Virtual screening of selective multitarget kinase inhibitors by combinatorial support vector machines.

Multitarget agents have been increasingly explored for enhancing efficacy and reducing countertarget activities and toxicities. Efficient virtual screening (VS) tools for searching selective multitarget agents are desired. Combinatorial support vector machines (C-SVM) were tested as VS tools for searching dual-inhibitors of 11 combinations of 9 anticancer kinase targets (EGFR, VEGFR, PDGFR, Src, FGFR, Lck, CDK1, CDK2, GSK3). C-SVM trained on 233-1,316 non-dual-inhibitors correctly identified 26.8%-57.3% (majority >36%) of the 56-230 intra-kinase-group dual-inhibitors (equivalent to the 50-70% yields of two independent individual target VS tools), and 12.2% of the 41 inter-kinase-group dual-inhibitors. C-SVM were fairly selective in misidentifying as dual-inhibitors 3.7%-48.1% (majority <20%) of the 233-1,316 non-dual-inhibitors of the same kinase pairs and 0.98%-4.77% of the 3,971-5,180 inhibitors of other kinases. C-SVM produced low false-hit rates in misidentifying as dual-inhibitors 1,746-4,817 (0.013%-0.036%) of the 13.56 M PubChem compounds, 12-175 (0.007%-0.104%) of the 168 K MDDR compounds, and 0-84 (0.0%-2.9%) of the 19,495-38,483 MDDR compounds similar to the known dual-inhibitors. C-SVM was compared to other VS methods Surflex-Dock, DOCK Blaster, kNN and PNN against the same sets of kinase inhibitors and the full set or subset of the 1.02 M Zinc clean-leads data set. C-SVM produced comparable dual-inhibitor yields, slightly better false-hit rates for kinase inhibitors, and significantly lower false-hit rates for the Zinc clean-leads data set. Combinatorial SVM showed promising potential for searching selective multitarget agents against intra-kinase-group kinases without explicit knowledge of multitarget agents.

Virtual screening of Abl inhibitors from large compound libraries by support vector machines.

Abl promotes cancers by regulating cell morphogenesis, motility, growth, and survival. Successes of several marketed and clinical trial Abl inhibitors against leukemia and other cancers and appearances of reduced efficacies and drug resistances have led to significant interest in and efforts for developing new Abl inhibitors. In silico methods of pharmacophore, fragment, and molecular docking have been used in some of these efforts. It is desirable to explore other in silico methods capable of searching large compound libraries at high yields and reduced false-hit rates. We evaluated support vector machines (SVM) as a virtual screening tool for searching Abl inhibitors from large compound libraries. SVM trained and tested by 708 inhibitors and 65,494 putative noninhibitors correctly identified 84.4 to 92.3% inhibitors and 99.96 to 99.99% noninhibitors in 5-fold cross validation studies. SVM trained by 708 pre-2008 inhibitors and 65 494 putative noninhibitors correctly identified 50.5% of the 91 inhibitors reported since 2008 and predicted as inhibitors 29,072 (0.21%) of 13.56M PubChem, 659 (0.39%) of 168K MDDR, and 330 (5.0%) of 6638 MDDR compounds similar to the known inhibitors. SVM showed comparable yields and substantially reduced false-hit rates against two similarity based and another machine learning VS methods based on the same training and testing data sets and molecular descriptors. These suggest that SVM is capable of searching Abl inhibitors from large compound libraries at low false-hit rates.

Functionalized chalcones with basic functionalities have antibacterial activity against drug sensitive Staphylococcus aureus.

A library of chalcones with basic functionalities were evaluated for antibacterial activity against drug sensitive strains of Staphylococcus aureus and Escherichia coli. The most active compounds were 2-52 and 2-57 (MIC 6.3 microM S. aureus). These compounds had no activity against E. coli (MIC>100 microM). Both compounds were characterized by a ring A that was substituted with 2-hydroxy-4,6-dimethoxy-3-(1-methylpiperidin-4-yl) groups. The phenolic OH and 1-methylpiperidinyl groups were required for activity but the phenolic OH may play a more critical role. While the compounds were comparable to licochalcone A in terms of antibacterial activity, they caused less hemolysis of sheep erythrocytes at high concentrations (100 microM). It was noted that the structural requirements for limiting hemolytic activity were less stringent than those required for antibacterial activity. The present findings suggest that the chalcone framework is an attractive template for optimization to achieve better potency, lower toxicity and a wider spectrum of antibacterial activity.

Quinone reductase induction activity of methoxylated analogues of resveratrol.

Agents that induce the activity of phase II enzymes play an important role in intervening with the carcinogenic process at the initiation stage. Resveratrol is well known for its chemopreventive activity against major stages of carcinogenesis. In this study, several methoxylated analogues of resveratrol were synthesized and evaluated for their ability to induce the activity of the phase II enzyme quinone reductase (QR). Methoxy groups serve to increase lipophilicity and improve metabolic stability. Compared to resveratrol, analogues with ortho-methoxy substituents were found to be more potent inducers of QR and to exert their activity in a qualitatively different manner. The greater induction activities associated with these stilbenoids serve as a useful starting point for the design of improved chemopreventive agents.

