SCHEDULE 13G 0001346824 XXXXXXXX LIVE Common Stock, par value $0.001 per share 08/11/2025 0001426800 Assembly Biosciences, Inc. 045396207 Two Tower Place, 7th Floor South San Francisco CA 94080 Rule 13d-1(c) RA Capital Management, L.P. DE 0.00 1530615.00 0.00 1530615.00 1530615.00 9.5 IA PN Peter Kolchinsky X1 0.00 1530615.00 0.00 1530615.00 1530615.00 9.5 HC IN Rajeev Shah X1 0.00 1530615.00 0.00 1530615.00 1530615.00 9.5 HC IN RA Capital Healthcare Fund, L.P. DE 0.00 1530615.00 0.00 1530615.00 1530615.00 9.5 PN Assembly Biosciences, Inc. Two Tower Place, 7th Floor, South San Francisco, CA, 94080. The names of the persons filing this report (collectively, the "Reporting Persons") are: RA Capital Management, L.P. ("RA Capital") Peter Kolchinsky Rajeev Shah RA Capital Healthcare Fund, L.P. (the "Fund") The Reporting Persons expressly disclaim status as a "group" for purposes of this Schedule 13G. The address of the principal business office of each of the Reporting Persons is: c/o RA Capital Management, L.P., 200 Berkeley Street, 18th Floor, Boston MA 02116 RA Capital and the Fund are Delaware limited partnerships. Dr. Kolchinsky and Mr. Shah are United States citizens. Y Row 9 of each Reporting Person's cover page to this Schedule 13G sets forth the aggregate number of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. The Fund directly holds (i) 1,020,410 shares of common stock, (ii) warrants (the "Class A Warrants") exercisable for up to 510,205 shares of common stock and (iii) warrants (the "Class B Warrants" and, together with the Class A Warrants, the "Warrants") exercisable for up to 510,205 shares of common stock. The Class A Warrants are immediately exercisable and will expire upon the earlier of (i) five years from the date of issuance and (ii) the date that is 30 days after the public announcement that the Issuer has achieved a predefined clinical milestone. The Class B Warrants are exercisable on or after November 15, 2026 and will expire on December 31, 2026, subject to their automatic termination in full in the event that the Issuer announces the completion of a non-dilutive capital raise of at least $75.0 million prior to November 15, 2026. The Warrants contain a provision (the "Beneficial Ownership Blocker") which precludes exercise of the Warrants to the extent that, following exercise, the Fund, together with its affiliates and other attribution parties, would own more than 9.99% of the common stock outstanding. RA Capital Healthcare Fund GP, LLC is the general partner of the Fund. The general partner of RA Capital is RA Capital Management GP, LLC, of which Dr. Kolchinsky and Mr. Shah are the controlling persons. RA Capital serves as investment adviser for the Fund and may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities of the Issuer held by the Fund. The Fund has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in the Fund's portfolio, including the shares of the Issuer's common stock reported herein. Because the Fund has divested voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, the Fund disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act. As managers of RA Capital, Dr. Kolchinsky and Mr. Shah may be deemed beneficial owners, for purposes of Section 13(d) of the Act, of any securities of the Issuer beneficially owned by RA Capital. RA Capital, Dr. Kolchinsky, and Mr. Shah disclaim beneficial ownership of the securities reported in this Schedule 13G other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13G shall not be deemed an admission that either RA Capital, Dr. Kolchinsky, or Mr. Shah is the beneficial owner of such securities for any other purpose. Row 11 of each Reporting Person's cover page to this Schedule 13G sets forth the percentages of common stock of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Such percentage is based upon the sum of (i) 15,560,009 shares of the Issuer's common stock outstanding as of August 11, 2025, as disclosed in the Issuer's prospectus supplement dated August 8, 2025 filed with the Securities and Exchange Commission (the "SEC") on August 11, 2025 and (ii) 510,205 shares of common stock issuable upon the exercise of the Class A Warrants. Row 5 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 6 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 7 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 8 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Y Y Y Y Y N By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect, other than activities solely in connection with a nomination under ?? 240.14a-11. Exhibit 99.1 Joint Filing Agreement RA Capital Management, L.P. /s/ Peter Kolchinsky 08/18/2025 Peter Kolchinsky /s/ Peter Kolchinsky 08/18/2025 Rajeev Shah /s/ Rajeev Shah 08/18/2025 RA Capital Healthcare Fund, L.P. /s/ Peter Kolchinsky 08/18/2025