Identification and Exploration of a Series of SARS-Cov-2 M<sup>Pro</sup> Cyano-Based Inhibitors Revealing Ortho-Substitution Effects within the P3 Biphenyl Group
Starting from a simple scaffold hopping exercise based on our previous exploration of cysteine protease inhibitors against legumain, compound <b>6a</b> was identified as a starting point for the development of a SARS-CoV-2 main protease (M<sup>Pro</sup>) inhibitor. Compound <b>6a</b> displayed submicromolar biochemical potency in the ultrasensitive assay developed by Drag and co-workers. Through an iterative structure-activity relationship campaign, we discovered an unexpected improvement in both biochemical and cellular potency through the incorporation of an ortho substituent within the P3 benzamide. X-ray crystallography revealed that incorporation of the ortho substituent caused a subtle but important binding enhancement of the P1 glutamate group within the M<sup>Pro</sup> S1 pocket. While incorporation of the ortho substituent improved the potency, the off-target selectivity against a panel of cysteine proteases and cell activity remained suboptimal. Further scanning of the P2 core revealed that incorporation of the 3.1.0 proline could address these issues and afford compound <b>22e</b>, a highly potent and cellularly active M<sup>Pro</sup> inhibitor.
Authors
- Marcin Drąg (ORCID: https://orcid.org/0000-0001-8510-1967)
- Richard D. Williams (ORCID: https://orcid.org/0000-0002-7710-2975)
- Christopher J. Scott (ORCID: https://orcid.org/0000-0002-7582-3808)
- Chloé James (ORCID: https://orcid.org/0000-0001-9553-2701)
- Anindita Nayak (ORCID: https://orcid.org/0000-0001-8735-4132)
- Mikołaj Żmudziński (ORCID: https://orcid.org/0000-0002-9792-9160)
- Shaun K. Olsen (ORCID: https://orcid.org/0000-0002-1265-7101)
- Digant Nayak (ORCID: https://orcid.org/0000-0003-3680-0846)
- Dirk Jochmans (ORCID: https://orcid.org/0000-0002-9265-6028)
- Priscila dos Santos Bury
- Johan Neyts (ORCID: https://orcid.org/0000-0002-0033-7514)
- Mohammad Afsar (ORCID: https://orcid.org/0000-0002-3062-9219)
- Emma Clyde-Allen
Institutions
- Wrocław University of Science and Technology (PL)
- Queen's University Belfast (GB)
- The University of Texas at San Antonio Health Science Center (US)
- Rega Institute for Medical Research (BE)
- Institute of Molecular Bioimaging and Physiology (IT)
- Institut de Recherche Vaccinale (FR)
- Cancer Research Institute of the Slovak Academy of Sciences (SK)
- Institute for the Future (US)
- Elucid Bioimaging (US)
- KU Leuven (BE)
Publication Details
- Journal
- ACS Medicinal Chemistry Letters
- Published
- 2025-09-25
- DOI
- https://doi.org/10.1021/acsmedchemlett.5c00301
- Primary Topic
- Computational Drug Discovery Methods
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Cancer Prevention and Research Institute of Texas
- UK Research and Innovation
- National Institutes of Health
- National Institute of General Medical Sciences
- Office of Research Infrastructure Programs, National Institutes of Health
- Argonne National Laboratory