Molecular Modeling of the Shigella flexneri Serogroup 3 and 5 O-Antigens and Conformational Relationships for a Vaccine Containing Serotypes 2a and 3a

Abstract

The pathogenic bacterium Shigella flexneri is a leading global cause of diarrheal disease. The O-antigen is the primary vaccine target and distinguishes the 30 serotypes reported. Except for serotype 6, all S. flexneri serotypes have a common backbone repeating unit (serotype Y), with variations in substitution creating the various serotypes. A quadrivalent vaccine containing serotypes 2a and 3a (as well as 6 and Shigella sonnei) is proposed to provide broad protection against non-vaccine S. flexneri serotypes through shared epitopes and conformations. Here we model the O-antigen (O-Ag) conformations of serogroups 3 and 5: a continuation of our ongoing systematic study of the S. flexneri O-antigens that began with serogroup 2. Our simulations show that S. flexneri serogroups 2, 3, and 5 all have flexible O-Ags, with substitutions of the backbone altering the chain conformations in different ways. Our analysis suggests three general heuristics for the effects of substitution on the Shigella O-Ag conformations: (1) substitution on rhamnose C reduces the extension of the O-Ag chain; (2) substitution at O-3 of rhamnose A restricts the O-Ags to predominantly helical conformations, (3) substitution at O-3 of rhamnose B has only a slight effect on conformation. The common O-Ag conformations across serotypes identified in this work support the assumption that a quadrivalent vaccine containing serotypes 2a and 3a could provide coverage against S. flexneri serotype 3b and serogroup 5.

Conformational and Immunogenicity Studies of the Shigella flexneri Serogroup 6 O-Antigen: The Effect of O-Acetylation

“…We used our established systematic approach to the modeling of polysaccharides, as follows [ 19 , 24 ]. To identify the preferred orientation of each glycosidic linkage, two-dimensional φ, ψ potential mean force (PMF) calculations were performed for the glycosidic linkages of all the disaccharide fragments of the O-Ag repeating units.…”

“…Chain length is an important consideration when modeling O-Ags, as a short chain may have insufficient molecular flexibility while long chains become extremely time consuming and too computationally expensive to model. S. flexneri exhibits a range of O-Ag chain lengths, however, 3RU is considered sufficient to represent O-Ag conformation (based on our previous work with S. flexneri and studies in mice) [ 15 , 19 , 20 , 25 , 26 ]. Furthermore, antibodies have been shown to only bind small fragments of the O-Ag between one and seven residues in length corresponding to 1–2 RU in the case of S. flexneri [ 27 ].…”

“…Molecular modeling of antigen conformations can provide insight into the likelihood of cross-protection between S. flexneri O-Ags [15,19]. We have previously modelled the 4Ac).…”

“…Molecular modeling of antigen conformations can provide insight into the likelihood of cross-protection between S. flexneri O-Ags [ 15 , 19 ]. We have previously modelled the conformations of S. flexneri serogroup Y, 2, 3, and 5 O-antigens [ 15 , 19 ]. The molecular dynamics simulations revealed that S. flexneri serotypes are highly flexible, with a wide distribution of conformations.…”

“…The molecular dynamics simulations revealed that S. flexneri serotypes are highly flexible, with a wide distribution of conformations. Substitutions of the backbone residues (glucosylation and/or O-acetylation) were found to limit the flexibility and distribution of conformations to varying degrees and we proposed three guiding heuristics to describe and predict the effect of substitutions [ 19 ]. Particularly of relevance to Sf 6 is that we found that substitution with O-factor 9 restricts the O-Ags to predominantly helical conformations.…”