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Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2

Background: The novel severe acute respiratory syndrome related corona virus-2 (SARS-CoV-2) belongs to the “Coronaviridae” family and order “Nidovirales”, which has caused the pandemic coronavirus disease 2019 (COVID-19). SARS-CoV-2 has been spread in more than a 100 countries, and more than a milli...

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Autores principales: Kumar, Vipul, Kancharla, Sudhakar, Kolli, Prachetha, Jena, Manoj
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8009247/
https://www.ncbi.nlm.nih.gov/pubmed/33841800
http://dx.doi.org/10.12688/f1000research.36371.1
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author Kumar, Vipul
Kancharla, Sudhakar
Kolli, Prachetha
Jena, Manoj
author_facet Kumar, Vipul
Kancharla, Sudhakar
Kolli, Prachetha
Jena, Manoj
author_sort Kumar, Vipul
collection PubMed
description Background: The novel severe acute respiratory syndrome related corona virus-2 (SARS-CoV-2) belongs to the “Coronaviridae” family and order “Nidovirales”, which has caused the pandemic coronavirus disease 2019 (COVID-19). SARS-CoV-2 has been spread in more than a 100 countries, and more than a million have lost their lives. Vaccination and immunization could be an effective strategy to combat fatal COVID-19. Methods: For identification of effective vaccine candidate against COVID-19, various immunoinformatics online tools and softwares were used to predict epitopes. Cytotoxic T cell epitopes, helper T cell epitopes, and B cell epitopes from three structural polyproteins (Spike, Membrane, and Nucleocapsid (SMN) based on the binding affinity towards MHC, antigenicity, non-allergenicity, and non-toxicity) were identified for vaccine development. The multiepitope based vaccine was constructed linking two additional adjuvants human beta-defensin-3 and human beta-defensin-2 at N and C terminal, respectively. Results: The constructed vaccine sequence was found to be a good antigen and non-allergen for the human body. The constructed vaccine was docked with the TLR-3 receptor.  The docked complex was further taken for molecular dynamics simulations and RMSD was calculated, which showed stable binding of the complex. The codon adaptation index (CAI) of 0.92 and GC content of 55.5% for E. coli (K12 strain) suggested efficient expression of the predicted vaccine. Conclusion: The current study can be helpful in the reduction of time and cost for further experimental validations and could give a valuable contribution against this pandemic.
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spelling pubmed-80092472021-04-08 Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2 Kumar, Vipul Kancharla, Sudhakar Kolli, Prachetha Jena, Manoj F1000Res Research Article Background: The novel severe acute respiratory syndrome related corona virus-2 (SARS-CoV-2) belongs to the “Coronaviridae” family and order “Nidovirales”, which has caused the pandemic coronavirus disease 2019 (COVID-19). SARS-CoV-2 has been spread in more than a 100 countries, and more than a million have lost their lives. Vaccination and immunization could be an effective strategy to combat fatal COVID-19. Methods: For identification of effective vaccine candidate against COVID-19, various immunoinformatics online tools and softwares were used to predict epitopes. Cytotoxic T cell epitopes, helper T cell epitopes, and B cell epitopes from three structural polyproteins (Spike, Membrane, and Nucleocapsid (SMN) based on the binding affinity towards MHC, antigenicity, non-allergenicity, and non-toxicity) were identified for vaccine development. The multiepitope based vaccine was constructed linking two additional adjuvants human beta-defensin-3 and human beta-defensin-2 at N and C terminal, respectively. Results: The constructed vaccine sequence was found to be a good antigen and non-allergen for the human body. The constructed vaccine was docked with the TLR-3 receptor.  The docked complex was further taken for molecular dynamics simulations and RMSD was calculated, which showed stable binding of the complex. The codon adaptation index (CAI) of 0.92 and GC content of 55.5% for E. coli (K12 strain) suggested efficient expression of the predicted vaccine. Conclusion: The current study can be helpful in the reduction of time and cost for further experimental validations and could give a valuable contribution against this pandemic. F1000 Research Limited 2021-01-23 /pmc/articles/PMC8009247/ /pubmed/33841800 http://dx.doi.org/10.12688/f1000research.36371.1 Text en Copyright: © 2021 Kumar V et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Kumar, Vipul
Kancharla, Sudhakar
Kolli, Prachetha
Jena, Manoj
Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title_full Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title_fullStr Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title_full_unstemmed Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title_short Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
title_sort reverse vaccinology approach towards the in-silico multiepitope vaccine development against sars-cov-2
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8009247/
https://www.ncbi.nlm.nih.gov/pubmed/33841800
http://dx.doi.org/10.12688/f1000research.36371.1
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