Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection

Methane is a greenhouse gas which poses a great threat to life on earth as its emissions directly contribute to global warming and methane has a 28-fold higher warming potential over that of carbon dioxide. Ruminants have been identified as a major source of methane emission as a result of methanoge...

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Autores principales:	Yuvaraj Dinakarkumar, Jothi Ramalingam Rajabathar, Selvaraj Arokiyaraj, Iyyappan Jeyaraj, Sai Ramesh Anjaneyulu, Shadakshari Sandeep, Chimatahalli Shanthakumar Karthik, Jimmy Nelson Appaturi, Lee D. Wilson
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	ruminants methane emission methyl-coenzyme M reductase phytochemicals in-silico screening molecular docking Mechanical engineering and machinery TJ1-1570
Acceso en línea:	https://doaj.org/article/cf1b0682b83c4e97819edf86fa14be39
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spelling	oai:doaj.org-article:cf1b0682b83c4e97819edf86fa14be392021-11-25T18:23:54ZAnti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection10.3390/mi121114252072-666Xhttps://doaj.org/article/cf1b0682b83c4e97819edf86fa14be392021-11-01T00:00:00Zhttps://www.mdpi.com/2072-666X/12/11/1425https://doaj.org/toc/2072-666XMethane is a greenhouse gas which poses a great threat to life on earth as its emissions directly contribute to global warming and methane has a 28-fold higher warming potential over that of carbon dioxide. Ruminants have been identified as a major source of methane emission as a result of methanogenesis by their respective gut microbiomes. Various plants produce highly bioactive compounds which can be investigated to find a potential inhibitor of methyl-coenzyme M reductase (the target protein for methanogenesis). To speed up the process and to limit the use of laboratory resources, the present study uses an in-silico molecular docking approach to explore the anti-methanogenic properties of phytochemicals from <i>Cymbopogon</i> <i>citratus</i>, <i>Origanum vulgare</i>, <i>Lavandula officinalis</i>, <i>Cinnamomum zeylanicum</i>, <i>Piper betle</i>, <i>Cuminum cyminum</i>, <i>Ocimum gratissimum</i>, <i>Salvia sclarea</i>, <i>Allium sativum</i>, <i>Rosmarinus officinalis</i> and <i>Thymus vulgaris</i>. A total of 168 compounds from 11 plants were virtually screened. Finally, 25 scrutinized compounds were evaluated against methyl-coenzyme M reductase (MCR) protein using the AutoDock 4.0 program. In conclusion, the study identified 21 out of 25 compounds against inhibition of the MCR protein. Particularly, five compounds: rosmarinic acid (−10.71 kcal/mol), biotin (−9.38 kcal/mol), α-cadinol (−8.16 kcal/mol), (3<i>R</i>,3a<i>S</i>,6<i>R</i>,6a<i>R</i>)-3-(2<i>H</i>-1,3-benzodioxol-4-yl)-6-(2<i>H</i>-1,3-benzodioxol-5-yl)-hexahydrofuro[3,4-<i>c</i>]furan-1-one (−12.21 kcal/mol), and 2,4,7,9-tetramethyl-5decyn4,7diol (−9.02 kcal/mol) showed higher binding energy towards the MCR protein. In turn, these compounds have potential utility as rumen methanogenic inhibitors in the proposed methane inhibitor program. Ultimately, molecular dynamics simulations of rosmarinic acid and (3<i>R</i>,3a<i>S</i>,6<i>R</i>,6a<i>R</i>)-3-(2<i>H</i>-1,3-benzodioxol-4-yl)-6-(2<i>H</i>-1,3-benzodioxol-5-yl)-hexahydrofuro[3,4-<i>c</i>]furan-1-one yielded the best possible interaction and stability with the active site of 5A8K protein for 20 ns.Yuvaraj DinakarkumarJothi Ramalingam RajabatharSelvaraj ArokiyarajIyyappan JeyarajSai Ramesh AnjaneyuluShadakshari SandeepChimatahalli Shanthakumar KarthikJimmy Nelson AppaturiLee D. WilsonMDPI AGarticleruminantsmethane emissionmethyl-coenzyme M reductasephytochemicalsin-silico screeningmolecular dockingMechanical engineering and machineryTJ1-1570ENMicromachines, Vol 12, Iss 1425, p 1425 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	ruminants methane emission methyl-coenzyme M reductase phytochemicals in-silico screening molecular docking Mechanical engineering and machinery TJ1-1570
