RNTX / Rein Therapeutics Inc. - Документы SEC, Годовой отчет, Доверенное заявление

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

S-1 Table of Contents As filed with the Securities and Exchange Commission on September 3, 2025 Registration No.

Calculation of Filing Fee Tables Form S-1 (Form Type) Rein Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities

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

Rein Therapeutics Wins U.K. Approval to Launch Phase 2 Clinical Trial of LTI-03 in Idiopathic Pulmonary Fibrosis

EX-99.1 Exhibit 99.1 Rein Therapeutics Wins U.K. Approval to Launch Phase 2 Clinical Trial of LTI-03 in Idiopathic Pulmonary Fibrosis AUSTIN, Texas, Aug. 19, 2025 (GLOBE NEWSWIRE) — Rein Therapeutics (“Rein”) (NASDAQ: RNTX), a biopharmaceutical company advancing a novel pipeline of first-in-class medicines to address significant unmet medical needs in orphan pulmonary and fibrosis indications, tod

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 19, 2025 REIN THERAPEUTICS,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 19, 2025 REIN THERAPEUTICS, INC.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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 ☐ 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: 001-38130 Rein Therapeutics, Inc.

Amended and Restated Bylaws, as amended.

Exhibit 3.5 AMENDED AND RESTATED BY-LAWS OF REIN THERAPEUTICS, INC. TABLE OF CONTENTS Page ARTICLE I STOCKHOLDERS 1 1.1 Place of Meetings 1 1.2 Annual Meeting 1 1.3 Special Meetings 1 1.4 Notice of Meetings 1 1.5 Voting List 1 1.6 Quorum 1 1.7 Adjournments 2 1.8 Voting and Proxies 2 1.9 Action at Meeting 2 1.10 Nomination of Directors 2 1.11 Notice of Business at Annual Meetings 4 1.12 Conduct of

Common Stock

Filed Pursuant to Rule 424(b)(5) Registration No. 333-287342 PROSPECTUS SUPPLEMENT (To Prospectus dated May 22, 2025) $8,066,607 Common Stock This prospectus supplement amends and supplements certain information in the prospectus, dated May 22, 2025, filed with the Securities and Exchange Commission as a part of our registration statement on Form S-3 (File No. 333-287342), which we refer to as the

Entry into a Material Definitive Agreement

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 29, 2025 REIN THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission F

Pre-Paid Advance Agreement, dated as of July 29, 2025, between the Registrant and YA II PN, Ltd.

EX-10.1 Exhibit 10.1 PREPAID ADVANCE AGREEMENT THIS PREPAID ADVANCE AGREEMENT (this “Agreement”) dated as of July 29, 2025 is made by and between YA II PN, LTD., a Cayman Islands exempt limited company (the “Investor”), and REIN THERAPEUTICS, INC., a Delaware corporation (the “Company”). The Investor and the Company may be referred to herein individually as a “Party” and collectively as the “Parti

Common Stock

Table of Contents Filed pursuant to Rule 424(b)(5) Registration No. 333-287342 PROSPECTUS SUPPLEMENT (To Prospectus Dated May 22, 2025) $6,000,000 Common Stock We are offering up to $6,000,000 of shares of our common stock, par value $0.001 per share, by this prospectus supplement and the accompanying prospectus, directly to YA II PN, Ltd., a Cayman Islands exempt limited partnership (“Yorkville”)

Standby Equity Purchase Agreement, dated as of July 29, 2025, between the Registrant and YA II PN, Ltd.

EX-10.2 Exhibit 10.2 STANDBY EQUITY PURCHASE AGREEMENT THIS STANDBY EQUITY PURCHASE AGREEMENT (this “Agreement”) dated as of July 29, 2025 is made by and between YA II PN, LTD., a Cayman Islands exempt limited company (the “Investor”), and REIN THERAPEUTICS, INC., a company incorporated under the laws of the State of Delaware (the “Company”). The Investor and the Company may be referred to herein

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 23, 2025 Rein Therapeutics, Inc.

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 8, 2025 Rein Therapeutics, Inc.

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. )

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)) ☐ Defin

Amendment No. 1 to Amended and Restated By-laws, dated July 10, 2025

Exhibit 3.1 AMENDMENT NO. 1 TO AMENDED AND RESTATED BY-LAWS OF REIN THERAPEUTICS, INC. The Board of Directors of Rein Therapeutics, Inc., a Delaware corporation (the “Corporation”), having resolved to amend the Amended and Restated By-laws of the Corporation (the “By-laws”) as set forth below, the By-laws are hereby amended as follows, effective as of July 10, 2025: 1. Article I, Section 1.6 of th

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, DC 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 24, 2025 Rein Therapeutics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 24, 2025 Rein Therapeutics, Inc.

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 10, 2025 Rein Therapeutics, Inc.

REIN THERAPEUTICS, INC. 12407 N. Mopac Expy., Suite 250 #390 Austin, Texas 78758

CORRESP REIN THERAPEUTICS, INC. 12407 N. Mopac Expy., Suite 250 #390 Austin, Texas 78758 May 21, 2025 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attn: Christopher Edwards Re: Rein Therapeutics, Inc. Registration Statement on Form S-3 File No. 333-287342 Request for Acceleration Ladies and Gentlemen: Pursuant

As filed with the Securities and Exchange Commission on May 16, 2025

Table of Contents As filed with the Securities and Exchange Commission on May 16, 2025 Registration No.

Form of Subordinated Note

EX-4.10 Exhibit 4.10 Form of Subordinated Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER

Calculation of Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Rein Therapeutics, Inc.

Form of Senior Note

EX-4.9 Exhibit 4.9 Form of Senior Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE

Form of Senior Indenture

EX-4.7 Exhibit 4.7 REIN THERAPEUTICS, INC. and Trustee INDENTURE Dated as of SENIOR DEBT SECURITIES CROSS-REFERENCE TABLE1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314(b

At the Market Offering Agreement, dated May 15, 2025, by and between the Registrant and H.C. Wainwright & Co., LLC

Exhibit 1.2 AT THE MARKET OFFERING AGREEMENT May 15, 2025 H.C. Wainwright & Co., LLC 430 Park Avenue New York, New York 10022 Ladies and Gentlemen: Rein Therapeutics, Inc., a corporation organized under the laws of Delaware (the “Company”), confirms its agreement (this “Agreement”) with H.C. Wainwright & Co., LLC (the “Manager”) as follows: 1. Definitions. The terms that follow, when used in this

Form of Subordinated Indenture

EX-4.8 Exhibit 4.8 REIN THERAPEUTICS, INC. and Trustee INDENTURE Dated as of SUBORDINATED DEBT SECURITIES CROSS-REFERENCE TABLE 1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.0

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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 ☐ 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: 001-38130 Rein Therapeutics, Inc.

Common Stock

424B5 Filed Pursuant to Rule 424(b)(5) Registration No. 333-265470 PROSPECTUS SUPPLEMENT (To Prospectus Dated June 16, 2022) Common Stock This prospectus supplement supplements the equity distribution agreement prospectus dated July 26, 2024 related to the offer and sale of shares of our common stock, $0.001 par value per share, pursuant to the Equity Distribution Agreement, dated July 26, 2024, o

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 15, 2025 Rein Therapeutics, Inc

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 15, 2025 Rein Therapeutics, Inc.

