Title of article :
A computational study at blocking probability of the SARS-CoV-2 spike protein through the binding of cellular receptors
Author/Authors :
Mohammadi ، Saeedeh Department of Physics - Shahid Rajaee Teacher Training University , Doustkhah ، Esmail International Center for Materials Nanoarchitechtonics (WPI-MANA) - National Institute for Materials Science (NIMS) , Salehi Chaleshtori ، Ahmad Reza Department of Medical Genetics - Faculty of Medical Sciences - Tarbiat Modares University , Esmailpour ، Mohammad Department of Physics - Azarbaijan Shahid Madani University , Zamani ، Farzad Institute of Scientific and Industrial Research (ISIR) - Osaka University , Esmailpour ، Ayoub Department of Physics - Shahid Rajaee Teacher Training University
Abstract :
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.
Keywords :
SARS , CoV , 2 , spike protein , homology modeling , molecular docking , dynamic simulation
Journal title :
Eurasian Chemical Communications
Journal title :
Eurasian Chemical Communications
