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Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development

Chikungunya is a mosquito-borne disease, caused by the member of the Togaviridae family belongs to the genus alphavirus, making it a major threat in all developing countries as well as some developed countries. The mosquito acts as a vector for the disease and carries the CHIK-Virus. To date there i...

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Autores principales: Saxena, Prashant, Mishra, Sanjay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223317/
https://www.ncbi.nlm.nih.gov/pubmed/32421074
http://dx.doi.org/10.1007/s10989-020-10038-2
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author Saxena, Prashant
Mishra, Sanjay
author_facet Saxena, Prashant
Mishra, Sanjay
author_sort Saxena, Prashant
collection PubMed
description Chikungunya is a mosquito-borne disease, caused by the member of the Togaviridae family belongs to the genus alphavirus, making it a major threat in all developing countries as well as some developed countries. The mosquito acts as a vector for the disease and carries the CHIK-Virus. To date there is no direct treatment available and that demands the development of more effective vaccines. In this study author employed Immune Epitope Database and Analysis Resource, a machine learning-based algorithm principally working on the Artificial Neural Network (ANN) algorithm, also known as (IEDB-ANN) for the prediction and analysis of Epitopes. A total of 173 epitopes were identified on the basis of IC50 values, among them 40 epitopes were found, sharing part with the linear B-cell epitopes and exposed to the cTAP1protein, and out of 40, 6 epitopes were noticed to show interactions with the cTAP with their binding energy ranging from − 3.61 to − 1.22 kcal/mol. The six epitopes identified were exposed to the HLA class I alleles and from this all revealed interaction with the HLA alleles and minimum binding energy that ranges from − 4.12 to − 5.88 kcal/mol. Besides, two T cell epitopes i.e. (145)KVFTGVYPE(153) and (395)STVPVAPPR(403) were found most promiscuous candidates. These promiscuous epitopes-HLA complexes were further analyzed by the molecular dynamics simulation to check the stability of the complex. Results obtained from this study suggest that the identified epitopes i.e. and (395)STVPVAPPR(403), are likely to be capable of passing through the lumen of ER to bind withthe HLA class I allele and provide new insights and potential application in the designing and development of peptide-based vaccine candidate for the treatment of chikungunya.
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spelling pubmed-72233172020-05-15 Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development Saxena, Prashant Mishra, Sanjay Int J Pept Res Ther Article Chikungunya is a mosquito-borne disease, caused by the member of the Togaviridae family belongs to the genus alphavirus, making it a major threat in all developing countries as well as some developed countries. The mosquito acts as a vector for the disease and carries the CHIK-Virus. To date there is no direct treatment available and that demands the development of more effective vaccines. In this study author employed Immune Epitope Database and Analysis Resource, a machine learning-based algorithm principally working on the Artificial Neural Network (ANN) algorithm, also known as (IEDB-ANN) for the prediction and analysis of Epitopes. A total of 173 epitopes were identified on the basis of IC50 values, among them 40 epitopes were found, sharing part with the linear B-cell epitopes and exposed to the cTAP1protein, and out of 40, 6 epitopes were noticed to show interactions with the cTAP with their binding energy ranging from − 3.61 to − 1.22 kcal/mol. The six epitopes identified were exposed to the HLA class I alleles and from this all revealed interaction with the HLA alleles and minimum binding energy that ranges from − 4.12 to − 5.88 kcal/mol. Besides, two T cell epitopes i.e. (145)KVFTGVYPE(153) and (395)STVPVAPPR(403) were found most promiscuous candidates. These promiscuous epitopes-HLA complexes were further analyzed by the molecular dynamics simulation to check the stability of the complex. Results obtained from this study suggest that the identified epitopes i.e. and (395)STVPVAPPR(403), are likely to be capable of passing through the lumen of ER to bind withthe HLA class I allele and provide new insights and potential application in the designing and development of peptide-based vaccine candidate for the treatment of chikungunya. Springer Netherlands 2020-02-03 2020 /pmc/articles/PMC7223317/ /pubmed/32421074 http://dx.doi.org/10.1007/s10989-020-10038-2 Text en © Springer Nature B.V. 2020 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
Saxena, Prashant
Mishra, Sanjay
Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title_full Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title_fullStr Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title_full_unstemmed Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title_short Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development
title_sort study of the binding pattern of hla class i alleles of indian frequency and ctap binding peptide for chikungunya vaccine development
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223317/
https://www.ncbi.nlm.nih.gov/pubmed/32421074
http://dx.doi.org/10.1007/s10989-020-10038-2
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