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Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia

Ebola virus (EBOV) belongs to Filoviridae family, a deadly virus that can cause severe viral haemorrhagic fevers (VHF) with a high fatality rate between 25 to 90 percent. Amongst EBOV proteins, the EBOV matrix protein VP40 is crucial in facilitating the transcription of the viral gene in the early s...

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Main Authors: Abd Halim, Khairul Bariyyah, Muhamad Yusoff, Muhamad Ariff, Samin, Noor Atikah
Format: Article
Language:English
English
Published: UTM Press 2022
Subjects:
Q Science (General)
Online Access:http://irep.iium.edu.my/99158/7/99158_Computational%20studies%20of%20potential%20ebola%20vp40_SCOPUS.pdf
http://irep.iium.edu.my/99158/8/99158_Computational%20studies%20of%20potential%20ebola%20vp40.pdf
http://irep.iium.edu.my/99158/
https://journals.utm.my/jurnalteknologi/article/view/17954/7962
https://doi.org/10.11113/jurnalteknologi.v84.17954
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spelling my.iium.irep.991582022-08-03T04:48:22Z http://irep.iium.edu.my/99158/ Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia Abd Halim, Khairul Bariyyah Muhamad Yusoff, Muhamad Ariff Samin, Noor Atikah Q Science (General) Ebola virus (EBOV) belongs to Filoviridae family, a deadly virus that can cause severe viral haemorrhagic fevers (VHF) with a high fatality rate between 25 to 90 percent. Amongst EBOV proteins, the EBOV matrix protein VP40 is crucial in facilitating the transcription of the viral gene in the early stage of infection. To date, there is no cure for EBOV and available chemical drugs were known to cause severe side effects. It is known that bioactive compounds from natural products can potentially combat this viral disease with fewer side effects. Therefore, this study aims to screen 15 bioactive compounds of medicinal plants from Malaysia. These compounds were docked against the RNA active site (Phe125 and Arg134) on VP40 matrix protein using AutoDock Vina. The ADMET properties and the toxicity class of the compounds were predicted computationally, and the compounds with good oral bioavailability were chosen for docking simulations. The top three docked compounds namely apigenin, epiexcelsin and kaempferol have a binding affinity of -4.6, -4.4 and -4.3 kJ/mol respectively. Our MD simulation study showed that epiexcelsin is the best candidate among the three selected compounds. Binding free energy calculation via molecular-mechanics Poisson Boltzmann surface area (MM- PBSA) method showed that epiexcelsin has the lowest binding free energy of -56.503 kJ/mol compared to apigenin (-40.344 kJ/mol) and kaemferol (- 27.329 kJ/mol). Our results suggest that epiexcelsin from local herbal plants can potentially be explored as a good candidate for further development of EBOV inhibitor targeting VP40. UTM Press 2022-06-30 Article PeerReviewed application/pdf en http://irep.iium.edu.my/99158/7/99158_Computational%20studies%20of%20potential%20ebola%20vp40_SCOPUS.pdf application/pdf en http://irep.iium.edu.my/99158/8/99158_Computational%20studies%20of%20potential%20ebola%20vp40.pdf Abd Halim, Khairul Bariyyah and Muhamad Yusoff, Muhamad Ariff and Samin, Noor Atikah (2022) Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia. Jurnal Teknologi (Sciences and Engineering), 84 (4). pp. 183-190. ISSN 0127-9696 E-ISSN 2180-3722 https://journals.utm.my/jurnalteknologi/article/view/17954/7962 https://doi.org/10.11113/jurnalteknologi.v84.17954
institution Universiti Islam Antarabangsa Malaysia
building IIUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider International Islamic University Malaysia
content_source IIUM Repository (IREP)
url_provider http://irep.iium.edu.my/
language English
English
topic Q Science (General)
spellingShingle Q Science (General)
Abd Halim, Khairul Bariyyah
Muhamad Yusoff, Muhamad Ariff
Samin, Noor Atikah
Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
description Ebola virus (EBOV) belongs to Filoviridae family, a deadly virus that can cause severe viral haemorrhagic fevers (VHF) with a high fatality rate between 25 to 90 percent. Amongst EBOV proteins, the EBOV matrix protein VP40 is crucial in facilitating the transcription of the viral gene in the early stage of infection. To date, there is no cure for EBOV and available chemical drugs were known to cause severe side effects. It is known that bioactive compounds from natural products can potentially combat this viral disease with fewer side effects. Therefore, this study aims to screen 15 bioactive compounds of medicinal plants from Malaysia. These compounds were docked against the RNA active site (Phe125 and Arg134) on VP40 matrix protein using AutoDock Vina. The ADMET properties and the toxicity class of the compounds were predicted computationally, and the compounds with good oral bioavailability were chosen for docking simulations. The top three docked compounds namely apigenin, epiexcelsin and kaempferol have a binding affinity of -4.6, -4.4 and -4.3 kJ/mol respectively. Our MD simulation study showed that epiexcelsin is the best candidate among the three selected compounds. Binding free energy calculation via molecular-mechanics Poisson Boltzmann surface area (MM- PBSA) method showed that epiexcelsin has the lowest binding free energy of -56.503 kJ/mol compared to apigenin (-40.344 kJ/mol) and kaemferol (- 27.329 kJ/mol). Our results suggest that epiexcelsin from local herbal plants can potentially be explored as a good candidate for further development of EBOV inhibitor targeting VP40.
format Article
author Abd Halim, Khairul Bariyyah
Muhamad Yusoff, Muhamad Ariff
Samin, Noor Atikah
author_facet Abd Halim, Khairul Bariyyah
Muhamad Yusoff, Muhamad Ariff
Samin, Noor Atikah
author_sort Abd Halim, Khairul Bariyyah
title Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
title_short Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
title_full Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
title_fullStr Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
title_full_unstemmed Computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of Malaysia
title_sort computational studies of potential ebola vp40 inhibitors using bioactive compounds from medicinal plants of malaysia
publisher UTM Press
publishDate 2022
url http://irep.iium.edu.my/99158/7/99158_Computational%20studies%20of%20potential%20ebola%20vp40_SCOPUS.pdf
http://irep.iium.edu.my/99158/8/99158_Computational%20studies%20of%20potential%20ebola%20vp40.pdf
http://irep.iium.edu.my/99158/
https://journals.utm.my/jurnalteknologi/article/view/17954/7962
https://doi.org/10.11113/jurnalteknologi.v84.17954
_version_ 1740825508703109120
score 13.211869

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