Synthesis and biological activity of a novel series of indole-derived PPARgamma agonists

Benzosuberene-sulfone analogues synthesis from Cedrus deodara oil and their therapeutic evaluation by computational analysis to treat type 2 diabetes

Benzosuberene-sulfone (BSS) analogues have been semi-synthesized following green approaches from himachalenes, which has been extracted from essential oil of Cedrus deodara. In this process, benzosuberene in presence of different aryl or alkyl sodium sulfinates, I₂ and potassium persulfate (K₂S₂O₈) in acetonitrile-water solvent conditions gave BSS-analogues at room temperature. Under this reaction, a facile endocyclic β-H elimination has been noticed for BSS-analogues synthesis instead of vinyl sulfones and the reason may be due to its specific structure and electronic environment. The BSS-compounds were obtained with moderate to excellent yields under mild conditions. All the compounds were computationally subjected to drug likeliness and toxicity prediction studies. Further, the synthesized molecules were evaluated under in-silico studies for their binding affinity towards the native Peroxisome Proliferator-Activated Receptor Gamma (PPARG), and two PPARG mutants (R357A and V290M). Both the mutant forms of PPARG are deficient in eliciting a response to treatment with full and partial agonists. Our computational studies suggested that the molecule 3q performed better than the standard drug (Rosiglitazone) in all three protein structures. This implies that our suggested molecule could act as a more potent antagonist to native PPARG and could also be developed to treat type-2 diabetes patients with R357A and V290M mutations, which didn't elicit any response to currently available drugs in the market.

Identification of a Novel PPAR-γ Agonist through a Scaffold Tuning Approach

Peroxisome proliferator-activated receptors (PPARs) are important targets in metabolic diseases including obesity, metabolic syndrome, diabetes, and non-alcoholic fatty liver disease. Recently, they have been highlighted as attractive targets for the treatment of cardiovascular diseases and chronic myeloid leukemia. The PPAR agonist structure is consists of a polar head, a hydrophobic tail, and a linker. Each part interacts with PPARs through hydrogen bonds or hydrophobic interactions to stabilize target protein conformation, thus increasing its activity. Acidic head is essential for PPAR agonist activity. The aromatic linker plays an important role in making hydrophobic interactions with PPAR as well as adjusting the head-to-tail distance and conformation of the whole molecule. By tuning the scaffold of compound, the whole molecule could fit into the ligand-binding domain to achieve proper binding mode. We modified indol-3-ylacetic acid scaffold to (indol-1-ylmethyl)benzoic acid, whereas 2,4-dichloroanilide was fixed as the hydrophobic tail. We designed, synthesized, and assayed the in vitro activity of novel indole compounds with (indol-1-ylmethyl)benzoic acid scaffold. Compound 12 was a more potent PPAR-γ agonist than pioglitazone and our previous hit compound. Molecular docking studies may suggest the binding between compound 12 and PPAR-γ, rationalizing its high activity.

Design, synthesis, and biological evaluation of a series of alkoxy-3-indolylacetic acids as peroxisome proliferator-activated receptor γ/δ agonists

A series of alkoxy-3-indolylacetic acid analogs has been discovered as peroxisome proliferator-activated receptor (PPAR) agonists. Structure-activity relationship study indicated that PPARα/γ/δ activities were dependent on the nature of the hydrophobic group, the attachment position of the alkoxy linker to the indole ring, and N-alkylation of indole nitrogen. Some compounds presented significant PPARγ/δ activity and molecular modeling suggested their putative binding modes in the ligand binding domain of PPARγ. Of these, compound 51 was selected for in vivo study via an evaluation of microsomal stability in mouse and human liver. Compound 51 lowered the levels of fasting blood glucose, insulin, and HbA1c without gain in body weight in db/db mice. When compound 51 was treated, hepatic triglycerides level and the size of adipocytes in white adipose tissue of db/db mice were also reduced as opposed to treatment with rosiglitazone. Taken together, compound 51 shows high potential warranting further studies in models for diabetes and related metabolic disorders and may be in use as a chemical tool for the understanding of PPAR biology.

A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding

BACKGROUND

A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation.

RESULTS

A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding.

CONCLUSIONS

The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.

