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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.
Hassan, Heba Ali; Hassan, Ahmed R; Mohamed, Eslam A R; Al-Khdhairawi, Ahmad; Karkashan, Alaa; Attar, Roba; Allemailem, Khaled S; Al Abdulmonem, Waleed; Shimizu, Kuniyoshi; Abdel-Rahman, Iman A M; Allam, Ahmed E.
  • Hassan HA; Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt.
  • Hassan AR; Desert Research Center, Medicinal and Aromatic Plants Department, Cairo 11753, Egypt.
  • Mohamed EAR; Department of Chemistry, Faculty of Science, Minia University, Minia 61511, Egypt.
  • Al-Khdhairawi A; Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia.
  • Karkashan A; Department of Biology, College of Sciences, University of Jeddah, Jeddah 21959, Saudi Arabia.
  • Attar R; Department of Biology, College of Sciences, University of Jeddah, Jeddah 21959, Saudi Arabia.
  • Allemailem KS; Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.
  • Al Abdulmonem W; Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia.
  • Shimizu K; Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
  • Abdel-Rahman IAM; Department of Pharmacognosy, Faculty of Pharmacy, South Valley University, Qena 83523, Egypt.
  • Allam AE; Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt.
Molecules ; 27(9)2022 May 04.
Article in English | MEDLINE | ID: covidwho-1820345
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-ß-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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Euphorbia / COVID-19 Type of study: Clinical Practice Guide / Risk factors Topics: Variants Limits: Humans Language: English Journal subject: Biology Year: 2022 Document Type: Article Affiliation country: Molecules27092929

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Euphorbia / COVID-19 Type of study: Clinical Practice Guide / Risk factors Topics: Variants Limits: Humans Language: English Journal subject: Biology Year: 2022 Document Type: Article Affiliation country: Molecules27092929