In silico identification of RBD subdomain of spike protein from Pro(322)-Thr(581) for applications in vaccine development against SARS-CoV2

The three-dimensional hybrid structures of coronavirus spike proteins including the C-terminal sequence and receptor binding motif (RBM) was remodeled and energy minimized. Further, protein-protein docking show that Receptor Binding Domain (RBD) of SARS-CoV 2 Lys(457)-Pro(490) bind on the surface of ACE2 receptor near N-terminal helices to form host-pathogen attachment. In this binding interface, SARS-CoV 2 shows a tight network of hydrogen bonds than other spike proteins from BtRsRaTG13-CoV, SARS-CoV, BtRsBeta-CoV, BtRsCoV-related, Pangolin-CoV (PCoV), human-CoV (hCoV), MERS-CoV (MCoV), Avian-CoV (ACoV) and PEDV1-CoV. Further studies show that subdomains from SARS-CoV 2 RBD Pro(322)-Thr(581), SARS-CoV RBD Pro(309)-Pro(575), BtRsRaTG13 RBD Thr(581)-Thr(323), BtRsBeta-CoV RBD Ser(311)-Thr(568), BtRsCoV-related Arg(306)-Pro(575) and PCoV RBD Gln(319)-Ser(589) show binding conformations with ACE2 like their full-length structures of spike proteins. In addition, the subdomains MCoV RBD Gly(372)-Val(616), ACoV RBD Gly(372)-Val(616) and PEDV1-CoV RBD Ala(315)-Tyr(675) also binds on the surface of ACE2 similar to their full-length spike proteins. The B-Cell epitope mapping also identified main antigenic determinants predicting that these nine subdomains are highly useful in recombinant vaccine development in inducing cross neutralizing antibodies against SARS-CoV 2 spike protein and inhibits its attachment with ACE2.