In silico design of a novel chimeric shigella IpaB fused to C terminal of clostridium perfringens enterotoxin as a vaccine candidate

This study aimed to design a novel chimeric protein in silico to serve as a serotype-independent vaccine candidate against Shigella. The chimera contains amino acid residues 240-460 of Shigella invasion plasmid antigen B (IpaB) and the C-terminus of Clostridium perfringens enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE290-319, IpaB-CPE184-319, IpaB-CPE194-319 and 537 newly designed IpaB-linker-CPE290-319 constructs with varying linker regions were predicted. These predicted 3D structures were merged with the 3D structures of native IpaB(240-460), CPE194-319, CPE184-319 and CPE290-319 to select the structure most similar to native IpaB and C-CPE. Several in silico tools were used to determine the suitability of the selected IpaB-C-CPE structure as a vaccine candidate. None of the 537 linkers was capable of preserving the native structure of CPE290-319 within the IpaB-linker-CPE290-319 structure. In silico analysis determined that the IpaB-CPE194-319 3D structure was the most similar to the 3D structure of the respective native CPE domain and that it was a stable chimeric protein exposing multiple B-cell epitopes. IpaB-CPE194-319 was designed for its capability to bind to human intestinal epithelial and M cells and to accumulate on these cells. The predicted B-cell epitopes are likely to be capable of inducing a mucosal antibody response in the human intestine against Shigella IpaB. This study also showed that the higher binding affinities of CPE184-319 and CPE194-319 to claudin molecules than those of CPE290-319 is the result of preserving the 3D structures of CPE184-319 and CPE194-319 when they are linked to the C-termini of other proteins.