Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs

COVID-19 is spreading rapidly yet there is no clinically proven drug available now. Soil-derived Streptomyces sp. GMR22 has a large genome size (11.4 Mbp) and a huge BGCs (Biosynthetic Gene Clusters) encoding secondary metabolites. This bacterium is a potential source for producing a wide variety of...

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Autores principales:	Yohana Nadia Melinda, Jaka Widada, Tutik Dwi Wahyuningsih, Rifki Febriansah, Ema Damayanti, Mustofa Mustofa
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Streptomyces Secondary metabolite SARS-CoV-2 AntiSMASH COVID-19 Science (General) Q1-390 Social sciences (General) H1-99
Acceso en línea:	https://doaj.org/article/e1f81f8991b24cd881baec6247e961fa
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spelling	oai:doaj.org-article:e1f81f8991b24cd881baec6247e961fa2021-12-02T05:02:33ZMetabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs2405-844010.1016/j.heliyon.2021.e08308https://doaj.org/article/e1f81f8991b24cd881baec6247e961fa2021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2405844021024117https://doaj.org/toc/2405-8440COVID-19 is spreading rapidly yet there is no clinically proven drug available now. Soil-derived Streptomyces sp. GMR22 has a large genome size (11.4 Mbp) and a huge BGCs (Biosynthetic Gene Clusters) encoding secondary metabolites. This bacterium is a potential source for producing a wide variety of compounds which are able to block SARS-CoV-2, the causative agent of COVID-19. This study aimed to predict the secondary metabolites of Streptomyces sp. GMR22 and to evaluate the ability as SARS-CoV-2 inhibitor. The AntiSMASH 5.0 was used for genome mining analysis and targeted liquid chromatography-high resolution mass spectrometry (LC-HRMS) was used for metabolite analysis. In silico molecular docking was performed on important target proteins of SARS-CoV-2 i.e., spike protein (PDB ID: 6LXT), Receptor Binding Domain (RBD)-ACE2 (Angiotensin-Converting Enzyme 2) (PDB ID: 6VW1), 3CLpro (3-chymotrypsin-like protease) (PDB ID: 6M2N), and RdRp (RNA-dependent RNA polymerase) (PDB ID: 6M71). Two compounds from GMR22 extract, echoside A and echoside B were confirmed by targeted LC-HRMS and potential as SARS-CoV-2 inhibitor. Echoside A and echoside B showed higher docking score than remdesivir as COVID-19 drug on four target proteins, i.e., spike protein (−7.9 kcal/mol and −7.8 kcal/mol), RBD-ACE2 (−7.5 kcal/mol and −8.2 kcal/mol), 3CLpro (−8.4 kcal/mol and −9.4 kcal/mol) and RdRp (−7.3 kcal/mol and −8.0 kcal/mol). A combination of genome mining and metabolomic approaches can be used as integrated strategy to elucidate the potential of GMR22 as a resource in the discovery of anti-COVID -19 compound.Yohana Nadia MelindaJaka WidadaTutik Dwi WahyuningsihRifki FebriansahEma DamayantiMustofa MustofaElsevierarticleStreptomycesSecondary metaboliteSARS-CoV-2AntiSMASHCOVID-19Science (General)Q1-390Social sciences (General)H1-99ENHeliyon, Vol 7, Iss 11, Pp e08308- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Streptomyces Secondary metabolite SARS-CoV-2 AntiSMASH COVID-19 Science (General) Q1-390 Social sciences (General) H1-99
spellingShingle	Streptomyces Secondary metabolite SARS-CoV-2 AntiSMASH COVID-19 Science (General) Q1-390 Social sciences (General) H1-99 Yohana Nadia Melinda Jaka Widada Tutik Dwi Wahyuningsih Rifki Febriansah Ema Damayanti Mustofa Mustofa Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
description	COVID-19 is spreading rapidly yet there is no clinically proven drug available now. Soil-derived Streptomyces sp. GMR22 has a large genome size (11.4 Mbp) and a huge BGCs (Biosynthetic Gene Clusters) encoding secondary metabolites. This bacterium is a potential source for producing a wide variety of compounds which are able to block SARS-CoV-2, the causative agent of COVID-19. This study aimed to predict the secondary metabolites of Streptomyces sp. GMR22 and to evaluate the ability as SARS-CoV-2 inhibitor. The AntiSMASH 5.0 was used for genome mining analysis and targeted liquid chromatography-high resolution mass spectrometry (LC-HRMS) was used for metabolite analysis. In silico molecular docking was performed on important target proteins of SARS-CoV-2 i.e., spike protein (PDB ID: 6LXT), Receptor Binding Domain (RBD)-ACE2 (Angiotensin-Converting Enzyme 2) (PDB ID: 6VW1), 3CLpro (3-chymotrypsin-like protease) (PDB ID: 6M2N), and RdRp (RNA-dependent RNA polymerase) (PDB ID: 6M71). Two compounds from GMR22 extract, echoside A and echoside B were confirmed by targeted LC-HRMS and potential as SARS-CoV-2 inhibitor. Echoside A and echoside B showed higher docking score than remdesivir as COVID-19 drug on four target proteins, i.e., spike protein (−7.9 kcal/mol and −7.8 kcal/mol), RBD-ACE2 (−7.5 kcal/mol and −8.2 kcal/mol), 3CLpro (−8.4 kcal/mol and −9.4 kcal/mol) and RdRp (−7.3 kcal/mol and −8.0 kcal/mol). A combination of genome mining and metabolomic approaches can be used as integrated strategy to elucidate the potential of GMR22 as a resource in the discovery of anti-COVID -19 compound.
format	article
author	Yohana Nadia Melinda Jaka Widada Tutik Dwi Wahyuningsih Rifki Febriansah Ema Damayanti Mustofa Mustofa
author_facet	Yohana Nadia Melinda Jaka Widada Tutik Dwi Wahyuningsih Rifki Febriansah Ema Damayanti Mustofa Mustofa
author_sort	Yohana Nadia Melinda
title	Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
title_short	Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
title_full	Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
title_fullStr	Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
title_full_unstemmed	Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs
title_sort	metabologenomics approach to the discovery of novel compounds from streptomyces sp. gmr22 as anti-sars-cov-2 drugs
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/e1f81f8991b24cd881baec6247e961fa
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Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs

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