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

In this section energetics of epitope attachment with MHC class II HLA-DRA, DRB was determined in presence and absence of NAG at the 10B epitope structure through molecular docking ( Figure 6 ). Docking results showed that without NAG, the binding efficiency of 10B epitope at the epitope binding site of MHC class II HLA-DRA, DRB molecule was very high. The copyright holder for this preprint (which was not peer-reviewed) is the .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 Though, epitope 8 A & B were also present at the surface of the spike glycoprotein but was found to wrapped with a short segment IGAEHVNNSYECD (651-663) carrying a glycosylation at N residue position 657 (Figure 7a) . As a result of which antibody accessibility to this epitope may also be difficult. Whereas, surface epitope 9 with sequence VRDPQTLEILDITPC (576-590) showed highest antigenecity of 1.1285 (Table 3) can recombine to gain entry into human cells are the points also to be noted [35] . SARS CoV-2 induced severe and often lethal lung failure is caused due to its inhibition of ACE-2 expression [36] . So, keeping the ACE-2 normal functioning but blocking viral entry is the most challenging The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.02.021725 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.02.021725 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the .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 Position of Epitope 9 in COVID 19 spike protein with no direct or indirect NAG attachment, PDB ID: 6svb (b). Among 10 best docking positions, 8 were found in epitope presenting site of MHC II HLA-DRB1, PDB ID: 5jlz (c). The best docking posture of epitope 9 with MHC II HLA-DRB1 (d) and its specific interaction pattern (e).