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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2

The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its va...

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Autores principales: Erol, Ismail, Kotil, Seyfullah Enes, Fidan, Ozkan, Yetiman, Ahmet E., Durdagi, Serdar, Ortakci, Fatih
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626284/
https://www.ncbi.nlm.nih.gov/pubmed/34837166
http://dx.doi.org/10.1007/s12602-021-09879-0
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author Erol, Ismail
Kotil, Seyfullah Enes
Fidan, Ozkan
Yetiman, Ahmet E.
Durdagi, Serdar
Ortakci, Fatih
author_facet Erol, Ismail
Kotil, Seyfullah Enes
Fidan, Ozkan
Yetiman, Ahmet E.
Durdagi, Serdar
Ortakci, Fatih
author_sort Erol, Ismail
collection PubMed
description The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein–protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than −7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of − 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant’s predicted binding affinity with −13.8 kcal/mol, −13.0 kcal/mol, and −12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12602-021-09879-0.
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spelling pubmed-86262842021-11-29 In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2 Erol, Ismail Kotil, Seyfullah Enes Fidan, Ozkan Yetiman, Ahmet E. Durdagi, Serdar Ortakci, Fatih Probiotics Antimicrob Proteins Article The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein–protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than −7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of − 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant’s predicted binding affinity with −13.8 kcal/mol, −13.0 kcal/mol, and −12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12602-021-09879-0. Springer US 2021-11-27 2023 /pmc/articles/PMC8626284/ /pubmed/34837166 http://dx.doi.org/10.1007/s12602-021-09879-0 Text en © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
Erol, Ismail
Kotil, Seyfullah Enes
Fidan, Ozkan
Yetiman, Ahmet E.
Durdagi, Serdar
Ortakci, Fatih
In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title_full In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title_fullStr In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title_full_unstemmed In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title_short In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
title_sort in silico analysis of bacteriocins from lactic acid bacteria against sars-cov-2
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626284/
https://www.ncbi.nlm.nih.gov/pubmed/34837166
http://dx.doi.org/10.1007/s12602-021-09879-0
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