Single-Molecule Analysis of SARS-CoV-2 Binding to C-Type Lectin Receptors

Abstract

Despite intense scrutiny throughout the pandemic, development of efficacious drugs against SARS-CoV-2 spread remains hindered. Understanding the underlying mechanisms of viral infection is fundamental for developing novel treatments. While angiotensin converting enzyme 2 (ACE2) is accepted as the key entry receptor of the virus, other infection mechanisms exist. Dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin (DC-SIGN) and its counterpart DC-SIGN-related (DC-SIGNR, also known as L-SIGN) have been recognized as possessing functional roles in COVID-19 disease and binding to SARS-CoV-2 has been demonstrated previously with ensemble and qualitative techniques. Here we examine the thermodynamic and kinetic parameters of the ligand-receptor interaction between these C-type lectins and the SARS-CoV-2 S1 protein using force-distance curve-based AFM and biolayer interferometry. We evidence that the S1 receptor binding domain is likely involved in this bond formation. Further, we employed deglycosidases and examined a nonglycosylated S1 variant to confirm the significance of glycosylation in this interaction. We demonstrate that the high affinity interactions observed occur through a mechanism distinct from that of ACE2.

Keywords: DC-SIGN; L-SIGN; SARS-CoV-2; atomic force microscopy; kinetics; protein glycosylation; single molecule.

Figure 1

Binding of SARS-CoV-2 to DC-SIGN and L-SIGN. SARS-CoV-2 binds cell surface receptors through the exposed trimeric S protein (A). Electron density map of the S1 trimer with glycans rendered in blue as seen from the side (B) and from the top of the RBD (C). Example of the experimental setup for binding assessment of model surfaces (D). A laser is focused on the back of the AFM cantilever, being reflected into a photodiode, which allows for detection of forces acting on the functionalized tip as it is approached and retracted from the surface, bringing RBD or S1 with DC-SIGN or L-SIGN; attached to the tip via a PEG linker was either the S1 protein, or the isolated RBD domain. On the model surface with which the tip was interacting was grafted either L-SIGN (teal) or DC-SIGN (red). The resulting BPs (E) between S1 (left) or RBD (right) functionalized tip and model surfaces (D) coated with L-SIGN (blue shades) or DC-SIGN (red shades); n > 8 for each condition. Significance as represented by p value was calculated using a student t test. BLI sensograms showing the kinetics of the interaction between DC-SIGN (F) and L-SIGN (G) with S1 protein expressed in HEK cells; fitting is indicated by dark lines.

Figure 2

Binding kinetics of S1 protein with L-SIGN and DC-SIGN. Free energy landscape of ligand–receptor binding dynamics as given by a two-state Bell–Evans model for single bond rupture (A). Retrieval of information from adhesion events (B), showing the determination of the force (B, top) and loading rate (ΔF/Δt) (B, middle) from curves that display binding events (B, top and middle), and an example of a retrieved curve with no binding event (B, bottom). DFS plots constructed from retrieved data for L-SIGN (C) and DC-SIGN (D) with contact time versus BP graphs (inset); solid line represents a least-squares fit of a monoexponential decay. DFS plots show the distribution of rupture forces as a function of loading rate (LR) for all data points. Solid line represents the Bell–Evans fit for single noncovalent bonds, whereas the Williams–Evans fit for a second uncorrelated bond is indicated by a dashed line.

Figure 3

Probing S1 binding to L-SIGN or DC-SIGN on live A549 cells. Binding of S1 is probed on A549 cells and A549 cells transfected with L-SIGN GFP (A). An example height map (B) with corresponding region indicated on a confocal micrograph (inset), GFP fluorescence in green; scale bars are 5 and 10 μm, respectively. Edge of the positive cell being examined is indicated with a dotted line in the height map. Grayscale adhesion map of the same cell (C) showing binding on the positive cell (left-hand side) and less on the negative cells (right-hand side), scale is 0–400 pN. Corresponding binding probability results for L-SIGN positive and negative cells (D), showing significantly higher binding on positive cells (n = 9 for L-SIGN expressing cells, n = 13 for control cells, individual points are representative of the result from an individual cell, hollow marker indicates the average BP, whiskers denote the data range, bisecting lines show the median, and the interquartile range is shown by the length of the box). Experimental setup for live cell experiments to assess DC-SIGN binding on transfected A549 cells (E). Height map and confocal micrograph (inset) of a DC-SIGN-OFP positive and negative cell (F), adhesion map of this region (G), and binding probability calculated from live cell adhesion maps (H) showing significantly higher binding probability for transfected cells (n = 6 in the case of both DC-SIGN expressing and control cells, individual points are representative of the result from an individual cell, hollow marker indicates the average BP, whiskers denote the data range, bisecting lines show the median, and the interquartile range is shown by the length of the box). Corresponding DFS plot for L-SIGN incorporating the data retrieved from living cell experiments (I) and resulting histograms (J). Corresponding DFS plot for DC-SIGN incorporating the data retrieved from living cell experiments (K) and resulting histograms (L).

Figure 4

Evaluating the role of glycosylation in binding behaviors observed between S1 and DC/L-SIGN. A multisurface experimental set up was utilized (A), wherein the BP was observed across multiple surfaces with the same tip, with ACE2 acting as a positive control. When S1 derived from E. coli was attached to the AFM tip (B), binding was conserved with ACE2 (brown lines), however was severely impacted for both DC-SIGN (red lines) and L-SIGN (teal lines). These findings were corroborated using BLI (B) wherein binding was not observed for DC-SIGN or L-SIGN, but maintained for ACE2. Enzymatic removal of glycans (C and D) and impact on BP was performed using a similar experimental setup, and binding was assessed for all three surfaces before and after the addition of N-glycosidase and O-glycosidase (E), or in the reverse order (F) (anti-ACE2 mAb being used as a control in both cases). To confirm that the importance of glycans only applies to certain interactions, BLI was performed using E. coli derived S1 with L-SIGN (G), and DC-SIGN (H) performing poorly and exhibiting very little wavelength shift due to lack of binding to the sensor, whereas ACE2 (I) gave a much larger shift, as S1 bound the receptor and thus coated the probe.