Rein Therapeutics Reports First Quarter 2025 Financial Results and Provides Business Update RENEW Phase 2 trial evaluating the safety, tolerability, and efficacy of LTI-03 in idiopathic pulmonary fibrosis (IPF) initiated with topline interim data exp

EX-99.1 Exhibit 99.1 Rein Therapeutics Reports First Quarter 2025 Financial Results and Provides Business Update RENEW Phase 2 trial evaluating the safety, tolerability, and efficacy of LTI-03 in idiopathic pulmonary fibrosis (IPF) initiated with topline interim data expected in the first half of 2026 Two abstracts accepted to the American Thoracic Society (ATS) 2025 International Conference Cash

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 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 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ 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 ☐ T

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ 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 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM       TO       Commission File

Form of Exchange Letter

Exhibit 10.2 REIN THERAPEUTICS, INC. 12407 N. Mopac Expy., Suite 250, #390 Austin, Texas 78758 April   , 2025 To the Holder of 2023 Warrant to Purchase Common Stock Re: Inducement Offer to Exchange 2023 Warrant to Purchase Common Stock Dear Holder: REIN THERAPEUTICS, INC. (formerly Aileron Therapeutics, Inc.) (the “Company”) is pleased to offer to you the opportunity to receive pre-funded warrants

Registration Rights Agreement, dated as of April 21, 2025, between the Company and Bios Purchaser

Exhibit 10.4 REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is dated as of April 21, 2025, by and among Rein Therapeutics, Inc., a Delaware corporation (the “Company”), and Bios 2024 Co-Invest, LP, a Delaware limited partnership (including its successors and assigns, “Purchaser”). This Agreement is made pursuant to the Pre-Funded Warrant Subscription Agreement,

Form of Inducement Letter

Exhibit 10.1 REIN THERAPEUTICS, INC. 12407 N. Mopac Expy., Suite 250, #390 Austin, Texas 78758 April  , 2025 Re: Inducement Offer to Exercise 2023 Warrant to Purchase Common Stock Dear Holder: REIN THERAPEUTICS, INC. (formerly Aileron Therapeutics, Inc.) (the “Company”) is pleased to offer to you the opportunity to exercise for cash the warrant to purchase shares of the Company’s common stock, par

Pre-Funded Warrant Subscription Agreement, dated as of April 21, 2025, between the Company and Bios Purchaser

Exhibit 10.3 PRE-FUNDED WARRANT SUBSCRIPTION AGREEMENT This Pre-Funded Warrant Subscription Agreement (this “Agreement”) is made as of April 21, 2025 by and between Rein Therapeutics, Inc., a Delaware corporation (the “Company”), and Bios 2024 Co-Invest, LP, a Delaware limited partnership (the “Purchaser”). WHEREAS, the parties desire to enter into this Agreement for the sale and issuance of pre-f

Form of Pre-Funded Warrant

Exhibit 4.1 THESE SECURITIES REPRESENTED HEREBY AND THE SECURITIES ISSUABLE UPON EXERCISE OF THESE SECURITIES HAVE NOT BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE BUT HAVE BEEN OR WILL BE ISSUED IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND, ACCORDINGLY, MAY NOT BE TRANSFERRED UNLESS (I) S

Entry into a Material Definitive Agreement

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): April 21, 2025 REIN THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Changes in Registrant's Certifying Accountant

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): April 16, 2025 Rein Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Letter from Marcum LLP regarding change in certifying accountant

Exhibit 16.1 April 17, 2025 Securities and Exchange Commission 100 F Street, N.E. Washington, DC 20549 Commissioners: We have read the statements made by Rein Therapeutics, Inc. under Item 4.01 of its Form 8-K dated April 17, 2025. We agree with the statements concerning our Firm in such Form 8-K; we are not in a position to agree or disagree with other statements of Rein Therapeutics, Inc. contai

Aileron Insider Trading Policy

Exhibit 19.1 Execution Version AILERON THERAPEUTICS, INC. INSIDER TRADING POLICY 1. BACKGROUND AND PURPOSE 1.1 Why Have We Adopted This Policy? The federal securities laws prohibit any member of the Board of Directors (a “Director”)or employee of Aileron Therapeutics, Inc. (together with its subsidiaries, the “Company”) from purchasing or selling Company securities on the basis of material nonpubl

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

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ 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 ☐ 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 001-38130 Rein Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 12b-25 NOTIFICATION OF LATE FILING (Check One):  ☒  Form 10-K ☐ Form 20-F ☐ Form 11-K ☐ Form 10-Q ☐ Form 10-D ☐ Form N-CEN ☐ Form N-CSR For Period Ended: December 31, 2024 ☐

NT 10-K SEC File Number 001-38130 CUSIP Number: 00887A204 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

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): January 10, 2025 Rein Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commissio

Certificate of Amendment of Restated Certificate of Incorporation of the Registrant, dated as of January 10, 2025

Exhibit 3.1 CERTIFICATE OF AMENDMENT TO RESTATED CERTIFICATE OF INCORPORATION OF AILERON THERAPEUTICS, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Aileron Therapeutics, Inc. (hereinafter called the “Corporation”), a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware, does hereby c

Amended and Restated Bylaws

Exhibit 3.2 AMENDED AND RESTATED BY-LAWS OF REIN THERAPEUTICS, INC. TABLE OF CONTENTS Page ARTICLE I STOCKHOLDERS 1 1.1 Place of Meetings 1 1.2 Annual Meeting 1 1.3 Special Meetings 1 1.4 Notice of Meetings 1 1.5 Voting List 1 1.6 Quorum 1 1.7 Adjournments 2 1.8 Voting and Proxies 2 1.9 Action at Meeting 2 1.10 Nomination of Directors 2 1.11 Notice of Business at Annual Meetings 4 1.12 Conduct of

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 14, 2024 Aileron Therapeutics, Inc.

Aileron Therapeutics Reports Third Quarter 2024 Financial Results and Recent Business Highlights Announced promising safety and positive biomarker data from Cohort 2 (5mg BID) of the Phase 1b clinical trial of LTI-03 in idiopathic pulmonary fibrosis

Exhibit 99.1 Aileron Therapeutics Reports Third Quarter 2024 Financial Results and Recent Business Highlights Announced promising safety and positive biomarker data from Cohort 2 (5mg BID) of the Phase 1b clinical trial of LTI-03 in idiopathic pulmonary fibrosis (IPF) patients demonstrating dose dependent effects in five biomarkers evaluated compared to low dose LTI-03 Data from Cohort 2 of the Ph

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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 ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 20, 2024 Aileron Therapeutics, Inc.

Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 14, 2024 Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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 ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Aileron Therapeutics Reports Second Quarter 2024 Financial Results and Business Highlights Announced positive data from Cohort 1 of the ongoing Phase 1b clinical trial of LTI-03 evaluating low dose LTI-03 (2.5 mg BID) in idiopathic pulmonary fibrosis

Exhibit 99.1 Aileron Therapeutics Reports Second Quarter 2024 Financial Results and Business Highlights Announced positive data from Cohort 1 of the ongoing Phase 1b clinical trial of LTI-03 evaluating low dose LTI-03 (2.5 mg BID) in idiopathic pulmonary fibrosis (“IPF”) patients, with positive trends observed in seven of the eight biomarkers evaluated Topline results from Cohort 2 evaluating high

Equity Distribution Agreement, dated July 26, 2024, by and between Aileron Therapeutics, Inc. and Citizens JMP Securities, LLC

Exhibit 1.1 Execution Version AILERON THERAPEUTICS, INC. $50,000,000 Common Stock EQUITY DISTRIBUTION AGREEMENT Dated: July 26, 2024 TABLE OF CONTENTS SECTION 1. Description of Securities 1 SECTION 2. Placements 2 SECTION 3. Sale of Placement Securities by the Placement Agent 3 SECTION 4. Suspension of Sales 3 SECTION 5. Representations and Warranties 4 SECTION 6. Sale and Delivery to the Placemen

Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-265470 PROSPECTUS SUPPLEMENT (To Prospectus Dated June 16, 2022) $50,000,000 Common Stock We have entered into an equity distribution agreement, or equity distribution agreement, with Citizens JMP Securities, LLC, or Citizens JMP, dated July 26, 2024, relating to the sale of shares of our common stock offered by this prospectu

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 26, 2024 Aileron Therapeutic

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 26, 2024 Aileron Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commissio

Common Stock

Filed Pursuant to Rule 424(b)(5) Registration No. 333-265470 PROSPECTUS SUPPLEMENT (To Prospectus Dated June 16, 2022) Common Stock This prospectus supplement supplements the sales agreement prospectus dated June 16, 2022 related to the offer and sale of shares of our common stock, $0.001 par value per share, pursuant to the Capital on Demand™ Sales Agreement, dated January 29, 2021, or the sales

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 R

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. )

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 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 5, 2024 Aileron Therapeutics

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 5, 2024 Aileron Therapeutics, Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission Fil

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 15, 2024 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File N

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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 ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Employment Agreement, dated as of December 13, 2018, by and between Lung Therapeutics, Inc. and Charles T. Garner.

