Ligand and Receptor Dynamics Contribute to the Mechanism of Graded PPARγ Agonism

Abstract

SUMMARY Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution NMR studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators.

Structure of REV-ERBβ Ligand-binding Domain Bound to a Porphyrin Antagonist

“…previously used NMR to demonstrate a dynamic mechanism by which ligands that bind to another nuclear receptor, PPAR␥, partially stabilize the PPAR␥ activation function-2 surface to provide full versus partial agonist activity (34). Protein NMR analysis of apo-REV-ERB␤-LBD reveals that approximately half of the residues comprising the LBD are dynamic (flexible) on the intermediate NMR time scale and are not observed in the NMR experiments.…”

“…Protein NMR analysis of apo-REV-ERB␤-LBD reveals that approximately half of the residues comprising the LBD are dynamic (flexible) on the intermediate NMR time scale and are not observed in the NMR experiments. Apo-PPAR␥ and RXR␣ also display a similar dynamic phenotype in the apo form (34,35), suggesting generally that the ligand-binding pockets of apo-ligand-regulated NR LBDs are conformationally dynamic.…”

Combined action of estrogen receptor agonists and antagonists in two-hybrid recombinant yeast in vitro

“…3, the antiestrogens decreased the induction ratios, without changing the EC 50 s of the concentration-response curves. This is because the dynamic interaction between ligands and receptors includes association, dissociation and recombination (Carroll et al, 2012;Hughes et al, 2012). The binding probability of a certain ligand depends on its proportion in the ligands cocktail.…”

Effects of Structural and Electronic Characteristics of Chalcones on the Activation of Peroxisome Proliferator-Activated Receptor Gamma

“…[10][11][12] For example, rosiglitazone stabilizes the PPARγ LBD into a single conformation, whereas partial agonists may alter the conformational dynamics of the receptor by binding in multiple orientations. 12) Furthermore, a recent study by Kumari and co-workers in which computer-aided virtual screening was used to identify novel chalcones as candidate PPARγ agonists also lends support to our observations. 13) Several of the top hits in that study were chalcones with high molecular weight, including some with naphthalene-like moieties.…”

“…However, our screen of 53 varied chalcones failed to identify any strict requirements for ligand binding, presumably due to the highly flexible PPARγ LBD. 12) This poses a significant challenge to the development of simple chalcones as novel PPARγ ligands. Nonetheless, our observations suggest that development of larger, complex chalcones or chalcone-like compounds with an electron rich group or sterically large groups such as napthyl on the carbonyl side should yield better PPARγ partial agonists.…”