Discovery of 3-Cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist.

The nuclear hormone receptor retinoic acid receptor-related orphan C2 (RORC2, also known as RORγt) is a promising target for the treatment of autoimmune diseases. A small molecule, inverse agonist of the receptor is anticipated to reduce production of IL-17, a key proinflammatory cytokine. Through a high-throughput screening approach, we identified a molecule displaying promising binding affinity for RORC2, inhibition of IL-17 production in Th17 cells, and selectivity against the related RORA and RORB receptor isoforms. Lead optimization to improve the potency and metabolic stability of this hit focused on two key design strategies, namely, iterative optimization driven by increasing lipophilic efficiency and structure-guided conformational restriction to achieve optimal ground state energetics and maximize receptor residence time. This approach successfully identified 3-cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide as a potent and selective RORC2 inverse agonist, demonstrating good metabolic stability, oral bioavailability, and the ability to reduce IL-17 levels and skin inflammation in a preclinical in vivo animal model upon oral administration.

Development of subtype-selective oestrogen receptor-based therapeutics.

The two oestrogen receptor subtypes α and ß are hormone-regulated modulators of intracellular signalling and gene expression. Regulation of oestrogen receptor activity is crucial not only for development and homeostasis but also for the treatment of various diseases and symptoms. Classical selective oestrogen receptor modulators are well established in the treatment of breast cancer and osteoporosis, but emerging data suggest that the development of subtype-selective ligands that specifically target either oestrogen receptor-α or oestrogen receptor-ß could be a more optimal approach for the treatment of cancer, cardiovascular disease, multiple sclerosis and Alzheimer's disease.

Thyroid receptor ligands. 6. A high affinity "direct antagonist" selective for the thyroid hormone receptor.

A new high-affinity thyroid hormone antagonist 6 with druglike properties was designed and synthesized. The compound behaved as an antagonist in a cell transactivation assay, and in a first in vivo experiment in rats.

Virtual screening for aryl hydrocarbon receptor binding prediction.

The overall goal of this study has been to validate computational models for predicting aryl hydrocarbon receptor (AhR) binding. Due to the unavailability of the AhR X-ray crystal structure we have decided to use QSARs models for the binding prediction virtual screening. We have built up CoMFA, Volsurf, and HQSAR models using as a training set 84 AhR ligands. Additionally, we have built a hybrid model combining two of the final selected models in order to give a single operational system. The results show that CoMFA, VolSurf, HQSAR, and the hybrid models gives good results (R(2) equal to 0.91, 0.79, 0.85, and 0.82 and q(2) 0.62, 0.58, 0.62, and 0.70, respectively). Since the techniques analyzed show a good correlation and good prediction also for an external test set, particularly the HQSAR and the hybrid model, we can conclude that these models can be used for predicting AhR binding in virtual screening.

Thyroid receptor ligands. Part 5: novel bicyclic agonist ligands selective for the thyroid hormone receptor beta.

Based on the examination of the crystal structure of rat TRbeta complexed with 3,5,3'-triiodo-l-thyronine (2) a novel TRbeta-selective indole derivative 6b was prepared and tested in vitro. This compound was found to be 14 times selective for TRbeta over TRalpha in binding and its beta-selectivity could be rationalized through the comparison of the X-ray crystallographic structures of 6b complexed with TRalpha and TRbeta.

Thyroid receptor ligands. Part 4: 4'-amido bioisosteric ligands selective for the thyroid hormone receptor beta.

Based on the examination of the X-ray crystallographic structures of the LBD of TRalpha and TRbeta in complex with KB-141 (2), a number of novel 4'-hydroxy bioisosteric thyromimetics were prepared. Optimal affinity and beta-selectivity (33 times), was found with a medium-sized alkyl-substituted amido group; iso-butyl (12c). It can be concluded that bioisosteric replacements of the 4'-hydroxy position represent a new promising class of TRbeta-selective synthetic thyromimetics.

Solid-phase synthesis of a 6-phenylquinolin-2(1H)-one library directed toward nuclear hormone receptors.

