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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1189786/full |
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| author | Shopnil Akash Imren Bayıl Md. Anisur Rahman Nobendu Mukerjee Nobendu Mukerjee Swastika Maitra Md. Rezaul Islam Sanchaita Rajkhowa Arabinda Ghosh Sami A. Al-Hussain Magdi E. A. Zaki Vikash Jaiswal Sanjit Sah Sanjit Sah Joshuan J. Barboza Ranjit Sah Ranjit Sah Ranjit Sah |
| author_facet | Shopnil Akash Imren Bayıl Md. Anisur Rahman Nobendu Mukerjee Nobendu Mukerjee Swastika Maitra Md. Rezaul Islam Sanchaita Rajkhowa Arabinda Ghosh Sami A. Al-Hussain Magdi E. A. Zaki Vikash Jaiswal Sanjit Sah Sanjit Sah Joshuan J. Barboza Ranjit Sah Ranjit Sah Ranjit Sah |
| author_sort | Shopnil Akash |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-13T02:46:52Z |
| format | Article |
| id | doaj.art-e46eb3fc5fe047c5b391486e065c48fb |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-13T02:46:52Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-e46eb3fc5fe047c5b391486e065c48fb2023-06-28T16:58:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-06-011410.3389/fmicb.2023.11897861189786Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulationShopnil Akash0Imren Bayıl1Md. Anisur Rahman2Nobendu Mukerjee3Nobendu Mukerjee4Swastika Maitra5Md. Rezaul Islam6Sanchaita Rajkhowa7Arabinda Ghosh8Sami A. Al-Hussain9Magdi E. A. Zaki10Vikash Jaiswal11Sanjit Sah12Sanjit Sah13Joshuan J. Barboza14Ranjit Sah15Ranjit Sah16Ranjit Sah17Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, BangladeshDepartment of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, TürkiyeDepartment of Pharmacy, Islamic University, Kushtia, BangladeshDepartment of Microbiology, West Bengal State University, Kolkata, West Bengal, IndiaDepartment of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, AustraliaDepartment of Microbiology, Adamas University, Kolkata, West Bengal, IndiaDepartment of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, BangladeshCentre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, IndiaMicrobiology Division, Department of Botany, Gauhati University, Gwahati, Assam, IndiaDepartment of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi ArabiaDepartment of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia0Department of Cardiovascular Research, Larkin Community Hospital, South Miami, FL, United States1Global Consortium for Public Health and Research, Datta Meghe Institute of Higher Education and Research, Jawaharlal Nehru Medical College, Wardha, India2SR Sanjeevani Hospital, Kayanpur, Siraha, Nepal3Escuela de Medicina, Universidad Cesar Vallejo, Trujillo, Peru4Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal5Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India6Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, IndiaMosquitoes 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1189786/fullWest Nile virusmolecular dockingmolecular dynamic simulationPCAdrug-likenessADMET |
| spellingShingle | Shopnil Akash Imren Bayıl Md. Anisur Rahman Nobendu Mukerjee Nobendu Mukerjee Swastika Maitra Md. Rezaul Islam Sanchaita Rajkhowa Arabinda Ghosh Sami A. Al-Hussain Magdi E. A. Zaki Vikash Jaiswal Sanjit Sah Sanjit Sah Joshuan J. Barboza Ranjit Sah Ranjit Sah Ranjit Sah Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation Frontiers in Microbiology West Nile virus molecular docking molecular dynamic simulation PCA drug-likeness ADMET |
| 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 | West Nile virus molecular docking molecular dynamic simulation PCA drug-likeness ADMET |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1189786/full |
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