How do common mutations in SARS-CoV-2’s spike affect its binding affinity with host cell receptors?

By Dr. Priyom Bose, Ph.D.May 21 2021

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the most severe global pandemic for a century. Globally, this virus has affected more than 165 million individuals and has claimed over 3.4 million lives. Several vaccines have received emergency authorization from various regulating bodies and subsequently, vaccination programs have commenced in many countries. More recently, with the emergence of SARS-CoV-2 variants, scientists have become concerned about the effectiveness of these vaccines and previous infection-induced immunity against the variants.

Following the onset of infection, SARS-CoV-2 penetrates the host cell by establishing an interaction between the virus’s Spike (S) protein with angiotensin-converting enzyme 2 (ACE2) on the host’s cell surfaces. The receptor-binding domain (RBD) of the S protein attaches with the membrane-distal portion of the ACE2 protein. Scientists have explained that the S protein forms a homotrimer that cleaves into two fragments, S1 and S2, that remain attached non-covalently. S1 contains RBD, whereas S2 mediates the fusion of membranes following the binding of S protein with ACE2.

Researchers have revealed that the mutation, which occurred in the Spike protein, has increased the infection rate. One of the virus strains that emerged in Europe and became dominant is D614G. This variant increased the density of intact Spike trimer on its surface by blocking premature dissociation of S1 from S2 following cleavage. However, the mutation in the N501Y occurred within the RBD domain, increasing the binding affinity for ACE2. These reports indicate that mutations that directly or indirectly result in increases in the binding of S protein to ACE2 cause an increase in virulence.

Antibodies produced during a previous case of COVID-19 or vaccine-induced immunity are targeted towards S protein, where the neutralizing antibodies attach to the Spike RBD domain. Some of the variants have mutations in their RBD domain, causing resistance to the neutralizing antibodies. However, the effect of these mutations on the affinity and kinetics of the binding of Spike RBD to ACE2 is not clear. A new study has been published on the bioRxiv* preprint server, which deals with the study of affinity and kinetic analysis of the interface between Spike RBD and ACE2 at physiological temperatures.

Study: Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics. Image Credit: Juan Gaertner / Shutterstock

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Previous studies have reported that both mutations of ACE2 (S19P, K26R) and RBD (N501Y, E484K, and S477N) result in the enhancement of the interactions between RBD and ACE2. The increase in the binding results in the lowering of dissociation rate constants (N501Y, S477N) and/or increases the association rate constants (N501Y, E484K). South African (B.1.351) and Brazilian (P.1) SARS-Cov-2 variants, which are caused by the K417N/T mutations, decrease the binding affinity. However, the presence of N501Y and E484K mutations (affinity enhancing) results in a four-fold enhancement in the affinity of RBD domains for ACE2.

Similar to previous studies, the current study has also revealed that the SARS-CoV-2 RBD attaches to ACE2 with an affinity of KD 74 nM at 37°C. However, the rate constant was found to be three times faster than the previously published literature. Scientists believe that this difference might be because previous studies had conducted their experiments at a lower temperature, which decreases the rate constant. Another reason could be that earlier kinetic studies were conducted in conditions where the diffusion rate of a soluble molecule to the sensor surface restricts the association rate. Additionally, the rebinding of dissociated molecules to the surface also lowers the calculated dissociation rate. To avoid these pitfalls, the present study has immobilized a very low level of ligand on the sensor surface.

The present study selected RBD mutants that have emerged independently and have become dominant in a particular place. In this study, researchers have revealed that N501Y, E484K, and S477N have enhanced the binding affinity of RBD for ACE2. This could be the property that enabled their selection. Several pieces of research indicate that increasing the Spike/ACE2 interaction would be beneficial for the virus. This is because the virus has started spreading very recently to humans from other mammalian hosts, for which it did not get the appropriate time for optimization for the affinity.

Scientists have further reported that mutations of RBD could result in evasion of the immune response. This is further validated by the observation that two variants with RBD mutations that escape antibody neutralization, namely, B.1.351 and P1, became dominant in the regions where the rate of previous SARS-CoV-2 infection was high. Both these variants underwent N501Y mutation. The current study reveals that K417N/T mutants present in both B.1.351 and P.1 variants, lowers the affinity of RBD for ACE2. Hence, these variants were selected as they can evade immune responses.  

The present study has identified the importance of the interaction between the RBD S477N and ACE2 S19P mutants. Further, the scientists recommended, based on their results as well as the available literature, that the N501Y and S477N mutations mainly increase transmission. The K417N/T mutations accelerate evasion of the immune system. Lastly, the E484K mutation expedites both transmissions as well as immune escape.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources