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 securities)

00887A 105

(CUSIP number)

Muneer A. Satter

c/o Satter Management Co., L.P.

676 N. Michigan Avenue, Suite 4000, Chicago, IL 60611

(312) 448-5500

COPY TO:

Robert M. Hayward, P.C.

Kirkland & Ellis LLP

300 N. LaSalle St.

Chicago, Illinois 60654

(312) 862-2000

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

January 6, 2021

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box.  ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

SCHEDULE 13D

SCHEDULE 13D

Item 3. Source and Amount of Funds.

Item 3 of the Prior Filings is amended by adding the following paragraph:

On January 6, 2021, the Company entered into a securities purchase agreement (the “Purchase Agreement”) with certain affiliates of the Reporting Person, pursuant to which the Company agreed to issue and sell to affiliates of the Reporting Person, in a registered direct offering (the “Offering”), an aggregate of 9,000,000 shares of Common Stock, at a purchase price per share of $1.10. The shares of Common Stock are being offered by the Company pursuant to a shelf registration statement on Form S-3 (File No. 333-226650) that was filed with the Securities and Exchange Commission, and a prospectus supplement thereunder. The Offering closed on January 8, 2021. The source of the funds for SMTP’s acquisition of shares in the Offering was capital committed by the partners of SMTP.

Item 5. Interest in Securities of the Issuer.

Paragraph (a) of Item 5 of the Prior Filings is hereby deleted and replaced as follows:

Amount beneficially owned: The Reporting Person beneficially owns an aggregate of 20,340,792 shares of Common Stock. The shares of Common Stock beneficially owned by the Reporting Person include (a) 1,025,076 shares of Common Stock that are held by Muneer A. Satter Revocable Trust for which the Reporting Person serves as trustee and, in such capacity, has sole voting and dispositive power over all such shares; (b) 1,231,044 shares of Common Stock that are held by various other trusts and other entities for which the Reporting Person serves as trustee, investment advisor or manager and, in such capacity, has sole voting and dispositive power over all such shares; (c) 14,353,329 shares of Common Stock that are held by SMTP for which the Reporting Person has sole voting and dispositive power over all such shares, and (d) subject to the ownership limitation described below, Warrants to purchase 3,731,343 shares of Common Stock held by SMTP for which the Reporting Person has sole voting and dispositive power over all such Warrants and the underlying shares of Common Stock.

Percent of class:

While the Reporting Person beneficially owns 20,340,792 shares of Common Stock, such amount only represents 19.9% of the total number of shares of Common Stock outstanding because the Warrants may not be exercised with respect to any portion of the Warrants, to the extent that such exercise would result in SMTP and its affiliates beneficially owning more than 19.9% of the outstanding Common Stock or outstanding voting power of the Company.

All percentages calculated in this Schedule 13D are based on 83,610,151 shares of Common Stock outstanding after the Offering as disclosed in the Prospectus Supplement filed by the Company with the Securities and Exchange Commission on January 7, 2021.

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

Item 6 of the Prior Filings is amended by adding the following paragraph:

Securities Purchase Agreement (2021)

The Purchase Agreement contains customary representations, warranties, covenants and agreements by the Company, customary conditions to closing, indemnification obligations, other obligations of the parties and termination provisions. The description of the Purchase Agreement included in this Schedule 13D does not purport to be a complete description and is qualified in its entirety by reference to the full text of such agreement, which is filed as part of this Schedule 13D and incorporated by reference herein.

Item 7. Material to be Filed as Exhibits.

Item 7 of the Prior Filings is amended by adding the following exhibit:

Exhibit D: Form of Securities Purchase Agreement (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K filed on January 7, 2021)

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: January 8, 2021

EXHIBIT INDEX