Structural determinants of ligand binding selectivity between the peroxisome proliferator- activated receptors H. Eric Xu*, Millard H. Lambert†, Valerie G. Montana, Kelli D. Plunket, Linda B. Moore, Jon L. Collins, Jeffery A. Oplinger, Steven A. Kliewer, Robert T. Gampe, Jr., David D. McKee, John T. Moore, and Timothy M. Willson‡ Nuclear Receptor Discovery Research, GlaxoSmithKline, Research Triangle Park, NC 27709 Edited by Michael G. Rosenfeld, University of California at San Diego, La Jolla, CA, and approved September 27, 2001 (received for review August 3, 2001) The peroxisome proliferator-activated receptors (PPARs) are tran- to an even wider range of FAs than either PPAR␥ or PPAR␦ scriptional regulators of glucose, lipid, and cholesterol metabolism. (10). However, no structure of the PPAR␣ LBD has been We report the x-ray crystal structure of the ligand binding domain available to explain these differences in ligand binding proper- of PPAR␣ (NR1C1) as a complex with the agonist ligand GW409544 ties. We now report the structure of the PPAR␣ LBD and the and a coactivator motif from the steroid receptor coactivator 1. identification of key determinants of ligand binding selectivity Through comparison of the crystal structures of the ligand binding between the three PPAR subtypes. domains of the three human PPARs, we have identified molecular determinants of subtype selectivity. A single amino acid, which is Materials and Methods tyrosine in PPAR␣ and histidine in PPAR␥, imparts subtype selec- Reagents and Assays. Rosiglitazone, pioglitazone, and farglitazar tivity for both thiazolidinedione and nonthiazolidinedione ligands. were synthesized as described (11). The synthesis of GW409544 The availability of high-resolution cocrystal structures of the three will be described elsewhere. Expression plasmids for the human PPAR subtypes will aid the design of drugs for the treatments of PPAR-GAL4 chimeras were prepared by inserting amplified metabolic and cardiovascular diseases. cDNAs encoding the LBDs into a modified pSG5 expression vector (Stratagene) containing the GAL4 DNA binding domain eroxisome proliferator-activated receptor (PPAR) ␣ (amino acids 1–147) and the simian virus 40 large T antigen P(NR1C1), PPAR␥ (NR1C3), and PPAR␦ (NR1C2) are nuclear localization signal (APKKKRKVG). For generation of members of the nuclear receptor family of ligand-activated the Y314H PPAR␣ mutant, the Tyr-314 codon (TAT nucleotide transcription factors that bind to fatty acids (FAs) and their sequence) was altered to a His codon (CAT) by Quick-Change metabolites (1). Although the PPARs were originally cloned as Mutagenesis (Stratagene). For generation of the H323Y PPAR␥ orphan receptors, their role in mammalian physiology has been mutant the His-323 codon (CAC) was altered to a Tyr codon uncovered through a process of reverse endocrinology (2) using (TAC). Cell-based reporter assays were performed by transient ␣ transfection in CV-1 cells using (UAS)5-tk-SPAP reporter con- high-affinity synthetic ligands as chemical tools. PPAR is the MEDICAL SCIENCES receptor for the fibrate class of lipid-lowering drugs (3), and structs as described (11). Transfections were performed using PPAR␥ is the receptor for the thiazolidinedione (TZD) class of Lipofectamine (Life Technologies, Grand Island, NY) according antidiabetic drugs (4). Recently, the function of PPAR␦ in the to the manufacturer’s instructions. A ␤-galactosidase expression regulation of reverse cholesterol transport and high-density plasmid was included in each transfection for use as a normal- lipoprotein metabolism was revealed through the use of a potent ization control. PPAR␦ agonist, GW501516 (5). Thus, the PPARs are FA- activated receptors that function as key regulators of glucose, Protein Expression. The human PPAR␣ LBD (amino acids 192– lipid, and cholesterol metabolism. 468 of GenBank No. S74349) tagged with MKKGHHHHHHG The marketed TZDs rosiglitazone and pioglitazone are effec- was expressed from the T7 promoter of plasmid vector pRSETA. tive glucose-lowering drugs that produce modest effects on lipids Bacterial cells (BL21DE3) transformed with this expression in patients with type 2 diabetes (1). Most diabetic patients have vector were grown at 24°C in 2YT broth with 50 mg͞liter Ϸ an abnormal lipid profile, including low levels of high density carbenicillin in shaker flasks to an OD600 of 5.0. Cells were lipoprotein and high levels of triglycerides, which may contribute harvested, resuspended with 20 ml of extract buffer (20 mM to their greatly increased burden of cardiovascular disease. Hepes, pH 7.5͞50 mM imidazole͞250 mM NaCl, and a trace of There is a resurgence of interest in the development of new lysozyme) per liter of cells and sonicated for 20 min on ice. The antidiabetic drugs that combine the insulin-sensitizing effects of lysed cells were centrifuged at 40,000 ϫ g for 40 min, and the PPAR␥ activation with the additional