Next Article in Journal
SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
Next Article in Special Issue
SARS-CoV-2: Ultrastructural Characterization of Morphogenesis in an In Vitro System
Previous Article in Journal
Replication and Spread of Oncolytic Herpes Simplex Virus in Solid Tumors
Previous Article in Special Issue
Evaluation of Clinical and Immune Responses in Recovered Children with Mild COVID-19
Article

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

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
*
Authors to whom correspondence should be addressed.
Academic Editors: Concetta Castilletti and Caijun Sun
Viruses 2022, 14(1), 119; https://doi.org/10.3390/v14010119 (registering DOI)
Received: 29 November 2021 / Revised: 3 January 2022 / Accepted: 4 January 2022 / Published: 10 January 2022
(This article belongs to the Special Issue SARS-CoV-2 Host Cell Interactions)
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. View Full-Text
Keywords: SARS-CoV-2; coronavirus surface protein S-spike; arbidol; molecular dynamics; molecular docking; pseudoviral system SARS-CoV-2; coronavirus surface protein S-spike; arbidol; molecular dynamics; molecular docking; pseudoviral system
Show Figures

Graphical abstract

MDPI and ACS Style

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, 14, 119. https://doi.org/10.3390/v14010119

AMA Style

Borisevich SS, Khamitov EM, Gureev MA, Yarovaya OI, Rudometova NB, Zybkina AV, Mordvinova ED, Shcherbakov DN, Maksyutov RA, Salakhutdinov NF. Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights. Viruses. 2022; 14(1):119. https://doi.org/10.3390/v14010119

Chicago/Turabian Style

Borisevich, Sophia S., Edward M. Khamitov, Maxim A. Gureev, Olga I. Yarovaya, Nadezhda B. Rudometova, Anastasiya V. Zybkina, Ekaterina D. Mordvinova, Dmitriy N. Shcherbakov, Rinat A. Maksyutov, and Nariman F. Salakhutdinov. 2022. "Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights" Viruses 14, no. 1: 119. https://doi.org/10.3390/v14010119

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop