Selective therapeutics for nuclear receptors would revolutionize treatment for endocrine disease. Specific control of nuclear receptor activity is challenging because the internal cavities that bind hormones can be virtually identical. Only one highly selective hormone analog is known for the thyroid receptor, GC-24, an agonist for human thyroid hormone receptor ␤. The compound differs from natural hormone in benzyl, substituting for an iodine atom in the 3 position. The benzyl is too large to fit into the enclosed pocket of the receptor. The crystal structure of human thyroid hormone receptor ␤ at 2.8-Å resolution with GC-24 bound explains its agonist activity and unique isoform specificity. The benzyl of GC-24 is accommodated through shifts of 3-4 Å in two helices. These helices are required for binding hormone and positioning the critical helix 12 at the C terminus. Despite these changes, the complex associates with coactivator as tightly as human thyroid hormone receptor bound to thyroid hormone and is fully active. Our data suggest that increased specificity of ligand recognition derives from creating a new hydrophobic cluster with ligand and protein components.A ll metazoan life depends on transcription control by the family of nuclear receptors. Nuclear receptors regulate development and differentiation as well as metabolism and physiology, and their dysfunction contributes to disorders such as diabetes, obesity, cardiovascular disease, and cancer (1). Synthetic hormone analogs have therapeutic potential for altering the function of many nuclear receptors, provided that they are receptor and isoform selective. Agonist ligands of peroxisome proliferator-activated receptor ␥ are currently used to treat type II diabetes (2-4). Estrogen analogs called selective estrogen receptor modulators that selectively block or activate estrogen receptor isoforms are applied in the therapy of breast cancer and osteoporosis (5, 6).Although investigations on structure-function relationships show that nuclear receptors possess unique features in regulation, their three-dimensional structures are similar. The ligandbinding domain (LBD) binds hormone and is interdependent on other domains that bind to DNA and coregulators or respond to posttranslational modifications (7). Within the LBD, the critically placed C-terminal helix 12 changes its position and binding surface in an allosteric response to hormone binding (8). The function of this conformational change is to shape the surface for binding of coregulators (9, 10). The coactivator complex attracts further cofactors, which are required for activation of the transcription of target genes (11, 12). The shape and size of the hormone-binding pocket, usually completely buried inside the protein, place severe restrictions on the design of ligands. Any subtle changes in the chemical structure of the hormone might alter the position of helix 12 and so determine the fate of the receptor as repressed or activated.The synthesis and evaluation of ligands for thyroid hormone receptor (...

Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPARγ ligand binding domain (LBD) and found that the ligand binding pocket (LBP) is occupied by bacterial medium chain fatty acids (MCFAs). We verified that MCFAs (C8–C10) bind the PPARγ LBD in vitro and showed that they are low-potency partial agonists that display assay-specific actions relative to TZDs; they act as very weak partial agonists in transfections with PPARγ LBD, stronger partial agonists with full length PPARγ and exhibit full blockade of PPARγ phosphorylation by cyclin-dependent kinase 5 (cdk5), linked to reversal of adipose tissue insulin resistance. MCFAs that bind PPARγ also antagonize TZD-dependent adipogenesis in vitro. X-ray structure B-factor analysis and molecular dynamics (MD) simulations suggest that MCFAs weakly stabilize C-terminal activation helix (H) 12 relative to TZDs and this effect is highly dependent on chain length. By contrast, MCFAs preferentially stabilize the H2-H3/β-sheet region and the helix (H) 11-H12 loop relative to TZDs and we propose that MCFA assay-specific actions are linked to their unique binding mode and suggest that it may be possible to identify selective PPARγ modulators with useful clinical profiles among natural products.

Background: PPARγ agonists improve insulin sensitivity but also evoke weight gain.Results: GQ-16 is a PPARγ partial agonist that blocks receptor phosphorylation by Cdk5 and improves insulin sensitivity in diabetic mice in the absence of weight gain.Conclusion: The unique binding mode of GQ-16 appears to be responsible for the compound's advantageous pharmacological profile.Significance: Similar compounds could have promise as anti-diabetic therapeutics.

