TABLE OF CONTENTS

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
SCHEDULE 14A
Proxy Statement Pursuant to Section 14(a) of the Securities
Exchange Act of 1934
(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
Metacrine, 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.

TABLE OF CONTENTS

MERGER PROPOSAL—YOUR VOTE IS VERY IMPORTANT


Dear stockholders of Equillium, Inc. and stockholders of Metacrine, Inc.:
As previously announced, the board of directors of Equillium, Inc., or Equillium, and the board of directors of Metacrine, Inc., or Metacrine, have approved an acquisition of Metacrine by Equillium. Equillium, Metacrine, Equillium Acquisition Sub, Inc., or Acquisition Sub I, Triumph Acquisition Sub, Inc., or Acquisition Sub II, and Triumph Merger Sub, Inc., or Merger Sub, entered into an Agreement and Plan of Merger, dated as of September 6, 2022, as amended on October 26, 2022, pursuant to which Merger Sub will merge with and into Metacrine, with Metacrine continuing as an indirect wholly owned subsidiary of Equillium, or the Merger.
If the transaction is completed, Metacrine stockholders will have the right to receive for each share of Metacrine common stock held by such stockholder (i) a portion of a share of Equillium common stock equal to the exchange ratio, or the Exchange Ratio, determined by dividing (x) (a) 125% of Metacrine’s net cash as of the closing of the Merger, or the Upfront Merger Consideration, by (b) the price per share of Equillium common stock determined based on the 10 day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the closing date of the Merger, provided that in no event will the price per share of Equillium common stock be less than $2.70 or greater than $4.50, or the Equillium Stock Price, by (y) the aggregate fully diluted shares of Metacrine, or Metacrine’s Closing Capitalization, plus (ii) any cash payable in lieu of fractional shares of Equillium’s common stock. The Exchange Ratio will not reflect changes in the market price of Metacrine common stock and will not reflect changes in the market price of Equillium common stock, except that the Exchange Ratio will reflect the 10-day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the closing date of the Merger, or the Closing Date.
For illustrative purposes only, we have provided the below assumptions and sensitivity analysis to inform your decision. Assuming (1) an Upfront Merger    Consideration of $33.75 million, which is based on Metacrine’s current forecasts of net cash as of December 23, 2022, the assumed closing date, or the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price of $2.70, which reflects the lowest trading price per share of Equillium common stock to be calculated for purposes of the Exchange Ratio, or the Floor Price, and the applicable per share price that would be used to determine the Exchange Ratio based on applying the 10-day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to November 8, 2022, the last trading day before November 9, 2022, and (3) Metacrine’s Closing Capitalization is 44,378,697, the aggregate fully diluted shares of Metacrine as of November 9, 2022, or the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.282.
Assuming (1) the Upfront Merger Consideration equals the Assumed Upfront Merger Consideration and (2) the Metacrine Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 increase to the Floor Price would decrease the Exchange Ratio to 0.258. Assuming (1) the Upfront Merger Consideration equals the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price of $4.50, which reflects the highest trading price per share of Equillium common stock to be calculated for purposes of the Exchange Ratio, or the Ceiling Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.169. Assuming (1) the Upfront Merger Consideration equals the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 decrease to the Ceiling Price would increase the Exchange Ratio to 0.179. Assuming (1) the Equillium Stock Price remains constant and (2) the Metacrine Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $1,000,000 increase or decrease in the Upfront Merger Consideration would increase or decrease, respectively, the Exchange Ratio by approximately 0.008.
We encourage you to obtain current market quotations of Equillium common stock and Metacrine common stock before voting.
Based on the Assumed Upfront Merger Consideration, Equillium estimates that it may issue between 7.5 and 12.5 million shares of its common stock to Metacrine equityholders in connection with the Closing. Upon completion of the Merger and based on the Assumed Upfront Merger Consideration and 34,352,084 shares of Equillium common stock outstanding as of November 9, 2022, we estimate that current Equillium stockholders will own between 82.08% and 73.32% of the outstanding common stock of the combined company and former Metacrine equityholders will own between 17.92% and 26.68% of the outstanding common stock of the combined company. If the actual facts are different from these assumptions (which they are likely to be), the percentage ownership retained by Equillium’s stockholders in the combined company will be different. The foregoing numbers are based on assumptions and illustrative and the actual percentage ownership in the combined company retained by Equillium’s stockholders at Closing will be calculated based on the actual numbers. Equillium common stock and Metacrine common stock are both traded on Nasdaq under the symbols “EQ” and “MTCR”, respectively. Upon completion of the Merger, Metacrine common stock will cease to be traded on Nasdaq.
At the special meeting of Equillium stockholders to be held virtually on December 20, 2022, Equillium stockholders will be asked to vote on (i) a proposal to approve the issuance of shares of Equillium common stock to Metacrine stockholders, which is a condition to completion of the Merger, or the Equillium stock issuance proposal, and (ii) a proposal to approve the adjournment from time to time of the Equillium virtual special meeting, if necessary, to solicit additional proxies if there are not sufficient votes to approve the issuance of shares of Equillium common stock in the Merger, which we refer to as the Equillium adjournment proposal.
At the special meeting of Metacrine stockholders to be held virtually on December 20, 2022, Metacrine stockholders will be asked to vote on (i) a proposal to adopt the Merger Agreement, or the Metacrine merger proposal and (ii) a proposal to approve the adjournment from time to time of the Metacrine virtual special meeting, if necessary, to solicit additional proxies if there are not sufficient votes to adopt the Merger Agreement, or the Metacrine adjournment proposal.
Only holders of record of Equillium common stock on November 9, 2022 (including shares of Equillium common stock held through a bank, broker or other nominee that is a stockholder of record of Equillum) and holders of record of Metacrine common stock on November 9, 2022 (including shares of Metacrine common stock held through a bank, broker or other nominee that is a stockholder of record of Metacrine) are entitled to attend and vote at the virtual special meeting of Equillium stockholders or the virtual special meeting of Metacrine stockholders, respectively, or any adjournment or postponement thereof.
We cannot complete the Merger unless the Metacrine stockholders and the Equillium stockholders approve the respective proposals related to the Merger. Your vote is very important, regardless of the number of shares you own. Whether or not you expect to attend the Equillium virtual special meeting or Metacrine virtual special meeting, as applicable, please vote your shares as promptly as possible by (1) accessing the Internet website specified on your proxy card, (2) calling the toll-free number specified on your proxy card, or (3) signing and returning all proxy cards that you receive in the postage-paid envelope provided, so that your shares may be represented and voted at the Equillium or the Metacrine virtual special meeting, as applicable. If you are a Metacrine stockholder, please note that a failure to vote your shares is the equivalent of a vote against the Merger. If you are an Equillium stockholder, please note that a failure to vote your shares may result in a failure to establish a quorum for the Equillium virtual special meeting.
The Equillium board of directors, or the Equillium Board, recommends that Equillium stockholders vote “FOR” the Equillium stock issuance proposal and, if necessary, “FOR” the Equillium adjournment proposal. The Metacrine board of directors, or the Metacrine Board, recommends that Metacrine stockholders vote “FOR” the Metacrine merger proposal and, if necessary, “FOR” the Metacrine adjournment proposal.
The obligations of Equillium and Metacrine to complete the Merger are subject to the satisfaction or waiver of several conditions set forth in the Merger Agreement. More information about Equillium, Metacrine and the Merger is contained in this joint proxy statement/prospectus. Equillium and Metacrine encourage you to read this entire joint proxy statement/prospectus carefully, including the section entitled “Risk Factors” beginning on page 30.
We look forward to the successful Merger of Equillium and Metacrine.
Sincerely,
Sincerely,
 
 
 
 
 
/s/ BRUCE D. STEEL
 
/s/ PRESTON KLASSEN
 
Bruce D. Steel
 
Preston Klassen, M.D., MHS
 
Chief Executive Officer, Director
 
President, Chief Executive Officer, Director
 
Equillium, Inc.
 
Metacrine, Inc.
 
 
 
 
NEITHER THE U.S. SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES COMMISSION HAS APPROVED OR DISAPPROVED OF THE SECURITIES TO BE ISSUED UNDER THIS JOINT PROXY STATEMENT/PROSPECTUS OR DETERMINED THAT THIS JOINT PROXY STATEMENT/PROSPECTUS IS ACCURATE OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL OFFENSE.
This joint proxy statement/prospectus is dated November 10, 2022 and is first being mailed to the stockholders of Equillium and stockholders of Metacrine on or about November 10, 2022.

TABLE OF CONTENTS

ABOUT THIS JOINT PROXY STATEMENT/PROSPECTUS
This joint proxy statement/prospectus, which forms part of a registration statement on Form S-4 filed with the Securities and Exchange Commission, or the SEC, by Equillium (File No. 333-268024), constitutes a prospectus of Equillium under Section 5 of the Securities Act of 1933, as amended, or the Securities Act, with respect to the shares of Equillium common stock proposed to be issued to Metacrine stockholders pursuant to the Merger Agreement. This document also constitutes a joint proxy statement under Section 14(a) of the Securities Exchange Act of 1934, as amended, or the Exchange Act. It also includes a notice of meeting with respect to the special meeting of Equillium stockholders, at which Equillium stockholders will be asked to vote upon the Equillium stock issuance proposal, and a notice of meeting with respect to the special meeting of Metacrine stockholders, at which Metacrine stockholders will be asked to vote on the Metacrine merger proposal.
Equillium has supplied all information contained in this joint proxy statement/prospectus relating to Equillium, Acquisition Sub I, Acquisition Sub II, and Merger Sub. Metacrine has supplied all information contained in or incorporated by reference into this joint proxy statement/prospectus relating to Metacrine. Equillium and Metacrine have both contributed information relating to the proposed transactions.
Before casting your vote, you should carefully review all the information contained or incorporated by reference into this joint proxy statement/prospectus. Neither Equillium nor Metacrine has authorized anyone to provide you with information that is different from that contained in, or incorporated by reference into, this joint proxy statement/prospectus. This joint proxy statement/prospectus is dated November 10, 2022. You should not assume that the information contained in, or incorporated by reference into, this joint proxy statement/prospectus is accurate as of any date other than the date on the front cover of those documents. Neither our mailing of this joint proxy statement/prospectus to Equillium stockholders or Metacrine stockholders nor the issuance by Equillium of common stock in connection with the Merger will create any implication to the contrary.
In deciding how to vote with respect to any of the proposals discussed herein, you must make your own independent examination of the merits and risks of the proposal. You should not construe anything included in this joint proxy statement/prospectus as investment, legal, business or tax advice, and should consult with your own advisors if you have questions concerning any of the matters described herein.
This joint proxy statement/prospectus does not constitute an offer to sell, or a solicitation of an offer to buy, any securities, or the solicitation of a proxy, in any jurisdiction in which or from any person to whom it is unlawful to make any such offer or solicitation in such jurisdiction. As permitted by SEC rules, this joint proxy statement/prospectus does not contain all of the information you can find in Equillium’s registration statement or its exhibits. For further information pertaining to Equillium and the shares of Equillium common stock to be issued in connection with the Merger, reference is made to that registration statement and its exhibits. Statements contained in this document or in any document incorporated into this document by reference as to the contents of any contract or other document referred to in this document or in other documents that are incorporated by reference into this document are not necessarily complete and, in each instance, reference is made to the copy of the applicable contract or other document filed as an exhibit to the registration statement or otherwise filed with the SEC. Each statement contained in this document is qualified in its entirety by reference to the underlying documents. You are encouraged to read the entire registration statement. You may obtain copies of the Form S-4 including documents incorporated by reference into the Form S-4 (and any amendments to those documents) by following the instructions under “Where You Can Find Additional Information.”
All references in this joint proxy statement/prospectus to “Metacrine” refer to Metacrine, Inc., a Delaware corporation (except that in connection with the description of its operations or business under the headings “Cautionary Statement Regarding Forward-Looking Statements” and “Risk Factors,” such term refers to the consolidated operations of Metacrine and its subsidiaries); all references in this joint proxy statement/prospectus to “Equillium” refer to Equillium, Inc., a Delaware corporation (except that in connection with the description of its operations or business under the headings “Cautionary Statement Regarding Forward-Looking Statements” and “Risk Factors,” such term refers to the consolidated operations of Equillium and its subsidiaries); all references to “Acquisition Sub I” refer to Equillium Acquisition Sub, Inc., a Delaware corporation and a wholly owned subsidiary of Equillium, formed in connection with the Merger, “Acquisition Sub II” refer to Triumph Acquisition Sub, Inc, a Delaware corporation and wholly owned subsidiary of Acquisition Sub I, formed in connection with the Merger, and “Merger Sub” refer to Triumph Merger Sub, Inc., a Delaware corporation and a wholly owned subsidiary of Acquisition Sub II, formed for the purpose of effecting the Merger. Unless otherwise indicated or as the context requires, all references to the “Merger Agreement” refer to the Agreement and Plan

TABLE OF CONTENTS

of Merger, dated as of September 6, 2022, among Equillium, Metacrine, Acquisition Sub I, Acquisition Sub II and Merger Sub, as amended on October 26, 2022, a copy of which is included as Annex A to this joint proxy statement/prospectus.
TRADEMARKS AND SERVICE MARKS
Equillium and Metacrine own or have rights to various trademarks, logos, service marks and trade names that each uses in connection with the operation of its business. Equillium and Metacrine each also own or have the rights to copyrights that protect the content of their respective products. Solely for convenience, the trademarks, service marks, trade names and copyrights referred to in this joint proxy statement/prospectus are listed without the ™, ® and © symbols, but such references do not constitute a waiver of any rights that might be associated with the respective trademarks, service marks, trade names and copyrights included or referred to in this joint proxy statement/prospectus.
ADDITIONAL INFORMATION
This joint proxy statement/prospectus incorporates important business and financial information about Equillium and Metacrine from other documents that are not included in or delivered with this joint proxy statement/prospectus. For a listing of documents incorporated by reference into this joint proxy statement/prospectus, please see the section entitled “Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus. This information is available to you without charge upon your request.
You can obtain the documents incorporated by reference into this joint proxy statement/prospectus by requesting them in writing or by telephone from the appropriate company at the following addresses and telephone numbers:
Equillium, Inc.

2223 Avenida de la Playa, Suite 105
La Jolla, California 92037
(858) 240-1200
Attn: Investor Relations
Metacrine, Inc.

4225 Executive Square, Suite 600
San Diego, CA 92037
(858) 369-7800
Attn: Investor Relations
Investors may also consult Equillium’s or Metacrine’s website for more information concerning the Merger described in this joint proxy statement/prospectus. Equillium’s website is www.Equilliumbio.com. Metacrine’s website is www.Metacrine.com. Information included on these websites is not incorporated by reference into this joint proxy statement/prospectus.
In addition, if you have questions about the Merger or the accompanying joint proxy statement/prospectus, would like additional copies of the joint proxy statement/prospectus, or need to obtain proxy cards or other information related to the proxy solicitation, for Metacrine stockholders, please call Morrow Sodali, LLC, the proxy solicitor for Metacrine, toll-free at (800) 662-5200, or, for Equillium stockholders, please call Equillium at (858) 240-1200 or email ir@equilliumbio.com. You will not be charged for any of these documents that you request.
If you would like to request any documents, please do so no later than five business days before the date of the relevant special meeting in order to receive timely delivery of such documents before such special meeting. Therefore, if you would like to request documents from Equillium, please do so by December 13, 2022 and if you would like to request documents from Metacrine, please do so by December 13, 2022 in order to receive such documents before the Equillium and Metacrine virtual special meetings, respectively.

TABLE OF CONTENTS


Equillium, Inc.
2223 Avenida de la Playa, Suite 105
La Jolla, California 92037
(858) 240-1200
NOTICE OF SPECIAL MEETING OF STOCKHOLDERS TO BE HELD ON DECEMBER 20, 2022

Virtual Meeting Only – No Physical Meeting Location
Dear Equillium stockholders:
We are pleased to invite you to attend the special meeting of the Equillium stockholders, which will be held on December 20, 2022, at 12:00 pm (Eastern Time), or the Equillium virtual special meeting. The Equillium virtual special meeting will be conducted via live webcast at www.virtualshareholdermeeting.com/EQ2022SM for the following purposes:
Equillium Proposal 1: To approve the issuance of shares of Equillium common stock to Metacrine stockholders in connection with the Merger contemplated by the Agreement and Plan of Merger, dated September 6, 2022, among Equillium, Inc., Equillium Acquisition Sub, Inc., Triumph Acquisition Sub, Inc., Triumph Merger Sub, Inc. and Metacrine, Inc., as amended on October 26, 2022, and as may be further amended from time to time, or the Merger Agreement. A copy of the Merger Agreement is attached as Annex A to the joint proxy statement/prospectus accompanying this notice. We refer to this proposal as the Equillium stock issuance proposal.
Equillium Proposal 2: To approve the adjournment from time to time of the Equillium virtual special meeting, if necessary, to solicit additional proxies if there are not sufficient votes to approve the Equillium stock issuance proposal. We refer to this proposal as the Equillium adjournment proposal.
Equillium will transact no other business at the special meeting except such business as may properly be brought before the special meeting or any adjournment or postponement thereof. Please refer to the attached joint proxy statement/prospectus for further information with respect to the business to be transacted at the Equillium virtual special meeting.
In order to attend the Equillium virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow the instructions found on your proxy card and/or voting authorization form.
At a meeting of the Equillium Board held on September 5, 2022, the Equillium Board determined that the Merger Agreement and the transactions contemplated thereby, including the issuance of shares of Equillium common stock to the Metacrine stockholders in connection with the Merger, are in the best interests of Equillium and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby.
The Equillium Board recommends that Equillium stockholders vote “FOR” the Equillium stock issuance proposal and “FOR” the Equillium adjournment proposal.
Holders of record of shares of Equillium common stock, at the close of business on December 20, 2022, or the Equillium record date, are entitled to notice of, and may vote at, the Equillium virtual special meeting and any adjournment of the special meeting. A list of Equillium stockholders entitled to vote at the Equillium virtual special meeting will be available for inspection at Equillium’s principal executive offices, located at 2223 Avenida de la Playa, Suite 105, San Diego, California 92037, at least 10 days prior to the date of the Equillium virtual special meeting and continuing through the date thereof for any purpose germane to the Equillium virtual special meeting, between the hours of 9:00 a.m. and 4:30 p.m., local time.

TABLE OF CONTENTS

Approval of the Equillium stock issuance proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (provided that a quorum exists). Approval of the Equillium adjournment proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (whether or not a quorum is present).
Important Notice Regarding the Availability of Proxy Materials for
the Special Meeting to Be Held on December 20, 2022 starting at 12:00 p.m. (Eastern Time) via live webcast at www.virtualshareholdermeeting.com/EQ2022SM
The proxy statement is available at www.virtualshareholdermeeting.com/EQ2022SM
Your vote is important. Whether or not you expect to attend the Equillium virtual special meeting virtually, we urge you to vote your shares as promptly as possible by (1) accessing the Internet website specified on your proxy card; (2) calling the toll-free number specified on your proxy card; or (3) signing and returning the enclosed proxy card in the postage-paid envelope provided, so that your shares may be represented and voted at the Equillium virtual special meeting. If your shares are held in “street name” through a bank, broker or other fiduciary, please follow the instructions on the voting instruction card furnished by the record holder. In lieu of receiving a proxy card, participants in certain benefit plans of Equillium and certain participating Equillium subsidiaries have been furnished with voting instruction cards, which are described in greater detail in the accompanying joint proxy statement/prospectus. If your shares are registered directly in your name with our transfer agent, American Stock Transfer & Trust Company, LLC, you are considered, with respect to those shares, the shareholder of record. In such case, these proxy materials are being sent directly to you.
If you have any questions or need assistance voting your shares, please call (858) 240-1200.
 
By Order of the Board of Directors,
 
 
 
/s/ BRUCE D. STEEL
 
Bruce D. Steel
 
Chief Executive Officer
 
San Diego, California
 
November 10, 2022
We are pleased to invite you to attend the Equillium virtual special meeting, conducted via live webcast, at www.virtualshareholdermeeting.com/EQ2022SM. You will not be able to attend the special meeting in person. Whether or not you expect to attend the virtual special meeting, please complete, date, sign and return the proxy card that may be delivered 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 virtual special meeting. Even if you have voted by proxy, you may still vote if you attend the virtual special 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 special meeting, you may be instructed to obtain a legal proxy form from your broker, bank or other nominee and to submit a copy in advance of the special meeting.

TABLE OF CONTENTS


Metacrine, Inc.

