Exploring the disruption of SARS-CoV-2 RBD binding to hACE2

Abstract

The COVID-19 pandemic was declared due to the spread of the novel coronavirus, SARS-CoV-2. Viral infection is caused by the interaction between the SARS-CoV-2 receptor binding domain (RBD) and the human ACE2 receptor (hACE2). Previous computational studies have identified repurposed small molecules that target the RBD, but very few have screened drugs in the RBD-hACE2 interface. When studies focus solely on the binding affinity between the drug and the RBD, they ignore the effect of hACE2, resulting in an incomplete analysis. We screened ACE inhibitors and previously identified SARS-CoV-2 inhibitors for binding to the RBD-hACE2 interface, and then conducted 500 ns of unrestrained molecular dynamics (MD) simulations of fosinopril, fosinoprilat, lisinopril, emodin, diquafosol, and physcion bound to the interface to assess the binding characteristics of these ligands. Based on MM-GBSA analysis, all six ligands bind favorably in the interface and inhibit the RBD-hACE2 interaction. However, when we repeat our simulation by first binding the drug to the RBD before interacting with hACE2, we find that fosinopril, fosinoprilat, and lisinopril result in a strongly interacting trimeric complex (RBD-drug-hACE2). Hydrogen bonding and pairwise decomposition analyses further suggest that fosinopril is the best RBD inhibitor. However, when lisinopril is bound, it stabilizes the trimeric complex and, therefore, is not an ideal potential drug candidate. Overall, these results reveal important atomistic interactions critical to the binding of the RBD to hACE2 and highlight the significance of including all protein partners in the evaluation of a potential drug candidate.

Keywords: ACE inhibitors; COVID-19; MM-GBSA; SARS-CoV-2; human ACE2 receptor; molecular dynamics; receptor binding domain; repurposed drugs.

FIGURE 1

RMSF of SARS-CoV-2 RBD and hACE2 structures for the 3 µs ensemble. (A) The RMSF of the RBD. (B) The RMSF of hACE2. For both graphs, the residues of the RMSF data enclosed in green are residues involved in the interface of the SARS-CoV-2 RBD–hACE2 interaction, according to Wang et al. (2020c).

FIGURE 2

Significant interactions for the SARS-CoV-2 RBD–hACE2 complex. Interactions detailed in Table 3 are displayed with hydrogen bonds depicted in purple.

FIGURE 3

SARS-CoV-2 RBD - hACE2 complex junction binding site. In the image, hACE2 is shown in gray and SARS-CoV-2 RBD is shown in cyan. Hydrogen bond acceptor sites are colored red, hydrogen bond donating sites are colored purple, and hydrophobic sites are colored yellow. The N-linked glycan bound to Asn90 is shown in orange. Site #2 on the 6LZG complex was predicted to have a SiteMap SScore of 1.002 and DScore of 1.017.

FIGURE 4

A visual representation of the various MM-GBSA energies that we used to evaluate binding. For all panels, the receptor defined for MM-GBSA calculations is in gray, and the defined ligand is in blue. (A) For the MM-GBSA_{Drug-(RBD+hACE2)} calculation, the RBD and hACE2 are taken together and treated as the receptor while each drug is treated as the ligand; therefore, the binding free energy is calculated between the drug and the RBD–hACE2 complex. (B) MM-GBSA_RBD-hACE2 is the binding free energy between the RBD and hACE2 with the ligand bound in the interface–though the drug is excluded from the calculation (shown in white)–it affects the conformations and interactions of RBD and hACE2. We subtract this value from the apo binding free energy between the RBD and hACE2, i.e., when no drug is bound. The average value of this apo energy is −31.23 (0.06) kcal/mol for the 3 μs ensemble. This difference is ΔΔG_{Bind, RBD-hACE2}, which tells us how the drug impacts the binding of RBD to hACE2. A positive ΔΔG_{Bind, RBD-hACE2} signifies that the drug inhibited the interaction between the RBD and hACE2. (C) MM-GBSA_{(RBD+Drug)-hACE2} represents the average binding free energy between hACE2 and the RBD–drug complex. The difference between MM-GBSA_{(RBD+Drug)-hACE2} and apo is ΔΔG_{Bind, (RBD+Drug)-hACE2}, which signifies the drug’s effects on the RBD–hACE2 interaction after the drug binds first to the RBD. Overall, ΔΔG_{Bind, (RBD+Drug)-hACE2} represents whether hACE2 prefers to bind to the drug-bound RBD or the apo RBD. A negative value signifies that the interaction between the drug-bound RBD and hACE2 is stronger than the interaction between apo RBD and hACE2. This suggests that the trimeric complex is more stable than the RBD–hACE2 apo complex. All values can be found in Table 4.

FIGURE 5

Comparison of MM-GBSA energies and percent dissociation. The x-axis represents the average MM-GBSA binding free energies between the RBD and hACE2 with a ligand present in the interface, MM-GBSA_RBD-hACE2. The y-axis (left side) represents the MM-GBSA binding free energies of the ligand interacting with the RBD–hACE2 complex, MM-GBSA_{Drug-(RBD+hACE2)}. The MM-GBSA_{Drug-(RBD+hACE2)} energies with respect to the x-axis are represented as circles. The y-axis (right side) represents the percent dissociations. These values with respect to the x-axis are triangles. The larger symbols depicted in orange represent ligands that were selected for further analyses. All other symbols are purple. All ligands, except physcion, are included and labeled next to each data point. Physcion was not included because it appeared to be an outlier once the data was visualized. The blue dashed line represents the apo MM-GBSA binding free energy, −31.23 (0.06) kcal/mol, in comparison to the MM-GBSA_RBD-hACE2 values.

FIGURE 6

All ligand poses. The starting pose of each ligand selected for further analysis based on the evaluation of the MM-GBSA values are depicted in the interface. The SARS-CoV-2 RBD is depicted in blue and hACE2 in gray. Fosinopril in pose 1 is shown in dark blue, fosinoprilat in pose 2 is shown in purple, fosinoprilat in pose 3 is shown in pink, and lisinopril in pose 1 in light green.

FIGURE 7

Visualization of drugs’ effects on residue interactions using dominant structures determined from clustering. The SARS-CoV-2 RBD is shown in blue and the hACE2 receptor is shown in gray. Clustering was used to determine the dominant structure of the ligand-bound complex throughout the 500 ns simulation. The percentage of the simulation that is represented by this dominant structure is in the top left corner of each panel. Hydrogen bonds between the drug and the RBD–hACE2 complex are depicted in pink. In all clusters, such hydrogen bonding persisted for at least 12% or more of each trajectory. Residue interactions between the RBD and hACE2 that were enhanced are shown in green and interactions that were disrupted are shown in red. (A) Fosinopril, depicted in beige, is bound in the interface. (B) Fosinoprilat pose 2, depicted in orange, is bound in the interface. (C) Fosinoprilat pose 3, depicted in light pink, is bound in the interface. Hydrogen bonds that were not present in the first dominant structure were visualized in the second dominant structure. (D) Lisinopril, depicted in brown, is bound in the interface. Hydrogen bonds that were not present in the first dominant structure were visualized in the second dominant structure.