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Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection
SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary p...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer US
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9759041/ https://www.ncbi.nlm.nih.gov/pubmed/36570051 http://dx.doi.org/10.1007/s11224-022-02113-9 |
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author | Singh, Satyendra Chauhan, Priya Sharma, Vinita Rao, Abhishek Kumbhar, Bajarang Vasant Prajapati, Vijay Kumar |
author_facet | Singh, Satyendra Chauhan, Priya Sharma, Vinita Rao, Abhishek Kumbhar, Bajarang Vasant Prajapati, Vijay Kumar |
author_sort | Singh, Satyendra |
collection | PubMed |
description | SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11224-022-02113-9. |
format | Online Article Text |
id | pubmed-9759041 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer US |
record_format | MEDLINE/PubMed |
spelling | pubmed-97590412022-12-19 Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection Singh, Satyendra Chauhan, Priya Sharma, Vinita Rao, Abhishek Kumbhar, Bajarang Vasant Prajapati, Vijay Kumar Struct Chem Original Research SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11224-022-02113-9. Springer US 2022-12-17 /pmc/articles/PMC9759041/ /pubmed/36570051 http://dx.doi.org/10.1007/s11224-022-02113-9 Text en © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. 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 | Original Research Singh, Satyendra Chauhan, Priya Sharma, Vinita Rao, Abhishek Kumbhar, Bajarang Vasant Prajapati, Vijay Kumar Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title | Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title_full | Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title_fullStr | Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title_full_unstemmed | Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title_short | Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection |
title_sort | identification of multi-targeting natural antiviral peptides to impede sars-cov-2 infection |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9759041/ https://www.ncbi.nlm.nih.gov/pubmed/36570051 http://dx.doi.org/10.1007/s11224-022-02113-9 |
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