and Nasdaq that bear upon the advisor's independence;rules; however, there is no requirement that any advisoradviser be independent.

During the past fiscal year, after taking into consideration the six factors prescribed byunder the SEC and Nasdaq described above,rules, the Compensation Committee engaged Radford, an AonHewittAon Hewitt Company, as its compensation consultants.consultant. Radford was selected because it is a well-known and respected national


compensation consulting firm that commonly provides information, recommendations and other executive compensation advice to compensation committees and management. The Compensation Committee has determined that (1) Radford satisfies applicable independence criteria and (2) Radford’s work does not raise any conflicts of interest, in each case under applicable Nasdaq and SEC rules and regulations. The Compensation Committee requested that Radford:


evaluate the efficacy of the Company'sCompany’s existing compensation strategy and practices in supporting and reinforcing the Company'sCompany’s long-term strategic goals; and


assist in refining the Company'sCompany’s compensation strategy and in developing and implementing an executive compensation program to execute that strategy.

As part of its engagement, Radford was requested by the Compensation Committee to develop a comparative group of companies and to perform analyses of competitive performance and compensation levels for that group; as well as conduct market research and analysis on annual and long-term incentive programs, salaries and equity plans; assist in developing target grant levels, target bonus levels and annual salaries for executive officers and other employees; provide the committee with advice and ongoing recommendations regarding material executive compensation decisions; and review the director compensation program. Radford ultimately developed recommendations that were presented to the Compensation Committee for its consideration. Following an active dialogue with Radford and resulting modifications, the Compensation Committee approved the modified Radford recommendations.

On May 25, 2017, the

The Compensation Committee amended its New Hire and Merit Equity Grant Delegation Policy pursuant to whichhas delegated authority was granted to Dr. Patel, as the sole member of the Equity Award Committee of the Board, the full authority of the Board, to grant equity-based awards to non-executive officer employees and consultants, within Board-approved guidelines, under the Company'sCompany’s 2016 Equity Incentive Plan (the "2016 Plan"“2016 Plan”). The purpose of this delegation of authority is to enhance the flexibility of optionequity-based award administration within the Company and to facilitate the timely grants of equity-based awards to service providers of the Company.

During fiscal 2017, Dr. Patel exercised his authority to grant options to purchase an aggregate of 408,623 shares to employees.

The Compensation Committee and the Board retain concurrent authority to make equity-based awards to employees and consultants who are eligible recipients under this policy pursuant to the 2016 Plan. The Compensation Committee receives periodic reports of grants made pursuant to this delegated authority.

During fiscal 2023, Dr. Patel exercised his authority to grant equity-based awards, including options and restricted stock units, totaling 1,162,650 shares in aggregate to employees and consultants.
Historically, the Compensation Committee has made most of the significant adjustments to annual compensation, determined bonus and equity-based awards and established new performance objectives at one

14


or more meetings held during the fourth and first quarterquarters of the year. However, the Compensation Committee also considers matters related to individual compensation, such as compensation for new executive hires, as well as high-level strategic issues, such as the efficacy of the Company'sCompany’s compensation strategy, potential modifications to that strategy and new trends, plans or approaches to compensation, at various meetings throughout the year. Generally, the Compensation Committee'sCommittee’s process comprises two related elements: the determination of compensation levels and the establishment of performance objectives for the current year. For executives other than the Chief Executive Officer, the Compensation Committee solicits and considers evaluations and recommendations submitted to the Committeecommittee by the Chief Executive Officer. In the case of the Chief Executive Officer, the evaluation of his performance is conducted by the Compensation Committee, which determines any adjustments to his compensation as well as awards to be granted. For all executives and directors as part of its deliberations, the Compensation Committee may review and consider, as appropriate, materials such as financial reports and projections, operational data, tax and accounting information, tally sheets that set forth the total compensation that may become payable to executives in various hypothetical scenarios, executive and director stock ownership information, companyCompany stock performance data, analyses of historical executive compensation levels and current


Company-wide compensation levels and recommendations of the Compensation Committee'sCommittee’s compensation consultant, including analyses of executive and director compensation paid at other companies identified by the consultant.

Compensation Committee Interlocks and Insider Participation

None of the members of the Compensation Committee is currently or has been at any time one of the Company'sCompany’s officers or employees. None of the Company'sCompany’s executive officers currently serves, or has served during the last year, as a member of the board or compensation committee of any entity that has one or more executive officers serving as a member of the Board or Compensation Committee.

Nominating and Corporate Governance Committee

The Nominating and Corporate Governance Committee of the Board is responsible for identifying, reviewing and evaluating candidates to serve as directors of the Company (consistent with criteria approved by the Board), reviewing and evaluating incumbent directors,; recommending to the Board for selection candidates for election to the Board,Board; making recommendations to the Board regarding the membership of the committees of the Board,Board; assessing the performance of management and the Board,Board; and developing a set of corporate governance principles for the Company.

The Nominating and Corporate Governance Committee is composed of three directors: Dr. Shanafelt, Dr. Selick and Dr. Khosla. All members of the Nominating and Corporate Governance Committee are independent (as independence is currently defined in Rule 5605(a)(2) of the Nasdaq listing standards). The Nominating and Corporate Governance Committee met three times during the fiscal year. The Board has adopted a written Nominating and Corporate Governance Committee charter that is available to stockholders in the "Corporate Governance" section of the Company's website at www.protagonist-inc.com.

The Nominating and Corporate Governance Committee believes that candidates for director should have certain minimum qualifications, including the ability to read and understand basic financial statements being over 21 years of age and having the highest personal integrity and ethics. The Nominating and Corporate Governance Committee also intends to considerconsiders such factors as possessing relevant expertise upon which to be able to offer advice and guidance to management, having sufficient time to devote to the affairs of the Company, having demonstrated excellence in his or her field, having the ability to exercise sound business judgment and having the commitment to rigorously represent the long-term interests of the Company'sCompany’s stockholders. However, the Nominating and Corporate Governance Committee retains the right to modify these qualifications from time to time. Candidates for director nominees are reviewed in the context of the current composition of the Board, the operating requirements of the Company and the long-term interests of stockholders. In conducting this assessment, the Nominating and Corporate Governance Committee typically considers diversity (as discussed below), age, skills and such other factors as it deems appropriate, given the current needs of the Board and the Company, to maintain a balance of knowledge, experience and capability.

The Nominating and Corporate Governance Committee appreciates the value of thoughtful Board refreshment and regularly identifies and considers qualities, skills and other director attributes that would enhance the composition of the Board. In the case of incumbent directors whose terms of office are set to expire, the Nominating and Corporate Governance Committee reviews these directors'directors’ overall service to the Company during their terms, including the number of meetings attended, level of participation, quality of performance and any other relationships and transactions that might impair the directors'directors’ independence. The Committeecommittee also takes into account the results of the Board's self-evaluation, conducted annually on a group and individual basis.Board’s self-evaluation. In the case of new director candidates, the Nominating and Corporate Governance Committee also determines whether the nominee is independent for Nasdaq purposes, which determination is based upon applicable Nasdaq listing standards, applicable SEC rules and regulations and the advice of counsel, if necessary. The Nominating and Corporate Governance Committee then uses its network

15


of contacts to compile a list of potential candidates, but may also engage, if it deems


appropriate, a professional search firm.firm (though it did not do so in 2023). The Nominating and Corporate Governance Committee conducts any appropriate and necessary inquiries into the backgrounds and qualifications of possible candidates after considering the function and needs of the Board. The Nominating and Corporate Governance Committee meets to discuss and consider the candidates'candidates’ qualifications and then selects a nominee for recommendation to the Board by majority vote.

for appointment or nomination and to the stockholders for election at the annual meeting.

The Nominating and Corporate Governance Committee will consider director candidates recommended by stockholders. The Nominating and Corporate Governance Committee does not intend to alter the manner in which it evaluates candidates recommended by stockholders in the same manner, including applying the minimum criteria set forth above, based on whether or not the candidate wasas candidates recommended by a stockholder.other sources. Stockholders who wish to recommend individuals for consideration by the Nominating and Corporate Governance Committee to become nominees for election to the Board may do so by delivering a written recommendation to the Nominating and Corporate Governance Committee atas described under “Stockholder Communications with the following address: 7707 Gateway Blvd., Suite 140, Newark, CA 94560.Board of Directors.” Submissions must include the full namesame information required under our Bylaws for nominating a director.
BOARD DIVERSITY
In addition to the factors discussed above, the Board and the Nominating and Corporate Governance Committee actively seek to achieve a diversity of occupational and personal backgrounds on the Board. The Nominating and Corporate Governance Committee considers a potential director candidate’s ability to contribute to the diversity of personal backgrounds on the Board, including with respect to gender, race, ethnic and national background, geography, age and sexual orientation. The Nominating and Corporate Governance Committee assesses its effectiveness in balancing these considerations in connection with its annual evaluation of the proposed nominee, a descriptioncomposition of the proposed nominee's business experience for at least the previous five years, complete biographicalBoard. In this regard, our current Board of seven directors includes one director (14%) who self-identifies as female and two directors (28%) who self-identify as racially/ethnically diverse or LTBTQ+.
In accordance with Nasdaq’s board diversity listing standards, we are disclosing aggregated statistical information a descriptionabout our Board’s self-identified gender and racial/ethnic characteristics and LGBTQ+ status as voluntarily confirmed to us by each of the proposed nominee's qualifications as a director and a representation that the nominating stockholder is a beneficial or record holder of the Company's stock and has been a holder for at least one year. Any such submission must be accompanied by the written consent of the proposed nominee to be named as a nominee and to serve as a director if elected.

our directors.

Board Diversity Matrix
(as of the date of this Proxy Statement)
Total number of directors – 7
Gender identity:FemaleMaleNon-
Binary
Did not
Disclose
Gender
Directors16
Number of directors who identify in any of the categories below:
African American or Black
Alaskan Native or Native American
Asian1
Hispanic or Latinx
Native Hawaiian or Pacific Islander
White15
Two or More Races or Ethnicities
LGBTQ+1
STOCKHOLDER COMMUNICATIONS WITH THE BOARD OF DIRECTORS

Historically, the Company has not provided

Stockholders and other interested parties may communicate with our Board or a formal process relatedparticular director by sending a letter addressed to stockholder communications with the Board. Nevertheless, every effort has been made to ensure that the views of stockholders are heard by the Board or individual directors, as applicable,a particular director to our Corporate Secretary at the address set

16


forth on the first page of this Proxy Statement. These communications will be compiled and thatreviewed by our Corporate Secretary, who will determine whether the communication is appropriate responses are provided to stockholders in a timely manner. The Company believes its responsiveness to stockholder communicationsfor presentation to the Board has been excellent.

or the particular director. The purpose of this screening is to allow the Board to avoid having to consider irrelevant or inappropriate communications (such as advertisements, solicitations and hostile communications).

To enable the Company to speak with a single voice, as a general matter, senior management serves as the primary spokesperson for the Company and is responsible for communicating with various constituencies, including stockholders, on behalf of the Company. Directors may participate in discussions with stockholders and other constituencies on issues where Board-level involvement is appropriate. In addition, the Board is kept informed by senior management of the Company’s stockholder engagement efforts.
CODE OF ETHICS

The Company has adopted the Protagonist Therapeutics, Inc. Code of Business Conduct and Ethics (the “Code”) that applies to all officers, directors and employees.employees, including our principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions. The Code of Business Conduct and Ethics is available in the "Corporate Governance"“Investors — Governance” section of the Company'sCompany’s website at www.protagonist-inc.com.www.protagonist-inc.com. If the Company makes any substantivecertain amendments to the Code of Business Conduct and Ethics or grants any waiver fromof a provision of the Code to any executive officer or director, the Company willintends to promptly disclose the nature of the amendment or waiver on its website.

website, to the extent required by applicable rules.

CORPORATE GOVERNANCE GUIDELINES

In July 2016,

The Board has adopted the Board documented the governance practices followed by the Company by adopting Corporate Governance Guidelines to assure thatserve as a framework for the Board will have the necessary authority and practices in place to review and evaluate the Company's business operations as needed and to make decisions that are independentgovernance of the Company's management.Company. The guidelines are also intended to align the interests of directors and management with those of the Company'sCompany’s stockholders. The Corporate Governance Guidelines set forth the Board’s practices the Board intends to follow with respect to boardBoard composition and selection, boardBoard diversity, Board meetings, and involvementoversight of senior management, Chief Executive Officer performance evaluation and succession planning, and boardBoard committees and compensation. The Corporate Governance Guidelines, as well as the charters for each committee of the Board, may be viewed inon the "Corporate Governance"“Investors — Governance” section of the Company'sCompany’s website at www.protagonist-inc.com.

www.protagonist-inc.com.

ANTI-HEDGING AND PLEDGING POLICY


Our insider trading policy prohibits our directors, executive officers and employees from engaging in the trading of derivative securities, short sales, transactions in put or call options, hedging transactions, pledges, holding equity securities in margin accounts or other inherently speculative transactions relating to our equity securities.
ENVIRONMENTAL, SOCIAL AND GOVERNANCE
Environmental, social and governance (“ESG”) matters are a priority to us. The Nominating and Corporate Governance Committee oversees this commitment, as well as our ESG initiatives and progress towards related goals and targets. We report on these programs and initiatives, including our drug access and pricing program, our diversity and inclusion priorities, and our community and stakeholder educational efforts related to our therapeutic focus areas. Additional information about our ESG initiatives is available in the “Community” section of the Company’s website at www.protagonist-inc.com.

