ANRO / Alto Neuroscience, Inc. - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

Asset Purchase Agreement, dated as of May 31, 2025, by and between the Registrant and Chase Therapeutics Corporation

Exhibit 10.1 CERTAIN INFORMATION HAS BEEN EXCLUDED FROM THIS AGREEMENT (INDICATED BY “[***]”) BECAUSE SUCH INFORMATION IS BOTH (A) NOT MATERIAL AND (B) IS THE TYPE THAT THE REGISTRANT CUSTOMARILY AND ACTUALLY TREATS AS PRIVATE OR CONFIDENTIAL. ASSET PURCHASE AGREEMENT by and between ALTO NEUROSCIENCE, INC. and CHASE THERAPEUTICS CORPORATION Dated as of May 31, 2025 ASSET PURCHASE AGREEMENT This As

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2025 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission file number 0

Alto Neuroscience Reports Second Quarter 2025 Financial Results and Recent Business Highlights – Acquisition of potentially best-in-class dopamine agonist combination product candidates, including ALTO-207, expands precision psychiatry pipeline; guid

Exhibit 99.1 Alto Neuroscience Reports Second Quarter 2025 Financial Results and Recent Business Highlights – Acquisition of potentially best-in-class dopamine agonist combination product candidates, including ALTO-207, expands precision psychiatry pipeline; guided by compelling PAX-D study results published in The Lancet Psychiatry – – ALTO-207 adds expected late-stage readout in treatment resist

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 12, 2025 ALTO NEUROSCIENCE

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 12, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 3, 2025 ALTO NEUROSCIENCE, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 3, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission Fi

Alto Neuroscience Identifies Biomarker and Reports Positive Pharmacodynamic Results from Exploratory Phase 2 Proof-of-Concept Trial of ALTO-203 – Demonstrated target engagement and response prediction for ALTO-203 by theta/beta ratio, a commonly used

Exhibit 99.1 Alto Neuroscience Identifies Biomarker and Reports Positive Pharmacodynamic Results from Exploratory Phase 2 Proof-of-Concept Trial of ALTO-203 – Demonstrated target engagement and response prediction for ALTO-203 by theta/beta ratio, a commonly used EEG index of cortical arousal and attentional control – – ALTO-203, a non-stimulant compound which demonstrated pro-cognitive and wake-p

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 26, 2025 ALTO NEUROSCIENCE,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 26, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission F

Entry into a Material Definitive Agreement, Unregistered Sales of Equity Securities, Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 31, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission Fi

Alto Neuroscience Announces Acquisition of Novel Dopamine Agonist Combination Product Candidate, Adding Late-Stage Readout in Treatment Resistant Depression Within Current Cash Runway – ALTO-207 (fka CTC-501) is a fixed-dose combination of pramipexol

Exhibit 99.1 Alto Neuroscience Announces Acquisition of Novel Dopamine Agonist Combination Product Candidate, Adding Late-Stage Readout in Treatment Resistant Depression Within Current Cash Runway – ALTO-207 (fka CTC-501) is a fixed-dose combination of pramipexole and ondansetron designed to induce rapid antidepressant effects while mitigating dose-limiting adverse events of pramipexole – – Alto h

Financial Statements and Exhibits, Results of Operations and Financial Condition, Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 13, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2025 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission file number

Alto Neuroscience Reports First Quarter 2025 Financial Results and Recent Business Highlights – Phase 2 proof-of-concept trials remain on track: Topline data expected from ALTO-203 in MDD in the second quarter of 2025 followed by ALTO-101 in schizoph

Exhibit 99.1 Alto Neuroscience Reports First Quarter 2025 Financial Results and Recent Business Highlights – Phase 2 proof-of-concept trials remain on track: Topline data expected from ALTO-203 in MDD in the second quarter of 2025 followed by ALTO-101 in schizophrenia in the second half of 2025 – – Late-stage programs advancing: Topline data expected from the Phase 2b trial of ALTO-300 in MDD in m

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. 1)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. 1) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.)

DEFA14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.) Filed by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number 001-419

Non-Employee Director Compensation Policy

Exhibit 10.9 ALTO NEUROSCIENCE, INC. NON-EMPLOYEE DIRECTOR COMPENSATION POLICY ADOPTED: JANUARY 16, 2024 AMENDED: MARCH 17, 2025 (i) Each member of the Board of Directors (the “Board”) of Alto Neuroscience, Inc. (the “Company”) who is not also serving as an employee of or consultant to the Company or any of its subsidiaries (each such member, an “Eligible Director”) will receive the compensation d

2025 Inducement Plan.

Exhibit 99.5 ALTO NEUROSCIENCE, INC. 2025 INDUCEMENT PLAN ADOPTED BY THE BOARD OF DIRECTORS: FEBRUARY 6, 2025 1. GENERAL. (a) Eligible Award Recipients. The only persons eligible to receive grants of Awards under this Plan are individuals who satisfy the standards for “employment inducement awards” under NYSE Listed Company Manual Section 303A.08. A person who previously served as an Employee or D

Power of Attorney. Reference is made to the signature page hereto.

As filed with the Securities and Exchange Commission on March 20, 2025 Registration No.

Alto Neuroscience Reports Full-Year 2024 Financial Results and Recent Business Highlights – Favorable outcome from interim analysis of ongoing ALTO-300 Phase 2b MDD trial; topline results expected in mid-2026 – – Completed enrollment in ALTO-203 Phas

Exhibit 99.1 Alto Neuroscience Reports Full-Year 2024 Financial Results and Recent Business Highlights – Favorable outcome from interim analysis of ongoing ALTO-300 Phase 2b MDD trial; topline results expected in mid-2026 – – Completed enrollment in ALTO-203 Phase 2 proof-of-concept MDD trial; on track to report topline data in the second quarter of 2025 – – Novel transdermal formulation of ALTO-1

Description of Securities

Exhibit 4.5 DESCRIPTION OF SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following description of the common stock of Alto Neuroscience, Inc., or the Company, and certain provisions of the Company’s amended and restated certificate of incorporation, or the restated certificate, and amended and restated bylaws, or restated bylaws, are summaries. These summa

2025 Inducement Plan

Exhibit 10.6 Alto Neuroscience, Inc. 2025 Inducement Plan Adopted by the Board of Directors: February 6, 2025 1.GENERAL. (a)Eligible Award Recipients. The only persons eligible to receive grants of Awards under this Plan are individuals who satisfy the standards for “employment inducement awards” under NYSE Listed Company Manual Section 303A.08. A person who previously served as an Employee or Dir

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 17, 2025 ALTO NEUROSCIENCE,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 17, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission

Insider Trading Policy

Exhibit 19.1 Alto Neuroscience, Inc. Insider Trading Policy (adopted February 1, 2024) Introduction During the course of your relationship with Alto Neuroscience, Inc. (“Alto”), you may receive material information that is not yet publicly available (“material nonpublic information”) about Alto or other publicly traded companies. Material nonpublic information may give you, or someone you pass tha

Form of Stock Option Grant Notice, Option Agreement, and Notice of Exercise under the 2025 Inducement Plan.