4225 Executive Square, Suite 600
San Diego, CA 92037
(858) 369-7800
NOTICE OF SPECIAL MEETING OF STOCKHOLDERS TO BE HELD ON DECEMBER 20, 2022

Virtual Meeting Only – No Physical Meeting Location
Dear Metacrine stockholders:
We are pleased to invite you to attend the special meeting of the Metacrine stockholders, which will be held on December 20, 2022, at 12:00p.m. (Eastern Time), or the Metacrine virtual special meeting. The Metacrine virtual special meeting will be conducted via live webcast at www.virtualshareholdermeeting.com/MTCR2022SM for the following purposes:
Metacrine Proposal 1: To adopt the Agreement and Plan of Merger, dated September 6, 2022, among Equillium, Inc., Equillium Acquisition Sub, Inc., Triumph Acquisition Sub, Inc., Triumph Merger Sub, Inc. and Metacrine, Inc., as amended on October 26, 2022, and as may be further amended from time to time, or the Merger Agreement. A copy of the Merger Agreement is attached as Annex A to the joint proxy statement/prospectus accompanying this notice. We refer to this proposal as the Metacrine merger proposal.
Metacrine Proposal 2: To approve the adjournment from time to time of the Metacrine virtual special meeting, if necessary, to solicit additional proxies if there are not sufficient votes to approve the Metacrine merger proposal. We refer to this proposal as the Metacrine adjournment proposal.
Metacrine will transact no other business at the special meeting except such business as may properly be brought before the special meeting or any adjournment or postponement thereof. Please refer to the attached joint proxy statement/prospectus for further information with respect to the business to be transacted at the Metacrine virtual special meeting.
In order to attend the Metacrine virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/MTCR2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
Pursuant to an action by unanimous written consent of the Metacrine Board dated September 5, 2022, the Metacrine Board determined that the Merger Agreement and the transactions contemplated thereby are in the best interests of Metacrine and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby and declared advisable and recommended that Metacrine’s stockholders adopt the Merger Agreement.
The Metacrine Board recommends that Metacrine stockholders vote “FOR” the Metacrine merger proposal and “FOR” the Metacrine adjournment proposal.
Holders of record of shares of Metacrine common stock, at the close of business on November 9, 2022, or the Metacrine record date, are entitled to notice of, and may vote at, the special meeting and any adjournment of the special meeting. A list of Metacrine stockholders entitled to vote at the Metacrine virtual special meeting will be available for inspection at Metacrine’s principal executive offices, located at 4225 Executive Square, Suite 600, San Diego, California 92037, at least 10 days prior to the date of the Metacrine virtual special meeting and continuing through the date thereof for any purpose germane to the Metacrine virtual special meeting, between the hours of 9:00 a.m. and 4:30 p.m., local time.
Approval of the Metacrine merger proposal requires the affirmative vote of holders of Metacrine common stock representing a majority of the outstanding shares of Metacrine common stock entitled to vote on such

TABLE OF CONTENTS

matter at the Metacrine virtual special meeting (provided that a quorum exists). Approval of the Metacrine adjournment proposal requires the affirmative vote of holders of Metacrine common stock representing a majority of votes cast on such matter at the Metacrine virtual special meeting (whether or not a quorum is present).
Your vote is important. Whether or not you expect to attend the Metacrine virtual special meeting virtually, we urge you to vote your shares as promptly as possible by (1) accessing the Internet website specified on your proxy card; (2) calling the toll-free number specified on your proxy card; or (3) signing and returning the enclosed proxy card in the postage-paid envelope provided, so that your shares may be represented and voted at the Metacrine virtual special meeting. If your shares are held in “street name” through a bank, broker or other fiduciary, please follow the instructions on the voting instruction card furnished by the record holder. In lieu of receiving a proxy card, participants in certain benefit plans of Metacrine and certain participating Metacrine subsidiaries have been furnished with voting instruction cards, which are described in greater detail in the accompanying joint proxy statement/prospectus. If your shares are registered directly in your name with our transfer agent, American Stock Transfer & Trust Company, LLC, you are considered, with respect to those shares, the shareholder of record. In such case, these proxy materials are being sent directly to you.
If you have any questions or need assistance voting your shares, please call our proxy solicitor, Morrow Sodali, LLC, toll-free at (800) 662-5200.
 
By Order of the Board of Directors,
 
 
 
 
 
/s/ PRESTON KLASSEN
 
Preston Klassen
President, Chief Executive Officer
 
San Diego, California
 
November 10, 2022
We are pleased to invite you to attend the Metacrine virtual special meeting, conducted via live webcast, at www.virtualshareholdermeeting.com/MTCR2022SM. You will not be able to attend the special meeting in person. Whether or not you expect to attend the virtual special meeting, please complete, date, sign and return the proxy card that may be delivered 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 virtual special meeting. Even if you have voted by proxy, you may still vote if you attend the virtual special 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 special meeting, you may be instructed to obtain a legal proxy form from your broker, bank or other nominee and to submit a copy in advance of the special meeting.

TABLE OF CONTENTS

TABLE OF CONTENTS
i

TABLE OF CONTENTS

QUESTIONS AND ANSWERS ABOUT THE MERGER AND THE VIRTUAL SPECIAL MEETINGS
The following are brief answers to certain questions that Equillium stockholders and Metacrine stockholders may have regarding the merger, the merger agreement, the issuance of shares of Equillium common stock in connection with the merger, the Equillium virtual special meeting, the Metacrine virtual special meeting, and other matters to be considered at the Equillium virtual special meeting and at the Metacrine virtual special meeting. Equillium and Metacrine urge you to carefully read the remainder of this joint proxy statement/prospectus and additional important information contained in the annexes and exhibits to, and the documents incorporated by reference into, this joint proxy statement/prospectus because the information in this section may not provide all of the information that might be important to you in determining how to vote. See “Where You Can Find More Information” beginning on page 141 in this joint proxy statement/ prospectus.
Q:
What is the proposed transaction?
A:
On September 6, 2022, Equillium, Metacrine, Acquisition Sub I, Acquisition Sub II, and Merger Sub, entered into the Merger Agreement. A copy of the Merger Agreement is attached to this joint proxy statement/prospectus as Annex A.
Under the terms of the Merger Agreement, Merger Sub will merge with and into Metacrine, with Metacrine continuing as an indirect, wholly owned subsidiary of Equillium, or the Merger. If the Merger is completed, holders of Metacrine common stock, or Metacrine stockholders, will have the right to receive for each share of Metacrine common stock held by such Metacrine stockholder (i) a portion of a share of Equillium common stock equal to the exchange ratio, or the Exchange Ratio, determined by dividing (x) (a) 125% of Metacrine’s net cash as of the closing of the Merger, or the Upfront Merger Consideration, by (b) the price per share of Equillium common stock determined based on the 10 day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the closing date of the Merger, provided that in no event will the price per share of Equillium common stock be less than $2.70 or greater than $4.50, or the Equillium Stock Price, by (y) the aggregate fully diluted shares of Metacrine, or Metacrine’s Closing Capitalization, plus (ii) any cash payable in lieu of fractional shares of Equillium’s common stock. The Exchange Ratio will not reflect changes in the market price of Metacrine common stock and will not reflect changes in the market price of Equillium common stock, except during the 10 trading days that are 10 trading days prior to the closing of the Merger. Holders of Equillium common stock, or Equillium stockholders, will not receive any merger consideration and will continue to hold their shares of Equillium common stock.
Q:
Why am I receiving this joint proxy statement/prospectus?
A:
In order to complete the Merger, among other things:
Equillium stockholders must vote to approve the issuance of shares of Equillium common stock to Metacrine stockholders in connection with the Merger, or the Equillium stock issuance proposal; and
Metacrine stockholders must vote to adopt the Merger Agreement, or the Metacrine merger proposal.
Equillium is holding a virtual special meeting of stockholders in order to obtain the stockholder approval necessary to approve the Equillium stock issuance proposal. Equillium stockholders will also be asked to approve the adjournment from time to time of the Equillium virtual special meeting if necessary to solicit additional proxies if there are not sufficient votes at the time of the Equillium virtual special meeting, or any adjournment or postponement thereof, to approve the stock issuance, or the Equillium adjournment proposal. It is important that Equillium stockholders vote on each of these matters, regardless of the number of shares owned.
Metacrine is holding a virtual special meeting of stockholders to obtain the stockholder approval necessary to approve the Metacrine merger proposal. In addition, Metacrine stockholders will also be asked to approve the adjournment from time to time of the Metacrine virtual special meeting if necessary to solicit additional proxies if there are not sufficient votes to approve the Metacrine merger proposal at the time of the Metacrine virtual special meeting or any adjournment or postponement thereof, or the Metacrine adjournment proposal. It is important that Metacrine stockholders vote their Metacrine common stock on each of these matters, regardless of the number of shares owned.
Your vote is important. We encourage you to vote as soon as possible.
1

TABLE OF CONTENTS

Q:
Who is soliciting my proxy?
A:
Proxies in the form enclosed with this joint proxy statement/prospectus are being solicited from the Equillium stockholders by the board of directors of Equillium, or the Equillium Board. Proxies in the form enclosed with this joint proxy statement/prospectus are being solicited from the Metacrine stockholders by the board of directors of Metacrine, or the Metacrine Board.
Q:
When and where will the meetings be held?
A:
The Equillium virtual special meeting will be held virtually on December 20, 2022, at 12:00 p.m. (Eastern Time). There will be no physical meeting location. In order to attend the Equillium virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
The Metacrine virtual special meeting will be held virtually on December 20, 2022, at 12:00 p.m. (Eastern Time). There will be no physical meeting location. In order to attend the Metacrine virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/MTCR2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
Q:
What will Metacrine stockholders receive in the Merger?
A:
In connection with the closing of the Merger, Metacrine stockholders will have the right to receive for each share of Metacrine common stock held by such Metacrine stockholder (i) a portion of a share of Equillium common stock equal to the Exchange Ratio, plus (ii) any cash payable in lieu of fractional shares of Equillium’s common stock. The Exchange Ratio was devised so that Metacrine stockholders would, in the aggregate, receive a number of shares of Equillium common stock equal to 125% of Metacrine’s net cash at the closing of the Merger. The price of a share of Equillium common stock for purposes of determining the number of shares to be issued will be based on the 10 day trading volume weighted average calculated 10 trading days prior to the closing of the Merger. That price may be more or less than the current price or the price on the last trading day before public announcement of the Merger, but in no event will it be less than $2.70 per share or more than $4.50 per share. The Exchange Ratio will not reflect changes in the market price of Metacrine common stock and will not reflect changes in the market price of Equillium common stock, except during the 10 trading days that are 10 trading days prior to the closing of the Merger.
For illustrative purposes only, we have provided the below assumptions and sensitivity analysis to inform your decision. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Floor Price, the applicable per share price that would be used to determine the Exchange Ratio based on applying the 10 day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to November 8, 2022, the last trading day before November 9, 2022, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.282.
Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to Metacrine’s Assumed Closing Capitalization, a $0.25 increase to the Floor Price would decrease the Exchange Ratio to 0.258. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Ceiling Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.169. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 decrease to the Ceiling Price would increase the Exchange Ratio by 0.179. Assuming (1) the Equillium Stock Price remains constant and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $1,000,000 increase or decrease in the Upfront Merger Consideration would increase or decrease, respectively, the Exchange Ratio by approximately 0.008.
We encourage you to obtain current market quotations of Equillium common stock and Metacrine common stock before voting.
2

TABLE OF CONTENTS

Equillium stockholders will continue to own their existing shares of Equillium common stock. Equillium common stock is currently traded on the Nasdaq under the symbol “EQ,” and Metacrine common stock is currently traded on the Nasdaq under the symbol “MTCR.”
We encourage you to obtain current market quotations of Equillium common stock and Metacrine common stock before voting.
Q:
After applying the Exchange Ratio, how will fractional shares be handled?
A:
No certificate or scrip representing fractional shares of Equillium common stock will be issued in connection with the Merger, and such fractional share interests shall not entitle the owner thereof to vote or to any other rights of an Equillium stockholder. AST, acting as agent for the holders of Metacrine common stock otherwise entitled to receive fractional shares of Equillium common stock at the Closing, will aggregate all fractional shares of Equillium common stock that would otherwise have been required to be distributed and cause them to be sold in the open market for the accounts of such holders. Each holder of Metacrine common stock who would otherwise have been entitled to receive a fraction of a share of Equillium common stock will receive cash, rounded to the nearest whole cent and without interest, in an amount equal to the proceeds from such sale by AST, if any, less applicable fees and expenses, including broker fees.
Q:
How does the Exchange Ratio affect the ownership of Equillium after completion of the Merger?
A:
The Exchange Ratio will determine the relative ownership percentages of the current Equillium stockholders and the current Metacrine stockholders in the combined company. The Exchange Ratio will not be definitively determined until shortly prior to the closing of the Merger.
Q:
How do Metacrine stockholders vote?
A:
If you are a stockholder of record of Metacrine, you may vote at the Metacrine virtual special meeting, vote by proxy over the telephone, vote by proxy through the internet or vote by proxy using the proxy card that may be delivered to you. Whether or not you plan to attend the Metacrine virtual special meeting, we urge you to vote by proxy to ensure your vote is counted. You may still attend the virtual special meeting and vote even if you have already voted by proxy.
VOTE DURING THE SPECIAL MEETING: To vote during the live webcast of the Metacrine virtual special meeting, you will need to visit www.virtualshareholdermeeting.com/MTCR2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form. Stockholders will be able to attend the Metacrine virtual special meeting platform beginning at 12:00 p.m. (Eastern Time) on December 20, 2022, by visiting www.virtualshareholdermeeting.com/MTCR2022SM.
TO VOTE BY PHONE: To vote over the telephone, dial (800) 690-6903 using any touch-tone telephone to transmit your voting instructions. Vote by 11:59 p.m. (Eastern Time) on December 19, 2022. Have your proxy card in hand when you call and then follow the instructions.
TO VOTE BY INTERNET: You can vote over the Internet at www.proxyvote.com. Vote by 11:59 p.m. (Eastern Time) on December 19, 2022. Have your proxy card in hand when you access the website and follow the instructions to obtain your records and to crease an electronic voting instruction form.
TO VOTE BY PROXY CARD: To vote using the proxy card, simply complete, sign and date the proxy card that may be delivered to you and return it promptly in the postage-prepaid envelope we have provided or return it to: Vote Processing, c/o Broadridge, 51 Mercedes Way, Edgewood, NY 11717. If you return your signed proxy card to us before the Metacrine virtual special meeting, we will vote your shares as you direct.
Beneficial Owner: Shares Registered in the Name of Broker or Bank
If you are a beneficial owner of shares registered in the name of your brokerage firm, bank or other agent, you should have received a voting instruction form with the proxy card delivered to you from that organization rather than from Metacrine. Simply complete and mail the voting instruction form to ensure that your vote is
3

TABLE OF CONTENTS

counted. Alternatively, you may vote by telephone or over the internet as instructed by your broker, bank or other agent. To vote at the Metacrine virtual special meeting, you will need to visit www.virtualshareholdermeeting.com/MTCR2022SM. You may be instructed to obtain a legal proxy from your broker, bank or other nominee and to submit a copy in advance of the Metacrine virtual special meeting. Further instruction will be provided to you as part of your registration process.
Internet proxy voting may be provided to allow you to vote your shares online, with procedures designed to ensure the authenticity 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.
Q:
How do Equillium stockholders vote?
A:
If you are a stockholder of record of Equillium, you may vote at the Equillium virtual special meeting, vote by proxy over the telephone, vote by proxy through the internet or vote by proxy using the proxy card that may be delivered to you. Whether or not you plan to attend the Equillium virtual special meeting, we urge you to vote by proxy to ensure your vote is counted. You may still attend the virtual special meeting and vote even if you have already voted by proxy.
VOTE DURING THE SPECIAL MEETING: To vote during the live webcast of the Equillium virtual special meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number included in your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
Stockholders will be able to attend the Equillium virtual special meeting platform beginning at 12:00 p.m. (Eastern Time) on December 20, 2022, by visiting www.virtualshareholdermeeting.com/EQ2022SM.
TO VOTE BY PHONE: To vote over the telephone, dial (800) 690-6903 using any touch-tone telephone to transmit your voting instructions. Vote by 11:59 p.m. (Eastern Time) on December 19, 2022. Have your proxy card in hand when you call and then follow the instructions.
TO VOTE BY INTERNET: You can vote over the Internet at www.proxyvote.com. Vote by 11:59 p.m. (Eastern Time) on December 19, 2022. Have your proxy card in hand when you access the website and follow the instructions to obtain your records and to crease an electronic voting instruction form.
TO VOTE BY PROXY CARD: To vote using the proxy card, simply complete, sign and date the proxy card that may be delivered to you and return it promptly in the postage-prepaid envelope we have provided or return it to Vote Processing, c/o Broadridge, 51 Mercedes Way, Edgewood, NY 11717. If you return your signed proxy card to us before the Equillium virtual special meeting, we will vote your shares as you direct.
Beneficial Owner: Shares Registered in the Name of Broker or Bank
If you are a beneficial owner of shares registered in the name of your brokerage firm, bank or other agent, you should have received a voting instruction form with the proxy card delivered to you from that organization rather than from Equillium. Simply complete and mail the voting instruction form to ensure that your vote is counted. Alternatively, you may vote by telephone or over the internet as instructed by your broker, bank or other agent. To vote at the Equillium virtual special meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM. You may be instructed to obtain a legal proxy from your broker, bank or other nominee and to submit a copy in advance of the Equillium virtual special meeting. Further instruction will be provided to you as part of your registration process.
Internet proxy voting may be provided to allow you to vote your shares online, with procedures designed to ensure the authenticity 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.
Q:
What are the voting deadlines?
A:
If you are an Equillium stockholder, the deadline for submitting a proxy using the Internet or the telephone
4

TABLE OF CONTENTS

is 11:59 p.m. (Eastern Time) on December 19, 2022. If you received your special meeting materials by mail, you may complete, sign and date the proxy card or voting instruction card and return it in the prepaid envelope. All holders of Equillium common stock as of the close of business on the record date for the Equillium virtual special meeting may vote virtually at the Equillium virtual special meeting. For detailed information, see the section entitled “The Equillium virtual special meeting.”
If you are a Metacrine stockholder, the deadline for submitting a proxy using the Internet or the telephone is 11:59 p.m. (Eastern Time) on December 19, 2022. If you received your special meeting materials by mail, you may complete, sign and date the proxy card or voting instruction card and return it in the prepaid envelope. All holders of Metacrine common stock as of the close of business on the record date may vote virtually at the Metacrine virtual special meeting. For detailed information, see the section entitled “The Metacrine virtual special meeting.”
Q:
What vote is required to approve each proposal at the Equillium virtual special meeting?
A:
Equillium Stock Issuance Proposal. Approval of the stock issuance proposal requires the affirmative vote of the holders of Equillium common stock representing a majority of the votes cast at the Equillium virtual special meeting (provided that a quorum exists). Failure to vote virtually or by proxy at the special meeting, abstentions, and broker non-votes (if any) will have no effect on the outcome of the Equillium stock issuance proposal. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Equillium Adjournment Proposal. Approval of the Equillium adjournment proposal requires the affirmative vote of the holders of Equillium common stock representing a majority of the votes cast at the Equillium virtual special meeting (whether or not a quorum is present). Failure to vote virtually or by proxy at the special meeting, abstentions, and broker non-votes (if any) will have no effect on the outcome of the Equillium adjournment proposal. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Q:
What vote is required to approve each proposal at the Metacrine virtual special meeting?
A:
Metacrine Merger Proposal. Approval of the Metacrine merger proposal requires the affirmative vote of a majority of the outstanding shares of Metacrine’s common stock. Failure to vote virtually or by proxy at the special meeting, abstentions, and broker non-votes (if any) will have the same effect as a vote against the Metacrine merger proposal. Shares of Metacrine common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Metacrine Adjournment Proposal. Approval of the Metacrine adjournment proposal requires the affirmative vote of the holders of Metacrine common stock representing a majority of the votes cast at the Equillium virtual special meeting (whether or not a quorum is present). Failure to vote virtually or by proxy at the special meeting, abstentions, and broker non-votes (if any) will have no effect on the outcome of the Metacrine adjournment proposal. Shares of Metacrine common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Q:
How does the Metacrine Board recommend that Metacrine stockholders vote?
A:
Pursuant to an action by unanimous written consent of the Metacrine Board dated September 5, 2022, the Metacrine Board determined that the Merger Agreement and the transactions contemplated thereby were in the best interests of Metacrine and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby and declared advisable and recommended that Metacrine’s stockholders adopt the Merger Agreement. The Metacrine Board recommends that Metacrine stockholders vote “FOR” the Metacrine merger proposal and “FOR” the Metacrine adjournment proposal.
Q:
How does the Equillium Board recommend that Equillium stockholders vote?
A:
At a meeting of the Equillium Board held on September 5, 2022, the Equillium Board determined that the Merger Agreement and the transactions contemplated thereby, including the issuance of shares of Equillium common stock to the Metacrine stockholders in connection with the Merger, were in the best interests of
5

TABLE OF CONTENTS

Equillium and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby. The Equillium Board recommends that Equillium stockholders vote “FOR” the Equillium stock issuance proposal and “FOR” Equillium adjournment proposal.
Q:
How many votes do I have?
A:
Equillium. You are entitled to one vote for each share of Equillium common stock that you owned as of the Equillium record date. As of the close of business on November 9, 2022, there were 34,352,084 outstanding shares of Equillium common stock. As of that date, 25.5% of the outstanding shares of Equillium common stock were beneficially owned by the directors and executive officers of Equillium.
Metacrine. You are entitled to one vote for each share of Metacrine common stock that you owned as of the Metacrine record date. As of the close of business on November 9, 2022, there were 42,569,515 outstanding shares of Metacrine common stock. As of that date, 8.4% of the outstanding shares of Metacrine common stock were beneficially owned by the directors and executive officers of Metacrine.
Q:
What will happen if I fail to vote or I abstain from voting?
A:
Equillium. If you are an Equillium stockholder, abstentions and broker “non-votes” have no effect on the outcome of the Equillium stock issuance proposal or the Equillium adjournment proposal. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Your failure to cast a vote virtually will also make it more difficult to meet the quorum requirement with respect to the Equillium stock issuance proposal.
Metacrine. If you are a Metacrine stockholder, failure to vote virtually or by proxy at the Metacrine virtual special meeting, abstentions, and broker non-votes (if any) will have the same effect as a vote against the Metacrine merger proposal. Shares of Metacrine common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon.
Q:
What are “broker non-votes”?
A:
Brokers who hold shares in street name for customers have the authority to vote on “routine” proposals when they have not received instructions from beneficial owners. However, brokers are precluded from exercising their voting discretion with respect to approval of non-routine matters, such as the Equillium stock issuance proposal and the Metacrine merger proposal, and, as a result, absent specific instructions from the beneficial owner of such shares, brokers are not empowered to vote those shares, referred to generally as “broker non-votes.” Broker non-votes, if any, will be treated as shares that are present at the virtual special meeting for purposes of determining whether a quorum exists but will not be counted or deemed present virtually or by proxy for the purpose of voting on the Equillium stock issuance proposal or the Metacrine merger proposal. Broker non-votes, if any, will have the same effect as a vote against the Metacrine merger proposal.
Q:
What constitutes a quorum?
A:
Equillium. The holders of a majority of the voting power of Equillium’s outstanding shares of common stock entitled to vote as of the close of business on the Equillium record date must be virtually present or represented by proxy to constitute a quorum to conduct the Equillium virtual special meeting. All shares of Equillium common stock represented at the Equillium virtual special meeting, including abstentions and broker non-votes, will be treated as present for purposes of determining the presence or absence of a quorum to conduct the Equillium virtual special meeting.
Metacrine. The holders of a majority of the voting power of Metacrine’s outstanding shares of common stock entitled to vote as of the close of business on the Metacrine record date must be virtually present or represented by proxy to constitute a quorum to conduct the Metacrine virtual special meeting. All shares of Metacrine common stock represented at the Metacrine virtual special meeting, including abstentions and broker non-votes will be treated as present for purposes of determining the presence or absence of a quorum to conduct the Metacrine virtual special meeting.
6

