Wild Type and Omicron SARS-CoV-2 Spike Receptor Binding Domains Bind Similarly to the Human ACE2 Receptor: An MM-GBSA Study

Abstract

SARS-CoV-2 is a coronavirus that has created a global pandemic. The virus contains a spike protein which has been shown to bind to the ACE2 receptor on the surface of human cells. Vaccines have been developed that recognize elements of the SARS-CoV-2 spike protein and they have been successful in preventing infection. Recently, the omicron variant of the SARS-CoV-2 virus was reported and quickly became a variant of concern due to its transmissibility. This variant contained an unusually large number (32) of point mutations, of which 15 of those mutations are in the receptor binding domain of the spike protein. In order to assess the differential binding ability of the wild type and omicron variant of the RBD spike protein to human ACE2 receptors, we conducted 2 μs of molecular dynamics simulation to estimate the binding affinities and behaviors. Based upon MM-GBSA binding affinity, center of mass distance measurements, ensemble clustering, pairwise residue decomposition and hydrogen bonding analysis, we can conclude that the 15 point mutations in the receptor binding domain do not increase the affinity of the spike protein for the human ACE2 receptor. The MM-GBSA binding estimations over a 2 μs trajectory, suggest that the wild type binds to ACE2 with a value of -29.69 kcal/mol while the omicron mutant binds with an energy value of -26.67 kcal/mol. These values are within the error estimates of the MM-GBSA method. While some mutations increase binding, more mutations diminish binding, leading to an overall similar picture of binding.

Investigation of SARS-CoV-2 lineages and mutations circulating in a university-affiliated hospital in South Korea analyzed using Oxford Nanopore MinION sequencing

“…Of the mutually detected mutations in the 3 Omicron subvariants, a previous study showed that Q493R and N501Y, along with S477N, formed a new interaction with human ACE2, which enhanced the binding of the Omicron variant to human ACE2 [ 16 ]. The Y505H mutation did not seem to have an impact on binding [ 17 ].…”