Computational Design and In Silico Evaluation of a Multi-Epitope Vaccine Candidate Targeting HIV Envelope Proteins

Paushali Pal

doi:10.36948/ijfmr.2026.v08i02.71872

Computational Design and In Silico Evaluation of a Multi-Epitope Vaccine Candidate Targeting HIV Envelope Proteins

Author(s)	Dr. Paushali Pal
Country	India
Abstract	Human Immunodeficiency Virus (HIV) remains a major global health challenge due to its high genetic variability and complex immune evasion mechanisms. In the present study, an immunoinformatics-based strategy was employed to design a multi-epitope vaccine candidate targeting envelope proteins associated with HIV entry pathways. The vaccine construct was evaluated through a series of computational analyses, including protein–protein docking, structural dynamics assessment, codon optimisation, and in silico cloning. Protein–protein docking was performed to investigate the interaction potential of the vaccine construct with host receptors involved in viral entry, including CD4, CCR5, and CXCR4. The docking results demonstrated favourable binding interactions with progressively stable docking scores across the receptor engagement stages, suggesting structural compatibility between the vaccine construct and host receptor systems. Post-docking interaction analysis identified hydrogen bonds, salt bridges, and hydrophobic contacts contributing to interface stability. Normal mode analysis was performed to examine the dynamic behaviour of the docked complexes, revealing a stable structural architecture with limited flexible regions primarily located in loop segments. Codon optimisation using the JCat server indicated efficient expression potential in Escherichia coli K12 with an optimal Codon Adaptation Index and balanced GC content. In silico cloning further confirmed successful integration of the vaccine gene into the pET-28a(+) expression vector. Overall, the computational results suggest that the designed multi-epitope construct exhibits favourable structural stability, receptor interaction potential, and expression feasibility, supporting its suitability for further experimental validation as a prospective HIV vaccine candidate.
Keywords	Multi-epitope vaccine, HIV, Immunoinformatics, molecular docking, protein–protein interaction, normal mode analysis, codon optimisation, in silico cloning
Field	Biology > Genetics / Molecular
Published In	Volume 8, Issue 2, March-April 2026
Published On	2026-03-19
DOI	https://doi.org/10.36948/ijfmr.2026.v08i02.71872

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Computational Design and In Silico Evaluation of a Multi-Epitope Vaccine Candidate Targeting HIV Envelope Proteins

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