Exhibit 99.6 ALTO NEUROSCIENCE, INC. STOCK OPTION GRANT NOTICE (2025 INDUCEMENT PLAN) Alto Neuroscience, Inc. (the “Company”), pursuant to its 2025 Inducement Plan (the “Plan”), has granted to you (“Optionholder”) an option to purchase the number of shares of the Common Stock set forth below (the “Option”). The Option is granted in compliance with NYSE Listed Company Manual Section 303A.08 as a ma

Subsidiaries of the Registrant

Exhibit 21.1 Subsidiaries of Alto Neuroscience, Inc. Name of Subsidiary Jurisdiction of Incorporation Alto Neuroscience (Australia) Pty Ltd Australia

Form of Option Grant Notice and Agreement, and Exercise Notice under the 2025 Inducement Plan

Exhibit 10.7 ALTO NEUROSCIENCE, INC. STOCK OPTION GRANT NOTICE (2025 INDUCEMENT PLAN) Alto Neuroscience, Inc. (the “Company”), pursuant to its 2025 Inducement Plan (the “Plan”), has granted to you (“Optionholder”) an option to purchase the number of shares of the Common Stock set forth below (the “Option”). The Option is granted in compliance with NYSE Listed Company Manual Section 303A.08 as a ma

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Form S-8 (Form Type) Alto Neuroscience, Inc.

JOINT FILING AGREEMENT

EXHIBIT 99.1 JOINT FILING AGREEMENT This Joint Filing Agreement, dated as of February 14, 2025, is by and among RA Capital Management, L.P., Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the foregoing are collectively referred to herein as the “Filers”). Each of the Filers may be required to file with the United States Securities and Exchange Commission a statement on Schedu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 12, 2025 ALTO NEUROSCIEN

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 12, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commissi

Alto Neuroscience Announces Favorable Outcome from Interim Analysis of ALTO-300 Phase 2b Major Depressive Disorder Trial – Interim analysis resulted in a recommendation to continue the study with a total targeted biomarker population of ~200 patients

Exhibit 99.1 Alto Neuroscience Announces Favorable Outcome from Interim Analysis of ALTO-300 Phase 2b Major Depressive Disorder Trial – Interim analysis resulted in a recommendation to continue the study with a total targeted biomarker population of ~200 patients in the final analysis sample – – Topline results are expected in mid-2026 – – The company recently reported an estimated preliminary 202

ALTO NEUROSCIENCE, INC. 650 Castro Street, Suite 450 Mountain View, California 94041

ALTO NEUROSCIENCE, INC. 650 Castro Street, Suite 450 Mountain View, California 94041 February 7, 2025 Via EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attn: Daniel Crawford Re: Alto Neuroscience, Inc. Registration Statement on Form S-3 (File No. 333-284667) Request for Acceleration of Effective Date Daniel Crawford: In acco

Form of Common Stock Warrant Agreement and Warrant Certificate

Exhibit 4.8 ALTO NEUROSCIENCE, INC. AND , AS WARRANT AGENT FORM OF COMMON STOCK WARRANT AGREEMENT DATED AS OF ALTO NEUROSCIENCE, INC. FORM OF COMMON STOCK WARRANT AGREEMENT THIS COMMON STOCK WARRANT AGREEMENT (this “Agreement”), dated as of [•], between ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), and [•], a [corporation] [national banking association] organized and existing un

Sales Agreement, dated as of February 3, 2025, by and between the Company and Leerink Partners LLC (incorporated by reference to Exhibit 1.2 of the Company’s Registration Statement on Form S-3 filed on February 3, 2025).

Exhibit 1.2 Alto Neuroscience, Inc. Shares of Common Stock ($0.0001 par value per share) SALES AGREEMENT February 3, 2025 LEERINK PARTNERS LLC 1301 Avenue of the Americas, 5th Floor New York, New York 10019 Ladies and Gentlemen: Alto Neuroscience, Inc., a Delaware corporation (the “Company”), confirms its agreement (this “Agreement”) with Leerink Partners LLC (the “Agent”), as follows: 1. Issuance

Form of Preferred Stock Warrant Agreement and Warrant Certificate

Exhibit 4.9 ALTO NEUROSCIENCE, INC. AND , AS WARRANT AGENT FORM OF PREFERRED STOCK WARRANT AGREEMENT DATED AS OF ALTO NEUROSCIENCE, INC. FORM OF PREFERRED STOCK WARRANT AGREEMENT THIS PREFERRED STOCK WARRANT AGREEMENT (this “Agreement”), dated as of [•], between ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), and [•], a [corporation] [national banking association] organized and ex

Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) ALTO NEUROSCIENCE, INC.

Form of Debt Indenture

EX-4.6 Exhibit 4.6 ALTO NEUROSCIENCE, INC., Issuer AND [TRUSTEE], Trustee INDENTURE Dated as of [•], 20 Debt Securities TABLE OF CONTENTS PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 5 Section 2.01 Designation and Terms of Securities 5 Section 2.02 Form of Securities and Trustee’s Certificat

Form of Debt Securities Warrant Agreement and Warrant Certificate

EX-4.10 Exhibit 4.10 ALTO NEUROSCIENCE, INC. AND , AS WARRANT AGENT FORM OF DEBT SECURITIES WARRANT AGREEMENT DATED AS OF ALTO NEUROSCIENCE, INC. FORM OF DEBT SECURITIES WARRANT AGREEMENT THIS DEBT SECURITIES WARRANT AGREEMENT (this “Agreement”), dated as of [•], between ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), and [•], a [corporation] [national banking association] organiz

Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 3, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commissio

As filed with the Securities and Exchange Commission on February 3, 2025

S-3 Table of Contents As filed with the Securities and Exchange Commission on February 3, 2025 Registration No.

