On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

Abstract

A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.

Keywords: ACE2; Antibody development; Antigenic analysis; Binding affinity; Computer simulation; Coronavirus; Electrostatic interactions; Epitopes; Host-pathogen interaction; Protein-protein interaction; SARS-CoV-2; pH effect.

Graphical abstract

Fig. 1

Crystal structure of the SARS-CoV-1 S RBD (PDB id 2AJF, chain E) and the modeled SARS-CoV-2 S RBD. See text for details regarding the modeling aspects. These macromolecules are shown, respectively, in blue and red in a ribbon representation. The RMSD between these structures is equal to 0.638Å.

Fig. 2

Crystal structure of SARS-CoV-1 S RBD complexed with ACE2 (PDB id 2AJF). Only standard amino acids of chain A (ACE2) and E (SARS-CoV-1 S RBD) are shown in a molecular representation using spheres for its atoms. Atoms are colored accordingly to their amino acids physical chemical properties: red for acid amino acids, blue for base amino acids and gray for non-titrating amino acids. For a better visualization of the interface, the ACE2 structure was translated ∼12 Å.

Fig. 3

Molecular structures of the SARS-CoV-2 S RBD complexed with fragments of the investigated monoclonal antibodies. Only standard amino acids are shown in a molecular representation using its surface. Atoms are colored accordingly to their amino acids physical chemical properties: red for acid amino acids, blue for base amino acids and gray for non-titrating amino acids. For a better visualization of the epitope-paratope interface, the structures of the Abs were translated ∼12 Å. The RBD of SARS-CoV-2 S protein is given by the modeled generated at the SWISS-MODEL workspace (YP_009724390.1). The fragments of the mAbs 80R (PDB id 2GHW), F26G19 (PDB id 3BGF) and m396 (PDB id 2G75) are shown using their original PDB structures. CR3022 was modeled as described in the text.

Fig. 4

Sequences alignment of SARS-CoV-1 and SARS-CoV-2 RBD (S1 subunit) proteins. Symbols between the two pairwise aligned sequences have the usual meaning: a) conservative amino acids where both sequences have the same residues are indicated by “|”; b) Similarities with a high score are marked with “;” and c) the ones with low positive score are indicated by “.”. Gaps are represented by “-”. Numbers are used to guide the identification of the amino acids sequence numbers. See text for more details.

Fig. 5

A sketch of the simulation model system for the constant-pH Monte Carlo simulations. A SARS-CoV-2 S RBD and the fragment of the mAb 80R (as given by the PDB id 2GHW) represented by a collection of charged Lennard-Jones spheres of radii R_i and valences z_i mimicking amino acids are surrounded by counter ions and added salt, implicitly described by the inverse Debye length κ. The solvent is represented by its static dielectric constant ε. Positive and negatively charged protein amino acids are represented in blue and red, respectively. The macromolecules's centers of mass are separated by a distance r. The cylindrical simulation box is defined by the length l_cyl and radius r_cyl. Translation (back and forward) and rotation (in all directions) possible movements are illustrated by the gray arrows while the protonation/deprotonation processes are indicated by the dashed arrows labeled with H⁺.

Fig. 6

Free energy profiles for the interaction of RBD proteins with ACE2. The simulated free energy of interactions [Δw(r)] between the centers of mass of the RBD proteins from both SARS-CoV-1 and SARS-CoV-2 and the ACE2 at different solution pH conditions. Salt concentration was fixed at 150 mM. The structures of these macromolecules were extracted from the PDB id 2AJF for SARS-CoV-1 S RBD and ACE. SARS-CoV-2 S RBD was built-up by modeling as described in the text. Simulations started with the two molecules placed at random orientation and separation distance. Results for the systems SARS-CoV-1 and SARS-CoV-2 are show as continuous and dashed lines, respectively.

Fig. 7

Free energy profiles for the interaction of RBD proteins with monoclonal antibodies. The simulated free energy of interactions [Δw(r)] between the centers of mass of the RBD proteins from both SARS-CoV-1 and SARS-CoV-2 and the monoclonal antibodies at pH 4.6. Salt concentration was fixed at 150 mM. See text for details about the structures of these macromolecules. Simulations started with the two molecules placed at random orientation and separation distance. Results for SARS-CoV-1 and SARS-CoV-2 are show as continuous and dashed lines, respectively. Different line colors are used for each fragment of the Abs: 80R (black), CR3022 (red), m396 (green) and F29G19 (blue). (a) Left panel: Full plot. (b) Right panel: The well depth region of the βw(r) for each studied complex.

Fig. 8

Molecular structures of a possible SARS-CoV-2 S RBD complexed with CR3022. Standard amino acids of SARS-CoV-2 S RBD (molecule at left) and CR3022 (molecule at right) are shown in a molecular representation using spheres and ribbons, respectively. Atoms are colored accordingly to their amino acids physical chemical properties: red for acid amino acids, blue for base amino acids and wheat/green for non-titrating amino acids. For a better visualization of the interface, the two macromolecules were placed ∼12 Å apart from each other. Suggested residues to be mutated to improve the functional properties of CR3022 are indicated by the labeled amino acids (K12, K170, R194) are represented using the ball-and-stick model.

Fig. 9

Free energy profile for the interaction of SARS-CoV-2 S RBD proteins with a new monoclonal antibody. The simulated free energy of interactions [Δw(r)] between the centers of mass of the SARS-CoV S RBD protein and CR3022’ at pH 4.6 (dashed line in orange). Salt concentration was fixed at 150 mM. See text for details about the structures of these macromolecules. Simulations started with the two molecules placed at random orientation and separation distance. The results for SARS-CoV-1-CR3022 and SARS-CoV-2-CR3022 (continuum and dashed lines in red) are also shown for comparison. This data was extracted from Fig. 6.

Fig. 10

Electrostatic epitopes. Primary sequences of the SARS-CoV-1 S RBD and the SARS-CoV-2 S RBD with the interface with ACE2 and the estimated antigenic regions (shown in blue) for 80R and CR3022 by the electrostatic method. Data obtained using the threshold |ΔpK_a|>0.01. Symbols between the two pairwise aligned sequences have the usual meaning: a) conservative amino acids where both sequences have the same residues are indicated by “|”; b) Similarities with a high score are marked with “;” and c) the ones with low positive score are indicated by “.”. Gaps are represented by “-”. Numbers are used to guide the identification of the amino acids sequence numbers.

Fig. 11

Electrostatic epitopes. Primary sequence of the SARS-CoV-2 S RBD with the estimated antigenic regions (shown in blue) for CR3022 and CR3022’ by the electrostatic method. Data for CR3022 is the same shown in Fig. 10. All other details are also as in Fig. 10.