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In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19
COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288047/ https://www.ncbi.nlm.nih.gov/pubmed/34291081 http://dx.doi.org/10.3389/fmolb.2021.637122 |
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author | Sankar, Muthumanickam Ramachandran, Balajee Pandi, Boomi Mutharasappan, Nachiappan Ramasamy, Vidhyavathi Prabu, Poorani Gurumallesh Shanmugaraj, Gowrishankar Wang, Yao Muniyandai, Brintha Rathinasamy, Subaskumar Chandrasekaran, Balakumar Bayan, Mohammad F. Jeyaraman, Jeyakanthan Halliah, Gurumallesh Prabu Ebenezer, Solomon King |
author_facet | Sankar, Muthumanickam Ramachandran, Balajee Pandi, Boomi Mutharasappan, Nachiappan Ramasamy, Vidhyavathi Prabu, Poorani Gurumallesh Shanmugaraj, Gowrishankar Wang, Yao Muniyandai, Brintha Rathinasamy, Subaskumar Chandrasekaran, Balakumar Bayan, Mohammad F. Jeyaraman, Jeyakanthan Halliah, Gurumallesh Prabu Ebenezer, Solomon King |
author_sort | Sankar, Muthumanickam |
collection | PubMed |
description | COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to now, no efficient drugs are available on the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiber officinale, Cuminum cyminum, Piper nigrum, Curcuma longa, and Allium sativum). In total, 227 phytocompounds were identified and screened against the proteins S-ACE2 and M(pro) through structure-based virtual screening approaches. Based on the binding affinity score, 30 active phytocompounds were selected. Amongst, the binding affinity for beta-sitosterol and beta-elemene against S-ACE2 showed −12.0 and −10.9 kcal/mol, respectively. Meanwhile, the binding affinity for beta-sitosterol and beta-chlorogenin against M(pro) was found to be −9.7 and −8.4 kcal/mol, respectively. Further, the selected compounds proceeded with molecular dynamics simulation, prime MM-GBSA analysis, and ADME/T property checks to understand the stability, interaction, conformational changes, binding free energy, and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for M(pro) were actively involved in the inhibition of viral entry. From the in silico analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19. |
format | Online Article Text |
id | pubmed-8288047 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-82880472021-07-20 In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 Sankar, Muthumanickam Ramachandran, Balajee Pandi, Boomi Mutharasappan, Nachiappan Ramasamy, Vidhyavathi Prabu, Poorani Gurumallesh Shanmugaraj, Gowrishankar Wang, Yao Muniyandai, Brintha Rathinasamy, Subaskumar Chandrasekaran, Balakumar Bayan, Mohammad F. Jeyaraman, Jeyakanthan Halliah, Gurumallesh Prabu Ebenezer, Solomon King Front Mol Biosci Molecular Biosciences COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to now, no efficient drugs are available on the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiber officinale, Cuminum cyminum, Piper nigrum, Curcuma longa, and Allium sativum). In total, 227 phytocompounds were identified and screened against the proteins S-ACE2 and M(pro) through structure-based virtual screening approaches. Based on the binding affinity score, 30 active phytocompounds were selected. Amongst, the binding affinity for beta-sitosterol and beta-elemene against S-ACE2 showed −12.0 and −10.9 kcal/mol, respectively. Meanwhile, the binding affinity for beta-sitosterol and beta-chlorogenin against M(pro) was found to be −9.7 and −8.4 kcal/mol, respectively. Further, the selected compounds proceeded with molecular dynamics simulation, prime MM-GBSA analysis, and ADME/T property checks to understand the stability, interaction, conformational changes, binding free energy, and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for M(pro) were actively involved in the inhibition of viral entry. From the in silico analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19. Frontiers Media S.A. 2021-07-05 /pmc/articles/PMC8288047/ /pubmed/34291081 http://dx.doi.org/10.3389/fmolb.2021.637122 Text en Copyright © 2021 Sankar, Ramachandran, Pandi, Mutharasappan, Ramasamy, Prabu, Shanmugaraj, Wang, Muniyandai, Rathinasamy, Chandrasekaran, Bayan, Jeyaraman, Halliah and Ebenezer. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Molecular Biosciences Sankar, Muthumanickam Ramachandran, Balajee Pandi, Boomi Mutharasappan, Nachiappan Ramasamy, Vidhyavathi Prabu, Poorani Gurumallesh Shanmugaraj, Gowrishankar Wang, Yao Muniyandai, Brintha Rathinasamy, Subaskumar Chandrasekaran, Balakumar Bayan, Mohammad F. Jeyaraman, Jeyakanthan Halliah, Gurumallesh Prabu Ebenezer, Solomon King In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title | In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title_full | In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title_fullStr | In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title_full_unstemmed | In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title_short | In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19 |
title_sort | in silico screening of natural phytocompounds towards identification of potential lead compounds to treat covid-19 |
topic | Molecular Biosciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288047/ https://www.ncbi.nlm.nih.gov/pubmed/34291081 http://dx.doi.org/10.3389/fmolb.2021.637122 |
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