spellingShingle	ruminants methane emission methyl-coenzyme M reductase phytochemicals in-silico screening molecular docking Mechanical engineering and machinery TJ1-1570 Yuvaraj Dinakarkumar Jothi Ramalingam Rajabathar Selvaraj Arokiyaraj Iyyappan Jeyaraj Sai Ramesh Anjaneyulu Shadakshari Sandeep Chimatahalli Shanthakumar Karthik Jimmy Nelson Appaturi Lee D. Wilson Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
description	Methane is a greenhouse gas which poses a great threat to life on earth as its emissions directly contribute to global warming and methane has a 28-fold higher warming potential over that of carbon dioxide. Ruminants have been identified as a major source of methane emission as a result of methanogenesis by their respective gut microbiomes. Various plants produce highly bioactive compounds which can be investigated to find a potential inhibitor of methyl-coenzyme M reductase (the target protein for methanogenesis). To speed up the process and to limit the use of laboratory resources, the present study uses an in-silico molecular docking approach to explore the anti-methanogenic properties of phytochemicals from <i>Cymbopogon</i> <i>citratus</i>, <i>Origanum vulgare</i>, <i>Lavandula officinalis</i>, <i>Cinnamomum zeylanicum</i>, <i>Piper betle</i>, <i>Cuminum cyminum</i>, <i>Ocimum gratissimum</i>, <i>Salvia sclarea</i>, <i>Allium sativum</i>, <i>Rosmarinus officinalis</i> and <i>Thymus vulgaris</i>. A total of 168 compounds from 11 plants were virtually screened. Finally, 25 scrutinized compounds were evaluated against methyl-coenzyme M reductase (MCR) protein using the AutoDock 4.0 program. In conclusion, the study identified 21 out of 25 compounds against inhibition of the MCR protein. Particularly, five compounds: rosmarinic acid (−10.71 kcal/mol), biotin (−9.38 kcal/mol), α-cadinol (−8.16 kcal/mol), (3<i>R</i>,3a<i>S</i>,6<i>R</i>,6a<i>R</i>)-3-(2<i>H</i>-1,3-benzodioxol-4-yl)-6-(2<i>H</i>-1,3-benzodioxol-5-yl)-hexahydrofuro[3,4-<i>c</i>]furan-1-one (−12.21 kcal/mol), and 2,4,7,9-tetramethyl-5decyn4,7diol (−9.02 kcal/mol) showed higher binding energy towards the MCR protein. In turn, these compounds have potential utility as rumen methanogenic inhibitors in the proposed methane inhibitor program. Ultimately, molecular dynamics simulations of rosmarinic acid and (3<i>R</i>,3a<i>S</i>,6<i>R</i>,6a<i>R</i>)-3-(2<i>H</i>-1,3-benzodioxol-4-yl)-6-(2<i>H</i>-1,3-benzodioxol-5-yl)-hexahydrofuro[3,4-<i>c</i>]furan-1-one yielded the best possible interaction and stability with the active site of 5A8K protein for 20 ns.
format	article
author	Yuvaraj Dinakarkumar Jothi Ramalingam Rajabathar Selvaraj Arokiyaraj Iyyappan Jeyaraj Sai Ramesh Anjaneyulu Shadakshari Sandeep Chimatahalli Shanthakumar Karthik Jimmy Nelson Appaturi Lee D. Wilson
author_facet	Yuvaraj Dinakarkumar Jothi Ramalingam Rajabathar Selvaraj Arokiyaraj Iyyappan Jeyaraj Sai Ramesh Anjaneyulu Shadakshari Sandeep Chimatahalli Shanthakumar Karthik Jimmy Nelson Appaturi Lee D. Wilson
author_sort	Yuvaraj Dinakarkumar
title	Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
title_short	Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
title_full	Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
title_fullStr	Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
title_full_unstemmed	Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection
title_sort	anti-methanogenic effect of phytochemicals on methyl-coenzyme m reductase—potential: in silico and molecular docking studies for environmental protection
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/cf1b0682b83c4e97819edf86fa14be39
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Anti-Methanogenic Effect of Phytochemicals on Methyl-Coenzyme M Reductase—Potential: In Silico and Molecular Docking Studies for Environmental Protection

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