Comparative Molecular Modelling of Capsular Polysaccharide Conformations in Streptococcus suis Serotypes 1, 2, 1/2 and 14 Identifies Common Epitopes for Antibody Binding

Abstract

Streptococcus suis is an encapsulated, commensal, potentially pathogenic bacterium that infects swine globally and causes sporadic life-threatening zoonotic septicemia and meningitis infections in humans. The capsular polysaccharide is a primary virulence factor for S. suis. As S. suis serotype 2 is the most prevalent serotype globally, the serotype 2 CPS is the primary target of current efforts to develop an effective glycoconjugate veterinary vaccine against S. suis. Possible cross-protection with related serotypes would broaden the coverage of a vaccine. The CPS in serotypes 2 and 1/2 differ at a single residue (Gal versus GalNAc), and both are similar to serotypes 1 and 14: all contain a terminal sialic acid on a side chain. However, despite this similarity, there is complex pattern of cross-protection for these serotypes, with varying estimations of the importance of sialic acid in a protective epitope. Further, a pentasaccharide without the terminal sialic acid has been identified as minimal epitope for serotype 2. Here we use molecular simulation to model the molecule conformations of the CPS in serotypes 2, 1/2, 1 and 14, as well as three vaccine candidate oligosaccharides. The common epitopes we identify assist in rationalizing the apparently contradictory immunological data and provide a basis for rational design of S. suis vaccines in the future.

Keywords: Streptococcus suis; antigen; capsular polysaccharide; carbohydrate epitopes; conformation; cross protection; molecular modelling and simulation.

FIGURE 1

Capsular polysaccharide repeating unit structures for Streptococcus suis serotypes 2, 14, 1/2 and 1 and 14 (Van Calsteren et al., 2010; Van Calsteren et al., 2013; Van Calsteren et al., 2016), as well as the structure of three Ss2 oligosaccharide vaccine candidates, labelled frag3, frag4 and frag5 (Zhang et al., 2021). The graphical representations use the Symbol Nomenclature for Glycans (SNFG) (Varki et al., 2015). Abbreviations: d-glucose (Glc), d-galactose (Gal), N-acetyl-d-glucosamine (GlcNAc), N-acetyl-d-galactosamine (GalNAc), l-rhamnose (Rha), N-acetyl-d-neuraminic acid (Neu5Ac).

FIGURE 2

The end-to-end distance, r, for the 6 RU S. suis CPS is here defined as the distance (Å) from the ring O5 in the backbone βDGal in the first and last RU, labelled in (A) on a sample Ss2 conformation. The simulation time series (left column) and corresponding histograms (right column) are graphed for (B) Ss2, (C) Ss1/2, (D) Ss1 and (E) Ss14. The first 200 ns of simulation are considered equilibration and are not shown. The average r value $\overline{r}$ (plotted as a dashed gray line on the time series graphs) and the standard deviation σ are listed on each histogram.

FIGURE 3

Main conformational families and associated percentages of the CPS molecules shown with the side chains in the PaperChain visualisation and the CPS backbone in a space-filling representation. Representative conformations for RU 2–5 (excluding the first and last RU) are shown for (A) Ss2; (B) Ss1/2; (C) Ss14; and (D) Ss1. Conformations are scaled according to their relative percentage occupancies, and clusters less than 6% are not shown. The residues in all representations are coloured in keeping with the SNFG, as follows: βdGal and βdGalNAc—yellow; αdGal—brown; βdGlc—blue; βlRha—green; αdNeu5Ac—purple.

FIGURE 4

Main conformational families and associated percentages of the side chains in RU 4 for (A) Ss2; (B) Ss1/2; (C) Ss14; and (D) Ss1. Conformational clusters of less than 10% occupancy are not shown. Potential epitopes are labelled on Ss2 in grey. The residues in all representations are coloured in keeping with the SNFG, as follows: βdGal and βdGalNAc—yellow; αdGal—brown; βdGlc and βdGlcNAc—blue; βlRha—green; αdNeu5Ac—purple; NAc—cyan.

FIGURE 5

Main conformational families and associated percentages of the sialic side chain in (A) RU 4 of Ss2 compared with the dominant conformation of the three Ss2 oligosaccharide vaccine candidates (B) frag3, (C) frag4 and (D) frag5 (Zhang et al., 2021). Conformational clusters with less than 10% occupancy are not shown. The residues in all representations are coloured in keeping with the SNFG, as follows: βdGal and βdGalNAc—yellow; αdGal—brown; βdGlc and βdGlcNAc—blue; βlRha—green; αdNeu5Ac—purple; NAc—cyan.