  Preliminary epidemiologic, phylogenetic and clinical findings suggest that
several novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
variants have increased transmissibility and decreased efficacy of several
existing vaccines. Four mutations in the receptor-binding domain (RBD) of the
spike protein that are reported to contribute to increased transmission.
Understanding physical mechanism responsible for the affinity enhancement
between the SARS-CoV-2 variants and ACE2 is the "urgent challenge" for
developing blockers, vaccines and therapeutic antibodies against the
coronavirus disease 2019 (COVID-19) pandemic. Based on a
hydrophobic-interaction-based protein docking mechanism, this study reveals
that the mutation N501Y obviously increased the hydrophobic attraction and
decrease hydrophilic repulsion between the RBD and ACE2 that most likely caused
the transmissibility increment of the variants. By analyzing the
mutation-induced hydrophobic surface changes in the attraction and repulsion at
the binding site of the complexes of the SARS-CoV-2 variants and antibodies, we
found out that all the mutations of N501Y, E484K, K417N and L452R can
selectively decrease or increase their binding affinity with some antibodies.
