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EyePoint Pharmaceuticals, Inc. 11,000,000 Shares of Common Stock Pre-Funded Warrants to Purchase 1,500,000 Shares of Common Stock We are offering 11,000,000 shares of our common stock, par value $0.001 per share, and, in lieu of common stock to certain investors thatso choose, pre-funded warrants to purchase 1,500,000 shares of our common stock pursuant to this prospectus supplement and theaccompanying prospectus. The public offering price of each share of common stock is $12.00, and the purchase price of each warrantequals the public offering price of each share of common stock, minus $0.001, which is the exercise price per share underlying the pre-funded warrants. This prospectus supplement also relates to the offering of the shares of our common stock issuable upon the exercise ofsuch pre-funded warrants. Our common stock is listed on The Nasdaq Global Market under the symbol “EYPT.” On October14, 2025, the closing price of ourcommon stock, as reported on The Nasdaq Global Market, was $13.16 per share. There is no established public trading market for thepre-funded warrants, and we do not expect a market to develop. We do not intend to list the warrants on The Nasdaq Global Market orany other national securities exchange or nationally recognized trading system. We have granted the underwriters an option for a period of 30 days to purchase up to an additional 1,875,000 shares of our common stockat the public offering price, less the underwriting discounts and commissions. Investing in our securities involves a high degree of risk. You should review carefully the risks and uncertainties referencedunder the heading “Risk Factors” onpageS-5of this prospectus supplement,page6 of the accompanying prospectus and inthe documents that are incorporated herein by reference. Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of thesesecurities or determined if this prospectus supplement or the accompanying prospectus is truthful or complete. Anyrepresentation to the contrary is a criminal offense. The underwriters expect to deliver the shares of common stock and the pre-funded warrants against payment on or about October 16,2025. Jefferies J.P.Morgan Citigroup October 14, 2025. Table of Contents Table of contents Prospectus supplement ABOUT THIS PROSPECTUS SUPPLEMENTPROSPECTUS SUPPLEMENT SUMMARYTHE OFFERINGRISK FACTORSNOTE REGARDING FORWARD-LOOKING STATEMENTSUSE OF PROCEEDSDILUTIONDESCRIPTION OF PRE-FUNDED WARRANTSMATERIAL U.S. FEDERAL INCOME TAX CONSEQUENCESUNDERWRITINGLEGAL MATTERSEXPERTSWHERE YOU CAN FIND MORE INFORMATIONINCORPORATION OF CERTAIN INFORMATION BY REFERENCE Prospectus ABOUT THIS PROSPECTUSFORWARD-LOOKING STATEMENTSMARKET, INDUSTRY AND OTHER DATASUMMARYRISK FACTORSUSE OF PROCEEDSPLAN OF DISTRIBUTIONGENERAL DESCRIPTION OF OUR SECURITIES Table of Contents About this prospectus supplement This prospectus supplement and the accompanying prospectus are part of a “shelf” registration statement on FormS-3that went effectiveupon our filing with the Securities and Exchange Commission, or SEC, on October14, 2025. Under the shelf registration statementprocess, we may from time to time offer and sell any combination of the securities described in the accompanying prospectus, of whichthis prospectus forms a part. This document is in two parts. The first part is this prospectus supplement, which describes the terms of this offering and also adds to andupdates information contained in the accompanying prospectus and the documents incorporated by reference herein or therein. Thesecond part, the accompanying prospectus, including the documents incorporated by reference into the accompanying prospectus,provides more general information. Generally, when we refer to this prospectus, we are referring to both parts of this document combined.To the extent there is a conflict between the information contained in this prospectus supplement and the information contained in theaccompanying prospectus or any document incorporated by reference herein or therein filed prior to the date of this prospectussupplement, you should rely on the information in this prospectus supplement; provided that if any statement in one of these documents isinconsistent with a statement in another document having a later date—for example, a document incorporated by reference in theaccompanying prospectus—the statement in the document having the later date modifies or supersedes the earlier statement. Neither we nor the underwriters have authorized anyone to provide information different from that contained in this prospectussupplement, the accompanying prospectus and any free writing prospectus that we have authorized for use in this offering. If anyoneprovides you with different or inconsistent information, you should not rely on it. Neither we nor the underwriters take any responsibility for,and can provide no assurance as to the reliability of, any other information