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Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling

SARS-CoV-2 triggered a worldwide medical crisis, affecting the world’s social, emotional, physical, and economic equilibrium. However, treatment choices and targets for finding a solution to COVID-19’s threat are becoming limited. A viable approach to combating the threat of COVID-19 is by unravelin...

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Autores principales: Balogun, Toheeb A., Chukwudozie, Onyeka S., Ogbodo, Uchechukwu C., Junaid, Idris O., Sunday, Olugbodi A., Ige, Oluwasegun M., Aborode, Abdullahi T., Akintayo, Abiola D., Oluwarotimi, Emmanuel A., Oluwafemi, Isaac O., Saibu, Oluwatosin A., Chuckwuemaka, Prosper, Omoboyowa, Damilola A., Alausa, Abdullahi O., Atasie, Nkechi H., Ilesanmi, Ayooluwa, Dairo, Gbenga, Tiamiyu, Zainab A., Batiha, Gaber E., Alkhuriji, Afrah Fahad, Al-Megrin, Wafa Abdullah I., De Waard, Michel, Sabatier, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9593047/
https://www.ncbi.nlm.nih.gov/pubmed/36304744
http://dx.doi.org/10.3389/fchem.2022.964446
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author Balogun, Toheeb A.
Chukwudozie, Onyeka S.
Ogbodo, Uchechukwu C.
Junaid, Idris O.
Sunday, Olugbodi A.
Ige, Oluwasegun M.
Aborode, Abdullahi T.
Akintayo, Abiola D.
Oluwarotimi, Emmanuel A.
Oluwafemi, Isaac O.
Saibu, Oluwatosin A.
Chuckwuemaka, Prosper
Omoboyowa, Damilola A.
Alausa, Abdullahi O.
Atasie, Nkechi H.
Ilesanmi, Ayooluwa
Dairo, Gbenga
Tiamiyu, Zainab A.
Batiha, Gaber E.
Alkhuriji, Afrah Fahad
Al-Megrin, Wafa Abdullah I.
De Waard, Michel
Sabatier, Jean-Marc
author_facet Balogun, Toheeb A.
Chukwudozie, Onyeka S.
Ogbodo, Uchechukwu C.
Junaid, Idris O.
Sunday, Olugbodi A.
Ige, Oluwasegun M.
Aborode, Abdullahi T.
Akintayo, Abiola D.
Oluwarotimi, Emmanuel A.
Oluwafemi, Isaac O.
Saibu, Oluwatosin A.
Chuckwuemaka, Prosper
Omoboyowa, Damilola A.
Alausa, Abdullahi O.
Atasie, Nkechi H.
Ilesanmi, Ayooluwa
Dairo, Gbenga
Tiamiyu, Zainab A.
Batiha, Gaber E.
Alkhuriji, Afrah Fahad
Al-Megrin, Wafa Abdullah I.
De Waard, Michel
Sabatier, Jean-Marc
author_sort Balogun, Toheeb A.
collection PubMed
description SARS-CoV-2 triggered a worldwide medical crisis, affecting the world’s social, emotional, physical, and economic equilibrium. However, treatment choices and targets for finding a solution to COVID-19’s threat are becoming limited. A viable approach to combating the threat of COVID-19 is by unraveling newer pharmacological and therapeutic targets pertinent in the viral survival and adaptive mechanisms within the host biological milieu which in turn provides the opportunity to discover promising inhibitors against COVID-19. Therefore, using high-throughput virtual screening, manually curated compounds library from some medicinal plants were screened against four main drivers of SARS-CoV-2 (spike glycoprotein, PLpro, 3CLpro, and RdRp). In addition, molecular docking, Prime MM/GBSA (molecular mechanics/generalized Born surface area) analysis, molecular dynamics (MD) simulation, and drug-likeness screening were performed to identify potential phytodrugs candidates for COVID-19 treatment. In support of these approaches, we used a series of computational modeling approaches to develop therapeutic agents against COVID-19. Out of the screened compounds against the selected SARS-CoV-2 therapeutic targets, only compounds with no violations of Lipinski’s rule of five and high binding affinity were considered as potential anti-COVID-19 drugs. However, lonchocarpol A, diplacol, and broussonol E (lead compounds) were recorded as the best compounds that satisfied this requirement, and they demonstrated their highest binding affinity against 3CLpro. Therefore, the 3CLpro target and the three lead compounds were selected for further analysis. Through protein–ligand mapping and interaction profiling, the three lead compounds formed essential interactions such as hydrogen bonds and hydrophobic interactions with amino acid residues at the binding pocket of 3CLpro. The key amino acid residues at the 3CLpro active site participating in the hydrophobic and polar inter/intra molecular interaction were TYR54, PRO52, CYS44, MET49, MET165, CYS145, HIS41, THR26, THR25, GLN189, and THR190. The compounds demonstrated stable protein–ligand complexes in the active site of the target (3CLpro) over a 100 ns simulation period with stable protein–ligand trajectories. Drug-likeness screening shows that the compounds are druggable molecules, and the toxicity descriptors established that the compounds demonstrated a good biosafety profile. Furthermore, the compounds were chemically reactive with promising molecular electron potential properties. Collectively, we propose that the discovered lead compounds may open the way for establishing phytodrugs to manage COVID-19 pandemics and new chemical libraries to prevent COVID-19 entry into the host based on the findings of this computational investigation.
