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Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study

(1) Background: SARS-CoV-2 Omicron BA.1 is the most common variation found in most countries and is responsible for 99% of cases in the United States. To overcome this challenge, there is an urgent need to discover effective inhibitors to prevent the emerging BA.1 variant. Natural products, particul...

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Autores principales: Hassan, Heba Ali, Hassan, Ahmed R., Mohamed, Eslam A. R., Al-Khdhairawi, Ahmad, Taha, Hala E., El-Tantawy, Hanan M., Abdel-Rahman, Iman A. M., Raslan, Ali E., Allemailem, Khaled S., Almatroudi, Ahmad, Alrumaihi, Faris, Alshiekheid, Maha A., Rehman, Hafiz Muzzammel, Abdelhamid, Mahmoud M., Abdel-Rahman, Islam M., Allam, Ahmed E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9600405/
https://www.ncbi.nlm.nih.gov/pubmed/36286057
http://dx.doi.org/10.3390/cimb44100342
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author Hassan, Heba Ali
Hassan, Ahmed R.
Mohamed, Eslam A. R.
Al-Khdhairawi, Ahmad
Taha, Hala E.
El-Tantawy, Hanan M.
Abdel-Rahman, Iman A. M.
Raslan, Ali E.
Allemailem, Khaled S.
Almatroudi, Ahmad
Alrumaihi, Faris
Alshiekheid, Maha A.
Rehman, Hafiz Muzzammel
Abdelhamid, Mahmoud M.
Abdel-Rahman, Islam M.
Allam, Ahmed E.
author_facet Hassan, Heba Ali
Hassan, Ahmed R.
Mohamed, Eslam A. R.
Al-Khdhairawi, Ahmad
Taha, Hala E.
El-Tantawy, Hanan M.
Abdel-Rahman, Iman A. M.
Raslan, Ali E.
Allemailem, Khaled S.
Almatroudi, Ahmad
Alrumaihi, Faris
Alshiekheid, Maha A.
Rehman, Hafiz Muzzammel
Abdelhamid, Mahmoud M.
Abdel-Rahman, Islam M.
Allam, Ahmed E.
author_sort Hassan, Heba Ali
collection PubMed
description (1) Background: SARS-CoV-2 Omicron BA.1 is the most common variation found in most countries and is responsible for 99% of cases in the United States. To overcome this challenge, there is an urgent need to discover effective inhibitors to prevent the emerging BA.1 variant. Natural products, particularly flavonoids, have had widespread success in reducing COVID-19 prevalence. (2) Methods: In the ongoing study, fifteen compounds were annotated from Echium angustifolium and peach (Prunus persica), which were computationally analyzed using various in silico techniques. Molecular docking calculations were performed for the identified phytochemicals to investigate their efficacy. Molecular dynamics (MD) simulations over 200 ns followed by molecular mechanics Poisson–Boltzmann surface area calculations (MM/PBSA) were performed to estimate the binding energy. Bioactivity was also calculated for the best components in terms of drug likeness and drug score. (3) Results: The data obtained from the molecular docking study demonstrated that five compounds exhibited remarkable potency, with docking scores greater than −9.0 kcal/mol. Among them, compounds 1, 2 and 4 showed higher stability within the active site of Omicron BA.1, with ΔG(binding) values of −49.02, −48.07, and −67.47 KJ/mol, respectively. These findings imply that the discovered phytoconstituents are promising in the search for anti-Omicron BA.1 drugs and should be investigated in future in vitro and in vivo research.
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spelling pubmed-96004052022-10-27 Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study Hassan, Heba Ali Hassan, Ahmed R. Mohamed, Eslam A. R. Al-Khdhairawi, Ahmad Taha, Hala E. El-Tantawy, Hanan M. Abdel-Rahman, Iman A. M. Raslan, Ali E. Allemailem, Khaled S. Almatroudi, Ahmad Alrumaihi, Faris Alshiekheid, Maha A. Rehman, Hafiz Muzzammel Abdelhamid, Mahmoud M. Abdel-Rahman, Islam M. Allam, Ahmed E. Curr Issues Mol Biol Article (1) Background: SARS-CoV-2 Omicron BA.1 is the most common variation found in most countries and is responsible for 99% of cases in the United States. To overcome this challenge, there is an urgent need to discover effective inhibitors to prevent the emerging BA.1 variant. Natural products, particularly flavonoids, have had widespread success in reducing COVID-19 prevalence. (2) Methods: In the ongoing study, fifteen compounds were annotated from Echium angustifolium and peach (Prunus persica), which were computationally analyzed using various in silico techniques. Molecular docking calculations were performed for the identified phytochemicals to investigate their efficacy. Molecular dynamics (MD) simulations over 200 ns followed by molecular mechanics Poisson–Boltzmann surface area calculations (MM/PBSA) were performed to estimate the binding energy. Bioactivity was also calculated for the best components in terms of drug likeness and drug score. (3) Results: The data obtained from the molecular docking study demonstrated that five compounds exhibited remarkable potency, with docking scores greater than −9.0 kcal/mol. Among them, compounds 1, 2 and 4 showed higher stability within the active site of Omicron BA.1, with ΔG(binding) values of −49.02, −48.07, and −67.47 KJ/mol, respectively. These findings imply that the discovered phytoconstituents are promising in the search for anti-Omicron BA.1 drugs and should be investigated in future in vitro and in vivo research. MDPI 2022-10-19 /pmc/articles/PMC9600405/ /pubmed/36286057 http://dx.doi.org/10.3390/cimb44100342 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hassan, Heba Ali
Hassan, Ahmed R.
Mohamed, Eslam A. R.
Al-Khdhairawi, Ahmad
Taha, Hala E.
El-Tantawy, Hanan M.
Abdel-Rahman, Iman A. M.
Raslan, Ali E.
Allemailem, Khaled S.
Almatroudi, Ahmad
Alrumaihi, Faris
Alshiekheid, Maha A.
Rehman, Hafiz Muzzammel
Abdelhamid, Mahmoud M.
Abdel-Rahman, Islam M.
Allam, Ahmed E.
Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title_full Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title_fullStr Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title_full_unstemmed Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title_short Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
title_sort targeting natural plant metabolites for hunting sars-cov-2 omicron ba.1 variant inhibitors: extraction, molecular docking, molecular dynamics, and physicochemical properties study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9600405/
https://www.ncbi.nlm.nih.gov/pubmed/36286057
http://dx.doi.org/10.3390/cimb44100342
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