Abstract
The Omicron variant (B.1.1.529) comprises 30 mutations on the spike glycoprotein (S), 15 of which are located on its receptor-binding domain (RBDOmicron). RBD interacts with the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors and plays a critical role in the host cell entry of the virus. We performed all-atom simulations of the RBDOmicron-PD in the presence of explicit water and ions. Simulations showed a considerably more extensive interactions network between RBDOmicron and PD compared to RBDWT, comprising a 250%, 10% and -25% change in the total number of salt bridges, hydrophobic interactions, hydrogen bonds at the S-ACE2 interface, respectively. Using the conformations sampled in each our MD trajectories, binding energies of two sets of RBDWT-PD and four sets of RBDOmicron-PD simulations were calculated via the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method, estimating ∼44% stronger binding energy for RBDOmicron compared to RBDWT. Our results suggest that an increase in the number of salt bridges in the S-ACE2 interface result in a higher binding strength of RBD to PD, which may result in a higher efficiency of the SARS-CoV-2 virus to infect host cells. Furthermore, RBDOmicron exhibits a more dispersed interaction network on both sides of the RBD-PD interaction surface compared to WT.
Competing Interest Statement
The authors have declared no competing interest.