Epitope-based peptide vaccine design and target site characterization against novel coronavirus disease caused by SARS-CoV-2

Lin Li; Ting Sun; Yufei He; Wendong Li; Yubo Fan; Jing Zhang

Peptide_binding_to_MHC_class_I_molecules tool of IEDB and HLA class I set [20] was utilized to predict T-cell epitopes for S protein. Percentile rank with threshold of 1% was used to filter out peptideallele with weak binding affinity. The antigenicity score of each peptide was calculated by VaxiJen v2.0 to evaluate its antigenicity. A peptide having both high antigenicity score and capacity to bind with larger number of alleles is considered to have high potentials to initiate a strong defense response. High stringent criteria were used to filter peptides with antigenicity score larger than or equal to 1 and the number of binding alleles larger than or equal to 3. Utilizing the evaluating method above, we obtained a total of 9 MHC class-I allele binding peptides ( Table 3) Peptide_binding_to_MHC_class_II_molecules tool of IEDB and HLA class II set [21] was utilized to predict T-cell epitopes for S protein. Percentile rank with threshold of 10% was used to filter out peptideallele with weak binding affinity. The antigenicity score of each peptide was calculated by VaxiJen v2.0 to evaluate its antigenicity. A high stringent standard was used to filter peptides with antigenicity score larger than or equal to 1 and the number of binding alleles larger than or equal to 5. As a result, we obtained a total of 13 MHC class-II allele binding peptides (