TABLE OF CONTENTS

Q:
What is the difference between a stockholder of record and a “street name” holder?
A:
If your shares are registered directly in your name, you are considered the stockholder of record with respect to those shares. If your shares are held in a stock brokerage account or by a bank, trust company or other nominee, then the broker, bank, trust company or other nominee is considered to be the stockholder of record with respect to those shares, while you are considered the beneficial owner of those shares. In the latter case, your shares are said to be held in “street name.”
Q:
If I am a beneficial owner of shares held in street name, how do I vote?
A:
If you are not a stockholder of record but instead hold your shares in a stock brokerage account, or if your shares are held by a bank, trust company or other nominee (that is, in street name), you must provide the record holder of your shares with instructions on how to vote your shares. If you are an Equillium stockholder but not a stockholder of record and you do not instruct your broker on how to vote your shares, your broker may not vote your shares on the Equillium stock issuance proposal or any adjournment proposal, which will have no effect on the vote on this proposal, assuming a quorum is present. If you are a Metacrine stockholder but not a stockholder of record and you do not instruct your broker on how to vote your shares, your broker may not vote your shares, which will have the same effect as a vote against the Metacrine merger proposal and, assuming a quorum is present, will have no effect on the outcome of the Metacrine adjournment proposal.
Please follow the voting instructions provided by your broker or nominee. Please note that you may not vote shares held in street name by returning a proxy card directly to Equillium or Metacrine or by voting virtually at your special meeting. Further, brokers who hold shares of Equillium common stock or Metacrine common stock on behalf of their customers may not give a proxy to Equillium or Metacrine to vote those shares without specific instructions from their customers.
Q:
What will happen if I return my proxy card without indicating how to vote?
A:
If you are an Equillium stockholder of record and you sign and return your proxy card without indicating how to vote on any particular proposal, the shares of Equillium common stock represented by your proxy will be counted as present for purposes of determining the presence of a quorum for the Equillium virtual special meeting and will be voted “FOR” that proposal.
If you are a Metacrine stockholder of record and you sign and return your proxy card without indicating how to vote on any particular proposal, the shares of Metacrine common stock represented by your proxy will be counted as present for purposes of determining the presence of a quorum for the Metacrine virtual special meeting and will be voted “FOR” that proposal.
Q:
Can I change my vote after I have returned a proxy or voting instruction card?
A:
Yes. You can change your vote at any time before your proxy is voted at the Equillium virtual special meeting or the Metacrine virtual special meeting, as applicable. You can do this in one of four ways:
you can send a signed notice of revocation;
you can grant a new, valid proxy bearing a later date;
you can vote again by telephone or the Internet at a later time; or
if you are a holder of record, by voting at the Equillium virtual special meeting or Metacrine virtual special meeting, as applicable, which will automatically cancel any proxy previously given, or you may revoke your proxy by attending such virtual special meeting, but your attendance alone will not revoke any proxy that you have previously given.
If you choose either of the first two methods, you must provide your notice of revocation or your new proxy to the Secretary of Equillium or Secretary of Metacrine, as applicable, prior to your shares being voted. If your shares are held in street name by your broker or nominee, you should contact them to change your vote.
Q:
What should I do if I receive more than one set of voting materials?
A:
Please vote each proxy card and voting instruction card that you receive. You may receive more than one set of voting materials, including multiple copies of this joint proxy statement/prospectus and multiple proxy
7

TABLE OF CONTENTS

cards or voting instruction cards. For example, stockholders who hold shares in more than one brokerage account will receive a separate voting instruction card for each brokerage account in which shares are held. If shares are held in more than one name, stockholders will receive more than one proxy or voting instruction card. In addition, if you are a stockholder of both Equillium and Metacrine, you may receive one or more proxy cards or voting instruction cards for Equillium and one or more proxy cards or voting instruction cards for Metacrine. If you are a stockholder of both Equillium and Metacrine, please note that a vote for the issuance of shares of Equillium common stock in the Merger pursuant to the terms of the Merger Agreement for the Equillium virtual special meeting will not constitute a vote for the proposal to adopt the Merger Agreement for the Metacrine virtual special meeting, and vice versa. Therefore, please vote each proxy and voting instruction card you receive, whether from Equillium or Metacrine.
Q:
Is there a list of stockholders entitled to vote at the Equillium and Metacrine virtual special meetings?
A:
The names of stockholders of record entitled to vote at the Equillium virtual special meeting will be available at the Equillium virtual special meeting and for 10 days prior to the Equillium virtual special meeting for any purpose germane to the special meeting, between the hours of 9:00 a.m. and 4:30 p.m. (Pacific Time), at Equillium’s principal executive offices located at 2223 Avenida de la Playa, Suite 105, La Jolla, California 92037, or by contacting Equillium’s corporate secretary.
The names of stockholders of record entitled to vote at the Metacrine virtual special meeting will be available at the Metacrine virtual special meeting and for 10 days prior to the Metacrine virtual special meeting for any purpose germane to the special meeting, between the hours of 9:00 a.m. and 4:30 p.m. (Pacific Time), at Metacrine’s principal executive offices located at 4225 Executive Square, Suite 600, San Diego, CA 92037, or by contacting Metacrine’s corporate secretary.
Q:
What happens if I am a Metacrine stockholder who sells my shares of Metacrine common stock before the Metacrine virtual special meeting?
A:
The record date for the Metacrine virtual special meeting is earlier than the Metacrine virtual special meeting. If you transfer your shares of Metacrine common stock after the Metacrine record date but before the Metacrine virtual special meeting, you will retain your right to vote at the Metacrine virtual special meeting, but will have transferred the right to receive the merger consideration in the Merger. In order to receive the merger consideration, you must hold your shares through the effective time of the Merger.
Q:
What happens if I am an Equillium stockholder who sells my shares of Equillium common stock before the Equillium virtual special meeting?
A:
The record date for the Equillium virtual special meeting is earlier than the Equillium virtual special meeting. If you transfer your shares of Equillium common stock after the Equillium record date but before the Equillium virtual special meeting, you will retain your right to vote at the Equillium virtual special meeting.
Q:
What will happen to my Metacrine stock options, restricted stock units and/or warrants at the time of the Merger?
A:
Treatment of Restricted Stock Unit Awards. At the effective time of the Merger, each Metacrine restricted stock unit outstanding immediately prior to such time, or a Metacrine RSU, whether vested or unvested, other than Metacrine RSUs held by any former employee, former service provider or director of Metacrine, will be assumed by Equillium and converted into a restricted stock unit for a number of shares of Equillium common stock, or an assumed RSU, equal to the product of (a) the number of shares of Metacrine common stock subject to such Metacrine RSU and (b) the Exchange Ratio (with any fractional shares rounded down to the nearest whole share). Except for the change to the number and type of shares, each assumed RSU will be subject to the same terms and conditions, including vesting, as were applicable to such Metacrine RSU prior to the Merger. At the effective time of the Merger, (a) each outstanding unvested Metacrine RSU held by a former employee, former service provider or director of Metacrine will be cancelled without the payment of any consideration and (b) each outstanding vested and unexercised Metacrine RSU held by a former employee, former service provider or director of Metacrine will be cancelled and converted into a
8

TABLE OF CONTENTS

right to receive a number of fully-vested shares of Equillium common stock equal to the product of (a) the number of shares of Metacrine common stock subject to such Metacrine RSU and (b) the Exchange Ratio (with any fractional shares rounded down to the nearest whole share).
Treatment of Stock Options. At the effective time of the Merger, each option to purchase Metacrine common stock that is outstanding and unexercised immediately prior to such time, or a Metacrine option, whether vested or unvested, other than any Metacrine option held by any former employee, former service provider or director of Metacrine, will be assumed by Equillium and converted into an option to acquire a number of shares of Equillium common stock, or an adjusted option, equal to the product of (a) the number of shares of Metacrine common stock subject to such Metacrine option and (b) the Exchange Ratio (rounded down to the nearest whole share). The per share exercise price of each adjusted option will be equal to (i) the per share exercise price of such Metacrine option immediately prior to the Merger divided by (ii) the Exchange Ratio (with the resulting price per share rounded up to the nearest whole cent). Except for the changes made to the number and type of shares and the exercise price, each adjusted option will be subject to the same terms and conditions, including vesting, as were applicable to such Metacrine option immediately prior to the Merger. At the effective time of the Merger, each unvested Metacrine option that is outstanding and unexercised as of immediately prior to such time and held by a former employee, former service provider or director of Metacrine will be cancelled without the payment of any consideration, and each vested Metacrine option that is outstanding and unexercised as of immediately prior to such time and held by a former employee, former service provider or director of Metacrine will be cancelled and converted into a right to receive a number of shares of Equillium common stock equal to the product of (x) the number of shares of Metacrine common stock subject to such Metacrine option multiplied by the excess, if any, of (1) the 10 day volume weighted average closing sale price of one share of Metacrine common stock for the 10 trading days prior to the effective time of the Merger (as adjusted as appropriate to reflect any stock splits, stock dividends, combinations, mergers, reorganizations, reclassifications or similar events), or the Metacrine Share Value over (2) the per share exercise price for shares subject to such Metacrine option, divided by (y) the Metacrine Share Value, multiplied by (z) the Exchange Ratio (rounded down to the nearest whole share).
Treatment of Warrants. At the effective time of the Merger, each of Metacrine’s warrants, or Metacrine Warrant, that is outstanding and unexercised immediately prior to the closing of the Merger will be automatically substituted into a warrant to purchase the number of shares of Equillium common stock equal to the product obtained by multiplying (i) the number of shares of Metacrine common stock subject to the Metacrine Warrant immediately prior to the closing of the Merger by (ii) the Exchange Ratio (rounding up to the nearest whole share). Each Metacrine Warrant will have an exercise price per share of Equillium common stock equal to (i) the exercise price per share provided in the Metacrine Warrant immediately prior to the closing of the Merger divided by (ii) the Exchange Ratio.
Treatment of ESPP. Following the date of the Merger Agreement, Metacrine has taken actions with respect to Metacrine’s 2020 Employee Stock Purchase Plan, or the ESPP, to provide that with respect to any offering periods in effect as of the date of the Merger Agreement, or the current purchase period, (i) no employee who is not a participant in the ESPP as of the date of the Merger Agreement may become a participant in the ESPP, and (ii) no employee participating in the current purchase period may increase his or her payroll contribution rate pursuant to the ESPP from the rate in effect immediately prior to the date of the Merger Agreement, except as required by applicable law. In addition, (A) the current purchase period will end on a specified trading day occurring at least 10 days prior to the date on which the Merger is expected to close; (B) there will be no offering periods following the current purchase period and (C) in all events, Metacrine shall terminate the ESPP prior to the effective time of the Merger.
Q:
How will the rights of Metacrine stockholders change after the Merger?
A:
Metacrine stockholders will receive shares of Equillium common stock in connection with the Merger and will no longer be stockholders of Metacrine following the Merger. Their rights as holders of Equillium common stock will be governed by the amended and restated certificate of incorporation of Equillium and Equillium’s amended and restated bylaws. For additional information on stockholder rights, see “Description of Capital Stock and Comparison of Rights of Equillium Stockholders and Metacrine Stockholdersbeginning on page 130 of this joint proxy statement/prospectus.
The rights of Equillium stockholders will remain the same as prior to the Merger.
9

TABLE OF CONTENTS

Q:
What are the material U.S. federal income tax consequences of the Merger to U.S. holders of Metacrine common stock?
A:
For U.S. federal income tax purposes, the receipt of the merger consideration by a U.S. Holder (as defined in the section captioned “Material U.S. Federal Income Tax Consequences of the Merger” in exchange for such U.S. Holder’s shares of our common stock in the merger is generally expected to be a taxable transaction for U.S. federal income tax purposes. In that case, such exchange will result in the recognition of gain or loss in an amount measured by the difference, if any, between the fair market value of the merger consideration that such U.S. Holder receives in the merger and such U.S. Holder’s adjusted tax basis in the shares of our common stock surrendered in the merger.
A Non-U.S. Holder (as defined in the section captioned “Material U.S. Federal Income Tax Consequences of the Merger”) generally will not be subject to U.S. federal income tax with respect to the exchange of our common stock for the Merger Consideration in the Merger unless such Non-U.S. Holder has certain connections to the United States, but may be subject to backup withholding tax unless the Non-U.S. Holder complies with certain certification procedures or otherwise establishes a valid exemption from backup withholding tax.
You should read the section entitled “Material U.S. Federal Income Tax Consequences” beginning on page 123 for a more complete discussion of the U.S. federal income tax consequences of the Merger. Tax matters can be complicated, and the tax consequences of the Merger to you will depend on your particular situation. You should consult your own tax advisors concerning the U.S. federal income tax consequences relating to the Merger in light of your particular circumstances and any consequences arising under U.S. federal non-income tax laws or the laws of any territory, state, local or non-U.S. taxing jurisdiction.
Q:
Are there any risks that I should consider in deciding how to vote?
A:
Yes. You should read and carefully consider the risk factors set forth in the section entitled “Risk Factors” beginning on page 30 of this joint proxy statement/prospectus. You also should read and carefully consider the risk factors of Equillium and Metacrine contained in the documents that are incorporated by reference into this joint proxy statement/prospectus.
Q:
What happens if the Merger is not completed?
A:
If the Merger is not completed for any reason, Metacrine stockholders will not receive the merger consideration issuable under the Merger Agreement. Instead, Equillium and Metacrine will remain separate public companies, and Metacrine expects that its common stock will continue to be registered under the Exchange Act and traded on the Nasdaq. In specified circumstances, either Equillium or Metacrine may be required to pay to the other party a termination fee, as described below.
Q:
Does Metacrine have to pay anything to Equillium if the Merger Agreement is terminated?
A:
In certain circumstances, depending on the reasons for termination of the Merger Agreement, Metacrine may have to pay Equillium a termination fee of $1.25 million. For a discussion of the circumstances under which a termination fee is payable by Metacrine applies, see “The Merger Agreement—Termination Fees; Liability for Breach.”
Q:
Does Equillium have to pay anything to Metacrine if the Merger Agreement is terminated?
A:
In certain circumstances, depending on the reasons for termination of the Merger Agreement, Equillium may have to pay Metacrine a termination fee of $1.75 million. For a discussion of the circumstances under which a termination fee is payable by Equillium applies, see “The Merger Agreement—Termination Fees; Liability for Breach
Q:
When do you expect the Merger to be completed?
A:
Metacrine and Equillium intend to complete the Merger as soon as reasonably practicable and currently anticipate the closing of the Merger to occur on December 23, 2022, following the satisfaction of all the conditions to completion of the Merger. However, the Merger is subject to the satisfaction or waiver of
10

TABLE OF CONTENTS

certain conditions and it is possible that factors outside the control of Metacrine and Equillium could result in the Merger being completed at a later time or not at all. There can be no assurances as to when or if the Merger will close. See “The Merger Agreement—Article VI Conditions.”
Q:
What do I need to do now?
A:
You should carefully read and consider the information contained in and incorporated by reference into this joint proxy statement/prospectus, including its annexes. Even if you plan to attend the Equillium virtual special meeting or the Metacrine virtual special meeting virtually, after carefully reading and considering the information contained in this joint proxy statement/prospectus, please vote promptly to ensure that your shares are represented at the Equillium virtual special meeting or the Metacrine virtual special meeting, as applicable.
Q:
Do I need to do anything with my Metacrine common stock certificates now?
A:
No. After the Merger is completed, if you held certificates representing shares of Metacrine common stock prior to the Merger, Equillium’s exchange agent American Stock Transfer & Trust Company, LLC, or the exchange agent, will send you a letter of transmittal and instructions for exchanging your shares of Metacrine common stock for the merger consideration. Upon surrender of the certificates for cancellation along with the executed letter of transmittal and other required documents described in the instructions, a Metacrine stockholder will receive the merger consideration. The shares of Equillium common stock you receive in the Merger will be issued in book-entry form.
If you are an Equillium stockholder, you are not required to take any action with respect to your Equillium stock certificates.
Q:
Do I need to do anything with my Metacrine common stock held in book-entry form now?
A:
No. After the Merger is completed, if you held shares of Metacrine common stock in book-entry form prior to the Merger, Equillium’s exchange agent will send you a letter of transmittal and instructions for exchanging your shares of Metacrine common stock for the merger consideration. Upon receipt of an agent’s message in customary form (or such other evidence, if any, as the exchange agent may reasonably request), along with the executed letter of transmittal and other required documents described in the instructions, a Metacrine stockholder will receive the merger consideration. The shares of Equillium common stock you receive in the Merger will be issued in book-entry form.
Q:
Are stockholders entitled to appraisal rights?
A:
Under Delaware law, the Metacrine stockholders are not entitled to appraisal rights in connection with the Metacrine merger proposal.
Under Delaware law, the Equillium stockholders are not entitled to appraisal rights in connection with the Equillium stock issuance proposal.
Q:
How can I contact Equillium’s or Metacrine’s transfer agent?
A:
You may contact Equillium’s or Metacrine’s transfer agent by writing to American Stock Transfer & Trust Company, LLC, 6201 15th Avenue, Brooklyn, NY 11219, or by telephoning (718) 921-8300.
Q:
Who should I contact if I have any questions about the proxy materials or about voting?
A:
If you have any questions about the proxy materials or if you need assistance submitting your proxy or voting your shares or need additional copies of this joint proxy statement/prospectus or the enclosed proxy card, you should, if you are an Equillium stockholder, contact Equillium by telephone at (858) 240-1200 or by email at ir@equilliumbio.com, and, if you are a Metacrine stockholder, contact Morrow Sodali, LLC, Metacrine’s proxy solicitor, by telephone toll-free at (800) 662-5200, by email at MTCR@investor.morrowsodali.com, or by mail at 509 Madison Avenue, Suite 1206, New York, NY 10022.
Q:
Who is the exchange agent in the Merger?
A:
American Stock Transfer & Trust Company, LLC will be the exchange agent for the Merger.
Q:
Where can I find more information about Equillium and Metacrine?
A:
You can find more information about Equillium and Metacrine from the various sources described under Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus.
11

TABLE OF CONTENTS

SUMMARY
This summary highlights selected information contained elsewhere in this joint proxy statement/prospectus and may not contain all the information that is important to you with respect to the Merger and the related matters being considered at the applicable special meeting. Equillium and Metacrine urge you to carefully read the remainder of this joint proxy statement/prospectus, including the annexes and exhibits attached to and the documents incorporated by reference into this joint proxy statement/prospectus. For a description of, and instructions as to how to obtain, this information, see “Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus. Certain items in this summary include a page reference directing you to a more complete description of that item.
Parties to the Merger
Equillium, Inc.
2223 Avenida de la Playa, Suite 105
La Jolla, California 92037
(858) 240-1200
Equillium was incorporated in the state of Delaware on March 16, 2017. Equillium is a clinical-stage biotechnology company leveraging deep understanding of immunology to develop novel products to treat severe autoimmune and inflammatory disorders with high unmet medical need. Equillium’s strategy is focused on advancing the clinical development of its product candidates, including potentially pursuing additional indications and acquiring new product candidates and platforms to expand its pipeline. Equillium intends to commercialize its product candidates either independently or through partnerships or otherwise monetize its pipeline through strategic transactions.
Since inception, Equillium has devoted substantially all of its efforts to organizing and staffing the company, business planning, raising capital, in-licensing rights to itolizumab (EQ001), conducting non-clinical research, filing three Investigational New Drug applications, conducting pre-clinical and clinical development of Equillium’s initial product candidate, itolizumab (EQ001), conducting business development activities such as the acquisition of Bioniz Therapeutics, Inc., in February 2022, preparing to initiate clinical studies of EQ101 and EQ102, and the general and administrative activities associated with operating a public company. Equillium has not generated revenues from its principal operations, and the sales and income potential of its business is unproven.
About Itolizumab
Itolizumab (EQ001) is a clinical-stage, first-in-class anti-CD6 monoclonal antibody that selectively targets the CD6-ALCAM pathway. This pathway plays a central role in modulating the activity and trafficking of T cells that drive a number of immuno-inflammatory diseases. Equillium acquired rights to itolizumab through an exclusive partnership with Biocon Limited.
About Equillium’s Multi-Cytokine Platform and Product Candidates EQ101 and EQ102
Equillium’s proprietary multi-cytokine platform, or MCP, generates rationally designed composite peptides that selectively block key cytokines at the shared receptor level targeting pathogenic cytokine redundancies and synergies while preserving non-pathogenic signaling. This approach provides multi-cytokine inhibition at the receptor level and is expected to avoid the broad immuno-suppression and off-target safety liabilities that may be associated with other therapeutic classes, such as JAK inhibitors. Many immune-mediated diseases are driven by the same combination of dysregulated cytokines, and Equillium believes identifying the key cytokines for these diseases will allow it to target and develop customized treatment strategies for multiple autoimmune and inflammatory diseases. Current MCP assets include EQ101, a first-in-class, tri-specific inhibitor of IL-2, IL-9 and IL-15, and EQ102, a first-in-class, selective inhibitor of IL-15 and IL-21.
This joint proxy statement/prospectus incorporates important business and financial information about Equillium from other documents that are not included in or delivered with this joint proxy statement/prospectus. For a list of the documents that are incorporated by reference, see “Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus.
12

