Selecting the Most Immunogenic Fragments on an Antigenic Protein for Designing DNA Vaccine Using Different Algorithms

Approaching novel techniques in delivering vaccines, DNA vaccines are the most interesting devices, which are the head of the 3rd generation of vaccination methods. Lack of requirement of purifying and downstream separation and expression made these vaccines more useful than subunit and peptide vaccines.However, DNA vaccines utilize endogenous pathways requiring B cells and other APCs to present their immunogen epitopes to CD4+ T helper cells for inducing humoral immune responses. Hence, MHC II epitope determination is a critical issue in designing endogenous DNA vaccines.Once, DNA vaccine reaches into the cell cytoplasm, it will express antigen protein.In the following research, a DNA Vaccine is designed against an antigenic glycoprotein of a rhabdovirus family to generate immunity before challenging wild virus. According to the delivery method used for this research, endosomal proteases have been considered to cut down antigen peptide bond into shorter MHC II epitope peptides. The pattern of cleavage of antigen can be predicted by protease databases and servers including endosomal specific proteases cleavage cut site patterns. In this research, both endosomal proteases pattern and MHC II binding epitopes (Linear and Conformational) have been predicted for designing an efficient protective DNA vaccine against viral diseases caused by Rhabdoviridae family.In order to linear MHC II epitope prediction, Propred[1], IEDB[2] and NetMHCII[3] servers were used while selecting scores above specified thresholds. Likewise, conformational MHC II epitopes have been analyzed with Discotope IEDB[4] server on the 3D structure of peptide sequence chains. On the other hand, specific proteases-mediated peptide cleavage pattern has been studied with PepCleave CD4+[5], and ExPasy PeptideCutter[6] servers.Also, predicted MHC binding epitopes were examined with SYFPEITHI[7] to determine epitope-MHC II binding affinity. Hence, gathered data shows the best-predicted epitopes located on the desired sequence which should be involved in designing DNA vaccine as insert fragments.Eventually, collected data obtained from different servers have been caparisoned and the most immunogen fragments have been selected for designing efficient DNA vaccine.

Keywords:

Epitope Prediction , Antigen , CD4+ , MHC II , DNA Vaccine