Exhibit 10.1 EMPLOYMENT AGREEMENT This Employment Agreement (this “Agreement’) is made and entered into as of December 13, 2018 (the “Effective Date”) by and between Lung Therapeutics, Inc. (the “Company”), and Charles T. Garner, an individual (“Executive”). RECITALS WHEREAS, the Company and Executive are currently parties to a Consulting Agreement dated October 1, 2018 (the “Consulting Agreement”

Retention Agreement, dated as of March 23, 2024, by and between Aileron Therapeutics, Inc. and Charles T. Garner.

Exhibit 10.3 AILERON THERAPEUTICS, INC. VIA ELECTRONIC DELIVERY March 23, 2024 Charles T. Gamer Re: Retention Agreement Dear Chuck: As we discussed, your employment with Aileron Therapeutics, Inc. (the “Company”) will terminate effective May 15, 2024 (the “Separation Date”).Through the Separation Date, you will continue to serve as the principal financial officer and principal accounting officer o

Letter Agreement, dated as of October 30, 2023, by and between Lung Therapeutics, Inc. and Charles T. Garner.

Exhibit 10.2 LUNG THERAPEUTICS, INC. October 30, 2023 Charles Garner [***] [***] Dear Mr. Garner: As you know, Lung Therapeutics, Inc. (the “Company”) previously entered into an Employment Agreement with you dated December 13, 2018 (the “Agreement”). The Company desires to modify the Agreement effective October 30, 2023, as follows: • Section 1.4.1 of the Agreement shall be modified to increase yo

Aileron Therapeutics Reports First Quarter 2024 Financial Results and Business Highlights Announced positive data from Cohort 1 of the Phase 1b clinical trial of LTI-03 in idiopathic pulmonary fibrosis (IPF) patients with positive trends observed in

Exhibit 99.1 Aileron Therapeutics Reports First Quarter 2024 Financial Results and Business Highlights Announced positive data from Cohort 1 of the Phase 1b clinical trial of LTI-03 in idiopathic pulmonary fibrosis (IPF) patients with positive trends observed in seven of the eight biomarkers evaluated Topline results from Cohort 2 evaluating high-dose LTI-03 (5 mg BID) expected in the third quarte

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 15, 2024 Aileron Therapeutics, Inc.

AILERON THERAPEUTICS, INC. Shares of Common Stock Warrants to Purchase Shares of Common Stock

Issuer Free Writing Prospectus dated May 1, 2024 Filed Pursuant to Rule 433 Registration No.

4,273,505 Shares of Common Stock Warrants to Purchase 4,273,505 Shares of Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-265470 PROSPECTUS SUPPLEMENT (To Prospectus dated June 16, 2022) 4,273,505 Shares of Common Stock Warrants to Purchase 4,273,505 Shares of Common Stock We are offering 4,273,505 shares of our common stock, par value $0.001 per share, and accompanying warrants to purchase 4,273,505 shares of our common stock. Each share of comm

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 1, 2024 Aileron Therapeutics, Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

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

As filed with the Securities and Exchange Commission on May 1, 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): May 1, 2024 Aileron Therapeutics, Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

Form of Warrant (incorporated by reference to Exhibit 4.1 of the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on May 1, 2024.)

Exhibit 4.1 COMMON STOCK PURCHASE WARRANT AILERON THERAPEUTICS, INC. Warrant Shares: Initial Exercise Date: May 3, 2024 CUSIP: 00887A 113 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the date

Underwriting Agreement, dated May 1, 2024, between Aileron Therapeutics, Inc. and Titan Partners Group LLC

Exhibit 1.1 4,273,505 SHARES OF COMMON STOCK WARRANTS TO PURCHASE 4,273,505 SHARES OF COMMON STOCK AILERON THERAPEUTICS, INC. UNDERWRITING AGREEMENT May 1, 2024 Titan Partners Group LLC, a division of American Capital Partners, LLC As the Representative of the Several underwriters, if any, named in Schedule I hereto 4 World Trade Center, 29th Floor New York, NY 10007 Ladies and Gentlemen: The unde

Aileron Therapeutics Announces Pricing of Underwritten Registered Direct Offering Priced At-The-Market Under Nasdaq Rules of up to Approximately $40 Million Includes initial funding of approximately $20 million, as well as the potential for additiona

Exhibit 99.1 Aileron Therapeutics Announces Pricing of Underwritten Registered Direct Offering Priced At-The-Market Under Nasdaq Rules of up to Approximately $40 Million Includes initial funding of approximately $20 million, as well as the potential for additional proceeds of approximately $20 million from exercise of three-year warrants issued in offering May 1, 2024 AUSTIN, Texas, May 01, 2024 (

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ 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 ☐ T

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ 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 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM      TO     

ALRN / Aileron Therapeutics, Inc. / Satter Muneer A Activist Investment

SC 13D/A 1 ff327154713da6-aileron.htm UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities Exchange Act of 1934 (Amendment No. 6) Aileron Therapeutics, Inc. (Name of issuer) Common Stock, par value $0.0

Exhibit 4.2

Exhibit 4.2 DESCRIPTION OF SECURITIES REGISTERED UNDER SECTION 12 OF THE EXCHANGE ACT OF 1934, AS AMENDED The following description of the common stock, par value $0.001 per share, of Aileron Therapeutics, Inc. (“us,” “our,” “we” or the “Company”), which is the only security of the Company registered under Section 12 of the Securities Exchange Act of 1934, as amended, summarizes certain informatio

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

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ 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 ☐ 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 001-38130 Aileron Therape

Lung Therapeutics, Inc.2013 Long-Term Incentive Plan, as amended

Exhibit 10.42 LUNG THERAPEUTICS, INC. 2013 LONG-TERM INCENTIVE PLAN This Lung Therapeutics, Inc. 2013 Long-Term Incentive Plan (the “Plan”) was adopted by the Board of Directors of Lung Therapeutics, Inc., a Texas corporation (the “Company”), effective as of October 23, 2013, subject to approval by the Company’s shareholders. The Plan was further amended on April 30, 2019 and again on June 28, 202

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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): April 15, 2024 Aileron Therapeutics, Inc.

Certificate of Amendment of Restated Certificate of Incorporation of the Registrant, dated as of February, 29, 2024

Exhibit 3.3 CERTIFICATE OF AMENDMENT TO RESTATED CERTIFICATE OF INCORPORATION OF AILERON THERAPEUTICS, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Aileron Therapeutics, Inc. (hereinafter call the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify as follows: F

Aileron Therapeutics, Inc. 2021 Stock Incentive Plan, as amended

Exhibit 10.11 AILERON THERAPEUTICS, INC. 2021 STOCK INCENTIVE PLAN 1. Purpose The purpose of this 2021 Stock Incentive Plan (the “Plan”) of Aileron Therapeutics, Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are expected to make important contributions to the Com

Aileron Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Business Update Topline results from Phase 1b study of LTI-03, a novel Caveolin-1-related peptide in development for the treatment of idiopathic pulmonary f

Exhibit 99.1 Aileron Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Business Update Topline results from Phase 1b study of LTI-03, a novel Caveolin-1-related peptide in development for the treatment of idiopathic pulmonary fibrosis, expected to be reported in the third quarter of 2024 Cash runway expected to fund operations and key milestones into the fourth

Aileron Therapeutics, Inc. Compensation Recovery Policy

Exhibit 97.1 AILERON THERAPEUTICS, INC. Compensation Recovery Policy This Compensation Recovery Policy (this “Policy”) is adopted by Aileron Therapeutics, Inc. (the “Company”) in accordance with Nasdaq Listing Rule 5608 (“Rule 5608”). This Policy is effective as of October 2, 2023 (the “Effective Date”). 1. Definitions (a) “Accounting Restatement” means a requirement that the Company prepare an ac

Subsidiaries of Aileron Therapeutics, Inc.

