Molecular dynamics and docking studies on potentially active natural phytochemicals for targeting SARS-CoV-2 main protease

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Sankaran S. K., Nair A. S.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol.41, no.14, pp.6459-6475, 2023 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 41 Issue: 14
  • Publication Date: 2023
  • Doi Number: 10.1080/07391102.2022.2107573
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE
  • Page Numbers: pp.6459-6475
  • Keywords: SARS-CoV-2, COVID19, Phytochemicals, DOCKTHOR, LibDock, Molecular dynamics
  • Bursa Uludag University Affiliated: No


In the present study, we screened eighty seven novel phytochemical compounds from four popular herbs, such as, Aegle Marmelos, Coleus Amboinicus, Aerva Lanata and Biophytum Sensitivum and identified the best three for targeting the main protease (M-pro) receptor of SARS-CoV-2. After categorizing all the phytochemicals based upon LibDock scores and hydrogen bonding interactions, the top ranked 26 compounds were further subjected for detailed Molecular dynamics (MD) study. From these screening we identified that Aegelinosides B leads the list with a high LibDock value of 142.50 (binding energy: -8.54 kcal/mol), which is better than several popular reference compounds namely, Tipranavir (LibDock score, 141.50), Saquinavir (125.34), Zopicole (122.9), Pirenepine (122.70), (115.37), Metixene (109.18), Oxiconazole Pimozide (138.00) and Rimonabant (91.88). Detailed analysis for structural stability (RMSD), C alpha fluctuations (RMSF), intermolecular hydrogen bond interactions, effect of solvent accessibility (SASA) and compactness (Rg) factors were performed for the best six compounds and it is found that they are very stable and exhibit folding behavior. Apart from the docking and MD tests, through further drug-likeness and toxicity tests, three compounds, such as, Aegelinosides B, Epicatechin, and Feruloyltyramine (LibDock scores, respectively, 142.50, 124.33 and 129.06) can be suggested for fighting SARS-CoV-2. Communicated by Ramaswamy H. Sarma