lipid-modifying activity of supernatant was loaded on a 100-ml Ni-agarose column. The the other PPAR subtypes. For example, the L-tyrosine analogue farglitazar (GI262570) has robust effects on glucose, high- density lipoprotein, and triglycerides in diabetic patients (6). The This paper was submitted directly (Track II) to the PNAS office. triglyceride-lowering activity of farglitazar may be a result of its Abbreviations: PPAR, peroxisome proliferator-activated receptor; TZD, thiazolidinedione; activity on PPAR␣. Although farglitazar is 1,000 times less LBD, ligand binding domain; FA, fatty acid; SRC1, steroid receptor coactivator 1. ␣ Data deposition: The atomic coordinates and structure factors have been deposited in the potent on PPAR , its peak plasma levels are above the EC50 for activation of this subtype (1, 6). Additional insight into the Protein Data Bank, www.rcsb.org (PDB ID codes 1K7L and 1K74). molecular determinants of PPAR subtype selectivity may have *To whom correspondence on the structure determination and requests for materials should be addressed. E-mail: [email protected]. important applications in the design of new diabetes drugs. ␥ ␦ †To whom correspondence on molecular modeling should be addresssed. E-mail: X-ray crystal structures of the PPAR and PPAR ligand [email protected]. binding domains (LBDs) revealed that the receptors contain a ‡To whom additional correspondence and reprint requests should be addressed. E-mail: much larger ligand binding pocket than other nuclear receptors [email protected]. (7–10). The size of this pocket may explain the ability of the The publication costs of this article were defrayed in part by page charge payment. This PPARs to bind a variety of naturally occurring and synthetic article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. lipophilic acids. Remarkably, PPAR␣ has been reported to bind §1734 solely to indicate this fact. www.pnas.org͞cgi͞doi͞10.1073͞pnas.241410198 PNAS ͉ November 20, 2001 ͉ vol. 98 ͉ no. 24 ͉ 13919–13924 Downloaded by guest on October 2, 2021 column was washed with 150 ml of buffer A (10% glycerol͞20 Table 1. Statistics of crystallographic data and structures mM Hepes, pH 7.5͞25 mM imidazole), and the protein was ␣͞ ␥͞ ␣͞ ͞ PPAR SRC1 PPAR RXR SRC1 eluted with a 450-ml gradient to buffer B (10% glycerol 20 mM Crystals with GW409544 with GW409544 Hepes, pH 7.5͞500 mM imidazole). The protein, which eluted at 20% buffer B, was diluted with 1 vol of buffer C (20 mM Hepes, Space group P212121 P212121 pH 7.5͞1 mM EDTA) and loaded on a 100-ml S-Sepharose Resolution, Å 20.0–2.5 20.0–2.3 column. The column was washed with a 100-ml buffer C, and the Unique reflections, N 49,991 24,986 PPAR␣ LBD was eluted with a 200-ml gradient to buffer D (20 Completeness, % 99.9 97.3 mM Hepes, pH 7.5͞10 mM DTT͞1 M ammonium acetate). The I͞␴ (last shell) 48.3 (5.7) 28.9 (3.3) PPAR␣ LBD was eluted from the column at 43% buffer D, Rsym*, % 5.4 5.7 which yielded 9 mg of protein per liter of cells, and was Ͼ95% Refinement statistics pure as determined by SDS͞PAGE analysis. The protein was R factor†,% 24.7 23.8 then diluted to 1 mg͞ml with buffer C such that the final buffer R free, % 28.5 27.9 composition was 220 mM ammonium acetate͞20 mM Hepes, pH rmsd‡ bond lengths, Å 0.012 0.011 7.5͞1 mM EDTA͞1 mM DTT. The diluted protein was ali- rmsd bond angles, ° 1.550 1.515 quoted, frozen, and stored at Ϫ80°C. The protein–ligand com- Total nonhydrogen atoms 9312 4408 plexes were prepared by adding 5-fold excess of GW409544 and *Rsym ϭ͚͉Iavg Ϫ Ii͉͚͞Ii. a 2-fold excess of a peptide from the steroid receptor coactivator † Rfactor ϭ͚͉FP Ϫ FPcalc͉͚͞Fp, where Fp and Fpcalc are observed and calculated 1 (SRC1) containing the sequence HSSLTERHKILHR- structure factors, Rfree is calculated from a randomly chosen 10% of reflec- LLQEGSPS (LxxLL motif underlined) and were concentrated to tions excluded from the refinement, and Rfactor is calculated for the remaining 10 mg͞ml. The PPAR␥͞RXR␣ heterodimer complex with 90% of reflections. GW409544 and 9-cis-retinoic acid was prepared as reported (9). ‡rmsd, the rms deviation from ideal geometry. Crystallization and Data Collection. The PPAR␣͞GW409544͞ SRC1 crystals were grown at room temperature in hanging drops lished results). GW409544 contains a vinylogous amide as the containing 1 ␮l of the protein–ligand solution and 1 ␮l of well L-tyrosine N-substituent, which contains three fewer carbon buffer (50 mM bis-Tris-propane, pH 7.5͞4–6% PEG 3350͞150 atoms than the benzophenone found in farglitazar. Aside from mM NaNO ͞16% 2,5-hexanediol͞1–3mMYCl). Before data this difference, the chemical structures of the compounds are 3 3 ␣ ϭ collection, crystals were transiently mixed with the well buffer identical. GW409544 activates PPAR with EC50 2.3 nM and ␥ ϭ ␦ that contained an additional 10% hexanediol and then were PPAR with EC50 0.28 nM, but shows no activation of PPAR ␮ flash-frozen in liquid nitrogen.