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

Frontiers in Pharmacology

Inna N. Kurbatskaia¹  Nikita A. Kuznetsov¹  Aydar A. Ishmukhametov¹  Elena N. Kaliberda²  Victoria I. Uvarova²  Anastasiia D. Fomina²  Vera D. Knorre³  Anatoly A. Bulygin³  Ivan V. Smirnov³  Alexandra A. Kuznetsova⁴  Alexandre Varnek⁴  Alexander G. Gabibov⁵  Alexey M. Egorov⁵  Maria Yu. Zakharova⁶  Dmitry I. Osolodkin⁷  Olga S. Fedorova⁸  Liubov I. Kozlovskaya⁸ 

[1] D IBP RAS” (Institute of Poliomyelitis), Moscow, Russia;;FSASI “Chumakov FSC R&Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia;Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia;Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia;Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia;Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, Strasbourg, France;Lomonosov Moscow State University, Moscow, Russia;

关键词: SARS-CoV-2;    main protease;    pre-steady-state kinetics;    substrate cleavage;    inhibitor binding;    molecular docking;   

DOI  :  10.3389/fphar.2021.773198

来源: DOAJ

【 摘 要 】

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, Mpro, 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 Mpro inhibitors have turned out to be promising anticoronaviral agents. Thus, an effective platform for quantitative screening of Mpro-targeting molecules is urgently needed. Here, we propose a pre–steady-state kinetic analysis of the interaction of Mpro with inhibitors as a basis for such a platform. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type Mpro and by its catalytically inactive mutant C145A. The enzyme induces conformational changes of the peptide during the reaction. The inhibition of Mpro 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 Mpro mutant interacts with PF-00835231 approximately 100-fold less effectively. Nevertheless, the binding constant of PF-00835231 toward C145A Mpro 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 Mpro.

【 授权许可】

Unknown