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

To screen CTL epitopes, the Immune Epitope Database (IEDB) tool "Proteasomal cleavage/TAP transport/MHC class I combined predictor" (http://tools.iedb.org/processing/) was used. [23] [24] [25] The total score generated by the tool is a combined score of proteasome, TAP (N-terminal interaction), major histocompatibility complex (MHC), and processing analysis scores. The score is generated using the combination of six methods, namely, Consensus, NN-align, SMM-align, Combinatorial Library, Sturniolo, and NetMHCIIpan. The IC50 (nM) value was also obtained using this IEDB tool. Epitopes with high, intermediate, and least affinity of binding to an HLA allele have IC50 values <50 nM, <500 nM, and <5,000 nM, respectively. Immunogenicity of the screened CTL epitopes was also obtained by the "MHC I Immunogenicity" tool of IEDB (http://tools.iedb.org/ immunogenicity/) with all parameters set to default (first, second, and C-terminus amino acids). 26 The tool predicts immunogenicity of a peptide MHC complex on the basis of physiochemical properties of amino acids and their position within the short peptide sequence.