CoChat
Sign Up
Cited by 198Peroxisome Proliferator-Activated ReceptorsNuclear Receptors and SignalingEstrogen and related hormone effects

An alternate binding site for PPARγ ligands

Open access
Hughes, Travis S., Giri, Pankaj Kumar, de Vera, Ian Mitchelle S., Marciano, David P., Kuruvilla, Dana S., Shin, Youseung, Blayo, Anne-Laure, Kamenecka, Theodore M. +3 more·2014·Nature Communications
DOI 10.1038/ncomms4571PMC PMC4070320
Open this paper in CoChat — free accountOpen PDF

Abstract

PPARγ is a target for insulin-sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/ncomms4571

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 63

  1. [1]Nwachukwu JC Nettles KW The nuclear receptor signalling scaffold: insights from full-length structures EMBO J 31 251 3 2012 22252143 PMC3261572
  2. [3]Chandra V Structure of the intact PPAR-gamma-RXR-alpha nuclear receptor complex on DNA Nature 456 350 356 2008 19043829 PMC2743566
  3. [4]Orlov I Rochel N Moras D Klaholz BP Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA EMBO J 31 291 300 2012 22179700 PMC3261568
  4. [5]Rochel N Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings Nat Struct Mol Biol 18 564 70 2011 21478865
  5. [6]Zhang J DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex Nat Struct Mol Biol 18 556 63 2011 21478866 PMC3087838
  6. [7]Moore JT Collins JL Pearce KH The nuclear receptor superfamily and drug discovery ChemMedChem 1 504 23 2006 16892386
  7. [8]Renaud JP Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid Nature 378 681 9 1995 7501014
  8. [9]Nagy L Schwabe JW Mechanism of the nuclear receptor molecular switch Trends Biochem Sci 29 317 24 2004 15276186
  9. [10]Choi JH Antidiabetic actions of a non-agonist PPARgamma ligand blocking Cdk5-mediated phosphorylation Nature 477 477 81 2011 21892191 PMC3179551
  10. [11]Choi JH Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARgamma by Cdk5 Nature 466 451 6 2010 20651683 PMC2987584
  11. [12]Hughes TS Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism Structure 20 139 50 2012 22244763 PMC3278220
  12. [13]Bruning JB Partial agonists activate PPARgamma using a helix 12 independent mechanism Structure 15 1258 71 2007 17937915
  13. [14]Waku T The nuclear receptor PPARgamma individually responds to serotonin- and fatty acid-metabolites Embo J 29 3395 407 2010 20717101 PMC2957204
  14. [15]Acton JJ 3rd Benzoyl 2-methyl indoles as selective PPARgamma modulators Bioorg Med Chem Lett 15 357 62 2005 15603954
  15. [16]Riepl H Sequential backbone assignment of peroxisome proliferator-activated receptor-gamma ligand binding domain J Biomol NMR 32 259 2005 16132831
  16. [17]Kleckner IR Foster MP An introduction to NMR-based approaches for measuring protein dynamics Biochim Biophys Acta 1814 942 68 2011 21059410 PMC3061256
  17. [18]Aci-Seche S Genest M Garnier N Ligand entry pathways in the ligand binding domain of PPARgamma receptor FEBS Lett 585 2599 603 2011 21782815
  18. [19]Genest D Ligand-escape pathways from the ligand-binding domain of PPARgamma receptor as probed by molecular dynamics simulations Eur Biophys J 37 369 79 2008 17929009
  19. [20]Leesnitzer LM Functional consequences of cysteine modification in the ligand binding sites of peroxisome proliferator activated receptors by GW9662 Biochemistry 41 6640 50 2002 12022867
  20. [21]Lee G T0070907, a selective ligand for peroxisome proliferator-activated receptor gamma, functions as an antagonist of biochemical and cellular activities J Biol Chem 277 19649 57 2002 11877444
  21. [22]Reibarkh M Malia TJ Wagner G NMR distinction of single- and multiple-mode binding of small-molecule protein ligands J Am Chem Soc 128 2160 1 2006 16478139 PMC2527406
  22. [23]Lamotte Y Synthesis and biological activities of novel indole derivatives as potent and selective PPARgamma modulators Bioorg Med Chem Lett 20 1399 404 2010 20079636
  23. [24]Shiraki T Alpha,beta-unsaturated ketone is a core moiety of natural ligands for covalent binding to peroxisome proliferator-activated receptor gamma J Biol Chem 280 14145 53 2005 15695504
  24. [25]Soares AF Covalent binding of 15-deoxy-delta12,14-prostaglandin J2 to PPARgamma Biochem Biophys Res Commun 337 521 5 2005 16198309
  25. [26]Itoh T Structural basis for the activation of PPARgamma by oxidized fatty acids Nat Struct Mol Biol 2008 PMC2939985 19172745
  26. [27]Lehmann JM An antidiabetic thiazolidinedione is a high affinity ligand for peroxisome proliferator-activated receptor gamma (PPAR gamma) J Biol Chem 270 12953 6 1995 7768881
  27. [28]Nolte RT Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma Nature 395 137 43 1998 9744270
  28. [29]Forman BM 15-Deoxy-Δ12,14-prostaglandin J2 is a ligand for the adipocyte determination factor PPARγ Cell 83 803 12 1995 8521497
  29. [30]Kliewer SA A prostaglandin J2 metabolite binds peroxisome proliferator-activated receptor gamma and promotes adipocyte differentiation Cell 83 813 9 1995 8521498
  30. [31]Li Y Molecular recognition of nitrated fatty acids by PPAR gamma Nat Struct Mol Biol 15 865 7 2008 18604218 PMC2538624
  31. [32]Waku T Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids J Mol Biol 385 188 99 2009 18977231
  32. [33]Waku T Shiraki T Oyama T Morikawa K Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands FEBS Lett 583 320 4 2009 19101554
