Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach

M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Salma Akter; A. S. M. Rubayet-Ul-Alam; Mohammad Anwar Siddique; Otun Saha; Md. Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain

The IEDB analysis resource tool was employed to identify T-cell epitopes in RBD nM identifies peptide binders recognized by T-cells, and this threshold can be used to select 215 peptides, we kept binding affinity within 50 nM to get better confidence level in predicting 216 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015164 doi: bioRxiv preprint epitopes for MHC-I and MHC-II alleles. The IEDB MHC-I prediction tool retrieved 77 T-cell 217 epitopes in RBD that interacted with 21 possible MHC-I alleles whereas the NTD domain 218 possessed 35 T-cell epitopes with 17 possible MHC-I alleles (Supplementary Data 1) . Similarly, 219 the IEDB MHC-II prediction tool generated 13-mer124 peptides from the RBD, and 10-mer 73 220 peptides in the NTD segments of the S protein that showed interaction with many different 221 and/or common MHC-II alleles with an IC 50 value ranging from 1.4 to 49.9 nM (Supplementary 222 Data 1). Furthermore, for MHC-I and MHC-II processing, the analysis tool of the IEDB 223 generates an overall score for each epitope's intrinsic potential of being a T-cell epitope based on 224 proteasomal processing, TAP transport, and MHC-binding efficiency (Supplementary Data 1). 225