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In silico screening of some compounds derived from the desert medicinal plant Rhazya stricta for the potential treatment of COVID-19.
Baeshen, Nabih A; Albeshri, Abdulaziz O; Baeshen, Naseebh N; Attar, Roba; Karkashan, Alaa; Abbas, Basma; Bouback, Thamer A; Aljaddawi, Abdullah A; Refai, Mohammed Y; Abdelkader, Hayam S; Al Tamim, Abdullah; Alowaifeer, Abdullah; Ahmed, Firoz; Baeshen, Mohammed N.
  • Baeshen NA; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
  • Albeshri AO; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
  • Baeshen NN; Department of Biology, College of Sciences and Arts, University of Jeddah, Khulais Campus, Jeddah, Saudi Arabia. nnbaeshen@uj.edu.sa.
  • Attar R; Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Karkashan A; Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Abbas B; Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Bouback TA; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
  • Aljaddawi AA; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
  • Refai MY; Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Abdelkader HS; Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Al Tamim A; Reference Laboratory for Food Chemistry, Saudi Food & Drug Authority (SFDA), Riyadh, Saudi Arabia.
  • Alowaifeer A; Reference Laboratory for Food Chemistry, Saudi Food & Drug Authority (SFDA), Riyadh, Saudi Arabia.
  • Ahmed F; Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
  • Baeshen MN; Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia. mnbaeshen@uj.edu.sa.
Sci Rep ; 12(1): 11120, 2022 07 01.
Article in English | MEDLINE | ID: covidwho-2028700
ABSTRACT
The latest coronavirus pandemic (SARS-CoV-2) poses an exceptional threat to human health and society worldwide. The coronavirus (SARS-CoV-2) spike (S) protein, which is required for viral-host cell penetration, might be considered a promising and suitable target for treatment. In this study, we utilized the nonalkaloid fraction of the medicinal plant Rhazya stricta to computationally investigate its antiviral activity against SARS-CoV-2. Molecular docking and molecular dynamics simulations were the main tools used to examine the binding interactions of the compounds isolated by HPLC analysis. Ceftazidime was utilized as a reference control, which showed high potency against the SARS-CoV-2 receptor binding domain (RBD) in an in vitro study. The five compounds (CID1, CID2, CID3, CID4, and CID5) exhibited remarkable binding affinities (CID1, - 8.9; CID2, - 8.7; and CID3, 4, and 5, - 8.5 kcal/mol) compared to the control compound (- 6.2 kcal/mol). MD simulations over a period of 200 ns further corroborated that certain interactions occurred with the five compounds and the nonalkaloidal compounds retained their positions within the RBD active site. CID2, CID4, and CID5 demonstrated high stability and less variance, while CID1 and CID3 were less stable than ceftazidime. The average number of hydrogen bonds formed per timeframe by CID1, CID2, CID3, and CID5 (0.914, 0.451, 1.566, and 1.755, respectively) were greater than that formed by ceftazidime (0.317). The total binding free energy calculations revealed that the five compounds interacted more strongly within RBD residues (CID1 = - 68.8, CID2 = - 71.6, CID3 = - 74.9, CID4 = - 75.4, CID5 = - 60.9 kJ/mol) than ceftazidime (- 34.5 kJ/mol). The drug-like properties of the selected compounds were relatively similar to those of ceftazidime, and the toxicity predictions categorized these compounds into less toxic classes. Structural similarity and functional group analyses suggested that the presence of more H-acceptor atoms, electronegative atoms, acidic oxygen groups, and nitrogen atoms in amide or aromatic groups were common among the compounds with the lowest binding affinities. In conclusion, this in silico work predicts for the first time the potential of using five R. stricta nonalkaloid compounds as a treatment strategy to control SARS-CoV-2 viral entry.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Plants, Medicinal / Apocynaceae / COVID-19 Drug Treatment Type of study: Experimental Studies / Prognostic study / Randomized controlled trials Topics: Traditional medicine Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-15288-2

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Plants, Medicinal / Apocynaceae / COVID-19 Drug Treatment Type of study: Experimental Studies / Prognostic study / Randomized controlled trials Topics: Traditional medicine Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-15288-2