  33. [34]Rogue A Comparative gene expression profiles induced by PPARgamma and PPARalpha/gamma agonists in human hepatocytes PLoS One 6 e18816 2011 21533120 PMC3078935
  34. [35]Hurtado O Daidzein has neuroprotective effects through ligand-binding-independent PPARgamma activation Neurochem Int 61 119 27 2012 22521773
  35. [36]Sikka S Chen L Sethi G Kumar AP Targeting PPARgamma Signaling Cascade for the Prevention and Treatment of Prostate Cancer PPAR Res 2012 968040 2012 23213321 PMC3504464
  36. [37]Akinyeke TO Stewart LV Troglitazone suppresses c-Myc levels in human prostate cancer cells via a PPARgamma-independent mechanism Cancer Biol Ther 11 1046 58 2011 21525782 PMC3142365
  37. [38]Lyles BE Akinyeke TO Moss PE Stewart LV Thiazolidinediones regulate expression of cell cycle proteins in human prostate cancer cells via PPARgamma-dependent and PPARgamma-independent pathways Cell Cycle 8 268 77 2009 19164938
  38. [39]Robbins GT Nie D PPAR gamma, bioactive lipids, and cancer progression Front Biosci 17 1816 34 2012 PMC3409468 22201838
  39. [40]Lea MA Sura M Desbordes C Inhibition of cell proliferation by potential peroxisome proliferator-activated receptor (PPAR) gamma agonists and antagonists Anticancer Res 24 2765 71 2004 15517883
  40. [41]Nettles KW Insights into PPARgamma from structures with endogenous and covalently bound ligands Nat Struct Mol Biol 15 893 5 2008 18769464
  41. [42]Li Y T2384, a novel antidiabetic agent with unique peroxisome proliferator-activated receptor gamma binding properties J Biol Chem 283 9168 76 2008 18263587
  42. [43]Moore TW Mayne CG Katzenellenbogen JA Minireview: Not picking pockets: nuclear receptor alternate-site modulators (NRAMs) Mol Endocrinol 24 683 95 2010 19933380 PMC2852352
  43. [44]Wang Y A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor β Proc Natl Acad Sci U S A 103 9908 11 2006 16782818 PMC1502552
  44. [45]Kojetin DJ Burris TP Jensen EV Khan SA Implications of the binding of tamoxifen to the coactivator recognition site of the estrogen receptor Endocr Relat Cancer 15 851 70 2008 18755852
  45. [46]Jensen EV Khan SA A two-site model for antiestrogen action Mech Ageing Dev 125 679 82 2004 15541763
  46. [47]Buzon V Carbo LR Estruch SB Fletterick RJ Estebanez-Perpina E A conserved surface on the ligand binding domain of nuclear receptors for allosteric control Mol Cell Endocrinol 348 394 402 2012 21878368
  47. [48]Grosdidier S Allosteric conversation in the androgen receptor ligand-binding domain surfaces Mol Endocrinol 26 1078 90 2012 22653923 PMC5416996
  48. [49]Estébanez-Perpiñá E A surface on the androgen receptor that allosterically regulates coactivator binding Proc Natl Acad Sci U S A 104 16074 9 2007 17911242 PMC1999396
  49. [50]Estébanez-Perpiñá E Structural insight into the mode of action of a direct inhibitor of coregulator binding to the thyroid hormone receptor Mol Endocrinol 21 2919 28 2007 17823305
  50. [51]Arnold LA Discovery of small molecule inhibitors of the interaction of the thyroid hormone receptor with transcriptional coregulators J Biol Chem 280 43048 55 2005 16263725
  51. [52]Sadana P Similarities and differences between two modes of antagonism of the thyroid hormone receptor ACS Chem Biol 6 1096 106 2011 21815645 PMC3199310
  52. [53]Mizwicki MT Identification of an alternative ligand-binding pocket in the nuclear vitamin D receptor and its functional importance in 1alpha,25 (OH)2-vitamin D3 signaling Proc Natl Acad Sci U S A 101 12876 81 2004 15326291 PMC516488
  53. [54]Mizwicki MT Bula CM Bishop JE Norman AW New insights into Vitamin D sterol-VDR proteolysis, allostery, structure-function from the perspective of a conformational ensemble model J Steroid Biochem Mol Biol 103 243 62 2007 17368177 PMC1906717
  54. [55]Mizwicki MT Bula CM Bishop JE Norman AW A perspective on how the Vitamin D sterol/Vitamin D receptor (VDR) conformational ensemble model can potentially be used to understand the structure-function results of A-ring modified Vitamin D sterols J Steroid Biochem Mol Biol 97 69 82 2005 16055325
  55. [56]Mizwicki MT Norman AW The vitamin D sterol-vitamin D receptor ensemble model offers unique insights into both genomic and rapid-response signaling Sci Signal 2 re4 2009 19531804
  56. [57]Menegaz D Vitamin D receptor (VDR) regulation of voltage-gated chloride channels by ligands preferring a VDR-alternative pocket (VDR-AP) Mol Endocrinol 25 1289 300 2011 21659475 PMC3146250
  57. [58]Motani A INT131: a selective modulator of PPAR gamma J Mol Biol 386 1301 11 2009 19452630
  58. [59]Solt LA Regulation of Circadian Behavior and Metabolism by Synthetic REV-ERB Agonists Nature 485 62 8 2012 22460951 PMC3343186
  59. [60]Findeisen M Brand T Berger S A 1H-NMR thermometer suitable for cryoprobes Magn Reson Chem 45 175 8 2007 17154329
  60. [61]Otten R Chu B Krewulak KD Vogel HJ Mulder FA Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins J Am Chem Soc 132 2952 60 2010 20148553
  61. [62]Kovrigin EL NMR line shapes and multi-state binding equilibria J Biomol NMR 2012 22610542
  62. [63]Chalmers MJ Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry Anal Chem 78 1005 14 2006 16478090
  63. [65]Pascal BD HDX workbench: software for the analysis of H/D exchange MS data J Am Soc Mass Spectrom 23 1512 21 2012 22692830 PMC3808162

