Proanthocyanidin B2 derived metabolites may be ligands for bile acid receptors S1PR2, PXR and CAR: an in silico approach

Abstract

Bile acids (BAs) act as signaling molecules via their interactions with various nuclear (FXR, VDR, PXR and CAR) and G-protein coupled (TGR5, M3R, S1PR2) BA receptors. Stimulation of these BA receptors influences several processes, including inflammatory responses and glucose and xenobiotic metabolism. BA profiles and BA receptor activity are deregulated in cardiometabolic diseases; however, dietary polyphenols were shown to alter BA profile and signaling in association with improved metabolic phenotypes. We previously reported that supplementing mice with a proanthocyanidin (PAC)-rich grape polyphenol (GP) extract attenuated symptoms of glucose intolerance in association with changes to BA profiles, BA receptor gene expression, and/or downstream markers of BA receptor activity. Exact mechanisms by which polyphenols modulate BA signaling are not known, but some hypotheses include modulation of the BA profile via changes to gut bacteria, or alteration of ligand-availability via BA sequestration. Herein, we used an in silico approach to investigate putative binding affinities of proanthocyanidin B2 (PACB2) and PACB2 metabolites to nuclear and G-protein coupled BA receptors. Molecular docking and dynamics simulations revealed that certain PACB2 metabolites had stable binding affinities to S1PR2, PXR and CAR, comparable to that of known natural and synthetic BA ligands. These findings suggest PACB2 metabolites may be novel ligands of S1PR2, CAR, and PXR receptors.Communicated by Ramaswamy H. Sarma.

Keywords: CAR; PXR; Polyphenols; S1PR2; bile acids; bile acids receptors; epicatechin; procyanidins.

Figure 1.. Binding affinities of BA receptors with PACB2 metabolites and BA ligands.

Heatmaps showing binding affinities (ΔG) between bile acids receptors (TGR5, M3R, S1PR2, FXR, VDR, PXR, and CAR) and A. PACB2 and 35 reported PACB2 metabolites and B. 32 bile acids and 4 non-bile-acid antagonists. Blue-white-red spectrum denotes ΔG scale, weak (-6) intermediate (-8), and strong (-10) binding affinities.

Figure 2.. Sankey diagrams of PACB2 metabolites (L2-L21) connected to tissue compartments they were identified in using UPLC-MS/MS.

PACB2 metabolites with competitive affinity to A. S1PR2, B. PXR, C. CAR using docking (Autodock Vina) and molecular dynamic simulations (YASARA). Thirty-five PACB2 metabolites were screened; only putative ligands with higher binding affinities than reported BA ligands for S1PR2, PXR, and CAR are shown. Computed IUPAC names of ligands can be found in Supplementary Online Material.

Figure 3.. S1PR2 interactions with known and putative ligands.

A. 3D schematic of S1PR2 protein (gold) showing active site interaction with previously reported ligands GDCA (colored blue), JTE-013 (colored red) as well as putative interactions with PACB2 metabolites L13 (colored green), L16 (colored purple), and L20 (colored orange). Interactions between S1PR2 amino acid residues and B. GDCA (natural agonist), C. JTE-013 (synthetic antagonist). Putative interactions between S1PR2 amino acid residues and D. L13, E. L16, F. L20. Residues in green form hydrogen bonds and residues in black form hydrophobic bonds.

Figure 4.. PXR interactions with known and putative ligands.

A. 3D schematic of PXR protein (green) showing active site interaction with previously reported ligands LCA (colored blue), SPA70 (colored red) as well as putative interactions with PACB2 metabolites L2 (colored green), L6 (colored purple), and L15 (colored orange). Interactions between PXR amino acid residues and B. LCA (natural agonist), C. SPA70 (synthetic antagonist). Putative interactions between PXR amino acid residues and D. L2, E. L10, F. L15. Residues in green form hydrogen bonds and residues in black form hydrophobic bonds.

Figure 5.. CAR interactions with known and putative ligands.

A. 3D schematic of CAR protein (violet) showing active site interaction with previously reported ligands LCA (colored blue), CINPA1 (colored red) as well as putative interactions with PACB2 metabolites L18 (colored green), L20 (colored purple), and L21 (colored orange). Interactions between CAR amino acid residues and B. LCA (natural agonist), C. CINPA1 (synthetic antagonist). Putative interactions between CAR amino acid residues and D. L18, E. L20, F. L21. Residues in green form hydrogen bonds and residues in black form hydrophobic bonds.

Figure 6.. Molecular dynamics simulations for movement of Cα-backbones of BA receptors and their known and putative ligands.

Root-mean square deviation (RMSD) values in Ångström (Å) for Cα-backbones (A, C, E) and ligands (B, D, F) of S1PR2, PXR and CAR. Legends show color key for each receptor-ligand pair investigated.