Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals

Abstract

Coinage metals like silver, gold and copper are historically known as materials with anti-infective properties; but the mechanism behind these properties is not yet clear, and several features seem to be effective in this regard. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up and down conformations of the S1 subunit of the SARS-CoV-2 spike protein with the (100) surface of Au, Ag and Cu. Our results revealed that spike protein is adsorbed onto the surface of these metals, being the Cu-metal with the highest interaction with the spike and Au, the metal which induces bigger structural changes in the spike. In our simulations, we considered the spike protein in both its up and down conformations. We found that the affinity of the metals for the up-conformation was higher than their affinity for the down conformation of the spike protein due to the interactions with the receptor binding domain that is exposed in the up conformation but hidden in the down conformation.

Comparing the present results for metals with those obtained in our previous MD simulations with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in the spike, larger than those obtained in our previous studies.