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Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plant...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178537/ https://www.ncbi.nlm.nih.gov/pubmed/34870149 http://dx.doi.org/10.1016/j.crphar.2021.100038 |
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author | Verma, Devvret Mitra, Debasis Paul, Manish Chaudhary, Priya Kamboj, Anshul Thatoi, Hrudayanath Janmeda, Pracheta Jain, Divya Panneerselvam, Periyasamy Shrivastav, Rakesh Pant, Kumud Das Mohapatra, Pradeep K. |
author_facet | Verma, Devvret Mitra, Debasis Paul, Manish Chaudhary, Priya Kamboj, Anshul Thatoi, Hrudayanath Janmeda, Pracheta Jain, Divya Panneerselvam, Periyasamy Shrivastav, Rakesh Pant, Kumud Das Mohapatra, Pradeep K. |
author_sort | Verma, Devvret |
collection | PubMed |
description | The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plants i.e. Eurycoma harmandiana, Sophora flavescens and Andrographis paniculata phyto-compounds against SARS-COV-2 papain-like protease (PL(pro)) and main protease (M(pro))/3-chymotrypsin-like protease (3CL(pro)). The interaction of protein targets and ligands was performed through AutoDock-Vina visualized using PyMOL and BIOVIA-Discovery Studio 2020. Molecular docking with canthin-6-one 9-O-beta-glucopyranoside showed highest binding affinity and less binding energy with both PL(pro) and M(pro)/3CL(pro) proteases and was subjected to molecular dynamic (MD) simulations for a period of 100ns. Stability of the protein-ligand complexes was evaluated by different analyses. The binding free energy calculated using MM-PBSA and the results showed that the molecule must have stable interactions with the protein binding site. ADMET analysis of the compounds suggested that it is having drug-like properties like high gastrointestinal (GI) absorption, no blood-brain barrier permeability and high lipophilicity. The outcome revealed that canthin-6-one 9-O-beta-glucopyranoside can be used as a potential natural drug against COVID-19 protease. |
format | Online Article Text |
id | pubmed-8178537 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-81785372021-06-05 Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components Verma, Devvret Mitra, Debasis Paul, Manish Chaudhary, Priya Kamboj, Anshul Thatoi, Hrudayanath Janmeda, Pracheta Jain, Divya Panneerselvam, Periyasamy Shrivastav, Rakesh Pant, Kumud Das Mohapatra, Pradeep K. Curr Res Pharmacol Drug Discov COVID-19 therapy The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plants i.e. Eurycoma harmandiana, Sophora flavescens and Andrographis paniculata phyto-compounds against SARS-COV-2 papain-like protease (PL(pro)) and main protease (M(pro))/3-chymotrypsin-like protease (3CL(pro)). The interaction of protein targets and ligands was performed through AutoDock-Vina visualized using PyMOL and BIOVIA-Discovery Studio 2020. Molecular docking with canthin-6-one 9-O-beta-glucopyranoside showed highest binding affinity and less binding energy with both PL(pro) and M(pro)/3CL(pro) proteases and was subjected to molecular dynamic (MD) simulations for a period of 100ns. Stability of the protein-ligand complexes was evaluated by different analyses. The binding free energy calculated using MM-PBSA and the results showed that the molecule must have stable interactions with the protein binding site. ADMET analysis of the compounds suggested that it is having drug-like properties like high gastrointestinal (GI) absorption, no blood-brain barrier permeability and high lipophilicity. The outcome revealed that canthin-6-one 9-O-beta-glucopyranoside can be used as a potential natural drug against COVID-19 protease. Elsevier 2021-06-05 /pmc/articles/PMC8178537/ /pubmed/34870149 http://dx.doi.org/10.1016/j.crphar.2021.100038 Text en © 2021 Published by Elsevier B.V. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | COVID-19 therapy Verma, Devvret Mitra, Debasis Paul, Manish Chaudhary, Priya Kamboj, Anshul Thatoi, Hrudayanath Janmeda, Pracheta Jain, Divya Panneerselvam, Periyasamy Shrivastav, Rakesh Pant, Kumud Das Mohapatra, Pradeep K. Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title | Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title_full | Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title_fullStr | Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title_full_unstemmed | Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title_short | Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
title_sort | potential inhibitors of sars-cov-2 (covid 19) proteases pl(pro) and m(pro)/ 3cl(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components |
topic | COVID-19 therapy |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178537/ https://www.ncbi.nlm.nih.gov/pubmed/34870149 http://dx.doi.org/10.1016/j.crphar.2021.100038 |
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