Abstract
BackgroundEvidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants. All the mechanisms of vaccine adjuvants ensuing immunostimulatory effects directly or indirectly stimulate antigen presenting cells (APCs). While numerous methods have been developed in the past for predicting B cell and T-cell epitopes; no method is available for predicting the peptides that can modulate the APCs.MethodsWe named the peptides that can activate APCs as A-cell epitopes and developed methods for their prediction in this study. A dataset of experimentally validated A-cell epitopes was collected and compiled from various resources. To predict A-cell epitopes, we developed support vector machine-based machine learning models using different sequence-based features.ResultsA hybrid model developed on a combination of sequence-based features (dipeptide composition and motif occurrence), achieved the highest accuracy of 95.71% with Matthews correlation coefficient (MCC) value of 0.91 on the training dataset. We also evaluated the hybrid models on an independent dataset and achieved a comparable accuracy of 95.00% with MCC 0.90.ConclusionThe models developed in this study were implemented in a web-based platform VaxinPAD to predict and design immunomodulatory peptides or A-cell epitopes. This web server available at http://webs.iiitd.edu.in/raghava/vaxinpad/ will facilitate researchers in designing peptide-based vaccine adjuvants.
Highlights
Evidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants
In the A-cell epitope dataset, the percentage composition of an amino acid residue was calculated for each epitope, and the average of these values was plotted in Fig. 2 for the corresponding amino acid
Host Defense Peptides have been realized as promising immunomodulators likely to become potential vaccine adjuvants [47]
Summary
Evidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants. All the mechanisms of vaccine adjuvants ensuing immunostimulatory effects directly or indirectly stimulate antigen presenting cells (APCs). Antigenic peptides by themselves are poorly immunogenic since they lack the capability of activating the innate immunity. There is a need for Vaccine adjuvants effectuate their action by a variety of mechanisms with all of them involving the antigen presenting cells (APCs) the dendritic cells [3]. One of these mechanisms is the activation of the pattern recognition receptors (PRRs) on the APCs that recognize conserved microbial molecular signatures.
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