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

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

研究成果: ジャーナルへの寄稿学術誌査読

1 被引用数 (Scopus)

抄録

(1) Background: Natural constituents are still a preferred route for counteracting the out-break 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 Omi-cron 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) Conclusion: 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.

本文言語英語
論文番号2929
ジャーナルMolecules
27
9
DOI
出版ステータス出版済み - 5月 1 2022

!!!All Science Journal Classification (ASJC) codes

  • 分析化学
  • 化学(その他)
  • 分子医療
  • 薬科学
  • 創薬
  • 物理化学および理論化学
  • 有機化学

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