Interactions between glucosides of the tip of the S1 subunit of SARS-CoV-2 spike protein and dry and wet surfaces of CuO and Cu-A model for the surfaces of coinage metals

Abstract

Despite their importance there is little knowledge at the atomic scale on the interactions between fragments of SARS-CoV-2 and inorganic materials. Such knowledge is important to understand the survival of the virus at surfaces and for the development of antiviral materials. Here is reported a study of the interactions between glucoside monomers of the tip of the S1 subunit of SARS-CoV-2 spike protein with dry and wet surfaces of CuO and Cu, performed with dispersion corrected density functional theory-DFT. The three glucoside monomers that constitute the tip of S1: 6VSB, 6VXX and 6X6P, were adsorbed onto dry and wet CuO(111) and Cu(110) with different orientations and surface alignments. There are large differences-of up to 1.3 eV-in binding energies between these monomers and the surfaces. These differences depend on: the type of surface; if the surface is wet or dry; if the glucosidic O-atom points towards or away from the surfaces; and to a smaller extent on the surface alignment of the monomers. All monomers bind strongly to the surfaces via molecular adsorption that does not involve bond breaking in the monomers at this stage. 6VSB has the larger adsorption energies-that reach 2.2 eV-due to its larger dipole moment. Both materials bind the monomers more strongly when their surfaces are dry. At Cu(110) the bonds are on average 1 eV stronger when the surface is dry when compared to wet. The difference between dry and wet CuO(111) is smaller, in the order of 0.2 eV. Overall, it is here shown that the stability of the monomers of the tip of the spike protein of the virus is very different at different surfaces. For a given surface the larger binding energies in dry conditions could explain the differences in the surface stability of the spike protein depending on the presence of moisture.

Keywords: DFT; Interactions with inorganic surfaces; Quantum mechanical modeling; SARS-CoV-2; Spike protein.

Graphical abstract

Fig. 1

Dry and wet surfaces of Cu(110) and CuO(111) employed in the study of the adsorption of the glucoside monomers. The axes A and B correspond to the following directions: A = [001], B = [$\stackrel{\circledR }{1}$10] in Cu(110); and A = [001], B = [011], in CuO(111). The black lines show the supercells. The bottom figures show the alignments of a glucoside relative to the axes A and B of the surfaces. These two alignments are designated by A and B, respectively. Cu (), O (), H (○).

Fig. 2

Top and side views of the optimized structures of the glucoside monomers in gas-phase with PDB IDs: 6VSB, 6VXX and 6X6P; isomers of 2-acetamido-2-deoxy-beta-D-glucopyranose. C (), O (), N () H (○). The conformation 6VSB is β while 6VXX and 6X6P are α.

Fig. 3

Adsorption geometries for the monomers 6VSB, 6VXX and 6X6P at dry CuO(111). The monomers are oriented as U or D and A or B (see beginning of Section 3.3 for explanation).

Fig. 4

Adsorption geometries for the monomers 6VSB, 6VXX and 6X6P at wet CuO(111). The monomers are oriented as U or D and A or B (see beginning of Section 3.3 for explanation).

Fig. 5

Adsorption geometries for the monomers 6VSB, 6VXX and 6X6P at dry Cu(110). The monomers are oriented as U or D and A or B (see beginning of Section 3.3 for explanation).

Fig. 6

Adsorption geometries for the monomers 6VSB, 6VXX and 6X6P at wet Cu(110). The monomers are oriented as U or D and A or B (see beginning of Section 3.3 for explanation).

Fig. 7

Adsorption energies for the monomers 6VSB, 6VXX and 6X6P at dry and wet surfaces of CuO(111) and Cu(110). The monomers are oriented as U or D and A or B (see beginning of Section 3.3 for explanation).

Fig. 8

Adsorption energies (ΔE_ads) for the monomers 6VSB, 6VXX and 6X6P at dry and wet surfaces of CuO(111) and Cu(110). Upper panels: average adsorption energies for each of the monomers obtained from the different orientations U or D and alignments A or B (see beginning of Section 3.3 for explanation). Lower panel: average adsorption energies for the three monomers in all conformations at each of the surfaces. The bars in the bottom figure are the standard deviations and represent the dispersion in the binding energies which in turn depend on the diversity of binding sites at the respective surface.