In silico design of a novel peptide-based vaccine candidate against Streptococcus pneumoniae

Streptococcus pneumoniae remains a leading bacterial pathogen causing pneumonia, meningitis, septicemia, and post-viral respiratory infections such as COVID-19. Despite licensed vaccines, efficacy is limited by serotype dependency, cost, and restricted coverage, highlighting the need for broad-spectrum alternatives. Protein-based vaccines with conserved antigens represent a promising strategy. This study aimed to design and evaluate an efficient peptide-based vaccine against pneumococcal virulence factors using immunoinformatics tools. Two major pneumococcal surface proteins were selected, and two immunodominant epitope-rich regions enriched in overlapping B-cell and MHC-II epitopes were identified and linked using a flexible linker. To enhance immunogenicity, human β-defensin-2 (hBD-2) was fused to the N-terminus with a rigid linker, and a His-tag was added at the C-terminus. The construct showed high predicted antigenicity (VaxiJen score: 0.917), was predicted to be non-allergenic, and exhibited favorable solubility and physicochemical properties. Structural modeling, refinement, discontinuous B-cell epitope mapping, docking with TLR4/MD2, molecular dynamics, and immune simulations were performed. The construct demonstrated favorable stability and safety, while B-cell epitope mapping indicated predicted immunogenic potential. Molecular docking predicted stable interactions with TLR4/MD2, with the top-ranked ClusPro complex showing an energy score of - 779.3. Normal mode analysis suggested structural flexibility and conformational stability of the complex. Immune simulations predicted potentially robust primary, secondary, and tertiary responses, including antibody production, memory cell generation, and IFN-γ induction. Integrating conserved immunodominant regions into a peptide-based construct with hBD-2 adjuvant through rational immunoinformatics resulted in a computationally predicted stable and immunogenic candidate that may potentially overcome serotype dependency and provide broader protection. In silico results suggest this peptide-based vaccine is a promising candidate, warranting further in vitro and in vivo validation.

The online version contains supplementary material available at https://doi.org/10.1007/s40203-026-00740-2.