17


PROPOSAL 2

ADVISORY VOTE ON EXECUTIVE COMPENSATION
Section 14A of the Exchange Act requires that the Company provide stockholders with the opportunity to cast an advisory (non-binding) vote to approve the compensation of our named executive officers (the “say-on-pay vote”).
The say-on-pay vote is a non-binding vote on the compensation of our named executive officers, as described in this Proxy Statement in the “Executive Compensation” section, the tabular disclosure regarding such compensation and the accompanying narrative disclosure. The say-on-pay vote is not a vote on our general compensation policies or the compensation of our Board.
Our philosophy in setting compensation policies for executive compensation is to strongly align our compensation program with stockholder interests, reflect market-best practices, continue to support our long-term business objectives and support talent retention. The “Executive Compensation” section provides a more detailed discussion of our executive compensation program and our compensation philosophy.
The vote under this Proposal 2 is advisory only and therefore not binding on us, the Board or our Compensation Committee. However, our Board, including our Compensation Committee, values the opinions of our stockholders, and we will consider the outcome of the say-on-pay vote when making future compensation decisions for our named executive officers. Unless the Board modifies its policy of holding annual say-on-pay advisory votes, the next say-on-pay vote is expected to occur at the 2025 Annual Meeting of Stockholders.
THE BOARD OF DIRECTORS RECOMMENDS
A VOTE “FOR” PROPOSAL 2.

18


PROPOSAL 3
RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING
FIRM

The Audit Committee of the Board has selected PricewaterhouseCoopersErnst & Young LLP (“EY”) as the Company'sCompany’s independent registered public accounting firmauditor for the fiscal year ending December 31, 20182024, and has further directed that management submit the selection of its independent registered public accounting firm for ratification by the stockholders at the Annual Meeting. PricewaterhouseCoopers LLP has audited the Company's financial statements since 2015.are asked to vote to ratify this selection. Representatives of PricewaterhouseCoopers LLPEY are expected to be present at the Annual Meeting. They will have an opportunity to make a statement if they so desire and willare expected to be available to respond to appropriate stockholder questions.

Neither the Company'sCompany’s Bylaws nor other governing documents or law require stockholder ratification of the selection of PricewaterhouseCoopers LLPEY as the Company'sCompany’s independent registered public accounting firm. However, the Audit Committee is submitting the selection of PricewaterhouseCoopers LLPEY to the stockholders for ratification as a matter of good corporate practice.governance. If the stockholders fail to ratify the selection, the Audit Committee will reconsider whether or not to retain that firm.EY as the Company’s independent auditor. Even if the selection is ratified, the Audit Committee in its discretion may direct the appointment of a different independent auditorsauditor at any time during the year if they determineit determines that such a change would be in the best interests of the Company and its stockholders.

The affirmative vote of the holders of a majority of the shares present in person or represented by proxy and entitled to vote on the matter at the Annual Meeting will be required to ratify the selection of PricewaterhouseCoopers LLP.

PRINCIPAL ACCOUNTANT

FEES BILLED BY ERNST & YOUNG LLP DURING FISCAL 2023 AND SERVICES

2022

The following table represents aggregatesummarizes the audit fees billed and expected to the Companybe billed by EY for the indicated fiscal years ended December 31, 2017 and December 31, 2016the fees billed by PricewaterhouseCoopers LLP,EY for all other services rendered during the Company's principal accountant.

indicated fiscal years.
Fiscal Year Ended
December 31,
20232022
Audit Fees(1)
$1,622,000$1,035,150
Audit-Related Fees(2)
Tax Fees(3)
35,80620,639
All Other Fees(4)
7,2003,405
Total Fees$1,665,006$1,059,194
 
 Fiscal Year Ended 
 
 2017 2016 

Audit Fees(1)

 $930,250 $1,273,377 

Audit-Related Fees(2)

     

Tax Fees(3)

  28,142  19,344 

All Other Fees(4)

  2,000   

Total Fees

 $960,392 $1,292,721 
(1)

(1)
"
Audit Fees"Fees” consist of fees billed for professional services rendered for the audit of the Company'sCompany’s consolidated financial statements included in the Company'sCompany’s Annual Report on Form 10-K and for the review of the financial statements included in the Company'sCompany’s Quarterly Reports on Form 10-Q, as well as services as are normally provided by the Company's independent registered public accounting firm,Company’s auditor, including statutory audits and services rendered in connection with statutory and regulatory filings or engagements for thosethe indicated fiscal years.years, and related expenses. The Audit Fees incurred in 20172023 also includeincluded fees of $200,850$185,000 related to services performed in connection with the Company's shelf registration statement on Form S-3Company’s at-the-market offerings and subsequent follow-on publiccommon stock offering, including comfort letters, consents and review of documents filed with the SEC. The Audit Fees incurred in 20162022 also includeincluded fees of $654,000$135,000 related to services performed in connection with the Company's initial public offering,Company’s at-the-market offerings and a shelf registration statement on Form S-3, including comfort letters, consents and review of documents filed with the SEC.

(2)
"
Audit-Related Fees"Fees” consist of fees billed for assurance and related services by the principal accountantauditor that are reasonably related to the performance of the audit or review of the Company'sCompany’s financial statements and are not reported under the Audit Fees category.
(3)
"
Tax Fees"Fees” in 20172023 and 20162022 consist primarily of fees billed for professional services rendered in connection with indirect tax compliance in foreign tax jurisdictions (Australia). As the Company's subsidiary is incorporated in Australia, a substantial portion of the Tax Fees are denominated in Australian Dollars (AUD) and have been translated into U.S. Dollars (USD) using the average exchange rate for each applicable period listed in the table below.
Name
 AUD : USD AUD USD 

2017 Average

  1.00 : 0.771 $36,500 $28,142 

2016 Average

  1.00 : 0.744 $26,000 $19,344 
(4)
(4)
"
All Other Fees"Fees” consist of fees related to products and services provided by the principal accountant,auditor, other than the services reported above. All Other Fees for 2017 were for access to an online database of automated disclosure checklists and accounting pronouncements and interpretations maintained by PricewaterhouseCoopers LLP.

All fees described above were pre-approved by the Audit Committee.

In connectionCommittee in accordance with the audit of the 2017 financial statements, the Company entered into an engagement agreement with PricewaterhouseCoopers LLP that sets forth the terms by which PricewaterhouseCoopers LLP will perform audit services for the Company. That agreement is subject to alternative dispute resolutionpre-approval policies and procedures and an exclusion of punitive damages.

During the fiscal year ended December 31, 2017, none of the total hours expended on the Company's financial audit by PricewaterhouseCoopers LLP were provided by persons other than PricewaterhouseCoopers LLP's full-time permanent employees.

described below.

PRE-APPROVAL POLICIES AND PROCEDURES

The Audit Committee has adopted a policypolicies and procedures for the pre-approval of audit and non-audit services rendered by the Company'sCompany’s independent registered public accounting firm, PricewaterhouseCoopers LLP.EY. The policy generally pre-approvesallows pre-approval of specified services in the defined categories of audit services, audit-related services and tax services, up to specified amounts. Pre-approval may also be given as part of the Audit Committee'sCommittee’s approval of

19


the scope of the engagement of the independent auditor or on an individual, explicit,specified, case-by-case basis before the independent auditor is engaged to provide each service. The pre-approval of services may be delegated to one or more of the Audit Committee'sCommittee’s members, but the decision must be reported to the full Audit Committee at its next scheduled meeting.

The Audit Committee has determined that the rendering of services other than auditlimited non-audit services by PricewaterhouseCoopers LLPEY is compatible with maintaining the principal accountant'sEY’s independence.


THE BOARD OF DIRECTORS RECOMMENDS

A VOTE IN FAVOR“FOR” PROPOSAL 3.

20


PROPOSAL 4
APPROVAL OF AN AMENDMENT TO OUR CERTIFICATE OF INCORPORATION TO INCREASE THE NUMBER OF AUTHORIZED SHARES
We are asking stockholders to approve an amendment to the Company’s Amended and Restated Certificate of Incorporation (the “Certificate of Incorporation”) to increase the number of authorized shares of common stock, par value $0.00001 per share, from 90,000,000 to 180,000,000, which would also have the effect of increasing the total number of authorized shares from 100,000,000 to 190,000,000 (the “Proposed Certificate Amendment”). Specifically, the Proposed Certificate Amendment, which our Board has approved and declared advisable, would amend Section A of Article IV of the Certificate of Incorporation as follows:
“A. This Company is authorized to issue two classes of stock to be designated, respectively, “Common Stock” and “Preferred Stock.” The total number of shares which the Company is authorized to issue is 190,000,000 shares. 180,000,000 shares shall be Common Stock, each having a par value of one-thousandth of one cent ($0.00001). 10,000,000 shares shall be Preferred Stock, each having a par value of one-thousandth of one cent ($0.00001).”
Under the Proposed Certificate Amendment, the authorized number of shares of preferred stock, of which none are currently outstanding, would remain unchanged.
Purpose of the Proposed Certificate Amendment
As of April 24, 2024, the Record Date, our common stock share utilization was approximately as follows:
Number of
Shares of
Common Stock
Authorized for issuance90,000,000
Issued and outstanding58,643,133
Reserved for issuance16,085,529

Available for future grant under employee equity incentive plans*
3,444,761

Outstanding awards under our employee equity incentive plans*
10,020,508

Outstanding warrants
2,620,260
Total share usage (issued and outstanding + reserved for issuance)74,728,662
Total share usage as a percentage of authorized83%
*
Includes the 2007 Stock Option and Incentive Plan, 2016 Plan, 2016 Employee Stock Purchase Plan (the “2016 ESPP”) and 2018 Inducement Plan.
As a result, only approximately 15,271,338 shares of our common stock (or 17% of the total authorized) remain available for future use.
Our Board believes that the availability of additional authorized shares of common stock is needed to provide us with additional flexibility to issue common stock for a variety of general corporate purposes as the Board may determine to be desirable. This includes, but is not limited to, raising equity capital, including any future at-the-market equity programs, using our common stock as consideration for acquisitions, mergers, business combinations or other corporate transactions, adopting additional employee benefit plans or reserving additional shares for issuance under existing plans and implementing stock splits. Unless our stockholders approve the Proposed Certificate Amendment, we may not have sufficient unissued and unreserved authorized shares to engage in similar transactions in the future.
Having additional authorized shares of common stock available for future use will allow us to issue additional shares of common stock without the expense and delay of arranging a special meeting of stockholders. We may seek a further increase in authorized shares from time to time in the future as considered appropriate by our Board.

21


Effect of the Proposed Certificate Amendment
The Proposed Certificate Amendment would not change the number of shares of common stock outstanding, nor will it have any immediate dilutive effect. However, the issuance of additional shares of common stock authorized by the Proposed Certificate Amendment may occur at times or under circumstances as to have a dilutive effect on earnings per share, book value per share or the percentage voting or ownership interest of the present holders of our common stock, none of whom have preemptive rights under the Certificate of Incorporation to subscribe for additional securities that we may issue.
The Proposed Certificate Amendment has been prompted by business and financial considerations. The Board currently is not aware of any attempt by a third party to accumulate shares of our common stock or take control of the Company by means of a merger, tender offer or solicitation in opposition to management or the Board. Moreover, we currently have no plans to issue newly authorized shares of common stock to discourage third parties from attempting to take over the Company. However, the Proposed Certificate Amendment could, under certain circumstances, have an anti-takeover effect or delay or prevent a change in control of the Company by providing the Company the capability to engage in actions that would be dilutive to a potential acquiror, to pursue alternative transactions, or to otherwise increase the potential cost to acquire control of the Company. Thus, while we currently have no intent to use the additional authorized shares as an anti-takeover device, the Proposed Certificate Amendment may have the effect of discouraging future unsolicited takeover attempts.
Once the Proposed Certificate Amendment is approved, no further action by the stockholders would be necessary prior to the issuance of additional shares of common stock unless required by law or Nasdaq listing rules. Each of the newly authorized shares of common stock will have the same rights and privileges as currently authorized shares of common stock. Adoption of the Proposed Certificate Amendment will not affect the rights of the holders of currently outstanding common stock, nor will it change the par value of the common stock.
A complete copy of the existing Certificate of Incorporation is available as an exhibit to the Company’s Annual Report on Form 10-K for the year ended December 31, 2023.
The Proposed Certificate Amendment is binding. If the Proposed Certificate Amendment is approved, we intend to file a Certificate of Amendment to our Certificate of Incorporation with the Secretary of State of the State of Delaware as soon as reasonably practicable after the Annual Meeting. The Proposed Certificate Amendment will become effective upon such filing.
THE BOARD OF DIRECTORS RECOMMENDS
A VOTE “FOR”
PROPOSAL 2.

4.



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EXECUTIVE OFFICERS

The following table sets forth certain information with respect to the Company'sCompany’s current executive officers asofficers. There are no family relationships among any of March 12, 2018.

our directors or executive officers.
NameAgePosition
Name
AgePosition

Dinesh V. Patel, Ph.D.

6167President, Chief Executive Officer and Director

David Y. Liu, Ph.D. 

Asif Ali
68Chief Scientific Officer and Head of Research & Development

Richard S. Shames, M.D. 

50
58Chief Medical Officer

Thomas P. O'Neil

53Executive Vice President, Chief Financial Officer
Suneel Gupta, Ph.D.66Chief Development Officer
Arturo Molina, M.D., M.S., F.A.C.P.65Chief Medical Officer

Dinesh V. Patel, Ph.D.

Biographical information for Dr. Patel is included above with the director biographies under the caption "Class“Class I Directors Continuing in Office Until the 20202026 Annual Meeting."

David Y. Liu, Ph.D.

