Altered affinity to ACE2 and reduced Fc functional antibodies to SARS-CoV-2 RBD variants

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains a formidable challenge to worldwide public health. The receptor binding domain (RBD) of the SARS-CoV-2 spike protein is a hotspot for mutations, reflecting its critical role at the ACE2 interface during viral entry. We comprehensively investigated the impact of RBD mutations, including 6 variants of concern (VOC) or interest (Alpha, Beta, Gamma, Delta, Kappa and Omicron) and 33 common point mutations, on IgG recognition, FcgR-engagement, and ACE2-binding inhibition in plasma from BNT162b2-vaccine recipients (two-weeks following second dose) and mild-to-moderate COVID-19 convalescent subjects using our custom bead-based 39-plex array. We observed that IgG-recognition and FcgR-binding antibodies were most profoundly decreased against Beta and Omicron RBDs, as well as point mutations G446S, found in Omicron, and N501T, a key mutation found in animal adapted SARS-CoV-2 viruses. Measurement of RBD-ACE2 binding affinity via Biolayer Interferometry showed all VOC RBDs have enhanced affinity to human ACE2. Furthermore we demonstrate that human ACE2 polymorphisms, E35K (rs1348114695), K26R (rs4646116) and S19P (rs73635825), have altered binding kinetics to the RBD of VOCs potentially affecting virus-host interaction and thereby host susceptibility.

High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2

“…This is followed by G446S, which is predicted to have a mild stabilizing effect. As we know, the N501Y mutant has been experimentally verified to increase the binding affinity ( Table 1 ), whereas the G446S mutation has been shown to slightly (by 1.6-fold) decrease the binding affinity [ 66 , 67 ]. The remaining three F486V, G496S and Y505H mutations are predicted to be mildly to moderately destabilizing.…”

“… Predicted versus experimentally reported binding affinity of spike receptor-binding domain with hACE2 for the G446S and N501Y mutations . The experimental values were taken from Table 1 and converted to ∆G [ 40 , 66 , 74 , 77 , 78 ]. The ∆∆G was calculated by subtracting the binding free energy of the WT spike (∆G WT ) from that of the mutant spike (∆G MUT ).…”

“… N.B. Experimental binding affinity (Kd in nM) of WT spike glycoprotein to hACE2: 29.4 ± 2.62 [ 66 ], 17 ± 0.6 [ 74 ], 10 ± 3.1 [ 76 ], 62.6 ± 7.7 [ 40 ], 75.1 [ 77 ], 16 [ 78 ]. nM.—data not available.…”