Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

Understanding thermodynamics and kinetics of the binding process of an antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bond, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant. Moreover, the fragment of NAb + RBD can be used as an affordable model to investigate the change of the binding process between mutations RBD and antibodies.