Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

Sanders, Brian C.; Pokhrel, Suman; Labbe, Audrey D.; Mathews, Irimpan I.; Cooper, Connor J.; Davidson, Russell B.; Phillips, Gwyndalyn; Weiss, Kevin L.; Zhang, Qiu; O'Neill, Hugh; Kaur, Manat; Schmidt, Jurgen G.; Reichard, Walter; Surendranathan, Surekha; Parvathareddy, Jyothi; Phillips, Lexi; Rainville, Christopher; Sterner, David E.; Kumaran, Desigan; Andi, Babak; Babnigg, Gyorgy; Joachimiak, Andrzej

doi:10.6082/96f47-32w17

Published March 28, 2023 | Version v1

Journal article Open

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

1. Oak Ridge National Laboratory
2. Stanford University
3. Stanford Synchrotron Radiation Lightsource
4. Los Alamos National Laboratory
5. University of Tennessee
6. Utah State University
7. Progenra Inc.
8. Brookhaven National Laboratory
9. University of Chicago

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M⁻¹ s⁻¹, achieves sub-μM EC₅₀ values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Notes

Due to the large number of authors, only the first 20 and the University of Chicago authors are included on the above author list. Please download the article for the complete list of authors.

Data availability

Structural data for the SARS-CoV-2 papain-like protease in complex with compound 7 were deposited in the Protein Data Bank (PDB) with accession code 8EUA. All other data generated or analyzed during this study are included in this published article (and its supplementary information files). Publicly available datasets used in this study are X-ray crystal structures of SARS-CoV-2 PLpro with accession codes PDB ID: 7JIR, 7CMD, 6WX4, 6W9C, 6WZU, 6XAA; a structure of UCH-L1 with PDB ID: 3KW5; and a structure of USP4 with PDB ID: 2Y6E. Source data are provided with this paper. Data are available from the corresponding authors upon request. Source data are provided with this paper.

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