Discovery and SAR study of novel dihydroquinoline-containing glucocorticoid receptor agonists

Structure-based virtual screening, molecular docking, molecular dynamics simulation and MM/PBSA calculations towards identification of steroidal and non-steroidal selective glucocorticoid receptor modulators

Glucocorticoids have been used in the treatment of many diseases including inflammatory and autoimmune diseases. Despite the wide therapeutic effects of synthetic glucocorticoids, the use of these compounds has been limited due to side effects such as osteoporosis, immunodeficiency, and hyperglycaemia. To this end, extensive studies have been performed to discover new glucocorticoid modulators with the aim of increasing affinity for the receptor and thus less side effects. In the present work, structure-based virtual screening was used for the identification of novel potent compounds with glucocorticoid effects. The molecules derived from ZINC database were screened on account of structural similarity with some glucocorticoid agonists as the template. Subsequently, molecular docking was performed on 200 selected compounds to obtain the best steroidal and non-steroidal conformations. Three compounds, namely ZINC_000002083318, ZINC_000253697499 and ZINC_000003845653, were selected with the binding energies of -11.5, -10.5, and -9.5 kcal/mol, respectively. Molecular dynamic simulations on superior structures were accomplished with the glucocorticoid receptor. Additionally, root mean square deviations, root mean square fluctuation, radius of gyration, hydrogen bonds, and binding-free energy analysis showed the binding stability of the proposed compounds compared to budesonide as an approved drug. The results demonstrated that all the compounds had suitable binding stability compared to budesonide, while ZINC_000002083318 showed a tighter binding energy compared to the other compounds.Communicated by Ramaswamy H. Sarma.

Rapid Assembly of Functionalized 2H-Chromenes and 1,2-Dihydroquinolines via Microwave-Assisted Secondary Amine-Catalyzed Cascade Annulation of 2-O/N-Propargylarylaldehydes with 2,6-Dialkylphenols

An efficient, secondary amine-catalyzed cascade annulation of 2-O/N-propargylarylaldehydes with 2,6-dialkylphenols was established to access biologically relevant functionalized 2H-chromenes and 1,2-dihydroquinolines tethered with a synthetically useful p-quinone methide scaffold in high yields under microwave irradiation and conventional heating conditions. The microwave-assisted strategy was convenient, clean, rapid, and high yielding in which the reactions were completed in just 15 min, and the yields obtained were up to 95%. This highly atom-economical domino process constructed two new C-C double bonds and a six-membered O/N-heterocyclic ring in a single synthetic operation. Its mechanism process was rationalized as involving sequential iminium ion formation, nucleophilic addition, and intramolecular annulation steps. Furthermore, the synthesized 2H-chromene derivatives were transformed into valuable indeno[2,1-c]chromenes, 5H-indeno[2,1-c]quinolines, and oxireno[2,3-c]chromene via a palladium-catalyzed double C-H bond activation process and epoxidation, respectively.

Solvent-Free Mechanosynthesis of Polysubstituted 1,2-Dihydroquinolines from Anilines and Alkyne Esters

A novel one-pot reaction of anilines with acetylenedicarboxylate diesters in the presence of boron trifluoride, iodine, and trifluoroacetic acid or methylsulfonic acid has been developed under solvent-free ball-milling conditions, affording a variety of polysubstituted 1,2-dihydroquinolines bearing multiple ester groups in moderate to excellent yields. The present protocol features mild reaction conditions, short reaction time, and feasibility of large-scale synthesis, providing a facile and practical alternative to 1,2-dihydroquinoline synthesis. Intriguingly, the generated 1,2-dihydroquinolines can be further transformed into quinoline derivatives.

Rh(iii)-Catalyzed [5 + 1] annulation of 2-alkenylanilides and 2-alkenylphenols with allenyl acetates

Herein, we report a mild and highly regioselective Rh(iii)-catalyzed non-oxidative [5 + 1] vinylic C-H annulation of 2-alkenylanilides with allenyl acetates, which has been elusive so far. The reaction proceeds via vinylic C-H activation, regioselective 2,3-migratory insertion, β-oxy elimination followed by nucleophilic cyclization to get direct access to 1,2-dihydroquinoline derivatives. The strategy was also successfully extended to C-H activation of 2-alkenylphenols for constructing chromene derivatives. In the overall [5 + 1] annulation, the allene serves as a one carbon unit. The acetate group on the allene is found to be crucial both for controlling the regio- and chemoselectivity of the reaction and also for facilitating β-oxy elimination. The methodology was scalable and also further extended towards late stage functionalization of various natural products.