Dr. Liu

Asif Ali
Mr. Ali has served as the Company's Chief Scientific Officer (CSO) since May 2013 and has served as CSO and Head of Research and Development since February 2016. Prior to Protagonist, Dr. Liu was the Chief Operating Officer and a cofounder of Trenovus, Inc., from 2010 to 2012. Prior to Trenovus, Dr. Liu wasCompany’s Executive Vice President, of Research at FibroGen Inc., from 2002 to 2010. Prior to Fibrogen, Dr. Liu served as Director of Inflammation Research at Scios, Inc., now part of Johnson & Johnson, from 1992 to 2002. Dr. Liu held a position as an academic researcher at Brigham and Women's Hospital, Harvard Medical School and was Instructor and Assistant Professor in the Department of Medicine, Harvard Medical School, from 1976 to 1986. Dr. Liu received his Ph.D. in Microbiology and Immunology from Michigan State University, and his B.S. in Chemistry from The University of Chicago.

Richard S. Shames, M.D.

Dr. Shames has served as the Company's Chief MedicalFinancial Officer since August 2015. He currently also serves as Adjunct Associate Clinical Professor of Pediatrics at Stanford University.April 2022. Prior to joining Protagonist, he served as Vice President, Finance and Chief Accounting Officer for Theravance Biopharma, Inc. (Nasdaq: TBPH), a multinational biopharmaceutical company, from September 2018 to February 2022, where his contributions and oversight included equity and asset-backed financings, strategic collaborations, finance operations, international tax planning and long-term business strategy. Prior to Theravance, Mr. Ali served as Vice President and Corporate Controller for Depomed, Inc. (now Assertio Holdings, Inc. (Nasdaq: ASRT)), a specialty pharmaceutical company, from June 2012 to June 2018, where he supported multiple product launches, product acquisitions and equity and asset-backed financings. From 2010 to 2011, he served as Director of Finance and Accounting for Nevada Property 1 LLC, a former public company that owned and operated the Cosmopolitan of Las Vegas, Nevada. From 2004 to 2009, Mr. Ali worked in public accounting in the life sciences practice of PricewaterhouseCoopers LLP, an accounting firm, where he held various positions of responsibility and left as a Senior Manager. Mr. Ali is a fellow of the Institute of Chartered Accountants in England & Wales, a qualification that he obtained in conjunction with studying accounting at the University of North London, United Kingdom (the combined studies are the U.S. equivalent of a B.S. in Business Administration with concentration in accounting). He also holds a C.P.A. license in California.

Suneel Gupta, Ph.D.
Dr. Gupta has served as the Company’s Chief Development Officer since May 2019, and previously served as the Company’s Executive Vice President of Clinical Pharmacology and Clinical Operations from January 2019 to May 2019. Prior to joining Protagonist, he was Chief Scientific Officer of Impax Pharmaceuticals, a pharmaceutical company, where he was responsible for all aspects of the company’s neurology and psychiatry research and development efforts, including research, development, clinical, regulatory and medical affairs, from 2008 to January 2019. Prior to Impax, Dr. Gupta was Senior Vice President and Chief Medical OfficerDistinguished Research Fellow at Aldea Pharmaceuticals,Johnson & Johnson (NYSE: JNJ), a multinational corporation, where he led early development from 2013 to 2015.2002 through 2008. Prior to Aldea, Dr. Shames was Distinguished Scientist, Clinical ResearchJohnson & Johnson, he held positions at ALZA Corporation, a pharmaceutical and Early Biologics Lead (Immunology) at Merck & Co., Inc.,medical systems company, from 2009 to 2013. Prior to joining Merck, Dr. Shames1989 through 2001, where he held positionsroles of increasing responsibility, at Facet Biotech (formerly PDL BioPharma),including serving as Vice President of Clinical Pharmacology & Product Discovery. Dr. Gupta serves on the scientific advisory boards of several pharmaceutical companies. Dr. Gupta received a Ph.D. in Pharmacokinetics from 1999 to 2009, most recently as Therapeutic Headthe University of ImmunologyManchester, UK in 1987 and Senior Medical Director. Prior to Facet, Dr. Shames held full time clinical faculty positionsdid a postdoctoral fellowship in Pediatric Allergy and Clinical ImmunologyPharmacology at Stanford University, from 1996 to 1999, and the University of California, San Francisco Schools of Medicine, from 1993 to 1996. Francisco.
Arturo Molina, M.D., M.S., F.A.C.P.
Dr. Shames received his M.D. from University of California, Davis School of Medicine and received a B.S. in Biological Sciences from Stanford University.

Thomas P. O'Neil

Mr. O'NeilMolina has served as the Company'sCompany’s Chief FinancialMedical Officer since February 2016. From March 2015November 2022. Prior to October 2015, Mr. O'Neiljoining Protagonist, he served as Chief FinancialMedical Officer of Arcadia Biosciences,for Sutro Biopharma, Inc. (Nasdaq: STRO), a biopharmaceutical company. From January 2014biotechnology company, where he established a world-class, Cross-Functional Clinical Development, Regulatory, Clinical Operations and Biometrics Team (CDRT) to July 2014, Mr. O'Neil served as Chief Financial Officer of Sorbent Therapeutics, Inc.advance development candidates and optimized leads towards


23


Investigational New Drug and registration-enabling clinical studies, from 2016 to 2022. Prior to Sutro, Dr. Molina was Vice President, Oncology Scientific Innovation at Johnson & Johnson (NYSE: JNJ), a biopharmaceutical company. From September 2011multinational corporation. Earlier in his career, Dr. Molina was Chief Medical Officer at Cougar Biotechnology Inc., until it was acquired by Johnson & Johnson in 2009. Dr. Molina was an Adjunct Professor in the Department of Hematology/Bone Marrow Transplantation at City of Hope Comprehensive Cancer Center, from 2002 to December 2013, Mr. O'Neil2004. Prior to that, he served as a consultantfaculty staff physician in the Department of Hematology/Bone Marrow Transplantation and Medical Oncology/Therapeutics Research from 1991 to Sorbent2002. Dr. Molina received his M.D. and M.S. in Physiology from Stanford University Medical Center, and a variety of health careB.A. in Psychology and technology companies. From December 2009 to August 2011, Mr. O'Neil served as Vice President of Finance & Administration of ChemGenex Pharmaceuticals Ltd., a biopharmaceutical company. From March 2007 to May 2009, Mr. O'Neil served as Vice President of Finance & Administration of Nodality, Inc., a biotechnology company. Mr. O'Neil holds a B.A. from Pomona CollegeB.S. in International Relations and an M.B.A.Zoology from the University of California, Los Angeles.

Texas, Austin. Dr. Molina maintains an Adjunct Clinical Faculty appointment in the Department of Medicine, division of Oncology, Stanford University School Medicine.



24


SECURITY OWNERSHIP OF

CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth certain information regarding the ownership of the Company'sCompany’s common stock as of March 12, 201815, 2024 by: (i) each director and nominee for director; (ii) each of the named executive officers named in the Summary Compensation Table;officers; (iii) all current executive officers and directors of the Company as a group; and (iv) all thosepersons and entities known by the Company to be beneficial owners of more than five percent of its common stock.

Beneficial Ownership(1)
Beneficial OwnerNumber of
Shares
Percent of
Total
5% Stockholders:
Farallon Partners, L.L.C. and its affiliated entities(2)
5,798,3409.9%
Biotechnology Value Fund, L.P. and its affiliated entities(3)
5,798,3409.9%
BlackRock, Inc.(4)
5,543,9029.5%
RTW Investments, L.P.(5)
5,315,5149.1%
The Vanguard Group, Inc.(6)
3,153,9165.4%
Named Executive Officers and Directors:
Dinesh V. Patel, Ph.D.(7)
1,959,7803.3%
Suneel Gupta, Ph.D.(8)
471,030*
Asif Ali(9)
59,108*
Harold E. Selick, Ph.D.(10)
204,586*
Bryan Giraudo(11)
157,566*
Sarah A. O’Dowd(12)
106,566*
Daniel N. Swisher, Jr.(13)
7,500*
William D. Waddill(14)
151,566*
Lewis T. Williams, M.D., Ph.D.(15)
139,566*
All current executive officers and directors as a group (10 persons)(16)
3,323,1425.4%
 
 Beneficial Ownership(1) 
Beneficial Owner
 Number of Shares Percent of Total 

5% Stockholders:

       

Adage Capital Partners, LP(2)

  2,056,576  9.7%

Canaan X L.P(3)

  2,453,255  11.6%

FMR LLC(4)

  3,071,949  14.5%

Johnson & Johnson Development Corporation(5)

  2,449,183  11.6%

Lilly Ventures Fund I, LLC(6)

  2,099,482  9.9%

Executive Officers and Directors:

       

Dinesh V. Patel, Ph.D.(7)

  510,336  2.4%

David Y. Liu, Ph.D.(8)

  108,083  * 

Richard S. Shames, M.D.(9)

  95,052  * 

Harold E. Selick, Ph.D.(10)

  44,284  * 

Chaitan Khosla, Ph.D.(11)

  37,925  * 

Sarah B. Noonberg, M.D., Ph.D.(12)

  3,333  * 

Armen B. Shanafelt, Ph.D.(13)

  2,113,482  10.0%

William D. Waddill(14)

  25,893  * 

Lewis T. Williams, M.D., Ph.D.(15)

  7,332  * 

All executive officers and directors as a group (10 persons)(16)

  3,013,468  13.8%

*
*
LessRepresents beneficial ownership of less than one percent.
percent of the outstanding common stock.
(1)

This table is based upon information supplied by officers, directors and principal stockholders and Schedules 13D and 13G filed with the SEC. Beneficial ownership is determined in accordance with the rules promulgated by the SEC. Under such rules, beneficial ownership includes any shares of common stock over which the person or group has sole or shared voting or investment power as well as any shares of common stock that the person or group has the right to acquire within 60 days after the date of this table. Unless otherwise indicated in the footnotes to this table and subject to community property laws where applicable, the Company believes that each of the stockholders named in this table has sole voting and investment power with respect to the shares indicated as beneficially owned. Applicable percentages are based on 21,148,52358,569,088 shares outstanding on March 12, 2018 adjusted as required by rules promulgated byof the SEC.date of this table. Pursuant to the rules of the SEC, the number of shares of common stock deemed outstanding includes shares issuable upon settlement of restricted stock units held by the respectivefor a person or group that will vestincludes shares of common stock such person or group has the right to acquire within 60 days of March 12, 2018 and pursuant to options held by the respective person or group that are currently exercisable or may be exercised within 60 daysdate of March 12, 2018.this table. Unless otherwise indicated, the address for each of beneficial owner is c/o Protagonist Therapeutics, Inc., 7707 Gateway Blvd., Suite 140, Newark, CACalifornia 94560.
(2)

This information is based solely upon a Schedule 13G/A filed jointly with the SEC on February 2, 2024 by Adageentities affiliated with Farallon Partners, L.L.C. (“Farallon General Partner”). Consists of (i) 380,977 shares held by Farallon Capital Partners, L.P. ("ACP"(“FCP”), Adage(ii) 390,700 shares held by Farallon Capital Institutional Partners, GP, L.L.C. ("ACPGP"L.P. (“FCIP”), Adage(iii) 126,312 shares held by Farallon Capital Advisors, L.C.C. ("ACA"Institutional Partners II, L.P. (“FCIP II”), Robert Atchinson(iv) 53,700 shares held by Farallon Capital Institutional Partners III, L.P. (“FCIP III”), (v) 71,000 shares held by Four Crossings Institutional Partners V, L.P. (“FCIP V”), (vi) 750,036 shares held by Farallon Capital Offshore Investors II, L.P. (“FCOI II”), (vii) 49,579 shares held by Farallon Capital (AM) Investors, L.P. (“FCAMI”), (viii) 165,370 shares held by Farallon Capital F5 Master I, L.P. (“F5MI”), (ix) 3,746,756 shares held by Farallon Healthcare Partners Master, L.P. (“FHPM,” and Phillip Gross on January 4, 2018. ACPGP servestogether with FCP, FCIP, FCIP II, FCIP III, FCIP V, FCOI II, FCAMI and F5MI, the “Farallon Funds”) and (x) 63,910 shares underlying certain exercisable warrants. Excludes 1,436,090 shares underlying certain warrants, the exercise of which is subject to a beneficial ownership limitation of 9.99% of the outstanding common stock. Farallon General Partner, as the (i) general partner of each of FCP, FCIP, FCIP II, FCIP III, FCOI II and FCAMI and (ii) the sole member of each of Farallon Institutional (GP) V, L.L.C. (“FCIP V General Partner”) and Farallon Healthcare Partners (GP), L.L.C. (“FHPM General Partner”), is deemed to be the beneficial owner of the shares held by each of the Farallon Funds other than F5MI. FCIP V General Partner, as the general partner of ACP and as such has discretion over the portfolio of securities beneficially owned by ACP. ACA is the managing member of ACPGP and directs ACPGP's operations. Robert Atchinson and Phillip Gross are the managing members of ACA. ACP has the power to dispose of and the power to vote the shares of the Company's common stock beneficially owned by it, which power may be exercised by its general partner, ACPGP. ACA, as managing member of ACPGP, directs ACPGP's operations. Messrs. Atchinson and Gross, as managing

    members of ACA, have shared power to vote the shares of the Company's common stock beneficially owned by ACP. Neither ACPGP, ACA, Mr. Atchinson nor Mr. Gross directly own any shares of the Company's common stock. By reason of the provisions of Rule 13d-3 of the Securities Exchange Act of 1934, as amended (the "Act"), ACPGP and ACAFCIP V, may be deemed to beneficially own the shares ownedheld by ACP. The address of ACP is 200 Clarendon Street, 52nd Floor, Boston, MA 02110.

