Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein

Cecylia S. Lupala; Xuanxuan Li; Jian Lei; Hong Chen; Jianxun Qi; Haiguang Liu; Xiao-dong Su

The physical interactions between the RBD and the ACE2 were quantified for the simulated structures. We considered the molecular mechanics energy E MM , which is We would like to point out that the energy E MM is the physical interaction between the RBD and the ACE2, rather than the binding energy, which requires accurately incorporating solvation energy and entropy. Furthermore, the standard deviations of E MM are 70.2 kJ/mol and 65.5 kJ/mol for the two complexes. Therefore, we infer that the binding affinities are comparable for CoV2-RBD/ACE2 and SARS-RBD/ACE2. The simulations started from the predicted and crystal models yielded very similar results (purple triangles). This is in line with a recent study, in which the authors showed similar binding affinity to human ACE2 for both SARS-CoV-2 and SARS-CoV spike proteins 29 .