First Amendment to Loan and Security Agreement, by and among the Registrant, K2 HealthVentures LLC, as lender, K2 HealthVentures LLC, as administrative agent for the Lender, and Ankura Trust Company, LLC, as collateral trustee for the Lender, dated as of January 13, 2025

Exhibit 10.1 FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT This FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”) is entered into as of January 13, 2025 (the “Restatement Effective Date”), by and among ALTO NEUROSCIENCE, INC., a Delaware corporation (“Borrower Representative”), each other Person party hereto as a borrower from time to time (together with Borrower Representative, c

Warrant to Purchase Stock, dated January 13, 2025, issued to K2 HealthVentures Equity Trust LLC

Exhibit 4.2 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE U.S. SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY U.S. STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR, IN THE OPINION OF LEGAL COUNSEL IN FORM A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 13, 2025 ALTO NEUROSCIENC

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 13, 2025 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commissio

Amended and Restated Warrant to Purchase Stock, dated January 13, 2025, issued to K2 HealthVentures Equity Trust LLC

Exhibit 4.1 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE U.S. SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY U.S. STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR, IN THE OPINION OF LEGAL COUNSEL IN FORM A

ANRO / Alto Neuroscience, Inc. / RA CAPITAL MANAGEMENT, L.P. - SC 13G/A Passive Investment

SC 13G/A 1 tm2427451d9sc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 1)* Alto Neuroscience, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 02157Q109 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of this Stateme

ANRO / Alto Neuroscience, Inc. / Etkin Amit - SC 13G Passive Investment

SC 13G 1 d873145dsc13g.htm SC 13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO §240.13d-1(b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO §240.13d-2 (Amendment No.  )* Alto Neuroscience, Inc. (Name of Issuer) Common Stock, $0.0001 par value per share (Title of Class of Securit

Joint Filing Agreement

EX-99.1 2 tm2427451d9ex1.htm EXHIBIT 1 EXHIBIT 1 AGREEMENT This Joint Filing Agreement, dated as of November 14, 2024 is by and among RA Capital Management, L.P., Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the foregoing are collectively referred to herein as the “Filers”). Each of the Filers may be required to file with the United States Securities and Exchange Commission

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 12, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2024 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission file num

Alto Neuroscience Reports Third Quarter 2024 Financial Results and Recent Business Highlights – Topline data from two MDD trials expected in the first half of 2025: Phase 2b trial of ALTO-300 as an adjunctive treatment and Phase 2a trial of ALTO-203

Exhibit 99.1 Alto Neuroscience Reports Third Quarter 2024 Financial Results and Recent Business Highlights – Topline data from two MDD trials expected in the first half of 2025: Phase 2b trial of ALTO-300 as an adjunctive treatment and Phase 2a trial of ALTO-203 in patients with anhedonia – – Additional Phase 2 studies ongoing: ALTO-101 in schizophrenia and ALTO-100 as an adjunctive treatment in b

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 22, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commissio

Alto Neuroscience Reports Topline Results from a Phase 2b Trial Evaluating ALTO-100 as a Treatment for Major Depressive Disorder – Treatment with ALTO-100 did not demonstrate improvement in depressive symptoms compared to placebo in patients with a m

Exhibit 99.1 Alto Neuroscience Reports Topline Results from a Phase 2b Trial Evaluating ALTO-100 as a Treatment for Major Depressive Disorder – Treatment with ALTO-100 did not demonstrate improvement in depressive symptoms compared to placebo in patients with a memory-based cognitive biomarker – – ALTO-100 demonstrated a favorable safety and tolerability profile, consistent with previously reporte

Alto Neuroscience Reports Second Quarter 2024 Financial Results and Recent Business Highlights – Completed enrollment of 301 patients in Phase 2b MDD study for ALTO-100; Investor Day focused on ALTO-100 planned for September 9, 2024; topline data exp

Exhibit 99.1 Alto Neuroscience Reports Second Quarter 2024 Financial Results and Recent Business Highlights – Completed enrollment of 301 patients in Phase 2b MDD study for ALTO-100; Investor Day focused on ALTO-100 planned for September 9, 2024; topline data expected in October 2024 – – Initiated multiple Phase 2 studies: ALTO-101 in schizophrenia, ALTO-203 in MDD with anhedonia, and ALTO-100 in

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 13, 2024 ALTO NEUROSCIENCE

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 13, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2024 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission file number 0

Convertible Loan Agreement, by and between the Registrant and The Wellcome Trust Limited, dated as of July 24, 2024.

EXHIBIT 10.1 EXECUTION VERSION (1) THE WELLCOME TRUST LIMITED (2) ALTO NEUROSCIENCE, INC. CONVERTIBLE LOAN AGREEMENT AWARD NUMBER 306439/Z/23/Z CONTENTS 1 INTERPRETATION 4 2 LOAN TO BE ADVANCED BY WELLCOME 14 3 INTEREST 16 4 CONVERSION OR REPAYMENT OPTION 17 5 WARRANTIES 19 6 LIMITS ON LIABILITY 20 7 AUDIT 21 8 TERMINATION 22 9 EVENTS OF DEFAULT 22 10 OBLIGATIONS OF THE COMPANY 24 11 PROJECT REPOR

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 24, 2024 ALTO NEUROSCIENCE,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 24, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission F

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 21, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2024 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission file number

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission Fi

Alto Neuroscience Reports First Quarter 2024 Financial Results and Recent Business Highlights – Initiated Phase 2 study of ALTO-203 in patients with MDD and anhedonia-– – Reported positive Phase 1 data with transdermal formulation of novel PDE4 inhib

Exhibit 99.1 Alto Neuroscience Reports First Quarter 2024 Financial Results and Recent Business Highlights – Initiated Phase 2 study of ALTO-203 in patients with MDD and anhedonia-– – Reported positive Phase 1 data with transdermal formulation of novel PDE4 inhibitor, ALTO-101; achieved significantly greater drug exposure with improved tolerability compared to oral administration – – Patient enrol

ANRO / Alto Neuroscience, Inc. / RA CAPITAL MANAGEMENT, L.P. - SC 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Alto Neuroscience, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 02157Q109 (CUSIP Number) March 19, 2024 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the ru

Description of Securities

Exhibit 4.4 DESCRIPTION OF SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following description of the common stock of Alto Neuroscience, Inc., or the Company, and certain provisions of the Company’s amended and restated certificate of incorporation, or the restated certificate, and amended and restated bylaws, or restated bylaws, are summaries. These summa

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 21, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission

