Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach

Srivastava, Sukrit; Kamthania, Mohit; Singh, Soni; Saxena, Ajay K; Sharma, Nishi

B-cell epitope prediction sequence-based B-cell epitope prediction Protein sequence-based linear B-cell epitopes were predicted by six different prediction methods available at "B Cell Epitope Prediction Tools" tool of IEDB server (http://tools. iedb.org/bcell/); these tools are based on the propensity scale method and physicochemical properties of the antigenic sequence. These methods include "BepiPred Linear Epitope Prediction" (propensity scale method such as hidden Markov model), "Chou & Fasman Beta-Turn Prediction", "Emini Surface Accessibility Prediction", "Karplus & Schulz Flexibility Prediction", "Kolaskar & Tongaonkar Antigenicity", and "Parker Hydrophilicity Prediction". [32] [33] [34] [35] [36] [37] structure-based B-cell epitope prediction Two structure-based B-cell epitope prediction methods, namely, DiscoTope 2.0 (Structure-based Antibody Prediction tool; http://tools.iedb.org/discotope/) and Ellipro (Antibody Epitope Prediction tool; http://tools.iedb.org/ellipro/), available in IEDB, were used for linear and discontinuous B-cell epitope prediction. 38, 39 The ElliPro method is based on the location of the residue in the protein's 3D structure. The residues lying outside of the ellipsoid covering 90% of the inner core residues of the protein score highest protrusion index (PI) of 0.9 and so on. Discontinuous epitopes predicted by ElliPro are clustered on the basis of distance R in Å between two residues' centers of mass lying outside the largest possible ellipsoid. The larger the value of R, the larger will be the number of discontinuous epitopes clustered. DiscoTope 2.0 is based on the number of contacts of the residues' Cα carbon atom with other Cα carbon atoms in the 3D structure within the 10 Å distance and the propensity of a residue to be a part of an epitope. Toxicity assessment of CTL and HTL epitopes and B-cell epitopes was performed by ToxinPred (http://crdd.osdd.net/ raghava/toxinpred/multi_submit.php) analysis. This analysis allows to identify highly toxic or nontoxic peptides. The analysis was performed by the "support vector machine (SVM) (SwissProt)-based" method with all the parameters set to default. 41 Overlapping residue analysis Multiple Sequence Alignment (MSA) analysis using the Clustal Omega tool (https://www.ebi.ac.uk/Tools/ msa/clustalo/) of European Bioinformatics Institute was performed for all the shortlisted CTL, HTL, and B-cell epitopes from 13 MERS-CoV proteins. 42 MSA by Clustal Omega virtually aligns any number of protein sequences and delivers accurate alignments.