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Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions

From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary tar...

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Autores principales: Tambunan, Usman Sumo Friend, Sipahutar, Feimmy Ruth Pratiwi, Parikesit, Arli Aditya, Kerami, Djati
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852757/
https://www.ncbi.nlm.nih.gov/pubmed/27147821
http://dx.doi.org/10.4137/BBI.S38378
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author Tambunan, Usman Sumo Friend
Sipahutar, Feimmy Ruth Pratiwi
Parikesit, Arli Aditya
Kerami, Djati
author_facet Tambunan, Usman Sumo Friend
Sipahutar, Feimmy Ruth Pratiwi
Parikesit, Arli Aditya
Kerami, Djati
author_sort Tambunan, Usman Sumo Friend
collection PubMed
description From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Vaccine is the most effective immunologic intervention. In this study, we use the epitope-based vaccine design from hemagglutinin and neuraminidase of H5N1 Indonesian strain virus by using immunoinformatics approach in order to predict the binding of B-cell and T-cell epitopes (class I and class II human leukocyte antigen [HLA]). BCPREDS was used to predict the B-cell epitope. Propred, Propred I, netMHCpan, and netMHCIIpan were used to predict the T-cell epitope. Two B-cell epitopes of hemagglutinin candidates and one B-cell epitope of neuraminidase candidates were obtained to bind T-cell CD4(+) (class II HLA), and also five T-cell epitope hemagglutinin and four T-cell epitope neuraminidase were obtained to bind T-cell CD8(+) (class I HLA). The visualization of epitopes was done using MOE 2008.10. It shows that the binding affinity of epitope–HLA was based on minimum binding free energy (ΔG(binding)). Based on this result, visualization, and dynamic simulation, four hemagglutinin epitopes (MEKIVLLLA, CPYLGSPSF, KCQTPMGAI, and IGTSTLNQR) and two neuraminidase epitopes (NPNQKIITI and CYPDAGEIT) were computed as having the best binding affinity from HLA ligand. The results mentioned above are from in silico experiments and need to be validated using wet experiment.
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spelling pubmed-48527572016-05-04 Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions Tambunan, Usman Sumo Friend Sipahutar, Feimmy Ruth Pratiwi Parikesit, Arli Aditya Kerami, Djati Bioinform Biol Insights Original Research From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Vaccine is the most effective immunologic intervention. In this study, we use the epitope-based vaccine design from hemagglutinin and neuraminidase of H5N1 Indonesian strain virus by using immunoinformatics approach in order to predict the binding of B-cell and T-cell epitopes (class I and class II human leukocyte antigen [HLA]). BCPREDS was used to predict the B-cell epitope. Propred, Propred I, netMHCpan, and netMHCIIpan were used to predict the T-cell epitope. Two B-cell epitopes of hemagglutinin candidates and one B-cell epitope of neuraminidase candidates were obtained to bind T-cell CD4(+) (class II HLA), and also five T-cell epitope hemagglutinin and four T-cell epitope neuraminidase were obtained to bind T-cell CD8(+) (class I HLA). The visualization of epitopes was done using MOE 2008.10. It shows that the binding affinity of epitope–HLA was based on minimum binding free energy (ΔG(binding)). Based on this result, visualization, and dynamic simulation, four hemagglutinin epitopes (MEKIVLLLA, CPYLGSPSF, KCQTPMGAI, and IGTSTLNQR) and two neuraminidase epitopes (NPNQKIITI and CYPDAGEIT) were computed as having the best binding affinity from HLA ligand. The results mentioned above are from in silico experiments and need to be validated using wet experiment. Libertas Academica 2016-04-28 /pmc/articles/PMC4852757/ /pubmed/27147821 http://dx.doi.org/10.4137/BBI.S38378 Text en © 2016 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
spellingShingle Original Research
Tambunan, Usman Sumo Friend
Sipahutar, Feimmy Ruth Pratiwi
Parikesit, Arli Aditya
Kerami, Djati
Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title_full Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title_fullStr Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title_full_unstemmed Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title_short Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
title_sort vaccine design for h5n1 based on b- and t-cell epitope predictions
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852757/
https://www.ncbi.nlm.nih.gov/pubmed/27147821
http://dx.doi.org/10.4137/BBI.S38378
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