A library of 6-phenylquinolin-2(1H)-ones with diversity at position 1 and the ortho, meta, and para positions of the pendant phenyl ring has been synthesized using solid-phase parallel synthetic techniques. A key step in the synthesis of the library is a tandem alkylation cleavage in which diversity can be introduced at position 1 simultaneously to the cleavage from the resin. The yields of this step were significantly improved over what has previously been reported by addition of cesium carbonate to scavenge the acid that is formed during the reaction. Furthermore, we have shown that the solid support linkage is tolerant to Suzuki coupling and etherification reaction conditions and that selective cleavage of the linkage can take place in the presence of esters. The resulting 6-phenylquinolin-2(1H)-one library was screened against a panel of nuclear hormone receptors (androgen, estrogen alpha and beta isoforms, glucocorticoid, mineralocorticoid, and progesterone). Certain members of this library display moderate affinity for several of these receptors, and consequently, the 6-phenylquinolin-2(1H)-one core of the library may be considered a privileged structure for nuclear hormone receptors. In contrast, other members of the library display high selectivity for a particular receptor. The highest affinity ligand (9{2,1,1}) possesses an affinity of 330 nM for the androgen receptor, whereas the most selective ligand (9{2,4,1}) displays an affinity of 900 nM for the androgen receptor and a selectivity of 140-fold over the next highest affinity receptor.

Mouse estrogen receptor beta isoforms exhibit differences in ligand selectivity and coactivator recruitment.

Estrogens exert their physiological effects through two estrogen receptor (ER) subtypes, ERalpha and ERbeta. In mouse, the cloning of an alternative splice variant of the wild-type ERbeta (mERbeta1), mERbeta2, which contains an 18 amino acid insertion in the ligand binding domain, contributed an additional level of complexity to estrogen signaling. In this study we have assayed the interaction of several known ligands with mERbeta1 and mERbeta2. The binding affinity of estradiol was 14-fold higher for mERbeta1 than for mERbeta2. In contrast, raloxifene was dramatically (8-fold) mERbeta2 selective. The selectivity for mERbeta2 was abolished when the 2-arylbenzothiophene core of the raloxifene molecule was tested for binding affinity, demonstrating that the 3-aroyl side chain of raloxifene plays an important role in contributing to its mERbeta2 selectivity. The opposite isoform selectivity found for estradiol and raloxifene in our ligand binding assay was also reflected in the transactivation assay system. That is, mERbeta2 required 10-fold greater estradiol concentrations for maximal activation compared to mERbeta1, whereas raloxifene was more potent in antagonizing estradiol-induced gene expression via mERbeta2 than mERbeta1. The raloxifene core behaved as a pure agonist. Furthermore, mERbeta2 showed significantly decreased estradiol-induced maximal transcriptional activity as compared to mERbeta1. A pull-down assay indicated that the interactions of TIF2 and RAP250 with mERbeta2 were weaker than with mERbeta1. To assess TIF2 and RAP250 interactions with ERs more quantitatively, we examined the interaction of LXXLL containing peptides derived from TIF2 and RAP250 with mERbeta1 and mERbeta2 using surface plasmon resonance analysis. Our results indicate that mERbeta2 interacts with both coactivators with lower affinity, which may explain its reduced transcriptional activity. Taken together, these results suggest that ligand selectivity and coactivator recruitment of the ERbeta isoforms constitute additional levels of specificity that influence the transcriptional response in estrogen target cells.

Reflections on the discovery and significance of estrogen receptor beta.

We have known for many years that estrogen is more than the female hormone. It is essential in the male gonads, and in both sexes, estrogen has functions in the skeleton and central nervous system, on behavior, and in the cardiovascular and immune systems. An important aspect of the discovery of estrogen receptor (ER) beta is that the diverse functions of estrogen can now be divided into those mediated by ERalpha and those mediated by ERbeta. Pharmacological exploitation of this division of the labors of estrogen is facilitated by the ligand-binding specificity and selective tissue distribution of the two ERs. Because the ligand binding domains of ERalpha and ERbeta are significantly different from each other, selective ligands can be (and have been) developed to target the estrogenic pathway that is malfunctioning, without interfering with the other estrogen-regulated pathways. Because of the absence of ERbeta from the adult pituitary and endometrium, ERbeta agonists can be used to target ERbeta with no risk of adverse effects from chemical castration and uterine cancer. Some of the diseases in which there is hope that ERbeta agonists will be of benefit are prostate cancer, autoimmune diseases, colon cancer, malignancies of the immune system, and neurodegeneration.

Thyroid receptor ligands. 3. Design and synthesis of 3,5-dihalo-4-alkoxyphenylalkanoic acids as indirect antagonists of the thyroid hormone receptor.

Based on the recently described concept of "indirect antagonism" of nuclear receptors, a series of thyroid hormone receptor (TR) antagonists were prepared, in which the outer ring of a thyromimetic was replaced with alkyl chains of variable length and branch. The results of a binding assay for the human TR and reporter cell assay revealed, within this series, a positive correlation between increasing bulk of the alkyl group and affinity to TRs. Compared with already reported TR antagonists, their affinities are within the same range, thus potentially representing a useful approach to novel and high affinity TR-antagonists.

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization.

