In-silico epitope-based vaccines design: progress, challenges and the road ahead

Introduction: In silico technologies are increasingly shaping vaccine development, supporting the field beyond empirical discovery toward rational, data-driven design. Contemporary computational pipelines enable rapid antigen screening, high-precision epitope-MHC binding prediction, structural modeling, and immune response simulations. These approaches are accelerating vaccine discovery not only for infectious diseases but also in oncology, where neoantigen prediction underpins personalized cancer immunotherapy. Areas covered: This review explores recent advances in computational pipelines for epitope-based vaccine design, covering antigen discovery; B- and T-cell epitope mapping; safety and specificity assessment; vaccine construct assembly with adjuvants and linkers; structural modeling; and immune-response simulations that predict efficacy in specific disease contexts using advanced platforms. It showcases applications in infectious diseases, including SARS-CoV-2, tuberculosis, and influenza, and poxivirus infections, as well as in cancer immunotherapy. It is based on literature obtained through searches utilizing PubMed, Scopus, and Web of Science databases covering publications up to 2025, using combinations of keywords such as epitope-based vaccines, reverse vaccinology, immunoinformatics, and immune system simulation. Expert opinion: In silico approaches offer a transformative advantage to vaccine research by delivering speed, cost-efficiency, and enhanced precision. Yet the predictive power of current computational pipelines is still constrained by algorithmic limitations and by their incomplete integration of immune-regulatory processes. Progress in artificial intelligence, multi-omics integration, and formal recognition of digital evidence by regulatory agencies will be crucial for narrowing the gap between computational predictions and experimental validation. Ultimately, combining predictive immunoinformatics with advanced immune simulations and rigorous verification could help establish in silico methodologies as a cornerstone of next-generation vaccine development.