SCHEDULE 13D/A 0001387131-22-000582 0001812049 XXXXXXXX LIVE 1 Common Stock, $0.0001 par value per share 08/05/2025 false 0001827087 92673K108 VIGIL NEUROSCIENCE, INC.

100 Forge Road, Suite 700 Watertown MA 02472

Ommer Chohan, CFO (857) 201-2700 300 Technology Square, 8th Floor Cambridge MA 02139 0001812049 N Atlas Venture Fund XII, L.P. b WC N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 PN 0001845875 N Atlas Venture Associates XII, L.P. b AF N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 PN 0001845871 N Atlas Venture Associates XII, LLC b AF N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 OO 0001759241 N Atlas Venture Opportunity Fund I, L.P. b WC N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 PN 0001780065 N Atlas Venture Associates Opportunity I, L.P. b AF N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 PN 0001780066 N Atlas Venture Associates Opportunity I, LLC b AF N DE 0.00 0.00 0.00 0.00 0.00 N 0.0 OO Common Stock, $0.0001 par value per share VIGIL NEUROSCIENCE, INC. 100 Forge Road, Suite 700 Watertown MA 02472 Item 1 of the Statement is amended and supplemented as follows: 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 January 21, 2022 (as amended, 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 4 of the Statement is hereby amended and supplemented as follows: On May 21, 2025, the Issuer entered into an Agreement and Plan of Merger (the "Merger Agreement") with Sanofi, a French societe anonyme ("Parent" or "Sanofi"), and Vesper Acquisition Sub Inc., a Delaware corporation and a wholly-owned subsidiary of Parent ("Merger Sub"), pursuant to which, Merger Sub would merge with and into the Issuer (the "Merger"), with the Issuer surviving the merger as a wholly-owned subsidiary of Parent. On August 4, 2025, at a special meeting of stockholders of the Issuer, the Issuer's stockholders voted to adopt the Merger Agreement. On August 5, 2025, the Merger closed and each share of the Issuer's Common Stock issued and outstanding, including all of the shares of Common Stock owned by the Reporting Persons, was converted into the right to receive (i) $8.00 per share of Common Stock in cash, without interest plus (ii) one contingent value right, representing the right to receive $2.00 payable in cash, conditioned upon satisfaction of a certain clinical milestone. As of the date hereof, the Reporting Persons no longer beneficially owns any securities of the Issuer or any percentage of the Issuer's outstanding Common Stock. As of the date hereof, the Reporting Persons no longer beneficially owns any securities of the Issuer. Except as descried herein, none of the Reporting Persons have purchased or sold any shares of Common Stock during the past 60 days. No other person is known to have the right to receive or the power to direct the receipt of dividends from, or any proceeds from the sale of, the shares of Common Stock beneficially owned by any of the Reporting Persons. The Reporting Persons ceased to be the beneficial owners of more than five percent of the Common Stock on August 5, 2025 by virtue of the closing of the Merger. Exhibit 99.1 - Joint Filing Agreement Atlas Venture Fund XII, L.P. /s/ Ommer Chohan 08/07/2025 Atlas Venture Associates XII, L.P. /s/ Ommer Chohan 08/07/2025 Atlas Venture Associates XII, LLC /s/ Ommer Chohan 08/07/2025 Atlas Venture Opportunity Fund I, L.P. /s/ Ommer Chohan 08/07/2025 Atlas Venture Associates Opportunity I, L.P. /s/ Ommer Chohan 08/07/2025 Atlas Venture Associates Opportunity I, LLC /s/ Ommer Chohan 08/07/2025