Prioritization of potential vaccine candidates and designing a multiepitope-based subunit vaccine against multidrug-resistant Salmonella Typhi str. CT18: A subtractive proteomics and immunoinformatics approach

Abstract Salmonella enterica serovar Typhi (S. Typhi), a causative agent of typhoid fever, is a Gram-negative, human-restricted pathogen that causes significant morbidity and mortality, particularly in developing countries. The currently available typhoid vaccines are not recommended to children below six years of age and have poor long-term efficacy. Due to these limitations and the emerging threat of multidrug-resistance (MDR) strains, the development of a new vaccine is urgently needed. The present study aims to design a multiepitope-based subunit vaccine (MESV) against MDR S. Typhi str. CT18 using a computational-based approach comprising subtractive proteomics and immunoinformatics. Firstly, we investigated the proteome of S. Typhi str. CT18 using subtractive proteomics and identified twelve essential, virulent, host non-homologous, and antigenic outer membrane proteins (OMPs) as potential vaccine candidates with low transmembrane helices (≤1) and molecular weight (≤110 kDa). The OMPs were mapped for cytotoxic T lymphocyte(CTL) epitopes, helper T lymphocyte (HTL) epitopes, and linear B lymphocyte (LBL) epitopes using various immunoinformatics tools and servers. A total of 6, 12, and 11 CTL, HTL, and LBL epitopes were shortlisted, respectively, based on their immunogenicity, antigenicity, allergenicity, toxicity, and hydropathicity potential. Four MESV constructs (MESVCs), MESVC-1, MESVC-2, MESVC-3, and MESVC-4, were designed by linking the CTL, HTL, and LBL epitopes with immune-modulating adjuvants, linkers, and PADRE (Pan HLA DR-binding epitope) sequences. The MESVCs were evaluated for their physicochemical properties, allergenicity, antigenicity, toxicity, and solubility potential to ensure their safety and immunogenic behavior. Secondary and tertiary structures of shortlisted MESVCs (MESVC-1, MESVC-3, and MESVC-4) were predicted, modeled, refined, validated, and then docked with various MHC I, MHC II, and TLR4/MD2 complex. Molecular dynamics (MD) simulation of the final selected MESVC-4 with TLR4/MD2 complex confirms its binding affinity and stability. Codon optimization and in silico cloning verified the translation efficiency and successful expression of MESVC-4 in E. coli str. K12. Finally, the efficiency of MESVC-4 to trigger an effective immune response was assessed by an in silico immune simulation. In conclusion, our findings show that the designed MESVC-4 can elicit humoral and cellular immune responses, implying that it may be used for prophylactic or therapeutic purposes. Therefore, it should be subjected to further experimental validations.