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Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study

COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompoun...

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Autores principales: Kar, Bipasa, Dehury, Budheswar, Singh, Mahender Kumar, Pati, Sanghamitra, Bhattacharya, Debdutta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007924/
https://www.ncbi.nlm.nih.gov/pubmed/35468453
http://dx.doi.org/10.1016/j.jmgm.2022.108192
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author Kar, Bipasa
Dehury, Budheswar
Singh, Mahender Kumar
Pati, Sanghamitra
Bhattacharya, Debdutta
author_facet Kar, Bipasa
Dehury, Budheswar
Singh, Mahender Kumar
Pati, Sanghamitra
Bhattacharya, Debdutta
author_sort Kar, Bipasa
collection PubMed
description COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompounds can be opted as good one. In this study, three hundred phytocompounds were screened virtually against two viral proteins namely main protease and spike protein. Molecular docking and dynamic simulation study was used to find binding affinity, structural stability and flexibility of the complex. Pharmacokinetic properties were studied through ADMET analysis. To understand energy variation of the complex structure free energy landscape analysis was performed. Among three hundred phytocompounds virtual screening, three phytocompounds were selected for detailed molecular interaction analysis. Oleanderolide, Proceragenin A and Balsaminone A, showed strong binding affinity against both the target proteins and reflected conformational stability throughout the MD run. Oleanderolide, proceragenin A and balsaminone A has docking score −9.4 kcal/mol, −8.6 kcal/mol, and −8.1 kcal/mol respectively against main protease and same −8.3 kcal/mol docking score against spike protein. These three phytocompounds has high gastrointestinal absorption capacity. They were unexplored till now for their antiviral activity. Their promising in silico results suggests that they can be promoted in the long run for development of new antiviral drugs.
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spelling pubmed-90079242022-04-14 Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study Kar, Bipasa Dehury, Budheswar Singh, Mahender Kumar Pati, Sanghamitra Bhattacharya, Debdutta J Mol Graph Model Article COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompounds can be opted as good one. In this study, three hundred phytocompounds were screened virtually against two viral proteins namely main protease and spike protein. Molecular docking and dynamic simulation study was used to find binding affinity, structural stability and flexibility of the complex. Pharmacokinetic properties were studied through ADMET analysis. To understand energy variation of the complex structure free energy landscape analysis was performed. Among three hundred phytocompounds virtual screening, three phytocompounds were selected for detailed molecular interaction analysis. Oleanderolide, Proceragenin A and Balsaminone A, showed strong binding affinity against both the target proteins and reflected conformational stability throughout the MD run. Oleanderolide, proceragenin A and balsaminone A has docking score −9.4 kcal/mol, −8.6 kcal/mol, and −8.1 kcal/mol respectively against main protease and same −8.3 kcal/mol docking score against spike protein. These three phytocompounds has high gastrointestinal absorption capacity. They were unexplored till now for their antiviral activity. Their promising in silico results suggests that they can be promoted in the long run for development of new antiviral drugs. Elsevier Inc. 2022-07 2022-04-14 /pmc/articles/PMC9007924/ /pubmed/35468453 http://dx.doi.org/10.1016/j.jmgm.2022.108192 Text en © 2022 Elsevier Inc. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Kar, Bipasa
Dehury, Budheswar
Singh, Mahender Kumar
Pati, Sanghamitra
Bhattacharya, Debdutta
Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title_full Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title_fullStr Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title_full_unstemmed Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title_short Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study
title_sort identification of phytocompounds as newer antiviral drugs against covid-19 through molecular docking and simulation based study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007924/
https://www.ncbi.nlm.nih.gov/pubmed/35468453
http://dx.doi.org/10.1016/j.jmgm.2022.108192
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