Abstract
BACKGROUND: Breast cancer (BC) remains a global health emergency, particularly HER2-positive subtypes, which are aggressive and resistant to conventional therapies. Despite advancements, therapeutic resistance and limited immune memory underline the need for novel treatment approaches such as multi-epitope vaccines. OBJECTIVE: This study investigates the design and effectiveness of a novel in silico multi-epitope vaccine that is capable of targeting HER2 in breast cancer using immunoinformatics, structural modeling, and immune simulation approaches. METHODS: UniProt was used to retrieve the HER2 protein sequences. Cytotoxic Tlymphocyte (CTL) and helper T lymphocyte (HTL) epitopes were predicted using IEDB and CTLPred, and filtered for antigenicity, IFN-γ production, and population coverage. The vaccine construct was designed by linking selected epitopes to PADRE, TAT peptide, and adjuvants using appropriate linker sequences. An evaluation of physicochemical, allergenic, and toxicological properties was carried out on the 322-amino-acid vaccine construct. Secondary and tertiary structures were predicted using PSIPRED and Robetta, refined with GalaxyRefine, and validated through Ramachandran plots, ERRAT, and ProSA-web. Molecular docking with TLR4 was conducted using HDOCK. Molecular dynamics simulations (MD) were performed with GROMACS for 100 ns and analyzed using RMSD, RMSF, PCA, DCCM, and MM-PBSA. Immune simulations were performed using C-ImmSim. RESULTS: The final vaccine construct was found to be non-allergenic, antigenic (VaxiJen score: 0.59) and stable (instability index: 23.18). Tertiary structure validation yielded a favorable Ramachandran distribution (83 %), an ERRAT score of 90.12, and a Z-score of -8.35. Docking showed strong binding to TLR4 (score:296.23, with 6 ion bridges and 7 hydrogen bonds). Stable conformation of the vaccine construct with low fluctuations and high interaction correlation was derived through MD simulations. MM-PBSA calculated a binding free energy of -112.71 kJ/mol. Immune simulations predicted robust humoral and cellular immune responses with increased IFN-γ, IL-2, CTLs, and memory B-cells. CONCLUSION: The proposed HER2-targeted multi-epitope vaccine confirmed promising immunogenicity, structural stability, and potential global population coverage. It represents a novel, rationally designed immunotherapy candidate against HER2-positive breast cancer. However, further in vitro and in vivo validations are required to confirm its clinical application.