Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ.

Jinsai Shang,Jared Bass,Hua Lin,Richard Brust,Douglas J Kojetin,Theodore M Kamenekca,Travis S Hughes,Miru Tang,Sarah A Mosure,Qingfeng Ge,Paola Munoz-Tello

doi:10.7554/elife.43320

Abstract

Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic ligand to the orthosteric pocket can push natural and endogenous PPARγ ligands (fatty acids) out of the orthosteric pocket towards an alternate ligand-binding site near the functionally important omega (Ω)-loop. X-ray crystallography, NMR spectroscopy, all-atom molecular dynamics simulations, and mutagenesis coupled to quantitative biochemical functional and cellular assays reveal that synthetic ligand and fatty acid cobinding can form a 'ligand link' to the Ω-loop and synergistically affect the structure and function of PPARγ. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of a natural or endogenous ligand with a synthetic ligand.

Highlights

Thiazolidinediones (TZDs), called glitazones, are synthetic agonists of the peroxisome proliferator-activated receptor gamma (PPARg) nuclear receptor with potent anti-diabetic efficacy in patients with type 2 diabetes (Soccio et al, 2014)
Using NMR spectroscopy, molecular dynamics simulations, isothermal titration calorimetry (ITC), and mutagenesis coupled to functional assays, we show that cobinding of a synthetic ligand and fatty acid affects the conformation of the activation function-2 (AF-2) surface, synergistically enhances coactivator interaction, and may affect PPARg transcription in cells
Synthetic ligands and FDA-approved anti-diabetic drugs that target the nuclear receptor PPARg are thought to compete with and completely displace natural/endogenous ligands upon binding to an orthosteric pocket to regulate PPARg activity. This competitive or ‘onefor-one’ orthosteric ligand exchange model was developed from crystal structures of PPARg bound to individual ligands, whereby structural overlay of these structures showed that the ligands have overlapping orthosteric binding modes

Summary

Introduction

Thiazolidinediones (TZDs), called glitazones, are synthetic agonists of the peroxisome proliferator-activated receptor gamma (PPARg) nuclear receptor with potent anti-diabetic efficacy in patients with type 2 diabetes (Soccio et al, 2014). After an increase in clinical use of TZD drugs such as rosiglitazone (Avandia) in the early 2000s, the use of TZDs in diabetic patients has dropped significantly due to adverse side effects, including bone loss and water retention. These observations have spawned efforts to determine the molecular mechanisms by which TZDs and other synthetic PPARg ligands exert beneficial antidiabetic effects and adverse effects.

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