Two-point mutations in the human glucocorticoid receptor have been studied by computer simulations to rationalize experimental data, where mutants comprising the V571M substitution improve both transcriptional activity and affinity for aldosterone despite large distances between the mutated residue and the coactivator-binding surface and ligand-binding pocket, respectively. Our molecular dynamics simulations show that the V571M mutation modifies the coactivator-binding site defined by helices 3, 4, and 12, and that specific structural rearrangement of the coactivator-binding site correlates well with transactivation data. A similar reorganization of the coactivator-binding cleft is observed in crystallographic structures of the estrogen receptor in the presence of coactivator peptide, compared with structures without peptide, indicating that induced fit for coactivator binding is a general phenomenon for nuclear receptors. These results suggest that the V571M substitution facilitates recruitment of coactivator protein by promotion of a conformational substate reducing the energetic penalty for the induced fit of the receptor-coactivator complex. Furthermore, our simulations of V571M mutants showed reduced fluctuations of residues lining the ligand-binding pocket. This indicates that a reduction of the entropic cost for ligand binding may explain the increased affinity of V571M mutants for certain ligands.

Oestrogen receptors and selective oestrogen receptor modulators: molecular and cellular pharmacology.

The early termination of the two arms of the Women's Health Initiative Trials has led to an increased interest and demand for selective oestrogen receptor modulators because of their potential to retain the benefits of hormone replacement therapy (oestrogen plus a gestagen) and at the same time avoid most of its severe adverse events. Selective oestrogen receptor modulators are a class of oestrogen receptor binding, small organic molecules that take advantage of the plasticity of the oestrogen receptors (alpha and beta, respectively), modulating the surface conformation of the oestrogen receptors upon binding in the respective ligand binding cavity. By doing so they affect the binding of various co-factors to the surface of the oestrogen receptors that, at least in part, explains why selective oestrogen receptor modulators may mimic the activity of oestrogen in some tissues where so desired, while opposing its activity in tissues where oestrogen-like activity is undesirable. Although selective oestrogen receptor modulators have many properties in common they also display unique activities including oestrogen receptor surface modulation and regulation of target gene expression. Selective oestrogen receptor modulators therefore offer the opportunity to develop pharmaceuticals with very distinct pharmacology and mechanism of action. Furthermore, these modulators offer the advantage of decreased risk for the development of breast and endometrial cancer and circumvent the need for combination with a gestagen. Most selective oestrogen receptor modulators in development bind with roughly equal affinity to both oestrogen receptor alpha and beta (balanced) and our view is that it is unlikely that a balanced selective oestrogen receptor modulator will inherit all desired effects of oestrogen (e.g. 17beta-oestradiol) and at the same time be devoid of all undesired effects. We therefore propose that the development of oestrogen receptor-subtype (alpha and beta, respectively) selective pharmaceuticals for specific applications (designer drugs) would better provide the benefits of hormone replacement therapy without its associated risks.

Liver-selective glucocorticoid antagonists: a novel treatment for type 2 diabetes.

Hepatic blockade of glucocorticoid receptors (GR) suppresses glucose production and thus decreases circulating glucose levels, but systemic glucocorticoid antagonism can produce adrenal insufficiency and other undesirable side effects. These hepatic and systemic responses might be dissected, leading to liver-selective pharmacology, when a GR antagonist is linked to a bile acid in an appropriate manner. Bile acid conjugation can be accomplished with a minimal loss of binding affinity for GR. The resultant conjugates remain potent in cell-based functional assays. A novel in vivo assay has been developed to simultaneously evaluate both hepatic and systemic GR blockade; this assay has been used to optimize the nature and site of the linker functionality, as well as the choice of the GR antagonist and the bile acid. This optimization led to the identification of A-348441, which reduces glucose levels and improves lipid profiles in an animal model of diabetes.

Identification of a functional variant of estrogen receptor beta in an African population.

In this study, we identified five novel polymorphisms in the estrogen receptor beta (ERbeta) gene in an African population. Interestingly, two of these variants are expected to change the amino acid sequence of the ERbeta protein. These changes correspond to an isoleucine to valine substitution at amino acid position 3 (I3V) and a valine to glycine substitution at position 320 (V320G), respectively. The functional consequences of these amino acid substitutions were determined in different in vitro assays. The I3V mutation displayed no differences with regard to transcriptional activity in a reporter assay, as compared with the wild-type receptor. The V320G mutation, however, showed significantly decreased maximal transcriptional activity in a reporter assay, although its binding affinity for 17beta-estradiol was not affected. A pull-down assay indicated that the interaction of full-length TIF2 with hERbetaV320G was weaker than with hERbetawt. Moreover, surface plasmon resonance analysis revealed reduced interaction of the V320G ERbeta variant with the NR box I and II modules of TIF2. To our knowledge, this represents the first identification of a functional polymorphism in the ERbeta gene. This novel polymorphism provides a tool for human genetic studies of diseases in the African population.

