Binding mechanism of SARS-CoV-2 spike protein with human ACE2 receptor
SARS-CoV-2 virus interacts via C-terminal domain of spike protein to human cell receptor protein hACE2. Amino acid residues residing at the interface play vital role in binding of SARS-CoV-2 CTD to hACE2. The detailed atomic level inves- tigation of interactions at binding interface of SARS-CoV-2 CTD/hACE2 provides indispensable information on better understanding of location for drug target. In the present work, we have studied the dynamical behaviour of the complex by ana- lyzing the
... lyzing the molecular dynamics (MD) trajectories. The major interacting residues of SARS-CoV-2 CTD and hACE2 have been identified by analyzing the non-bonded interactions such as hydrogen bondings, salt bridges, hydrophobic interactions, van der Waals interactions etc. Umbrella sampling method has been used to estimate the binding free energy for in-depth understanding of binding mechanism between virus protein and host receptor. The binding free energy difference, key residues at the interface, important atomic interactions and contact surface areas have been compared with the molecular complex of SARS-CoV and hACE2. Relatively larger contact surface area, more non-bonded interactions as well as greater binding free energy provide the evidence for favorable binding of SARS-CoV-2 with hACE2 receptor than SARS-CoV.