Synthesis and biological activities of novel indole derivatives as potent and selective PPARgamma modulators

Starting from the structure of Telmisartan, a new series of potent and selective PPARgamma modulators was identified. The synthesis, in vitro and in vivo evaluation of the most potent compounds are reported and the X-ray structure of compound 7b bound to the PPARgamma ligand binding domain is described.

Thiazolidinediones and the preservation of beta-cell function, cellular proliferation and apoptosis

The thiazolidinediones (TZDs) or glitazones are pharmaceutical agents that have profound effects on energy expenditure and conservation. They also exert significant anti-inflammatory effects and influence cell proliferation and cell death. The drugs are primarily used in clinical practice in the treatment of patients with type 2 diabetes mellitus, a disorder of insulin resistance that occurs when the pancreatic beta-cells are unable to produce adequate amounts of insulin to maintain euglycaemia. Loss of pancreatic beta-cell function in type 2 diabetes is progressive and often precedes overt diabetes by 10 years or more, as was shown by the United Kingdom Prospective Diabetes Study. Any therapeutic or preventive approach that would limit or reverse loss of beta-cell function in diabetes would have profound effects on the morbidity associated with this widespread disease. Evidence suggesting a potential role of TZDs in preserving beta-cell function in type 2 diabetes as well as the ability of these agents to exert anti-inflammatory and proapoptotic anticancer effects, and their ability to promote cellular proliferation in various organs is reviewed.

A potent indole-3-carbinol derived antitumor agent with pleiotropic effects on multiple signaling pathways in prostate cancer cells

Indole-3-carbinol has emerged as a promising chemopreventive agent due to its in vivo efficacy in various animal models. However, indole-3-carbinol exhibits weak antiproliferative potency and is unstable in acidic milieu. Thus, this study was aimed at exploiting indole-3-carbinol to develop potent antitumor agents with improved chemical stability. This effort culminated in OSU-A9 {[1-(4-chloro-3-nitrobenzenesulfonyl)-1H-indol-3-yl]-methanol}, which is resistant to acid-catalyzed condensation, and exhibits 100-fold higher apoptosis-inducing activity than the parent compound. Relative to indole-3-carbinol, OSU-A9 displays a striking qualitative similarity in its effects on the phosphorylation or expression of multiple signaling targets, including Akt, mitogen-activated protein kinases, Bcl-2 family members, survivin, nuclear factor-kappaB, cyclin D1, p21, and p27. The ability of OSU-A9 to concurrently modulate this broad range of signaling targets underscores its in vitro and in vivo efficacy in prostate cancer cells. Nevertheless, despite this complex mode of mechanism, normal prostate epithelial cells were less susceptible to the antiproliferative effect of OSU-A9 than PC-3 and LNCaP prostate cancer cells. Treatment of athymic nude mice bearing established s.c. PC-3 xenograft tumors with OSU-A9 at 10 and 25 mg/kg i.p. for 42 days resulted in a 65% and 85%, respectively, suppression of tumor growth. Western blot analysis of representative biomarkers in tumor lysates revealed significant reductions in the intratumoral levels of phosphorylated (p-) Akt, Bcl-xL, and RelA, accompanied by robust increases in p-p38 levels. In conclusion, the ability of OSU-A9 to target multiple aspects of cancer cell survival with high potency suggests its clinical value in prostate cancer therapy.

Design and synthesis of novel N-sulfonyl-2-indole carboxamides as potent PPAR-γ binding agents with potential application to the treatment of osteoporosis

The synthesis and structure-activity relationships of a novel series of N-sulfonyl-2-indole carboxamides that bind to peroxisome proliferator-activated receptor gamma (PPAR-gamma) are reported. Chemical optimization of the series led to the identification of 4q (IC(50)=50 nM) as a potent binding agent of PPAR-gamma. Also reported is preliminary cell based data suggesting the use of these compounds in the treatment of osteoporosis.

Structure-based de novo design, synthesis, and biological evaluation of the indole-based PPARγ ligands (I)

MCSS and LeapFrog, two de novo drug design programs, were used for the novel indole-based PPARgamma ligands' study. The designed compounds were synthesized and tested for the PPARgamma protein binding activities in vitro. Out of the compounds that were synthesized, two molecules (compounds 14d and 7d) possessed potent PPARgamma protein binding activity close to rosiglitazone in vitro.