TABLE OF CONTENTS

Equillium Acquisition Sub, Inc.
Triumph Acquisition Sub, Inc.
Triumph Merger Sub, Inc.
2223 Avenida de la Playa, Suite 105
La Jolla, California 92037
(858) 240-1200
Acquisition Sub I, a direct wholly owned subsidiary of Equillium, is a Delaware corporation formed on September 1, 2022, for the purpose of forming Merger Sub, and subsequently, Acquisition Sub II. Upon completion of the Merger, Acquisition Sub I will continue to exist as a direct wholly owned subsidiary of Equillium.
Acquisition Sub II, a direct wholly owned subsidiary of Acquisition Sub I, is a Delaware corporation formed on October 20, 2022 for the purposes of holding all outstanding shares of Merger Sub. Upon completion of the Merger, Acquisition Sub II will continue to exist as a direct wholly owned subsidiary of Acquisition Sub I.
Merger Sub, a direct wholly owned subsidiary of Acquisition Sub II, is a Delaware corporation formed on September 1, 2022, for the purposes of effecting the Merger. Upon completion of the Merger, Merger Sub will be merged with and into Metacrine, with Metacrine continuing as a direct wholly owned subsidiary of Acquisition Sub II.
Each of Acquisition Sub I, Acquisition Sub II, and Merger Sub have not conducted any activities other than those incidental to their formation and the matters contemplated by the Merger Agreement.
Metacrine, Inc.
4225 Executive Square, Suite 600
San Diego, CA 92037
(858) 369-7800
Metacrine was incorporated in the state of Delaware on September 17, 2014. Metacrine is a clinical-stage biopharmaceutical company currently focused on discovering and developing differentiated therapies for patients with gastrointestinal, or GI, diseases. Metacrine’s most advanced program, MET642, targets the farnesoid X receptor, or FXR, which is central to modulating GI and liver diseases. Metacrine has not generated revenues from its principal operations, and the sales and income potential of its business is unproven.
This joint proxy statement/prospectus incorporates important business and financial information about Metacrine from other documents that are not included in or delivered with this joint proxy statement/prospectus. For a list of the documents that are incorporated by reference, see “Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus.
Risk Factors
Before voting at the Equillium virtual special meeting or the Metacrine virtual special meeting, you should carefully consider all of the information contained in or as incorporated by reference into this joint proxy statement/prospectus, as well as the specific factors under the heading “Risk Factors” beginning on page 30 of this joint proxy statement/prospectus.
The Merger and the Merger Agreement
A copy of the Merger Agreement is attached as Annex A to this joint proxy statement/prospectus. Equillium and Metacrine encourage you to read the entire Merger Agreement carefully because it is the principal document governing the Merger. For more information on the Merger Agreement, see the section entitled “The Merger Agreement” beginning on page 15 of this joint proxy statement/prospectus.
Effects of the Merger; Merger Consideration
If the conditions set forth in the Merger Agreement are satisfied or waived, Merger Sub will merge with and into Metacrine. Metacrine will survive the Merger and will continue as a direct wholly owned subsidiary of Equillium.
13

TABLE OF CONTENTS

In the Merger, each share of Metacrine common stock issued and outstanding immediately prior to the effective time of the Merger will be automatically converted at the effective time into the right to receive the Exchange Ratio, with cash paid in lieu of fractional shares. The Exchange Ratio will not reflect changes in the market price of Metacrine common stock and will not reflect changes in the market price of Equillium common stock, except during the 10 trading days that are 10 trading days prior to the closing of the Merger. Equillium stockholders will not receive any merger consideration and will continue to hold their existing shares of Equillium common stock.
Treatment of Metacrine Equity Awards and Warrants
For a description of the treatment of Metacrine equity awards and warrants, see “Treatment of Metacrine Equity Awards and Warrants” beginning on page 70 of this joint proxy statement/prospectus.
Material U.S. Federal Income Tax Consequences of the Merger (See page 123)
It is expected that, for U.S. federal income tax purposes, the Merger will be a taxable transaction. In that event, a U.S. holder of Metacrine common stock will recognize gain or loss for U.S. federal income tax purposes upon the exchange of such holder's shares of Metacrine common stock for the Merger Consideration in the Merger.
The discussion of U.S. federal income tax consequences of the Merger contained in this joint proxy statement/prospectus is intended to provide only a general summary and is not a complete analysis or description of all potential U.S. federal income tax consequences of the Merger. The discussion does not address tax consequences that may vary with, or are contingent on, individual circumstances. In addition, it does not address the effects of any non-U.S., state or local tax laws.
For a more complete discussion of the material U.S. federal income tax consequences of the Merger, please carefully review the information set forth in the section entitled “Material U.S. Federal Income Tax Consequences”.
The tax consequences of the Merger to any particular stockholder will depend on that stockholder’s particular facts and circumstances. Accordingly, you are urged to consult your own tax advisor as to the specific tax consequences of the Merger, including the effects of U.S. federal, state, local, non-U.S. and other tax laws.
Equillium’s Reasons for the Merger; Recommendation of the Equillium Board (See page 87)
At a meeting of the Equillium Board held on September 5, 2022, the Equillium Board determined that the Merger Agreement and the transactions contemplated thereby, including the issuance of shares of Equillium common stock to the Metacrine stockholders in connection with the Merger, are in the best interests of Equillium and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby, including the issuance of shares of Equillium common stock in connection with the Merger.
For the factors considered by the Equillium Board in reaching its decision to approve the Merger Agreement, see the section entitled “The Merger—Equillium’s Reasons for the Merger; Recommendation of the Stock Issuance by the Equillium Board” beginning on page 87.
The Equillium Board recommends that Equillium stockholders vote “FOR” the proposal to issue shares of Equillium common stock in connection with the Merger and “FOR” the Equillium adjournment proposal.
Metacrine’s Reasons for the Merger; Recommendation of the Metacrine Board (See page 88)
Pursuant to an action by unanimous written consent of the Metacrine Board dated September 5, 2022, the Metacrine Board determined that the Merger Agreement and the transactions contemplated thereby was in the best interests of Metacrine and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby and declared advisable and recommended that Metacrine’s stockholders adopt the Merger Agreement.
For the factors considered by the Metacrine Board in reaching its decision to approve the Merger Agreement, see the section entitled “The Merger—Metacrine’s Reasons for the Merger; Recommendation of the Merger by the Metacrine Board” beginning on page 88 of this joint proxy statement/prospectus.
14

TABLE OF CONTENTS

The Metacrine Board recommends that Metacrine stockholders vote “FOR” the Metacrine merger proposal and “FOR” the Metacrine adjournment proposal.
Opinion of Equillium’s Financial Advisor (See page 96)
Equillium retained Vantage Point Advisors, Inc., or VPA, as its financial advisor in connection with the Merger. Representatives of VPA reviewed the financial terms of the proposed transaction with the Equillium Board. At the conclusion of the discussion, VPA rendered its opinion to the Equillium Board, which was confirmed by delivery of a written opinion, dated September 6, 2022, to the effect that, as of that date and based on and subject to various assumptions, qualifications and limitations described in its opinion, the Merger was fair, from a financial point of view, to Equillium’s common stockholders. VPA’s financial analysis and written opinion is described below in “The Merger—Opinion of Equillium’s Financial Advisor” beginning on page 96.
The full text of the written opinion of VPA, dated September 6, 2022, which sets forth assumptions made, procedures followed, matters considered and limitations on the review undertaken in connection with the opinion, is attached as Annex B to this joint proxy statement/prospectus. VPA provided its opinion for the information and assistance of the Equillium Board in connection with its consideration of the Merger. The VPA opinion is not a recommendation as to how any Equillium stockholder should vote with respect to the issuance of shares of Equillium common stock in connection with the Merger or any other matter. For a description of the opinion that the Equillium Board received from VPA, see the section entitled “The Merger—Opinion of Equillium’s Financial Advisor” beginning on page 96.
Opinions of Metacrine’s Financial Advisor (See page 103)
Metacrine retained MTS Health Partners, L.P., or MTS Partners, as its financial advisor in connection with the Merger. MTS Securities, LLC, or MTS Securities or MTS, an affiliate of MTS Partners, rendered oral opinions to the Metacrine Board on September 2, 2022 and October 19, 2022, and subsequently confirmed by delivery of a written opinion dated as of September 2, 2022 and October 19, 2022, respectively, that as of such dates and based upon and subject to the assumptions made, procedures followed, matters considered and qualifications and limitations set forth in each written opinion and described below, the Exchange Ratio employed in the Merger pursuant to the Merger Agreement was fair to the holders of Metacrine common stock (other than the Excluded Shares (as defined in MTS’s written opinions)) from a financial point of view. The full text of MTS’s written opinion, dated September 2, 2022, is attached as Annex C-1 to this joint proxy statement/prospectus, and the full text of MTS’s written opinion, dated October 19, 2022, is attached as Annex C-2 to this joint proxy statement/prospectus, and both are incorporated by reference in this joint proxy statement/prospectus in their entirety. The description of MTS’s opinions set forth below is qualified in its entirety by reference to the full text of MTS’s opinions. MTS’s opinions were directed to the Metacrine Board, in its capacity as such, and addressed only the fairness from a financial point of view of the Exchange Ratio pursuant to the Merger Agreement to the holders of shares of Metacrine common stock (other than the Excluded Shares) as of the date of each such opinion. They did not address any other aspects or implications of the Merger or in any manner address the prices at which the Equillium common stock would trade following consummation of the Merger or at any time and were not intended to and did not express any opinion or recommendation as to how the stockholders of Equillium or Metacrine should vote at the stockholders’ meetings to be held in connection with the Merger.
For a description of the opinions that the Metacrine Board received from MTS, see “The Merger—Opinions of Metacrine’s Financial Advisor” beginning on page 103 of this joint proxy statement/prospectus.
The Merger Agreement (See page 57)
The terms and conditions of the Merger are contained in the Merger Agreement, which is attached to this joint proxy statement/prospectus as Annex A. You should read the Merger Agreement carefully, as it is the legal document that governs the Merger.
Conditions to Completion of the Merger (See page 72)
As more fully described in this joint proxy statement/prospectus and in the Merger Agreement, the completion of the Merger depends on a number of conditions being satisfied or, where legally permissible, waived. These conditions include, among others, receipt of the requisite approvals of Equillium stockholders and
15

TABLE OF CONTENTS

Metacrine stockholders, the absence of any law or order prohibiting the Merger, the shares of Equillium common stock to be issued in connection with the Merger having been approved for listing on the Nasdaq, the effectiveness of the registration statement of which this joint proxy statement/prospectus forms a part, the correctness of all representations and warranties made by the parties in the Merger Agreement and performance by the parties of their obligations under the Merger Agreement (subject in each case to certain materiality standards), the performance of obligations required under the Merger Agreement by Equillium and Metacrine, no material adverse effect having occurred with respect to Equillium or Metacrine, the delivery of customary closing deliverables and Metacrine’s net cash at the closing of the Merger being no less than $23,000,000.
We cannot be certain when, or if, the conditions to the Merger will be satisfied or waived, or that the Merger will be completed.
Termination of the Merger Agreement (See page 73)
At any time before the effective time of the Merger, whether before or after Equillium’s and Metacrine’s respective stockholder votes, the parties may terminate the Merger Agreement by mutual written consent.
At any time before the effective time of the Merger, either party may terminate the Merger Agreement:
if the Merger does not close on or before 11:59 p.m. Pacific Standard time on January 2, 2023, or the termination date (provided that this termination right is not available to a party whose material breach of the Merger Agreement is the primary cause of, or resulted in, such failure to close by the termination date);
if the Metacrine stockholder approval is not obtained (provided that this termination is not available to Metacrine if its material breach of any provision of the Merger Agreement is the primary cause of, or resulted in, such failure to obtain the Metacrine stockholder approval);
if the Equillium stockholder approval is not obtained (provided that this termination right is not available to Equillium if its material breach of the Merger Agreement is the primary cause of, or resulted in, such failure to obtain the Equillium stockholder approval); or
if any law or judgment permanently restraining, enjoining or otherwise prohibiting consummation of the Merger shall become final and non-appealable (provided that this termination right is not available to a party if its material breach of any provision under the Merger Agreement has been the cause of, or resulted in the failure of the Merger to be consummated).
At any time before the effective time of the Merger, Metacrine may terminate the Merger Agreement if, (a) prior to the time the Equillium stockholder approval is obtained, (i) the Equillium Board effects a change in recommendation in relation to the stock issuance proposal contained in this joint proxy/prospectus statement (ii) Equillium fails to include the Equillium Board recommendation in this joint proxy statement/prospectus, (iii) Equillium Board failed to publicly reaffirm its recommendation to approve the Equillium stock issuance proposal within 10 Business Days after Metacrine so requests in writing following the public disclosure of any acquisition proposal with any person other than Metacrine, (iv) a tender offer or exchange offer for outstanding shares of Equillium capital shall have been commenced (other than by Metacrine or an affiliate of Metacrine) and Equillium Board shall have recommended that the stockholders of Equillium tender their shares in such tender or exchange offer or, within 10 Business Days after the commencement of such tender or exchange offer, the Equillium Board shall have failed to recommend against acceptance of such offer; or (v) Equillium materially breaches or fails to perform its non-solicitation obligations pursuant to the Merger Agreement, or clauses (i) through (v) collectively, an Equillium triggering event, (b) prior to or after the time the Metacrine stockholder approval is obtained, Equillium or Merger Sub breaches any representation, warranty, covenant or agreement made by Equillium or Merger Sub under the Merger Agreement (subject to certain procedures and materiality exceptions) such that the closing condition related to the correctness of certain representations and warranties or performance of covenants or agreements of Equillium are not met or (c) prior to the time the Metacrine stockholder approval is obtained, subject to compliance with certain terms and conditions, the Metacrine Board authorizes Metacrine to enter into an alternative acquisition agreement pursuant to a superior proposal and Metacrine pays to Equillium the required termination fee.
At any time before the effective time of the Merger, Equillium may terminate the Merger Agreement if, (a) prior to the time the Metacrine stockholder approval is obtained, (i) the Metacrine Board effects a change in
16

TABLE OF CONTENTS

recommendation in relation to the Metacrine merger proposal, (ii) Metacrine fails to include the Metacrine merger proposal in this joint proxy statement/prospectus, (iii) the Metacrine Board shall have failed to publicly reaffirm its recommendation to approve Metacrine merger proposal within 10 Business Days after Equillium so requests in writing following the public disclosure of any acquisition proposal with any person other than Equillium, (iv) a tender offer or exchange offer for outstanding Metacrine common stock shall have been commenced (other than by Equillium or an Affiliate of Equillium) and the Metacrine Board shall have recommended that the stockholders of Metacrine tender their shares in such tender or exchange offer or, within 10 Business Days after the commencement of such tender or exchange offer, the Metacrine Board shall have failed to recommend against acceptance of such offer, or (v) Metacrine materially breaches or fails to perform the non-solicitation provisions of the Merger Agreement, or clauses (i) through (v) collectively, a Metacrine triggering event, (b) prior to or after the time the Equillium stockholder approval is obtained, Metacrine breaches any representation, warranty, covenant or agreement made by Metacrine under the Merger Agreement (subject to certain procedures and materiality exceptions) such that the closing condition related to the correctness of certain representations and warranties or performance of covenants or agreements of Metacrine are not met or (c) prior to the time the Equillium stockholder approval is obtained, the Equillium Board authorizes Equillium to enter into an alternative acquisition agreement pursuant to a superior proposal and Equillium pays to Metacrine the required termination fee.
Termination Fees (See page 75)
If the Merger Agreement is terminated (i) by Equillium following a Metacrine triggering event or (ii) by Metacrine to enter into a superior proposal, Metacrine shall pay Equillium a fee equal to $1,250,000 within two business days after such termination in the case of clause (i) or concurrently with such termination in the case of clause (ii).
Further, (i) the Merger Agreement is terminated by Equillium or Metacrine due to a failure to close the Merger by the termination date or failure to obtain the Metacrine stockholder approval, (ii) prior to such termination referred to in clause (i) of this sentence, but after the date of the Merger Agreement, a bona fide acquisition proposal with respect to Metacrine shall have been announced or publicly disclosed to Metacrine or its stockholders and not publicly withdrawn, and (iii) within 12 months after the date of a termination in either of the cases referred to in clause (i) of this sentence, Metacrine consummates an acquisition proposal with respect to Metacrine or enters into an agreement contemplating an acquisition proposal with respect to Metacrine that is subsequently consummated, then Metacrine will pay Equillium a fee equal to $1,250,000, concurrently with such consummation; provided that solely for purposes of this provision, the term “acquisition proposal” shall have the meaning assigned to such term with respect to Metacrine in “No Solicitation of Alternative Proposals” discussed below, beginning on page 65, except that the references to “20% or more” shall be deemed to be references to “50% or more”.
If the Merger Agreement is terminated (i) by Metacrine following an Equillium triggering event or (ii) by Equillium to enter into a superior proposal, then Equillium shall, within two business days after such termination in the case of clause (i) or concurrently with such termination in the case of clause (ii), pay Metacrine a fee equal to $1,750,000.
Further, if (i) the Merger Agreement is terminated by Equillium or Metacrine due to a failure to close the Merger by the termination date or failure to obtain the Equillium stockholder approval, (ii) prior to such termination referred to in clause (i) of this sentence, but after the date of the Merger Agreement, a bona fide acquisition proposal with respect to Equillium shall have been publicly made or publicly disclosed to Equillium or its stockholders and not publicly withdrawn, and (iii) within 12 months after the date of a termination in either of the cases referred to in clause (i) of this sentence, Equillium consummates an acquisition proposal with respect to Equillium or enters into an agreement contemplating an acquisition proposal with respect to Equillium that is subsequently consummated, then Equillium shall pay Metacrine a fee equal to $1,750,000, concurrently with such consummation; provided that solely for purposes of this provision, the term “acquisition proposal” shall have the meaning assigned to such term with respect to Equillium in “No Solicitation of Alternative Proposals” discussed below, beginning on page 65, except that the references to “twenty (20%) or more” shall be deemed to be references to “50% or more”. In no event shall Metacrine be required to pay a termination fee on more than one occasion. In no event shall Equillium be required to pay a termination fee on more than one occasion.
17

TABLE OF CONTENTS

Regulatory Matters
Neither Equillium nor Metacrine is aware of any material regulatory approvals or actions that are required for completion of the Merger. It is presently contemplated that if any such additional regulatory approvals or actions are required, those approvals or actions will be sought. There can be no assurance, however, that any additional approvals or actions will be obtained.
Accounting Treatment (See page 122)
Equillium prepares its consolidated financial statements in accordance with accounting principles generally accepted in the United States, or GAAP. The Merger will be accounted for using the acquisition method of accounting, with Equillium treated as the acquiror. Please see the section entitled “The Merger—Accounting Treatment” on page 122 of this joint proxy statement/prospectus.
Appraisal Rights (See page 122)
Under Delaware law, the Metacrine stockholders are not entitled to appraisal rights in connection with the Merger or any other transaction contemplated by the Merger Agreement.
Under Delaware law, the Equillium stockholders are not entitled to appraisal rights in connection with the issuance of shares of Equillium common stock in the Merger pursuant to the terms of the Merger Agreement.
Metacrine’s Executive Officers and Directors Have Financial Interests in the Merger That Differ from the Interests of Metacrine Stockholders (See page 118)
Certain members of the Metacrine Board and certain executive officers of Metacrine may be deemed to have financial interests in the Merger that are in addition to, or different from, the interests of other Metacrine stockholders generally. The Metacrine Board was aware of these interests and considered them, among other matters, in approving the Merger and the Merger Agreement and in making the recommendation that Metacrine stockholders adopt the Merger Agreement. These potential interests include:
Accelerated vesting of equity awards upon the Effective Time of the Merger and upon certain terminations of employment or service following the Effective Time of the Merger;
Following the Effective Time, it is expected that Dr. Klassen will be appointed to the Equillium Board;
Cash severance and other benefits upon certain terminations of employment or service following the Effective Time of the Merger; and
Indemnification by the combined company for liabilities for acts or omissions occurring at or prior to the Effective Time of the Merger.
For additional details about these interests, see “Financial Interests of Metacrine Directors and Executive Officers in the Merger” beginning on page 118 of this joint proxy statement/prospectus.
Rights of Metacrine Stockholders Will Change as a Result of the Merger (See page 130)
As a result of the Merger, Metacrine stockholders will become holders of shares of Equillium common stock, and their rights will be governed by the Amended and Restated Certificate of Incorporation of Equillium and Equillium’s Amended and Restated Bylaws (instead of the Amended and Restated Certificate of Incorporation of Metacrine and Metacrine’s Amended and Restated Bylaws) and the General Corporation Law of Delaware, or the DGCL. Following the Merger, former Metacrine stockholders will have different rights as holders of Equillium common stock than they had as Metacrine stockholders due to differences in the organizational documents of Equillium and Metacrine. For additional information on stockholder rights, see “Description of Capital Stock and Comparison of Rights of Equillium Stockholders and Metacrine Stockholders” beginning on page 130 of this joint proxy statement/prospectus.
18

TABLE OF CONTENTS

The Equillium virtual special meeting
The Equillium virtual special meeting will be held by live webcast at 12:00 p.m. (Eastern Time), on December 20, 2022. There will be no physical meeting location. In order to attend the Equillium virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number shown on your proxy card. At the Equillium virtual special meeting, Equillium stockholders will be asked to consider and vote upon the following proposals:
the Equillium stock issuance proposal; and
the Equillium adjournment proposal.
Only holders of record of shares of Equillium common stock at the close of business on November 9, 2022, the Equillium record date, will be entitled to notice of, and to vote at, the Equillium virtual special meeting and any postponements or adjournments thereof. Holders of Equillium common stock at the close of business on the Equillium record date may cast one vote for each share of Equillium common stock so held, including (i) shares held directly in the name of the holder of record and (ii) shares held on behalf of the holder as the beneficial owner in street name through a broker, bank, or other nominee. On the Equillium record date, there were outstanding a total of 34,352,084 shares of common stock entitled to vote at the Equillium virtual special meeting.
Approval of the Equillium stock issuance proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (provided that a quorum exists). Approval of the Equillium adjournment proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (whether or not a quorum is present).
The Metacrine virtual special meeting
The Metacrine virtual special meeting will be held by live webcast at 12:00 p.m. (Eastern Time), on December 20, 2022. There will be no physical meeting location. In order to attend the Metacrine virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/MTCR2022SM and enter the 16-digit Control Number shown on your proxy card. At the Metacrine virtual special meeting, Metacrine stockholders will be asked to consider and vote upon the following proposals:
the Metacrine merger proposal; and
the Metacrine adjournment proposal.
Only holders of record of shares of Metacrine common stock at the close of business on November 9, 2022, the Metacrine record date, will be entitled to notice of, and to vote at, the Metacrine virtual special meeting and any postponements or adjournments thereof. Holders of Metacrine common stock at the close of business on the Metacrine record date may cast one vote for each share of Metacrine common stock so held, including (i) shares held directly in the name of the holder of record and (ii) shares held on behalf of the holder as the beneficial owner in street name through a broker, bank, or other nominee. On the Metacrine record date, there were outstanding a total of 42,569,515 shares of Metacrine common stock entitled to vote at the Metacrine virtual special meeting.
Completion of the Merger is conditioned on the approval of the Metacrine merger proposal. Approval of the Metacrine merger proposal requires the affirmative vote of the holders of Metacrine’s common stock representing a majority of the outstanding shares of Metacrine common stock entitled to vote on such matter at the Metacrine virtual special meeting (provided that a quorum exists). Approval of the Metacrine adjournment proposal requires the affirmative vote of the holders of shares of Metacrine common stock representing a majority of the votes cast on such matter at the Metacrine virtual special meeting (whether or not a quorum is present).
19

