Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery.

Autor:	Zakharova MY; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia., Kuznetsova AA; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia., Uvarova VI; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia., Fomina AD; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia.; Lomonosov Moscow State University, Moscow, Russia., Kozlovskaya LI; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia.; Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia., Kaliberda EN; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia., Kurbatskaia IN; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia., Smirnov IV; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.; Lomonosov Moscow State University, Moscow, Russia., Bulygin AA; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia., Knorre VD; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia., Fedorova OS; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia., Varnek A; Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, Strasbourg, France., Osolodkin DI; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia.; Lomonosov Moscow State University, Moscow, Russia.; Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia., Ishmukhametov AA; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia.; Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia., Egorov AM; FSASI 'Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow, Russia.; Lomonosov Moscow State University, Moscow, Russia., Gabibov AG; Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.; Lomonosov Moscow State University, Moscow, Russia.; Department of Biology and Biotechnology, Higher School of Economics, Moscow, Russia., Kuznetsov NA; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia.; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
Jazyk:	angličtina
Zdroj:	Frontiers in pharmacology [Front Pharmacol] 2021 Dec 06; Vol. 12, pp. 773198. Date of Electronic Publication: 2021 Dec 06 (Print Publication: 2021).
DOI:	10.3389/fphar.2021.773198
Abstrakt:	The design of effective target-specific drugs for COVID-19 treatment has become an intriguing challenge for modern science. The SARS-CoV-2 main protease, M pro , responsible for the processing of SARS-CoV-2 polyproteins and production of individual components of viral replication machinery, is an attractive candidate target for drug discovery. Specific M pro inhibitors have turned out to be promising anticoronaviral agents. Thus, an effective platform for quantitative screening of M pro -targeting molecules is urgently needed. Here, we propose a pre-steady-state kinetic analysis of the interaction of M pro with inhibitors as a basis for such a platform. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type M pro and by its catalytically inactive mutant C145A. The enzyme induces conformational changes of the peptide during the reaction. The inhibition of M pro by boceprevir, telaprevir, GC-376, PF-00835231, or thimerosal was investigated. Detailed pre-steady-state kinetics of the interaction of the wild-type enzyme with the most potent inhibitor, PF-00835231, revealed a two-step binding mechanism, followed by covalent complex formation. The C145A M pro mutant interacts with PF-00835231 approximately 100-fold less effectively. Nevertheless, the binding constant of PF-00835231 toward C145A M pro is still good enough to inhibit the enzyme. Therefore, our results suggest that even noncovalent inhibitor binding due to a fine conformational fit into the active site is sufficient for efficient inhibition. A structure-based virtual screening and a subsequent detailed assessment of inhibition efficacy allowed us to select two compounds as promising noncovalent inhibitor leads of SARS-CoV-2 M pro . Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2021 Zakharova, Kuznetsova, Uvarova, Fomina, Kozlovskaya, Kaliberda, Kurbatskaia, Smirnov, Bulygin, Knorre, Fedorova, Varnek, Osolodkin, Ishmukhametov, Egorov, Gabibov and Kuznetsov.)
Databáze:	MEDLINE
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