How do common mutations in SARS-CoV-2 spikes affect the binding affinity for host cell receptors?

The rapid epidemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the most serious pandemic of the first century. Globally, the virus affects more than 165 million people and kills more than 3.4 million people. Some vaccines have received urgent permits from various regulators, and vaccination programs have since been launched in many countries. Recently, with the advent of SARS-CoV-2 mutants, scientists have become concerned about the effectiveness of these vaccines and their previous infection-induced immunity to the mutants.

After the onset of infection, SARS-CoV-2 invades the host cell by establishing an interaction between the viral peplomer (S) protein and angiotensin converting enzyme 2 (ACE2) on the host cell surface. The receptor binding domain (RBD) of the S protein attaches to the distal part of the membrane of the ACE2 protein. Scientists explain that the S protein forms a homotrimer, which is cleaved into two fragments, S1 and S2, and remains uncovalent. S1 contains RBD, which mediates membrane fusion following the binding of S protein to ACE2.

Researchers have found that mutations that occur in Spike protein, The infection rate is increasing. One of the virus strains that emerged and became dominant in Europe is D614G. This variant increased the density of intact spike trimers on its surface by blocking the premature dissociation of S1 from S2 after cleavage. However, the mutation in N501Y occurred within the RBD domain, increasing the binding affinity for ACE2. These reports indicate that mutations that directly or indirectly result in increased binding of the S protein to ACE2 cause increased toxicity.

Antibodies produced during previous cases of COVID-19 or vaccine-induced immunization target the S protein. Neutralizing antibody Connect to the SpikeRBD domain. Some mutants have mutations in the RBD domain, causing resistance to neutralizing antibodies. However, the effect of these mutations on the affinity and kinetics of spike RBD binding to ACE2 is unclear.New research published in bioRxiv* A preprint server that handles research on the affinity and kinetic analysis of the interface between spike RBD and ACE2 at physiological temperatures.

Previous studies have reported that mutations in both ACE2 (S19P, K26R) and RBD (N501Y, E484K, and S477N) enhance the interaction between RBD and ACE2. An increase in binding results in a decrease in the dissociation rate constant (N501Y, S477N) and / or an increase in the association rate constant (N501Y, E484K). SARS-Cov-2 mutants in South Africa (B.1.351) and Brazil (P.1) caused by the K417N / T mutation reduce binding affinity. However, the presence of N501Y and E484K mutations (enhanced affinity) enhances the affinity of the RBD domain for ACE2 by a factor of four.

Similar to previous studies, current studies have shown that SARS-CoV-2RBD attaches to ACE2 at 37 ° C with an affinity for KD74nM. However, the rate constant was found to be three times faster than previously published literature. Scientists believe that this difference may be due to previous studies conducting experiments at lower temperatures. This will reduce the rate constant. Another reason may be that early kinetic studies were conducted under the condition that the rate of diffusion of soluble molecules on the sensor surface limits the rate of association. In addition, when the dissociated molecule recombines the surface, the calculated dissociation rate also decreases. To avoid these pitfalls, we fixed very low levels of ligand on the sensor surface in this study.

In this study, we selected RBD mutants that appeared independently and became predominant at specific locations. In this study, researchers found that N501Y, E484K, and S477N enhanced the binding affinity of RBD for ACE2. This could be a property that allowed their choice. Some studies have shown that increasing spike / ACE2 interactions is beneficial to the virus. This is because the virus has only recently begun to spread to humans from other mammalian hosts, and has not had the appropriate time to optimize affinity.

Scientists further report that mutations in RBD can lead to evasion of the immune response. This is further verified by the observation that two mutants with RBD mutations that evade antibody neutralization, namely B.1.351 and P1, prevailed in areas with previously high SARS-CoV-2 infection rates. I will. Both of these mutants have undergone the N501Y mutation. Current studies have shown that K417N / T mutants present in both B.1.351 and P.1 variants reduce the affinity of RBD for ACE2. Therefore, these mutants were selected because they can evade the immune response.

This study identified the importance of the interaction between RBDS477N and the ACE2S19P mutant. In addition, scientists recommended that mutations in N501Y and S477N predominantly increase infection, based on their results and available literature. The K417N / T mutation accelerates immune system evasion. Finally, the E484K mutation promotes both transmission and immune evasion.

*Important Notices

bioRxiv publishes unpeer-reviewed preliminary scientific reports and should not be considered definitive, guide clinical / health-related behaviors, or be treated as established information.