Incentive Compensation Recoupment Policy

Exhibit 97 ALTO NEUROSCIENCE, INC. Incentive Compensation Recoupment Policy 1.Introduction The Board of Directors (the “Board”) of Alto Neuroscience, Inc., a Delaware corporation (the “Company”), has determined that it is in the best interests of the Company and its stockholders to adopt this Incentive Compensation Recoupment Policy (this “Policy”) providing for the Company’s recoupment of Recover

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 OR o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number 001-419

Alto Neuroscience Reports Full Year 2023 Financial Results and Recent Business Highlights – Reported positive results from ALTO-100 and ALTO-300 Phase 2a studies demonstrating prospective replication of response prediction using Alto’s Precision Psyc

Exhibit 99.1 Alto Neuroscience Reports Full Year 2023 Financial Results and Recent Business Highlights – Reported positive results from ALTO-100 and ALTO-300 Phase 2a studies demonstrating prospective replication of response prediction using Alto’s Precision Psychiatry Platform™ – – Patient enrollment on track across Phase 2b MDD studies for two lead product candidates – – Successful completion of

Subsidiaries of the Registrant

Exhibit 21.1 Subsidiaries of Alto Neuroscience, Inc. Name of Subsidiary Jurisdiction of Incorporation Alto Neuroscience (Australia) Pty Ltd Australia

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 8, 2024 ALTO NEUROSCIENCE, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-41944 83-4210124 (State or Other Jurisdiction of Incorporation) (Commission F

ANRO / Alto Neuroscience, Inc. / Falcon Edge Capital, LP - ALTO NEUROSCIENCE, INC. Passive Investment

SC 13G 1 p24-0728sc13g.htm ALTO NEUROSCIENCE, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Alto Neuroscience, Inc. (Name of Issuer) Common stock, par value $0.0001 per share (Title of Class of Securities) 02157Q109 (CUSIP Number) February 6, 2024 (Date of Event Which Requires Filing of this Statement) Check

JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k)

EX-99.1 2 p24-0737exhibit99.htm JOINT FILING AGREEMENT EXHIBIT 99.1 JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k) The undersigned acknowledge and agree that the foregoing statement on Schedule 13G is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13G shall be filed on behalf of each of the undersigned without the necessity of filing a

ANRO / Alto Neuroscience, Inc. / Point72 Asset Management, L.P. - ALTO NEUROSCIENCE, INC. Passive Investment

SC 13G 1 p24-0737sc13g.htm ALTO NEUROSCIENCE, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Alto Neuroscience, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 02157Q109 (CUSIP Number) February 6, 2024 (Date of Event Which Requires Filing of this Statement) Check

2024 Equity Incentive Plan.

Exhibit 99.3 ALTO NEUROSCIENCE, INC. 2024 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: JANUARY 23, 2024 APPROVED BY THE STOCKHOLDERS: JANUARY 25, 2024 IPO DATE: FEBRUARY 1, 2024 1. GENERAL. (a) Successor to Prior Plan. The Plan is the successor to the Prior Plan. As of the Effective Date, no additional awards may be granted under the Prior Plan, and all outstanding awards granted under

As filed with the Securities and Exchange Commission on February 6, 2024

As filed with the Securities and Exchange Commission on February 6, 2024 Registration No.

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 6, 2024 Alto Neuroscience, Inc. (Exact name of registrant as specified in its charter) Delaware 001-41944 83-4210124 (State or other jurisdiction of incorporation) (Commissio

Amended and Restated Certificate of Incorporation of the Registrant

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ALTO NEUROSCIENCE, INC. Alto Neuroscience, Inc., a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the “DGCL”), does hereby certify that: ONE: The name of this corporation is Alto Neuroscience, Inc. The date of filing of the original certificate of incorporation of this

Amended and Restated Bylaws of the Registrant

Exhibit 3.2 AMENDED AND RESTATED BYLAWS OF ALTO NEUROSCIENCE, INC. (A DELAWARE CORPORATION) SECTION 1. OFFICES Section 1.1 Registered Office. The registered office of Alto Neuroscience, Inc. (the “Corporation”) in the State of Delaware and the name of the Corporation’s registered agent at such address shall be as set forth in the certificate of incorporation of the Corporation (as the same may be

2024 Employee Stock Purchase Plan.

Exhibit 99.6 ALTO NEUROSCIENCE, INC. 2024 EMPLOYEE STOCK PURCHASE PLAN ADOPTED BY THE BOARD OF DIRECTORS: JANUARY 23, 2024 APPROVED BY THE STOCKHOLDERS: JANUARY 25, 2024 IPO DATE: FEBRUARY 1, 2024 1. GENERAL; PURPOSE. (a) The Plan provides a means by which Eligible Employees of the Company and certain Designated Companies may be given an opportunity to purchase shares of Common Stock. The Plan per

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Form S-8 (Form Type) ALTO NEUROSCIENCE, INC.

8,040,000 Shares Common Stock

Table of Contents Filed pursuant to Rule 424(b)(4) Registration Nos. 333-276495 and 333-276828 8,040,000 Shares Common Stock We are offering 8,040,000 shares of our common stock. This is our initial public offering, and prior to this offering there has been no public market for our common stock. The initial public offering price is $16.00 per share. Our common stock has been approved for listing o

As filed with the Securities and Exchange Commission on February 1, 2024.

As filed with the Securities and Exchange Commission on February 1, 2024. Registration No. 333-      UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Alto Neuroscience, Inc. (Exact name of registrant as specified in its charter) Delaware 2834 83-4210124 (State or other jurisdiction of incorporation or organizat

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Tables Form S-1 (Form Type) Alto Neuroscience, Inc.

[Signature Page Follows]

January 30, 2024 VIA EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Lauren Hamill, Tim Buchmiller, Li Xiao, Mary Mast Re: Alto Neuroscience, Inc. Registration Statement on Form S-1, as amended File No. 333-276495 Acceleration Request Requested Date: Thursday, February 1, 2024 Requested Time: 4:30

Alto Neuroscience, Inc. 369 South San Antonio Road Los Altos, CA 94022

Alto Neuroscience, Inc. 369 South San Antonio Road Los Altos, CA 94022 January 30, 2024 VIA EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Lauren Hamill, Tim Buchmiller, Li Xiao, Mary Mast Re: Alto Neuroscience, Inc. Registration Statement on Form S-1, as amended (File No. 333-276495) Request for

Form 8-A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-A FOR REGISTRATION OF CERTAIN CLASSES OF SECURITIES PURSUANT TO SECTION 12(b) OR (g) OF THE SECURITIES EXCHANGE ACT OF 1934 Alto Neuroscience, Inc. (Exact name of registrant as specified in its charter) Delaware 83-4210124 (State or other jurisdiction of incorporation or organization) (I.R.S. Employer Identification No.