TABLE OF CONTENTS

UNAUDITED PRO FORMA CONDENSED COMBINED FINANCIAL INFORMATION
The following unaudited pro forma condensed combined financial information is presented to illustrate the estimated effects of the proposed Merger.
The unaudited pro forma condensed combined balance sheet information as of June 30, 2022 is based upon and derived from the historical financial information of Equillium and Metacrine and gives effect to the Merger as if such acquisition had occurred on June 30, 2022. The unaudited pro forma condensed combined statements of operations and comprehensive loss for the year ended December 31, 2021 and the six months ended June 30, 2022 are also based upon and derived from the historical financial information of Equillium and Metacrine and give effect to the Merger as if it occurred on January 1, 2021. In addition, the unaudited pro forma condensed combined statements of operations and comprehensive loss for the year ended December 31, 2021 and the six months ended June 30, 2022 are also based upon and derived from the historical financial information of Bioniz, Inc., or Bioniz, which was acquired by Equillium on February 14, 2022 and give effect to the Bioniz acquisition as if it occurred on January 1, 2021, or the Bioniz Acquisition and together with the Merger, the Acquisitions.
The unaudited pro forma condensed combined financial information should be read in conjunction with:
Equillium’s audited consolidated financial statements and accompanying notes as of and for the year ended December 31, 2021, as contained in its Annual Report on Form 10-K filed on March 23, 2022 with the SEC.
Equillium’s unaudited condensed consolidated financial statements and accompanying notes as of and for the six months period ended June 30, 2022, as contained in its Quarterly Report on Form 10-Q filed on August 15, 2022 with the SEC.
Metacrine’s audited consolidated financial statements and accompanying notes as of and for the year ended December 31, 2021, as contained in its Annual Report on Form 10-K filed on March 30, 2022 with SEC.
Metacrine’s unaudited condensed consolidated financial statements and accompanying notes as of and for the six months period ended June 30, 2022, as contained in its Quarterly Report on Form 10-Q filed on August 9, 2022 with the SEC.
The other information contained in or incorporated by reference into this filing.
Additional information about the basis of presentation of this information is provided in Note 1 hereto.
The unaudited pro forma condensed combined financial information is provided for informational purposes only and is not necessarily indicative of the operating results or financial position that would have occurred if the Acquisitions had been completed as of the dates set forth above, nor is it indicative of the future results or financial position of the combined company. In connection with the pro forma financial information, Equillium allocated the purchase price using its best estimates of fair value. Accordingly, the pro forma Merger price adjustments are preliminary and subject to further adjustments as additional information becomes available and as additional analyses are performed. The unaudited pro forma condensed combined financial information also does not give effect to the potential impact of current financial conditions, any anticipated synergies, operating efficiencies or cost savings that may result from the Merger or any integration costs. The unaudited pro forma condensed combined statements of operations and comprehensive loss do not reflect certain amounts resulting from the Merger that were determined to be of a non-recurring nature.
The unaudited pro forma condensed combined financial information was prepared in accordance with Article 11 of Regulation S-X. Equillium has accounted for the Merger using the acquisition method of accounting, in accordance with FASB Accounting Standards Codification, or ASC, Topic 805 “Business Combinations”, or ASC 805. Equillium preliminarily determined that the Merger constitutes an acquisition of assets instead of a business combination as substantially all of the fair value of the gross assets acquired was concentrated in a group of similar identifiable assets, and therefore, the Merger was not considered a business combination.
After the closing of the Merger, Equillium will complete the valuations necessary to finalize the required purchase price allocation based upon the fair market values as of the actual closing date of the Merger, at which time the final allocation of the purchase price will be determined. The pro forma financial information contained in this joint proxy statement/prospectus is also based upon certain assumptions with respect to the amount of net
20

TABLE OF CONTENTS

cash to be received from Metacrine at the closing of the Merger and the number of shares of Equillium common stock to be issued to Metacrine at closing of the Merger. Differences between preliminary estimates in the pro forma financial information presented herein and the final acquisition accounting will occur and could have a material impact on the pro forma financial information. In this regard, differences between those preliminary estimates and the actual net cash received from Metacrine at the closing of the Merger and the number of shares of Equillium common stock ultimately issued to Metacrine at closing of the Merger would result in changes to various components of the unaudited pro forma condensed combined balance sheet, including cash and cash equivalents, common stock and additional paid-in capital, and various components of the unaudited pro forma condensed combined statements of operations, including in-process research and development expense, net loss per share and weighted-average shares used in computing net loss per share.
The unaudited pro forma condensed combined financial information has been prepared by Equillium in accordance with SEC Regulation S-X Article 11 and is not necessarily indicative of the condensed combined financial position or results of operations that would have been realized had the Acquisitions been completed as of the dates indicated above, nor is it meant to be indicative of any anticipated combined financial position or future results of operations that Equillium will experience after the Merger is completed. In addition, the accompanying unaudited pro forma condensed combined statements of operations and comprehensive loss do not include any pro forma adjustments to reflect expected cost savings or restructuring actions which may be achievable or the impact of any non-recurring expenses and one-time transaction-related costs that may be incurred as a result of the Acquisitions.
Description of the Merger
Equillium, Metacrine, Acquisition Sub I, Acquisition Sub II and Merger Sub entered into the Merger Agreement dated September 6, 2022 and amended on October 26, 2022. Pursuant to the Merger Agreement, Merger Sub will be merged with and into Metacrine, and Metacrine will continue as the surviving corporation and an indirect, wholly owned subsidiary of Equillium. In connection with the Merger, all of the issued and outstanding shares of common stock of Metacrine, par value $0.0001 per share, or the Shares, will be cancelled and converted into the right to receive consideration per share consisting of (i) the Exchange Ratio, which is determined by dividing (x) (a) 125% of Metacrine’s net cash as of the closing of the Merger, or the Closing, by (b) the price per share of common stock of Equillium, par value $0.0001 per share, or Equillium common stock determined based on the 10-day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the Closing date, provided that the price per share of Equillium common stock shall be no less than $2.70 and no more than $4.50 by (y) the aggregate fully diluted shares of Metacrine, plus (ii) any cash payable in lieu of fractional shares of Equillium’s common stock. As defined in the Merger Agreement, net cash consists of Metacrine’s cash and cash equivalents, deposits, prepaid expenses, and short-term investments, adjusted by certain factors including the full payoff amount of Metacrine’s existing term debt having an outstanding principal of $15 million. Net cash is estimated to be approximately $27.0 million at Closing, assuming a Closing on December 23, 2022. In addition, Equillium has agreed to terms on an amended debt facility with Metacrine’s current lender, K2 HealthVentures LLC, whereby at the Closing Equillium would assume Metacrine’s existing loan, subject to certain modifications. Concurrent with the Closing, Equillium intends to retire its existing debt facility with Oxford Finance LLC and SVB, which has an outstanding principal balance of $10 million as of June 30, 2022.
Consummation of the Merger is subject to certain closing conditions, including Metacrine’s net cash being no less than $23 million, the absence of certain legal impediments, the effectiveness of a registration statement to which this joint proxy statement/prospectus is a part, adoption of the Merger Agreement by the holders of a majority of Metacrine’s outstanding common stock at Metacrine’s virtual special meeting, and approval of the issuance of shares of Equillium common stock in the Merger by the holders of shares of Equillium common stock representing a majority of the votes cast at Equillium’s virtual special meeting.
21

TABLE OF CONTENTS

UNAUDITED PRO FORMA CONDENSED COMBINED BALANCE SHEET
As of June 30, 2022
(In thousands)
 
Equillium,
Inc.
Metacrine,
Inc.
Pro Forma
Adjustments
Notes
Equillium,
Inc.
Unaudited
Pro Forma
Combined
Assets
 
 
 
 
 
Current assets:
 
 
 
 
 
Cash and cash equivalents
$23,808
$45,348
$(6,508)
A
 
 
 
 
(3,747)
B
 
 
 
 
(10,600)
C
 
 
 
 
(893)
B
 
 
 
 
(150)
D
47,258
Short-term investments
33,754
10,182
 
43,936
Prepaid expenses and other current assets
2,920
3,611
 
6,531
Total current assets
60,482
59,141
(21,898)
 
97,725
Property and equipment, net
451
 
451
Operating lease right-of-use assets
1,418
 
1,418
Other assets
121
 
121
Total assets
$62,472
$59,141
$(21,898)
 
$99,715
Liabilities and stockholders’ equity
 
 
 
 
 
Current liabilities:
 
 
 
 
 
Accounts payable
$5,091
$503
$
 
$5,594
Accrued expenses
5,377
2,150
 
7,527
Current portion of operating lease liabilities
434
 
434
Current portion of long-term notes payable
4,286
(4,286)
C
Total current liabilities
15,188
2,653
(4,286)
 
13,555
Long-term notes payable
5,992
13,616
(5,992)
C
 
 
 
 
1,384
D
 
 
 
 
(150)
D
 
 
 
 
(208)
D
14,642
Other non-current liabilities
1,388
(1,388)
D
Long-term operating lease liabilities
1,025
 
1,025
Total liabilities
22,205
17,657
(10,640)
 
29,222
Commitments and contingencies
 
 
 
 
 
Stockholders’ equity:
 
 
 
 
 
Common Stock
3
4
(4)
E
 
 
 
 
1
H
4
Additional paid-in capital
201,936
243,595
(243,595)
E
 
 
 
 
33,346
H
 
 
 
 
208
D
235,490
Accumulated other comprehensive loss
(149)
(20)
20
E
(149)
Accumulated deficit
(161,523)
(202,095)
202,095
E
 
 
 
 
(893)
B
 
 
 
 
(322)
C
 
 
(2,114)
I
(164,852)
Total stockholders’ equity
40,267
41,484
(11,258)
 
70,493
Total liabilities and stockholders’ equity
$62,472
$59,141
$(21,898)
 
$99,715
See notes to unaudited pro forma condensed combined financial statements
22

TABLE OF CONTENTS

UNAUDITED PRO FORMA CONDENSED COMBINED STATEMENT OF OPERATIONS AND
COMPREHENSIVE LOSS
For the Year Ended December 31, 2021
(In thousands, except share and per share data)
 
Equillium,
Inc.
Historical
December 31,
2021
Bioniz,
Inc.
Historical
December 31,
2021
Pro Forma
Adjustments
(Acquisition
of Bioniz)
Notes
Equillium,
Inc.
Unaudited
Pro Forma
Results
(Adjusted for
Acquisition
of Bioniz)
Metacrine,
Inc.
Historical
December 31,
2021
Pro Forma
Adjustments
(Acquisition
of
Metacrine)
Notes
Equillium,
Inc.
Unaudited
Pro Forma
Results
Combined
Research and development
$26,379
$3,277
$
 
$29,656
$45,474
$
 
$75,130
Acquired in-process research and development
23,049
I
23,049
2,114
I
25,163
General and administrative
11,407
2,181
 
13,588
15,605
 
29,193
Total operating expenses
37,786
5,458
23,049
 
66,293
61,079
2,114
 
129,486
Loss from operations
(37,786)
(5,458)
(23,049)
 
(66,293)
(61,079)
(2,114)
 
(129,486)
Other expense, net:
 
 
 
 
 
 
 
 
 
Interest expense
(1,073)
 
(1,073)
(1,202)
1,073
F
(1,202)
Interest income
57
 
 
 
57
102
 
159
Other expense, net
(250)
14,997
(15,000)
G
(253)
(28)
 
(281)
Total other expense, net
(1,266)
14,997
(15,000)
 
(1,269)
(1,128)
1,073
 
(1,324)
Net loss
$(39,052)
$9,539
$(38,049)
 
$(67,562)
$(62,207)
$(1,041)
 
$(130,810)
Other comprehensive income, net:
 
 
 
 
 
 
 
 
 
Unrealized loss on available-for-sale securities, net
(59)
 
(59)
(6)
 
(65)
Foreign currency translation gain
218
 
218
 
218
Total other comprehensive income, net
159
 
159
(6)
 
153
Comprehensive loss
$(38,893)
$9,539
$(38,049)
 
$(67,403)
$(62,213)
$(1,041)
 
$(130,657)
Net loss per share, basic and diluted
$(1.36)
 
$(2.01)
$(2.29)
 
$(2.85)
Weighted-average number of common shares outstanding, basic and diluted
28,806,310
4,820,230
H
33,626,540
27,188,864
(14,838,231)
H
45,977,173
See notes to unaudited pro forma condensed combined financial statements
23

TABLE OF CONTENTS

UNAUDITED PRO FORMA CONDENSED COMBINED STATEMENT OF OPERATIONS AND
COMPREHENSIVE LOSS
For the Six Months Ended June 30, 2022
(In thousands, except share and per share data))
 
Equillium,
Inc.
Historical
June 30,
2022
Bioniz,
Inc.
Historical
January 1-
February 13,
2022
Pro Forma
Adjustments
(Acquisition
of Bioniz)
Notes
Equillium,
Inc.
Unaudited
Pro Forma
Results
(Adjusted for
Acquisition
of Bioniz)
Metacrine,
Inc.
Historical
June 30,
2022
Pro Forma
Adjustments
(Acquisition
of
Metacrine)
Notes
Equillium,
Inc.
Unaudited
Pro Forma
Results
Combined
Research and development
$20,251
$123
 
 
$20,374
$8,989
 
 
$29,363
Acquired in-process research and development
23,049
 
(23,049)
I
 
 
 
General and administrative
7,581
211
 
7,792
8,894
 
 
16,686
Restructuring charges
 
902
 
 
902
Gain from lease termination and asset sale
 
(508)
 
(508)
Total operating expenses
50,881
334
(23,049)
 
28,166
18,277
 
46,443
Loss from operations
(50,881)
(334)
23,049
 
(28,166)
(18,277)
 
(46,443)
Other expense, net:
 
 
 
 
 
 
 
 
 
Interest expense
(515)
 
(515)
(925)
515
F
(925)
Interest income
90
 
90
90
 
180
Other expense, net
(240)
 
(240)
(30)
 
(270)
Total other expense, net
(665)
 
(665)
(865)
515
 
(1,015)
Net loss
$(51,546)
$(334)
$23,049
 
$(28,831)
$(19,142)
$515
 
$(47,458)
Other comprehensive loss, net:
 
 
 
 
 
 
 
 
 
Unrealized loss on available-for-sale securities, net
(234)
 
(234)
(15)
 
(249)
Foreign currency translation gain
223
 
223
 
223
Total other comprehensive loss, net
(11)
 
(11)
(15)
 
(26)
Comprehensive loss
$(51,557)
$(334)
$23,049
 
$(28,842)
$(19,157)
$515
 
$(47,484)
Net loss per share, basic and diluted
$(1.56)
 
$(0.87)
$(0.45)
 
$(1.04)
Weighted-average number of common shares outstanding, basic and diluted
33,085,917
 
33,085,917
42,278,932
(29,928,299)
H
45,436,550
See notes to unaudited pro forma condensed combined financial statements
24

TABLE OF CONTENTS

1. Basis of presentation
The historical consolidated financial information of Equillium has been adjusted in the accompanying unaudited pro forma condensed combined financial information to give effect to pro forma events that are (i) directly attributable to the Acquisitions, (ii) factually supportable, and (iii) with respect to the unaudited pro forma condensed combined statements of operations and comprehensive loss, are expected to have a continuing impact on the results of operations.
The unaudited pro forma condensed combined financial statements were prepared in accordance with the regulations of the SEC and are intended to show how the Acquisitions might have affected the historical financial statements. The unaudited pro forma condensed combined financial information set forth herein is based upon the consolidated financial statements of Equillium, Bioniz and Metacrine. The unaudited pro forma condensed combined financial information is presented as if the Merger had been completed on June 30, 2022 with respect to the unaudited pro forma condensed combined balance sheet as of June 30, 2022 and as of January 1, 2021 with respect to the unaudited pro forma condensed combined statements of operations and comprehensive loss for the year ended December 31, 2021 and the six month period ended June 30, 2022 for both the Acquisitions. The unaudited pro forma condensed combined financial statements have also been adjusted to give effect to pro forma events that are directly attributable to the Acquisitions, factually supportable and expected to have a continuing impact on the combined results.
Equillium’s combined financial information has been prepared in accordance with Generally Accepted Accounting Principles in the United States, or GAAP, as issued by the Financial Accounting Standards Board, or FASB. Metacrine’s and Bioniz’s financial information has been historically prepared in accordance with GAAP.
The unaudited pro forma condensed combined financial information is presented for informational purposes only and is not necessarily indicative of the combined financial position or results of operations had the Merger occurred as of the dates indicated, nor is it meant to be indicative of any anticipated combined financial position or future results of operations that the combined company will experience after the completion of the Merger. To the extent there are significant changes to the combined company’s business following completion of the Merger, the assumptions and estimates set forth in the unaudited pro forma condensed combined financial statements could change significantly.
Equillium determined the Merger constitutes an acquisition of assets instead of a business combination as substantially all of the fair value of the gross assets acquired was concentrated in a group of similar identifiable assets, and therefore, the acquisition was not considered a business. Asset acquisitions are accounted for by allocating the cost of the acquisition, including transaction costs, to the individual assets acquired and liabilities assumed on a relative fair value basis without recognition of goodwill.
Equillium determined the Merger meets the definition of an acquisition of a business as defined in Rule 8-04 of Regulation S-X of the SEC. The accompanying unaudited pro forma condensed combined financial information was prepared for the purpose of complying with Rule 8-04 of Regulation S-X of the SEC and for inclusion in Equillium’s filings with the SEC.
2. Accounting Policies
Following the execution of the Merger Agreement, Equillium will conduct a review of accounting policies of Metacrine in an effort to determine if differences in accounting policies require restatement or reclassification of results of operations or reclassification of assets or liabilities to conform to Equillium’s accounting policies and classifications. Equillium may identify differences among the accounting policies of Equillium and Metacrine that, when conformed, could have a material impact on this unaudited pro forma condensed combined financial information. During the preparation of this unaudited pro forma condensed combined financial information, Equillium was not aware of any material differences between accounting policies of Equillium and Metacrine to conform to Equillium’s financial presentation, and accordingly, this unaudited pro forma condensed combined financial information does not assume any material differences in accounting policies among Equillium and Metacrine.
25

TABLE OF CONTENTS

3. Consideration Transferred
The calculation of the estimated preliminary purchase consideration is as follows:
Estimated equity consideration
In connection with the Merger, all of the issued and outstanding Shares will be cancelled and converted into the right to receive consideration per share consisting of (i) the Exchange Ratio, plus (ii) any cash payable in lieu of fractional shares of Equillium’s common stock.
Each of Metacrine’s stock options, or Options, that is outstanding as of immediately prior to the effectiveness of the Merger, or the Effective Time, will (i), if held by a continuing employee or service provider, be substituted automatically into an Equillium option award to purchase the number of shares of Equillium common stock equal to the number of Shares subject to the Option immediately prior to the Effective Time multiplied by the Exchange Ratio, and (ii) if the Option is held by a former employee, service provider or director of Metacrine, (x) to the extent unvested, be cancelled without the payment of any consideration and (y) to the extent vested, be cancelled and converted into a right to receive the number of shares of Equillium common stock equal to (1) the number of Shares subject to the Option immediately prior to the Effective time multiplied by the excess, if any, of Metacrine’s price per Share based on the 10 day trading volume weighted average price per Share calculated 10 trading days prior to the Closing date over the per share exercise price for the Shares underlying the Option immediately prior to the Effective Time, or the Metacrine Share Value, divided by (2) the Metacrine Share Value multiplied by the Exchange Ratio.
Each of Metacrine’s restricted stock unit awards, or the RSUs, that is outstanding as of immediately prior to the Effective Time will (i), if held by a continuing employee or service provider, whether vested or unvested, be substituted automatically into an Equillium restricted stock unit award with respect to a number of shares of Equillium common stock equal to the product obtained by multiplying the total number of Shares subject to the RSU immediately prior to the Effective Time by the Exchange Ratio, and (ii) if the RSU is held by a former employee, service provider or director of Metacrine, (x) to the extent unvested, be cancelled without the payment of any consideration and (y) to the extent vested, be cancelled and converted into a right to receive the number of shares of Equillium common stock equal to the product obtained by multiplying the total number of Shares subject to the RSU immediately prior to the Effective Time by the Exchange Ratio.
Each of Metacrine’s warrants, or the Warrants, that is outstanding and unexercised immediately prior to the Effective Time will be automatically substituted into a warrant to purchase the number of shares of Equillium common stock equal to the product obtained by multiplying the number of Shares subject to the Warrant immediately prior to the Effective Time by the Exchange Ratio. Each Warrant will have an exercise price per share of Equillium common stock equal to exercise price per Share immediately prior to the Effective Time divided by the Exchange Ratio.
Estimated number of shares of the combined company to be owned by Metacrine stockholders
12,350,633
Multiplied by the assumed price per share of Equillium common stock(1)
$2.70
Estimated equity consideration
$33,346,709
(1)
Represents the floor price of the collar as Equillium’s stock price was trading below the floor as of November 8, 2022. The number of Equillium shares actually issued at closing will be based on the actual 10-day volume weighted average closing price of Equillium common stock calculated 10 trading days preceding the closing.
For illustrative purposes only, we have calculated the potential number of shares Equillium would issue in connection with the closing of the Merger based on the assumptions and sensitivity analysis set forth herein.
Based on (1) the Estimated equity consideration of $33,346,709, or the Pro Forma Assumed Upfront Merger Consideration, and (2) an Equillium Stock Price equal to the Floor Price, Equillium would issue 12,350,633 shares of common stock.
Keeping the Pro Forma Assumed Upfront Merger Consideration constant, a $0.25 increase from the Floor Price would decrease the number of shares of common stock Equillium issues at the Closing by 1,046,664. Keeping the Equillium stock price constant, a $1 million increase or decrease in the Assumed Upfront Merger Consideration would increase or decrease, respectively, the number of shares of common stock to be issued by Equillium by 462,963 shares. Keeping the Pro Forma Assumed Upfront Merger Consideration constant, and
26