Cited by

Sorted by citations

Authors
Hughes, T. S., Giri, P. K., de Vera, I. M. S., Marciano, D. P., Kuruvilla, D. S., Shin, Y., Blayo, A.-L., Kamenecka, T. M., Burris, T. P., Griffin, P. R., & Kojetin, D. J.
Affiliations
Scripps Research Institute (US)
Corresponding author
Kojetin, Douglas J.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2014-04-07
Volume
5
Issue
1
Pages
3571-3571
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms4571
PMC
PMC4070320
OpenAlex
W2062429936
Cited by
198
References
2
Citations by year
2026: 16 · 2025: 17 · 2024: 18 · 2023: 7 · 2022: 15 · 2021: 17 · 2020: 15 · 2019: 22 · 2018: 23 · 2017: 15 · 2016: 13 · 2015: 13 · 2014: 7
FWCI
6.70
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Florida Department of Health (1KN-09)
  • University of Cincinnati
  • National Institutes of Health (DK101871)
  • National Institute of Diabetes and Digestive and Kidney Diseases (DK101871, R01DK101871, DK097890, F32DK097890)
  • National Center for Research Resources (S10RR027270)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Peroxisome Proliferator-Activated Receptors
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Nuclear Receptors and Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Estrogen and related hormone effects
Keywords
PPARγ, ligand binding, thiazolidinediones, insulin-sensitizing drugs, allosteric modulation, receptor conformational change, transcriptional activation, adverse effects, diabetes mellitus, nuclear receptor structure
MeSH terms
Binding Sites, Ligands, PPAR gamma

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review