Consent of Husseini Manji, M.D. as director nominee

Exhibit 99.1 CONSENT OF DIRECTOR NOMINEE Pursuant to Rule 438 of Regulation C promulgated under the Securities Act of 1933, as amended (the "Securities Act"), in connection with the Registration Statement on Form S-1 (the "Registration Statement") of Alto Neuroscience, Inc., the undersigned hereby consents to being named and described as a person who will become a director of Alto Neuroscience, In

2024 Equity Incentive Plan

Exhibit 10.3 ALTO NEUROSCIENCE, INC. 2024 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: JANUARY 23, 2024 APPROVED BY THE STOCKHOLDERS: JANUARY 25, 2024 IPO DATE: [] 1. GENERAL. (a) Successor to Prior Plan. The Plan is the successor to the Prior Plan. As of the Effective Date, no additional awards may be granted under the Prior Plan, and all outstanding awards granted under the Prior Pla

2024 Employee Stock Purchase Plan

Exhibit 10.6 ALTO NEUROSCIENCE, INC. 2024 EMPLOYEE STOCK PURCHASE PLAN ADOPTED BY THE BOARD OF DIRECTORS: JANUARY 23, 2024 APPROVED BY THE STOCKHOLDERS: JANUARY 25, 2024 IPO DATE: [] 1. GENERAL; PURPOSE. (a) The Plan provides a means by which Eligible Employees of the Company and certain Designated Companies may be given an opportunity to purchase shares of Common Stock. The Plan permits the Compa

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-1 Alto Neuroscience, Inc. Table 1: Newly Registered Securities Security  Type  Security Class Title Fee  Calculation  or Carry  Forward  Rule  Amount  Registered(1)  Proposed  Maximum  Offering  Price Per  Unit(2)  Maximum Aggregate Offering Price(3) Fee Rate Amount of Registration Fee(4) Fees to Be Paid  Equity  Common Stock,  par value  $0.0001

As filed with the Securities and Exchange Commission on January 29, 2024.

S-1/A Table of Contents As filed with the Securities and Exchange Commission on January 29, 2024.

Form of Underwriting Agreement

Exhibit 1.1 [•] Alto Neuroscience, Inc. UNDERWRITING AGREEMENT [Date], 2024 JEFFERIES LLC COWEN AND COMPANY, LLC STIFEL, NICOLAUS & COMPANY, INCORPORATED As Representatives of the several Underwriters c/o JEFFERIES LLC 520 Madison Avenue New York, New York 10022 c/o COWEN AND COMPANY, LLC 599 Lexington Avenue New York, NY 10022 c/o STIFEL, NICOLAUS & COMPANY, INCORPORATED 787 7th Avenue, 11th Floo

As filed with the Securities and Exchange Commission on January 29, 2024.

S-1/A As filed with the Securities and Exchange Commission on January 29, 2024. Registration No. 333-276495 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Amendment No. 2 to FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Alto Neuroscience, Inc. (Exact Name of Registrant as Specified in Its Charter) Delaware 2834 83-4210124 (State or Other Jurisdiction of

Form of RSU Award Grant Notice and Agreement under the 2024 Equity Incentive Plan

Exhibit 10.5 ALTO NEUROSCIENCE, INC. RSU AWARD GRANT NOTICE (2024 EQUITY INCENTIVE PLAN) Alto Neuroscience, Inc. (the “Company”) has awarded to you (the “Participant”) the number of restricted stock units specified and on the terms set forth below in consideration of your services (the “RSU Award”). Your RSU Award is subject to all of the terms and conditions as set forth herein and in the Company

Form of Option Grant Notice and Agreement, and Exercise Notice under the 2024 Equity Incentive Plan

Exhibit 10.4 ALTO NEUROSCIENCE, INC. STOCK OPTION GRANT NOTICE (2024 EQUITY INCENTIVE PLAN) Alto Neuroscience, Inc. (the “Company”), pursuant to its 2024 Equity Incentive Plan (the “Plan”), has granted to you (“Optionholder”) an option to purchase the number of shares of the Common Stock set forth below (the “Option”). Your Option is subject to all of the terms and conditions as set forth herein a

Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant (as currently in effect)

Exhibit 3.5 CERTIFICATE OF AMENDMENT TO AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ALTO NEUROSCIENCE, INC. Alto Neuroscience, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the “General Corporation Law”), does hereby certify that: FIRST: The name of the Corporation is Alto Neuroscience, Inc. The

Form of Amended and Restated Bylaws of the Registrant, to be effective immediately prior to the closing of this offering

Exhibit 3.4 AMENDED AND RESTATED BYLAWS OF ALTO NEUROSCIENCE, INC. (A DELAWARE CORPORATION) SECTION 1. OFFICES Section 1.1 Registered Office. The registered office of Alto Neuroscience, Inc. (the “Corporation”) in the State of Delaware and the name of the Corporation’s registered agent at such address shall be as set forth in the certificate of incorporation of the Corporation (as the same may be

Form of Common Stock Certificate

Exhibit 4.1 INCORPORATED UNDER THE CUSIP 02157Q 10 9 LAWS OF THE STATE SEE REVERSE FOR CERTAIN OF DELAWARE DEFINITIONS AND LEGENDS This certifies that BY: COUNTERSIGNED is the record holder ofAND EQUINITI FULLY PAID AND NONASSESSABLE SHARES OF COMMON STOCK, $0.0001 PAR VALUE PER SHARE, OF ALTO NEUROSCIENCE, INC. TRUST transferable on the books of the Corporation in person or by duly authorized att

Form of Indemnification Agreement between the Registrant and each of its directors and executive officers

Exhibit 10.7 ALTO NEUROSCIENCE, INC. INDEMNIFICATION AGREEMENT THIS INDEMNIFICATION AGREEMENT (this “Agreement”) dated as of      , 20  , is made by and between ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), and        (“Indemnitee”). RECITALS A. The Company desires to attract and retain the services of highly qualified individuals as directors, officers, and employees, and agent

Form of Amendment to Employment Offer Letter

Exhibit 10.9 [Date] [Name] [Address] Re: Amendment to Employment Terms Dear [Name]: Alto Neuroscience, Inc. (the “Company”) is pleased to provide you with this amendment to certain employment terms contained in your employee offer letter (“Offer Letter Amendment”). This Offer Letter Amendment amends in part the offer of employment executed between you and the Company on [Month Day], 2023 (the “Pri

