Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site

Rennie, M. L. , Arkinson, C., Chaugule, V. K. and Walden, H. (2022) Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site. Science Advances, 8(39), eabq6353. (doi: 10.1126/sciadv.abq6353) (PMID:36170365) (PMCID:PMC9519042)

Abstract

Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase 1 clinical trials, have been established, their binding mode is unknown. Here, we use cryo–electron microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5-Å resolution, with and without ML323, we find an unusual binding mode in which the inhibitor disrupts part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1.

• Item Type: Articles
• Additional Information: Funding: European Research Council (ERC-2015-CoG-681582) ICLUb consolidator grant to H.W. 13. Medical Research Council (MC_UU_120164/12) to H.W.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Chaugule, Dr Viduth and Arkinson, Connor and Rennie, Dr Martin and Walden, Professor Helen
• Authors: Rennie, M. L., Arkinson, C., Chaugule, V. K., and Walden, H.
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: Science Advances
• Publisher: American Association for the Advancement of Science
• ISSN: 2375-2548
• ISSN (Online): 2375-2548
• Published Online: 28 September 2022
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Science Advances 8(39): eabq6353
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
302391		Regulation of DNA interstrand crosslink repair by ubiquitin.	Helen Walden	European Research Council (ERC)	681506	Institute of Molecular, Cell & Systems Biology