Development of a novel multi-epitope vaccine against triple-negative breast cancer targeting A-kinase anchoring protein 3 using bioinformatics

Abstract

A-Kinase Anchoring Protein 3 (AKAP3), a Cancer-Testis Antigen (CTA), is involved in cell proliferation and is aberrantly expressed in triple-negative breast cancer (TNBC), making it a promising target for immunotherapy. This study aimed to design a novel multi-epitope vaccine targeting AKAP3 using immunoinformatics approaches. Predicted CTL, HTL, and B-cell epitopes were selected based on their immunogenicity, antigenicity, non-allergenicity, and non-toxicity. The final construct integrated three epitopes from each category, connected by appropriate linkers (EAAAK, AAY, GPGPG, KK) and adjuvanted with the 50S ribosomal protein L7/L12 to enhance the immune response. Population coverage analysis indicated high accessibility, with 99.28 % in Indonesia, 99.4 % in Southeast Asia, and 100 % globally. Structural modeling and validation confirmed the vaccine's stability and immunogenic profile. Molecular docking demonstrated strong binding affinity to TLR-4 (−839.8 kcal/mol), supported by stable interactions in molecular dynamics simulations. Immune simulations further predicted the robust activation of both cellular and humoral immunity. In silico cloning confirmed compatibility with the pET28a(+) expression system for potential recombinant production. Collectively, these findings support the designed vaccine as a promising candidate for TNBC immunotherapy, warranting further in vitro and in vivo evaluation.