Triphenyltin isoselenocyanate: a novel nuclear retinoid X receptor ligand with antiproliferative and cytotoxic properties in cell lines derived from human breast cancer.

Several commercially available triorganotin compounds were previously found to function as agonist ligands for nuclear retinoid X receptor (RXR) molecules. Triphenyltin isoselenocyanate (TPT-NCSe), a novel selenium atom containing a derivative of triorganotin origin, was found to represent a new cognate bioactive ligand for RXRs. TPT-NCSe displayed a concentration- and time-dependent decrease in the cell viability in both human breast carcinoma MCF-7 (estrogen receptor positive) and MDA­MB­231 (triple negative) cell lines. Reactive oxygen species levels generated in response to TPT-NCSe were significantly higher in both carcinoma cell lines treated with TPT-NCSe when compared to mock-treated samples. Treatment with 500 nM TPT-NCSe caused a decrease in SOD1 and increased SOD2 mRNA in MCF-7 cells. The levels of SOD2 mRNA were more increased following the treatment with TPT-NCSe along with 1 µM all-trans retinoic acid (AtRA) in MCF-7 cells. An increased superoxide dismutase SOD1 and SOD2 mRNA levels were also detected in combination treatment of 500 nM TPT-NCSe and 1 µM AtRA in TPT-NCSe-treated MDA-MB-231 cells. The data have also shown that TPT-NCSe induces apoptosis via a caspase cascade triggered by the mitochondrial apoptotic pathway. TPT-NCSe modulates the expression levels of apoptosis­related proteins, Annexin A5, Bcl­2 and BAX family proteins, and finally, it enhances the expression levels of its cognate nuclear receptor subtypes RXRalpha and RXRbeta.

Structural and clinical characterization of CYP11B2 inhibition by dexfadrostat phosphate.

Aldosterone synthase (CYP11B2) represents a promising drug target because its genetic dysregulation is causally associated with cardiovascular disease, its autonomous activity leads to primary aldosteronism, and its deficiency leads to salt wasting syndromes. The serendipitous discovery that the dextro-rotatory stereoisomer of the racemic aromatase (CYP19A1) inhibitor CGS16949A mediates potent CYP11B2 inhibition led to the purification and clinical development of dexfadrostat phosphate. To characterize the pharmacophore of dexfadrostat phosphate, structure-based enzyme coordination with CYP11B2, CYP11B1 and CYP19A1 was combined with steroid turnover upon in vitro and clinical treatment. Dexfadrostat, but not its 5S-enantiomer (5S-fadrozole), precisely coordinates with the catalytic heme moiety in the space of the CYP11B2 substrate binding pocket forming a tight and stable complex. Conversely, neither rigid nor flexible docking led to a plausible coordination geometry for dexfadrostat in steroid 11ß-hydroxylase (CYP11B1 - orthologue to CYP11B2) or in CYP19A1. The inhibitory preference of dexfadrostat was confirmed in vitro using an adrenal cortex-derived cell line. Dexfadrostat phosphate treatment of healthy subjects in the context of a clinical phase 1 study led to a dose-dependent decrease in urinary aldosterone secretion, accompanied by an increase in urinary corticosterone and deoxycorticosterone metabolites. Increased urinary corticosterone metabolites are indicative of CYP11B2 (18-oxidase) inhibition with clinical features reminiscent of patients with inborn corticosterone methyloxidase type II deficiency. An off-target effect on CYP19A1 was not observed as indicated by no clinical changes in testosterone and estradiol levels. Therefore, dexfadrostat exhibits the ideal structural features for binding and catalytic inhibition of CYP11B2 but not CYP11B1. Clinically, treatment with dexfadrostat phosphate leads to suppression of aldosterone levels by inhibiting predominantly one or both final CYP11B2-mediated reactions.

Virtual screening and biological evaluation to identify pharmaceuticals potentially causing hypertension and hypokalemia by inhibiting steroid 11ß-hydroxylase.