Enantioselective [2+2] Cycloaddition of 1,2-Dihydroquinolines with 3-Olefinic Oxindoles via Brønsted Acid Catalysis

Two complementary regiodivergent Brønsted acid-catalyzed atom-economic [2+2] cycloaddition and ene reaction of 1,2-dihydroquinolines with 3-olefinic oxindoles are reported. In the presence of a chiral phosphoramide catalyst, the [2+2] cycloaddition affords...

Modular Access to Spiro-dihydroquinolines via Scandium-Catalyzed Dearomative Annulation of Quinolines with Alkynes

The catalytic enantioselective construction of three-dimensional molecular architectures from planar aromatics such as quinolines is of great interest and importance from the viewpoint of both organic synthesis and drug discovery, but there still exist many challenges. Here, we report the scandium-catalyzed asymmetric dearomative spiro-annulation of quinolines with alkynes. This protocol offers an efficient and selective route for the synthesis of spiro-dihydroquinoline derivatives containing a quaternary carbon stereocenter with an unprotected N-H group from readily accessible quinolines and diverse alkynes, featuring high yields, high enantioselectivity, 100% atom-efficiency, and broad substrate scope. Experimental and density functional theory studies revealed that the reaction proceeded through the C-H activation of the 2-aryl substituent in a quinoline substrate by a scandium alkyl (or amido) species followed by alkyne insertion into the Sc-aryl bond and the subsequent dearomative 1,2-addition of the resulting scandium alkenyl species to the C═N unit in the quinoline moiety. This work opens a new avenue for the dearomatization of quinolines, leading to efficient and selective construction of spiro molecular architectures that were previously difficult to access by other means.

Iron-catalyzed carboarylation of alkynes via activation of π-activated alcohols: rapid synthesis of substituted benzofused six-membered heterocycles

An Fe(OTf)3-catalysed carboarylation of alkynes is reported for the straightforward synthesis of densely substituted 1,2-dihydroquinolines from N-propargyl anilides and π-activated alcohols. The reaction provides a new method for the synthesis of highly substituted benzofused six-membered heterocycles by the formation of two carbon-carbon bonds and one ring in a single step. The power of the methodology was further extended to the synthesis of substituted chromene and thiochromene derivatives in high yields. In addition, substituted quinoline derivatives were also achieved in a single step in the presence of FeCl3 through detosylation/aromatisation. A number of control experiments have been performed and a plausible mechanism has also been proposed to explain the formation of the products.

Facile syntheses of tetrahydroquinolines and 1,2-dihydroquinolines via vinylogous cascade hydride transfer/cyclization

The medicinally significant 3-monosubstituted tetrahydroquinolines and 1,2-dihydroquinolines were controllably constructed via redox-neutral vinylogous cascade condensation/[1,5]-hydride transfer/cyclization in EtOH.

Appendix A. dithioloquinolinethiones as new potential multitargeted antibacterial and antifungal agents: Synthesis, biological evaluation and molecular docking studies

Herein we report the design, synthesis, molecular docking study and evaluation of antimicrobial activity of ten new dithioloquinolinethiones. The structures of compounds were confirmed by ¹H NMR, ¹³C NMR and HPLC-HRMS. Before evaluation of their possible antimicrobial activity prediction of toxicity was performed. All compounds showed antibacterial activity against eight Gram positive and Gram negative bacterial species. All compounds appeared to be more active than ampicillin and almost all than streptomycin. The best antibacterial activity was observed for compound 8c 4,4,8-trimethyl-5-{[(4-phenyl-5-thioxo-4,5-dihydro-1,3,4-thiadiazol-2-yl)thio]acetyl}-4,5-dihydro-1H-[1,2]dithiolo[3,4c]quino lone-1-thione). The most sensitive bacterium En.cloacae followed by S. aureus, while L.monocytogenes was the most resistant. All compounds were tested for antifungal activity also against eight fungal species. The best activity was expressed by compound 8d (5-[(4,5-Dihydro-1,3-thiazol-2-ylthio)acetyl]-4,4-dimethyl-4,5-dihydro-1H-[1,2]dithiolo[3,4-c]quinoline-1-thione). The most sensitive fungal was T. viride, while P. verrucosum var. cyclopium was the most resistant one. All compounds were more potent as antifungal agent than reference compound bifonazole and ketoconazole. The docking studies indicated a probable involvement of E. coli DNA GyrB inhibition in the anti-bacterial mechanism, while CYP51ca inhibition is probably responsible for antifungal activity of tested compounds. It is interesting to mention that docking results coincides with experimental.

A one pot three-component reaction for the preparation of dihydroquinolines with two different ketones and aromatic amines

A three component reaction with two different ketones and aromatic amines was firstly investigated. The difference in reactivity between ordinary ketones and ketone esters allowed for the production of 1,2-DHQs efficiently. The possible Skraup reaction with 2 equiv. of the same ketones was prohibited due to the fast formation of imines.

