Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations

The N234 and N343-linked glycans of the SARS-CoV 2 spike protein are known to stabilize the up-conformation of its receptor-binding domains (RBDs), enabling human angiotensin enzyme 2 (hACE2) receptor binding. However, the effect of spike-hACE2 binding on these important glycans remains poorly understood, and these changes could have implications in the development of drugs that inhibit viral entry. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations of the hACE2-free and hACE2-bound spike protein are performed. Biophysical analyses were focused on the accessibility of three previously suggested druggable pockets underneath the three RBD subunits. A shielding effect by N234-linked glycans on the components of their adjacent pockets was observed. Although deshielding of central scaffold residues was observed in the hACE2-bound state, pocket A's accessibility was reduced due to an increase in NTD_B-RBD_B contacts, restricting entry into the pocket. For pocket B, changes in N234_C and N343_C expose the central scaffold residues in the bound state, increasing accessibility. In Pocket C, increased shielding due to N234_A was found in the bound state, reducing accessibility. Despite these changes, the pockets remain accessible to ligands in both states and are still valid targets for drug development studies.