Exhibit 21.1 Subsidiaries of Aileron Therapeutics, Inc. Subsidiary State/Country of Formation Lung Therapeutics, LLC Delaware Lung Therapeutics Australia Pty Ltd Australia Lung Therapeutics Limited Ireland

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 12b-25 NOTIFICATION OF LATE FILING (Check one):  ☒ Form 10-K  ☐ Form 20-F  ☐ Form 11-K  ☐ Form 10-Q ☐ Form 10-D  ☐ Form N-CEN  ☐ Form N-CSR For Period Ended: December 31, 20

SEC File Number   001-38130 CUSIP Number 00887A204 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 25, 2024 Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 11, 2024 Aileron Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 11, 2024 Aileron Therapeutics, Inc.

Aileron Therapeutics Announces CEO Transition Current President and Chief Operating Officer, Brian Windsor, Ph.D., appointed Chief Executive Officer Dr. Windsor to lead Aileron into a new era focused on advancing a pipeline of first-in-class medicine

EX-99.1 Exhibit 99.1 Aileron Therapeutics Announces CEO Transition Current President and Chief Operating Officer, Brian Windsor, Ph.D., appointed Chief Executive Officer Dr. Windsor to lead Aileron into a new era focused on advancing a pipeline of first-in-class medicines for orphan pulmonary and fibrosis diseases WALTHAM, Mass., Mar. 12, 2024 (GLOBE NEWSWIRE) – Aileron Therapeutics, Inc. (“Ailero

ALRN / Aileron Therapeutics, Inc. / Satter Muneer A Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities Exchange Act of 1934 (Amendment No. 5) Aileron Therapeutics, Inc. (Name of issuer) Common Stock, par value $0.001 (Title of class of securities) 0088

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 29, 2024 Aileron Therapeutics, Inc.

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 28, 2024 Aileron Therapeutics, Inc.

US00887A2042 / AILERON THERAPEUTICS WAR 3/29/24 / BIOTECHNOLOGY VALUE FUND L P - AMENDMENT NO. 2 TO SCHEDULE 13G Passive Investment

SC 13G/A 1 sc13ga207422alrn02142024.htm AMENDMENT NO. 2 TO SCHEDULE 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 RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. 2)1 Aileron Therapeutics Inc. (Name of Issuer) Common Stock, $0.001 pa

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 9, 2024 Aileron Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 9, 2024 Aileron Therapeutics, Inc.

US00887A2042 / AILERON THERAPEUTICS WAR 3/29/24 / Kapnick Scott Passive Investment

SC 13G/A 1 ff296379813ga3-kapnick.htm SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 3) Aileron Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 00887A204 (CUSIP Number) December 31, 2023 (Date of Event Which Requires Filing of this Statement) Check the approp

February 1, 2024

February 1, 2024 VIA EDGAR SUBMISSION Securities and Exchange Commission Division of Corporation Finance 100 F Street, NE Washington, DC 20549 Attention: Lauren Hamill Re: Aileron Therapeutics, Inc.

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.  )

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)) ☐ Defi

Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Aileron Therapeutics, Inc.

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

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

Form S-3 Table of Contents As filed with the Securities and Exchange Commission on January 29, 2024 Registration No.

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 29, 2024 Aileron Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 29, 2024 Aileron Therapeutics, Inc.

Lung Therapeutics, Inc.2013 Long-Term Incentive Plan, as amended

Exhibit 99.1 LUNG THERAPEUTICS, INC. 2013 LONG-TERM INCENTIVE PLAN The Lung Therapeutics, Inc. 2013 Long-Term Incentive Plan (the “Plan”) was adopted by the Board of Directors of Lung Therapeutics, Inc., a Texas corporation (the “Company”), effective as of October 23, 2013, subject to approval by the Company’s shareholders. ARTICLE 1 PURPOSE The purpose of the Plan is to attract and retain the ser

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

As filed with the Securities and Exchange Commission on January 29, 2024 Registration No.

Amended and Restated Patent and Technology License Agreement, effective as of December 19, 2013, by and between Lung Therapeutics, Inc. and the Board of Regents of The University of Texas System, on behalf of The University of Texas Health Science Center at Tyler, as amended by First Amendment, effective as of May 4, 2017.

EX-10.2 Exhibit 10.2 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. AMENDED AND RESTATED PATENT & TECHNOLOGY LICENSE AGREEMENT This Amended and Restated Patent and Technology License Agreement (“Agreement”), effective a

Amended and Restated License Agreement, effective as of September 1, 2018, by and between Lung Therapeutics, Inc. and Medical University of South Carolina Foundation for Research Development.

EX-10.4 Exhibit 10.4 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. AMENDED AND RESTATED LICENSE AGREEMENT by and between MUSC FOUNDATION FOR RESEARCH DEVELOPMENT and LUNG THERAPEUTICS, INC. THIS AMENDED AND RESTATED AG

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 25, 2024 Aileron Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 25, 2024 Aileron Therapeutics, Inc.

Exclusive License Agreement, dated as of November 12, 2020, by and between Lung Therapeutics, Inc. and Taiho Pharmaceutical Co. Ltd.

EX-10.1 Exhibit 10.1 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. EXCLUSIVE LICENSE AGREEMENT between TAIHO PHARMACEUTICAL CO., LTD. and LUNG THERAPEUTICS, INC. a Texas corporation Dated as of November 12, 2020 TABLE

Patent License Agreement, effective as of May 21, 2015, by and between Lung Therapeutics, Inc. and the University of Texas at Austin, on behalf of The University of Texas System, as amended by Amendment #1, dated as of January 26, 2017, Amendment #2, dated as of November 19, 2018, Amendment #3, effective as of June 20, 2019, and Amendment #4, dated as of April 28, 2023.

EX-10.3 Exhibit 10.3 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. Patent License Agreement Agreement No. PM1504101 This Patent License Agreement is between the Licensor and the Licensee identified below (collectively,

License Agreement, effective as of March 8, 2018, by and between Lung Therapeutics, Inc. and Vivarta Therapeutics, L.L.C.

EX-10.5 Exhibit 10.5 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. LICENSE AGREEMENT by and between VIVARTA THERAPEUTICS, L.L.C. and LUNG THERAPEUTICS, INC. THIS LICENSE AGREEMENT, (the “Agreement”) effective as of Mar

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

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS Page Independent Auditor’s Report 2 Consolidated Balance Sheets as of December 31, 2022 and 2021 4 Consolidated Statements of Operations and Comprehensive Loss for the years ended December 31, 2022 and 2021

EX-99.1 Exhibit 99.1 INDEX TO CONSOLIDATED FINANCIAL STATEMENTS Page Independent Auditor’s Report 2 Consolidated Balance Sheets as of December 31, 2022 and 2021 4 Consolidated Statements of Operations and Comprehensive Loss for the years ended December 31, 2022 and 2021 5 Consolidated Statements of Convertible Preferred Stock and Stockholders’ Deficit for the years ended December 31, 2022 and 2021

INDEX TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS OF LUNG THERAPEUTICS, INC. Page Condensed Consolidated Balance Sheets as of September 30, 2023 and December 31, 2022 (unaudited) 2 Condensed Consolidated Statements of Operations and Comp

EX-99.2 Exhibit 99.2 INDEX TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS OF LUNG THERAPEUTICS, INC. Page Condensed Consolidated Balance Sheets as of September 30, 2023 and December 31, 2022 (unaudited) 2 Condensed Consolidated Statements of Operations and Comprehensive Loss for the Nine Months ended September 30, 2023 and 2022 (unaudited) 3 Condensed Consolidated Statements of Convertib

SELECTED HISTORICAL FINANCIAL DATA AND UNAUDITED PRO FORMA CONDENSED COMBINED FINANCIAL INFORMATION

EX-99.3 Exhibit 99.3 SELECTED HISTORICAL FINANCIAL DATA AND UNAUDITED PRO FORMA CONDENSED COMBINED FINANCIAL INFORMATION Selected Historical Condensed Financial Data of Aileron The following tables summarize financial data of Aileron Therapeutics, Inc., a Delaware corporation (“Aileron” or the “Company”). The statement of operations data for the nine months ended September 30, 2023, and 2022 and t

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 8-K/A 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 30, 2023 Aileron Therapeu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 8-K/A 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 30, 2023 Aileron Therapeutics, Inc.

Notice of Delisting or Failure to Satisfy a Continued Listing Rule or Standard; Transfer of Listing, Changes in Registrant's Certifying Accountant

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 4, 2024 Aileron Therapeutics, Inc.

