Abstract
Understanding thermodynamics and kinetics of the
binding process of 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, 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.