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spelling pubmed-95930472022-10-26 Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling Balogun, Toheeb A. Chukwudozie, Onyeka S. Ogbodo, Uchechukwu C. Junaid, Idris O. Sunday, Olugbodi A. Ige, Oluwasegun M. Aborode, Abdullahi T. Akintayo, Abiola D. Oluwarotimi, Emmanuel A. Oluwafemi, Isaac O. Saibu, Oluwatosin A. Chuckwuemaka, Prosper Omoboyowa, Damilola A. Alausa, Abdullahi O. Atasie, Nkechi H. Ilesanmi, Ayooluwa Dairo, Gbenga Tiamiyu, Zainab A. Batiha, Gaber E. Alkhuriji, Afrah Fahad Al-Megrin, Wafa Abdullah I. De Waard, Michel Sabatier, Jean-Marc Front Chem Chemistry SARS-CoV-2 triggered a worldwide medical crisis, affecting the world’s social, emotional, physical, and economic equilibrium. However, treatment choices and targets for finding a solution to COVID-19’s threat are becoming limited. A viable approach to combating the threat of COVID-19 is by unraveling newer pharmacological and therapeutic targets pertinent in the viral survival and adaptive mechanisms within the host biological milieu which in turn provides the opportunity to discover promising inhibitors against COVID-19. Therefore, using high-throughput virtual screening, manually curated compounds library from some medicinal plants were screened against four main drivers of SARS-CoV-2 (spike glycoprotein, PLpro, 3CLpro, and RdRp). In addition, molecular docking, Prime MM/GBSA (molecular mechanics/generalized Born surface area) analysis, molecular dynamics (MD) simulation, and drug-likeness screening were performed to identify potential phytodrugs candidates for COVID-19 treatment. In support of these approaches, we used a series of computational modeling approaches to develop therapeutic agents against COVID-19. Out of the screened compounds against the selected SARS-CoV-2 therapeutic targets, only compounds with no violations of Lipinski’s rule of five and high binding affinity were considered as potential anti-COVID-19 drugs. However, lonchocarpol A, diplacol, and broussonol E (lead compounds) were recorded as the best compounds that satisfied this requirement, and they demonstrated their highest binding affinity against 3CLpro. Therefore, the 3CLpro target and the three lead compounds were selected for further analysis. Through protein–ligand mapping and interaction profiling, the three lead compounds formed essential interactions such as hydrogen bonds and hydrophobic interactions with amino acid residues at the binding pocket of 3CLpro. The key amino acid residues at the 3CLpro active site participating in the hydrophobic and polar inter/intra molecular interaction were TYR54, PRO52, CYS44, MET49, MET165, CYS145, HIS41, THR26, THR25, GLN189, and THR190. The compounds demonstrated stable protein–ligand complexes in the active site of the target (3CLpro) over a 100 ns simulation period with stable protein–ligand trajectories. Drug-likeness screening shows that the compounds are druggable molecules, and the toxicity descriptors established that the compounds demonstrated a good biosafety profile. Furthermore, the compounds were chemically reactive with promising molecular electron potential properties. Collectively, we propose that the discovered lead compounds may open the way for establishing phytodrugs to manage COVID-19 pandemics and new chemical libraries to prevent COVID-19 entry into the host based on the findings of this computational investigation. Frontiers Media S.A. 2022-10-11 /pmc/articles/PMC9593047/ /pubmed/36304744 http://dx.doi.org/10.3389/fchem.2022.964446 Text en Copyright © 2022 Balogun, Chukwudozie, Ogbodo, Junaid, Sunday, Ige, Aborode, Akintayo, Oluwarotimi, Oluwafemi, Saibu, Chuckwuemaka, Omoboyowa, Alausa, Atasie, Ilesanmi, Dairo, Tiamiyu, Batiha, Alkhuriji, Al-Megrin, De Waard and Sabatier. 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 Chemistry
Balogun, Toheeb A.
Chukwudozie, Onyeka S.
Ogbodo, Uchechukwu C.
Junaid, Idris O.
Sunday, Olugbodi A.
Ige, Oluwasegun M.
Aborode, Abdullahi T.
Akintayo, Abiola D.
Oluwarotimi, Emmanuel A.
Oluwafemi, Isaac O.
Saibu, Oluwatosin A.
Chuckwuemaka, Prosper
Omoboyowa, Damilola A.
Alausa, Abdullahi O.
Atasie, Nkechi H.
Ilesanmi, Ayooluwa
Dairo, Gbenga
Tiamiyu, Zainab A.
Batiha, Gaber E.
Alkhuriji, Afrah Fahad
Al-Megrin, Wafa Abdullah I.
De Waard, Michel
Sabatier, Jean-Marc
Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title_full Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title_fullStr Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title_full_unstemmed Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title_short Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling
title_sort discovery of putative inhibitors against main drivers of sars-cov-2 infection: insight from quantum mechanical evaluation and molecular modeling
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9593047/
https://www.ncbi.nlm.nih.gov/pubmed/36304744
http://dx.doi.org/10.3389/fchem.2022.964446
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