Power of Attorney

EX-99.2 3 tm2330603d2ex99-2.htm EXHIBIT 99.2 Exhibit 99.2 POWER OF ATTORNEY The undersigned hereby constitute and appoint Daniel Schwarz, the lawful attorney-in-fact and agent with full power and authority to execute and file on the undersigned’s behalf, any and all instruments including Forms 3, 4 and 5, and Schedules 13D and 13G (collectively, the “Filings”), and any amendments, supplements or s

Joint Filing Agreement

EX-99.1 2 tm2330603d2ex99-1.htm EXHIBIT 99.1 Exhibit 99.1 JOINT FILING AGREEMENT In accordance with Rule 13d-1(k) promulgated under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree to the joint filing with all other Reporting Persons (as such term is defined in the Schedule 13G referred to below) on behalf of each of them of a statement on Schedule 13G (including amend

US00887A2042 / AILERON THERAPEUTICS WAR 3/29/24 / BIOS Fund I, LP - 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. )* AILERON THERAPEUTICS, INC. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 00887A204 (CUSIP Number) October 31, 2023 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate th

US00887A2042 / AILERON THERAPEUTICS WAR 3/29/24 / Satter Muneer A Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities Exchange Act of 1934 (Amendment No. 4) Aileron Therapeutics, Inc. (Name of issuer) Common Stock, par value $0.001 (Title of class of securities) 0088

Letter from PricewaterhouseCoopers LLP regarding change in certifying accountant

Exhibit 16.1 October 31, 2023 Securities and Exchange Commission 100 F Street, N.E. Washington, DC 20549 Commissioners: We have read the statements made by Aileron Therapeutics, Inc. (copy attached), which we understand will be filed with the Securities and Exchange Commission, pursuant to Item 4.01 of Form 8-K of Aileron Therapeutics, Inc. dated October 30, 2023. We agree with the statements conc

Aileron Therapeutics Announces Acquisition of Lung Therapeutics Acquisition includes multiple clinical stage, orphan pulmonary disease candidates, including LTI-03, a Caveolin-1-related peptide in development for the treatment of idiopathic pulmonary

Exhibit 99.1 Aileron Therapeutics Announces Acquisition of Lung Therapeutics Acquisition includes multiple clinical stage, orphan pulmonary disease candidates, including LTI-03, a Caveolin-1-related peptide in development for the treatment of idiopathic pulmonary fibrosis (IPF) Financing proceeds of approximately $18 million from a private placement anticipated to fund completion of the ongoing Ph

Regulation FD Disclosure, Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Entry into a Material Definitive Agreement, Unregistered Sales of Equity Securities, Changes in Registrant's Certifying Accountant, Completion of Acquisition or Disposition of Assets

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 30, 2023 Aileron Therapeutics, Inc.

Certificate of Designation of Series X Non-Voting Convertible Preferred Stock

Exhibit 3.1 AILERON THERAPEUTICS, INC. CERTIFICATE OF DESIGNATION OF PREFERENCES, RIGHTS AND LIMITATIONS OF SERIES X NON-VOTING CONVERTIBLE PREFERRED STOCK PURSUANT TO SECTION 151 OF THE DELAWARE GENERAL CORPORATION LAW Aileron Therapeutics, Inc., a Delaware corporation (the “Corporation”), in accordance with the provisions of Section 103 of the Delaware General Corporation Law (the “DGCL”) does h

Letter Agreement, dated as of February 11, 2023, by and between Lung Therapeutics, Inc. and Brian Windsor, Ph.D.

Exhibit 10.4 LUNG THERAPEUTICS, INC. February 11, 2023 Brian Windsor [***] [***] Dear Dr. Windsor, As you know, Lung Therapeutics Inc. (the “Company”) previously entered into an Employment Agreement with you dated February 1, 2015 (“Agreement”). The Company desires to modify the Agreement effective February 26, 2020, the date of the Board of Directors meeting at which the Board approved an incenti

Agreement and Plan of Merger, dated October 31, 2023, by and among Aileron Therapeutics, Inc., AT Merger Sub I, Inc., AT Merger Sub II, LLC and Lung Therapeutics, Inc.

Exhibit 2.1 AGREEMENT AND PLAN OF MERGER by and among AILERON THERAPEUTICS, INC. AT MERGER SUB I, INC., AT MERGER SUB II, LLC and LUNG THERAPEUTICS, INC. Dated as of October 31, 2023 TABLE OF CONTENTS Page ARTICLE I CERTAIN GOVERNANCE MATTERS 3 Section 1.1 Parent Matters 3 Section 1.2 First Step Surviving Company Matters 4 Section 1.3 Surviving Company Matters 4 ARTICLE II THE MERGER 5 Section 2.1

Forward-Looking Statements This presentation and various remarks we make during this presentation contain forward-looking statements of Aileron Therapeutics, Inc. (“Aileron”, the “Company”, “we”, “our” or “us”) within the meaning of the Private Secur

CORPORATE PRESENTATION OCTOBER 2023 Merger Announcement Exhibit 99.2 Forward-Looking Statements This presentation and various remarks we make during this presentation contain forward-looking statements of Aileron Therapeutics, Inc. (“Aileron”, the “Company”, “we”, “our” or “us”) within the meaning of the Private Securities Litigation Reform Act of 1995, including statements with respect to: future

Letter Agreement, dated as of October 30, 2023, by and between Lung Therapeutics, Inc. and Brian Windsor, Ph.D.

Exhibit 10.5 LUNG THERAPEUTICS, INC. October 30, 2023 Brian Windsor [***] [***] Dear Dr. Windsor: As you know, Lung Therapeutics, Inc. (the “Company”) previously entered into an Employment Agreement with you dated February 1, 2015, as modified by Letter Agreement dated February 11, 2023 (collectively, the “Agreement”). The Company desires to modify the Agreement effective October 30, 2023, as foll

Executive Employment Agreement, dated as of February 1, 2014, by and between Lung Therapeutics, Inc. and Brian Windsor, Ph.D., as amended

Exhibit 10.3 LUNG THERAPEUTICS, INC. EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (this “Agreement”) is entered into as of February 1, 2014 (the “Effective Date”) by and between Lung Therapeutics, Inc., a Texas corporation (the “Company”), and James Brian Windsor (“Executive”). R E C I T A L S WHEREAS, the Company considers it essential to its best interests and the best inte

Form of Warrant to Purchase Common Stock issued pursuant to the Stock and Warrant Purchase Agreement

Exhibit 4.1 FORM OF WARRANT NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN

Form of Registration Rights Agreement, by and among Aileron Therapeutics, Inc. and certain purchasers named therein

Exhibit 10.2 REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is dated as of November 2, 2023, by and among Aileron Therapeutics, Inc., a Delaware corporation (the “Company”), and the several purchasers signatory hereto (each, including its successors and assigns, a “Purchaser” and collectively, the “Purchasers”). This Agreement is made pursuant to the Stock and

Stock and Warrant Purchase Agreement, dated as of October 31, 2023, by and among Aileron Therapeutics, Inc. and each purchaser identified on Annex A thereto

Exhibit 10.1 STOCK AND WARRANT PURCHASE AGREEMENT THIS STOCK AND WARRANT PURCHASE AGREEMENT (this “Agreement”) is dated as of October 31, 2023, by and among Aileron Therapeutics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on Annex A hereto (each, including its successors and assigns, a “Purchaser” and collectively, the “Purchasers”). BACKGROUND A. The Company and e

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 OR ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Waiver Under Amended and Restated License Agreement, dated as of February 19, 2010, by and among the Registrant, President and Fellows of Harvard College and Dana-Farber Cancer Institute, Inc.

Exhibit 10.1 WAIVER UNDER LICENSE AGREEMENT July 19, 2023 THIS WAIVER UNDER LICENSE AGREEMENT (this “Waiver”) is made as of the date first written above (the “Effective Date”) by and among President and Fellows of Harvard College (“Harvard”), Dana-Farber Cancer Institute, Inc. (“DFCI”, and together with Harvard, the “Licensors”) and Aileron Therapeutics, Inc. (“Licensee”) with respect to that cert

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 OR ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Separation and Release of Claims Agreement, dated as of April 24, 2023, between the Registrant and D. Allen Annis, Ph.D.