(3)
This information is based in part upon a Schedule 13G filed jointly with the SEC by Canaan X L.P. and Canaan Partners X LLC on January 26, 2017. Canaan Partners X LLC is theFCIP V. Farallon F5 (GP), L.L.C. (“F5MI General Partner”), as general partner of Canaan X L.P. andF5MI, may be deemed to have sole investment and voting power overbeneficially own the shares held by Canaan X L.P. Brenton K. Ahrens, Stephen M. Bloch, Daniel T. Ciporin, Wende S. Hutton, Maha S. Ibrahim, Deepak Kamra, Nina Kjellson, Guy M. Russo, Tim Shannon and Hrach Simonian are the managing membersF5MI. FHPM General Partner, as general partner of Canaan Partners X LLC. Investment, voting and dispositive decisions with respectFHPM, may be deemed to beneficially own the shares held by Canaan X L.P. are made byFHPM. Joshua J. Dapice,

25


Philip D. Dreyfuss, Hannah E. Dunn, Richard B. Fried, Varun N. Gehani, Nicolas Giauque, David T. Kim, Michael G. Linn, Rajiv A. Patel, Thomas G. Roberts, Jr., Edric C. Saito, William Seybold, Daniel S. Short, Andrew J. M. Spokes, John R. Warren and Mark C. Wehrly (the “Farallon Individuals”), each of whom is a managing member or senior managing member of Farallon General Partner, and a manager or senior manager, as the managerscase may be, of Canaan Partners X LLC, collectively. The managers of Canaan Partners X LLC do not have beneficial ownership (withinFCIP V General Partner, F5MI General Partner and FHPM General Partner, may each be deemed to beneficially own the meaning of Rule 13d-3 promulgated under the Act) of any shares held by Canaan X L.P.the Farallon Funds. Each of the Farallon General Partner, the FCIP V General Partner, the F5MI General Partner, the FHPM General Partner and the Farallon Individuals disclaims any beneficial ownership of the shares and warrants. The address for Canaan X L.P.of each of the entities and persons above is 285 Riverside Avenue,c/o Farallon Capital Management, L.L.C., One Maritime Plaza, Suite 250, Westport, CT 06880.
(4)
2100, San Francisco, CA 94111.
(3)
This information is based solely upon a Schedule 13G/A filed jointly with the SEC by FMR LLC and Abigail P. Johnson on February 13, 2018.14, 2024 by entities affiliated with Biotechnology Value Fund, L.P. (“BVF”). Consists of (i) 3,101,857 shares held by BVF, (ii) 2,344,241 shares held by Biotechnology Value Fund II, L.P. (“BVF2”), (iii) 238,172 shares held by Biotechnology Value Trading Fund OS LP (“Trading Fund OS”), (iv) 60,038 shares held in certain Partners Managed Accounts and (v) 54,032 shares underlying certain pre-funded warrants. Excludes 1,151,220 shares underlying certain pre-funded warrants, the exercise of which is subject to a beneficial ownership limitation of 9.99% of the outstanding common stock. BVF I GP LLC (“BVF GP”), as the general partner of BVF, may be deemed to beneficially own the shares beneficially owned by BVF. BVF II GP LLC (“BVF2 GP”), as the general partner of BVF2, may be deemed to beneficially own the shares beneficially owned by BVF2. BVF Partners OS Ltd. (“Partners OS”), as the general partner of Trading Fund OS, may be deemed to beneficially own the shares beneficially owned by Trading Fund OS. BVF GP Holdings LLC (“BVF GPH”), as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the shares beneficially owned in the aggregate by BVF and BVF2. BVF Partners L.P. (“Partners”), as the investment manager of BVF, BVF2 and Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the shares beneficially owned in the aggregate by BVF, BVF2 and Trading Fund OS, and the shares held in the Partners Managed Accounts. BVF Inc., as the general partner of Partners, may be deemed to beneficially own the shares beneficially owned by Partners. Mark N. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the shares beneficially owned by BVF Inc. BVF GP disclaims beneficial ownership of the shares beneficially owned by BVF. BVF2 GP disclaims beneficial ownership of the shares beneficially owned by BVF2. Partners OS disclaims beneficial ownership of the shares beneficially owned by Trading Fund OS. BVF GPH disclaims beneficial ownership of the shares beneficially owned by BVF and BVF2. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the shares beneficially owned by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Accounts. The address for BVF, BVF GP, BVF2, BVF2 GP, BVF GPH, Partners, BVF Inc. and Mr. Lampert is 44 Montgomery Street, 40th Floor, San Francisco, CA 94104. The address of Trading Fund OS and Partners OS is PO Box 309 Ugland House, Grand Cayman, KY1-1104, Cayman Islands.
(4)
This information is based solely upon a Schedule 13G/A reports that FMR LLC heldfiled with the SEC on January 24, 2024 by BlackRock, Inc. (“BlackRock”). BlackRock has sole voting power over 396,120with respect to 5,458,848 shares and no shared voting power and sole dispositive power of 3,071,949 shares and no shared dispositive power. Abigail P. Johnson is a director, the vice chairman, the chief executive officer and the president of FMR LLC and has sole dispositive power over 3,071,949 shares. Members of the Johnson family, including Abigail P. Johnson, are the predominant owners, directly or through trusts, of Series B voting common shares of FMR LLC, representing 49% of the voting power of FMR LLC. The Johnson family group and all other Series B stockholders have entered into a stockholders' voting agreement under which all Series B voting common shares will be voted in accordance with the majority vote of Series B voting common shares. Accordingly, through their ownership of voting common shares and the execution of the stockholders' voting agreement, members of the Johnson family may be deemed, under the Investment Company Act of 1940, as amended (the "Investment Company Act"), to form a controlling group with respect to FMR LLC. Neither FMR LLC nor Abigail P. Johnson has the sole power to vote or direct the voting of the shares owned directly by the various investment companies registered under the Investment Company Act (the "Fidelity Funds") advised by Fidelity Management & Research Company ("FMR Co."), a wholly owned subsidiary of FMR LLC, which power resides with the Fidelity Funds' Boards of Trustees. FMR Co. carries out the voting of the shares under written guidelines established by the Fidelity Funds' Boards of Trustees.5,543,902 shares. The address for FMR LLCof BlackRock is 245 Summer Street, Boston, MA 02210.
50 Hudson Yards, New York, NY 10001.
(5)

This information is based in partsolely upon a Schedule 13G13G/A jointly filed jointly with the SEC on February 14, 2024 by Johnson & Johnson ("J&J"),RTW Investments, LP and Johnson & Johnson Innovation-JJDC, Inc. ("JJDC") on August 19, 2016. JJDC is a wholly-owned subsidiary of J&J. The securities held by J&JRoderick Wong, M.D. RTW Investments, LP and JJDC are directly beneficially owned by JJDC. J&J may be deemed to indirectly beneficially own the securities that are directly beneficially owned by JJDC. The board of directors of JJDC, which consists of Paulus StoffelsDr. Wong have shared voting and Steven Rosenberg, has shared investment and voting controldispositive power with respect to thethese shares, which are directly held by JJDCcertain funds to which RTW Investments, LP is the investment adviser. Dr. Wong is the Managing Partner and has delegated responsibility therefor to the managementChief Investment Officer of JJDC to take such actions on behalf of JJDC. As such, no individual member of the JJDC board of directors is deemed to hold any beneficial ownership or reportable pecuniary interest in the shares held by JJDC. No individual representative of JJDC shall be deemed (i) a beneficial owner of, or (ii) to have a reportable pecuniary interest in, the shares held by JJDC.RTW Investments, LP. The address of JJDCRTW Investments, LP and Dr. Wong is One Johnson & Johnson Plaza,40 10th Avenue, Floor 7, New Brunswick, NJ 08933.
York, NY 10014.
(6)
LV Management
This information is based solely upon a Schedule 13G/A filed with the SEC on February 13, 2024 by the Vanguard Group, LLC ("LVMG"Inc (“Vanguard”) is the management company for Lilly Ventures Fund I, LLC ("LVFI") and. Vanguard has dispositiveshared voting power over the shares held by LVFI. As such, LVMG

    may be deemed to indirectly beneficially own the shares held by LVFI. LVMG's voting and dispositive decisions with respect to the78,615 shares, held by LVFI are made by LVMG's management committee, which consistssole dispositive power with respect to 3,029,991 shares and shared dispositive power with respect to 123,925 shares. The address of Ed Torres, Steve Hall and Armen Shanafelt (collectively, the "Management Committee Members"). The mailing addresses of the beneficial ownersVanguard is 115 West Washington Street, Suite 1680 South, Indianapolis, IN 46204.

100 Vanguard Blvd., Malvern, PA 19355.
(7)

Includes 314,3711,479,657 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
(8)
Consiststhe date of 102,555this table.
(8)
Includes 323,587 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
(9)
Consiststhe date of 93,346this table.
(9)
Includes (i) 55,671 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
(10)
Consiststhe date of 44,284this table and (ii) 3,437 restricted stock units vesting within 60 days of the date of this table.
(10)
Includes 176,590 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
(11)
Consiststhe date of 37,925this table.
(11)
Includes 18,000 shares held indirectly by the Bryan and Courtney Giraudo Trust and 139,566 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
the date of this table.
(12)

Consists of 3,333106,566 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
the date of this table.
(13)
Includes 14,000
Consists of 7,500 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018 and the shares held by LVFI referenced in footnote (6) above. Dr. Shanafelt's business addresses is 115 West Washington Street, Suite 1680 South, Indianapolis, IN 46204.
date of this table.
(14)

Consists of 25,893139,566 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
the date of this table.
(15)

Consists of 7,332139,566 shares issuable pursuant to stock options exercisable within 60 days of March 12, 2018.
the date of this table.
(16)

Includes 707,327(i) 2,630,065 shares that certain executive officers and directors of the Company have the rightissuable pursuant to acquirestock options exercisable within 60 days of March 12, 2018 pursuant to the exercisedate of outstanding options.this table and (ii) 3,437 restricted stock units vesting within 60 days of the date of this table.



26


DELINQUENT SECTION 16(A) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

REPORTS

Section 16(a) of the Exchange Act requires the Company'sour directors, and executive officers and persons who beneficially own more than ten percent10% of a registered class of the Company'sour equity securities to file with the SEC initial reports of ownership and reports of changes in ownership of our common stock and other equity securities. To our knowledge, based solely on our review of Forms 3, 4 and 5 filed with the SEC or written representations that no Form 5 was required, during the year ended December 31, 2023 we believe that our directors, officers and persons who beneficially own more than 10% of a registered class of our equity securities timely filed all reports required under Section 16(a) of the Company. Officers, directors and greater than ten percent stockholders are required by SEC regulationExchange Act, except that, due to furnish the Company with copies of all Section 16(a) forms they file.

During fiscal 2017, Dr. Noonberg timely reported all transactions but a timely filedadministrative error, one Form 4 containedto report a typographical errorsell-to-cover transaction for Dr. Molina was filed late.


27


EXECUTIVE COMPENSATION
In accordance with SEC transition rules, in this Proxy Statement, we are continuing to provide executive compensation disclosures under the exercise priceSEC’s scaled disclosure framework. Accordingly, our reporting obligations with respect to our named executive officers (“NEOs”) extend only to the individuals who served as the principal executive officer and the next two most highly compensated executive officers as of the end of the prior fiscal year, as well as up to two additional individuals for whom disclosure would have been provided based on their compensation levels but for the fact that the individual was not serving as an option to purchase common stock. This error was corrected by amendingexecutive officer at the previous Form 4 report.

end of the prior fiscal year. Our NEOs for 2023 include Dr. Patel, our President and Chief Executive Officer, Dr. Gupta, our Chief Development Officer, and Mr. Ali, our Executive Vice President, Chief Financial Officer.


EXECUTIVE COMPENSATION

The following table sets forth information regarding compensation awarded to or earned by the executive officers listed belowour NEOs during the years ended December 31, 20172023 and December 31, 2016. As an emerging growth company, the Company complies with the executive compensation disclosure rules applicable to "smaller reporting companies," as such term is defined in the rules promulgated under the Securities Act of 1933, as amended (the "Securities Act"), which require compensation disclosure for the principal executive officer and the two most highly compensated executive officers other than the principal executive officer at December 31, 2017. These three officers are referred to as the named executive officers (the "Named Executive Officers").


2022.

SUMMARY COMPENSATION TABLE FOR FISCAL 2017

2023
NameYear
Salary
($)
(1)
Stock
Awards
($)
(2)(3)
Option
Awards
($)
(2)
Non-Equity
Incentive Plan 
Compensation
($)
(4)
All Other
Compensation
($)
(5)
Total ($)
Dinesh V. Patel, Ph.D.
President and Chief
Executive Officer
2023655,2006,041,100360,36010,9127,067,572
2022630,000897,8134,211,963242,55010,9125,993,238
Suneel Gupta, Ph.D.
Chief Development Officer
2023515,205251,0061,245,977193,12510,8762,216,189
2022500,000359,1251,684,785130,00010,8942,684,804
Asif Ali
EVP, Chief Financial Officer(6)
2023447,000129,306641,867178,8005,2421,402,215
Name and Principal Position
 Year Salary
($)(1)
 Option
Awards
($)(2)
 Non-Equity
Incentive Plan
Compensation
($)(3)
 All Other
Compensation
($)(4)
 Total
($)
 

Dinesh V. Patel, Ph.D. 

  2017  475,000    309,000  6,088  790,088 

President and Chief

  2016  400,000  4,430,240  160,000    4,990,240 

Executive Officer

                   

David Y. Liu, Ph.D. 

  
2017
  
357,000
  
  
186,000
  
9,168
  
552,168
 

Chief Scientific Officer and

  2016  310,000  922,707  93,000    1,325,707 

Head of Research & Development

                   

Richard S. Shames, M.D. 

