SARS-CoV-2 Spike Protein Unlikely to Bind to Integrins via the Arg-Gly-Asp (RGD) Motif of the Receptor Binding Domain: Evidence From Structural Analysis and Microscale Accelerated Molecular Dynamics

Abstract

The Receptor Binding Domain (RBD) of SARS-CoV-2 virus harbors a sequence of Arg-Gly-Asp tripeptide named RGD motif, which has also been identified in extracellular matrix proteins that bind integrins as well as other disintegrins and viruses. Accordingly, integrins have been proposed as host receptors for SARS-CoV-2. However, given that the microenvironment of the RGD motif imposes a structural hindrance to the protein-protein association, the validity of this hypothesis is still uncertain. Here, we used normal mode analysis, accelerated molecular dynamics microscale simulation, and protein-protein docking to investigate the putative role of RGD motif of SARS-CoV-2 RBD for interacting with integrins. We found, that neither RGD motif nor its microenvironment showed any significant conformational shift in the RBD structure. Highly populated clusters of RBD showed no capability to interact with the RGD binding site in integrins. The free energy landscape revealed that the RGD conformation within RBD could not acquire an optimal geometry to allow the interaction with integrins. In light of these results, and in the event where integrins are confirmed to be host receptors for SARS-CoV-2, we suggest a possible involvement of other residues to stabilize the interaction.

Molecular dynamics simulations of cRGD-conjugated PEGylated TiO2 nanoparticles for targeted photodynamic therapy

“…3a, since the other 5 clusters represent less than 1% of the conformations adopted during the production phase. Previous experimental and computational findings [64][65][66][67] have proven a direct link between the biological activity of RGD peptides and some of their intrinsic structural parameters. Three criteria were proposed for the assessment of biological activity of RGD-containing peptides [64,65] and they are illustrated in Fig.…”

“…Previous experimental and computational findings [64][65][66][67] have proven a direct link between the biological activity of RGD peptides and some of their intrinsic structural parameters. Three criteria were proposed for the assessment of biological activity of RGD-containing peptides [64,65] and they are illustrated in Fig. 3c: (i) the distance d1 between the positively (Asp) and negatively (Arg) charged groups, i.e., between the C ζ Arg and the C γ Asp; (ii) the distance d2 between the C β of Arg and Asp;…”

“…As previously stated in Section 3.1.1, several experimental works suggest the evaluation of a particular set of geometrical criteria (see Fig. 3c for further details) to assess the potential biological activity of RGD-containing peptides towards integrins [64,65]. Here, we retake the same analysis done for the single cRGD molecule in water (Table 1), further evaluating this set of geometrical parameters for the cRGDconjugated ligands in the NP-PEG-cRGD10, NP-PEG-cRGD20 and NP-PEG-cRGD50 nanodevices.…”

Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition

“…In fact, it is well known that, despite other Coronaviridae, the Spike S1 domain from SARS-CoV-2 uniquely contains the RGD (Arg-Gly-Asp) sequence, a motif strongly conserved in all integrins protein ligands (Ludwig et al, 2021). This motif has been proposed as the attachment site for integrins so far (Makowski et al, 2021;Sigrist et al, 2020;Simons et al, 2021), although, recently, also interactions RGD-independent between Spike and other integrins have been suggested (Beaudoin et al, 2021;Othman et al, 2022).…”

Coagulopathy in COVID-19 and anticoagulation clinical trials

“…Early studies noted the presence of an RGD motif in the RBD of SARS-CoV-2 spike glycoprotein, leading to the hypothesis that RGD binding integrins may be involved in SARS-CoV-2 infection [ 20 , 21 ]. However, a recent molecular dynamics microscale simulation did not support this hypothesis [ 22 ]. Unlike the RGD motifs of known integrin ligands, usually located in a flexible loop (so-called RGD finger), the SARS2-S RGD motif resides in a rigid α-helical structure, leaving the sidechain orientation unfavorable for integrin binding.…”