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Conducting the RBD of SARS-CoV-2 Omicron Variant with Phytoconstituents from Euphorbia dendroides to Repudiate the Binding of Spike Glycoprotein Using Computational Molecular Search and Simulation Approach

Authors :
Heba Ali Hassan
Ahmed R. Hassan
Eslam A.R. Mohamed
Ahmad Al-Khdhairawi
Alaa Karkashan
Roba Attar
Khaled S. Allemailem
Waleed Al Abdulmonem
Kuniyoshi Shimizu
Iman A. M. Abdel-Rahman
Ahmed E. Allam
Source :
Molecules, Vol 27, Iss 9, p 2929 (2022)
Publication Year :
2022
Publisher :
MDPI AG, 2022.

Abstract

(1) Background: Natural constituents are still a preferred route for counteracting the outbreak of COVID-19. Essentially, flavonoids have been found to be among the most promising molecules identified as coronavirus inhibitors. Recently, a new SARS-CoV-2 B.1.1.529 variant has spread in many countries, which has raised awareness of the role of natural constituents in attempts to contribute to therapeutic protocols. (2) Methods: Using various chromatographic techniques, triterpenes (1–7), phenolics (8–11), and flavonoids (12–17) were isolated from Euphorbia dendroides and computationally screened against the receptor-binding domain (RBD) of the SARS-CoV-2 Omicron variant. As a first step, molecular docking calculations were performed for all investigated compounds. Promising compounds were subjected to molecular dynamics simulations (MD) for 200 ns, in addition to molecular mechanics Poisson–Boltzmann surface area calculations (MM/PBSA) to determine binding energy. (3) Results: MM/PBSA binding energy calculations showed that compound 14 (quercetin-3-O-β-D-glucuronopyranoside) and compound 15 (quercetin-3-O-glucuronide 6″-O-methyl ester) exhibited strong inhibition of Omicron, with ΔGbinding of −41.0 and −32.4 kcal/mol, respectively. Finally, drug likeness evaluations based on Lipinski’s rule of five also showed that the discovered compounds exhibited good oral bioavailability. (4) Conclusions: It is foreseeable that these results provide a novel intellectual contribution in light of the decreasing prevalence of SARS-CoV-2 B.1.1.529 and could be a good addition to the therapeutic protocol.

Details

Language :
English
ISSN :
14203049
Volume :
27
Issue :
9
Database :
Directory of Open Access Journals
Journal :
Molecules
Publication Type :
Academic Journal
Accession number :
edsdoj.1376b8c93bbd4a2b8bee11aca3a88d0f
Document Type :
article
Full Text :
https://doi.org/10.3390/molecules27092929