| Item 1. | Security and Issuer |
| (a) | Title of Class of Securities:
Common Stock, par value $0.001 per share |
| (b) | Name of Issuer:
SEPTERNA, INC. |
| (c) | Address of Issuer's Principal Executive Offices:
250 East Grand Avenue, South San Francisco,
CALIFORNIA
, 94080. |
Item 1 Comment:
This Amendment No. 1 (this "Amendment No. 1" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on November 4, 2024 (the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 1 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. |
| Item 2. | Identity and Background |
|
| (a) | This Schedule 13D/A is being filed on behalf of RA Capital Management, L.P. ("RA Capital"), Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the "Fund"). The foregoing entities and individuals are collectively referred to herein as the "Reporting Persons." The agreement among the Reporting Persons to file this Schedule 13D/A jointly in accordance with Rule 13d-1(k) of the Act is attached hereto as Exhibit 99.1.
The Reporting Persons' ownership of the Issuer's securities includes (i) 4,777,415 shares of common stock held directly by the Fund; (ii) 725,443 shares of common stock held directly by RA Capital Nexus Fund III, L.P. (the "Nexus Fund III"); and (iii) a total of 22,466 shares of common stock underlying vested stock options (right to buy) held by Dr. Simson for the benefit of RA Capital.
RA Capital Healthcare Fund GP, LLC is the general partner of the Fund and RA Capital Nexus Fund III GP, LLC is the general partner of the Nexus Fund III. 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 each of the Fund and the Nexus Fund III 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 or the Nexus Fund III. Each of the Fund and the Nexus Fund III has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in its portfolio, including the shares of the Issuer's common stock reported herein. Because each of the Fund and the Nexus Fund III has divested itself of voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, each of the Fund and the Nexus Fund III disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act and therefore disclaims any obligation to report ownership of the reported securities under 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 13D other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13D 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. |
| (b) | The address of the principal business office of each of the Reporting Persons is 200 Berkeley Street, 18th Floor, Boston, MA 02116. |
| (c) | The Fund is a private investment vehicle. RA Capital provides investment management services to the Fund and the Nexus Fund III. The principal occupation of each of Dr. Kolchinsky and Mr. Shah is investment management. |
| (d) | During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors). |
| (e) | During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree of final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws. |
| (f) | See Item 6 of the cover pages. |
| Item 5. | Interest in Securities of the Issuer |
| (a) | Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D/A set forth the aggregate number of shares of common stock and percentage of the shares of common stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon 46,676,947 shares of common stock outstanding as of August 5, 2026, as reported in the Issuer's Quarterly Report on Form 10-Q filed with the SEC on August 10, 2026, and giving effect to stock options, to the extent exercisable within 60 days hereof, as referenced herein. |
| (b) | Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D/A set forth the number of shares of common stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference. |
| (c) | Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days.
Purchaser/ No. Price Per
Transaction Seller Date Shares Share ($)
Vest Stock Option (Right to Buy) RA Capital 06/17/2026 16,623 (1)
Vest Stock Option (Right to Buy) RA Capital 07/28/2026 835 (2)
Block Sale Fund 08/12/2026 746,500 42.50
Block Sale Nexus Fund III 08/12/2026 746,500 42.50
(1) This option represents a right to purchase a total of 16,623 shares of the Issuer's common stock, which vested in full on June 17, 2026. These options have an exercise price of $10.24 per share.
(2) This option represents a right to purchase a total of 13,356 shares of the Issuer's common stock, which began vesting on January 28, 2025 in 16 substantially equal quarterly installments, subject to Dr. Simson's continued service to the Issuer through each vesting date. These options have an exercise price of $6.81 per share.
|
| (d) | No person (other than the Reporting Persons) is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the shares of common stock subject to this 13D/A. |
| (e) | Not applicable. |
| Item 7. | Material to be Filed as Exhibits. |
| | Exhibit 99.1 Joint Filing Agreement (incorporated by reference to Exhibit 1 to the Reporting Persons' Schedule 13D filed with the SEC on November 4, 2024). |
