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The two SARS-CoV-2 proteases, i. e. the main protease (Mpro ) and the papain-like protease (PLpro ), which hydrolyze the viral polypeptide chain giving functional non-structural proteins, are essential for viral replication and are medicinal chemistry targets. We report a high-throughput mass spectrometry (MS)-based assay which directly monitors PLpro catalysis in vitro. The assay was applied to investigate the effect of reported small-molecule PLpro inhibitors and selected Mpro inhibitors on PLpro catalysis. The results reveal that some, but not all, PLpro inhibitor potencies differ substantially from those obtained using fluorescence-based assays. Some substrate-competing Mpro inhibitors, notably PF-07321332 (nirmatrelvir) which is in clinical development, do not inhibit PLpro . Less selective Mpro inhibitors, e. g. auranofin, inhibit PLpro , highlighting the potential for dual PLpro /Mpro inhibition. MS-based PLpro assays, which are orthogonal to widely employed fluorescence-based assays, are of utility in validating inhibitor potencies, especially for inhibitors operating by non-covalent mechanisms.

Original publication

DOI

10.1002/cmdc.202200016

Type

Journal article

Journal

ChemMedChem

Publication Date

04/05/2022

Volume

17

Keywords

Nucleophilic cysteine protease, PF-07321332/nirmatrelvir, SARS-CoV-2 main protease/Mpro, SARS-CoV-2 papain-like protease/PLpro, viral protease inhibition, Antiviral Agents, COVID-19, Coronavirus Papain-Like Proteases, Humans, Lactams, Leucine, Mass Spectrometry, Nitriles, Peptide Hydrolases, Proline, Protease Inhibitors, SARS-CoV-2