In Silico Design and Comprehensive Evaluation of a Novel Multi-Epitope Vaccine Candidate Against Chandipura Virus
- 1lovely professional university
Abstract
Chandipura virus (CHPV), an emerging arthropod-borne member of the Rhabdovirdae family, is an acute neurotropic pathogen responsible for explosive outbreak of acute encephalitis syndrome (AES) predominantly in pediatric cohorts. with mortality rates exceeding 70%, seizures, and death within 24 to 48 hours. the complete lack of approved antiviral therapies or preventive vaccine makes this a severe global health threat. to address this ,our study utilized a computational reverse vaccinology approach to design and structurally evaluate a novel epitope-based vaccine construct. and computationally validate a 104-amino-acid chimeric peptide vaccine candidate targeting immunoinformatics screening confirmed that the construct possesses strong predicted protective antigencity (VaxiJen >0.40) complete absence of allergenicity across multiple machine-learning models (AllerTopv2.0 and AllergenFP v1.0),and zero cellular or hemolytic toxicity (ToxinPred SVM regression score < 0.0). physicochemical characterization via EXPASY ProtParam established an 11.76 kDa construct comprising 1,653 atoms, with a theoretical isoelectric point of 7.78 an instability index of 39.92 (classifying the protein as physically stable), an aliphatic index of 81.73, and a grand average of Hydropathicity (GRAVY) of -0.350. These values confirm the construct is highly soluble in aqueous environments, which is necessary for physiological delivery. to prepare for expression, the sequence was reverse translated by codon-optimized for escherichia coli strain K12. JCat analysis returned a codonasaptation index (CAI) of 0.956 alongside of GC content of 61.48%. Subsequent in silico cloning successfully placed the 315 bp expression cassette into the pET-28a(+) vector, directly downstream of the T7 promoter. next, we evaluated receptor interaction by docking the construct against human Toll-Like Receptor 4 (TLR4;PDB ID: 4G8A). Using Hawkrank score of -5845.39 We validated this affinity with MM/GBSA calculations, which revealed a strong net binding free energy ({Delta}Gbind) of -29.12 kcal/mol, because static dicking cannot account for molecular flexibility, we then performed normal mode analysis (NMA) via the iMODS server. this dynamic simulation demonstrated structural stability throughout the construct was analyzed. The analysis found a fundamental eigenvalue of 4.62422*10-. the covariance matrix and elastic network showed highly correlated residue motions. to predict the vaccine's effectiveness we ran a 70-day simulation with C-Immsim. the data showed antigen clearance along with a strong primary IgM response successfully changed into IgG1 and IgG2 antibodies levels. The model also predicted an increase in active helper T cells. it also showed production of Th1 cytokines (inf-{gamma} and IL-2). this computer result prove the immune health of the chandipura virus construct. they give a reason to move this candidate forward for recombinants expression and in vivo preclinical testing.
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BibTeX
@misc{yella2026silico,
title = {{In Silico Design and Comprehensive Evaluation of a Novel Multi-Epitope Vaccine Candidate Against Chandipura Virus}},
author = {S. Yella and h. singh},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.14.758945},
url = {https://www.biorxiv.org/content/10.64898/2026.10.14.758945v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - In Silico Design and Comprehensive Evaluation of a Novel Multi-Epitope Vaccine Candidate Against Chandipura Virus
AU - S. Yella
AU - h. singh
PY - 2026
DA - 2026/10/14
PB - bioRxiv
DO - 10.64898/2026.10.14.758945
UR - https://www.biorxiv.org/content/10.64898/2026.10.14.758945v1
AB - Chandipura virus (CHPV), an emerging arthropod-borne member of the Rhabdovirdae family, is an acute neurotropic pathogen responsible for explosive outbreak of acute encephalitis syndrome (AES) predominantly in pediatric cohorts. with mortality rates exceeding 70%, seizures, and death within 24 to 48 hours. the complete lack of approved antiviral therapies or preventive vaccine makes this a severe global health threat. to address this ,our study utilized a computational reverse vaccinology approach to design and structurally evaluate a novel epitope-based vaccine construct. and computationally validate a 104-amino-acid chimeric peptide vaccine candidate targeting immunoinformatics screening confirmed that the construct possesses strong predicted protective antigencity (VaxiJen >0.40) complete absence of allergenicity across multiple machine-learning models (AllerTopv2.0 and AllergenFP v1.0),and zero cellular or hemolytic toxicity (ToxinPred SVM regression score < 0.0). physicochemical characterization via EXPASY ProtParam established an 11.76 kDa construct comprising 1,653 atoms, with a theoretical isoelectric point of 7.78 an instability index of 39.92 (classifying the protein as physically stable), an aliphatic index of 81.73, and a grand average of Hydropathicity (GRAVY) of -0.350. These values confirm the construct is highly soluble in aqueous environments, which is necessary for physiological delivery. to prepare for expression, the sequence was reverse translated by codon-optimized for escherichia coli strain K12. JCat analysis returned a codonasaptation index (CAI) of 0.956 alongside of GC content of 61.48%. Subsequent in silico cloning successfully placed the 315 bp expression cassette into the pET-28a(+) vector, directly downstream of the T7 promoter. next, we evaluated receptor interaction by docking the construct against human Toll-Like Receptor 4 (TLR4;PDB ID: 4G8A). Using Hawkrank score of -5845.39 We validated this affinity with MM/GBSA calculations, which revealed a strong net binding free energy ({Delta}Gbind) of -29.12 kcal/mol, because static dicking cannot account for molecular flexibility, we then performed normal mode analysis (NMA) via the iMODS server. this dynamic simulation demonstrated structural stability throughout the construct was analyzed. The analysis found a fundamental eigenvalue of 4.62422*10-. the covariance matrix and elastic network showed highly correlated residue motions. to predict the vaccine's effectiveness we ran a 70-day simulation with C-Immsim. the data showed antigen clearance along with a strong primary IgM response successfully changed into IgG1 and IgG2 antibodies levels. The model also predicted an increase in active helper T cells. it also showed production of Th1 cytokines (inf-{gamma} and IL-2). this computer result prove the immune health of the chandipura virus construct. they give a reason to move this candidate forward for recombinants expression and in vivo preclinical testing.
ER -