Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ
- The Scripps Research Institute, United States
- University of Montana, United States
- Southern Illinois University, United States
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.
Data availability
Crystal structures and diffraction data have been deposited in the PDB under accession codes 5UGM, 6AVI, 6AUG, 6MCZ, 6MD0, 6MD1, 6MD2, and 6MD4.
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PPARgamma LBD complexed with rosiglitazoneBiological Magnetic Resonance Bank, 17975.
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Human PPAR gamma in complex with nonanoic acidsProtein Data Bank, 4EM9.
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Crystal Structure of PPARg in complex with T2384Protein Data Bank, 3K8S.
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Human PPAR gamma ligand binding domain in complex with MCC555Protein Data Bank, 3B0Q.
Article and author information
Author details
Funding
National Institute of Diabetes and Digestive and Kidney Diseases (R01DK101871)
- Douglas J Kojetin
American Heart Association (16- POST27780018)
- Richard Brust
National Science Foundation (1659594)
- Sarah A Mosure
The Scripps Research Institute
- Sarah A Mosure
National Institute of Diabetes and Digestive and Kidney Diseases (R00DK103116)
- Travis S Hughes
National Institute of Diabetes and Digestive and Kidney Diseases (F32DK108442)
- Richard Brust
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Shang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ
eLife 7:e43320.
https://doi.org/10.7554/eLife.43320
Further reading
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- Structural Biology and Molecular Biophysics
Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor transcription factor that regulates gene expression programs in response to ligand binding. Endogenous and synthetic ligands, including covalent antagonist inhibitors GW9662 and T0070907, are thought to compete for the orthosteric pocket in the ligand-binding domain (LBD). However, we previously showed that synthetic PPARγ ligands can cooperatively cobind with and reposition a bound endogenous orthosteric ligand to an alternate site, synergistically regulating PPARγ structure and function (Shang et al., 2018). Here, we reveal the structural mechanism of cobinding between a synthetic covalent antagonist inhibitor with other synthetic ligands. Biochemical and NMR data show that covalent inhibitors weaken—but do not prevent—the binding of other ligands via an allosteric mechanism, rather than direct ligand clashing, by shifting the LBD ensemble toward a transcriptionally repressive conformation, which structurally clashes with orthosteric ligand binding. Crystal structures reveal different cobinding mechanisms including alternate site binding to unexpectedly adopting an orthosteric binding mode by altering the covalent inhibitor binding pose. Our findings highlight the significant flexibility of the PPARγ orthosteric pocket, its ability to accommodate multiple ligands, and demonstrate that GW9662 and T0070907 should not be used as chemical tools to inhibit ligand binding to PPARγ.
