Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q498R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Among the Q493K and Q493R, we report that Q493R shows stronger binding to ACE2 than Q493K due to increased interactions. Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our results could help explain the Omicron variant's prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.

Figure 1.

(A) Average force profiles of WT (red), Alpha (blue), Delta (gray), and Omicron variants (brown for Q493K and gold for Q493R) as a function of the distance between the center of mass of ACE2 and RBD. (B) The initial structure of Omicron (Q493R). Mutated residues from the WT are shown as solid sticks that are grouped and magnified into three panels with labels on the right. RBD and ACE2 are respectively colored in light gray (top) and yellow (bottom). All N-glycans, water, and ions are hidden for clarity.

Figure 2.

Two-dimensional contact maps of residues in RBD-ACE2 interface at D = 53 Å. (A) Interacting residue pairs between RBD^WT and ACE2. RBD residues subjected to mutation are marked with colored circles at the bottom: (B) brown for Omicron Q493K and (C) gold for Omicron Q493R. The contact frequency is displayed with colors from light blue to dark blue. Solid and transparent boxes on the map respectively represent increased and decreased interactions between RBD and ACE2 upon mutations. (D) A summary of RBD mutations in the Omicron variants.

Figure 3.

(A) The average number of contacts between RBD residues 498 and 501 and ACE2. (B and C) Representative snapshots at D = 55 Å of (B) Omicron Q493R and (C) WT. (D) The average number of contacts of Omicron variants between residues in RBD and ACE2 and (E and F) their interacting snapshots of (E) Q493K and (F) Q493R at D = 53 Å. (G) The average number of contacts between RBD residues and ACE2 and (H and I) key interaction pairs at D = 80 Å of (H) WT and (I) Omicron Q493R. The overall color scheme is the same as in Figure 1 (i.e., red for WT, brown for Omicron Q493K, and gold for Omicron Q493R). Interacting residues are presented as solid sticks, and residues losing their interactions are depicted as transparent sticks.

Figure 4.

(A) Microscale thermophoresis (MST) analysis of the interaction between ACE2 and RBD of the WT or Omicron variants. Error bars represent standard deviations from five individual repeat measurements. The binding affinities were determined by fitting the data with the ‘K_d’ model of the MO Affinity software. (B) Affinities of ACE2 binding to RBD variants detected by MST. The MST responses were fitted to the 1:1 binding model. The K_d rates are shown as fit ± one standard deviation. Data of the WT, Alpha, Beta, and Delta variants were adapted from our prior study.