TABLE OF CONTENTS

assuming an Equillium stock price equal to the Ceiling Price, Equillium would issue 7,410,380 shares. Keeping the Pro Forma Assumed Upfront Merger Consideration constant, a $0.25 decrease from the Ceiling Price would increase the number of shares of common stock Equillium issues at the Closing by 435,904.
Fair value of the Metacrine outstanding stock options and restricted stock units
The estimated fair value of the outstanding Options and RSUs are included in the consideration transferred in accordance with ASC 805. Because no Metacrine employees will be continuing following Closing, the outstanding Options and RSUs which are vested and in-the-money at the Effective Time will be exchanged into shares of common stock of Equillium based on the Exchange Ratio, those shares of common stock being an allocation of the total shares of common stock issued in the Merger as described above, with no incremental consideration attributed to such equity awards. There is no future service requirement. Any unvested Options or RSUs will be cancelled at the Effective Time.
Fair value of warrants to be issued by Equillium to Metacrine warrant holders
Each Warrant that is outstanding and unexercised immediately prior to the Merger will be automatically substituted into a warrant to purchase the number of shares of Equillium common stock equal to the product obtained by multiplying the number of Shares subject to the Warrant immediately prior to the Merger by the Exchange Ratio. Each Warrant will have an exercise price per share of Equillium common stock equal to exercise price per Share immediately prior to the Effective Time divided by the Exchange Ratio. The fair value of the warrants to purchase common stock to be issued to the Metacrine debt holders will be allocated to the pro forma long-term notes payable balance.
The total estimated equity consideration was recorded to common stock at par ($0.0001 per share) and the remainder to additional paid-in capital.
Total estimated preliminary purchase consideration consists of the following:
Estimated equity consideration
$33,346,709
Estimated fair value of the outstanding Metacrine stock options and RSUs
$
Estimated fair value of the outstanding Metacrine warrants
$
Total estimated preliminary purchase consideration
$33,346,709
4. Preliminary Purchase Price Allocation
The summary of the preliminary estimated purchase price allocation is as follows (in thousands):
Description
Fair
Value
Assets acquired:
 
Cash
$45,275
Prepaid expenses and other current assets
3,611
Total assets acquired
48,886
Liabilities assumed:
 
Accounts payable
503
Accrued expenses
2,150
Debt
15,000
Total liabilities assumed
17,653
Net assets acquired
31,233
In-Process R&D
2,114
Adjusted value of assets acquired
$33,347
27

TABLE OF CONTENTS

5. Pro Forma Adjustments
The unaudited pro forma adjustments included in the unaudited pro forma condensed combined financial statements are based on preliminary estimates that may change significantly as additional information is obtained, are as follows:
(A)
Reflects expected use of $6.5 million of Metacrine’s cash-on-hand for costs related to the closing of the Merger including costs directly attributable to the acquisition such as severance and directors and officers liability tail insurance.
(B)
To reduce cash based on the expected transaction costs, see Note 6.
(C)
To reflect the assumed payoff of the Equillium debt held with Oxford Finance and SVB along with a prepayment penalty fee of 1% of the outstanding principal as of June 30, 2022.
(D)
To reflect the assumption of a $15.0 million loan with K2 HealthVentures LLC payment of a $150,000 amendment fee and warrants issued with a fair value of approximately $0.2 million. Both the amendment fee and the fair value of the warrants are recorded as a debt discount, which is classified as a contra-liability against long-term notes payable.
(E)
To reflect the elimination of Metacrine’s historical equity accounts.
(F)
To eliminate the historical interest expense attributed to Equillium’s debt.
(G)
To reverse the income recognized under Bioniz during the year ended December 31, 2021 attributed to the termination of the Almirall option agreement which is considered to be a non-recurring item.
(H)
To reflect the unaudited pro forma condensed combined basic and diluted earnings per share for the periods presented that have been adjusted by the 4,820,230 shares of common stock issued in connection with the Bioniz acquisition and the estimated 12,350,633 shares of common stock to be issued in connection with the Merger, which are assumed outstanding for the year ended December 31, 2021 for pro forma purposes, and to reflect the fair value of the estimated preliminary purchase price consideration totaling $33.3 million as an increase to common stock and additional paid-in capital in the unaudited pro forma condensed combined balance sheet as of June 30, 2022.
(I)
To record the acquired in-process research and development in the unaudited pro forma condensed combined statement of operations and comprehensive loss for the year ended December 31, 2021 for the Bioniz and Mergers as if they were completed on January 1, 2021 and to record the acquired in-process research and development in the unaudited pro forma condensed combined balance sheets as of June 30, 2022 as if the Merger were completed on June 30, 2022.
6. Transaction Costs
The pro forma adjustment related to Merger costs of $4.6 million reflected in accumulated deficit consists of the estimated accrual to be incurred by Equillium and Metacrine in connection with the Merger which was not reflected in each of the historical consolidated balance sheets. Approximately $3.7 million of the estimated Merger costs is attributable to Metacrine, and approximately $0.9 million of the estimated Merger costs is attributable to Equillium.
These Merger-related costs are not expected to have a continuing impact on the results of the combined company. There were no material Merger-related costs included in the historical results of operations of Equillium or Metacrine requiring pro forma adjustment.
28

TABLE OF CONTENTS

COMPARATIVE STOCK PRICE DATA AND DIVIDENDS
Equillium common stock and Metacrine common stock are both traded on the Nasdaq under the symbols “EQ” and “MTCR”, respectively. The following table presents the high and low price per share of Equillium common stock and Metacrine common stock on September 6, 2022, the last full trading day before public announcement that Equillium and Metacrine had entered into the Merger Agreement, and November 8, 2022, the last practicable trading day before the date of this joint proxy statement/prospectus.
 
Equillium common
stock
Metacrine
common stock
Date
High
Low
Close
High
Low
Close
September 6, 2022
$2.77
$2.63
$2.73
$0.47
$0.44
$0.47
November 8, 2022
$1.79
$1.67
$1.72
$0.43
$0.39
$0.40
For illustrative purposes, the following table provides equivalent high and low price per share of Metacrine common stock on each of the specified dates. These equivalent high and low price per share amounts reflect the fluctuating value of Equillium common stock that Metacrine stockholders would receive in exchange for each share of Metacrine common stock if the Merger were completed on either of these dates and assuming an Exchange Ratio of 0.282.
 
Equillium common
stock
Metacrine Equivalent Per
Share
Date
High
Low
Close
High
Low
Close
September 6, 2022
$2.77
$2.63
$2.73
$0.78
$0.74
$0.77
November 8, 2022
$1.79
$1.68
$1.71
$0.50
$0.47
$0.48
The market value of the shares of Equillium common stock to be issued in exchange of shares of Metacrine common stock upon the completion of the Merger will not be known at the time of the Equillium and Metacrine virtual special meetings. The above tables show only historical comparisons. Because (1) the market prices of Equillium common stock and Metacrine common stock will likely fluctuate prior to the Merger, (2) the Equillium stock price used for the purposes of calculating the Exchange Ratio is determined based on the 10 day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the Closing date, provided that in no event will the price per share of Equillium common stock be less than $2.70 or greater than $4.50 and (3) Metacrine’s Closing net cash and aggregate fully diluted capitalization will not be known until shortly prior to the Closing, these comparisons may not provide meaningful information to (i) Equillium stockholders in determining whether to approve the issuance of shares of Equillium common stock to holders of Metacrine common stock in connection with the Merger pursuant to the Merger Agreement or (ii) Metacrine stockholders in determining whether to adopt the Merger Agreement. Equillium stockholders and Metacrine stockholders are encouraged to obtain current market quotations for shares of Equillium common stock and Metacrine common stock and to review carefully the other information contained in this joint proxy statement/prospectus or incorporated by reference in this joint proxy statement/prospectus in considering whether to approve the issuance of shares of Equillium common stock in connection with the Merger pursuant to the terms of the Merger Agreement, in the case of Equillium stockholders, and whether to adopt the Merger Agreement, in the case of Metacrine stockholders. See the section entitled “Where You Can Find More Information” beginning on page 141 of this joint proxy statement/prospectus.
Holders
As of 5:00 p.m. (Eastern Time) on the record date for the Equillium virtual special meeting, 34,352,084 shares of Equillium common stock, held by 49 holders of record, were outstanding and entitled to vote at the Equillium virtual special meeting. As of 5:00 p.m. (Eastern Time) on the record date for the Metacrine virtual special meeting, 42,569,515 shares of Metacrine common stock, held by 35 holders of record, were outstanding and entitled to vote at the Metacrine virtual special meeting.
29

TABLE OF CONTENTS

RISK FACTORS
In addition to the other information included and incorporated by reference into this joint proxy statement/prospectus, including the matters addressed in the section entitled “Cautionary Statement Regarding Forward-Looking Statements,” you should carefully consider the following risks before deciding whether to vote for the adoption and approval of the Merger Agreement, in the case of Metacrine stockholders, or for the issuance of shares of Equillium common stock in connection with the Merger, in the case of Equillium stockholders. In addition, you should read and consider the risks associated with each of the businesses of Equillium and Metacrine because these risks will also affect the combined company. These risks can be found in Equillium’s and Metacrine’s respective Quarterly Reports on Form 10-Q for the fiscal quarter ended June 30, 2022, both of which are filed with the SEC and incorporated by reference into this joint proxy statement/prospectus. You should also read and consider the other information in this joint proxy statement/prospectus and the other documents incorporated by reference into this joint proxy statement/prospectus. See the section entitled “Where You Can Find More Information,” beginning on page 141 of this joint proxy statement/prospectus.
Risk Factors Relating to the Merger
The Merger may not be completed on the terms or timeline currently contemplated, or at all. Equillium stockholders and Metacrine stockholders will be subject to a number of material risks if the Merger is not completed.
The consummation of the Merger is subject to numerous conditions, including (1) the approval by the Metacrine stockholders of the Metacrine Merger proposals, (2) the approval by the Equillium stockholders of the Equillium Merger proposals, (3) the effectiveness of the Registration Statement on Form S-4 of which the joint proxy statement and prospectus forms a part, (4) Metacrine’s net cash at the Closing being no less than $23,000,000, and (5) other customary closing conditions. See the section “The Merger Agreement – Conditions to Completion of Merger.”
If the Merger is not completed for any reason, including the failure to complete the Merger by January 2, 2023 (or such later date to which such date may be extended in accordance with the terms of the Merger Agreement), the price of Equillium common stock and/or the price of the Metacrine common stock, par value $0.0001, or Metacrine common stock, may decline to the extent that the market price of Equillium common stock or Metacrine common stock, as applicable, reflects or previously reflected positive market assumptions that the Merger would be completed and the related benefits would be realized. In addition, Equillium and Metacrine have expended and will continue to expend significant management time and resources and have incurred and will continue to incur significant expenses due to legal, advisory, printing and financial services fees related to the Merger. These expenses must be paid regardless of whether the Merger is consummated. If the Merger is not consummated because the Merger Agreement is terminated, Equillium may be required under certain circumstances to pay Metacrine a termination fee of $1,750,000 or Metacrine may be required under certain circumstances to pay Equillium a termination fee of $1,250,000. There is no assurance that the Merger will be consummated. If the Merger is not timely completed, Equillium and Metacrine may have to materially alter their respective business plans, including pausing and/or terminating their current and planned clinical trials and the development of their respective product candidates.
The Merger may be completed even if certain events occur prior to the Closing that materially and adversely affect Metacrine and Equillium.
In general, either party can refuse to complete the Merger if there is a material adverse change affecting the other party between the signing date of the Merger Agreement, and the Closing. However, certain types of changes do not permit either party to refuse to complete the Merger, even if such change could have a material adverse effect on Equillium and Metacrine, including, subject to certain exceptions, among others:
changes or conditions generally affecting the industries in which Equillium or Metacrine, as applicable, operate;
general economic or political conditions or securities, credit, financial or other capital markets conditions, in each case in the United States or any foreign jurisdiction;
any failure, in and of itself, by Equillium or Metacrine, as applicable, to meet any internal or published projections, forecasts, estimates or predictions in respect of revenues, earnings or other financial or operating metrics for any period;
30

TABLE OF CONTENTS

the public announcement or pendency of the transactions contemplated hereby;
any change, in and of itself, in the market price or trading volume of Equillium’s or Metacrine’s, as applicable, securities or in its credit ratings;
any change in applicable law, regulation or GAAP;
geopolitical conditions, the outbreak or escalation of hostilities, any acts of war, sabotage or terrorism, or any escalation;
any hurricane, tornado, flood, earthquake or other natural disaster;
any epidemic, pandemic or disease outbreak (including Covid-19) and any action by a governmental entity in response thereto;
any litigation arising from allegations of a breach of fiduciary duty or other violation of applicable law relating to the Merger Agreement or the transactions contemplated thereby;
any adverse effects, adverse events or safety observations or reports of new side effects, adverse events or safety observations with respect to Equillium’s or Metacrine’s, as applicable, product candidates that are not reasonably expected to materially affect the likelihood or timing of FDA approval;
any change or modification to any development program of Equillium; or
any taking of any action required pursuant to the Merger Agreement, or not required by the Merger Agreement but taken at the written request of the other party.
If one or more material adverse changes occur and Metacrine and Equillium still complete the Merger, the stock price of the combined company following the Closing may suffer. This in turn may reduce the value of the shares of Equillium common stock to the stockholders of the combined company. See “The Merger Agreement” beginning on page 57 for more information.
The Exchange Ratio will not be determined until shortly prior to the date of the Closing and Equillium and Metacrine stockholders may not know the number of shares to be issued in the Merger or the Exchange Ratio at the time of the stockholder special meetings.
In connection with the Merger, all of the issued and outstanding shares of Metacrine common stock, will be cancelled and converted into the right to receive consideration per share consisting of (i) the exchange ratio, or the Exchange Ratio, determined by dividing (x) (a) 125% of Metacrine’s net cash as of the Closing, or the Upfront Merger Considerations, divided by (b) the price per share of Equillium common stock determined based on the 10 day trading volume weighted average price per share of Equillium common stock calculated 10 trading days prior to the Closing date, provided that in no event will the price per share of Equillium common stock, or the Equillium Stock Price, be less than $2.70 or greater than $4.50 by (y) the aggregate fully diluted shares of Metacrine, or Metacrine’s Closing Capitalization, plus (ii) any cash payable in lieu of fractional shares of Equillium common stock.
The Exchange Ratio is adjustable, as described above, and the price per share of Equillium common stock may be subject to change prior to, during and following the period during which the price per share of Equillium common stock is set for purposes of the Exchange Ratio. Changes in Metacrine’s net cash as of Closing and the price of Equillium common stock prior to the Merger, will each affect the market value of the Merger consideration that Metacrine stockholders actually receive upon the Closing. Stock price changes may result from a variety of factors (many of which are beyond Metacrine’s and Equillium’s control), including the following factors:
changes in Equillium’s and Metacrine’s respective businesses, operations, financial position or prospects;
changes in market assessments of the business, operations, financial position or prospects of either company or the combined company;
manipulation to affect the Exchange Ratio leading up to the Closing;
market assessments of the likelihood that the Merger will be completed;
interest rates, general market, political and economic conditions and other factors generally affecting the price of Equillium’s common stock; and
31

TABLE OF CONTENTS

federal, state and local legislation, governmental regulation and legal developments affecting the businesses of Metacrine or Equillium.
Under the Merger Agreement, there will be no adjustment to the Exchange Ratio for changes in the market price of Equillium common stock within 10 trading days of the Closing, and neither company is permitted to terminate the Merger Agreement or resolicit the vote of Equillium stockholders or Metacrine stockholders solely because of changes in the market price of either company’s stock. You are encouraged to obtain current market quotations for shares of Metacrine common stock and for shares of Equillium common stock before voting.
Because the Merger will be completed after the date of the respective special stockholder meetings, if the special stockholder meeting occurs prior to the finalization of the Closing net cash or more than 10 trading days prior to the Closing, at the time of the applicable special stockholder meeting, the Equillium or Metacrine stockholders may not know the Exchange Ratio or the exact market value of the Equillium common stock that Metacrine stockholders will receive upon completion of the Merger.
subject to the $4.50 per share ceiling, if the 10-day volume weighted average price per share of Equillium common stock increases after the special stockholder meeting but during the window used for determining the Exchange Ratio, Metacrine stockholders can expect to receive less shares of Equillium common stock than was estimated at the time of the special stockholder meeting; and
subject to the $2.70 per share floor, if the 10-day volume weighted average price per share of Equillium common stock decreases after the special stockholder meeting but during the window used for determining the Exchange Ratio, Metacrine stockholders can expect to receive more shares of Equillium common stock than was estimated at the time of the special stockholder meeting.
For illustrative purposes only, we have calculated the potential Exchange Ratio based on the assumptions and sensitivity analysis set forth herein. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Floor Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.282. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 increase to the Floor Price would decrease the Exchange Ratio to 0.258. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Ceiling Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.169. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 decrease to the Ceiling Price would increase the Exchange Ratio to 0.179. Assuming (1) the Equillium Stock Price remains constant and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $1,000,000 increase or decrease in the Upfront Merger Consideration would increase or decrease, respectively, the Exchange Ratio by approximately 0.008.
We encourage you to obtain current market quotations of Equillium common stock, Metacrine common stock and consider the foregoing risk before voting. See the section “The Merger Agreement – Treatment of Metacrine Equity Awards and Warrants” beginning on page 70 for more information.
Failure to complete the Merger could negatively affect the stock prices and the future business and financial results of Equillium and Metacrine.
If the Merger is not completed, the ongoing businesses of Equillium and Metacrine may be adversely affected and Equillium and Metacrine will be subject to several risks, including the following:
the possibility that Equillium may be required to pay Metacrine a termination fee of $1,750,000, if the Merger is terminated under qualifying circumstances described under “The Merger Agreement – Termination Fees; Liability for Breach”;
the possibility that Metacrine may be required to pay Equillium a termination fee of $1,250,000 under qualifying circumstances described under “The Merger Agreement – Termination Fees; Liability for Breach”;
the incurrence of costs and expenses relating to the proposed Merger, such as financing, legal, accounting, financial advisor, filing, printing and mailing fees and expenses;
32

TABLE OF CONTENTS

the possibility that Metacrine will be unable to find another potential strategic partner, advance its product candidates, and, as a result, elect to liquidate and dissolve its business;
the possibility that Equillium will be unable to raise sufficient capital or enter into one or more strategic transactions to enable it to carry on its current business plan, including its current and planned clinical trials or expand its pipeline;
the possibility of a change in the trading price of Equillium common stock to the extent current trading prices reflect a market assumption that the Merger will be completed;
the possibility that Equillium or Metacrine could suffer potential negative reactions from their respective employees, partners and vendors; and
the possibility that Equillium or Metacrine could suffer adverse consequences associated with their respective management's focus on the Merger instead of on pursuing other opportunities that could have been beneficial to each company, in each case, without realizing any of the benefits contemplated by the Merger.
In addition, if the Merger is not completed, Equillium or Metacrine could be subject to litigation related to any failure to complete the Merger or to perform their respective obligations under the Merger Agreement.
If the Merger is not completed, Equillium and Metacrine cannot assure their stockholders that these risks will not materialize and will not materially affect the business, financial results and stock prices of Equillium or Metacrine. See the section “The Merger Agreement – Termination of the Merger Agreement” beginning on page 57 for more information.
Metacrine’s net cash at the Closing is subject to change, which could result in Metacrine Stockholders owning a smaller percentage of the combined organization and could even result in the conditions to Closing not being satisfied.
For purposes of the Merger Agreement, Metacrine cash is subject to certain reductions, including, without limitation, certain short and long term liabilities, unpaid expenses related to the Merger, the purchase of a six-year tail to Metacrine’s directors and officers liability insurance policy, and certain other unpaid obligations, including change of control payments, severance and similar payments payable to its current and former employees, the expected cost and expenses of Metacrine liability arising from legal proceedings, payments in order to terminate certain agreements, and payments (up to the unpaid deductible) under D&O insurance reasonably expected to be paid in connection with legal proceedings. In the event the amount of Metacrine’s net cash at the Closing is less than anticipated, Metacrine’s stockholders could hold a significantly smaller portion of the combined organization. Additionally, the Merger Agreement includes a closing condition that requires Metacrine deliver a minimum net cash of $23 million at the Closing. In the event that Metacrine’s net cash falls below this threshold, Equillium would not be obligated to, but may in its sole discretion elect to, consummate the Merger, which would further reduce Metacrine stockholders holding a smaller portion of the combined organization. See the section “The Merger Agreement – Representations and Warranties” beginning on page 60 for more information.
Equillium has the right to pursue certain strategic transactions and to issue and sell equity and convertible securities subject to certain limitations, the occurrence of which may impact Metacrine’s stockholders’ decisions to vote for the Metacrine merger proposals.
The Merger Agreement allows Equillium to issue, sell or agree to issue or sell shares of Equillium capital stock and/or other equity and convertible securities of Equillium that in the aggregate would not equal or exceed 20% of Equillium’s outstanding capital stock, calculated as of the date of the Merger Agreement, without Metacrine’s consent. Any such issuance or sale of Equillium equity or convertible securities may result in Metacrine stockholders holding a smaller portion of the combined organization. Additionally, in limited circumstances, Equillium may enter into and consummate a strategic transaction to exclusively license or sell, or grant an option to exclusively license or sell, certain of its assets, including Equillium’s rights to develop, manufacture and commercialize EQ001 (itolizumab) without Metacrine’s consent. Should such a transaction occur, it is likely to materially impact Equillium’s stock price and its current and future business plans. Metacrine stockholders should consider these possibilities or the lack of such possibilities, among other things disclosed in this joint proxy/prospectus, in determining whether to vote for the Metacrine merger proposals. See the section “The Merger Agreement – Conduct of Business” beginning on page 62 for more information.
33