SEPARATION AND RELEASE OF CLAIMS AGREEMENT This Separation and Release of Claims Agreement (the “Agreement”) is made by and between Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2023 OR ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Consulting Agreement, dated as of April 15, 2023, between the Registrant and D. Allen Annis, Ph.D.

CONSULTING AGREEMENT THIS CONSULTING AGREEMENT (the “Agreement”) is entered into as of April 15, 2023 by and between Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31 , 2022 OR ☐

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31 , 2022 OR ☐ 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-

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

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 OR ☐ 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 001-38130 Aileron Therape

Form of Restricted Stock Unit Agreement under 2021 Stock Incentive Plan

Exhibit 10.13 Aileron Therapeutics, Inc. Restricted Stock Unit Agreement Aileron Therapeutics, Inc. (the “Company”) hereby grants the following restricted stock units pursuant to its 2021 Stock Incentive Plan. The terms and conditions attached hereto are also a part hereof. Notice of Grant Name of recipient (the “Participant”): Grant Date: Number of restricted stock units (“RSUs”) granted: Vesting

Form of Stock Option Agreement under 2021 Stock Incentive Plan

Exhibit 10.12 AILERON THERAPEUTICS, INC. STOCK OPTION AGREEMENT Aileron Therapeutics, Inc. (the “Company”) hereby grants the following stock option pursuant to its 2021 Stock Incentive Plan. The terms and conditions attached hereto are also a part hereof. Notice of Grant Name of optionee (the “Participant”): Grant Date: Incentive Stock Option or Nonstatutory Stock Option: Number of shares of the C

Costs Associated with Exit or Disposal Activities, 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): February 16, 2023 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission F

ALRN / Aileron Therapeutics Inc / Kapnick Scott Passive Investment

SC 13G/A 1 ff175953013ga2-kapnick.htm SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2) Aileron Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 00887A105 (CUSIP Number) December 31, 2022 (Date of Event Which Requires Filing of this Statement) Check the approp

US00887A2042 / AILERON THERAPEUTICS WAR 3/29/24 / BIOTECHNOLOGY VALUE FUND L P - AMENDMENT NO. 1 TO THE SCHEDULE 13G Passive Investment

SC 13G/A 1 sc13ga107422alrn02142023.htm AMENDMENT NO. 1 TO THE SCHEDULE 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 RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. 1)1 Aileron Therapeutics Inc. (Name of Issuer) Common Stock, $0.00

Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Material Modification to Rights of Security Holders, Financial Statements and Exhibits

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 November 10, 2022 Date of Report (Date of earliest event reported) AILERON THERAPEUTICS, INC. (Exact Name of Registrant as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Certificate of Amendment of Restated Certificate of Incorporation of the Registrant, dated as of November 10, 2022

Exhibit 3.1 CERTIFICATE OF AMENDMENT TO RESTATED CERTIFICATE OF INCORPORATION OF AILERON THERAPEUTICS, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Aileron Therapeutics, Inc. (hereinafter called the ?Corporation?), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify as follows:

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2022 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

EX-10.1

Separation and Release of Claims Agreement, dated July 8, 2022, by and between the Company and Vojislav Vukovic, M.D., Ph.D.

EX-10.1 2 alrn-ex101.htm EX-10.1 Exhibit 10.1 SEPARATION AND RELEASE OF CLAIMS AGREEMENT This Separation and Release of Claims Agreement (the “Agreement”) is made by and between Aileron Therapeutics, Inc. (the “Company”), having its principal place of business at 285 Summer Street, Suite 101, Boston, MA 02210, and Vojislav Vukovic, M.D., Ph.D., having an address at 1111 E Sunrise Blvd, Apt 505, Fo

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

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 8, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File N

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): June 29, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-265470 PROSPECTUS $14,024,100 Common Stock We have entered into a Capital on Demand? Sales Agreement, or sales agreement, with JonesTrading Institutional Services LLC and William Blair & Company, L.L.C., each an Agent and collectively, the Agents, dated January 29, 2021, relating to the sale of shares of our common stock. Unde

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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): June 15, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

AILERON THERAPEUTICS, INC. 285 Summer Street, Suite 101 Boston, Massachusetts 02210

CORRESP 1 filename1.htm AILERON THERAPEUTICS, INC. 285 Summer Street, Suite 101 Boston, Massachusetts 02210 June 14, 2022 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Re: Aileron Therapeutics, Inc. Registration Statement on Form S-3 File No. 333-265470 Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 461 promu

June 13, 2022

June 13, 2022 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

Form of Senior Indenture

Exhibit 4.5 AILERON THERAPEUTICS, INC. and Trustee INDENTURE Dated as of SENIOR DEBT SECURITIES CROSS-REFERENCE TABLE1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314(b) In

Form of Senior Note

Exhibit 4.7 Form of Senior Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE OF THE

Form of Subordinated Indenture

Exhibit 4.6 AILERON THERAPEUTICS, INC. and Trustee INDENTURE Dated as of SUBORDINATED DEBT SECURITIES CROSS-REFERENCE TABLE1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314

As filed with the Securities and Exchange Commission on June 7, 2022

Table of Contents As filed with the Securities and Exchange Commission on June 7, 2022 Registration No.

Notice of Delisting or Failure to Satisfy a Continued Listing Rule or Standard; Transfer of Listing

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 7, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File N

Calculation of Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Aileron Therapeutics, Inc.

Form of Subordinated Note

Exhibit 4.8 Form of Subordinated Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

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 5, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File N

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2022 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

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): April 25, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

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. )

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)) ? Defin

definitive proxy statement

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. )

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

Common Stock

Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 AMENDMENT NO. 1 To Prospectus Supplement dated January 29, 2021 (To Prospectus dated July 15, 2019) $16,929,022 Common Stock This Amendment No. 1 to Prospectus Supplement, or this Amendment, amends and supplements the information in the prospectus, dated July 15, 2019, filed as part of our registration statement on Form S-3 (File No. 333

Form of Restricted Stock Unit Agreement under 2021 Stock Incentive Plan

Exhibit 10.13 Aileron Therapeutics, Inc. Restricted Stock Unit Agreement Aileron Therapeutics, Inc. (the ?Company?) hereby grants the following restricted stock units pursuant to its 2021 Stock Incentive Plan. The terms and conditions attached hereto are also a part hereof. Notice of Grant Name of recipient (the ?Participant?): Grant Date: Number of restricted stock units (?RSUs?) granted: Vesting

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

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2021 OR ? 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 001-38130 Aileron Therape

Form of Stock Option Agreement under 2021 Stock Incentive Plan

Exhibit 10.12 AILERON THERAPEUTICS, INC. STOCK OPTION AGREEMENT Aileron Therapeutics, Inc. (the ?Company?) hereby grants the following stock option pursuant to its 2021 Stock Incentive Plan. The terms and conditions attached hereto are also a part hereof. Notice of Grant Name of optionee (the ?Participant?): Grant Date: Incentive Stock Option or Nonstatutory Stock Option: Number of shares of the C

ALRN / Aileron Therapeutics Inc / Kapnick Scott Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1) Aileron Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 00887A105 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursua

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): January 5, 2022 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission Fil

Notice of Delisting or Failure to Satisfy a Continued Listing Rule or Standard; Transfer of Listing

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): December 6, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2021 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

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): September 16, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (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): September 13, 2021 Aileron Therap

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): September 13, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Restated Certificate of Incorporation of the Registrant, as amended (incorporated by reference to Exhibit 3.1 of the Company’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on August 11, 2021.)

Exhibit 3.1 RESTATED CERTIFICATE OF INCORPORATION OF AILERON THERAPEUTICS, INC. (originally incorporated on August 6, 2001 under the name Renegade Therapeutics, Inc.) FIRST: The name of the Corporation is Aileron Therapeutics, Inc. SECOND: The address of the Corporation?s registered office in the State of Delaware is Corporation Trust Center, 1209 Orange Street, in the City of Wilmington, County o

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

As filed with the Securities and Exchange Commission on August 11, 2021

As filed with the Securities and Exchange Commission on August 11, 2021 Registration No.

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): July 1, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File N

Certificate of Amendment of Restated Certificate of Incorporation of Aileron Therapeutics, Inc.