  
2017
  
357,000
  
  
179,000
  
3,279
  
539,279
 

Chief Medical Officer

  2016  326,000  909,533  96,578  420  1,332,531 

(1)
(1)
The amounts in the "Salary"“Salary” column reflect each Named Executive Officer'sNEO’s base salary plus any additional amounts paid for unused accrued vacation or sick time.
salary.
(2)

The amounts in the "Option Awards" column“Stock Awards” and “Option Awards” columns reflect the aggregate grant date fair value of restricted stock units (“RSUs”), performance stock units (“PSUs”) and stock options, as applicable, granted during the calendar year and computed in accordance with the provisions of Accounting Standards Codification (ASC)(“ASC”) 718, Compensation—Compensation — Stock Compensation. The valuation assumptions used in determining such amounts aremethodology of these awards is described in the notes to the Company'sCompany’s financial statements included in its Annual Report on Form 10-K for the year ended December 31, 2017.2023. These amounts do not reflect the actual economic value that will be realized by the Named Executive OfficerNEO upon the vesting of the RSUs, PSUs and stock options, the exercise of the stock options, or the sale of the common stock underlying such stock options.awards. As required by SEC rules, the amounts shown exclude the impact of estimated forfeitures related to service-based vesting conditions. With respect to option awards only, the Named Executive OfficersNEOs will only realize compensation to the extent the trading price of the common stock is greater than the exercise price of such stock options.
(3)

PSUs granted in 2022 were deemed to have no reportable accounting grant date value because the performance goal was not likely to be achieved as of the grant date. The PSUs granted in 2022 vested 100% on May 31, 2023, the date that the Compensation Committee determined, in its sole discretion, that the Company’s forecasted cash and cash equivalents were sufficient to fund the Company’s operations through at least December 31, 2025. The maximum value of the PSUs at grant date for 2022, assuming the performance conditions were achieved, was $262,800 for Dr. Patel and $105,120 for Dr. Gupta.
(4)
The amounts in the "Non-Equity“Non-Equity Incentive Plan Compensation"Compensation” column for 20172023 reflect cash bonuses earned for the 20172023 fiscal year, which were paid in 2018,2024, based on the achievement of certain predetermined corporate objectives specified by the Board, including operating targets and research and development outcomes. In February 2018,December 2023, the Compensation Committee determined that the Company met 130%100% of its 20172023 corporate objectives and approved the amount of each

    Named Executive Officer's NEO’s bonus. The amount of the bonus that each named executive officerNEO earned for the fiscal year ended on December 31, 20172023 is listed in the table below.

Name2023 Base
Salary ($)
Target
Bonus
(As a % of
Base Salary)
Amount of
Bonus
Earned ($)
Dinesh V. Patel, Ph.D.655,20055%360,360
Suneel Gupta, Ph.D.515,20540%193,125
Asif Ali447,50040%178,800

Name
 2017
Base Salary
($)
 Target Bonus Amount of
Bonus Earned
($)
 

Dinesh V. Patel, Ph.D. 

  475,000  50% 309,000 

David Y. Liu, Ph.D. 

  357,000  40% 186,000 

Richard Shames, M.D. 

  357,000  40% 179,000 
28

(4)

(5)
The amounts noted for 20172023 include $6,088$6,858 in group term life insurance for Dr.Drs. Patel $9,168 inand Gupta and $1,242 group term life insurance for Dr. LiuMr. Ali, and $3,104$4,000 in group term life insurance401(k) plan matching contributions paid by the Company for Dr. Shames.each of Drs. Patel and Gupta and Mr. Ali. The amounts noted for 20172023 for Drs. Patel and 2016Gupta also include $175 and $420, respectively,premiums paid for elective LifeLock identity protection services pursuant to Company-wide policy.
(6)
Mr. Ali was not an NEO in gym membership reimbursements for Dr. Shames.2022.



29


NARRATIVE TO SUMMARY COMPENSATION TABLE

EXECUTIVE EMPLOYMENT ARRANGEMENTS WITH NAMED EXECUTIVE OFFICERS

Employment Agreement with Dinesh V. Patel, Ph.D.

The

In December 2008, the Company entered into an employment agreement with Dinesh V. Patel. Ph.D.,Dr. Patel, the Company'sCompany’s President and Chief Executive Officer, in December 2008, which was subsequentlyas amended in December 2015. The employment agreement provides for2015, pursuant to which he commenced employment. For 2024, Dr. Patel will receive an initialannual base salary of $315,000, which has been subsequently increased a number of times$681,410, with the most recent increase to $520,000, effective as of January 1, 2018. The employment agreement also provides for an initial annual cashtarget bonus of up to 30%55% of Dr. Patel'sthat base salary, which has been subsequently increased a number of times with the most recent increase to 50% of Dr. Patel's base salary, effective as of January 1, 2017.salary. The amount, if any, of such bonus with respect to any calendar year is based on the achievement of predetermined corporate and personal objectives as determined by the Board in its discretion.

Offer Letter Agreement with David Y. Liu,Suneel Gupta, Ph.D.

The

In December 2018, the Company entered into an offer letter agreement with David Liu, Ph.D.,Dr. Gupta, the Company'sCompany’s Chief ScientificDevelopment Officer, in May 2013. The offer letter provides forpursuant to which he commenced employment. For 2024, Dr. Gupta will receive an initialannual base salary of $250,000, which has been subsequently increased a number of times$530,500, with the most recent increase to $410,000, effective as of January 1, 2018. The offer letter also provides for an initial annual cashtarget bonus of up to 25% of Dr. Liu's base salary, which has been subsequently increased a number of times with the most recent increase to 40% of Dr. Liu'sthat base salary, effective as of January 1, 2017.salary. The amount, if any, of such bonus with respect to any calendar year is based on the achievement of predetermined corporate and personal objectives as determined by the Board in its discretion.

Offer Letter Agreement with Richard Shames, M.D.

TheAsif Ali

In March 2022, the Company entered into an offer letter agreement with Richard Shames, M.D.,Mr. Ali, the Company'sCompany’s Executive Vice President, Chief MedicalFinancial Officer, pursuant to which he commenced employment and, as an inducement to his commencement of employment, he received a grant of 82,500 stock options and 13,750 RSUs, in August 2015.each case pursuant to the Company’s 2018 Inducement Plan. The offer letter provides forstock options vested 25% after one year of continuous service and continue to vest in equal monthly installments over the subsequent three years, subject to continued service through each such vesting date. The RSUs vest in four equal installments on each anniversary of the date of grant subject to continued service through each such vesting date. For 2024, Mr. Ali will receive an initialannual base salary of $321,000, which has been subsequently increased a number of times$465,000, with the most recent increase to $400,000, effective as of January 1, 2018. The offer letter also provides for an initial annual cashtarget bonus of up to 25% of Dr. Shames's base salary, which has been subsequently increased a number of times with the most recent increase to 40% of Dr. Shames'sthat base salary, effective as of January 1, 2017.salary. The amount, if any,


of such bonus with respect to anythe calendar year is based on the achievement of predetermined corporate and personal objectives as determined by the Board in its discretion.

POTENTIAL PAYMENTS UPON TERMINATION OR CHANGE IN CONTROL

The Company is party to an Employee Severance Agreement with each of its Named Executive OfficersNEOs and certain of its other executives. If the Company terminates the employee'semployee’s employment without "cause"“cause” or the employee terminates employment for "good reason" (each“good reason” ​(each as defined in the agreement), the employee will receive: (a) salary continuation for 12 months, for the Chief Executive Officer, or nine months, for the other Named Executive OfficersNEOs (18 months and 12 months, respectively, in the case of a change in control termination); (b) COBRA continuation for the salary continuation period (or an equivalent cash payment if required by law); (c) in the case of a change in control termination only, a monthly payment equal to one twelfth of the target bonus for the severance period; and (d) in the case of a change in control termination only, acceleration of the vesting (and exercisability, if relevant) of equity awards held as of the date of termination. A "change“change in control termination"termination” is a termination by the Company without "cause"“cause” or the employee for "good reason"“good reason” that occurs within twelve months following the date of a "change“change in control" (ascontrol,” as defined in the agreement).agreement. Payments and benefits under the agreement are subject to the execution of an effective release.


OUTSTANDING EQUITY AWARDS AT FISCAL YEAR END

The following table shows for the fiscal year ended December 31, 2017,2023, certain information regarding outstanding equity awards at fiscal year end for the Named Executive Officers.

NEOs.



30


OUTSTANDING EQUITY AWARDS AT DECEMBER 31, 2017

2023
Option AwardsStock Awards
Equity Incentive
Plan Awards
Grant DateNumber of
Securities
Underlying
Unexercised
Options
(#)
Exercisable
Number of
Securities
Underlying
Unexercised
Options
(#)
Unexercisable
Option
Exercise
Price
($)
Vesting
Commencement
Date
Option
Expiration
Date
Number of
Shares or
Units of
Stock
That
Have Not
Vested
(#)
Market
Value of
Shares or
Units of
Stock
That
Have Not
Vested
($)
Number of
Unearned
Shares,
Units or
Other
Rights
That
Have Not
Vested
(#)
Market
or Payout
Value of
Unearned
Shares,
Units or
Other
Rights
That
Have Not
Yet
Vested
($)
Dinesh V. Patel, Ph.D.04/29/201654,000$4.2104/25/201604/28/2026
10/11/2016320,000$21.5808/10/201610/10/2026
02/28/2018150,000$16.9502/28/201802/27/2028
08/15/201854,700$8.5808/05/201808/14/2028
02/28/2019(1)172,500$8.0202/28/201902/27/2029
02/28/2020(1)225,2089,792$7.8002/28/202002/27/2030
02/26/2021(1)(2)(3)159,37565,625$23.5702/26/202102/25/203125,000573,25025,000573,250
02/15/2022(1)(4)85,937101,563$28.7302/15/202202/14/203220,834477,724
01/16/2023(1)137,500462,500$12.1701/16/202301/15/2033
Suneel Gupta, Ph.D.01/15/201950,000$7.3801/07/201901/14/2029
02/28/2019(1)45,000$8.0202/28/201902/27/2029
02/28/2020(1)81,4583,542$7.8002/28/202002/27/2030
02/26/2021(1)(2)(3)56,66623,334$23.5702/26/202102/25/203112,000275,16012,000275,160
02/15/2022(1)(4)34,37540,625$28.7302/15/202202/14/20328,334191,099
01/16/2023(1)(4)28,35995,391$12.1701/16/202301/15/203320,625472,931
Asif Ali04/18/2022(5)(6)34,37548,125$19.1904/18/202204/17/203210,313236,477
01/16/2023(1)(4)14,60949,141$12.1701/16/202301/15/203310,625243,631
(1)
The shares subject to the option vest as to 1/48 of the shares in equal monthly installments following the vesting commencement date, subject to the holder continuing to provide services through the applicable vesting date. The option is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the twelve months following the acquisition as described in “— Potential Payments upon Termination or Change in Control” above.
(2)
100% of the stock award vests three years from the grant date subject to the holder continuing to provide services through the applicable vesting date. The award is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the twelve months following the acquisition as described in “— Potential Payments upon Termination or Change in Control” above.
(3)
100% of the equity incentive plan award vests upon the first to occur of a submission of (i) a New Drug Application to the U.S. Food and Drug Administration or (ii) a European Union marketing authorization for a product candidate, subject to the holder continuing to provide services through the applicable vesting date. The award is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the twelve months following the acquisition as described in “— Potential Payments upon Termination or Change in Control” above.
(4)
1/3 of the stock award shares vest in equal yearly installments over three years subject to the holder continuing to provide services through the applicable vesting date. The award is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the twelve months following the acquisition as described in “— Potential Payments upon Termination or Change in Control” above.
(5)
25% of the stock award shares vest in equal yearly installments over four years subject to the holder continuing to provide services through the applicable vesting date. The award is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the twelve months following the acquisition as described in “— Potential Payments upon Termination or Change in Control” above.

31

 
 Grant Date Number of
Securities
Underlying
Unexercised
Options
(#)
Exercisable
 Number of
Securities
Underlying
Unexercised
Options
(#)
Unexercisable
 Option
Exercise
Price
($)
 Vesting
Commencement
Date
 Option
Expiration
Date
 

Dinesh V. Patel, Ph.D. 

  09/26/2013(1) 11,298   $0.87  10/01/2013  09/26/2023 

  10/22/2014(1) 25,488  18,599 $1.89  11/01/2014  10/22/2024 

  10/28/2015(2) 19,551  58,653 $1.16  09/01/2015  10/28/2025 

  04/29/2016(3) 3,541  37,944 $4.21  04/25/2016  04/29/2026 

  04/29/2016(3) 70,930  66,327 $4.21  04/25/2016  04/29/2026 

  10/11/2016(3) 106,666  211,607 $21.58  08/10/2016  10/11/2026 

  10/11/2016(3)   1,727 $21.58  08/10/2016  10/11/2026 

David Y. Liu, Ph.D. 

  
09/26/2013

(1)
 
23,767
  
 
$

0.87
  
10/01/2013
  
09/26/2023
 

  10/22/2014(1) 6,834  4,642 $1.89  11/01/2014  10/22/2024 

  03/26/2015(2) 4,124  1,875 $1.89  04/01/2015  03/26/2025 

  10/28/2015(2) 20,053  15,603 $1.16  09/01/2015  10/28/2025 

  04/29/2016(3) 12,091  26,740 $4.21  04/25/2016  04/29/2026 

  10/11/2016(3) 18,589  36,060 $21.58  08/10/2016  10/11/2026 

  10/11/2016(3) 3,077  7,274 $21.58  08/10/2016  10/11/2026 

Richard S. Shames, M.D. 

