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An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13

INTRODUCTION AND OBJECTIVE: Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host...

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Autores principales: Kumar, Sushant, Kumari, Khushboo, Azad, Gajendra Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier España, S.L.U. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977615/
https://www.ncbi.nlm.nih.gov/pubmed/37362836
http://dx.doi.org/10.1016/j.vacun.2023.02.001
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author Kumar, Sushant
Kumari, Khushboo
Azad, Gajendra Kumar
author_facet Kumar, Sushant
Kumari, Khushboo
Azad, Gajendra Kumar
author_sort Kumar, Sushant
collection PubMed
description INTRODUCTION AND OBJECTIVE: Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host immune surveillance. Therefore, this study was designed to study SARS-CoV-2 Nsp13 protein, its epitopes and evolution. METHODS: Clustal Omega was used to identify mutations in Nsp13 protein. Secondary structure and disorder score was predicted by CFSSP and PONDR-VSL2 webservers. Protein stability was predicted by DynaMut webserver. B cell epitopes were predicted by IEDB DiscoTope 2.0 tools and their 3D structures were represented by discovery studio. Antigenicity and allergenicity of epitopes were predicted by Vaxijen2.0 and AllergenFPv.1.0. Physiochemical properties of epitopes were predicted by Toxinpred, HLP webserver tool. RESULTS: Our data revealed 182 mutations in Nsp13 among Indian SARS-CoV-2 isolates, which were characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were analysed. Furthermore, eighteen mutations reside in these Nsp13 epitopes. CONCLUSIONS: We report appearance of eighteen mutations in the predicted twenty-one epitopes of Nsp13. Among these, at least seven epitopes closely matches with the functionally validated epitopes. Altogether, our study shows the pattern of evolution of Nsp13 epitopes and their probable implications.
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spelling pubmed-99776152023-03-02 An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13 Kumar, Sushant Kumari, Khushboo Azad, Gajendra Kumar Vacunas Original INTRODUCTION AND OBJECTIVE: Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host immune surveillance. Therefore, this study was designed to study SARS-CoV-2 Nsp13 protein, its epitopes and evolution. METHODS: Clustal Omega was used to identify mutations in Nsp13 protein. Secondary structure and disorder score was predicted by CFSSP and PONDR-VSL2 webservers. Protein stability was predicted by DynaMut webserver. B cell epitopes were predicted by IEDB DiscoTope 2.0 tools and their 3D structures were represented by discovery studio. Antigenicity and allergenicity of epitopes were predicted by Vaxijen2.0 and AllergenFPv.1.0. Physiochemical properties of epitopes were predicted by Toxinpred, HLP webserver tool. RESULTS: Our data revealed 182 mutations in Nsp13 among Indian SARS-CoV-2 isolates, which were characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were analysed. Furthermore, eighteen mutations reside in these Nsp13 epitopes. CONCLUSIONS: We report appearance of eighteen mutations in the predicted twenty-one epitopes of Nsp13. Among these, at least seven epitopes closely matches with the functionally validated epitopes. Altogether, our study shows the pattern of evolution of Nsp13 epitopes and their probable implications. Elsevier España, S.L.U. 2023-03-02 /pmc/articles/PMC9977615/ /pubmed/37362836 http://dx.doi.org/10.1016/j.vacun.2023.02.001 Text en © 2023 Elsevier España, S.L.U. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Original
Kumar, Sushant
Kumari, Khushboo
Azad, Gajendra Kumar
An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title_full An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title_fullStr An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title_full_unstemmed An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title_short An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13
title_sort immunoinformatics approach to study the epitopes of sars-cov-2 helicase, nsp13
topic Original
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977615/
https://www.ncbi.nlm.nih.gov/pubmed/37362836
http://dx.doi.org/10.1016/j.vacun.2023.02.001
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