Thyroid receptor ligands. Part 2: Thyromimetics with improved selectivity for the thyroid hormone receptor beta.

A set of thyromimetics having improved selectivity for TR-beta1 were prepared by replacing the 3'-isopropyl group of 2 and 3 with substituents having increased steric bulk. From this limited SAR study, the most potent and selective compounds identified were derived from 2 and contained a 3'-phenyl moiety bearing small hydrophobic groups meta to the biphenyl link. X-ray crystal data of 15c complexed with TR-beta1 LBD shows methionine 442 to be displaced by the bulky R3' phenyl ethyl amide side chain. Movement of this amino acid side chain provides an expanded pocket for the bulky side chain while the ligand-receptor complex retains full agonist activity.

Thyroid receptor ligands. 1. Agonist ligands selective for the thyroid receptor beta1.

Endogenous thyroid receptor hormones 3,5,3',5'-tetraiodo-l-thyronine (T(4), 1) and 3,5,3'-triiodo-l-thyronine (T(3), 2) exert a significant effects on growth, development, and homeostasis in mammals. They regulate important genes in intestinal, skeletal, and cardiac muscles, the liver, and the central nervous system, influence overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood and overall sense of well being. The literature suggests many or most effects of thyroid hormones on the heart, in particular on the heart rate and rhythm, are mediated through the TRalpha(1) isoform, while most actions of the hormones on the liver and other tissues are mediated more through the TRbeta(1) isoform of the receptor. Some effects of thyroid hormones may be therapeutically useful in nonthyroid disorders if adverse effects can be minimized or eliminated. These potentially useful features include weight reduction for the treatment of obesity, cholesterol lowering for treating hyperlipidemia, amelioration of depression, and stimulation of bone formation in osteoporosis. Prior attempts to utilize thyroid hormones pharmacologically to treat these disorders have been limited by manifestations of hyperthyroidism and, in particular, cardiovascular toxicity. Consequently, development of thyroid hormone receptor agonists that are selective for the beta-isoform could lead to safe therapies for these common disorders while avoiding cardiotoxicity. We describe here the synthesis and evaluation of a series of novel TR ligands, which are selective for TRbeta(1) over TRalpha(1). These ligands could potentially be useful for treatment of various disorders as outlined above. From a series of homologous R(1)-substituted carboxylic acid derivatives, increasing chain length was found to have a profound effect on affinity and selectivity in a radioreceptor binding assay for the human thyroid hormone receptors alpha(1) and beta(1) (TRalpha(1) and TRbeta(2)) as well as a reporter cell assay employing CHOK1-cells (Chinese hamster ovary cells) stably transfected with hTRalpha(1) or hTRbeta(1) and an alkaline phosphatase reporter-gene downstream thyroid response element (TRAFalpha(1) and TRAFbeta(1)). Affinity increases in the order formic, acetic, and propionic acid, while beta-selectivity is highest when the R(1) position is substituted with acetic acid. Within this series 3,5-dibromo-4-[(4-hydroxy-3-isopropylphenoxy)phenyl]acetic acid (11a) and 3,5-dichloro-4-[(4-hydroxy-3-isopropylphenoxy)phenyl]acetic acid (15) were found to reveal the most promising in vitro data based on isoform selectivity and were selected for further in vivo studies. The effect of 2, 11a, and 15 in a cholesterol-fed rat model was monitored including potencies for heart rate (ED(15)), cholesterol (ED(50)), and TSH (ED(50)). Potency for tachycardia was significantly reduced for the TRbeta selective compounds 11a and 15 compared with 2, while both 11a and 15 retained the cholesterol-lowering potency of 2. This left an approximately 10-fold therapeutic window between heart rate and cholesterol, which is consistent with the action of ligands that are approximately 10-fold more selective for TRbeta(1). We also report the X-ray crystallographic structures of the ligand binding domains of TRalpha and TRbeta in complex with 15. These structures reveal that the single amino acid difference in the ligand binding pocket (Ser277 in TRalpha or Asn331 in TRbeta) results in a slightly different hydrogen bonding pattern that may explain the increased beta-selectivity of 15.

A designed P1 cysteine mimetic for covalent and non-covalent inhibitors of HCV NS3 protease.

The difluoromethyl group was designed by computational chemistry methods as a mimetic of the canonical P1 cysteine thiol for inhibitors of the hepatitis C virus NS3 protease. This modification led to the development of competitive, non-covalent inhibitor 4 (K(i) 30 nM) and reversible covalent inhibitors (6, K(i) 0.5 nM; and 8 K*(i) 10 pM).