In silico design of a multi epitope vaccine for epithelial cancer immunotherapy-a comparative study

Abstract

Epithelial cancers remain a leading cause of morbidity and mortality worldwide, and many patients either fail or cannot tolerate conventional therapies. Cancer immunotherapy, particularly multi-epitope peptide and mRNA vaccines, has emerged as a promising strategy to induce precise, durable anti-tumor immune responses while limiting systemic toxicity. Leveraging tumor-associated and cancer-testis antigens as well as oncogenic drivers enables rational vaccine design tailored to epithelial malignancies such as breast, lung, colorectal and cervical cancers. This study presents a comparative analysis of in silico based multi epitope vaccine construction against epithelial cancer targeting 4 different proteins. Each protein was evaluated for vaccine antigenicity, physicochemical properties and structural stability using immune informative approach to identify the most suitable vaccine candidate. Various tools were used to identify the different epitopes of HTL, CTL, Bcell, which were connected using suitable linkers. Physicochemical properties were also check for the prepared vaccine through using Protparam. Molecular Docking was done with TLR-3 for checking the residual interaction. Among the proteins investigated, fascin1 emerged as the most promising candidate demonstrating superior vaccine antigenicity, favorable physical properties and structural stability. Collectively, this approach is expected to yield a structurally stable, antigenic, and globally applicable multi-epitope vaccine candidate capable of eliciting coordinated humoral and cellular immunity against epithelial cancers, warranting subsequent in vitro and in vivo validation.