PPARα Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates

Abstract

Summary Most triacylglycerol-lowering fibrates have been developed in the 1960s–1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARα), was identified. Twenty-one ligand-bound PPARα structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARα ligand-binding domain, which are composed of a “Center” and four “Arm” regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARα agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARα potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARα ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs.

Mechanisms Mediating the Regulation of Peroxisomal Fatty Acid Beta-Oxidation by PPARα

“…Recent publications to date on studies based on X-ray crystallography, referenced in the protein data bank website (PDB; http://www.pdb.org/, accessed on 1 July 2021), provide fascinating, detailed insight into the LBD domain structure, albeit limited to comparing it with other PPAR receptors. It describes a relatively large Y-shaped hydrophobic cavity in the PPARα-LBD pocket volume of 1400 Å 3 [68], which allows PPARα to interact with a broad range of structurally distinct natural and synthetic ligands [67,69]. (6,12,21,179,230) amino acids, the corepressor site is marked with a red half-sphere, and the coactivator binding site is shown with a green ring.…”

“…This group of compounds includes various insecticides (2,4-dichlorophenoxyacetic acid); herbicides (phenoxyacetate derivatives) [110]; surfactants (perfluorooctanoic acid-PFOA); organic chlorinated hydrocarbons solvents such as perchloroethylene and trichloroethylene [111]; food flavors [112]; leukotriene D4 receptor antagonists [113]; phthalate plasticizers, such as di-(2-ethylhexyl)-phthalate and di-(2-ethylhexyl) adipate [114]; and amphipathic carboxylic acids [98]. The latter form the hypolipidemic fibrate class of drugs, acknowledged as the archetypal PPARα agonists, including clofibrates [88,89]; pemafibrates [67,69]; fenofibrates [67], and ciprofibrates [115]. It is notable that certain synthetic ligands are designed to act as dual agonists, like muraglitazar [93], that target both PPARα and PPARγ isotypes; others act as pan-agonists that activate all PPAR receptors like bezafibrates [92]; or as a PPARα partial agonist such as GW9662 [69], known as a PPARγ-selective antagonist (Figure 5).…”

Structural Basis for Anti-non-alcoholic Fatty Liver Disease and Diabetic Dyslipidemia Drug Saroglitazar as a PPAR α/γ Dual Agonist

“…3) Meanwhile, PPARδ is ubiquitously expressed and has some physiological functions related to those of PPARα, such as energy dissipation (e.g., fatty acid β-oxidation), and those of PPARγ, such as insulin sensitivity enhancement. 4) It is on account of these characteristics that PPARs have been used as therapeutic targets against various metabolic diseases. 4) Fibrates such as fenofibrate and bezafibrate, which are synthetic PPARα agonists, are widely used to treat hypertriglyceridemia, whereas "thiazolidinediones (glitazones)" such as rosiglitazone and pioglitazone, which are synthetic PPARγ agonists, are antidiabetic drugs with potent insulin-sensitizing effects that confer long-term glycemic control.…”

“…4) It is on account of these characteristics that PPARs have been used as therapeutic targets against various metabolic diseases. 4) Fibrates such as fenofibrate and bezafibrate, which are synthetic PPARα agonists, are widely used to treat hypertriglyceridemia, whereas "thiazolidinediones (glitazones)" such as rosiglitazone and pioglitazone, which are synthetic PPARγ agonists, are antidiabetic drugs with potent insulin-sensitizing effects that confer long-term glycemic control. PPARδ agonists are not yet clinically available, but it is expected that they will be used in the treatment of metabolic/cardiovascular diseases.…”

“…PPARδ agonists are not yet clinically available, but it is expected that they will be used in the treatment of metabolic/cardiovascular diseases. 4) Human PPARα/γ/δ-ligand binding pockets (LBPs) share 62-71% amino acid sequence identity and form similar "Y"shape structures, enclosed by α-helices and β-sheets, 1) that consist of the Center and Arm I-III regions (the nomenclature of LBD differs depending on the researcher; here we use our nomenclature 5) ). The PPARα/γ-LBD pockets are significantly larger than the PPARδ-LBD pocket because of the narrowing of the pocket adjacent to the Activating Function-2 (AF-2) helix 12 6) ; the data describe the 1400 Å 3 , 1440 Å 3 , and 1300 Å 3 LBP cavities for PPARα, PPARγ, and PPARδ, respectively.…”