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

Recognition of B-cell epitopes depended on predictions of linear epitopes, antigenicity, hydrophilicity, accessibility of surface, beta-turn and flexibility [24] . B-cell epitopes of S protein were predicted using IEDB [17] . A total of 23 and 26 linear epitopes (Supplementary Table 3a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.25.965434 doi: bioRxiv preprint abundance in known B-cell epitopes. The antigenic tendency value of S protein was estimated to be 1.041 (average), 0.866(minimum) and 1.261 (maximum) (Fig. 1B) . Hydrophilic region is important in initiating immune response, which is generally uncovered on the surface of protein. Parker hydrophilicity of S protein was found to be 1.238 (average), -7.629 (minimum) and 7.743 (maximum) (Fig. 1C) . To find the surface availability of B-cell epitopes, Emini surface accessibility was predicted for S protein with average of 1 , minimum of 0.042, and maximum of 6.051 (Fig. 1D) . Exposed on the surface and hydrophilic in nature making beta turn a vital structure in starting the defense response. Therefore, we predicted Chou and Fasman beta turn to gain the result, 0.997 (average), 0.541 (minimum) and 1.484 (maximum) in S protein (Fig. 1E ). As the parts of epitope connecting with antibodies are typically elastic in nature, we predicted Karplus and Schulz flexibility of S protein and the result was 0.993 (average), 0,876 (minimum), and 1.125(maximum) (Fig. 1F) . A total of 262 B-cell epitopes were selected based on the combination of the results (Supplementary Table 3a ). BcePred [18] was used to predict B-cell epitopes using accessibility, antigenic propensity, exposed surface, flexibility, hydrophilicity, polarity and turns. Overall, we obtained totally 129 B-cell epitopes (Supplementary Table 3b ). Table 1 ). The four B-cell epitopes were mapped to the 3D structure of SARS-CoV-2 S protein (PDB ID: 6VSB), showing that 'VLGQSKRVDFCGKG' and 'GLTGTGVLTESNKK' are in less-exposed region (Figure 2 A, and B) , while 'VRQIAPGQTGKIAD' and 'KIADYNYKLPDDFT' locate in the spike head which is the most exposed region (Figure 2 C) . Discontinuous B-cell epitopes were predicted by Discotope 2.0 using A, B, and C chain of 3D structure of S protein (PDB ID: 6VSB), respectively. The positions of discontinuous epitopes were mapped on the surface of 3D structure of S protein ( Figure 3A ). Most discontinuous B-cell epitopes were mapped on the fully-exposed 'spike head' region ( Figure 3B ) and less-exposed 'spike stem', while a few located in the 'spike root' region of the spike (Supplementary Table 3c ).