title: Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization.
abstract: Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.
authors.affiliation: Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil.
authors.forename: Amanda
authors.initials: A
authors.lastname: Bernardes
authors.forename: Paulo C T
authors.initials: PC
authors.lastname: Souza
authors.forename: João R C
authors.initials: JR
authors.lastname: Muniz
authors.forename: Clarisse G
authors.initials: CG
authors.lastname: Ricci
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Ayers
authors.forename: Nili M
authors.initials: NM
authors.lastname: Parekh
authors.forename: André S
authors.initials: AS
authors.lastname: Godoy
authors.forename: Daniela B B
authors.initials: DB
authors.lastname: Trivella
authors.forename: Peter
authors.initials: P
authors.lastname: Reinach
authors.forename: Paul
authors.initials: P
authors.lastname: Webb
authors.forename: Munir S
authors.initials: MS
authors.lastname: Skaf
authors.forename: Igor
authors.initials: I
authors.lastname: Polikarpov
mesh_terms: D000893:Anti-Inflammatory Agents / Q000737:chemistry / Q000378:metabolism; D002478:Cells, Cultured; D018360:Crystallography, X-Ray; D004305:Dose-Response Relationship, Drug; D006801:Humans; D015850:Interleukin-6 / Q000378:metabolism; D016209:Interleukin-8 / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D047493:PPAR alpha / Q000819:agonists* / Q000737:chemistry*; D011487:Protein Conformation; D011743:Pyrimidines / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000893:Anti-Inflammatory Agents; D015850:Interleukin-6; D016209:Interleukin-8; D047493:PPAR alpha; D011743:Pyrimidines; C006253:pirinixic acid
keywords: AF-2; DBD; DMEM; DNA-binding domain; Dulbecco's modified Eagle's medium; HCEC; LBD; MD; PBS; PCA; PDB; PPAR; PPARα; Protein Data Bank; RMSF; activation function 2; crystal structure; dry eye disease; human corneal epithelial cells; ligand-binding domain; molecular dynamics; peroxisome proliferator-activated receptor; phosphate-buffered saline; principal component analysis; protein and ligand interaction; root-mean-square fluctuation