In silico prediction of T- and B-cell epitopes in PmpD: First step towards to the design of a Chlamydia trachomatis vaccine

Abstract

BackgroundChlamydia trachomatis is the most common sexually transmitted bacterial infection globally. Currently, there are no vaccines available despite the efforts made to develop a protective one. Polymorphic membrane protein D (PmpD) is an attractive immunogen candidate as it is conserved among strains and it is target of neutralizing antibodies. However, its high molecular weight and its complex structure make it difficult to handle by recombinant DNA techniques. Our aim is to predict B-cell and T-cell epitopes of PmpD.MethodA sequence (Genbank AAK69391.2) having 99–100% identity with various serovars of C. trachomatis was used for predictions. NetMHC and NetMHCII were used for T-cell epitope linked to MHC I or MHC II alleles prediction, respectively. BepiPred predicted linear B-cell epitopes. For three dimensional epitopes, PmpD was homology-modeled by Raptor X. Surface epitopes were predicted on its globular structure using DiscoTope.ResultsNetMHC predicted 271 T-cell epitopes of 9-12aa with weak affinity, and 70 with strong affinity to MHC I molecules. NetMHCII predicted 2903 T-cell epitopes of 15aa with weak affinity, and 742 with strong affinity to MHC II molecules. Twenty four linear B-cell epitopes were predicted. Raptor X was able to model 91% of the three-dimensional structure whereas 57 residues of discontinuous epitopes were suggested by DiscoTope. Six regions containing B-cell and T-cell epitopes were identified by at least two predictors.ConclusionsPmpD has potential B-cell and T-cell epitopes distributed throughout the sequence. Thus, several fragments were identified as valuable candidates for subunit vaccines against C. trachomatis.

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“…Particularly, amino acid substitutions (E484K and N501Y) in conformational epitopes were found in the RBD of the S protein (yellow). Reports suggested that amino acid substitutions of the conformational epitopes lead to viral reinfection and changes of vaccine efficacy ( Russi et al, 2018 ). Thus, our in silico study suggests that the mRNA vaccine efficacy partially changes against the variants ( Russi et al, 2018 ; Sahin et al, 2020 ), although this should also be examined in vitro and in vivo .…”

Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface

“…This interaction is at the core of the adaptive immune system, which among others is responsible for immunological memory and antigen-specific responses in vertebrates [ 2 ]. The ability to identify these binding areas in the antigen’s sequence or structure is important for the development of synthetic vaccines [ 3 , 4 , 5 ], diagnostic tests [ 6 ], and immunotherapeutics [ 7 , 8 ], especially in the COVID-19 era. Focus on these applications through the lens of epitope discovery has gained attention over the years, especially in regard to the safety benefits of synthetic vaccine development [ 9 ].…”

Linear B-cell epitope prediction for in silico vaccine design: a performance review of methods available via command-line interface

“…This interaction is at the core of the adaptive immune system, where among others is responsible for immunological memory and antigenspecific responses in vertebrates. The ability to identify these binding areas in the antigen's sequence or structure is important for the development of synthetic vaccines [1][2][3], diagnostic tests [4] and immunotherapeutics [5,6]. Focus on these applications, through the lens of epitope discovery, has gained attention over the years, especially in regard to the safety benefits of synthetic vaccine development [7].…”