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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Autores principales:	Jaka Fajar Fatriansyah, Raihan Kenji Rizqillah, Muhamad Yusup Yandi, Fadilah, Muhamad Sahlan
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2022
Materias:	SARS-CoV-2 Molecular docking Molecular dynamics Drug discovery Sulabiroin-A Science (General) Q1-390
Acceso en línea:	https://doaj.org/article/87027c300a354a73923d2d1f259b5547
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spelling	oai:doaj.org-article:87027c300a354a73923d2d1f259b55472021-11-24T04:27:06ZMolecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-21018-364710.1016/j.jksus.2021.101707https://doaj.org/article/87027c300a354a73923d2d1f259b55472022-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1018364721003694https://doaj.org/toc/1018-3647Molecular 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.Jaka Fajar FatriansyahRaihan Kenji RizqillahMuhamad Yusup Yandi FadilahMuhamad SahlanElsevierarticleSARS-CoV-2Molecular dockingMolecular dynamicsDrug discoverySulabiroin-AScience (General)Q1-390ENJournal of King Saud University: Science, Vol 34, Iss 1, Pp 101707- (2022)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 Molecular docking Molecular dynamics Drug discovery Sulabiroin-A Science (General) Q1-390
spellingShingle	SARS-CoV-2 Molecular docking Molecular dynamics Drug discovery Sulabiroin-A Science (General) Q1-390 Jaka Fajar Fatriansyah Raihan Kenji Rizqillah Muhamad Yusup Yandi Fadilah Muhamad Sahlan Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
description	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.
format	article
author	Jaka Fajar Fatriansyah Raihan Kenji Rizqillah Muhamad Yusup Yandi Fadilah Muhamad Sahlan
author_facet	Jaka Fajar Fatriansyah Raihan Kenji Rizqillah Muhamad Yusup Yandi Fadilah Muhamad Sahlan
author_sort	Jaka Fajar Fatriansyah
title	Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
title_short	Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
title_full	Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
title_fullStr	Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
title_full_unstemmed	Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
title_sort	molecular docking and dynamics studies on propolis sulabiroin-a as a potential inhibitor of sars-cov-2
publisher	Elsevier
publishDate	2022
url	https://doaj.org/article/87027c300a354a73923d2d1f259b5547
work_keys_str_mv	AT jakafajarfatriansyah moleculardockinganddynamicsstudiesonpropolissulabiroinaasapotentialinhibitorofsarscov2 AT raihankenjirizqillah moleculardockinganddynamicsstudiesonpropolissulabiroinaasapotentialinhibitorofsarscov2 AT muhamadyusupyandi moleculardockinganddynamicsstudiesonpropolissulabiroinaasapotentialinhibitorofsarscov2 AT fadilah moleculardockinganddynamicsstudiesonpropolissulabiroinaasapotentialinhibitorofsarscov2 AT muhamadsahlan moleculardockinganddynamicsstudiesonpropolissulabiroinaasapotentialinhibitorofsarscov2
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Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

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