TABLE OF CONTENTS

Metacrine stockholders and Equillium stockholders will not be entitled to appraisal rights in the Merger.
Appraisal rights are statutory rights that, if applicable under law, enable stockholders to dissent from an extraordinary transaction, such as a merger, and to demand that the corporation pay the fair value for their shares as determined by a court in a judicial proceeding instead of receiving the consideration offered to stockholders in connection with the extraordinary transaction.
Under the DGCL § 262(b), stockholders do not have appraisal rights if the shares of stock they hold, as of the record date for determination of stockholders entitled to vote at the meeting of stockholders to act upon a merger, are either (i) listed on a national securities exchange or (ii) held of record by more than 2,000 holders. Notwithstanding the foregoing, appraisal rights are available if stockholders are required by the terms of the merger agreement to accept for their shares anything other than (a) shares of stock of the surviving corporation, (b) shares of stock of another corporation that will either be listed on a national securities exchange or held of record by more than 2,000 holders, (c) cash instead of fractional shares or (d) any combination of clauses (a) through (c).
Equillium stockholders will not be entitled to appraisal rights in the Merger with respect to their Equillium shares. Metacrine shares are listed on Nasdaq and are expected to continue to be so listed on the record date for the Metacrine virtual special meeting. Because holders of shares of Metacrine common stock will receive shares of Equillium common stock in the Merger and cash in lieu of fractional shares, holders of shares of Metacrine common stock will also not be entitled to appraisal rights in the Merger with respect to their shares of Metacrine common stock.
The Merger Agreement contains provisions that could discourage a potential competing acquiror of either Equillium or Metacrine or could result in any competing proposal being at a lower price than it might otherwise be.
The Merger Agreement contains “no-shop” provisions that, subject to limited exceptions, restrict Metacrine’s and Equillium’s ability to solicit, encourage, facilitate or discuss competing third-party proposals to acquire all or a significant part of Equillium or Metacrine. In addition, the other party generally has an opportunity to offer to modify the terms of the proposed merger in response to any competing acquisition proposals that may be made before such board of directors may withdraw or qualify its recommendation regarding the proposals described herein. In specified circumstances, Equillium or Metacrine may be required to pay a termination fee to the other party due to the termination of the Merger Agreement.
These provisions could discourage a potential competing acquiror that might have an interest in acquiring all or a significant part of Equillium or Metacrine from considering or proposing that acquisition, even if it were prepared to pay consideration with a higher value than that market value proposed to be received or realized in the Merger, or might result in a potential competing acquiror proposing to pay a lower price than it might otherwise have proposed to pay because of the added expense of the termination fee or expenses that may become payable in certain circumstances.
If the Merger Agreement is terminated and either Equillium or Metacrine attempts to seek another business combination, there is no assurance that either Equillium or Metacrine, as applicable, may be able to negotiate a transaction with another party on terms comparable or better than the terms of the Merger. See the section “The Merger Agreement – No Solicitation of Alternative Proposals” beginning on page 65 for more information.
The pendency of the Merger could adversely affect the business and operations of Equillium and Metacrine.
In connection with the Merger, some prospective partners of each of Equillium and Metacrine may delay or defer decisions or reduce their level of business with either or both of the companies, any of which could negatively affect the financials and business plans of Equillium and Metacrine, regardless of whether the Merger is completed. In addition, due to operating covenants in the Merger Agreement, each of Equillium and Metacrine may be unable, during the pendency of the Merger, to pursue strategic transactions, undertake significant capital projects, undertake certain significant financing transactions and otherwise pursue other actions without the consent of the other party or as otherwise discussed elsewhere in these risk factors, even if such actions would prove beneficial. Any of these effects could adversely affect Equillium’s or Metacrine’s respective business prior to the completion of the Merger. Moreover, the pursuit of the Merger and the preparation for the integration of the companies may place a significant burden on the management and personnel of both companies. The diversion of management's attention away from operating the companies in the ordinary course could adversely affect Equillium’s and Metacrine’s financial results and the advancement of their respective product candidates.
34

TABLE OF CONTENTS

Current Equillium stockholders will have a reduced ownership and voting power in the combined company after the Merger.
After the completion of the Merger, the current securityholders of Equillium and Metacrine will own a smaller percentage of the combined company than their ownership in their respective companies prior to the Merger.
The aggregate value for each share of Metacrine common stock will not be determined until shortly prior to the closing of the Merger. For illustrative purposes only, we have provided the below assumptions and sensitivity analysis to inform your decision.
Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Floor Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.282. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 increase to the Floor Price would decrease the Exchange Ratio to 0.258. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration, (2) an Equillium Stock Price equal to the Ceiling Price, and (3) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, the Exchange Ratio would equal 0.169. Assuming (1) an Upfront Merger Consideration equal to the Assumed Upfront Merger Consideration and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $0.25 decrease to the Ceiling Price would increase the Exchange Ratio to 0.179. Assuming (1) the Equillium Stock Price remains constant and (2) Metacrine’s Closing Capitalization is equal to the Assumed Metacrine Closing Capitalization, a $1,000,000 increase or decrease in the Upfront Merger Consideration would increase or decrease, respectively, the Exchange Ratio by approximately 0.008. We encourage you to obtain current market quotations of Equillium common stock and Metacrine common stock before voting.
Based on the Assumed Upfront Merger Consideration, Equillium estimates that it may issue between 7.5 and 12.5 million shares of its common stock to Metacrine stockholders in connection with the Closing. Based on the Assumed Upfront Merger Consideration and 34,352,084 shares of Equillium common stock outstanding as of November 9, 2022, we estimate that current Equillium stockholders will own between 82.08% and 73.32% of the outstanding common stock of the combined company and former Metacrine equityholders will own between 17.92% and 26.68% of the outstanding common stock of the combined company.
Equillium stockholders and Metacrine stockholders currently have the right to vote for their respective directors and on certain other matters affecting their company. If and when the Merger occurs, each Equillium stockholder will remain a stockholder of Equillium with a percentage ownership of Equillium that will be smaller than the stockholder’s percentage of Equillium prior to the Merger (without considering such stockholder’s current ownership of Metacrine shares, if any). Correspondingly, each Metacrine stockholder who receives shares of Equillium common stock will become an Equillium stockholder with a percentage ownership of Equillium that will be smaller than the stockholder’s percentage ownership of Metacrine (without considering such stockholder’s current ownership of Equillium common stock). Equillium stockholders will have less voting power in Equillium than they currently have, and former Metacrine stockholders will have less voting power in Equillium than they now have in Metacrine. Each of Equillium and Metacrine’s pre-Merger stockholders, respectively, as a group, will be able to exercise less influence over the management and policies of the combined company following the consummation of the Merger than immediately prior to the consummation of the Merger. See the section “The Merger Agreement – Treatment of Metacrine Equity Awards and Warrants” beginning on page 70 for more information.
The market price of shares of Equillium common stock may be affected by factors different from those that historically have affected shares of Metacrine common stock and will continue to fluctuate after the Merger.
Upon completion of the Merger, holders of Metacrine common stock will become holders of Equillium common stock. Equillium’s business differs from that of Metacrine in certain respects, and, accordingly, the financial position or results of operations and/or cash flows of Equillium after the Merger, as well as the market price of shares of Equillium common stock, may be affected by factors different from those currently affecting the financial position or results of operations and/or cash flows of Metacrine. In addition, the stock market has experienced significant price and volume fluctuations in recent times which, if they continue to occur, could have a material adverse effect on the market for, or liquidity of, the Equillium common stock, regardless of Equillium's actual operating performance. As a result, the market price of shares of Equillium common stock may fluctuate significantly following completion of the Merger, and holders of Metacrine common stock could lose some or all of the value of their investment in Equillium common stock.
35

TABLE OF CONTENTS

Directors and executive officers of Equillium and Metacrine have financial interests in the Merger that may be different from, or in addition to, those of other Equillium stockholders and Metacrine stockholders, which could have influenced their decisions to support or approve the Merger.
In considering whether to approve the proposals at the special meetings, Equillium and Metacrine stockholders should recognize that directors and executive officers of Equillium and Metacrine have interests in the Merger that may differ from, or that are in addition to, their interests as stockholders of Equillium and stockholders of Metacrine. The Equillium Board and the Metacrine Board were aware of these interests at the time each approved the Merger Agreement. These interests may cause Equillium's and Metacrine's directors and executive officers to view the Merger differently than you may view it as a stockholder. The interests include, among others, severance benefits, continued indemnification and the right to accelerated vesting. For example, Metacrine previously entered into severance and bonus agreements with certain members of management that provide them with cash severance payments, certain health insurance coverage and the acceleration of their outstanding equity awards in the event their employment is terminated in connection with a change of control of Metacrine.
The opinions obtained by the Equillium Board and Metacrine Board from their respective financial advisors do not and will not reflect changes in circumstances after the date of such opinions.
The Equillium Board received a written opinion, or the VPA Opinion, dated September 6, 2022 from Vantage Point Advisors, Inc., its financial advisor, that the Merger transaction was fair, from a financial point of view, to the Equillium common stockholders, as of such date, and based on and subject to the qualifications, limitations and assumptions set forth in the VPA Opinion (including, without limitation, the accuracy and completeness of the audited and unaudited financial statements, forecasts and other information provided to it by the Equillium Board and the assurances from the Equillium Board that they were unaware of any facts or circumstances that would make the VPA Opinion incomplete or misleading). The VPA Opinion did not constitute a recommendation to the Equillium Board (or any member thereof) as to how it should vote with respect to the Merger transaction. The Metacrine Board received written opinions from MTS, an affiliate of its financial advisor MTS Health Partners, LP, or MTS Partners, dated September 2, 2022, or the September MTS Opinion, and October 19, 2022, or the October MTS Opinion and together with the September Opinion, the MTS Opinions, that as of such dates and based upon and subject to the assumptions made, procedures followed, matters considered and qualifications and limitations on the scope of review undertaken by MTS, as set forth in the MTS Opinions, the Exchange Ratio employed in the Merger pursuant to the Merger Agreement was fair to the holders of shares of Metacrine common stock (other than Excluded Shares), from a financial point of view. Changes in the operations or prospects of Equillium or Metacrine, general market and economic conditions and other factors that may be beyond the control of Equillium and Metacrine, and on which the above-described opinions were based, may alter the value of Equillium or Metacrine or the prices of shares of Equillium Common stock or Metacrine common stock by the time the Merger is completed. Except for the October MTS Opinion, Equillium and Metacrine have not obtained, and do not expect to request, updated opinions from their respective financial advisors. None of the above-listed opinions speak to any date other than the date of such opinion. See the sections “The Merger Agreement – Opinion of Equillium’s Financial Advisor” beginning on page 96, and “The Merger Agreement – Opinions of Metacrine’s Financial Advisor” beginning on page 103 for more information.
Due to the Merger, the ability of Equillium to use Metacrine's net operating losses to offset future taxable income may be restricted and these net operating losses could expire or otherwise be unavailable.
As of December 31, 2021, Metacrine had federal net operating loss carryforwards, which we refer to as NOLs, of approximately $164.5 million. In general, under Section 382 of the Code, a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-ownership change NOLs to offset future taxable income. As of December 31, 2021, Metacrine has not completed a Section 382 limitation study. If the Merger is completed, Metacrine's existing NOLs may be subject to limitations. In addition, if Equillium undergoes any subsequent ownership change, its ability to utilize NOLs would be limited.
The Merger is intended to be a taxable transaction and does not qualify as a “reorganization” for U.S. federal income tax purposes. U.S. holders will be required to recognize gain or loss for U.S. federal income tax purposes at the time of the exchange of their Metacrine common stock for the merger consideration in the Merger.
U.S. holders of Metacrine common stock will recognize gains or losses for U.S. federal income tax purposes on each share of Metacrine common stock surrendered in the Merger in an amount equal to the difference between (1) the fair market value of the merger consideration received in exchange for such surrendered share upon completion
36

TABLE OF CONTENTS

of the Merger and (2) the holder's basis in the share of Metacrine common stock surrendered. Any gain or loss recognized would be long-term capital gain or loss if the U.S. holder's holding period in a particular block of Metacrine common stock exceeds one year at the effective time of the Merger. Long-term capital gain of non-corporate U.S. holders (including individuals) is taxed at reduced U.S. federal income tax rates. See the section “Material U.S. Federal Income Tax Consequences” beginning on page 123 for more information.
Risk Factors Relating to Equillium Following the Merger
Operational Risks
Equillium expects to incur substantial costs and expenses related to the Merger.
Equillium expects to incur substantial costs and expenses in connection with completing the Merger and integrating Metacrine’s business. While Equillium has assumed that a certain level of transaction and integration costs and expenses would be incurred, there are a number of factors beyond its control that could affect the total amount or the timing of its integration costs and expenses, including any Metacrine liabilities that arise, or become known, following the Closing. Many of the costs and expenses that will be incurred, by their nature, are difficult to estimate accurately at the present time. Due to these factors, the transaction and integration costs and expenses could be greater or could be incurred over a longer period of time than Equillium currently expects.
Equillium intends to enter into an arrangement to assume Metacrine’s existing debt facility and to retire Equillium’s current debt facility, which, regardless of whether such arrangement is consummated, will have a material impact on Equillium’s financials.
In connection with the Closing, Equillium intends to enter into an arrangement with Metacrine’s current lender, K2 HealthVentures LLC, to amend and assume Metacrine’s current debt facility with an outstanding principal balance of $15 million, or the K2 Debt Arrangement. If Equillium and K2 HealthVentures LLC are able to consummate the K2 Debt Arrangement, Equillium would retire its existing debt facility with Oxford Finance LLC and Silicon Valley Bank, which currently has an outstanding principal amount of $10 million, or the Existing Debt Facility. After retiring the Existing Debt Facility and as a result of the Merger, Equillium anticipates adding approximately $35 million in cash to its balance sheet at the Closing. As a condition of the K2 Debt Arrangement, K2 HealthVentures LLC may require Equillium to provide additional warrant coverage, which, if issued and exercised, would dilute both Equillium and Metacrine stockholders’ ownership in the combined organization.
There are no assurances that Equillium and K2 HealthVentures LLC will be able to agree on terms mutually acceptable to each other with respect to the K2 Debt Arrangement. If Equillium and K2 HealthVentures LLC are unable to agree on acceptable terms for the K2 Debt Arrangement, Metacrine’s existing debt facility with K2 HealthVentures LLC will be retired at the Closing. If Metacrine’s existing debt facility is retired at the Closing, Equillium would expect to add approximately $27 million in cash to its balance sheet at the Closing and continue to maintain its Existing Debt Facility.
The restrictions and obligations contained in the K2 Debt Arrangement, if consummated, may differ from those under the Existing Debt Facility and Metacrine’s existing debt facility. Equillium anticipates the terms of the K2 Debt Arrangement will subject its business to the risks normally associated with debt financing, including the following risks:
Equillium’s cash flow may be insufficient to meet required payments of principal and interest, or require Equillium to dedicate a substantial portion of its cash flow to pay its debt and the interest associated with its debt rather than to other areas of its business;
it may be more difficult for Equillium to obtain additional financing in the future for its operations, working capital requirements, capital expenditures, debt service or other general requirements;
Equillium may be more vulnerable in the event of adverse economic and industry conditions or a downturn in its business;
Equillium may be placed at a competitive disadvantage compared to its competitors that have less debt;
Equillium may be subject to limitations with respect to its activities including certain future strategic transactions; and
37

TABLE OF CONTENTS

Equillium may not be able to refinance at all or on favorable terms, as its debt matures.
If any of the above risks occurred, Equillium’s financial condition and results of operations could be materially adversely affected. See section “Description of the Merger” beginning on page 21 for more information.
Equillium will require additional capital to fund its operations, which may not be available on acceptable terms, or at all. Failure to obtain this necessary capital when needed may force Equillium to delay, limit or terminate certain of its product development programs, commercialization efforts or other operations.
The development of biotechnology product candidates is capital-intensive. As Equillium conducts non-clinical research and clinical development of its product candidates, Equillium will need substantial additional funds to maintain and expand its capabilities in a variety of areas including research, clinical development, regulatory affairs, product quality assurance, and pharmacovigilance. In addition, if Equillium obtains marketing approval for any of its product candidates, Equillium expects to incur significant commercialization expenses for marketing, sales, manufacturing and distribution. Some of those commercialization investments may be made at-risk in advance of receiving an approval. Because the outcome of any preclinical study or clinical trial is highly uncertain, we cannot reasonably estimate the actual amounts necessary to successfully complete the development and commercialization of our drug candidates. Accordingly, we will need to obtain substantial additional funding in connection with our continuing operations. If we are unable to raise capital when needed or on attractive terms, we could be forced to delay, reduce or eliminate our research and development programs or any future commercialization efforts.
Based on Equillium’s current operating plan, Equillium believes that its existing cash and cash equivalents, together with the cash proceeds from the Merger, will be sufficient to fund its operating expenses and capital expenditure requirements through at least calendar year 2023. In particular, Equillium expects the cash proceeds from the Merger, together with its existing cash and cash equivalents, will allow it to advance its clinical development plans through topline data from the EQUALISE study, interim data from its planned Phase 2 study of EQ101 in alopecia areata and interim data from its planned Phase 1 study of EQ102 in healthy volunteers as well as in subjects with celiac disease. Equillium’s operating plan may change as a result of many factors currently unknown to it, and Equillium may need to seek additional funding sooner than planned.
Until such time as Equillium can generate significant revenue from sales of its product candidates, if ever, Equillium expects to finance its cash needs through equity offerings, debt financings or other capital sources, including potentially grants, collaborations, licenses or other similar arrangements. Accordingly, Equillium will need to continue to rely on additional financing to achieve its business objectives. If Equillium is unable to raise additional capital when needed, its ability to grow and support its business and to respond to market challenges could be significantly limited, which could have a material adverse effect on its business, financial condition and results of operations. Any additional capital raising efforts may divert Equillium’s management from their day-to-day activities, which may adversely affect its ability to develop and, if approved, commercialize its current and any future drug candidates. Additional funding may not be available on acceptable terms, or at all.
If the combined company is unable to compete effectively, the results of operations of the combined company will be materially and adversely affected.
The competitors of the combined company include major pharmaceutical and biotechnology companies, academic institutions, government agencies, public and private research institutions, and smaller or early stage companies, of which many are well-capitalized. The competitiveness of the combined company, is based on factors including the efficacy, safety and convenience of our product candidates, our combined ability to raise capital and enter into strategic transactions, and recruiting and retaining qualified scientific and management personnel and establishing clinical trial sites and patient registration for clinical trials. If the combined company is unable to compete based on such factors, the combined company's results of operations and business prospects could be harmed.
The combined company will have numerous product candidates and two discovery platforms and will need to prioritize its research programs and focus development of its product candidates on the potential treatment of certain indications. As a result, the combined company may forego or delay pursuit of opportunities with other indications or for any future product candidates that later prove to have greater commercial potential. The resource allocation decisions of the combined company may cause it to fail to capitalize on viable commercial products or profitable market opportunities. Such failure may result in the combine company being unable to
38

TABLE OF CONTENTS

raise additional capital to continue to fund its existing programs and operations, and could lead to stockholders losing all or substantially all of their investment in Equillium.
The business operations of the combined company will be subject to various and changing federal, state, local and foreign laws and regulations that could result in costs or sanctions that adversely affect the business and results of operations of the combined company.
The combined company will operate in an increasingly complex regulatory environment. Businesses in the countries in combined company will operate are subject to local, legal and political environments and regulations including with respect to employment, tax, statutory supervision and reporting and trade restriction. These regulations and environments are also subject to change.
Adjusting business operations to changing environments and regulations may be costly and could potentially render the particular business operations uneconomical, which may adversely affect the profitability of the combined company or lead to a change in the business operations.
Notwithstanding the best efforts of the combined company, it may not be in compliance with all regulations in the countries in which it operates at all times and may be subject to sanctions, penalties or fines as a result. These sanctions, penalties or fines may materially and adversely impact the profitability of the combined.
Other Risks
The historical and unaudited pro forma condensed combined financial information included elsewhere in this joint proxy statement/prospectus may not be representative of Equillium’s results after the Merger, and accordingly, you have limited financial information on which to evaluate the combined company.
Equillium and Metacrine will continue to operate as separate companies prior to the Merger. Equillium and Metacrine have no prior history as a combined company. The historical financial statements of Metacrine may be different from those that would have resulted had Metacrine been operated as part of Equillium. The pro forma condensed combined financial information appearing elsewhere herein has been presented for informational purposes only and is not necessarily indicative of the financial position or results of operations that actually would have occurred had the Merger been completed as of the dates indicated, nor is it indicative of the future operating results or financial position of the combined company. The unaudited pro forma condensed combined financial information reflects adjustments, which are based upon preliminary estimates, to allocate the aggregate consideration to Metacrine assets and liabilities. The aggregate consideration allocation reflected in the pro forma condensed combined financial information included in this joint proxy statement/prospectus is preliminary, and the final allocation of the aggregate consideration will be based upon the actual aggregate consideration and the fair value of the assets and liabilities of Metacrine as of the date of the completion of the Merger. The unaudited pro forma condensed combined financial information does not reflect future events that may occur after the Merger, including the incurrence of costs related to the planned integration of Metacrine, any future non-recurring charges resulting from the Merger, or consider potential effects of future market conditions on expense efficiencies, if any. The unaudited pro forma financial information presented in this joint proxy statement/prospectus is based in part on certain assumptions regarding the Merger that Equillium believes are reasonable under the circumstances. Equillium cannot assure you that the assumptions will prove to be accurate over time.
The Equillium and Metacrine prospective financial information is inherently subject to uncertainties.
While presented with numeric specificity, the Equillium and Metacrine prospective financial information provided in this document was prepared based on numerous variables and assumptions (including, but not limited to, those related to industry performance and competition and general business, economic, market and financial conditions, and additional matters specific to Equillium or Metacrine business, as applicable, including the possibility of consummating certain other strategic transactions) that are inherently subjective and uncertain and are largely beyond the control of the respective management of each. As a result, actual results may differ from the prospective financial information. Important factors that may affect actual results and cause these projected financial forecasts to not be achieved include, but are not limited to, risks and uncertainties relating to Equillium’s or Metacrine’s business, as applicable (including each company’s ability to achieve strategic goals, objectives and targets over applicable periods) and general industry, business, competitive and economic conditions.
39

