Advanced descriptors for long-range noncovalent interactions between SARS-CoV-2 spikes and polymer surfaces

2022

Preprint

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.

Section: Resultsmentioning

confidence: 99%

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

2022

Preprint

“…Furthermore, because of the presence of two different conformations (up and down states) for S pro [71,72] and their equal proportion on the surface of virion [73]; the interactions of both of the conformations with the metal surfaces are investigated and compared. Most of the published MD simulation studies have only investigated the interaction of the up-conformation of S pro (S up ) with the surface of the materials, and very rare studies have considered the interaction of down-conformation (S down ), as well [74]. Finally, we hope the results of this study might pave the way for developing a new generation of virucidal materials/coatings based on metals.…”

Section: Introductionmentioning

confidence: 89%

“…The all-atom molecular dynamics (MD) simulation method is used to clarify the mechanism, molecular, and atomic details of these adsorptions and also to complement our previous works on the interaction between SARS-CoV-2 and different types of hard and soft materials. , Furthermore, because of the presence of two different conformations (up and down states) for S pro , and their equal proportion on the surface of the virion, the interactions of both of the conformations with the metal surfaces are investigated and compared. Most of the published MD simulation studies have only investigated the interaction of the up-conformation of S pro (S up ) with the surface of the materials, and very rare studies have considered the interaction of down-conformation (S down ) as well …”

Section: Introductionmentioning

confidence: 99%

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

2022

Langmuir

A prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. 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 with the (100) surface of Au, Ag, and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, with Cu being the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up-conformation Sup (one receptor binding domain exposed) and down-conformation Sdown (no exposed receptor binding domain). We found that the affinity of the metals for the up-conformation was higher than their affinity for the down-conformation. The structural changes in the spike in the up-conformation were also larger than the changes in the down-conformation. Comparing the present results for metals with those obtained in our previous MD simulations of Sup with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in Sup, larger than those obtained in our previous studies.

“… 20 Most of the published MD simulation studies have only investigated the interaction of the up conformation of S protein with the surface of the materials, and only a few studies have considered the interaction of down conformation, as well. 21 Hence, in the present study, we investigate the interaction between up and down conformations of the S protein and a polystyrene slab using the all-atom MD simulation method. The specific objectives of this study are: (i) to clarify the molecular and atomic details of the interaction between SARS-CoV-2 virus and polystyrene ( Figure 1 ); (ii) to reveal the difference between up and down conformations of the S protein for interaction with polystyrene surface; and (iii) to complement our previous works on the interaction between SARS-CoV-2 and different types of materials (hard, soft, hydrophobic, and hydrophilic surfaces).…”

Section: Introductionmentioning

confidence: 99%

“…High-resolution experimental images of SARS-CoV-2 virions reveal that the proportion of up and down conformations of the S protein are approximately 1:1 . Most of the published MD simulation studies have only investigated the interaction of the up conformation of S protein with the surface of the materials, and only a few studies have considered the interaction of down conformation, as well . Hence, in the present study, we investigate the interaction between up and down conformations of the S protein and a polystyrene slab using the all-atom MD simulation method.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface

2022

J. Chem. Inf. Model.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity.