Molecular dynamics simulations reveal the importance of conformational changes, glycosylation, mutations, and drug repurposing for the Sars-Cov-2 spike protein

The protein responsible for the first steps of SARS-CoV-2 cell invasion, the spike protein, has received much attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new threat. Molecular dynamics (MD) in particular, has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. Here, we review the main findings of MD studies on the spike protein, including flexibility of the stalk region, the role of the glycans on the surface of the S protein, the effect of mutations on biding to ACE2, the change from the down conformation to the up conformation, and progress in drug repurposing.