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A computational study at blocking probability of the SARS-CoV-2 spike protein through the binding of cellular receptors

In this paper, the SARS-CoV-2 spike encoding gene sequences were analyzed to find the structural homology of S proteins. The S protein of SARS-CoV-2 was obtained from homology modeling and the protein-protein docking was performed to elucidate sites active in S protein for ACE2, dipeptidyl peptidase 4 (DPP4), chemokine receptor 5 (CCR5), and AXL. The two crucial binding sites of S protein, known as RBD and CTD, were investigated. Three-dimensional structures of 8 possible RBD/CTD-receptor complexes were evaluated using molecular dynamic (MD) simulations. The best simulation models of the SARS-CoV-2 S protein active sites with the receptors were obtained for the ACE2 receptor (PDB:6VW1), providing 99.5% and 98.5% coverage for CTD and RBD, respectively. The SARS-CoV- 2 S protein may connect with the ACE2 receptor via the RBD sites of the S protein and the ACE2 peptidase domain (PD), which can be blocked by encoding gene sequence in the active sites of S protein, offering an attractive protection approach against this novel SARS-CoV-2 virus.