Thyroid hormone (TH) actions are mediated by nuclear receptors (TRs ␣ and ␤) that bind triiodothyronine (T 3 , 3,5,3-triiodo-L-thyronine) with high affinity, and its precursor thyroxine (T 4 , 3,5,3,5-tetraiodo-L-thyronine) with lower affinity. T 4 contains a bulky 5 iodine group absent from T 3 . Because T 3 is buried in the core of the ligand binding domain (LBD), we have predicted that TH analogues with 5 substituents should fit poorly into the ligand binding pocket and perhaps behave as antagonists. We therefore examined how T 4 affects TR activity and conformation. We obtained several lines of evidence (ligand dissociation kinetics, migration on hydrophobic interaction columns, and non-denaturing gels) that TR-T 4 complexes adopt a conformation that differs from TR-T 3 complexes in solution. Nonetheless, T 4 behaves as an agonist in vitro (in effects on coregulator and DNA binding) and in cells, when conversion to T 3 does not contribute to agonist activity. We determined x-ray crystal structures of the TR␤ LBD in complex with T 3 and T 4 at 2.5-Å and 3.1-Å resolution. Comparison of the structures reveals that TR␤ accommodates T 4 through subtle alterations in the loop connecting helices 11 and 12 and amino acid side chains in the pocket, which, together, enlarge a niche that permits helix 12 to pack over the 5 iodine and complete the coactivator binding surface. While T 3 is the major active TH, our results suggest that T 4 could activate nuclear TRs at appropriate concentrations. The ability of TR to adapt to the 5 extension should be considered in TR ligand design. Thyroid hormone (TH)1 plays important regulatory roles in metabolism, homeostasis, and development by binding and altering the transcriptional regulatory properties of two related nuclear receptors (NRs), the thyroid hormone receptors (TRs) ␣ and ␤ (1, 2). Most TH produced in the thyroid gland is secreted in the form of thyroxine (T 4 ; 3,5,3Ј,5Ј-tetraiodo-L-thyronine) (2, 3). The thyroid gland also produces smaller amounts of triiodothyronine (T 3 ; 3,5,3Ј-triiodo-L-thyronine) and reverse T 3 (rT 3 ; 3,3Ј,5Ј-triiodo-L-thyronine), and 80% of T 4 is converted to T 3 and rT 3 in peripheral tissues by two selenium deiodinases, which are tissue-specific (4). Current beliefs are that T 3 is the dominant active form of TH; T 3 binds the TRs with an affinity about 20 -30 times higher than that of T 4 (5-9), and some studies suggest that T 3 is present at higher concentrations in the nucleus than T 4 (10, 11). Nonetheless, the question of whether T 4 is simply a prohormone or an active TH species is not completely resolved. T 4 exerts rapid nongenomic effects at several loci distinct from TRs (12). Moreover, saturating levels of T 4 activate transcription of TH-responsive genes in cell culture (see for example Ref. 5). Whereas it is possible that at least some of this activity is due to T 3 generated from T 4 in the cell, these results suggest that T 4 may act as a TR agonist. Normal concentrations of plasma-free T 4 are about 4 -6-fold higher than th...

Thyroid hormone (3,5,3-triiodo-L-thyronine, T3) is an endocrine hormone that exerts homeostatic regulation of basal metabolic rate, heart rate and contractility, fat deposition, and other phenomena (1, 2). T3 binds to the thyroid hormone receptors (TRs) and controls their regulation of transcription of target genes. The binding of TRs to thyroid hormone induces a conformational change in TRs that regulates the composition of the transcriptional regulatory complex. Recruitment of the correct coregulators (CoR) is important for successful gene regulation. In principle, inhibition of the TR-CoR interaction can have a direct influence on gene transcription in the presence of thyroid hormones. Herein we report a high throughput screen for small molecules capable of inhibiting TR coactivator interactions. One class of inhibitors identified in this screen was aromatic ␤-aminoketones, which exhibited IC 50 values of ϳ2 M. These compounds can undergo a deamination, generating unsaturated ketones capable of reacting with nucleophilic amino acids. Several experiments confirm the hypothesis that these inhibitors are covalently bound to TR. Optimization of these compounds produced leads that inhibited the TR-CoR interaction in vitro with potency of ϳ0.6 M and thyroid signaling in cellular systems. These are the first small molecules irreversibly inhibiting the coactivator binding of a nuclear receptor and suppressing its transcriptional activity. Thyroid hormone receptors (TRs)3 regulate development, growth, and metabolism (1, 2). The TRs are nuclear receptors (NR), part of a superfamily whose members function as hormone-activated transcription factors (3). The majority of thyroid hormone responses are induced by regulation of transcription by the thyroid hormone T3 (4). Two genes, THRA and THRB encode the two protein isoforms TR␣ and TR␤, which yield four distinct subtypes by alternative splicing (5). Several functional domains of TRs have been identified: a ligand-independent transactivation domain (AF-1) on the amino terminus, a central DNA binding domain, a ligand binding domain (LBD), and a carboxylterminal ligand dependent activation function (AF-2) (6). TR binds specific sequences of DNA in the 5Ј-flanking regions of T3-responsive genes, known as thyroid response elements, most often as a heterodimer with the retinoid X receptor (7). Both unliganded and liganded TRs can bind thyroid response elements and regulate genes under their control. The unliganded TR complex can recruit a nuclear receptor corepressor (NCoR) or a silencing mediator of retinoic acid to silence basal transcription (8). In the presence of T3, TRs undergo a conformational change with the result that the composition of the coregulator complex can change with strong effects on transcriptional regulation. Several coactivator proteins have been identified (9). The best studied group of coactivators is the p160 or steroid receptor coactivator (SRC) proteins (7) including SRC1 (10), SRC2 (11,12), and SRC3 (13). Another group of ligand-dependent-interactin...