Natural diketones as potential covalent ligands for SARS-CoV-2 proteins: an in silico docking study
https://doi.org/10.29235/1561-8331-2022-58-3-280-285
Abstract
Our computer-aided protein-ligand docking test using Autodock Vina software allowed to reveal the potential of few α- and β-diketones from plants and alternative living organisms as covalent ligands for few proteins of coronavirus SARS-CoV-2 – a causative agent of COVID-19. It has been established that values for energy of binding (docking score, Ebind, kcal/mol) less than –7.5 and for distances of ligands’ carbonyl groups to side chain nitrogens of arginine residues of some coronaviral enzymes within 0.4 nm have been true for β-diketones 6-gingerdione (Pubchem code CID162952), 8-gingerdione (CID14440537), tetrahydrocurcumine (CID124072) as well as α-diketone wallitaxane E (CID132967478). The in silico revealed interactions are interesting to be verified in vitro and they point out a possibility of investigation of the compounds and related natural materials as tools for struggle against coronaviral infections.
Supporting agencies: The work was supported by BRFFR grant X19COVID-030
About the Authors
Ya. V. Faletrov
Belarusian State University; Research Institute for Physical Chemical Problems, Belarusian State University
Belarus
Belarus
Faletrov Yaroslav V. – Ph. D. (Chemistry), Associate Professor, doctoral student of the Department of Macromolecular Compounds, Leading Researcher.
14, Leningradskaya str., 220006, Minsk
V. A. Staravoitava
Research Institute for Physical Chemical Problems, Belarusian State University
Belarus
Belarus
Staravoitava Victoryia A. – Research Assistant trainee of the Laboratory of Biochemistry of Medical Drugs.
14, Leningradskaya str., 220006, Minsk
H. I. Pozniak
Belarusian State University
Belarus
Belarus
Pozniak Hleb I. – 5th-year Student of the Faculty.
4, Nezavisimosti ave., 220030, Minsk
V. M. Shkumatov
Belarusian State University; Research Institute for Physical Chemical Problems, Belarusian State University
Belarus
Belarus
Shkumatov Vladimir M. – Corresponding Member of the National Academy of Sciences of Belarus, D. Sc. (Biology), Professor, Head of the Laboratory.
14, Leningradskaya str., 220006, Minsk
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