Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA

Abstract

Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA) supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86%) among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world.

Figure 1

Flow diagram of the methodology.

Figure 2

Cluster analysis of the HLA alleles for both MHC molecules through heat map representation. (a) Representing the cluster of the MHC-I. (b) Representing the cluster of MHC-II molecules. Epitopes are clustered on the basis of interaction with HLA and shown as red colour indicating strong interaction with appropriate annotation. Yellow zone indicates the weaker interaction. Here, all the available alleles are shown only.

Figure 3

MSA-based location identification of the different epitopes within the SPATE proteins of Shigella and their homologue in E. coli. In this figure, gi|647302223|, gi|446956855|, gi|844758686|, and gi|446956853| represent the S. flexneri, S. sonnei, S. boydii, and S. dysenteriae, respectively. E. coli represented by gi|693049347| and gi|699401135|.

Figure 4

The three-dimensional model of SPATE subfamily protein SigA with the proposed epitopes VTARAGLGY (magenta), FHTVTVNTL (yellow), HTTWTLTGY (green), and IELAGTLTL (red). The superficial localities of the epitopes indicate their surface accessibility.

Figure 5

The configurational frustration index of the predicted model of the SigA. (a) This analysis detects the stability and energy differences of the 3D structure of the protein. Colours are in accordance with their frustration index. The red colour regions are highly frustrated and the green colour regions are not frustrated. The frustrated residues are able to change their identity and also displace the location in any favourable conditions. (b) The locations of our proposed epitopes are described by different colours. The epitopes HTTWTLTGY (cyan) and IELAGTLTL (blue) are well outside of the frustrated regions and securing their stability. On the other hand, the epitopes VTARAGLGY (yellow) and FHTVTVNTL (orange) are in the frustrated regions and unable to secure their stability.

Figure 6

Population coverage analysis for the top predicted epitope based on the HLA interaction. Here, the whole world populations are assessed for the proposed epitope. The combined prediction for both of the MHC has been shown. Here, the number 1 bar for all the analyses represents out-predicted epitope. Notes: in the graphs, the line (-o-) represents the cumulative percentage of population coverage of the epitopes; the bars represent the population coverage for each epitope.

Figure 7

Docking analysis of the predicted epitope IELAGTLTL and HLA-E allele. (a) Representing the oriented view of the interaction and assuring the perfect binding. (b) Representing the cartoon view. (c) Embodying the interacted residues with the peptide.

Figure 8

Docking analysis of the predicted epitope KAIELAGTLTLTGTP and HLA-DQA1 allele. (a) Representing the oriented view of the interaction and assuring the perfect binding. (b) Representing the cartoon view. (c) Embodying the interacted residues with the peptide.

Figure 9

B-cell epitope prediction. (a) Kolaskar and Tongaonkar antigenicity prediction of the proposed epitope with a threshold value of 1.037. (b) Emini surface accessibility prediction of the proposed epitope, with a threshold value of 1.0. (c) Parker hydrophilicity prediction of the epitope, with a threshold of −0.352. Notes: the x-axis and y-axis represent the sequence position and antigenic propensity, respectively. The regions above the threshold are antigenic (desired), shown in yellow.