6AN1

Crystal structure of the complex between PPARgamma LBD and the ligand AM-879


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.687 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Screening for PPAR Non-Agonist Ligands Followed by Characterization of a Hit, AM-879, with Additional No-Adipogenic and cdk5-Mediated Phosphorylation Inhibition Properties.

Ribeiro Filho, H.V.Bernardi Videira, N.Bridi, A.V.Tittanegro, T.H.Helena Batista, F.A.de Carvalho Pereira, J.G.de Oliveira, P.S.L.Bajgelman, M.C.Le Maire, A.Figueira, A.C.M.

(2018) Front Endocrinol (Lausanne) 9: 11-11

  • DOI: 10.3389/fendo.2018.00011

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptor gamma (PPARγ) is a member of a nuclear receptor superfamily and acts as a ligand-dependent transcription factor, playing key roles in maintenance of adipose tissue and in regulation of glucose and lipid home ...

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a member of a nuclear receptor superfamily and acts as a ligand-dependent transcription factor, playing key roles in maintenance of adipose tissue and in regulation of glucose and lipid homeostasis. This receptor is the target of thiazolidinediones, a class of antidiabetic drugs, which improve insulin sensitization and regulate glycemia in type 2 diabetes. Despite the beneficial effects of drugs, such as rosiglitazone and pioglitazone, their use is associated with several side effects, including weight gain, heart failure, and liver disease, since these drugs induce full activation of the receptor. By contrast, a promising activation-independent mechanism that involves the inhibition of cyclin-dependent kinase 5 (CDK5)-mediated PPARγ phosphorylation has been related to the insulin-sensitizing effects induced by these drugs. Thus, we aimed to identify novel PPARγ ligands that do not possess agonist properties by conducting a mini-trial with 80 compounds using the sequential steps of thermal shift assay, 8-anilino-1-naphthalenesulfonic acid fluorescence quenching, and a cell-based transactivation assay. We identified two non-agonist PPARγ ligands, AM-879 and P11, and one partial-agonist, R32. Using fluorescence anisotropy, we show that AM-879 does not dissociate the NCOR corepressor in vitro , and it has only a small effect on TRAP coactivator recruitment. In cells, AM-879 could not induce adipocyte differentiation or positively regulate the expression of genes associated with adipogenesis. In addition, AM-879 inhibited CDK5-mediated phosphorylation of PPARγ in vitro . Taken together, these findings supported an interaction between AM-879 and PPARγ; this interaction was identified by the analysis of the crystal structure of the PPARγ:AM-879 complex and evidenced by AM-879's mechanism of action as a putative PPARγ non-agonist with antidiabetic properties. Moreover, we present an optimized assay pipeline capable of detecting ligands that physically bind to PPARγ but do not cause its activation as a new strategy to identify ligands for this nuclear receptor.


    Organizational Affiliation

    Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Centre de Biochimie Structurale CNRS, Université de Montpellier, Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
286Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BKY
Query on BKY

Download SDF File 
Download CCD File 
A
4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)methyl]phenoxy}methyl)benzoic acid
C24 H16 O5
NRIDPHPNVUPLOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.687 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.321α = 90.00
b = 61.366β = 102.65
c = 118.450γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
MOSFLMdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil2016/22246-0

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection