Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development

Amrita Banerjee; Dipannita Santra; Smarajit Maiti

Comparative analysis between glycosylated and non-glycosylated protein revealed some structural modification at the epitope locations. Among the identified epitopes 10B with sequence ITPGTNTSNQVAVLY (598-612) was found with N linked glycosylation at 603 position. The structural modification of this epitope was analyzed using non-glycosylated protein structure of COVID 19 (Acc. No.: NC_045512.2:21563-25384) and gltcosylated COVID 19 protein (PDB ID: 6vsb). Effect of glycosylation on protein structures revealed that glycosylated conformation was more organised (Figure 5a ) than non-glycosylated one (Figure 5b ). Secondary structural comparison between two epitopes showed more organised structure with attached NAG residue (Figure 5d ) whereas a shorter β-sheet structure was observed when NAG is removed from the structure (Figure 5c ). The peptide interactive site of 10B epitope was blocked due to NAG attachment. As a result of which antibody binding to the antigen may hamper. The NAG residue directly binds with N or ASN amino acid residue (Figure 5e ). So the removal of . CC-BY-ND 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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/10.1101/2020.04.02.021725 doi: bioRxiv preprint NAG from the spike glycoprotein structure is difficult. Structural distortion between glycosylated and non-glycosylated epitope 10B at tertiary level indicated that removal of NAG may distort the structure of epitope (Figure 5f ). Again that may hamper the proper antigenantibody binding.