Population coverage of MHC-I and MHC-II alleles of the selected epitopes.

Population coverage of MHC-I and MHC-II alleles of the selected epitopes.</p

Fig 7 -

Molecular dynamics (MD) simulation results A) C7-putative nitroreductase RMSD analysis B) RMSF analysis of Cα atoms C) H-bond estimation during 100 ns simulation D) Radius of gyration (Rg) analysis.</p

Pharmit scores and RMSD values of the top 10 hit compounds obtained from pharmacophore-based virtual screening using the Pharmit server.

Pharmit scores and RMSD values of the top 10 hit compounds obtained from pharmacophore-based virtual screening using the Pharmit server.</p

S6 Fig -

The individual RMSF graphs of protein (A) and protein-C7 complex (B). (TIF)</p

Immunogenicity analysis of non-human homologous overlapping epitopes.

Immunogenicity analysis of non-human homologous overlapping epitopes.</p

Molecular interactions between receptor molecules (Chain A) and vaccine construct (Chain B).

Molecular interactions between receptor molecules (Chain A) and vaccine construct (Chain B).</p

Codon optimization index graph of vaccine construct determined by JCAT server.

Codon optimization index graph of vaccine construct determined by JCAT server.</p

Codon optimization of vaccine construct.

Prevention of Clostridium difficile infection is challenging worldwide owing to its high morbidity and mortality rates. C. difficile is currently being classified as an urgent threat by the CDC. Devising a new therapeutic strategy become indispensable against C. difficile infection due to its high rates of reinfection and increasing antimicrobial resistance. The current study is based on core proteome data of C. difficile to identify promising vaccine and drug candidates. Immunoinformatics and vaccinomics approaches were employed to construct multi-epitope-based chimeric vaccine constructs from top-ranked T- and B-cell epitopes. The efficacy of the designed vaccine was assessed by immunological analysis, immune receptor binding potential and immune simulation analyses. Additionally, subtractive proteomics and druggability analyses prioritized several promising and alternative drug targets against C. difficile. These include FMN-dependent nitroreductase which was prioritized for pharmacophore-based virtual screening of druggable molecule databases to predict potent inhibitors. A MolPort-001-785-965 druggable molecule was found to exhibit significant binding affinity with the conserved residues of FMN-dependent nitroreductase. The experimental validation of the therapeutic targets prioritized in the current study may worthy to identify new strategies to combat the drug-resistant C. difficile infection.</div

Protein-protein interaction of pathogen protein CD630_32050 (putative nitroreductase) with PDB ID: 3GFA acquired from STRING database.

Protein-protein interaction of pathogen protein CD630_32050 (putative nitroreductase) with PDB ID: 3GFA acquired from STRING database.</p

Fig 6 -

(A) The active site of the protein CD630_32050 was used to create a pharmacophore model. The characteristics are denoted by different colors. White represents a hydrogen-bond donor, yellow represents a hydrogen acceptor, green represents hydrophobic properties, and aromatic represents aromatic features (pink). (B) The molecular interactions of the top hit docked compound (CD630_32050) within the substrate-binding site. The nature of protein-ligand interactions is shown in different colors.</p