Several drugs were found after their market approval to unexpectedly inhibit adrenal 11ß-hydroxylase (CYP11B1)-dependent cortisol synthesis. Known side-effects of CYP11B1 inhibition include hypertension and hypokalemia, due to a feedback activation of adrenal steroidogenesis, leading to supraphysiological concentrations of 11-deoxycortisol and 11-deoxycorticosterone that can activate the mineralocorticoid receptor. This results in potassium excretion and sodium and water retention, ultimately causing hypertension. With the risk known but usually not addressed in preclinical evaluation, this study aimed to identify drugs and drug candidates inhibiting CYP11B1. Two conceptually different virtual screening methods were combined, a pharmacophore based and an induced fit docking approach. Cell-free and cell-based CYP11B1 activity measurements revealed several inhibitors with IC50 values in the nanomolar range. Inhibitors include retinoic acid metabolism blocking agents (RAMBAs), azole antifungals, α2-adrenoceptor ligands, and a farnesyltransferase inhibitor. The active compounds share a nitrogen atom embedded in an aromatic ring system. Structure activity analysis identified the free electron pair of the nitrogen atom as a prerequisite for the drug-enzyme interaction, with its pKa value as an indicator of inhibitory potency. Another important parameter is drug lipophilicity, exemplified by etomidate. Changing its ethyl ester moiety to a more hydrophilic carboxylic acid group dramatically decreased the inhibitory potential, most likely due to less efficient cellular uptake. The presented work successfully combined different in silico and in vitro methods to identify several previously unknown CYP11B1 inhibitors. This workflow facilitates the identification of compounds that inhibit CYP11B1 and therefore pose a risk for inducing hypertension and hypokalemia.

Combination of In Silico and In Vitro Screening to Identify Novel Glutamate Carboxypeptidase II Inhibitors.

Glutamate carboxypeptidase II (GCPII) is a metalloprotease implicated in neurological diseases and prostate oncology. While several classes of potent GCPII-specific inhibitors exist, the development of novel active scaffolds with different pharmacological profiles remains a challenge. Virtual screening followed by in vitro testing is an effective means for the discovery of novel active compounds. Structure- and ligand-based pharmacophore models were created based on a dataset of known GCPII-selective ligands. These models were used in a virtual screening of the SPECS compound library (∼209.000 compounds). Fifty top-scoring virtual hits were further experimentally tested for their ability to inhibit GCPII enzymatic activity in vitro. Six hits were found to have moderate to high inhibitory potency with the best virtual hit, a modified xanthene, inhibiting GCPII with an IC50 value of 353 ± 24 nM. The identification of this novel inhibitory scaffold illustrates the applicability of pharmacophore-based modeling for the discovery of GCPII-specific inhibitors.

Microwave Catheter Navigation System for the Radiofrequency Liver Ablation.

Thermal ablation is a well-known method used in interventional radiology to treat cancer. The treatment success is closely related to the exact catheter location in the treated area. Current navigation methods are based mostly on ultrasound or computed tomography. This work explores the possibility of tracking the catheter position during ablation treatment of hepatocellular carcinomas (HCC) using an ultra-wideband (UWB) antenna array and microwave radar imaging based on the "Delay and Sum" (DAS) algorithm. The feasibility was first numerically studied on a simple homogeneous liver model. A heterogeneous anthropomorphic 3D model of the treated region consisting of the main organs within the treated area was then used. Various standard radiofrequency ablation (RFA) catheters were placed virtually in the heterogeneous model. The location and orientation of the antenna elements of the developed imaging system and the applied frequency band were studied. Subsequently, an experimental setup consisting of a 3D printed homogeneous anthropomorphic model, eight UWB dipole antennas, and catheters was created and used in a series of measurements. The average accuracy determining the catheter position from simulated and experimental data was 3.88 ± 0.19 and 6.13 ± 0.66 mm, which are close to the accuracy of clinical navigation systems.

Identification of Novel Dopamine D2 Receptor Ligands-A Combined In Silico/In Vitro Approach.

Diseases of the central nervous system are an alarming global problem showing an increasing prevalence. Dopamine receptor D2 (D2R) has been shown to be involved in central nervous system diseases. While different D2R-targeting drugs have been approved by the FDA, they all suffer from major drawbacks due to promiscuous receptor activity leading to adverse effects. Increasing the number of potential D2R-targeting drug candidates bears the possibility of discovering molecules with less severe side-effect profiles. In dire need of novel D2R ligands for drug development, combined in silico/in vitro approaches have been shown to be efficient strategies. In this study, in silico pharmacophore models were generated utilizing both ligand- and structure-based approaches. Subsequently, different databases were screened for novel D2R ligands. Selected virtual hits were investigated in vitro, quantifying their binding affinity towards D2R. This workflow successfully identified six novel D2R ligands exerting micro- to nanomolar (most active compound KI = 4.1 nM) activities. Thus, the four pharmacophore models showed prospective true-positive hit rates in between 4.5% and 12%. The developed workflow and identified ligands could aid in developing novel drug candidates for D2R-associated pathologies.

