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An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor

The deadliest recent pandemic outbreak of COVID-19 disease has severely damaged the socio-economic health of the people globally. Due to unavailability of any effective vaccine or treatment the human beings are still struggling to overcome the pandemic condition. In an attempt to discover anti-COVID...

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Autores principales: Aljarba, Nada H., Hasnain, Md Saquib, Bin-Meferij, Mashael Mohammed, Alkahtani, Saad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Authors. Published by Elsevier B.V. on behalf of King Saud University. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250415/
https://www.ncbi.nlm.nih.gov/pubmed/35811756
http://dx.doi.org/10.1016/j.jksus.2022.102214
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author Aljarba, Nada H.
Hasnain, Md Saquib
Bin-Meferij, Mashael Mohammed
Alkahtani, Saad
author_facet Aljarba, Nada H.
Hasnain, Md Saquib
Bin-Meferij, Mashael Mohammed
Alkahtani, Saad
author_sort Aljarba, Nada H.
collection PubMed
description The deadliest recent pandemic outbreak of COVID-19 disease has severely damaged the socio-economic health of the people globally. Due to unavailability of any effective vaccine or treatment the human beings are still struggling to overcome the pandemic condition. In an attempt to discover anti-COVID molecule, we used in-silico approach and reported 160 natural polyphenols to identify the most promising druggable HITs that can further used for drug discovery process. The co-crystallized structure COVID protease enzyme (PDB id 6LU7) was used. HTVS, MD simulation, binding energy calculations and in-silico ADME calculation were done and analyzed. Depending upon the scores three compounds galangin, nalsudaldain and rhamnezine were identified and the docking score were found to be −7.704, −6.51, −4.212 respectively. These docked complexes were further subjected to MD simulation runs over a 100 ns time and the RMSD and RMSF values were determined. The RMSD values of three compounds were found to be 2.9 Å, 7.6 Å & 9.5 Å respectively and the lowest RMSF values suggested the steady stability of ligand–protein complexes. The binding free energies (ΔG) of compounds with protein were found to be −49.8, −56.45, −62.87 kJ/mole. Moreover, in-silico ADME calculations indicated the drug likeliness properties of these molecules. By considering all these in-silico results the identified HITs would be the most probable anti-COVID drug molecules that can be further taken in wet lab and can act as lead for development of newer inhibitor of COVID-19 main protease enzyme.
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spelling pubmed-92504152022-07-05 An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor Aljarba, Nada H. Hasnain, Md Saquib Bin-Meferij, Mashael Mohammed Alkahtani, Saad J King Saud Univ Sci Original Article The deadliest recent pandemic outbreak of COVID-19 disease has severely damaged the socio-economic health of the people globally. Due to unavailability of any effective vaccine or treatment the human beings are still struggling to overcome the pandemic condition. In an attempt to discover anti-COVID molecule, we used in-silico approach and reported 160 natural polyphenols to identify the most promising druggable HITs that can further used for drug discovery process. The co-crystallized structure COVID protease enzyme (PDB id 6LU7) was used. HTVS, MD simulation, binding energy calculations and in-silico ADME calculation were done and analyzed. Depending upon the scores three compounds galangin, nalsudaldain and rhamnezine were identified and the docking score were found to be −7.704, −6.51, −4.212 respectively. These docked complexes were further subjected to MD simulation runs over a 100 ns time and the RMSD and RMSF values were determined. The RMSD values of three compounds were found to be 2.9 Å, 7.6 Å & 9.5 Å respectively and the lowest RMSF values suggested the steady stability of ligand–protein complexes. The binding free energies (ΔG) of compounds with protein were found to be −49.8, −56.45, −62.87 kJ/mole. Moreover, in-silico ADME calculations indicated the drug likeliness properties of these molecules. By considering all these in-silico results the identified HITs would be the most probable anti-COVID drug molecules that can be further taken in wet lab and can act as lead for development of newer inhibitor of COVID-19 main protease enzyme. The Authors. Published by Elsevier B.V. on behalf of King Saud University. 2022-10 2022-07-02 /pmc/articles/PMC9250415/ /pubmed/35811756 http://dx.doi.org/10.1016/j.jksus.2022.102214 Text en © 2022 The Authors Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Original Article
Aljarba, Nada H.
Hasnain, Md Saquib
Bin-Meferij, Mashael Mohammed
Alkahtani, Saad
An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title_full An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title_fullStr An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title_full_unstemmed An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title_short An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor
title_sort in-silico investigation of potential natural polyphenols for the targeting of covid main protease inhibitor
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250415/
https://www.ncbi.nlm.nih.gov/pubmed/35811756
http://dx.doi.org/10.1016/j.jksus.2022.102214
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