  
10/28/2015

(4)
 
42,392
  
32,978
 
$

1.16
  
09/01/2015
  
10/28/2025
 

  04/29/2016(4) 9,745  23,529 $4.21  04/25/2016  04/29/2026 

  10/11/2016(3) 17,956  35,797 $21.58  08/10/2016  10/11/2026 

  10/11/2016(3) 3,710  7,537 $21.58  08/10/2016  10/11/2026 

(1)

(6)
25% of the shares subject to the option vest on the first anniversary of the vesting commencement date, and the remainder vests in 36 equal monthly installments thereafter, subject to the holder continuing to provide services through the applicable vesting date. The option is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the sixtwelve months following the acquisition as described in "—“— Potential Payments upon Termination or Change of Control"in Control” above.
(2)
The option vests as to 1/48 of the shares on the last day of each month following the vesting commencement date, subject to the holder continuing to provide services through the applicable vesting date. The option is subject to accelerated vesting in the event of an acquisition and in the event of a qualifying termination that occurs in the six months following the acquisition as described in "—Potential Payments upon Termination or Change of Control" above.
(3)
The option vests as to 1/48 of the shares on the last day of each month following the vesting commencement date, subject to the holder continuing to provide services through the applicable vesting date.
(4)
25% of the shares subject to the option vest on the first anniversary of the vesting commencement date, and the remainder vests in 36 equal monthly installments thereafter on the last day of each month, subject to the holder continuing to provide services through the applicable vesting date.


OPTION EXERCISES

The following table shows information regarding option exercises during the fiscal year ended December 31, 2017, with respect to the named executive officers.

Name
 Number of
Shares Acquired
Upon Exercise
(#)
 Value Realized
Upon Exercise
($)
 

Dinesh V. Patel, Ph.D. 

  65,461  748,684 

David Y. Liu, Ph.D. 

  15,750  204,649 

Richard S. Shames, M.D. 

  7,058  106,657 

NONQUALIFIED DEFERRED COMPENSATION

The companyCompany does not maintain any nonqualified deferred compensation plans. The Board may elect to provide the Company'sCompany’s officers and other employees with nonqualified deferred compensation benefits in the future if it determines that doing so is in the Company'sCompany’s best interests.

401(K) PLAN

The Company maintains a tax-qualified retirement plan that provides eligible U.S. employees with an opportunity to save for retirement on a tax advantaged basis. Eligible employees may defer eligible compensation subject to applicable annual Internal Revenue Code of 1986, as amended (the "Code"“IRC”), limits. The 401(k) plan permits participants to make both pre-tax and certain after-tax (Roth) deferral contributions. These contributions are allocated to each participant'sparticipant’s individual account and are then invested in selected investment alternatives according to the participant'sparticipant’s directions. Employees are immediately and fully vested in their contributions. Currently,The Company may make contributions to this plan at its discretion. For the years ended December 31, 2023 and 2022, the Company does not make matching contributions or discretionary contributionsmatched 50% of each employee’s contribution up to the 401(k) plan.a maximum of $4,000. The 401(k) plan is intended to be qualified under Section 401(a) of the CodeIRC with the 401(k) plan'splan’s related trust intended to be exempt under Section 501(a) of the Code.IRC. As a tax qualified retirement plan, contributions to the 401(k) plan and earnings on those contributions are not taxable to the employees until distributed from the 401(k) plan.


INCENTIVE COMPENSATION CLAWBACK POLICY
We have adopted a Compensation Recoupment (Clawback) Policy, which is intended to comply with the requirements of Nasdaq Listing Standard 5608 implementing Rule 10D-1 under the Exchange Act. In the event the Company is required to prepare an accounting restatement of the Company’s financial statements due to material non-compliance with any financial reporting requirement under the federal securities laws, the Company will recover, on a reasonably prompt basis, the excess incentive-based compensation received by any covered executive during the prior three fiscal years that exceeds the amount that the executive otherwise would have received had the incentive-based compensation been determined based on the restated financial statements.
PAY VERSUS PERFORMANCE
As required by Section 953(a) of the Dodd-Frank Wall Street Reform and Consumer Protection Act, and Item 402(v) of Regulation S-K, we are providing the following information about the relationship between executive compensation actually paid and certain financial performance of the Company.
Year
Summary
Compensation
Table
Total for
PEO
(1)
Compensation
Actually
Paid to
PEO
(2)
Average
Summary
Compensation
Table Total
for Non-PEO
NEOs
(3)
Average
Compensation
Actually
Paid to
Non-PEO
NEOs
(4)
Value of
Initial
Fixed $100
Investment
Based On
Total
Shareholder
Return
(5)
Net Loss(6)
2023$7,067,572$15,327,386$1,809,202$4,027,890$113.74$(75,955,225)
2022$5,993,238$(5,174,369)$2,466,805$(1,687,548)$54.12$(127,393,315)
2021$5,544,733$12,111,993$2,222,969$4,761,991$169.64$(125,550,748)
(1)
The dollar amounts reported are the amounts of total compensation reported in our Summary Compensation Table for each of 2023, 2022 and 2021 for Dr. Patel, our President and Chief Executive Officer.
(2)
The dollar amounts reported represent the amount of “compensation actually paid,” as computed in accordance with SEC rules.

32


The dollar amounts do not reflect the actual amount of compensation earned by or paid during the applicable year. In accordance with SEC rules, the following adjustments were made to total compensation in 2023 to determine the compensation actually paid:
YearReported
Summary
Compensation
Table Total
for PEO
Reported
Value of
Equity
Awards
(a)
Equity
Award
Adjustments
(b)
Compensation
Actually
Paid to
PEO
2023$7,067,572$(6,041,100)$14,300,914$15,327,386
(a)
The grant date fair value of equity awards represents the total of the amounts reported in the “Stock Awards” and “Option Awards” columns in the Summary Compensation Table for the applicable year.
(b)
The equity award adjustments for each applicable year include the addition (or subtraction, as applicable) of the following: (i) the year-end fair value of any equity awards granted in the applicable year that are outstanding and unvested as of the end of the year; (ii) the amount of change as of the end of the applicable year (from the end of the prior fiscal year) in fair value of any awards granted in prior years that are outstanding and unvested as of the end of the applicable year; (iii) for awards that are granted and vest in same applicable year, the fair value as of the vesting date; (iv) for awards granted in prior years that vest in the applicable year, the amount equal to the change as of the vesting date (from the end of the prior fiscal year) in fair value; (v) for awards granted in prior years that are determined to fail to meet the applicable vesting conditions during the applicable year, a deduction for the amount equal to the fair value at the end of the prior fiscal year; and (vi) the dollar value of any dividends or other earnings paid on stock or option awards in the applicable year prior to the vesting date that are not otherwise reflected in the fair value of such award or included in any other component of total compensation for the applicable year. The valuation assumptions used to calculate fair values did not materially differ from those disclosed at the time of grant. The amounts deducted or added in calculating the equity award adjustments for 2023 are as follows:
YearYear End
Fair
Value of
Outstanding
and Unvested
Equity
Awards
Granted
During
the Year
Year over
Year Change
in Fair
Value of
Outstanding
and Unvested
Equity
Awards
Granted in
Prior Years
Fair
Value as
of Vesting
Date of
Equity
Awards
Granted and
Vested in
the Year
Change
in Fair
Value from
Prior Year
End to
Vesting Date
of Equity
Awards
Granted
in Prior
Years that
Vested in
the Year
Total
Equity
Award
Adjustments
2023$7,980,906$2,109,745$2,149,606$2,060,657$14,300,914
(3)
The dollar amounts reported represent the average of the amounts reported for the Company’s NEOs as a group (excluding our CEO) in the “Total” column of the Summary Compensation Table in each applicable year. The names of each of the NEOs (excluding our CEO) included for purposes of calculating the average amounts in 2023 are Suneel Gupta, Ph.D. and Asif Ali, and in 2022 and 2021 are Suneel Gupta, Ph.D. and David Y. Liu, Ph.D.
(4)
The dollar amounts reported represent the average amount of “compensation actually paid” to the NEOs as a group (excluding our CEO), as computed in accordance with SEC rules. The dollar amounts do not reflect the actual average amount of compensation earned by or paid to the NEOs as a group (excluding our CEO) during the applicable year. In accordance with the SEC rules, the following adjustments were made to average total compensation for the NEOs as a group (excluding our CEO) for 2023 to determine the compensation actually paid, using the same methodology described above in Note 2:
YearAverage
Reported
Summary
Compensation
Table
Total for
Non-PEO
NEOs
Average
Reported
Value of
Equity
Awards
Average
Equity
Awards
Adjustments
(a)
Average
Compensation
Actually
Paid to
Non-PEO
NEO
2023$1,809,202$(1,134,078)$3,352,766$4,027,890

33


(a)
The amounts deducted or added in calculating the total average equity award adjustments are as follows:
YearAverage
Year End
Fair
Value of
Outstanding
and Unvested
Equity
Awards
Granted
During the
Year
Year over
Year Average
Change in
Fair
Value of
Outstanding
and Unvested
Equity
Awards
Granted in
Prior Years
Average
Fair Value
as of
Vesting
Date of
Equity
Awards
Granted and
Vested in
the Year
Average
Change in
Fair Value
from Prior
Year End
to Vesting
Date of
Equity
Awards
Granted in
Prior Years
that Vested
in the Year
Total
Average
Equity
Award
Adjustments
2023$1,605,304$686,027$335,868$725,567$3,352,766
(5)
Cumulative total shareholder return (“TSR”) is calculated by dividing the sum of the cumulative amount of dividends for the measurement period, assuming dividend reinvestment, and the difference between the Company’s share price at the end and the beginning of the measurement period by the Company’s share price at the beginning of the measurement period.
(6)
The dollar amounts reported represent the amount of net loss reflected in the Company’s audited financial statements for the applicable year.
Analysis of the Information Presented in the Pay versus Performance Table
The Company’s executive compensation program reflects a variable pay-for-performance philosophy. While the Company utilizes several performance measures to align executive compensation with Company performance, all of those Company measures are not presented in the Pay versus Performance table. Moreover, the Company generally seeks to incentivize long-term performance, and therefore does not specifically align the Company’s performance measures with compensation that is actually paid (as computed in accordance with SEC rules) for a particular year. In accordance with SEC rules, the Company is providing the following graphs depicting the relationships between information presented in the Pay versus Performance table.
Compensation Actually Paid and Cumulative TSR
[MISSING IMAGE: bc_companytsr-4c.jpg]

34


Compensation Actually Paid and Net Loss
[MISSING IMAGE: bc_netloss-4c.jpg]

35


DIRECTOR COMPENSATION

The following table shows for the fiscal year ended December 31, 20172023 certain information with respect to the compensation of all non-employee directors of the Company:


NON-EMPLOYEE DIRECTOR COMPENSATION FOR FISCAL 2017

2023
NameFees Earned
or Paid
in Cash ($)
Option
Awards
($)
(1)(2)
Total
($)
Bryan Giraudo60,000296,517356,517
Sarah Noonberg, M.D., Ph.D.(3)
25,000591,741616,741
Sarah A. O’Dowd45,000296,517341,517
Harold E. Selick, Ph.D.98,750296,517395,267
Daniel N. Swisher, Jr.7,174530,982538,156
William D. Waddill67,500296,517364,017
Lewis T. Williams, M.D., Ph.D.55,000296,517351,517
Name
 Fees Earned or
Paid in Cash
($)
 Option Awards
($)(1)(2)
 All Other
Compensation
($)
 Total
($)
 

Julie Papanek Grant(3)

  52,500  59,183    111,683 

Chaitan Khosla, Ph.D.(4)

  43,750  59,183  10,000  112,933 

Sarah B. Noonberg, M.D., Ph.D. 

  2,582  260,124    262,706 

Harold E. Selick, Ph.D. 

  83,750  59,183    142,933 

Armen B. Shanafelt, Ph.D. 

  55,000  59,183    114,183 

William D. Waddill

  60,000  59,183    119,183 

Lewis T. Williams, M.D., Ph.D. 

  22,637  153,106    175,743 

(1)
(1)
The amounts in the "Option Awards"“Option Awards” column reflect the aggregate grant date fair value of stock options granted during the calendar year and the aggregate incremental fair value of stock options modified during the calendar year, in each case computed in accordance with the provisions of

    Accounting Standards Codification (ASC) ASC 718, Compensation—Compensation — Stock Compensation. The valuation assumptions used in determining such amounts are described in the notes to the Company'sCompany’s financial statements included in its Annual Report on Form 10-K for the year ended December 31, 2017.2023. These amounts do not reflect the actual economic value that will be realized by the directors upon the vesting of the stock options, the exercise of the stock options, or the sale of the common stock underlying such stock options.

(2)

The aggregate number of stock option awards for each non-employee director that were outstanding as of the end of fiscal year 20172023 is shown in the table below. Our non-employee directors did not hold any other outstanding stock awards as follows:
of such date.
(3)
Dr. Noonberg served on the Board until the 2023 Annual Meeting of Stockholders, after which time she provided consulting services through January 31, 2024. Her stock options continued to vest through such date and her vested options will remain outstanding until April 30, 2024. She did not receive any other compensation in exchange for such consulting services, but the change in vesting provisions resulted in incremental fair value ($295,224) as described in footnote (1).
Name
Name
Aggregate Number
of
Option Awards

Outstanding as of

December 31, 2017

Julie Papanek Grant(3)

2023
10,666

Chaitan Khosla, Ph.D. 

Bryan Giraudo
66,638131,000

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

(1)
24,00099,000

Sarah A. O’Dowd

98,000
Harold E. Selick, Ph.D.

77,020174,514

Armen B. Shanafelt, Ph.D. 

Daniel N. Swisher, Jr.
36,00045,000

William D. Waddill

48,975143,975

Lewis T. Williams, M.D., Ph.D.

24,000131,000
(3)
Ms. Grant resigned from(1)
Dr. Noonberg served on the Board effective December 12, 2017. Aggregate numberuntil the 2023 Annual Meeting of option awards outstanding at December 31, 2017 represents vested awards at termination, all ofStockholders, after which were exercised prior to March 12, 2018.
(4)
During 2017, Dr. Khosla received cash compensation for providingtime she provided consulting services through January 31, 2024. Her stock options continued to the Companyvest through such date and her vested options will remain outstanding until April 30, 2024. She did not receive any other compensation in the amount of $10,000.
exchange for such consulting services.

