Rational design of a multi epitope vaccine against Salmonella typhi via subtractive proteomics, reverse vaccinology and molecular modeling

Salmonella enterica subsp. enterica serotype Typhi (Salmonella typhi) is the cause of typhoid fever, a severe public health issue in impoverished countries with inadequate sanitation. Despite the availability of therapies, infection rates remain high, underscoring the critical need for an effective and long-lasting vaccine. In this study, we used an integrated in silico strategy to develop a multi-epitope vaccine for 122 S. Typhi strains. A core proteome study identified 2,637 conserved proteins, while subtractive proteomics discovered three non-homologous, virulent, antigenic, and non-allergenic proteins: major curlin subunit, outer membrane protein A, and a hypothetical protein. Four B-cell and ten T-cell epitopes (four HTL and six CTL) were predicted and chosen for vaccine development using immunoinformatics methods. In order to improve immunogenicity, these epitopes were adjuvanted with human beta-defensin-2 and linked by suitable linkers in the final vaccine design. Molecular docking demonstrated binding energies of -305.76 kcal/mol (TLR4), -254.28 kcal/mol (MHC-I), and - 270.85 kcal/mol (MHC-II), confirming stable interactions of the vaccine with TLR4 and MHC class I and II molecules. Molecular dynamics simulations showed that the vaccine-receptor complexes were structurally stable and compact. A robust and long-lasting immune response was also suggested by an immunological simulation study, which showed increased numbers of memory B and T cells, IL-2, and IFN-γ. Together, these results show how computational pipelines can speed up the development of bacterial vaccines and support the multi-epitope vaccine's potential as a viable option for typhoid fever prevention.