Rational design of multi-epitope vaccine for Chandipura virus using an immunoinformatics approach

Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL...

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Vydáno v:	PloS one Ročník 20; číslo 10; s. e0335147
Hlavní autoři:	Naderian, Ramtin, Ahmad, Sajjad, Rahmanian, Mojgan, Aghaamoo, Shahrzad, Rahbar, Aryan, Pajand, Omid, Alizadeh, Akram, Nazarian, Shahin, Sanami, Samira, Eslami, Majid
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 01.10.2025 Public Library of Science (PLoS)
Témata:	Allergens Animals Antibodies Antigenicity Antigens Bioinformatics Computational Biology - methods COVID-19 vaccines Cytotoxicity Disease transmission Encephalitis Epidemics Epitopes Epitopes, B-Lymphocyte - chemistry Epitopes, B-Lymphocyte - immunology Epitopes, T-Lymphocyte - chemistry Epitopes, T-Lymphocyte - immunology Genomes Glycoproteins Humans Immune response Immune system Immunoinformatics Infectious diseases Interferon Interleukin 2 Lymphocytes B Lymphocytes T Molecular docking Molecular Docking Simulation Molecular dynamics Molecular Dynamics Simulation Peptides Protein structure Proteins Rhabdoviridae Infections - immunology Rhabdoviridae Infections - prevention & control TLR4 protein Toll-Like Receptor 4 - chemistry Toll-Like Receptor 4 - immunology Toll-like receptors Toxicity Toxins Vaccines Vesiculovirus - immunology Viral Vaccines - chemistry Viral Vaccines - immunology Viruses India
ISSN:	1932-6203, 1932-6203
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Abstract	Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL epitopes, 2 HTL epitopes, and 1 linear B-cell epitope from glycoprotein (G) with 1 EAAAK linker, 10 AAY linkers, 2 GPGPG linkers, 1 KK linker, and adjuvant (RS-09 peptide). We predicted and optimized the vaccine’s protein structure. Furthermore, the vaccine 3D structure was docked with Toll-like receptor 4 (TLR4) using the Cluspro 2.0 server, and the docked complex was analyzed using molecular dynamics (MD) simulation by the assisted model building with energy refinement (AMBER) v.20 package. The vaccine’s immune simulation profile was determined, and the vaccine sequence was reverse translated and in silico cloned into the pET28a (+). The vaccine’s population coverage was 99.79% across the worldwide. The vaccine was soluble, non-allergenic and non-toxic, with high levels of antigenicity. The quality of the vaccine’s 3D structure improved following refining, and the number of residues in the most favoured regions of the Ramachandran plot increased by 94.2%. The molecular docking, with a docking score of −1157 kcal/mol, and MD simulation results revealed a robust interaction and remarkable stability between the vaccine and TLR4. The immune response simulation indicated a decrease in antigen levels and an increase in interferon‐gamma (IFN‐γ) and interleukin-2 (IL-2) concentrations after each injection. In silico results indicate that this vaccine possesses significant promise against CHPV; however, laboratory and animal studies are necessary to validate our findings.
AbstractList	Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL epitopes, 2 HTL epitopes, and 1 linear B-cell epitope from glycoprotein (G) with 1 EAAAK linker, 10 AAY linkers, 2 GPGPG linkers, 1 KK linker, and adjuvant (RS-09 peptide). We predicted and optimized the vaccine’s protein structure. Furthermore, the vaccine 3D structure was docked with Toll-like receptor 4 (TLR4) using the Cluspro 2.0 server, and the docked complex was analyzed using molecular dynamics (MD) simulation by the assisted model building with energy refinement (AMBER) v.20 package. The vaccine’s immune simulation profile was determined, and the vaccine sequence was reverse translated and in silico cloned into the pET28a (+). The vaccine’s population coverage was 99.79% across the worldwide. The vaccine was soluble, non-allergenic and non-toxic, with high levels of antigenicity. The quality of the vaccine’s 3D structure improved following refining, and the number of residues in the most favoured regions of the Ramachandran plot increased by 94.2%. The molecular docking, with a docking score of −1157 kcal/mol, and MD simulation results revealed a robust interaction and remarkable stability between the vaccine and TLR4. The immune response simulation indicated a decrease in antigen levels and an increase in interferon‐gamma (IFN‐γ) and interleukin-2 (IL-2) concentrations after each injection. In silico results indicate that this vaccine possesses significant promise against CHPV; however, laboratory and animal studies are necessary to validate our findings. Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL epitopes, 2 HTL epitopes, and 1 linear B-cell epitope from glycoprotein (G) with 1 EAAAK linker, 10 AAY linkers, 2 GPGPG linkers, 1 KK linker, and adjuvant (RS-09 peptide). We predicted and optimized the vaccine's protein structure. Furthermore, the vaccine 3D structure was docked with Toll-like receptor 4 (TLR4) using the Cluspro 2.0 server, and the docked complex was analyzed using molecular dynamics (MD) simulation by the assisted model building with energy refinement (AMBER) v.20 package. The vaccine's immune simulation profile was determined, and the vaccine sequence was reverse translated and in silico cloned into the pET28a (+). The vaccine's population coverage was 99.79% across the worldwide. The vaccine was soluble, non-allergenic and non-toxic, with high levels of antigenicity. The quality of the vaccine's 3D structure improved following refining, and the number of residues in the most favoured regions of the Ramachandran plot increased by 94.2%. The molecular docking, with a docking score of -1157 kcal/mol, and MD simulation results revealed a robust interaction and remarkable stability between the vaccine and TLR4. The immune response simulation indicated a decrease in antigen levels and an increase in interferon-gamma (IFN-γ) and interleukin-2 (IL-2) concentrations after each injection. In silico results indicate that this vaccine possesses significant promise against CHPV; however, laboratory and animal studies are necessary to validate our findings.Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL epitopes, 2 HTL epitopes, and 1 linear B-cell epitope from glycoprotein (G) with 1 EAAAK linker, 10 AAY linkers, 2 GPGPG linkers, 1 KK linker, and adjuvant (RS-09 peptide). We predicted and optimized the vaccine's protein structure. Furthermore, the vaccine 3D structure was docked with Toll-like receptor 4 (TLR4) using the Cluspro 2.0 server, and the docked complex was analyzed using molecular dynamics (MD) simulation by the assisted model building with energy refinement (AMBER) v.20 package. The vaccine's immune simulation profile was determined, and the vaccine sequence was reverse translated and in silico cloned into the pET28a (+). The vaccine's population coverage was 99.79% across the worldwide. The vaccine was soluble, non-allergenic and non-toxic, with high levels of antigenicity. The quality of the vaccine's 3D structure improved following refining, and the number of residues in the most favoured regions of the Ramachandran plot increased by 94.2%. The molecular docking, with a docking score of -1157 kcal/mol, and MD simulation results revealed a robust interaction and remarkable stability between the vaccine and TLR4. The immune response simulation indicated a decrease in antigen levels and an increase in interferon-gamma (IFN-γ) and interleukin-2 (IL-2) concentrations after each injection. In silico results indicate that this vaccine possesses significant promise against CHPV; however, laboratory and animal studies are necessary to validate our findings. Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a multi-epitope vaccine for CHPV using immunoinformatics approaches. In this study, a multi-epitope vaccine construct was developed by combining 11 CTL epitopes, 2 HTL epitopes, and 1 linear B-cell epitope from glycoprotein (G) with 1 EAAAK linker, 10 AAY linkers, 2 GPGPG linkers, 1 KK linker, and adjuvant (RS-09 peptide). We predicted and optimized the vaccine's protein structure. Furthermore, the vaccine 3D structure was docked with Toll-like receptor 4 (TLR4) using the Cluspro 2.0 server, and the docked complex was analyzed using molecular dynamics (MD) simulation by the assisted model building with energy refinement (AMBER) v.20 package. The vaccine's immune simulation profile was determined, and the vaccine sequence was reverse translated and in silico cloned into the pET28a (+). The vaccine's population coverage was 99.79% across the worldwide. The vaccine was soluble, non-allergenic and non-toxic, with high levels of antigenicity. The quality of the vaccine's 3D structure improved following refining, and the number of residues in the most favoured regions of the Ramachandran plot increased by 94.2%. The molecular docking, with a docking score of -1157 kcal/mol, and MD simulation results revealed a robust interaction and remarkable stability between the vaccine and TLR4. The immune response simulation indicated a decrease in antigen levels and an increase in interferon-gamma (IFN-γ) and interleukin-2 (IL-2) concentrations after each injection. In silico results indicate that this vaccine possesses significant promise against CHPV; however, laboratory and animal studies are necessary to validate our findings.
Author	Aghaamoo, Shahrzad Sanami, Samira Rahmanian, Mojgan Nazarian, Shahin Naderian, Ramtin Eslami, Majid Ahmad, Sajjad Pajand, Omid Alizadeh, Akram Rahbar, Aryan
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/41129557$$D View this record in MEDLINE/PubMed
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Copyright	Copyright: © 2025 Naderian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 2025 Naderian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2025 Naderian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Snippet	Chandipura virus (CHPV) is endemic in India, with frequent outbreaks reported. No approved medicines or vaccines exist for CHPV. We aimed to develop a...
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SubjectTerms	Allergens Animals Antibodies Antigenicity Antigens Bioinformatics Computational Biology - methods COVID-19 vaccines Cytotoxicity Disease transmission Encephalitis Epidemics Epitopes Epitopes, B-Lymphocyte - chemistry Epitopes, B-Lymphocyte - immunology Epitopes, T-Lymphocyte - chemistry Epitopes, T-Lymphocyte - immunology Genomes Glycoproteins Humans Immune response Immune system Immunoinformatics Infectious diseases Interferon Interleukin 2 Lymphocytes B Lymphocytes T Molecular docking Molecular Docking Simulation Molecular dynamics Molecular Dynamics Simulation Peptides Protein structure Proteins Rhabdoviridae Infections - immunology Rhabdoviridae Infections - prevention & control TLR4 protein Toll-Like Receptor 4 - chemistry Toll-Like Receptor 4 - immunology Toll-like receptors Toxicity Toxins Vaccines Vesiculovirus - immunology Viral Vaccines - chemistry Viral Vaccines - immunology Viruses
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Title	Rational design of multi-epitope vaccine for Chandipura virus using an immunoinformatics approach
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