Diarylcyclopropane hydroxamic acid inhibitors of histone deacetylase 4 designed by combinatorial approach and QM/MM calculations.

Inhibitors of histone deacetylase superfamily (HDAC), which induce cell cycle arrest, trigger cell death and reduce angiogenesis appear as promising anti-cancer drugs targeting the epigenetic regulation of gene expression. Approved HDAC inhibitors were found effective against haematological and solid malignancies, other HDACIs are currently in clinical trials for the treatment of neurological diseases or immune disorders. Among those, diarylcyclopropane hydroxamic acids (DCHA) were found to be potent and selective inhibitors of the class IIa HDACs, specifically HDAC4, a pharmacological target for the treatment of Huntington's disease and muscular atrophy. Crystallographic analysis revealed that one of the aryl groups of the DCHA fills the lower specificity pocket of the HDAC4 catalytic site that is specific for the class IIa HDACs. We have used computer-assisted combinatorial chemistry, hybrid quantum mechanics/molecular mechanics (QM/MM) with implicit solvation and QSAR models to optimize DCHA inhibitors and propose more potent DCHA analogues. The QM/MM approach has been selected since the process of inhibitor binding to the catalytic zinc and polar amino acid residues of the deacetylase active site induces considerable rearrangement of electron density of the inhibitor. Virtual combinatorial library consisting of 12180 DCHA analogues was focused by means of structure-based evaluation to form a small combinatorial subset enriched in potentially interesting inhibitor candidates. Two validated QSAR models making use of computed relative binding affinities of the DCHA inhibitors to the HDAC4 (ΔΔGcomQM/MM) were utilized to estimate the inhibitory potencies of the new analogues. The predicted half-maximal inhibitory concentrations (IC50pre) of the designed analogues fall into the low nanomolar concentration range and their predicted ADME properties are also favourable. The best designed DCHA analogues contain indazole, phenylpiperidine, phenyloxazole or hydroxypyridine moieties and stabilize bound inhibitors by hydrogen bonds to the catalytic water molecule and backbone carbonyl groups of the deacetylase active site residues. This makes them more potent and more specific inhibitors towards the HDAC4 isoform than the known diarylcyclopropane hydroxamic acids. The analogues are recommended for synthesis and experimental verification of inhibitory potencies in medicinal chemistry laboratories.

How accurate is the description of ligand-protein interactions by a hybrid QM/MM approach?

During the last decades, the application of hybrid quantum mechanical/molecular mechanical (QM/MM) methods has been extended to the field of drug design. In principle, the approximate QM/MM approach offers a more complete description of drug-receptor non-covalent interactions. This is especially true when charge or proton transfer, chelation of metal ions or strong polarization of ligand and protein or surface chemical groups are involved. The aim of this work was to assess the accuracy of calculated non-covalent ligand-protein interaction energies ([Formula: see text]) obtained by the hybrid QM/MM approach employed in QSite/Jaguar of Schrödinger's Small-Molecule Drug Discovery Suite on a set of small-molecule model systems when compared to rigorous QM calculations. The QM/MM approach was used at the density functional theory (DFT) level of theory with 6-31G* basis set, hybrid B3LYP functional and OPLS-2005 force field (DFT-B3LYP/6-31G*//OPLS-2005), a popular combination frequently used in studies on larger and complex biological systems such as drug-receptor complexes. In this work, we did not attempt to compute the most precise interaction energies of the model systems. We rather tried to assess the performance of the approximate QM/MM vs. full QM approach at the same computationally accessible level. For effective use of the QM/MM approach it is essential to select an appropriate QM region of the studied systems. To aid the selection of specific protein residues or functional groups to be included in the QM region, we evaluated the effect of its size, composition and symmetry on the accuracy of the QM/MM calculated [Formula: see text]. This was performed by means of a set of model clusters with well-defined configurations, which mimic the basic types of non-covalent interactions in proteins. Based on these systematic quantitative comparisons, recommendations for the addition of chemical groups or protein residues into the QM region are proposed for the popular DFT-B3LYP/6-31G*//OPLS-2005 QM/MM approach, leading to a more realistic description of ligand-protein interactions. These guidelines can have a significant bearing on computational drug or material research employing hybrid QM/MM methods by providing an estimate of the accuracy that can be expected from QM/MM studies. Graphical abstract An approximate hybrid QM/MM approach at the DFT-B3LYP/6-31G*//OPLS-2005 level was systematically assessed for the accuracy of description of non-covalent interactions on a series of six small-molecule model systems using the QSite and Jaguar modules of Schrödinger. Guidelines for rational selection of receptor residues or function groups to be included in the QM region around the ligand were proposed based on the achieved accuracy of computed ligand-protein interaction energies obtained by QM/MM vs. the full QM approach.

