Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

Molecular docking and dynamics simulations were conducted to investigate the antiviral activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin, and remdesivir as control ligands. The parameters calculated were docking score and binding energy/molecular mechanics-...

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Bibliographic Details
Published in:Journal of King Saud University. Science 2022-01, Vol.34 (1), p.101707-101707, Article 101707
Main Authors: Fatriansyah, Jaka Fajar, Rizqillah, Raihan Kenji, Yandi, Muhamad Yusup, Fadilah, Sahlan, Muhamad
Format: Article
Language:English
Subjects:
Drug discovery
Molecular docking
Molecular dynamics
Original
SARS-CoV-2
Sulabiroin-A
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Summary:Molecular docking and dynamics simulations were conducted to investigate the antiviral activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin, and remdesivir as control ligands. The parameters calculated were docking score and binding energy/molecular mechanics-generalized born surface area (MMGBSA), root mean square displacement (RMSD), and root mean square fluctuation (RMSF). Docking and MMGBSA scores showed that all the ligands demonstrate an excellent candidate as an inhibitor, and the order of both scores is hesperidin, remdesivir, quercetin, and sulabiroin-A. The molecular dynamics simulation showed that all the ligands are good candidates as inhibitors. Although the fluctuation of Sulabiroin-A is relatively high, it has less protein–ligand interaction time than other ligands. Overall, there is still a good possibility that sulabiroin-A can be used as an alternative inhibitor if a new structure of receptor SARS-CoV-2 is used.
ISSN:1018-3647
2213-686X
DOI:10.1016/j.jksus.2021.101707