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Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation
Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus’s ability to infiltrate and establish itself in increasing numbers of nations has made it a persistent threat to public health worldwide. Despite the widespread occurrence of this potentially fatal disease, no effective t...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338848/ https://www.ncbi.nlm.nih.gov/pubmed/37455711 http://dx.doi.org/10.3389/fmicb.2023.1189786 |
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author | Akash, Shopnil Bayıl, Imren Rahman, Md. Anisur Mukerjee, Nobendu Maitra, Swastika Islam, Md. Rezaul Rajkhowa, Sanchaita Ghosh, Arabinda Al-Hussain, Sami A. Zaki, Magdi E. A. Jaiswal, Vikash Sah, Sanjit Barboza, Joshuan J. Sah, Ranjit |
author_facet | Akash, Shopnil Bayıl, Imren Rahman, Md. Anisur Mukerjee, Nobendu Maitra, Swastika Islam, Md. Rezaul Rajkhowa, Sanchaita Ghosh, Arabinda Al-Hussain, Sami A. Zaki, Magdi E. A. Jaiswal, Vikash Sah, Sanjit Barboza, Joshuan J. Sah, Ranjit |
author_sort | Akash, Shopnil |
collection | PubMed |
description | Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus’s ability to infiltrate and establish itself in increasing numbers of nations has made it a persistent threat to public health worldwide. Despite the widespread occurrence of this potentially fatal disease, no effective treatment options are currently on the market. As a result, there is an immediate need for the research and development of novel pharmaceuticals. To begin, molecular docking was performed on two possible West Nile virus target proteins using a panel of twelve natural chemicals, including Apigenin, Resveratrol, Hesperetin, Fungisterol, Lucidone, Ganoderic acid, Curcumin, Kaempferol, Cholic acid, Chlorogenic acid, Pinocembrin, and Sanguinarine. West Nile virus methyltransferase (PDB ID: 2OY0) binding affinities varied from −7.4 to −8.3 kcal/mol, whereas West Nile virus envelope glycoprotein affinities ranged from −6.2 to −8.1 kcal/mol (PDB ID: 2I69). Second, substances with larger molecular weights are less likely to be unhappy with the Lipinski rule. Hence, additional research was carried out without regard to molecular weight. In addition, compounds 01, 02, 03, 05, 06, 07, 08, 09, 10 and 11 are more soluble in water than compound 04 is. Besides, based on maximum binding affinity, best three compounds (Apigenin, Curcumin, and Ganoderic Acid) has been carried out molecular dynamic simulation (MDs) at 100 ns to determine their stability. The MDs data is also reported that these mentioned molecules are highly stable. Finally, advanced principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, binding free energy and dynamic cross correlation matrix (DCCM) theoretical study is also included to established mentioned phytochemical as a potential drug candidate. Research has indicated that the aforementioned natural substances may be an effective tool in the battle against the dangerous West Nile virus. This study aims to locate a bioactive natural component that might be used as a pharmaceutical. |
format | Online Article Text |
id | pubmed-10338848 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-103388482023-07-14 Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation Akash, Shopnil Bayıl, Imren Rahman, Md. Anisur Mukerjee, Nobendu Maitra, Swastika Islam, Md. Rezaul Rajkhowa, Sanchaita Ghosh, Arabinda Al-Hussain, Sami A. Zaki, Magdi E. A. Jaiswal, Vikash Sah, Sanjit Barboza, Joshuan J. Sah, Ranjit Front Microbiol Microbiology Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus’s ability to infiltrate and establish itself in increasing numbers of nations has made it a persistent threat to public health worldwide. Despite the widespread occurrence of this potentially fatal disease, no effective treatment options are currently on the market. As a result, there is an immediate need for the research and development of novel pharmaceuticals. To begin, molecular docking was performed on two possible West Nile virus target proteins using a panel of twelve natural chemicals, including Apigenin, Resveratrol, Hesperetin, Fungisterol, Lucidone, Ganoderic acid, Curcumin, Kaempferol, Cholic acid, Chlorogenic acid, Pinocembrin, and Sanguinarine. West Nile virus methyltransferase (PDB ID: 2OY0) binding affinities varied from −7.4 to −8.3 kcal/mol, whereas West Nile virus envelope glycoprotein affinities ranged from −6.2 to −8.1 kcal/mol (PDB ID: 2I69). Second, substances with larger molecular weights are less likely to be unhappy with the Lipinski rule. Hence, additional research was carried out without regard to molecular weight. In addition, compounds 01, 02, 03, 05, 06, 07, 08, 09, 10 and 11 are more soluble in water than compound 04 is. Besides, based on maximum binding affinity, best three compounds (Apigenin, Curcumin, and Ganoderic Acid) has been carried out molecular dynamic simulation (MDs) at 100 ns to determine their stability. The MDs data is also reported that these mentioned molecules are highly stable. Finally, advanced principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, binding free energy and dynamic cross correlation matrix (DCCM) theoretical study is also included to established mentioned phytochemical as a potential drug candidate. Research has indicated that the aforementioned natural substances may be an effective tool in the battle against the dangerous West Nile virus. This study aims to locate a bioactive natural component that might be used as a pharmaceutical. Frontiers Media S.A. 2023-06-28 /pmc/articles/PMC10338848/ /pubmed/37455711 http://dx.doi.org/10.3389/fmicb.2023.1189786 Text en Copyright © 2023 Akash, Bayıl, Rahman, Mukerjee, Maitra, Islam, Rajkhowa, Ghosh, Al-Hussain, Zaki, Jaiswal, Sah, Barboza and Sah. 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 | Microbiology Akash, Shopnil Bayıl, Imren Rahman, Md. Anisur Mukerjee, Nobendu Maitra, Swastika Islam, Md. Rezaul Rajkhowa, Sanchaita Ghosh, Arabinda Al-Hussain, Sami A. Zaki, Magdi E. A. Jaiswal, Vikash Sah, Sanjit Barboza, Joshuan J. Sah, Ranjit Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title | Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title_full | Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title_fullStr | Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title_full_unstemmed | Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title_short | Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
title_sort | target specific inhibition of west nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338848/ https://www.ncbi.nlm.nih.gov/pubmed/37455711 http://dx.doi.org/10.3389/fmicb.2023.1189786 |
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