Stereoisomers of oseltamivir - synthesis, in silico prediction and biological evaluation.

Oseltamivir is an important antiviral drug, which possess three chirality centers in its structure. From eight possible stereoisomers, only two have been synthesized and evaluated so far. We describe herein the stereoselective synthesis, computational activity prediction and biological testing of another three diastereoisomers of oseltamivir. These isomers have been synthesized using stereoselective organocatalytic Michael addition, cyclization and reduction. Their binding to viral neuraminidase N1 of influenza A virus was evaluated by quantum-chemical calculations and their anti-influenza activities were tested by an in vitro virus-inhibition assay. All three isomers displayed antiviral activity lower than that of oseltamivir, however, one of the stereoisomers, (3S,4R,5S)-isomer, of oseltamivir showed in vitro potency towards the Tamiflu-sensitive influenza viral strain A/Perth/265/2009(H5N1) comparable to Tamiflu.

Selective inhibitors of zinc-dependent histone deacetylases. Therapeutic targets relevant to cancer.

Histone deacetylases (HDACs), which act on acetylated histones and/or other non-histone protein substrates, represent validated epigenetic targets for the treatment of cancer and other human diseases. The inhibition of HDAC activity was shown to induce cell cycle arrest, differentiation, apoptosis as well as a decrease in proliferation, angiogenesis, migration, and cell resistance to chemotherapy. Targeting single HDAC isoforms with selective inhibitors will help to reveal the role of individual HDACs in cancer development or uncover further biological consequences of protein acetylation. This review focuses on conventional zinc-containing HDACs. In its first part, the biological role of individual HDACs in various types of cancer is summarized. In the second part, promising HDAC inhibitors showing activity both in enzymatic and cell-based assays are surveyed with an emphasis on the inhibitors selective to the individual HDACs.

Melatonin improves the restoration of endothelium-derived constricting factor signalling and inner diameter in the rat femoral artery after cessation of L-NAME treatment.

OBJECTIVE: Melatonin is suggested to be beneficial in several pathological conditions including arterial hypertension. One of the mechanisms proposed for its antihypertensive action is the protection against endothelial dysfunction. We investigated whether melatonin can accelerate the recovery from N(G)-nitro-L-arginine-methyl ester (L-NAME)-induced hypertension after the cessation of L-NAME administration. METHODS: Male adult Wistar rats (n=40) were randomized into 3 treated groups: 5-week L-NAME, 5-week L-NAME + 3-week vehicle, 5-week L-NAME + 3-week melatonin and into 2 age-matched control groups. The blood pressure was measured in the carotid artery. The NO-signalling was represented by NO-synthase activity and expression in the aorta and NO-mediated relaxations of femoral and mesenteric arteries. The endothelium-derived-constricting factor (EDCF)-signalling was represented by aortic cyclooxygenase-2 expression and femoral EDCF-mediated contractions. Oxidative load was determined in the aorta based on conjugated dienes concentration and inner diameter was measured in femoral arteries. RESULTS: L-NAME caused hypertension, reduced NO-signalling and arterial diameter and increased oxidative load and EDCF-signalling. While the NO-signalling was restored spontaneously 3 weeks after L-NAME cessation, the EDCF-signalling, oxidative load and arterial remodeling were completely restored only when melatonin treatment was administered during the recovery period. The blood pressure regression was comparable between spontaneous and melatonin recovery. CONCLUSION: Although melatonin did not accelerate blood pressure reduction, it attenuated EDCF-contractions and oxidative load and enlarged arterial diameter. These effects may be beneficial for cardiovascular protection.