Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus

The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-depende...

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Autores principales:	Muhammad Arba, Andry Nur-Hidayat, Ida Usman, Arry Yanuar, Setyanto Tri Wahyudi, Gilbert Fleischer, Dylan James Brunt, Chun Wu
Formato:	article
Lenguaje:	EN
Publicado:	Department of Chemistry, Universitas Gadjah Mada 2020
Materias:	Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/27197eeb09c144cd8d6c76c544435626
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spelling	oai:doaj.org-article:27197eeb09c144cd8d6c76c5444356262021-12-02T16:11:23ZVirtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus1411-94202460-157810.22146/ijc.56120https://doaj.org/article/27197eeb09c144cd8d6c76c5444356262020-10-01T00:00:00Zhttps://jurnal.ugm.ac.id/ijc/article/view/56120https://doaj.org/toc/1411-9420https://doaj.org/toc/2460-1578The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-dependent RNA polymerase. It is the key enzyme in the viral replication machinery, and it does not exist in human beings, therefore its targeting has been considered as a strategic approach. Here we describe the identification of potential hits from Indonesian Herbal and ZINC databases. The pharmacophore modeling was employed followed by molecular docking and dynamics simulation for 40 ns. 151 and 14480 hit molecules were retrieved from Indonesian herbal and ZINC databases, respectively. Three hits that were selected based on the structural analysis were stable during 40 ns, while binding energy prediction further implied that ZINC1529045114, ZINC169730811, and 9-Ribosyl-trans-zeatin had tighter binding affinities compared to Remdesivir. The ZINC169730811 had the strongest affinity toward RdRp compared to the other two hits including Remdesivir and its binding was corroborated by electrostatic, van der Waals, and nonpolar contribution for solvation energies. The present study offers three hits showing tighter binding to RdRp based on MM-PBSA binding energy prediction for further experimental verification.Muhammad ArbaAndry Nur-HidayatIda UsmanArry YanuarSetyanto Tri WahyudiGilbert FleischerDylan James BruntChun WuDepartment of Chemistry, Universitas Gadjah MadaarticleChemistryQD1-999ENIndonesian Journal of Chemistry, Vol 20, Iss 6, Pp 1430-1440 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Chemistry QD1-999
spellingShingle	Chemistry QD1-999 Muhammad Arba Andry Nur-Hidayat Ida Usman Arry Yanuar Setyanto Tri Wahyudi Gilbert Fleischer Dylan James Brunt Chun Wu Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
description	The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-dependent RNA polymerase. It is the key enzyme in the viral replication machinery, and it does not exist in human beings, therefore its targeting has been considered as a strategic approach. Here we describe the identification of potential hits from Indonesian Herbal and ZINC databases. The pharmacophore modeling was employed followed by molecular docking and dynamics simulation for 40 ns. 151 and 14480 hit molecules were retrieved from Indonesian herbal and ZINC databases, respectively. Three hits that were selected based on the structural analysis were stable during 40 ns, while binding energy prediction further implied that ZINC1529045114, ZINC169730811, and 9-Ribosyl-trans-zeatin had tighter binding affinities compared to Remdesivir. The ZINC169730811 had the strongest affinity toward RdRp compared to the other two hits including Remdesivir and its binding was corroborated by electrostatic, van der Waals, and nonpolar contribution for solvation energies. The present study offers three hits showing tighter binding to RdRp based on MM-PBSA binding energy prediction for further experimental verification.
format	article
author	Muhammad Arba Andry Nur-Hidayat Ida Usman Arry Yanuar Setyanto Tri Wahyudi Gilbert Fleischer Dylan James Brunt Chun Wu
author_facet	Muhammad Arba Andry Nur-Hidayat Ida Usman Arry Yanuar Setyanto Tri Wahyudi Gilbert Fleischer Dylan James Brunt Chun Wu
author_sort	Muhammad Arba
title	Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
title_short	Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
title_full	Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
title_fullStr	Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
title_full_unstemmed	Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus
title_sort	virtual screening of the indonesian medicinal plant and zinc databases for potential inhibitors of the rna-dependent rna polymerase (rdrp) of 2019 novel coronavirus
publisher	Department of Chemistry, Universitas Gadjah Mada
publishDate	2020
url	https://doaj.org/article/27197eeb09c144cd8d6c76c544435626
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Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus

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