Structure-based design of indole propionic acids as novel PPARα/γ co-agonists

In the quest for novel PPARalpha/gamma co-agonists as putative drugs for the treatment of type 2 diabetes and dyslipidemia, we have used a structure-based design approach to identify propionic acids with a 1,5-disubstituted indole scaffold as potent PPARalpha/gamma activators. Compounds 13, 24, and 28 are examples of submicromolar dual agonists with different alpha/gamma EC50 ratios that are selective against the delta-isoform. Analysis of the X-ray complex structure of PPARgamma with the indole propionic acid 13 provides a rationalization for some of the observed SAR.

2D QSAR of PPARγ agonist binding and transactivation

Multilinear QSAR models are developed for the largest and most diverse set of PPARgamma agonists treated hitherto. Binding of these small molecules to the human nuclear receptor PPARgamma is described by models that are built on simple 2D molecular descriptors and nevertheless are of good quality and predictive power (e.g., 144 compounds, 10 descriptors, r2=0.79, r2(cv)=0.76). The models presented are thoroughly validated by crossvalidation, randomization experiments, bootstrapping, and training set/test set partitioning. They may therefore be helpful in the design of new antidiabetic drug candidates. For gene transactivation, the functional activity of the agonists, a corresponding model for a similarly diverse compound set is of somewhat lower statistical quality.

Novel Indole-Based Peroxisome Proliferator-Activated Receptor Agonists: Design, SAR, Structural Biology, and Biological Activities

The synthesis and structure-activity relationship studies of novel indole derivatives as peroxisome proliferator-activated receptor (PPAR) agonists are reported. Indole, a drug-like scaffold, was studied as a core skeleton for the acidic head part of PPAR agonists. The structural features (acidic head, substitution on indole, and linker) were optimized first, by keeping benzisoxazole as the tail part, based on binding and functional activity at PPARgamma protein. The variations in the tail part, by introducing various heteroaromatic ring systems, were then studied. In vitro evaluation led to identification of a novel series of indole compounds with a benzisoxazole tail as potent PPAR agonists with the lead compound 14 (BPR1H036) displaying an excellent pharmacokinetic profile in BALB/c mice and an efficacious glucose lowering activity in KKA(y) mice. Structural biology studies of 14 showed that the indole ring contributes strong hydrophobic interactions with PPARgamma and could be an important moiety for the binding to the protein.

Benzoyl 2-methyl indoles as selective PPARγ modulators

Routine screening for human PPAR ligands yielded compounds 1 and 2, both of which were sub-micromolar hPPARgamma agonists. Synthetic modifications of these leads led to a series of potent substituted 3-benzyl-2-methyl indoles, a subset of which were noted to be selective PPARgamma modulators (SPPARgammaMs). SPPARgammaM 24 displayed robust anti-diabetic activity with an improved therapeutic window in comparison to a PPARgamma full agonist in a rodent efficacy model.

2-Alkoxydihydrocinnamates as PPAR agonists. Activity modulation by the incorporation of phenoxy substituents

Herein we describe a series of potent and selective PPARgamma agonists with moderate PPARalpha affinity and little to no affinity for other nuclear receptors. In vivo studies in a NIDDM animal model (ZDF rat) showed that these compounds are efficacious at low doses in glucose normalization and plasma triglyceride reduction. Compound 1b (LY519818) was selected from our SAR studies to be advanced to clinical evaluation for the treatment of type II diabetes.

A new class of peroxisome proliferator-activated receptor γ (PPARγ) agonists that inhibit growth of breast cancer cells: 1,1-Bis(3′-indolyl)-1-(p-substituted phenyl)methanes