Exhibit 3.1 CERTIFICATE OF AMENDMENT OF RESTATED CERTIFICATE OF INCORPORATION OF AILERON THERAPEUTICS, INC. (Pursuant to Section 242 of the General Corporation Law of the State of Delaware) Aileron Therapeutics, Inc. (the ?Corporation?), a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware, does hereby certify as follows

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Financial Statements and Exhibits, 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): June 15, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

AILERON THERAPEUTICS, INC. 2021 STOCK INCENTIVE PLAN

Exhibit 99.1 AILERON THERAPEUTICS, INC. 2021 STOCK INCENTIVE PLAN 1. Purpose The purpose of this 2021 Stock Incentive Plan (the ?Plan?) of Aileron Therapeutics, Inc., a Delaware corporation (the ?Company?), is to advance the interests of the Company?s stockholders by enhancing the Company?s ability to attract, retain and motivate persons who are expected to make important contributions to the Comp

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

Sublease Agreement, dated March 26, 2021, by and among the Company, Vittoria Industries North America, Inc. and Waterfront Equity Partners, LLC

Exhibit 10.1 DocuSign Envelope ID: 7B2CF802-FA2C-4771-BA88-9E593E041528 Execution Version SUBLEASE This Sublease (this ?Sublease?) is entered into as of this 26th day of March, 2021, by and among Vittoria Industries North America, Inc., a Delaware corporation (?Sublandlord?), Aileron Therapeutics, Inc., a Delaware corporation (?Subtenant?), and Waterfront Equity Partners, LLC, a Massachusetts limi

“Proposal 3: Approval of 2021 Stock Incentive Plan”

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

- 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)) ? Defin

- PRE 14A

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

Entry into a Material Definitive Agreement

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 26, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

Annual Report - 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2020 OR ? 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 001-38130 Aileron Therape

- S-8

As filed with the Securities and Exchange Commission on March 24, 2021 Registration No.

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): March 2, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission File

By signing below, Prudential Financial, Inc. certifies that, to the best of its

13G HTML File DOCUMENT TYPE SC 13G/A TEXT SECURITIES AND EXCHANGE COMMISSION Washington, D.

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AILERON THERAPEUTICS, INC. 290 Pleasant Street, Unit 112 Watertown, MA 02472 February 5, 2021 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Re: Aileron Therapeutics, Inc. Registration Statement on Form S-3 File No. 333-252587 Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 461 promulgated under the Securities

- S-3

S-3 Table of Contents As filed with Securities and Exchange Commission on January 29, 2021 Registration No.

Capital on Demand™ Sales Agreement, dated January 29, 2021, by and among Aileron Therapeutics, Inc. and JonesTrading Institutional Services LLC and William Blair & Company, L.L.C.

EX-1.1 Exhibit 1.1 Aileron Therapeutics, Inc. Common Stock ($0.001 par value per share) Capital on Demand™ Sales Agreement January 29, 2021 JonesTrading Institutional Services LLC 757 Third Avenue, 23rd Floor New York, NY 10017 William Blair & Company, L.L.C. 150 North Riverside Plaza Chicago, Illinois 60606 Ladies and Gentlemen: Aileron Therapeutics, Inc., a Delaware corporation (the “Company”) c

Entry into a Material Definitive Agreement, Financial Statements and Exhibits - 8-K

8-K 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 29, 2021 Aileron Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38130 13-4196017 (State or other jurisdiction of incorporation) (Co

Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 PROSPECTUS SUPPLEMENT (To Prospectus Dated July 15, 2019) $30,000,000 Common Stock We have entered into a Capital on Demand™ Sales Agreement with JonesTrading Institutional Services LLC and William Blair & Company, L.L.C., each an Agent and collectively, the Agents, dated January 29, 2021, relating to the sale of

Joint Filing Agreement

Exhibit 99.1 Joint Filing Agreement The undersigned hereby agree that the Statement on Schedule 13G dated January 19, 2021 with respect to the shares of Common Stock, par value $0.001 of Aileron Therapeutics Inc., and any further amendments thereto executed by each and any of the undersigned shall be filed on behalf of each of the undersigned pursuant to and in accordance with the provisions of Ru

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendm

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. )1 Aileron Therapeutics Inc. (Name of Issuer) Common Stock, par value $0.001 (Title of Class of Securities) 00887A105 (CUSIP Number) January 6

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities

SC 13D/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities Exchange Act of 1934 (Amendment No. 3) Aileron Therapeutics, Inc. (Name of issuer) Common Stock, par value $0.001 (Title of class of securit

Form of Securities Purchase Agreement

EX-10.1 Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of January 6, 2021, between Aileron Therapeutics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on the signature pages hereto (each, including its successors and assigns, a “Purchaser” and collectively the “Purchasers”). WHEREAS, subject to the terms an

32,630,983 Shares Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 Prospectus Supplement (To Prospectus Dated July 15, 2019) 32,630,983 Shares Common Stock We are offering 32,630,983 shares of our common stock to certain institutional investors pursuant to this prospectus supplement and accompanying prospectus at an offering price of $1.10 per share. Our common stock is listed on

Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Other Events - 8-K

8-K 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 6, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Aileron Therapeutics Announces $35.9 Million Registered Direct Offering

EX-99.1 Exhibit 99.1 Aileron Therapeutics Announces $35.9 Million Registered Direct Offering WATERTOWN, Mass., January 6, 2021 –(GLOBE NEWSWIRE) — Aileron Therapeutics, Inc. (Nasdaq: ALRN), today announced that it has entered into definitive agreements with fundamental healthcare investors for the purchase and sale of 32,630,983 of its shares of common stock at a purchase price of $1.10 per share

Other Events - 8-K

8-K 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 6, 2021 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 PROSPECTUS SUPPLEMENT (To Sales Agreement Prospectus Dated July 15, 2019) $11,896,613 Common Stock We have entered into a Capital on Demand™ Sales Agreement, or the sales agreement, with JonesTrading Institutional Services LLC, or JonesTrading, dated July 1, 2019, relating to the sale of shares of our common stock

Regulation FD Disclosure, Other Events - 8-K

8-K 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): December 21, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2020 OR ? 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: 001-38130 Aileron Therapeutics, Inc.

Prevention of Chemotherapy-induced Myelosuppression in SCLC Patients Treated with the Dual MDMX/MDM2 Inhibitor ALRN-6924 Zoran Andric1, Timur Ceric2, Mirko Stanetic3, Milan Rancic4, Marko Jakopovic5, Santiago Ponce Aix6, Rodryg Ramlau7, Egbert Smit8,

EX-99.1 Exhibit 99.1 Prevention of Chemotherapy-induced Myelosuppression in SCLC Patients Treated with the Dual MDMX/MDM2 Inhibitor ALRN-6924 Zoran Andric1, Timur Ceric2, Mirko Stanetic3, Milan Rancic4, Marko Jakopovic5, Santiago Ponce Aix6, Rodryg Ramlau7, Egbert Smit8, Malgorzata Ulanska9, Christopher Caldwell10, Dora Ferrari10, Allen Annis10, Vojislav Vukovic10, Bojan Zaric11 1CHC Bezanijska Ko

Regulation FD Disclosure, Financial Statements and Exhibits, Other Events - 8-K

8-K 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 24, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commissio

10,551,899 Shares of Common Stock

424B3 Table of Contents Filed pursuant to Rule 424(b)(3) Registration No. 333-249319 PROSPECTUS 10,551,899 Shares of Common Stock This prospectus relates to the resale, from time to time, of up to 10,551,899 shares of our common stock, par value $0.001 per share, by the selling stockholder, Lincoln Park Capital Fund, LLC, which we refer to as Lincoln Park or the selling stockholder. The shares of

AILERON THERAPEUTICS, INC. 490 Arsenal Way, Suite 210 Watertown, MA 02472

AILERON THERAPEUTICS, INC. 490 Arsenal Way, Suite 210 Watertown, MA 02472 October 13, 2020 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Re: Aileron Therapeutics, Inc. Registration Statement on Form S-1 File No. 333-249319 Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 461 promulgated under the Securities Act

Registration Statement - S-1

S-1 Table of Contents As filed with Securities and Exchange Commission on October 5, 2020 Registration No.

Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 PROSPECTUS SUPPLEMENT (To Sales Agreement Prospectus Dated July 15, 2019) $4,194,699 Common Stock We have entered into a Capital on Demand™ Sales Agreement, or the sales agreement, with JonesTrading Institutional Services LLC, or JonesTrading, dated July 1, 2019, relating to the sale of shares of our common stock.

Entry into a Material Definitive Agreement, Unregistered Sales of Equity Securities, Financial Statements and Exhibits, Other Events - 8-K

8-K 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): September 21, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commiss

Purchase Agreement, dated as of September 21, 2020, by and between the Company and Lincoln Park Capital Fund, LLC

EX-10.1 Exhibit 10.1 PURCHASE AGREEMENT THIS PURCHASE AGREEMENT (the “Agreement”), dated as of September 21, 2020, by and between AILERON THERAPEUTICS, INC., a Delaware corporation (the “Company”), and LINCOLN PARK CAPITAL FUND, LLC, an Illinois limited liability company (the “Investor”). Capitalized terms used herein and not otherwise defined herein are defined in Section 1 hereof. WHEREAS: Subje

Registration Rights Agreement, dated as of September 21, 2020, by and between the Company and Lincoln Park Capital Fund, LLC

EX-10.2 Exhibit 10.2 REGISTRATION RIGHTS AGREEMENT THIS REGISTRATION RIGHTS AGREEMENT (this “Agreement”), dated as of September 21, 2020, by and between AILERON THERAPEUTICS, INC., a Delaware corporation (the “Company”), and LINCOLN PARK CAPITAL FUND, LLC, an Illinois limited liability company (together with its permitted assigns, the “Buyer”). Capitalized terms used herein and not otherwise defin

Aileron Therapeutics Announces Common Stock Purchase Agreement for up to $15 Million with Lincoln Park Capital

EX-99.1 Exhibit 99.1 Aileron Therapeutics Announces Common Stock Purchase Agreement for up to $15 Million with Lincoln Park Capital WATERTOWN, Mass., September 21, 2020 — Aileron Therapeutics, Inc. (NASDAQ: ALRN), today announced it has entered into a common stock purchase agreement (“Purchase Agreement”) for up to $15 million with Lincoln Park Capital Fund, LLC (“LPC”), a Chicago-based institutio

Regulation FD Disclosure, Other Events - 8-K

8-K 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): September 14, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commiss

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CORRESP AILERON THERAPEUTICS, INC. 490 Arsenal Way, Suite 210 Watertown, MA 02472 August 19, 2020 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Re: Aileron Therapeutics, Inc. Registration Statement on Form S-3 File No. 333-244367 Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 461 promulgated under the Securit

- S-3

S-3 Table of Contents As filed with Securities and Exchange Commission on August 11, 2020 Registration No.

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2020 OR ☐ 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: 001-38130 Aileron Therapeutics, Inc.

Submission of Matters to a Vote of Security Holders

8-K 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 17, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission F

Other Events

8-K 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 11, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission F

ALRN / Aileron Therapeutics Inc. / Satter Muneer A - SC 13D/A Activist Investment

SC 13D/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A (Rule 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) Under the Securities Exchange Act of 1934 (Amendment No. 2) Aileron Therapeutics, Inc. (Name of issuer) Common Stock, par value $0.001 (Title of class of securit

ALRN / Aileron Therapeutics Inc. / Kapnick Scott Passive Investment

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 Aileron Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 00887A105 (CUSIP Number) April 2, 20191 (Date of Event Whi

Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Other Events

8-K 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 4, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission Fi

9,090,910 Shares Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 Prospectus Supplement (To Prospectus Dated July 15, 2019) 9,090,910 Shares Common Stock We are offering 9,090,910 shares of our common stock. Our common stock is listed on the Nasdaq Capital Market under the symbol “ALRN.” On June 2, 2020, the last reported sale price of our common stock on the Nasdaq Capital Mark

Underwriting Agreement, dated June 4, 2020, by and between the Company and William Blair & Company, L.L.C.

EX-1.1 Exhibit 1.1 AILERON THERAPEUTICS, INC. Common Stock, par value $0.001 per share Underwriting Agreement June 4, 2020 William Blair & Company, L.L.C. As representative of the several Underwriters named in Schedule I hereto, c/o William Blair & Company, L.L.C. 150 North Riverside Plaza Chicago, Illinois 60606 Ladies and Gentlemen: Aileron Therapeutics, Inc., a Delaware corporation (the “Compan

Aileron Therapeutics Announces Pricing of Public Offering of Common Stock

EX-99.1 Exhibit 99.1 Aileron Therapeutics Announces Pricing of Public Offering of Common Stock WATERTOWN, Mass., June 4, 2020 (GLOBE NEWSWIRE) — Aileron Therapeutics (NASDAQ: ALRN) announced today the pricing of an underwritten public offering of 9,090,910 shares of its common stock at a public offering price of $1.10 per share, for aggregate gross proceeds of $10.0 million, before deducting under

SUBJECT TO COMPLETION, DATED JUNE 3, 2020

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 The information in this preliminary prospectus supplement is not complete and may be changed. A registration statement relating to these securities has been filed with the Securities and Exchange Commission and is effective. This preliminary prospectus supplement and the accompanying prospectus are not an offer to

Common Stock

424B5 Filed Pursuant to Rule 424(b)(5) Registration No. 333-226650 PROSPECTUS SUPPLEMENT (To Prospectus Dated July 15, 2019) Common Stock This prospectus supplement supplements the prospectus dated July 15, 2019 related to the offer and sale of shares of our common stock, $0.001 par value per share, pursuant to a Capital on Demand™ Sales Agreement, or the Sales Agreement, dated July 1, 2019, with

Regulation FD Disclosure, Financial Statements and Exhibits, Other Events

8-K 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 1, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission Fi

ALRN-6924: Ongoing Ph1b Clinical Trial in Small Cell Lung Cancer Patients Receiving Topotecan Dose Optimization N = 18 ALRN-6924 24h before topotecan 3 dose levels tested Expansion commenced Schedule Optimization N = 20 ALRN-6924 6h before topotecan

EX-99.1 Interim data from Phase 1b dose optimization trial Exhibit 99.1 ALRN-6924: Ongoing Ph1b Clinical Trial in Small Cell Lung Cancer Patients Receiving Topotecan Dose Optimization N = 18 ALRN-6924 24h before topotecan 3 dose levels tested Expansion commenced Schedule Optimization N = 20 ALRN-6924 6h before topotecan Test up to 2 dose levels Start enrollment planned for June 2020 Endpoints % wi

Form 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2020 OR ☐ 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: 001-38130 Aileron Therapeutics, Inc.

- DEFA14A

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))

definitive proxy statement

DEF 14A Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

Regulation FD Disclosure, Other Events

8-K 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): April 22, 2020 Aileron Therapeutics, Inc. (Exact Name of Company as Specified in Charter) Delaware 001-38130 13-4196017 (State or Other Jurisdiction of Incorporation) (Commission

ALRN / Aileron Therapeutics Inc. / Novartis Bioventures Ltd - SC 13D/A Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. 6)* Aileron Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 00887A 105 (CUSIP Number) Bart Dzikowski Secretary of the Board Novartis Bioventures Ltd. Lichtstrasse 35 CH-4056 Basel, Switzerland +41 6

ALRN / Aileron Therapeutics Inc. PRE 14A - - PRE 14A

PRE 14A 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))

Joint Filing Agreement

Exhibit 99.1 CUSIP No. 0087A 105 Schedule 13D Joint Filing Agreement In accordance with Rule 13d-1(k)(1) promulgated under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree to the joint filing with each other on behalf of each of them of such a statement on Schedule 13D (including amendments thereto) with respect to the Common Stock beneficially owned by each of them of

Joint Filing Agreement

Exhibit 99.1 CUSIP No. 0087A 105 Schedule 13D Joint Filing Agreement In accordance with Rule 13d-1(k)(1) promulgated under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree to the joint filing with each other on behalf of each of them of such a statement on Schedule 13D (including amendments thereto) with respect to the Common Stock beneficially owned by each of them of