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Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins
AIM: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. MATERIALS & METHODS: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Om...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Future Medicine Ltd
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241455/ http://dx.doi.org/10.2217/fvl-2022-0184 |
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author | Alanzi, Abdullah R Parvez, Mohammad K Al-Dosari, Mohammed S |
author_facet | Alanzi, Abdullah R Parvez, Mohammad K Al-Dosari, Mohammed S |
author_sort | Alanzi, Abdullah R |
collection | PubMed |
description | AIM: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. MATERIALS & METHODS: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes. RESULTS: Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness. CONCLUSION: Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike. |
format | Online Article Text |
id | pubmed-10241455 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Future Medicine Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-102414552023-06-06 Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins Alanzi, Abdullah R Parvez, Mohammad K Al-Dosari, Mohammed S Future Virol Research Article AIM: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. MATERIALS & METHODS: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes. RESULTS: Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness. CONCLUSION: Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike. Future Medicine Ltd 2023-06-01 2023-05 /pmc/articles/PMC10241455/ http://dx.doi.org/10.2217/fvl-2022-0184 Text en © 2023 Future Medicine Ltd https://creativecommons.org/licenses/by/4.0/This work is licensed under the Creative Commons Attribution 4.0 License (https://creativecommons.org/licenses/by/4.0/) |
spellingShingle | Research Article Alanzi, Abdullah R Parvez, Mohammad K Al-Dosari, Mohammed S Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title | Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title_full | Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title_fullStr | Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title_full_unstemmed | Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title_short | Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins |
title_sort | structure-based virtual identification of natural inhibitors of sars-cov-2 and its delta and omicron variant proteins |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241455/ http://dx.doi.org/10.2217/fvl-2022-0184 |
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