1,1-Bis(3′-indolyl)-1-(p-trifluoromethylphenyl)methane (DIM-C-pPhCF3) and several p-substituted phenyl analogues have been investigated as a new class of peroxisome proliferator-activated receptor γ (PPARγ) agonists. Structure-activity studies in PPARγ-dependent transactivation assays in MCF-7 breast cancer cells show that 5–20 μm concentrations of compounds containing p-trifluoromethyl, t-butyl, cyano, dimethylamino, and phenyl groups were active, whereas p-methyl, hydrogen, methoxy, hydroxyl, or halogen groups were inactive as PPARγ agonists. Induction of PPARγ-dependent transactivation by 15-deoxy-Δ12,14-prostaglandin J2 (PGJ2) and DIM-C-pPhCF3 was inhibited in MCF-7 cells cotreated with the PPARγ-specific antagonist N-(4′-aminopyridyl)-2-chloro-5-nitrobenzamide. In mammalian two-hybrid assays, DIM-C-pPhCF3 and PGJ2 (5–20 μm) induced interactions of PPARγ with steroid receptor coactivator (SRC) 1, SRC2 (TIFII), and thyroid hormone receptor-associated protein 220 but not with SRC3 (AIB1). In contrast, DIM-C-pPhCF3, but not PGJ2, induced interactions of PPARγ with PPARγ coactivator-1. C-substituted diindolylmethanes inhibit carcinogen-induced rat mammary tumor growth, induce differentiation in 3T3-L1 preadipocytes, inhibit MCF-7 cell growth and G0/G1-S phase progression, induce apoptosis, and down-regulate cyclin D1 protein and estrogen receptor α in breast cancer cells. These compounds are a novel class of synthetic PPARγ agonists that induce responses in MCF-7 cells similar to those observed for PGJ2.

Eigenvalue Analysis of Peroxisome Proliferator-Activated Receptor γ Agonists

Eigenvalue analysis (EVA) was conducted on a series of potent agonists of peroxisome proliferator-activated receptor gamma (PPARgamma). Predictive EVA quantitative structure-activity relationship (QSAR) models were established using the SYBYL package, which had conventional r2 and cross-validated coefficient (q2) values up to 0.920 and 0.587 for the AM1 method and 0.863 and 0.586 for the PM3 method, respectively. These models were validated by a test set containing 18 compounds. The capability to predict by these two models for PPARgamma agonists, with the best predictive r2pred value of 0.614 for AM1 and 0.822 for PM3 methods, set a successful example for applying a similar approach in building QSAR models for PPARalpha and -delta that could potentially offer a new opportunity in the design of novel PPAR modulators.

Therapeutic role of peroxisome proliferator-activated receptors in obesity, diabetes and inflammation

Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor family and play a significant role in regulation of lipid metabolism, hepatic peroxisomal enzyme expression, insulin sensitivity and glucose homeostasis. PPARs have been classified into three subtypes encoded by different genes: PPARalpha (NR1C1), PPARdelta (NR1C2), and PPARgamma (NR1C3). Each subtype of PPARs appears to be differently expressed in a tissue-specific manner because of their binding to specific consensus DNA sequences, known as PPREs (peroxisome proliferator response elements). Thus, PPARs have emerged as potential molecular targets for the design and synthesis of a different class of compounds, considering the conformation of receptors for the treatment of human metabolic disorders. This review covers the rapid progress made in functional analysis of PPARs and progress made towards the identification of ligands for each subtype receptor.

Peroxisome proliferator-activated receptor gamma (PPARgamma) and its ligands: a review

Peroxisome proliferator-activated receptor gamma (PPARgamma) is a member of a class of nuclear hormone receptors intimately involved in the regulation of expression of myriad genes that regulate energy metabolism, cell differentiation, apoptosis and inflammation. Although originally discovered as a pivotal regulator of adipocyte differentiation, the roles that this transcription factor play in physiology and pathophysiology continue to grow as researchers discover its influence in the function of many cell types. This review highlights the roles that PPARgamma play in the regulation of gene expression associated with normal cell physiology as well as the pathophysiology of multiple diseases including obesity, diabetes and cancer. Additionally, naturally occurring and pharmaceutical ligands for the receptor as well as the potential role of PPARgamma as the receptor responsible for fatty acid-induced effects on gene expression will be described.

Peroxisome proliferator-activated receptors

An exciting and rapidly evolving area in vascular biology and atherosclerosis research over the past 3 years has been the establishment of peroxisome proliferator-activated receptor (PPAR) expression in the vascular and inflammatory cells, and the emerging picture of the roles these ligand-activated nuclear receptor/transcription factors might play in vascular biology and atherosclerosis. Such work is all the more compelling given the ongoing clinical use of PPAR activators in patients. Thiazolidinediones (PPAR-g agonists) are used as insulin sensitizers in diabetic patients known to be at extraordinarily high risk for cardiovascular disease, whereas fibrates (PPAR-a agonists) are used to treat dyslipidemia, particularly in the case of high triglycerides and low high-density lipoprotein cholesterol.