Form of Amended and Restated Certificate of Incorporation of the Registrant, to be effective immediately prior to the closing of this offering

Exhibit 3.2 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ALTO NEUROSCIENCE, INC. Alto Neuroscience, Inc., a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the “DGCL”), does hereby certify that: ONE: The name of this corporation is Alto Neuroscience, Inc. The date of filing of the original certificate of incorporation of this

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Divakar Gupta +1 212 479 6474 [email protected] VIA EDGAR January 25, 2024 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Lauren Hamill Tim Buchmiller Li Xiao Mary Mast Re: Alto Neuroscience, Inc. Correspondence filed January 19, 2024 File No. 333-276495 Ladies and Gentlemen: On behalf of Alto Neurosci

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Divakar Gupta +1 212 479 6474 [email protected] VIA EDGAR January 24, 2024 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Lauren Hamill Tim Buchmiller Li Xiao Mary Mast Re: Alto Neuroscience, Inc. Correspondence filed January 19, 2024 File No. 333-276495 Ladies and Gentlemen: On behalf of Alto Neurosci

*FOIA Confidential Treatment Request* Confidential Treatment Requested by Alto Neuroscience, Inc. in connection with its Registration Statement on Form S-1 (File No. 333-276495)

Divakar Gupta +1 212 479 6474 [email protected] VIA EDGAR *FOIA Confidential Treatment Request* Confidential Treatment Requested by Alto Neuroscience, Inc. in connection with its Registration Statement on Form S-1 (File No. 333-276495) January 19, 2024 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Lau

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Divakar Gupta T: (212) 479-6474 [email protected] Via EDGAR January 12, 2024 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attention: Lauren Hamill Tim Buchmiller Li Xiao Mary Mast Re: Alto Neuroscience, Inc. Amendment No. 1 to Draft Registration Statement on Form S-1 Submitted December 28, 2023 CIK No. 000

Amended and Restated Bylaws of the Registrant, as currently in effect

Exhibit 3.3 BYLAWS OF ALTO NEUROSCIENCE, INC. Adopted March 25, 2019 TABLE OF CONTENTS Page ARTICLE I — MEETINGS OF STOCKHOLDERS 1 1.1 Place of Meetings 1 1.2 Annual Meeting 1 1.3 Special Meeting 1 1.4 Notice of Stockholders’ Meetings 1 1.5 Quorum 2 1.6 Adjourned Meeting; Notice 2 1.7 Conduct of Business 2 1.8 Voting 2 1.9 Stockholder Action by Written Consent Without a Meeting 3 1.10 Record Dates

License Agreement, by and between the Registrant and Sanofi, dated as of May 18, 2021

Exhibit 10.11 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. LICENSE AGREEMENT between SANOFI and ALTO NEUROSCIENCE, INC. Dated as of May 18, 2021 LICENSE AGREEMENT This License Agreement (this “Agreement”) is made a

Assignment and Assumption Agreement, by and between the Registrant and Palisade Bio, Inc. (formerly Seneca Biopharma, Inc., formerly Neuralstem Inc.), dated as of October 18, 2021

Exhibit 10.15 ASSIGNMENT AND ASSUMPTION AGREEMENT This ASSIGNMENT AND ASSUMPTION AGREEMENT (the “Agreement”), is dated as of October 18, 2021 (“Agreement Date”), by and between Palisade Bio, Inc., a Delaware corporation formerly known as Neuralstem Inc. (“Assignor”) and Alto Neuroscience, Inc., a Delaware corporation (the “Assignee”). WHEREAS Assignor and Assignee are parties to that certain Asset

Form of Option Grant Notice and Agreement, Exercise Notice, Early Exercise Notice, and Restricted Award Notice under the 2019 Equity Incentive Plan

Exhibit 10.2 ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN STOCK OPTION AGREEMENT Unless otherwise defined herein, the terms defined in the 2019 Equity Incentive Plan (the “Plan”) shall have the same defined meanings in this Stock Option Agreement (the “Option Agreement”). I.   NOTICE OF STOCK OPTION GRANT Name: Address: The undersigned Participant has been granted an Option to purchase Commo

Patent and Know-How License Agreement, by and between the Registrant and Cerecor Inc. (k/n/a Avalo Therapeutics, Inc.), dated as of May 28, 2021

Exhibit 10.12 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. PATENT AND KNOW-HOW LICENSE AGREEMENT by and between CERECOR INC. and ALTO NEUROSCIENCE, INC. 1 PATENT AND KNOW-HOW LICENSE AGREEMENT THIS PATENT AND KNOW-

Amended and Restated Certificate of Incorporation of the Registrant, as currently in effect

Exhibit 3.1 Execution Version AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ALTO NEUROSCIENCE, INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) ALTO NEUROSCIENCE, INC., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “General Corporation Law”), DOES HEREBY C

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Table Form S-1 Alto Neuroscience, Inc. Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price(1)(2) Fee Rate Amount of Registration Fee Fees to Be Paid Equity Common Stock, par value $0.0001 per share 457(o) — — $10

Amended and Restated Investor Rights Agreement, by and among the Registrant and certain of its stockholders, dated as of November 20, 2023

Exhibit 4.2 Execution Version ALTO NEUROSCIENCE, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT THIS AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT (this “Agreement”), is made as of November 20, 2023, by and among ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), each of the investors listed on Schedule A hereto, each of which is referred to in this Agreement as an “Investo

Form of Employment Offer Letter for executive officers

Exhibit 10.8 [Date] [Name] [Address] Re: Offer of Employment Dear [Name]: You are currently employed by Alto Neuroscience, Inc. (the “Company”) in the position of [POSITION] (“[abbreviated title]”) with an original start date of [INSERT]. Your employment is subject to the terms and conditions set forth in this letter agreement (the “Agreement”). Certain terms set forth herein are defined in Sectio

Subsidiaries of the Registrant

Exhibit 21.1 Subsidiaries of Alto Neuroscience, Inc. Name of Subsidiary Jurisdiction of Incorporation Alto Neuroscience (Australia) Pty Ltd Australia

As filed with the Securities and Exchange Commission on January 12, 2024.

S-1 Table of Contents As filed with the Securities and Exchange Commission on January 12, 2024.