The p-toluenesulfonic acid catalyzed single pot synthesis of tetracyclic 1,2-dihydroquinolines: a metal free approach

A simple, convenient and efficient metal free approach towards the synthesis of polysubstituted 1,2-dihydroquinolines.

Efficient synthesis of functionalized dihydroquinolines, quinolines and dihydrobenzo[b]azepine via an iron(iii) chloride-catalyzed intramolecular alkyne–carbonyl metathesis of alkyne tethered 2-amino benzaldehyde/acetophenone derivatives

Iron-catalyzed synthesis of dihydroquinolines, quinolines and dihydrobenzo[b]azepine.

Regioselective synthesis of 1,2-dihydroquinolines by a solvent-free MgBr2-catalyzed multicomponent reaction

A highly efficient and regioselective synthesis of 1,2-dihydroquinolines via a multicomponent reaction between an aniline and two ketones is described. This reaction was catalyzed by magnesium bromide and carried out under solvent-free conditions. When the reaction was performed by using 3-substituted anilines and nonsymmetrically substituted ketones, principally a single product was found among the four expected regioisomers. A variety of anilines and ketones, including cyclic ketones, were evaluated providing a series of 1,2-dihydroquinolines with diverse substitution patterns. A study of the mechanism is discussed. There is evidence of the in situ formation of the imine as a result of the reaction between the aniline and one of the ketones, before annulation to the heterocyclic ring.

Non-steroidal Dissociated Glucocorticoid Receptor Agonists

Synthetic glucocorticoids, such as dexamethasone and prednisolone, are amongst the most commonly used drugs due to their potent and efficacious anti-inflammatory and immunosuppressive properties. However, their long-term and/or high-dose administration is limited by a number of deleterious side-effects, including glucocorticoid-induced diabetes and osteoporosis. Glucocorticoids exert their effects through binding to the glucocorticoid receptor. Since the discovery of multiple differentiated down-stream functions of the glucocorticoid-bound receptor, such as gene transrepression and transactivation, researchers in academia and industry have been on a quest to discover novel glucocorticoids that achieve functional selectivity, hence dissociating the desired anti-inflammatory from the undesired side-effects. This review describes the current state of discovery and development of non-steroidal glucocorticoid receptor agonists. Several small-molecule drug candidates have advanced into clinical trials, and have shown promising early biomarker data, as well as beneficial effects in topical applications. However, a clinically efficacious and systemically available glucocorticoid with significantly reduced side-effects as compared to current steroidal drugs, the “Holy Grail” in immunology, is still elusive.

Exploring Structure-Activity Data Using the Landscape Paradigm

In this article we present an overview of the origin and applications of the activity landscape view of structure-actvitiy relationship data as conceived by Maggiora. Within this landscape, different regions exemplify different aspects of SAR trends - ranging from smoothly varying trends to discontinuous trends (also termed activity cliffs). We discuss the various definitions of landscapes and cliffs that have been proposed as well as different approaches to the numerical quantification of a landscape. We then highlight some of the landscape visualization approaches that have been developed, followed by a review of the various applications of activity landscapes and cliffs to topics in medicinal chemistry and SAR analysis.

Rank order entropy: why one metric is not enough

The use of Quantitative Structure-Activity Relationship models to address problems in drug discovery has a mixed history, generally resulting from the misapplication of QSAR models that were either poorly constructed or used outside of their domains of applicability. This situation has motivated the development of a variety of model performance metrics (r(2), PRESS r(2), F-tests, etc.) designed to increase user confidence in the validity of QSAR predictions. In a typical workflow scenario, QSAR models are created and validated on training sets of molecules using metrics such as Leave-One-Out or many-fold cross-validation methods that attempt to assess their internal consistency. However, few current validation methods are designed to directly address the stability of QSAR predictions in response to changes in the information content of the training set. Since the main purpose of QSAR is to quickly and accurately estimate a property of interest for an untested set of molecules, it makes sense to have a means at hand to correctly set user expectations of model performance. In fact, the numerical value of a molecular prediction is often less important to the end user than knowing the rank order of that set of molecules according to their predicted end point values. Consequently, a means for characterizing the stability of predicted rank order is an important component of predictive QSAR. Unfortunately, none of the many validation metrics currently available directly measure the stability of rank order prediction, making the development of an additional metric that can quantify model stability a high priority. To address this need, this work examines the stabilities of QSAR rank order models created from representative data sets, descriptor sets, and modeling methods that were then assessed using Kendall Tau as a rank order metric, upon which the Shannon entropy was evaluated as a means of quantifying rank-order stability. Random removal of data from the training set, also known as Data Truncation Analysis (DTA), was used as a means for systematically reducing the information content of each training set while examining both rank order performance and rank order stability in the face of training set data loss. The premise for DTA ROE model evaluation is that the response of a model to incremental loss of training information will be indicative of the quality and sufficiency of its training set, learning method, and descriptor types to cover a particular domain of applicability. This process is termed a "rank order entropy" evaluation or ROE. By analogy with information theory, an unstable rank order model displays a high level of implicit entropy, while a QSAR rank order model which remains nearly unchanged during training set reductions would show low entropy. In this work, the ROE metric was applied to 71 data sets of different sizes and was found to reveal more information about the behavior of the models than traditional metrics alone. Stable, or consistently performing models, did not necessarily predict rank order well. Models that performed well in rank order did not necessarily perform well in traditional metrics. In the end, it was shown that ROE metrics suggested that some QSAR models that are typically used should be discarded. ROE evaluation helps to discern which combinations of data set, descriptor set, and modeling methods lead to usable models in prioritization schemes and provides confidence in the use of a particular model within a specific domain of applicability.

