Integrated computational approach towards identification of HSPG and ACE2 mimicking moieties for SARS-CoV-2 inhibition

Abstract

A key step to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is to prevent the entry of the virus into the host cells. The receptor-binding domains (RBDs) of spike proteins of SARS-CoV and other human coronaviruses utilize heparan sulfate proteoglycans (HSPGs) as the primary receptors for their accumulation on the cell surface and then scan for binding to the main entry receptor angiotensin-converting enzyme 2 (ACE2). SARS-CoV and SARS-CoV-2 share structurally similar RBDs and therefore, it is possible that SARS-COV-2 primarily binds to HSPGs followed by binding to the ACE2 receptors. A promising strategy to inhibit virus infection is to circulate exogenous bioactive moieties structurally mimicking cellular HSPG and ACE2 which act as decoy receptors binding to SARS-CoV-2 and competitively inhibit virus entry to the host cells mediated by cellular-bound HSPG and ACE2. Using a molecular docking tool, we identified carboxymethyl benzyl amide sulfonate (CMBS) and polyanetholesulfonic acid (PAS) as the suitable HSPG mimicking ligands, and Paenibacillus sp. B38-derived carboxypeptidase (B38-CAP) and Bacillus subtilis-derived carboxypeptidase (BS-CAP) as the potential ACE2-like enzymes having a strong binding affinity to the spike proteins as that of cellular HSPG and ACE2. Further, the binding stability and compactness of these moieties with SARS-CoV-2 were analyzed through molecular dynamics (MD) simulations, and the results indicated that these moieties form well-stable complexes with the RBD of spike proteins. The identified moieties could be conjugated to the surfaces of non-toxic nanoparticles to provide multiple interactions to efficiently shield SARS-CoV-2, and inhibit viral entry to the host cells.

Keywords: ACE2; HSPG; Inhibition; Mimicking moieties; Molecular docking; Molecular dynamics simulations; SARS-CoV-2.

Fig. 1

Schematic of the SARS-CoV-2 virus entry inhibition mechanism in the presence of a soluble form of exogenous heparin sulfate proteoglycan (HSPG) and angiotensin-converting enzyme II (ACE2) mimicking moieties. (A) Conventional entry of virus to the cells via binding with HSPG and ACE2 receptors of the host cell membrane (B) Proposed mechanism of inhibition of virus entry to the cell by circulating bioactive chemical moieties structurally mimicking cellular HSPG and ACE2.

Fig. 2

Crystallographic images of the protein structures studied in this work. (A) RBD domain of spike protein of SARS-CoV-2 (PDB Id: 6M0J) (B) cellular angiotensin-converting enzyme 2 (ACE2) (PDB ID: 1R4L) (C) B38-CAP (GenBank, LC406946) (D) BA-CAP (GenBank, LC417450) (E) BS-CAP (PDB ID: 3HQ2).

Fig. 3

Docked poses of (A) heparin sulfate proteoglycan (HSPG) (B) carboxymethyl benzyl amide sulfonate (CMBS) (C) polyanetholesulfonic acid (PAS) ligands during their interaction with the RBD of the spike protein of SARS-CoV-2, obtained from Discovery Studio Visualizer 2021. Hydrogen and other several bonds were involved in the interaction between RBD and ligands.

Fig. 4

2-dimensional structures showing the amino acid residues binding with heparin sulfate proteoglycan (HSPG) ligand indicating the type of bond and distance at which the bonds are formed in (A) heparin sulfate proteoglycans (HSPG) (B) carboxymethyl benzyl amide sulfonate (CMBS) (C) poly anethole sulfonic acid (PAS) during docking with the RBD of the spike protein of SARS-CoV-2.

Fig. 5

Amino acid interaction at the protein–protein interfaces obtained from the docking results. (A) RBD and cellular angiotensin-converting enzyme 2 (ACE2) (B) RBD and BS-CAP (C) RBD and B-38 CAP. The maroon color indicates the RBD of the spike protein.

Fig. 6

RMSD plots of Cα atoms of RBD of SARS-CoV-2 during its complex formation with (A) cellular HSPG (B) CMBS and (C) PAS, in comparison to the RMSD of the respective free RBDs and free ligands.

Fig. 7

RMSF (A) and Rg (B) plots of Cα atoms of RBD of SARS-CoV-2 during its complex formation with cellular HSPG, CMBS, and PAS ligands.

Fig. 8

RMSD (A), RMSF (B), and Rg (C) plots of Cα atoms of RBD of SARS-CoV-2 during its complex formation with cellular ACE2, BS-CAP, and B38-CAP proteins.