In September 2016, the Board adopted a non-employee director compensation policy. The Compensation Committee made certain changes to the non-employee director compensation policy effective as of January 1, 2020, May 16, 2022, January 1, 2023 (to increase the number of options granted as part of the annual equity award from 20,000 to 30,000) and October 26, 2023 (to increase the number of options granted as part of the initial equity award from 30,000 to 45,000). Pursuant to this policy, the Company compensates its non-employee directors with a combination of cash and equity. The annual cash compensation contained in this policy, set forth below, is payable in equal quarterly installments, in arrears followingadvance during the endlast month of each quarter in which service occurred, prorated for any months of partial service.


36



Annual Board Service Retainer:


Non-employee directors other than the non-executive chairperson: $40,000


Non-executive chairperson: $70,000

$75,000

Annual Committee Service Retainer (Chairperson):


Chairperson of the Audit Committee: $15,000

$20,000

Chairperson of the Compensation Committee: $10,000

$15,000

Chairperson of the Nominating and Corporate Governance Committee: $7,500

$10,000

Chairperson of the Research Committee: $10,000

Annual Committee Service Retainer (Non-Chairperson):


Audit Committee: $7,500

$10,000

Compensation Committee: $5,000

$7,500

Nominating and Corporate Governance Committee: $3,750$5,000

\


Research Committee: $5,000
The Company'sCompany’s non-employee director compensation policy also provides for equity compensation to each non-employee director as follows:


Initial Grant: At the time he or she joins the Board, each new non-employee director will receive an initial stock option grant to purchase 24,00045,000 shares of common stock andstock. The awards shall vest in equal monthly installments over three years.


Annual Grant: Each non-employee director will also be granted an option to purchase 12,00030,000 shares of common stock on the date of each Annual Meeting of stockholders whichsame day as the annual employee refresher awards. The awards shall vest at the earlier of (i) one year or (ii) the next Annual Meeting of stockholders.

in equal monthly installments over twelve months.

All options granted to the Company'sCompany’s non-employee directors under the policy will vest in full upon the completion of a change in control.


NON-EMPLOYEE DIRECTOR COMPENSATION FOR FISCAL 2024
After consultation with Radford and pursuant to the compensation review process described above, effective January 1, 2024, the number of shares subject to the annual option grant to be awarded in fiscal year 2024 to our non-employee directors was set at 25,700 shares.

37


EQUITY COMPENSATION PLAN INFORMATION

The following table provides certain information with respect to all of the Company'sCompany’s equity compensation plans in effect as of December 31, 2017.

2023.
Plan Category(1)
Number of
Securities to
Be Issued
Upon Exercise
of Outstanding
Options,
Warrants
and Rights
(a)
Weighted
Average
Exercise
Price of
Outstanding
Options,
Warrants
and Rights
(2)
(b)
Number of
Securities
Remaining
Available
for Issuance
Under Equity
Compensation
Plans (Excluding
Securities
Reflected in
Column (a))
(c)
Equity compensation plans approved by securities holders:
2007 Stock Option and Incentive Plan146,371(3)$3.89
2016 Equity Incentive Plan7,594,673(4)$17.101,035,798(5)
2016 Employee Stock Purchase Plan1,459,902(6)
Equity compensation plans not approved by securities holders:
2018 Inducement Plan(7)
920,990(8)$19.56548,722
Total8,662,034$17.213,044,422
Plan Category(1)
 Number of securities
to be issued upon
exercise of
outstanding options,
warrants and rights
(a)
 Weighted-average
exercise price of
outstanding options,
warrants and rights($)(2)
(b)
 Number of securities
remaining available
for issuance under
equity compensation
plans
(excluding securities
reflected
in column (a))
(c)
 

Equity compensation plans approved by security holders:

          

2007 Stock Option and Incentive Plan

  1,058,741(3)$2.57   

2016 Equity Incentive Plan

  1,379,410(4)$20.09  531,039(5)

2016 Employee Stock Purchase Plan

      268,554(6)

(1)
(1)
The equity compensation plans are described in Note 1311 to our financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2017.
2023.
(2)

The weighted-average exercise price of outstanding stock options granted under equity compensation plans approved by securities holders was $9.70.
$16.82. The weighted-average exercise price of outstanding options granted under all equity compensation plans was $17.21. RSUs and PSUs do not have an exercise price and therefore have not been included in the calculations.
(3)

As of December 31, 2017,2023, there were 1,058,741146,371 shares of common stock subject to outstanding stock options under the 2007 Stock Option and Incentive Plan.
(4)

As of December 31, 2017,2023, there were 1,379,4106,888,433 shares of common stock subject to outstanding stock options, 630,740 shares to be issued pursuant to the vesting of unvested RSUs and 75,500 shares to be issued pursuant to the vesting of unvested PSUs upon achievement of performance conditions under the 2016 Equity Incentive Plan (the "2016 Plan").
Plan.
(5)

The reserve for shares available under the 2016 Plan will automatically increase on January 1st each year by an amount equal to 4 percent of the total number of outstanding shares of our capital stock on December 31st of the preceding fiscal year, or a lesser number of shares determined by the Board. Shares subject to stock awards granted under our 2016 Plan that expire or cancel without being exercised in full, or that are paid out in cash rather than in shares, do not reduce the number of shares available for issuance under our 2016 Plan. Additionally, shares issued pursuant to stock awards under our 2016 Plan that we repurchase or that are forfeited, as well as shares used to pay the exercise price of a stock award or to satisfy the tax withholding obligations related to a stock award, become available for future grant under our 2016 Plan.
(6)

The reserve for shares available under the 2016 Employee Stock Purchase Plan (the "2016 ESPP")ESPP will automatically increase on January 1st each year by the lesser of: (i) 1%one percent of the total number of outstanding shares of our capital stock outstanding on December 31st of the preceding fiscal year, (ii) 300,000 shares, or (iii) such other number of shares determined by the Board. As of December 31, 2017,2023, an aggregate of 268,5541,459,902 shares remained available for future issuance under the 2016 ESPP.ESPP, including 38,749 shares subject to purchase during the purchase period in effect on December 31, 2023.


(7)
In February 2020, the Board approved the Amended and Restated 2018 Inducement Plan, a non-stockholder approved stock plan, under which it reserved and authorized up to 1,250,000 shares of the Company’s common stock in order to award options and RSUs to persons that were not previously employees or directors of the Company, or following a bona fide period of non- employment, as an inducement material to such persons entering into employment with the Company, within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. The Board approved a further amendment and restatement in February 2022 to reserve and authorize an additional 500,000 shares of the Company’s common stock thereunder (as amended and restated in February 2022, the “2018 Inducement Plan”). The 2018 Inducement Plan is administered by the Board or the Compensation Committee of the Board, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2018 Inducement Plan expire no later than ten years from the date of grant.
(8)
As of December 31, 2023, there were 887,239 shares of common stock subject to outstanding stock options and 33,751 shares to be issued pursuant to the vesting of unvested RSUs under the 2018 Inducement Plan.

38


TRANSACTIONS WITH RELATED PERSONS AND INDEMNIFICATION

RELATED-PERSON TRANSACTIONS POLICY AND PROCEDURES

In 2016, the

The Company has adopted a written Related-Person Transactions Policy that sets forth the Company'sCompany’s policies and procedures regarding the identification, review, consideration and approval or ratification of "related-persons“related-persons transactions." For purposes of the Company'sCompany’s policy only, a "related-person transaction"“related-person transaction” is a transaction, arrangement or relationship (or any series of similar transactions, arrangements or relationships) in which the Company and any "related person"“related person” are participants involving an amount that exceeds $120,000. Transactions involving compensation for services provided to the Company as an employee, director, consultant or similar capacity by a related person are not covered by this policy. A related person is any executive officer, director, or more than 5% stockholder of the Company, including any of their immediate family members, and any entity owned or controlled by such persons.

Except as otherwise described, the foregoing policies and procedures were followed with respect to the transactions described below.
CERTAIN RELATED-PERSON TRANSACTIONS

The following is a summary of transactions since January 1, 20172022 in which the Company participated, in which the amount involved exceeded or will exceed $120,000, and in which any of the Company'sCompany’s directors, executive officers or holdersbeneficial owners of more than 5% of the Company's capitalCompany’s common stock or any members of their immediate family had or will have a direct or indirect material interest, other than compensation arrangements which are described under "Executive Compensation"“Executive Compensation” and "Director“Director Compensation."

Janssen License and Collaboration Agreement

2018 OFFERING
On May 26, 2017,August 6, 2018, the Company entered into a securities purchase agreement (the “Securities Purchase Agreement”) with certain accredited investors, including entities affiliated with BVF and Janssen Biotech, Inc., ("Janssen"entities affiliated with the Farallon General Partner (the “Investors”), oneeach a holder of more than 5% of the Janssen Pharmaceutical CompaniesCompany’s common stock, relating to the issuance and sale of Johnson & Johnson,2,750,000 shares of the Company’s common stock at a negotiated purchase price of $8.00 per share, for aggregate net proceeds of $21.7 million, after deducting offering expenses payable by us. In concurrent private placements, the Company issued the Investors warrants to purchase an aggregate of 2,750,000 shares of the Company’s common stock (each, a “Warrant” and, collectively, the “Warrants”). Each Warrant was exercisable from August 8, 2018 through August 8, 2023. In connection with the issuance and sale of the common stock and Warrants, the Company granted the investors certain registration rights with respect to the Warrants and the underlying shares.
In August 2023, prior to the expiration of the Warrants, the Company entered into certain agreements with the Investors and their affiliates under which the Company agreed to allow the Warrants to be exercised in exchange for pre-funded warrants representing the same number of shares underlying the Warrants with an exercise price of $0.001 per share (the “Pre-Funded Warrants”). Subsequent to the execution of the agreements and prior to the expiration of the Warrants, all outstanding Warrants were exercised for gross proceeds of $34.4 million in exchange for 44,748 shares of the Company’s common stock and Pre-Funded Warrants to purchase 2,705,252 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Pre-Funded Warrants) with an exercise price of $0.001 per share. The Pre-Funded Warrants will expire upon the day they are exercised in full. The Pre-Funded Warrants are exercisable at any time prior to expiration except that the Pre-Funded Warrants cannot be exercised by the Investors if, after giving effect thereto, the Investors would beneficially own more than 9.99% of the Company’s common stock, subject to certain exceptions.
WARRANT EXCHANGE
On December 21, 2018, the Company entered into an exclusive licenseexchange agreement with entities affiliated with BVF (the “Exchanging Stockholders”), pursuant to which the Company exchanged an aggregate of 1,000,000 shares of common stock owned by the Exchanging Stockholders for pre-funded warrants (the “Exchange Warrants”) to purchase an aggregate of 1,000,000 shares of common stock (subject to adjustment in the event of stock splits, recapitalizations and collaboration agreement forother similar events affecting common stock), with an exercise

39


price of $0.00001 per share. The Exchange Warrants expire ten years from the development, manufacture and commercializationdate of PTG-200 worldwide forissuance. The Exchange Warrants are exercisable at any time prior to expiration except that the treatmentExchange Warrants cannot be exercised by the Exchanging Stockholders if, after giving effect thereto, the Exchanging Stockholders would beneficially own more than 9.99% of Crohn's disease ("CD") and ulcerative colitis ("UC"). Janssen is a related partythe Company’s common stock, subject to certain exceptions. The holders of the Exchange Warrants will not have the right to vote on any matter except to the Companyextent required by Delaware law. The Exchange Warrants were issued without registration under the Securities Act of 1933, as Johnson & Johnson Innovation—JJDC, Inc.amended (the “Securities Act”), a significant stockholderin reliance on the exemption from registration contained in Section 3(a)(9) of the Securities Act. During the year ended December 31, 2019, Exchange Warrants to purchase 600,000 shares were net exercised, resulting in the issuance of 599,997 shares of common stock. During the year ended December 31, 2022, Exchange Warrants to purchase 400,000 shares were net exercised, resulting in the issuance of 399,997 shares of common stock. As of December 31, 2023, there were no outstanding Exchange Warrants.
2023 PUBLIC OFFERING
On April 4, 2023, the Company entered into an underwriting agreement with J.P. Morgan Securities LLC, Jefferies LLC and Janssen are both subsidiaries of JohnsonPiper Sandler & Johnson. PTG-200 is the Company's oral Interleukin 23 receptor ("IL-23R") antagonist drug candidate currently in development. The Janssen License and Collaboration Agreement became effective on July 13, 2017. Upon the effectivenessCo., as representatives of the agreement,several underwriters named therein, relating to the Company receivedpublic offering, issuance and sale of an aggregate of 5,750,000 shares of common stock at a non-refundable, upfront cash paymentpublic offering price of $50.0$20.00 per share (the “Offering”), including shares issued upon exercise in full by the underwriters of their option to purchase additional shares, for aggregate gross proceeds of $115.0 million, from Janssen.

Under the Janssen Licensebefore deducting underwriting discounts and Collaboration Agreement, the Company granted to Janssen an exclusive worldwide license to develop, manufacturecommissions and commercialize PTG-200 and related IL-23R compounds for all indications, including CD and UC. The Company is responsible, at its own expense, for the conductoffering expenses.