Rational ligand-based virtual screening and structure-activity relationship studies in the ligand-binding domain of the glucocorticoid receptor-α

The interest in developing synthetic glucocorticoids (GCs) arises from the utility of endogenous steroids as potent anti-inflammatory and immunosuppressant agents. The first GCs to be discovered, such as cortisol or dexamethasone, still represent the main treatment for conditions of the inflammatory process, despite the fact that they carry a significant risk of side effects. Hence, there is a continuing need to find drugs that preserve the immune effects of GCs without the side effects, such as those on metabolism (diabetes), bone tissue (osteoporosis), muscles (myopathy), eyes and skin. In this review, we focus on the recent use of ligand-based computational approaches in glucocorticoid receptor (GR) drug-design efforts for the determination of novel GR ligands. We examine a number of ligand-based (similarity searches, pharmacophore screens and quantitative structure-activity relationships) approaches that have been implemented in recent years. A recent virtual high-throughput screening similarity search was successful in developing a novel series of nonsteroidal GR antagonists. Additionally, there has been considerable success in ligand-based structure-analysis relationship generation and lead optimization studies for the GR. Future trends toward integrated GR ligand design incorporating ligand- and structure-based methodologies are inevitable.

The ups and downs of structure-activity landscapes

In this chapter we discuss the landscape view of structure-activity relationships (SARs). The motivation for such a view is that SARs come in a variety of forms, such as those where small changes in structure lead to small changes in activity or where small structural lead to significant changes in activity (also termed activity cliffs). Thus, an SAR dataset is viewed as a landscape comprised of smooth plains, rolling hills, and jagged gorges. We review the history of this view and early quantitative approaches that attempted to encode the landscape. We then discuss some recent developments that directly characterize structure-activity landscapes, in one case with the goal of highlighting activity cliffs while the other allows one to resolve different types of SAR that may be present in a dataset. We highlight some applications of these approaches, such as predictive model development and SAR elucidation, to SAR datasets obtained from the literature. Finally, we conclude with a summary of the landscape approach and why it provides an intuitive and rigorous alternative to standard views of structure-activity data.

Antitrypanosomal activity of 1,2-dihydroquinolin-6-ols and their ester derivatives

The current chemotherapy for second stage human African trypanosomiasis is unsatisfactory. A synthetic optimization study based on the lead antitrypanosomal compound 1,2-dihydro-2,2,4-trimethylquinolin-6-yl 3,5-dimethoxybenzoate (TDR20364, 1a) was undertaken in an attempt to discover new trypanocides with potent in vivo activity. While 6-ether derivatives were less active than the lead compound, several N1-substituted derivatives displayed nanomolar IC(50) values against T. b. rhodesiense STIB900 in vitro, with selectivity indexes up to >18000. 1-Benzyl-1,2-dihydro-2,2,4-trimethylquinolin-6-yl acetate (10a) displayed an IC(50) value of 0.014 microM against these parasites and a selectivity index of 1700. Intraperitoneal administration of 10a at 50 (mg/kg)/day for 4 days caused a promising prolongation of lifespan in T. b. brucei STIB795-infected mice (>14 days vs 7.75 days for untreated controls). Reactive oxygen species were produced when T. b. brucei were exposed to 10a in vitro, implicating oxidative stress in the trypanocidal mode of action of these 1,2-dihydroquinoline derivatives.

Structure--activity landscape index: identifying and quantifying activity cliffs

A new method for analyzing a structure-activity relationship is proposed. By use of a simple quantitative index, one can readily identify "structure-activity cliffs": pairs of molecules which are most similar but have the largest change in activity. We show how this provides a graphical representation of the entire SAR, in a way that allows the salient features of the SAR to be quickly grasped. In addition, the approach allows us view the SARs in a data set at different levels of detail. The method is tested on two data sets that highlight its ability to easily extract SAR information. Finally, we demonstrate that this method is robust using a variety of computational control experiments and discuss possible applications of this technique to QSAR model evaluation.