Asset Transfer Agreement, by and between the Registrant and Palisade Bio, Inc. (formerly Seneca Biopharma, Inc., formerly Neuralstem Inc.), dated as of October 18, 2021

Exhibit 10.14 ASSET TRANSFER AGREEMENT This ASSET TRANSFER AGREEMENT (this “Agreement”) is entered into as of October 18, 2021 (the “Agreement Date”), by and between Alto Neuroscience, Inc., a Delaware corporation (“Buyer”), and Palisade Bio, Inc. (formerly Seneca Biopharma, Inc.), a Delaware corporation (“Seller”) (Buyer and Seller are each referred to herein as a “Party” and together as the “Par

Exclusive License Agreement, by and between Dow Agrosciences LLC and Neuralstem, Inc., dated as of December 1, 2016.

Exhibit 10.13 CERTAIN INFORMATION HAS BEEN EXCLUDED FROM THIS AGREEMENT (INDICATED BY “[***]”) BECAUSE SUCH INFORMATION IS BOTH (A) NOT MATERIAL AND (B) IS THE TYPE THAT THE REGISTRANT CUSTOMARILY AND ACTUALLY TREATS AS PRIVATE OR CONFIDENTIAL. EXCLUSIVE LICENSE AGREEMENT BY AND BETWEEN DOW AGROSCIENCES LLC and NEURALSTEM, INC. December 1, 2016 CONFIDENTIAL EXCLUSIVE LICENSE AGREEMENT This EXCLUSI

Warrant to Purchase Preferred Stock, dated December 16, 2022, issued to K2 HealthVentures Equity Trust LLC

Exhibit 4.3 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTAN

Asset Purchase Agreement, by and between the Registrant and Teva Pharmaceutical Industries, Ltd., dated as of October 4, 2021

Exhibit 10.16 CERTAIN INFORMATION HAS BEEN EXCLUDED FROM THIS AGREEMENT (INDICATED BY “[***]”) BECAUSE SUCH INFORMATION IS BOTH (A) NOT MATERIAL AND (B) IS THE TYPE THAT THE REGISTRANT CUSTOMARILY AND ACTUALLY TREATS AS PRIVATE OR CONFIDENTIAL. CONFIDENTIAL FOR EXECUTION ASSET PURCHASE AGREEMENT This Asset Purchase Agreement (this “Agreement”) is made and entered into as of October 4, 2021 (the “E

Joint Development and License Agreement, by and between the Registrant and MedRx Co., Ltd., dated as of September 25, 2023

Exhibit 10.17 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. JOINT DEVELOPMENT AND LICENSE AGREEMENT This JOINT DEVELOPMENT AND LICENSE AGREEMENT (this “Agreement”) is made and entered into as of September 25, 2023 (

Loan and Security Agreement, by and among the Registrant, K2 HealthVentures LLC, as a lender, and the other lenders from time to time party thereto, or collectively the Lender, K2 HealthVentures LLC, as administrative agent for the Lender, and Ankura Trust Company, LLC, as collateral agent for the Lender, dated as of December 16, 2022

Exhibit 10.9 LOAN AND SECURITY AGREEMENT This LOAN AND SECURITY AGREEMENT (as amended, restated, amended and restated, supplemented or otherwise modified from time to time, this “Agreement”) dated as of December 16, 2022 (the “Closing Date”) is entered into among ALTO NEUROSCIENCE, INC., a Delaware corporation (“Borrower Representative”), and each other Person party hereto as a borrower from time

2019 Equity Incentive Plan

Exhibit 10.1 ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN As Amended on November 21, 2020, April 29, 2021, April 4, 2022, November 16, 2023 1. Purposes of the Plan. The purposes of this Plan are: • to attract and retain the best available personnel for positions of substantial responsibility, • to provide additional incentive to Employees, Directors and Consultants, and • to promote the succ

Exclusive License Agreement With Equity, by and between the Registrant and The Board of Trustees of the Leland Stanford Junior University, dated as of December 6, 2019, as amended as of May 18, 2020 and December 11, 2023

Exhibit 10.10 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. EXCLUSIVE LICENSE AGREEMENT WITH EQUITY This Agreement (“Agreement”) between THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY (“Stanford”), a

Cooley LLP 55 Hudson Yards New York, NY 10001 t: +1 212 479 6000 f: +1 212 479 6275 cooley.com

Divakar Gupta T: (212) 479-6474 [email protected] Via EDGAR December 28, 2023 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attention: Lauren Hamill Tim Buchmiller Li Xiao Mary Mast Re: Alto Neuroscience, Inc. Draft Registration Statement on Form S-1 Submitted on November 22, 2023 CIK No. 0001999480 Ladies

AT-WILL EMPLOYMENT, CONFIDENTIAL INFORMATION, INVENTIONS ASSIGNMENT AND ARBITRATION AGREEMENT

Exhibit 10.8 [Date] [Name] [Address] Re: Offer of Employment Dear [Name]: You are currently employed by Alto Neuroscience, Inc. (the “Company”) in the position of [POSITION] (“[abbreviated title]”) with an original start date of [INSERT].1 Your employment is subject to the terms and conditions set forth in this letter agreement (the “Agreement”). Certain terms set forth herein are defined in Secti

EXCLUSIVE LICENSE AGREEMENT BY AND BETWEEN DOW AGROSCIENCES LLC NEURALSTEM, INC. December 1, 2016

Exhibit 10.13 CERTAIN INFORMATION HAS BEEN EXCLUDED FROM THIS AGREEMENT (INDICATED BY “[***]”) BECAUSE SUCH INFORMATION IS BOTH (A) NOT MATERIAL AND (B) IS THE TYPE THAT THE REGISTRANT CUSTOMARILY AND ACTUALLY TREATS AS PRIVATE OR CONFIDENTIAL. EXCLUSIVE LICENSE AGREEMENT BY AND BETWEEN DOW AGROSCIENCES LLC and NEURALSTEM, INC. December 1, 2016 CONFIDENTIAL EXCLUSIVE LICENSE AGREEMENT This EXCLUSI

PATENT AND KNOW-HOW LICENSE AGREEMENT by and between CERECOR INC. ALTO NEUROSCIENCE, INC.

Exhibit 10.12 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. PATENT AND KNOW-HOW LICENSE AGREEMENT by and between CERECOR INC. and ALTO NEUROSCIENCE, INC. 1 PATENT AND KNOW-HOW LICENSE AGREEMENT THIS PATENT AND KNOW-

ASSIGNMENT AND ASSUMPTION AGREEMENT

Exhibit 10.15 ASSIGNMENT AND ASSUMPTION AGREEMENT This ASSIGNMENT AND ASSUMPTION AGREEMENT (the “Agreement”), is dated as of October 18, 2021 (“Agreement Date”), by and between Palisade Bio, Inc., a Delaware corporation formerly known as Neuralstem Inc. (“Assignor”) and Alto Neuroscience, Inc., a Delaware corporation (the “Assignee”). WHEREAS Assignor and Assignee are parties to that certain Asset

As submitted confidentially to the Securities and Exchange Commission on December 28, 2023. This Amendment No. 1 to the draft registration statement has not been publicly filed with the Securities and Exchange Commission and all information herein re

Table of Contents As submitted confidentially to the Securities and Exchange Commission on December 28, 2023.

