The evolution of the spike protein and hACE2 interface of SARS-CoV-2 omicron variants determined by hydrogen bond formation

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December 2019. As of mid-2021, the delta variant was the primary type; however, in January 2022, the omicron (BA.1) variant rapidly spread and became the dominant type in the United States. In June 2022, its subvariants surpassed previous variants in different temporal and spatial situations. To investigate the high transmissibility of omicron variants, we assessed the complex of spike protein 1 receptor-binding domain (S1RBD) and human angiotensin-converting enzyme 2 (hACE2) from the Protein Data Bank (6m0j, 7a91, 7mjn, 7v80, 7v84, 7v8b, 7wbl and 7xo9) and directly mutated specific amino acids to simulate several variants, including variants of concern (alpha, beta, gamma, delta), variants of interest (delta plus, epsilon, lambda, mu, mu without R346K) and omicron variants (BA.1, BA.2, BA.2.12.1, BA.4, BA.5). Molecular dynamics (MD) simulations for 100 ns under physiological conditions were then performed. We found that the omicron S1RBD-hACE2 complexes become more compact with increases in hydrogen-bond interactions at the interface, which is related to the transmissibility of SARS-CoV-2. Moreover, the relaxation time of hydrogen bonds is relatively short among the omicron variants, which implies that the interface conformation alterations are fast. From the molecular perspective, PHE486 and TYR501 in omicron S1RBDs need to involve hydrogen bonds and hydrophobic interactions on the interface. Our study provides structural features of the dominant variants that explain the evolution trend and their increased contagiousness and could thus also shed light on future variant changes.

Keywords: SARS-CoV-2; human angiotensin-converting enzyme 2 (hACE2); molecular dynamics; molecular evolution; omicron variant; spike protein 1 receptor-binding domain (S1RBD).