Is Antagonism of E/Z-Guggulsterone at the Farnesoid X Receptor Mediated by a Noncanonical Binding Site? A Molecular Modeling Study

Abstract

Guggulsterone 1, the active principle of guggulipid, has been used in ethnic medicine for thousands of years for its antinflammatory and antilipidemic activities. The activities of 1 are apparently mediated by its interaction with an array of nuclear receptors, including endocrine steroid receptors and metabolic lipid receptors. Although relatively weak, the activity at the metabolic farnesoid X receptor (FXR) is particularly intriguing, as 1 is, so far, the only antagonist known for this receptor, with a peculiar ability of gene selective modulation. We report here a systematic study aimed at identifying the potential binding pocket of 1 at FXR. Although 1 could be docked into the canonical binding site, we identified a novel, so far undescribed binding pocket, localized near the loop region between helix 1 and helix 2. This novel binding pocket may explain some of the peculiar characteristics of 1 when acting at FXR.

Conformational dynamics of human FXR-LBD ligand interactions studied by hydrogen/deuterium exchange mass spectrometry: Insights into the antagonism of the hypolipidemic agent Z-guggulsterone

“…In addition, the region 388–396 was also found as being protected against exchange-in in presence of GG. Interestingly, these two protected regions coincide with a noncanonical binding site that was predicted by docking studies by Meyer et al [48]. In their model, GG s noncanonical interaction involves Tyr-260 (helix 1), the partial sequence Lys-262 to Met-265 (helix 1 – helix 2 loop), Thr-386 (helix 8) and Ile-390 (helix 8) [48].…”

“…Although GG has a steroidal scaffold, it has an all trans and quasi planar ABCD ring system in contrast to bile acids in which ring A and B are conjugated in a cis configuration [48]. In the absence of a co-crystal structure of FXR-LBD in complex with GG, the current HDX-MS results advance our understanding of the molecular determinants that govern the interaction of GG with the FXR-LBD.…”

“…6A and B reveal that the N-terminal regions of the FXR-LBD (residues 201–278) showed slightly higher protection against exchange-in in the GG-bound state compared to conformational states induced by the two agonists studied. Interestingly, recent molecular modeling studies have predicted a novel noncanonical binding site for GG near the loop region located between helix 1 and helix 2 [48] with Gln267 playing a key role in binding of the unusual second coactivator peptide which is visible in the 6ECDCA-bound FXR-LBD crystal structure (PDB ID 1OSV). The observed protection against exchange-in in the N-terminal region in presence of GG is consistent with the prediction of a non-canonical ligand binding site in that region of the LBD [48].…”

Beyond Bile Acids: Targeting Farnesoid X Receptor (FXR) with Natural and Synthetic Ligands

“…Docking studies advanced the hypothesis that E-and Zguggulsterone could bind to FXR occupying an accessory "back door" pocket which faces the loop region between helix H1 and helix H2 (Fig. 3) [36]. Such hypothetical model of interaction has been recently confirmed by Maier and colleagues in an experimental study that used amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry to investigate conformational changes in the ligand binding domain of FXR upon ligand binding [37].…”

“…8), characterized by improved in vivo pharmacokinetic properties with respect to previous series of derivatives. Recently, beneficial effects of Px-102 (36) have been reported in lowering lipid levels in animal models [97], and in preventing tumor growth in a liver cancer model [20]. In October 2012, researchers at Phenex Pharmaceuticals announced the successful completion of phase I clinical studies for Px-102 (ClinicalTrials.gov identifiers: NCT01998659, NCT01998672), reporting that this compound is safe and well tolerated at all doses tested in healthy subjects.…”