ASSET TRANSFER AGREEMENT

Exhibit 10.14 ASSET TRANSFER AGREEMENT This ASSET TRANSFER AGREEMENT (this “Agreement”) is entered into as of October 18, 2021 (the “Agreement Date”), by and between Alto Neuroscience, Inc., a Delaware corporation (“Buyer”), and Palisade Bio, Inc. (formerly Seneca Biopharma, Inc.), a Delaware corporation (“Seller”) (Buyer and Seller are each referred to herein as a “Party” and together as the “Par

ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN As Amended on November 21, 2020, April 29, 2021, April 4, 2022, November 16, 2023

Exhibit 10.1 ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN As Amended on November 21, 2020, April 29, 2021, April 4, 2022, November 16, 2023 1. Purposes of the Plan. The purposes of this Plan are: • to attract and retain the best available personnel for positions of substantial responsibility, • to provide additional incentive to Employees, Directors and Consultants, and • to promote the succ

JOINT DEVELOPMENT AND LICENSE AGREEMENT

Exhibit 10.17 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. JOINT DEVELOPMENT AND LICENSE AGREEMENT This JOINT DEVELOPMENT AND LICENSE AGREEMENT (this “Agreement”) is made and entered into as of September 25, 2023 (

ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN STOCK OPTION AGREEMENT

Exhibit 10.2 ALTO NEUROSCIENCE, INC. 2019 EQUITY INCENTIVE PLAN STOCK OPTION AGREEMENT Unless otherwise defined herein, the terms defined in the 2019 Equity Incentive Plan (the “Plan”) shall have the same defined meanings in this Stock Option Agreement (the “Option Agreement”). I.   NOTICE OF STOCK OPTION GRANT Name: Address: The undersigned Participant has been granted an Option to purchase Commo

LICENSE AGREEMENT ALTO NEUROSCIENCE, INC. Dated as of May 18, 2021

Exhibit 10.11 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. LICENSE AGREEMENT between SANOFI and ALTO NEUROSCIENCE, INC. Dated as of May 18, 2021 LICENSE AGREEMENT This License Agreement (this “Agreement”) is made a

EXCLUSIVE LICENSE AGREEMENT WITH EQUITY

Exhibit 10.10 Certain information has been excluded from this agreement (indicated by “[***]”) because such information is both (a) not material and (b) is the type that the registrant customarily and actually treats as private or confidential. EXCLUSIVE LICENSE AGREEMENT WITH EQUITY This Agreement (“Agreement”) between THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY (“Stanford”), a

ASSET PURCHASE AGREEMENT

Exhibit 10.16 CERTAIN INFORMATION HAS BEEN EXCLUDED FROM THIS AGREEMENT (INDICATED BY “[***]”) BECAUSE SUCH INFORMATION IS BOTH (A) NOT MATERIAL AND (B) IS THE TYPE THAT THE REGISTRANT CUSTOMARILY AND ACTUALLY TREATS AS PRIVATE OR CONFIDENTIAL. CONFIDENTIAL FOR EXECUTION ASSET PURCHASE AGREEMENT This Asset Purchase Agreement (this “Agreement”) is made and entered into as of October 4, 2021 (the “E

BYLAWS OF ALTO NEUROSCIENCE, INC. Adopted March 25, 2019

Exhibit 3.3 BYLAWS OF ALTO NEUROSCIENCE, INC. Adopted March 25, 2019 TABLE OF CONTENTS Page ARTICLE I — MEETINGS OF STOCKHOLDERS 1 1.1 Place of Meetings 1 1.2 Annual Meeting 1 1.3 Special Meeting 1 1.4 Notice of Stockholders’ Meetings 1 1.5 Quorum 2 1.6 Adjourned Meeting; Notice 2 1.7 Conduct of Business 2 1.8 Voting 2 1.9 Stockholder Action by Written Consent Without a Meeting 3 1.10 Record Dates

AMENDED AND RESTATED CERTIFICATE OF INCORPORATION ALTO NEUROSCIENCE, INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware)

Exhibit 3.1 Execution Version AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ALTO NEUROSCIENCE, INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) ALTO NEUROSCIENCE, INC., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “General Corporation Law”), DOES HEREBY C

LOAN AND SECURITY AGREEMENT

Exhibit 10.6 LOAN AND SECURITY AGREEMENT This LOAN AND SECURITY AGREEMENT (as amended, restated, amended and restated, supplemented or otherwise modified from time to time, this “Agreement”) dated as of December 16, 2022 (the “Closing Date”) is entered into among ALTO NEUROSCIENCE, INC., a Delaware corporation (“Borrower Representative”), and each other Person party hereto as a borrower from time

As submitted confidentially to the Securities and Exchange Commission on November 22, 2023. This draft registration statement has not been publicly filed with the Securities and Exchange Commission and all information herein remains strictly confiden

Table of Contents As submitted confidentially to the Securities and Exchange Commission on November 22, 2023.

WARRANT TO PURCHASE PREFERRED STOCK Company: Alto Neuroscience, Inc., a Delaware corporation Class of Stock: Series B Preferred Stock, or, at Holder’s election, Next Round Stock. Number of Shares: A number equal to (a)(i) 0.0375, multiplied by (ii) t

Exhibit 4.3 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTAN

ALTO NEUROSCIENCE, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT

Exhibit 4.2 Execution Version ALTO NEUROSCIENCE, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT THIS AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT (this “Agreement”), is made as of November 20, 2023, by and among ALTO NEUROSCIENCE, INC., a Delaware corporation (the “Company”), each of the investors listed on Schedule A hereto, each of which is referred to in this Agreement as an “Investo

Subsidiaries of Alto Neuroscience, Inc. Name of Subsidiary Jurisdiction of Incorporation Alto Neuroscience (Australia) Pty Ltd Australia

Exhibit 21.1 Subsidiaries of Alto Neuroscience, Inc. Name of Subsidiary Jurisdiction of Incorporation Alto Neuroscience (Australia) Pty Ltd Australia