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Pre-FundedWarrants to Purchase 1,128,949 Shares of Common Stock 4D Molecular Therapeutics, Inc. is offering 8,385,809 shares of its common stock, par value $0.0001 per share, and, in lieu of shares of commonstock to certain investors,pre-fundedwarrants to purchase 1,128,949 shares of our common stock. The purchase price of eachpre-fundedwarrant is$10.5099, and the exercise price of eachpre-fundedwarrant will equal $0.0001 per share. This prospectus supplement also relates to the offering of theshares of our common stock issuable upon the exercise of suchpre-fundedwarrants. Our common stock is listed on the Nasdaq Global Select Market under the symbol “FDMT.” There is no established public trading market for thepre-fundedwarrants, and we do not expect a market to develop. We do not intend to list thepre-fundedwarrants on the Nasdaq Global Select Market orany other national securities exchange or nationally recognized trading system. On November5, 2025, the last reported sale price of our common stockon the Nasdaq Global Select Market was $10.51per share. See the section titled “Risk Factors” beginning on pageS-8of this prospectus supplement and in the documentsincorporated or deemed to be incorporated by reference into this prospectus supplement and the accompanying prospectus,to read about factors you should consider before deciding to invest in our securities. Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities orpassed upon the accuracy or adequacy of this prospectus supplement. Any representation to the contrary is a criminal offense. Evercore ISIRBC Capital Markets Leerink Partners Table of Contents TABLE OF CONTENTS ABOUT THIS PROSPECTUS SUPPLEMENTPROSPECTUS SUPPLEMENT SUMMARYTHE OFFERINGRISK FACTORSCAUTIONARY STATEMENT REGARDING FORWARD-LOOKING STATEMENTSMARKET AND INDUSTRY DATAUSE OF PROCEEDSDIVIDEND POLICYDILUTIONDESCRIPTION OFPRE-FUNDEDWARRANTSMATERIAL U.S. FEDERAL INCOME TAX CONSEQUENCESUNDERWRITINGLEGAL MATTERSEXPERTSWHERE YOU CAN FIND MORE INFORMATIONINCORPORATION BY REFERENCE ABOUT THIS PROSPECTUSSPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTSWHERE YOU CAN FIND MORE INFORMATION; INCORPORATION BY REFERENCETHE COMPANYRISK FACTORSUSE OF PROCEEDSDESCRIPTION OF CAPITAL STOCKDESCRIPTION OF DEBT SECURITIES DESCRIPTION OF WARRANTSGLOBAL SECURITIESPLAN OF DISTRIBUTIONLEGAL MATTERSEXPERTS Table of Contents ABOUT THIS PROSPECTUS SUPPLEMENT This document is in two parts. The first part is this prospectus supplement, which describes the specific terms of this offering of common stockandpre-fundedwarrants and also adds to and updates information contained in the accompanying prospectus and the documents incorporated byreference into this prospectus supplement and the accompanying prospectus. The second part is the accompanying prospectus dated August9, 2023,included in our registration statement on FormS-3(FileNo.333-273845),which was declared effective by the Securities and Exchange Commission(the “SEC”) on August15, 2023, along with the documents incorporated by reference therein, which provides more general information, some of whichmay not apply to this offering. Generally, when we refer to this prospectus, we are referring to both parts of this document combined. To the extent thereis a conflict between the information contained in this prospectus supplement, on the one hand, and the information contained in the accompanyingprospectus or in any document incorporated by reference that was filed with the SEC before the date of this prospectus supplement, on the other hand,you should rely on the information contained in this prospectus supplement. If any statement in one of these documents is inconsistent with a statementin another document having a later date—for example, a document incorporated by reference in the accompanying prospectus—the statement in thedocument having the later date modifies or supersedes the earlier statement. This prospectus supplement and the accompanying prospectus are part of a “shelf” registration statement that we filed with the SEC. Under thisshelf registration process, we may offer from time to time various securities, of which this offering of shares of our common stock andpre-fundedwarrants is a part. Such registration statement also includes exhibits that provide more detail on the matters discussed in this prospectus supplement andthe accompanying prospectus. You should read this prospectus supplement, the accompanying prospectus, including the information incorporated byreference herein and therein, the exhibits filed with the SEC, and any free writing prospectus that we have authorized for use in connection with thisoffering, in their entirety before making an investment decision. We have not, and the underwriters have not, authorized anyone to provide you with information, or to make any representation, different from thatcontained or incorporated by reference in this pro