Certain of the Phase 1 clinical trial for PTG-200, and Janssen will be responsible forpurchasers or their affiliates were, or became upon the conduct of a potential Phase 2 clinical trial for PTG-200 in CD, including filing the Investigational New Drug ("IND") application. All such clinical trials will be conducted in accordance with a mutually agreed upon clinical development plan and budget. Development costs for the Phase 2 clinical trial will be shared between the parties on an 80%/20% basis, with Janssen assuming the larger share. Should Janssen elect to retain its license following completion of the Phase 2 clinical trial, it will be responsible, at its own expense, for the manufacture, continued developmentOffering, beneficial holders of seeking regulatory approval for, and commercialization of PTG-200 worldwide. The parties' development activities under the Janssen License and Collaboration Agreement through the Phase 2 clinical trial will be overseen by a joint governance structure which will have equal representation by both parties unless both parties mutually agree to disband such structure or the Company has provided written notice to Janssen of its intention to disband and no longer participate in such structure.

The Company is eligible to receive a $25.0 million payment upon filingmore than 5% of the IND. FollowingCompany’s common stock. The Board approved the conclusion of the planned Phase 2a portion of the Phase 2 clinical trial, if Janssen elects to maintain its

Offering.

license rights and continue the development of PTG-200 in the Phase 2b portion of such clinical trial (the "First Opt-in Election"), the Company would be eligible to receive a $125.0 million payment. Following the conclusion of the planned Phase 2b portion of the Phase 2 clinical trial, if Janssen elects again to maintain its license rights (the "Second Opt-in Election"), the Company would be eligible to receive a $200.0 million payment. In addition to the opt-in fees, the Company is eligible to receive additional potential development, regulatory and sales milestone payments of up to an aggregate of $590.0 million, and tiered royalties paid as a percentage of Janssen's worldwide net sales at rates ranging from ten to the mid-teens, with certain customary reductions under certain circumstances. If Janssen does not make either the First Opt-in Election or the Second Opt-in Election, the Janssen License and Collaboration Agreement will terminate. If Janssen does not make the Second Opt-in Election, or if at any time after the Second Opt-in Election, Janssen terminates the Janssen License and Collaboration Agreement, the Company would be obligated to pay Janssen a low single-digit royalty on worldwide net sales of PTG-200. The Company would also have an option to provide up to 30% of the required U.S. details for PTG-200 to prescribers, using its own sales force personnel, upon commercial launch in the United States. If such right is exercised by the Company, the Company's detailing costs would be reimbursed by Janssen at a mutually agreed cost per primary detailing equivalent.

The Janssen License and Collaboration Agreement contains customary representations, warranties and covenants by the Company and Janssen and includes an obligation by the Company not to develop or commercialize other compounds which also target IL-23R outside of the Janssen License and Collaboration Agreement until completion of the Phase 2b portion of the Phase 2 clinical trial. Each of the Company and Janssen is required to indemnify the other party against all losses and expenses related to breaches of its representations, warranties and covenants under the Janssen License and Collaboration Agreement.

The Janssen License and Collaboration Agreement remains in effect until the royalty obligations cease following patent and regulatory expiry, unless terminated earlier. Either the Company or Janssen may terminate the Janssen License and Collaboration Agreement for uncured material breach. Janssen retains the right to terminate the Janssen License and Collaboration Agreement for convenience and without cause on written notice of a certain period to the Company. Upon a termination of the Janssen License and Collaboration Agreement, all rights revert back to the Company, and in certain circumstances, if such termination occurs during ongoing clinical trials, Janssen would, if requested, provide certain financial and operational support to the Company for the completion of such trials.

INDEMNIFICATION

The Company provides indemnification for its directors and executive officers so that they will be free from undue concern about personal liability in connection with their service to the Company. Under the Company's Amended and Restated Bylaws (the "Restated Bylaws"), the Company is required to indemnify its directors and executive officers to the extent not prohibited under Delaware or other applicable law. The Company has also entered into indemnity agreements with certain officers and directors. These agreements provide, among other things, that the Company will indemnify the officer or director, under the circumstances and to the extent provided for in the agreement, for expenses, damages, judgments, fines and settlements he or she may be required to pay in actions or proceedings which he or she is or may be made a party by reason of his or her position as a director, officer or other agent of the Company, and otherwise to the fullest extent permitted under Delaware law and the Restated Bylaws.



HOUSEHOLDING OF PROXY MATERIALS

The SEC has adopted rules that permit companies and intermediaries (e.g., brokers) to satisfy the delivery requirements for Notices of Internet Availability of Proxy Materials or other Annual Meeting Materialsmaterials with respect to two or more stockholders sharing the same address by delivering a single Notice of Internet Availability of Proxy Materials or other Annual Meeting Materialsmaterials addressed to those stockholders. This process, which is commonly referred to as "householding,"“householding,” potentially means extra convenience for stockholders and cost savings for companies.

This year, a number of brokers with account holders who are Protagonist stockholders will be "householding"“householding” the Company'sCompany’s proxy materials. A single Notice of Internet Availability of Proxy Materials will be delivered to multiple stockholders sharing an address unless contrary instructions have been received from the affected stockholders. Once you have received notice from your broker that they will be "householding"“householding” communications to your address, "householding"“householding” will continue until you are notified otherwise or until you revoke your consent. If, at any time, you no longer wish to participate in "householding"“householding” and would prefer to receive a separate Notice of Internet Availability of Proxy Materials, please notify your broker or Protagonist.Protagonist, and we will promptly deliver a separate Notice of Internet Availability of Proxy Materials to you. Direct your written request to Protagonist Therapeutics, Inc., c/o Thomas O'Neil, Chief Financial OfficerMatthew Gosling, Executive Vice President, General Counsel, at 7707 Gateway Blvd., Suite 140, Newark, California 94560 or contact Thomas O'NeilMatthew Gosling at (510) 474-0971.474-0170. Stockholders who currently receive multiple copies of the Notices of Internet Availability of Proxy Materials at their addresses and would like to request "householding"“householding” of their communications should contact their brokers.



OTHER MATTERS

The Board knows of no other matters thatWe will be presented for consideration at the Annual Meeting. If any other matters are properly brought before the meeting, it is the intention of the persons named in the accompanying proxy to vote on such matters in accordance with their best judgment.

By Order of the Board of Directors

/s/ Dinesh V. Patel

Dinesh V. Patel, Ph.D.
President and Chief Executive Officer



April 18, 2018


Aprovide a copy of the Company'sCompany’s Annual Report to the Securities and Exchange Commission on Form 10-K for the year ended December 31, 2017 is available2023, without charge, upon the written or oral request of a stockholder. Please send a written request to: Corporate Secretary, Protagonist Therapeutics, Inc., 7707 Gateway Blvd., Suite 140, Newark, California 94560.


94560 or call (510) 474-0170.


VOTE BY INTERNET - www.proxyvote.com

PROTAGONIST THERAPEUTICS, INC.

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TO

40

[MISSING IMAGE: px_24protagonistpage01-bw.jpg]
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PROTAGONIST THERAPEUTICS, INC.

For
All

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Except

To withhold authority to vote for any individual nominee(s), mark “For All Except” and write the number(s) of the nominee(s) on the line below.

The Board of Directors recommends you vote FOR the following:

o

o

o

1.

To elect the three nominees for Class II director named below to serve until the 2021 Annual Meeting of Stockholders and until their successors have been duly elected and qualified.

Nominees:

01)  Chaitan Khosla, Ph.D.

02)  William D. Waddill

03)  Lewis T. “Rusty” Williams, M.D., Ph.D.

The Board of Directors recommends you vote FOR the following proposal:

For

Against

Abstain

2.   To ratify the selection by the Audit Committee of the Board of PricewaterhouseCoopers LLP as Protagonist Therapeutics’ independent registered public accounting firm for the fiscal year ending December 31, 2018.

o

o

o

NOTE: The Board of Directors knows of no other matters that will be presented for consideration at the 2018 Annual Meeting of Stockholders. If any other matters are properly brought before the 2018 Annual Meeting of Stockholders, it is the intention of the person named in the proxy card to vote on such matters in accordance with their best judgment.

For address changes and/or comments, please check this box and write them on the back where indicated.

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DETACH AND RETURN THIS PORTION ONLYV44889-P10544For Against Abstain! ! !PROTAGONIST THERAPEUTICS, INC.7707 GATEWAY BLVD.SUITE 140NEWARK, CA 94560PROTAGONIST THERAPEUTICS, INC.1. To elect the Class II director nominees named below tohold office until the 2027 Annual Meeting of Stockholdersand until their successors are duly elected and qualified.The Board of Directors recommends you vote FORthe following nominees:Nominees:01) Sarah A. O'Dowd02) William D. Waddill03) Lewis T. "Rusty" Williams, M.D., Ph.D.The Board of Directors recommends you vote FOR Proposals 2, 3 and 4:NOTE: The Board of Directors knows of no other matters that will be presented for consideration at the 2024 Annual Meeting of Stockholders. If any othermatters are properly brought before the 2024 Annual Meeting of Stockholders or any postponement or adjournment thereof, it is the intention of the proxiesnamed in the proxy card to vote on such matters in accordance with their best judgment.3. To ratify the selection of Ernst & Young LLP as our independent

V.1.1

registered public accounting firm for the fiscal year ending December 31, 2024.4. To approve an amendment to our Certificate of Incorporation to increase the number of authorized shares of our common stock from 90,000,000 to180,000,000.2. To approve, on an advisory basis, the compensation of our named executive officers.Please sign exactly as your name(s) appear(s) hereon. When signing as attorney, executor,administrator, trustee or guardian, please add your title as such. When signing as jointtenants, all parties in the joint tenancy must sign. If a signer is a corporation, please sign infull corporate name by duly authorized officers.! ! !ForAllWithholdAllFor AllExceptTo withhold authority to vote for any individualnominee(s), mark "For All Except" and write thenumber(s) of the nominee(s) on the line below.! ! !! ! !SCAN TOVIEW MATERIALS & VOTE wVOTE BY INTERNETBefore The Meeting - Go to www.proxyvote.com or scan the QR Barcode aboveUse the Internet to transmit your voting instructions. Vote by 11:59 p.m. Eastern Time onJune 19, 2024. Have your proxy card in hand when you access the web site and followthe instructions to obtain your records and to create an electronic voting instruction form.During The Meeting - Go to www.virtualshareholdermeeting.com/PTGX2024You may attend the meeting via the Internet and vote during the meeting. Have the informationthat is printed in the box marked by the arrow available and follow the instructions.VOTE BY PHONE - 1-800-690-6903Use any touch-tone telephone to transmit your voting instructions. Vote by11:59 p.m. Eastern Time on June 19, 2024. Have your proxy card in hand when you call andthen follow the instructions.VOTE BY MAILMark, sign and date your proxy card and return it in the postage-paid envelope wehave provided or return it to Vote Processing, c/o Broadridge, 51 Mercedes Way,Edgewood, NY 11717.



Important

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V44890-P10544Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting:

Meeting to be held on June 20, 2024:The Notice and Proxy Statement and Form 10-KAnnual Report are available at www.proxyvote.com.

PROTAGONISTwww.proxyvote.com.PROTAGONIST THERAPEUTICS, INC.

AnnualINC.Annual Meeting of Stockholders

May 29, 2018 11:StockholdersJune 20, 2024 10:00 AM

This PTThis proxy is solicited by the Board of Directors

TheDirectorsThe stockholder(s) hereby appoints Thomas O’Neil,appoint(s) Dinesh V. Patel and Matthew Gosling, each as proxy,proxies and attorneys-in-fact, with the power to act without the other and with the power to appoint his substitute, and hereby authorize(s) himeach to represent and to vote, as designated on the reverse side of this ballot,form, all of the shares of Common Stock of PROTAGONIST THERAPEUTICS, INC. that the stockholders stockholder(s) is/are entitled to vote at the Annual Meeting of Stockholders to be held live via the Internet at 11:10:00 AM, PDTPT on May 29, 2018, June 20, 2024,at Pacific Research Center, Conference Center, 7677 Gateway Blvd., Newark, CA 94560,www.virtualshareholdermeeting.com/PTGX2024, and at any adjournment or postponement thereof.

Thisthereof.This proxy, when properly executed, will be voted in the manner directed herein.herein and in the discretion of the proxies with respect to such other business that may properly come before the meeting and any adjournments or postponements thereof. If no such direction is made but the card is signed, this proxy will be voted in accordance with the Board of Directors’Directors' recommendations.

Address Changes/Comments:

(If you noted In the event that any Address Changes/Comments above, please mark corresponding boxof the nominees named on the reverse side.)

Continuedside of this form are unavailable for election or unable to serve, the shares represented by this proxy may be voted for a substitute nominee selected by the Board of Directors.Continued and to be signed on reverse side




QuickLinks

PROPOSAL 1 ELECTION OF DIRECTORS
THE BOARD OF DIRECTORS RECOMMENDS A VOTE IN FAVOR OF EACH NAMED NOMINEE.
INFORMATION REGARDING THE BOARD OF DIRECTORS AND CORPORATE GOVERNANCE
PROPOSAL 2 RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
THE BOARD OF DIRECTORS RECOMMENDS A VOTE IN FAVOR OF PROPOSAL 2.
EXECUTIVE OFFICERS
SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
SECTION 16(A) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE
EXECUTIVE COMPENSATION
SUMMARY COMPENSATION TABLE FOR FISCAL 2017
NARRATIVE TO SUMMARY COMPENSATION TABLE
OUTSTANDING EQUITY AWARDS AT FISCAL YEAR END
OUTSTANDING EQUITY AWARDS AT DECEMBER 31, 2017
OPTION EXERCISES
DIRECTOR COMPENSATION
NON-EMPLOYEE DIRECTOR COMPENSATION FOR FISCAL 2017
EQUITY COMPENSATION PLAN INFORMATION
TRANSACTIONS WITH RELATED PERSONS AND INDEMNIFICATION
HOUSEHOLDING OF PROXY MATERIALS
OTHER MATTERS

0001377121 ptgx:EquityAwardsAdjustmentsChangeInFairValueAsOfVestingDateOfPriorYearAwardsVestedDuringCurrentYearMember ecd:NonPeoNeoMember 2023-01-01 2023-12-31