Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein-Montmorillonite Interactions

Abstract

The spike (S) protein of SARS-CoV-2 has been found to play a decisive role in the cell entry mechanism of the virus and has been the prime target of most vaccine development efforts. Although numerous vaccines are already in use and more than half of the world population has been fully vaccinated, the emergence of new variants of the virus poses a challenge to the existing vaccines. Hence, developing an effective drug therapy is a crucial step in ending the pandemic. Nanoparticles can play a crucial role as a drug or a drug carrier and help tackle the pandemic effectively. Here, we performed explicit all-atom molecular dynamics simulations to probe interactions between S protein and Montmorillonite (MMT) nano clay surface. We built two systems with different counterions (Na⁺ and Ca²⁺), namely Na-MMT and Ca-MMT, to investigate the effect of different ions on S protein-MMT interaction. Structural modification of S protein was observed in the presence of MMT surface, particularly the loss of helical content of S protein. We revealed that electrostatic and hydrophobic interactions synergistically govern the S protein-MMT interactions. However, hydrophobic interactions were more pronounced in the Na-MMT system than in Ca-MMT. We also revealed residues and glycans of S protein closely interacting with the MMT surface. Interestingly, N165 and N343, which we found to be closely interacting with MMT in our simulations, also have a critical role in cell entry and in thwarting the cell's immune response in recent studies. Overall, our work provides atomistic insights into S protein-MMT interaction and enriches our understanding of the nanoparticle-S protein interaction mechanism, which will help develop advanced therapeutic techniques in the future.