Amendment No. 2 to Collaboration and License Agreement

Exhibit 10.13

Amendment No. 2 to Collaboration and License Agreement

This Amendment No. 2 to Collaboration and License Agreement (this “Amendment No. 2”) is made and effective as of August 5, 2015, by and between Proteostasis Therapeutics, Inc., a corporation existing under the laws of the State of Delaware, having a place of business at 200 Technology Square, 4^th Floor, Cambridge, MA 02139 (“PTI”) and Astellas Pharma Inc., a Japanese corporation having its principal place of business at 5-1 Nihonbashi-Honcho 2-Chome, Chuo-ku, Tokyo 103-8411, Japan (“Astellas”). Each of Astellas and PTI is sometimes referred to individually herein as a “Party” and collectively as the “Parties”.

Reference is hereby made to that certain Collaboration and License Agreement dated November 4, 2014 and amended May 1, 2015, by and between the Parties (as amended, the “Agreement”). Capitalized terms used, but not defined herein shall have the meanings ascribed to such terms in the Agreement.

WHEREAS, the Parties now wish to further amend the Agreement pursuant to the terms and conditions set forth herein;

NOW, THEREFORE, in consideration of the premises, the mutual covenants contained herein and other valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Parties hereby agree as follows:

1. Section 2.2 is deleted in its entirety and replaced with the following language:

“2.2 Project Selection; Research Term Extension. During the first two (2) years after the Effective Date, Astellas may specify up to two (2) Additional Projects to be conducted under the Collaboration (along with the Initial Project). If any such Additional Projects are specified by Astellas during the first two (2) years after the Effective Date, the Research Term for the Agreement will be extended through the completion of the last Project. If either Party notifies the other Party that it desires to extend the Research Term for any Project beyond its initial term, the other Party will reasonably consider such request and the Parties will discuss such extension.”

2. Except as amended hereby, all other terms of the Agreement shall remain unchanged and in full force and effect.

3. This Amendment No. 2 will be governed by, and construed in accordance with, the laws of the state of New York, without taking into consideration any choice of law principles that would lead to the application of the laws of another jurisdiction.

Signatures Appear on the Page Immediately Following

IN WITNESS WHEREOF, the Parties have caused this Amendment No. 2 to be executed by their duly authorized representatives.

2