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SCHEDULE 13D/A 0001855502 XXXXXXXX LIVE 2 Common Stock, $0.0001 par value per share 06/05/2025 false 0001827087 92673K108 Vigil Neuroscience, Inc. 100 Forge Road Suite 700 Watertown MA 02472 Jean-Philippe Kouakou-Zebouah (857) 254-9500 Vida Ventures GP III, L.L.C. 40 Broad Street, Suite 201 Boston MA 02109 0001855504 N Vida Ventures III, L.P. b WC N DE 0 2835464 0 2835464 2835464 N 6.1 PN (1) All shares are held of record by Vida III (as defined in Item 2(a) of the Original Schedule 13D (as defined below)). Vida III GP (as defined in Item 2(a) of the Original Schedule 13D) is the general partner of each of Vida III and Vida III-A (as defined in Item 2(a) of the Original 13D) and may be deemed to have voting, investment, and dispositive power with respect to these securities. Each of the Investment Committee (as defined in the Original Schedule 13D) and the members thereof may be deemed to share voting, investment and dispositive power with respect to these securities. (2) Based upon 46,671,534 shares of the Issuer's Common Stock outstanding as of April 30, 2025, as set forth in the Issuer's quarterly report on Form 10-Q for the quarter ended March 31, 2025, filed with the Securities and Exchange Commission ("Commission") on May 7, 2025 (the "Form 10-Q"). 0001855503 N Vida Ventures III-A, L.P. b WC N DE 0 6536 0 6536 6536 N 0 PN (1) All shares are held of record by Vida III-A. Vida III GP is the general partner of each of Vida III and Vida III-A and may be deemed to have voting, investment, and dispositive power with respect to these securities. Each of the Investment Committee and the members thereof may be deemed to share voting, investment and dispositive power with respect to these securities. (2) Based upon 46,671,534 shares of the Issuer's Common Stock outstanding as of April 30, 2025, as set forth in the Form 10-Q. 0001855502 N Vida Ventures GP III, L.L.C. b AF N DE 0 2842000 0 2842000 2842000 N 6.1 OO (1) Consists of (i) 2,835,464 shares held by Vida III and (ii) 6,536 shares held by Vida III-A. Vida III GP is the general partner of each of Vida III and Vida III-A and may be deemed to have voting, investment, and dispositive power with respect to these securities. Each of the Investment Committee and the members thereof may be deemed to share voting, investment and dispositive power with respect to these securities. (2) Based upon 46,671,534 shares of the Issuer's Common Stock outstanding as of April 30, 2025, as set forth in the Form 10-Q. Common Stock, $0.0001 par value per share Vigil Neuroscience, Inc. 100 Forge Road Suite 700 Watertown MA 02472 Explanatory Note: This Amendment No. 2 (this Amendment) amends and supplements the Schedule 13D originally filed by the Reporting Persons with the SEC on February 10, 2023, as amended by that Amendment No. 1 filed with the SEC on October 9, 2024 (collectively, the Original Schedule 13D). Only those items that are hereby reported are amended; all other items reported in the Original Schedule 13D remain unchanged. Information given in response to each item shall be deemed incorporated by reference in all other items, as applicable. Capitalized terms not defines in this Amendment have the meanings ascribed to them in the Original Schedule 13D. This Amendment is being filed by Vida III, Vida III-A, and Vida III GP (each as defined in the Original 13D) and together with Vida III and Vida III-A, the "Reporting Persons")). Stefan Vitorovic, a reporting person on the Original 13D, is no longer a member of Vida III GP, and accordingly, is no longer a Reporting Person. The Reporting Persons expressly disclaim status as a "group" for purposes of this Schedule 13D. The agreement among the Reporting Persons to file jointly in accordance with the provisions of Rule 13d-1(k)(1) under the Act is attached to the Original 13D as Exhibit 1 thereto. Other than those securities reported herein as being held directly by such Reporting Person, each Reporting Person disclaims beneficial ownership of all securities reported in this Amendment except to the extent of such Reporting Person's pecuniary interest therein. The information set forth in Item 2(b) of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 2(c) of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 2(d) of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 2(e) of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 2(f) of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 3 of the Original Schedule 13D is incorporated herein by reference. The information set forth in Item 4 of the Original Schedule 13D is incorporated herein by reference. See Items 7-11 of the cover pages of this Amendment No. 2. The information reported on such cover pages is reported as of June 6, 2025. See Items 7-11 of the cover pages of this Amendment No. 2. The information reported on such cover pages is reported as of June 6, 2025. On June 5, 2025, Vida III sold 594,558 shares of Common Stock at a weighted average price per share of $7.8838 for aggregate proceeds of $4,687,386.65. On June 5, 2025, Vida III-A sold 1,371 shares of Common Stock at a weighted average price per share of $7.8838 for aggregate proceeds of $10,805.25. On June 6, 2025, Vida III sold 1,574,371 shares of Common Stock at a weighted average price per share of $7.8755 for aggregate proceeds of $12,398,957.24. On June 6, 2025, Vida III-A sold 3,629 shares of Common Stock at a weighted average price per share of $7.8755 for aggregate proceeds of $28,581.76. The information set forth in Item 5(d) of the Original Schedule 13D is incorporated herein by reference. N/A The information set forth in Item 6 of the Original Schedule 13D is incorporated herein by reference. Vida Ventures III, L.P. By: Vida Ventures GP III, L.L.C., its General Partner /s/ Jean-Philippe Kouakou-Zebouah Managing Member 06/09/2025 Vida Ventures III-A, L.P. By: Vida Ventures GP III, L.L.C., its General Partner /s/ Jean-Philippe Kouakou-Zebouah Managing Member 06/09/2025 Vida Ventures GP III, L.L.C. /s/ Jean-Philippe Kouakou-Zebouah Managing Member 06/09/2025