Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights | Sciact - CRIS-system of Boreskov Institute of Catalysis

Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights Full article

Journal

Viruses
, E-ISSN: 1999-4915

Output data

Year: 2022, Volume: 14, Number: 1, Article number : 119, Pages count : 21 DOI: 10.3390/v14010119

Tags

SARS-CoV-2; coronavirus surface protein S-spike; arbidol; molecular dynamics; molecular docking; pseudoviral system

Authors

Borisevich Sophia S. ¹ , Khamitov Edward M. ¹ , Gureev Maxim A. ^2,3 , Yarovaya Olga I. ⁴ , Rudometova Nadezhda B. ⁵ , Zybkina Anastasiya V. ⁵ , Mordvinova Ekaterina D. ⁴ , Shcherbakov Dmitriy N. ⁵ , Maksyutov Rinat A. ⁵ , Salakhutdinov Nariman F. ⁴

Affiliations

1	Ufa Federal Research Center, Laboratory of Chemical Physics, Ufa Institute of Chemistry, RAS, Octyabrya pr., 71, 450054 Ufa, Russia
2	Research Center “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
3	Department of Computational Biology, Sirius University of Science and Technology, 354349 Sochi, Russia
4	Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent'ev Av., 630090 Novosibirsk, Russia
5	State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559 Novosibirsk, Russia

In this work, we evaluated the antiviral activity of Arbidol (Umifenovir) against SARS-CoV-2 using a pseudoviral system with the glycoprotein S of the SARS-CoV-2 virus on its surface. In order to search for binding sites to protein S of the virus, we described alternative binding sites of Arbidol in RBD and in the ACE-2-RBD complex. As a result of our molecular dynamics simulations combined with molecular docking data, we note the following fact: wherever the molecules of Arbidol bind, the interaction of the latter affects the structural flexibility of the protein. This interaction may result both in a change in the shape of the domain–enzyme binding interface and simply in a change in the structural flexibility of the domain, which can subsequently affect its affinity to the enzyme. In addition, we examined the possibility of Arbidol binding in the stem part of the surface protein. The possibility of Arbidol binding in different parts of the protein is not excluded. This may explain the antiviral activity of Arbidol. Our results could be useful for researchers searching for effective SARS-CoV-2 virus inhibitors targeting the viral entry stage.

Borisevich S.S. , Khamitov E.M. , Gureev M.A. , Yarovaya O.I. , Rudometova N.B. , Zybkina A.V. , Mordvinova E.D. , Shcherbakov D.N. , Maksyutov R.A. , Salakhutdinov N.F.
Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights
Viruses. 2022. V.14. N1. 119 :1-21. DOI: 10.3390/v14010119 WOS Scopus РИНЦ ANCAN PMID OpenAlex

Submitted:	Nov 29, 2021
Accepted:	Jan 4, 2022
Published print:	Jan 10, 2022

Web of science:	WOS:000749830700001
Scopus:	2-s2.0-85122799818
Elibrary:	48142966
Chemical Abstracts:	2022:216953
Chemical Abstracts (print):	178:286550
PMID:	35062323
OpenAlex:	W4205305236

DB	Citing
OpenAlex	10
Web of science	8
Scopus	8