TABLE OF CONTENTS

Equillium and Metacrine may be targets of securities class action and derivative lawsuits which could result in substantial costs and may delay or prevent the Merger from being completed.
Securities class action lawsuits and derivative lawsuits are often brought against public companies that have entered into merger agreements. Even if the lawsuits are without merit, defending against these claims could result in substantial costs and divert management time and resources. An adverse judgment could result in monetary damages, which could have a negative impact on Equillium’s and Metacrine’s respective liquidity and financial condition. Additionally, if a plaintiff is successful in obtaining an injunction prohibiting completion of the Merger, then that injunction may delay or prevent the Merger from being completed, which may adversely affect Equillium’s and Metacrine’s respective business, financial position and results of operations.
Other Risks Related to Equillium’s Business and Metacrine’s business
Equillium’s and Metacrine’s businesses are, and following completion of the transaction Equillium will continue to be, subject to the risks described above and in Equillium’s Annual Report on Form 10-K for the fiscal year ended December 31, 2022, as amended and as updated by subsequent Quarterly Reports on Form 10-Q and Current Reports on Form 8-K and Metacrine’s Quarterly Report on Form 10-Q for the fiscal quarter ended September 30, 2022, as amended and as updated by subsequent Current Reports on Form 8-K, all of which are filed with the SEC and incorporated by reference into this joint proxy statement/prospectus. See “Where You Can Find More Information” beginning on page 141 for the location of information incorporated by reference in this joint proxy statement/prospectus.
40

TABLE OF CONTENTS

CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS
This joint proxy statement/prospectus and the documents incorporated by reference into this joint proxy statement/prospectus contain forward-looking statements. These forward-looking statements are based on current expectations and beliefs and involve numerous risks and uncertainties that could cause actual results to differ materially from expectations. These forward-looking statements should not be relied upon as predictions of future events as it cannot be assured that the events or circumstances reflected in these statements will be achieved or will occur. You can identify forward-looking statements by the use of forward-looking terminology including “anticipates,” “believes,” “could,” “seeks,” “estimates,” “expects,” “intends,” “may,” “plans,” “potential,” “predicts,” “projects,” “pro forma,” “should,” “will,” “would,” or the negative of these words and phrases or other variations of these words and phrases or comparable terminology. All statements other than statements of historical fact are statements that could be deemed forward-looking statements. For example, forward-looking statements include, but are not limited to statements about:
expected timing, completion, effects and potential benefits of the Merger;
statements of the plans, strategies and objectives of management with respect to the approval and closing of the Merger;
Metacrine’s and Equillium’s ability to solicit a sufficient number of proxies to approve matters related to the consummation of the Merger;
the expected Exchange Ratio and relative ownership percentages of the stockholders of Metacrine and Equillium in the combined company following the Closing;
the expected level of Metacrine Net Cash at the Closing;
the expected board of directors of Equillium;
any statements regarding future economic conditions, growth rate, market opportunity or performance of the combined company;
Equillium’s plans, if any, and timing to divest or enter into strategic partnerships with respect to its or Metacrine’s legacy assets;
the Metacrine-Prepared Projections;
research and development plans, including planned preclinical studies and clinical trials, including for itolizumab, EQ101 and EQ102;
the ability to obtain or maintain the listing of Equillium common stock on Nasdaq following the Merger;
Equillium’s and Metacrine’s respective officers and directors potentially having conflicts of interest with approving the Merger;
economic, business, competitive, and/or regulatory factors affecting the business of Equillium and Metacrine;
the occurrence of any other event, change or other circumstances that could give rise to the termination of the Merger Agreement;
satisfaction or waiver (if applicable) of the conditions to the Merger; and
statements of belief and any statement of assumptions underlying any of the foregoing.
For a discussion of the factors that may cause Equillium, Metacrine or the combined company’s actual results, performance or achievements following the Closing to differ materially from any future results, performance or achievements expressed or implied in such forward-looking statements, or for a discussion of risk associated with the ability of Equillium and Metacrine to complete the Merger and the effect of the Merger on the business of Equillium, Metacrine and the combined company following the completion of the Merger, see the section titled “Risk Factors” in this joint proxy statement/prospectus. Additional factors that could cause actual results to differ materially from those expressed in the forward-looking statements are discussed in reports filed with the SEC by Equillium and Metacrine. See the section titled “Where You Can Find More Information” in this joint proxy statement/prospectus. There can be no assurance that the Merger will be completed, or if it is completed, that it will close within the anticipated time period or that the expected benefits of the Merger will be realized.
41

TABLE OF CONTENTS

If any of these risks or uncertainties materializes or any of these assumptions proves incorrect, the results of Equillium, Metacrine or the combined company following completion of the Merger could differ materially from the forward-looking statements. All forward-looking statements in this joint proxy statement/prospectus are current only as of the date on which the statements were made. Equillium and Metacrine do not undertake any obligation (and expressly disclaim any such obligation) to publicly update any forward-looking statement to reflect events or circumstances after the date on which any statement is made or to reflect the occurrence of unanticipated events, except as required by applicable law.
In addition, statements that “Equillium believes” or “Metacrine believes” and similar statements reflect Equillium’s or Metacrine’s beliefs and opinions on the relevant subject. These statements are based upon information available to Equillium or Metacrine, as the case may be, as of the date of this joint proxy statement/prospectus, and while Equillium or Metacrine, as the case may be, believes such information forms a reasonable basis for such statements, such information may be limited or incomplete, and such statements should not be read to indicate that such party has conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and investors are cautioned not to unduly rely upon these statements.
42

TABLE OF CONTENTS

THE EQUILLIUM VIRTUAL SPECIAL MEETING
This joint proxy statement/prospectus is being mailed on or about November 10, 2022, to holders of record of Equillium common stock as of the close of business on November 9, 2022, and constitutes notice of the Equillium virtual special meeting in conformity with the requirements of the DGCL.
This joint proxy statement/prospectus is being provided to Equillium stockholders as part of a solicitation of proxies by the Equillium Board for use at the Equillium virtual special meeting and at any adjournments or postponements of the Equillium virtual special meeting. Equillium stockholders are encouraged to read the entire document carefully, including the annexes to and documents incorporated by reference into this document, for more detailed information regarding the Merger Agreement.
Date, Time and Place of the Equillium virtual special meeting
The Equillium virtual special meeting will be held via live webcast on December 20, 2022, starting at 12:00 p.m. (Eastern Time). There will be no physical meeting location. In order to attend the Equillium virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
Purpose of the Equillium virtual special meeting
At the Equillium virtual special meeting, Equillium stockholders will be asked to consider and vote upon the following proposals:
Equillium Proposal 1: To approve the Equillium stock issuance proposal.
Equillium Proposal 2: To approve the Equillium adjournment proposal.
Recommendation of the Equillium Board
At a meeting of the Equillium Board held on September 5, 2022, the Equillium Board determined that the Merger Agreement and the transactions contemplated thereby, including the issuance of shares of Equillium common stock to the Metacrine stockholders in connection with the Merger, are in the best interests of Equillium and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby.
The Equillium Board recommends that Equillium stockholders vote “FOR” the Equillium stock issuance proposal and “FOR” the Equillium adjournment proposal.
See also the section entitled “The Merger—Reasons for the Merger; Recommendation of the Merger by the Equillium Board” beginning on page 87.
Record Date for the Equillium virtual special meeting; Stock Entitled to Vote
Only holders of record of shares of Equillium common stock at the close of business on November 9, 2022, the record date for the Equillium virtual special meeting, will be entitled to notice of, and to vote at, the Equillium virtual special meeting and any postponements or adjournments thereof. Holders of Equillium common stock at the close of business on the Equillium record date may cast one vote for each share of Equillium common stock that you owned as of the Equillium record date, including (i) shares held directly in the name of the holder of record and (ii) shares held on behalf of the holder as the beneficial owner in street name through a broker, bank, or other nominee.
On the Equillium record date, there were outstanding a total of 34,352,084 shares of Equillium common stock entitled to vote at the Equillium virtual special meeting.
Solicitation of Proxies
The cost of proxy solicitation for the Equillium virtual special meeting, if any, and expenses for the filing, printing and mailing of this joint proxy statement/prospectus will be borne by Equillium. In addition to the use of the mail, proxies may be solicited by officers and directors and regular employees of Equillium, without additional remuneration, by personal interview, telephone, electronic communication or otherwise. Equillium will
43

TABLE OF CONTENTS

also request brokerage firms, nominees, custodians and fiduciaries to forward proxy materials to the beneficial owners of shares held of record on the Equillium record date and will provide customary reimbursement to such firms for the cost of forwarding these materials. Equillium has not retained a proxy solicitor to assist in its solicitation of proxies.
Quorum
The holders of a majority of the voting power of Equillium’s outstanding shares of common stock entitled to vote as of the close of business on the Equillium record date must be virtually present or represented by proxy to constitute a quorum to conduct the Equillium virtual special meeting. All shares of Equillium common stock represented at the Equillium virtual special meeting, including abstentions and broker non-votes (shares held by a broker or nominee that are represented at the meeting, but with respect to which the broker or nominee is not instructed by the beneficial owner of such shares to vote on the particular proposal), will be treated as present for purposes of determining the presence or absence of a quorum to conduct the Equillium virtual special meeting.
Vote Required
Equillium Stock Issuance Proposal. Approval of the Equillium stock issuance proposal requires the affirmative vote of the holders of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (provided that a quorum exists).
Equillium Adjournment Proposal. Approval of the Equillium adjournment proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of votes cast on such matter at the Equillium virtual special meeting (whether or not a quorum is present).
The chairperson of the Equillium virtual special meeting may, if necessary, adjourn the Equillium virtual special meeting for the purpose of soliciting additional proxies (whether or not a quorum exists).
Abstentions and Broker Non-Votes
If you are an Equillium stockholder, abstentions and broker “non-votes” have no effect on the outcome of the stock issuance proposal or the Equillium adjournment proposal. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon. If you are an Equillium stockholder of record and you sign and return your proxy card without indicating how to vote on any particular proposal, the shares of Equillium common stock represented by your proxy will be counted as present for purposes of determining the presence of a quorum for the Equillium virtual special meeting and will be voted “FOR” that proposal. Your failure to cast a vote will also make it more difficult to meet the quorum requirement with respect to organizing the meeting.
Voting Power of Equillium’s Directors and Executive Officers
On the Equillium record date, 25.5% of the outstanding Equillium common stock was held by Equillium directors and executive officers and their respective affiliates. Equillium currently expects that its directors and executive officers will vote their shares in favor of Equillium stock issuance proposal and the Equillium adjournment proposal.
Attending the Equillium virtual special meeting
All holders of Equillium common stock, including stockholders of record and stockholders who hold shares through banks, brokers or other nominees, are invited to virtually attend the Equillium virtual special meeting. Stockholders of record can vote at the special meeting. In order to attend the Equillium virtual special meeting, as well as vote and submit your questions during the live webcast of the meeting, you will need to visit www.virtualshareholdermeeting.com/EQ2022SM and enter the 16-digit Control Number shown on your proxy card. Please be sure to follow instructions found on your proxy card and/or voting authorization form.
Voting of Proxies by Record Stockholders
A proxy card is enclosed for use by Equillium stockholders of record. Equillium requests that its record stockholders sign the accompanying proxy and return it promptly in the enclosed postage-paid envelope. You may also vote your shares by telephone or through the Internet. Information and applicable deadlines for voting
44

TABLE OF CONTENTS

by telephone or through the Internet are set forth on the enclosed proxy card. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon. If you are an Equillium stockholder of record and you sign and return your proxy card without indicating how to vote on any particular proposal, the shares of Equillium common stock represented by your proxy will be counted as present for purposes of determining the presence of a quorum for the Equillium virtual special meeting and will be voted “FOR” that proposal.
At the date hereof, Equillium management has no knowledge of any business that will be presented for consideration at the special meeting and which would be required to be set forth in this joint proxy statement/prospectus other than the matters set forth in Equillium’s accompanying Notice of Special Meeting of Stockholders. In accordance with Equillium’s bylaws and Delaware law, business transacted at the Equillium virtual special meeting will be limited to those matters set forth in such notice. Nonetheless, if any other matter is properly presented at the Equillium virtual special meeting for consideration, it is intended that the persons named in the enclosed proxy and acting thereunder will vote in accordance with their best judgment on such matter.
Your vote is important. Whether or not you expect to attend the Equillium virtual special meeting in person, we urge you to vote your shares as promptly as possible by (1) accessing the Internet website specified on your proxy card; (2) calling the toll-free number specified on your proxy card; or (3) signing and returning the enclosed proxy card in the postage-paid envelope provided, so that your shares may be represented and voted at the Equillium virtual special meeting.
Shares Held in Street Name
If you hold your shares of Equillium common stock in a stock brokerage account or if your shares are held by a bank or nominee (that is, in street name), you must provide the record holder of your shares with instructions on how to vote your shares if you wish them to be counted. Please follow the voting instructions provided by your broker, bank or nominee. Please note that you may not vote shares held in street name by returning a proxy card directly to Equillium or by voting at the Equillium virtual special meeting. Further, brokers who hold shares of Equillium common stock on behalf of their customers may not vote those shares without specific instructions from their customers.
If you hold your Equillium common stock in street name and you do not instruct your broker on how to vote any of your shares, your broker may not vote those shares. For a discussion of the consequences of such broker non-votes, see “The Equillium virtual special meeting—Abstentions and Broker Non-Votes” beginning on page 44 of this joint proxy statement/prospectus.
Revocability of Proxies and Changes to an Equillium Stockholder’s Vote
If you are a holder of shares of Equillium common stock as of the record date for the Equillium virtual special meeting, you have the power to revoke your proxy at any time before your proxy is voted at the Equillium virtual special meeting. You can revoke your proxy in one of four ways:
you can send a signed notice of revocation that is received by Equillium prior to your shares being voted, stating that you would like to revoke your proxy, to Equillium’s corporate secretary at Equillium’s corporate headquarters, 2223 Avenida de la Playa, Suite 105, La Jolla, California 92037;
you can grant a new, valid proxy bearing a later date (by Internet, telephone or mail) that is received by Equillium prior to your shares being voted;
you can vote again by telephone or the Internet at a later time; or
if you are a holder of record, by voting at the Equillium virtual special meeting, which will automatically cancel any proxy previously given, or you may revoke your proxy by attending the virtual special meeting, but your attendance alone will not revoke any proxy that you have previously given.
The latest dated completed proxy will be the one that counts. Written notices of revocation and other communications with respect to the revocation of any proxies should be addressed to:
Equillium, Inc.
2223 Avenida de la Playa, Suite 105
La Jolla, California 92037
Attn: Corporate Secretary
45

TABLE OF CONTENTS

If you are an Equillium stockholder whose shares of Equillium common stock are held in “street name” by a bank, broker, or other nominee, you may revoke your proxy or voting instructions and vote your shares in person at the Equillium virtual special meeting only in accordance with applicable rules and procedures as employed by your bank, broker, or other nominee. If your shares are held in “street name” in an account at a bank, broker, or other nominee, you must follow the directions you receive from your bank, broker, or other nominee in order to change or revoke your proxy or voting instructions and should contact your bank, broker, or other nominee to do so.
Adjournments
Although it is not currently expected, the Equillium virtual special meeting may be adjourned for the purpose of soliciting additional proxies if Equillium has not received sufficient proxies to constitute a quorum or sufficient votes for approval of the Equillium stock issuance proposal. Adjourning the Equillium virtual special meeting requires the affirmative vote of the holders of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (whether or not a quorum is present), or in the case that no Equillium stockholders are present at the Equillium virtual special meeting, any Equillium officer entitled to preside at or to act as secretary of the Equillium virtual special meeting may adjourn the Equillium virtual special meeting. Pursuant to the Equillium bylaws, notice need not be given of any such adjourned meeting if the time and place thereof are announced at the meeting at which adjournment is taken. If the adjournment is for more than 30 days or if after the adjournment a new record date is fixed for the adjourned meeting, a notice of the adjourned meeting shall be given to each stockholder of record entitled to vote at the Equillium virtual special meeting. At any adjourned meeting, any business may be transacted which might have been transacted at the original meeting. If the Equillium virtual special meeting is adjourned, stockholders who have already sent in their proxies will be allowed to revoke them at any time prior to their use. The Merger Agreement provides that the Equillium virtual special meeting will not be adjourned to a date that is more than 15 calendar days after the date for which the Equillium virtual special meeting was originally scheduled.
Postponements
At any time prior to convening the Equillium virtual special meeting, the Equillium Board may postpone the Equillium virtual special meeting for any reason without the approval of the Equillium stockholders. The Merger Agreement provides that the Equillium virtual special meeting will not be postponed to a date that is more than 15 calendar days after the date for which the Equillium virtual special meeting was originally scheduled. Although it is not currently expected, the Equillium Board may postpone the Equillium virtual special meeting for the purpose of soliciting additional proxies if Equillium has not received sufficient proxies to constitute a quorum or sufficient votes for approval of the Equillium stock issuance proposal. If the Equillium virtual special meeting is postponed, stockholders who have already sent in their proxies will be allowed to revoke them at any time prior to their use.
Stockholder List
A list of Equillium stockholders entitled to vote at the Equillium virtual special meeting will be available for inspection at Equillium’s principal executive offices, located at 2223 Avenida de la Playa, Suite 105, La Jolla, California 92037, at least 10 days prior to the date of the Equillium virtual special meeting and continuing through the date thereof for any purpose germane to the Equillium virtual special meeting, between the hours of 9:00 a.m. and 4:30 p.m., local time.
Tabulation of Votes
A representative of Equillium’s mailing and tabulating agent, Broadridge Financial Solutions, will tabulate the votes and Equillium’s corporate secretary will act as inspector of elections.
How You Can Reduce the Number of Copies of Equillium’s Proxy Materials You Receive
Equillium has adopted a procedure approved by the Securities and Exchange Commission called “householding.” Under this procedure, stockholders of record who have the same address and last name and who do not participate in electronic delivery of proxy materials will receive only one copy of the proxy materials,
46

TABLE OF CONTENTS

unless one or more of these stockholders notifies Equillium that they wish to continue receiving individual copies. This procedure reduces Equillium’s printing costs and postage fees. Stockholders who wish to participate in householding will continue to receive separate proxy cards.
If you are eligible for householding, but you and other stockholders of record with whom you share an address currently receive multiple copies of the proxy materials, or if you hold stock in more than one account, and, in either case, you wish to receive only a single copy of the proxy materials for your household, please contact your broker.
If you participate in householding and wish to receive a separate copy of the proxy materials, or if you do not wish to continue to participate in householding and prefer to receive separate copies of the proxy materials in the future, please contact your broker or Equillium. Direct your written request to Equillium, Inc., Investor Relations, 2223 Avenida de la Playa, Suite 105, La Jolla, California 92037 or contact Investor Relations at (858) 240-1200 or by email at ir@equilliumbio.com.
Beneficial owners can request information about householding from their banks, brokers, or other holders of record.
Assistance
If you need assistance in completing your proxy card or have questions regarding the Equillium virtual special meeting, please contact Investor Relations at (858) 240-1200 or email ir@equilliumbio.com.
47

TABLE OF CONTENTS

EQUILLIUM PROPOSALS

Equillium Proposal 1: The Equillium Stock Issuance Proposal
Equillium stockholders are asked to approve the issuance of shares of Equillium common stock to Metacrine stockholders in connection with the Merger contemplated by the Merger Agreement. Equillium stockholders should carefully read this joint proxy statement/prospectus in its entirety, including the documents incorporated by reference and the Merger Agreement, for more detailed information concerning the Merger Agreement and the Equillium stock issuance proposal. For a detailed discussion of the terms of the Merger Agreement and the Merger, including the proposed Equillium stock issuance, see the information about the Merger and the Merger Agreement throughout this joint proxy statement/prospectus, including the information set forth in the section entitled “The Merger Agreement” beginning on page 57 of this joint proxy statement/prospectus. A copy of the Merger Agreement is attached as Annex A to this joint proxy statement/prospectus.
Approval of the Equillium stock issuance proposal is a condition to completion of the Merger. If the Equillium stock issuance proposal is not approved, the Merger will not occur. For a detailed discussion of the conditions of the Merger, see “The Merger Agreement—Conditions to Completion of the Merger” beginning on page 72 of this joint proxy statement/prospectus.
Approval of the Equillium stock issuance proposal requires the affirmative vote of the holders of shares of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (provided that a quorum exists). For the Equillium stock issuance proposal, abstentions and broker “non-votes” will have no effect on the outcome of the proposal. If an Equillium stockholder returns a signed proxy card without indicating voting preferences on such proxy card, the shares of Equillium common stock represented by that proxy will be counted as present for purposes of determining the presence of a quorum for the Equillium virtual special meeting and all of such shares will be voted as recommended by the Equillium Board.
At a meeting of the Equillium Board held on September 5, 2022, the Equillium Board determined that the Merger Agreement and the transactions contemplated thereby, including the issuance of shares of Equillium common stock to the Metacrine stockholders in connection with the Merger, were in the best interests of Equillium and its stockholders, and approved the Merger Agreement and the Merger, the execution of the Merger Agreement and the consummation of the transactions contemplated thereby.
IF YOU ARE AN EQUILLIUM STOCKHOLDER, THE EQUILLIUM BOARD
RECOMMENDS THAT YOU VOTE “FOR” THE PROPOSAL TO ISSUE SHARES OF
EQUILLIUM COMMON STOCK IN THE MERGER.
******************************************************************************
48

TABLE OF CONTENTS

Equillium Proposal 2: The Equillium Adjournment Proposal
This proposal would permit the Equillium Board to adjourn from time to time the Equillium virtual special meeting, if necessary, to solicit additional proxies if there are not sufficient votes to approve the Equillium stock issuance proposal.
Pursuant to Equillium’s bylaws, notice need not be given of any such adjourned meeting if the time and place thereof are announced at the meeting at which the adjournment is taken. If the adjournment is for more than 30 days or if, after the adjournment, a new record date is fixed for the adjourned meeting, a notice of the adjourned meeting shall be given to the Equillium stockholders of record entitled to vote at the adjourned meeting. At any adjourned meeting, any business may be transacted which might have been transacted at the original meeting.
Approval of the Equillium adjournment proposal requires the affirmative vote of the holders of Equillium common stock representing a majority of the votes cast on such matter at the Equillium virtual special meeting (whether or not a quorum is present). For the Equillium adjournment proposal, abstentions and broker “non-votes” will have no effect on the outcome of the proposal. Shares of Equillium common stock represented by properly executed, timely received and unrevoked proxies will be voted in accordance with the instructions indicated thereon. If an Equillium stockholder returns a signed proxy card without indicating voting preferences on such proxy card, the shares of Equillium common stock represented by that proxy will be counted as present for purposes of determining the presence of a quorum for the Equillium virtual special meeting and all of such shares will be voted as recommended by the Equillium Board.
IF YOU ARE AN EQUILLIUM STOCKHOLDER, THE EQUILLIUM BOARD
RECOMMENDS THAT YOU VOTE “FOR” THE PROPOSAL TO PERMIT THE