Chalcones: an update on cytotoxic and chemoprotective properties.

Chalcone is a unique template that is associated with several biological activities. In this review, an update of the cytotoxic and chemoprotective activities of chalcones is provided. Cytotoxicity against tumour cell lines may be the result of disruption of the cell cycle, inhibition of angiogenesis, interference with p53-MDM2 interaction, mitochondrial uncoupling or induction of apoptosis. Structural requirements for cytotoxic activity vary according to the mechanisms of action. For anti-mitotic activity, the presence of methoxy substituents, alpha-methylation of the enone moiety and the presence of 2' oxygenated substituents are favourable features. Conformational restraint of the chalcone template generally leads to a decrease in cytotoxic activity. Chemoprotection by chalcones may be a consequence of their antioxidant properties, mediated via inhibition or induction of metabolic enzymes, by an anti-invasive effect or a reduction in nitric oxide production. Hydroxyl and prenyl substituents are associated with antioxidant properties and induction of quinone reductase activities. The thiol reactivity of chalcones is likely to contribute to both cytotoxic and chemoprotective properties of these compounds.

Antimalarial alkoxylated and hydroxylated chalcones [corrected]: structure-activity relationship analysis.

Chalcones with 2',3',4'-trimethoxy, 2',4'-dimethoxy, 4'-methoxy, 4'-ethoxy, 2',4'-dihydroxy, and 4'-hydroxy groups on ring B were synthesized and evaluated in vitro against Plasmodium falciparum (K1) in a [3H] hypoxanthine uptake assay. The other ring A was quinoline, pyridine, naphthalene, or phenyl rings with electron-donating or electron-withdrawing substituents of varying lipophilicities. Trimethoxy 6 and 27, dimethoxy 7, 8, 29, and methoxy 31 analogues had good in vitro activities (IC(50) < 5 microM). 3-Quinolinyl ring A derivatives were well represented among the active compounds. Hydroxylated chalcones were less active than the corresponding alkoxylated analogues. When evaluated in vivo, 8 and 208 were comparable to chloroquine in extending the lifespan of infected mice. Multivariate data analysis showed that in vitro activity was mainly determined by the properties of ring B. Quantitative structure-activity relationship models with satisfactory predictive ability were obtained for various B ring chalcones using projections to latent structures. A model with good predictability was proposed for 19 active chalcones. Size and hydrophobicity were identified as critical parameters.

Synthesis and pharmacological characterization of O-alkynyloximes of tropinone and N-methylpiperidinone as muscarinic agonists.

A number of O-alkynyloximes of tropinone and N-methyl-4-piperidinone have been synthesized and evaluated for muscarinic activity. The affinities of these oximes were tested in homogenates of cerebral cortex, heart, and submandibulary glands from rats using [3H]pirenzepine and [3H]-N-methylscopolamine as radioligands. The oximes bind to the cortical muscarinic receptors with pKi values varying from 3 to 7. Higher binding affinities were observed for the O-alkynyl tropinone oximes than the corresponding piperidinone analogues. Binding to the muscarinic sites in the heart and submandibulary glands was also observed but with lower affinities. Good M1 subtype selectivity (10-fold or greater) was observed with some oximes (26a, 28a, 32a) at the cortical sites. These oximes also attenuated scopolamine-induced impairment of the water mask task in mice. Functional assays for M3 activity on the rat aorta showed that all oximes possessed M3 agonist action but M2 agonist activity was not observed at the endothelium-denuded rabbit aorta. Analysis of the quantitative structure-activity relationship (QSAR) indicated that the Connolly surface area is an important determinant of activity, accounting for 70% of the variation in cortical binding affinity among the oximes.

Synthesis of some novel amodiaquine analogues as potential antimalarial and antifilarial compounds.

Ten amodiaquine analogues, which are hybridized molecules of amodiaquine and diethylcarbamazine, were designed and synthesized. Six analogues, all bearing a basic tertiary amino function at their side chain, were active against Plasmodium berghei in mice and inhibited the mobility of adult worms and microfilariae of Breinlia booliati in vitro. They were inactive against Litomosoides carinii in Mastomys natalensis. The most active antimalarial compound, 7-chloro-4-[alpha-[[N-(4-methyl-1-piperazinyl)carbonyl]amino]-4-hydroxy-m-toluidino]quinoline, had twice the activity of amodiaquine. O-Methylation and N-ethylation generally reduced antimalarial activity. Analogues which lack a basic tertiary amino function at their side chain were also lacking in both antimalarial and antifilarial activities.

Long-acting contraceptive agents: furylalkylcarboxylic acid esters of norethisterone.

5-Methyl- and 5-ethyl-furylalkylcarboxylic esters of norethisterone (17 alpha-ethynyl-17 beta-hydroxyestr-4-en-3-one) were prepared in high yield in the presence of thallous ethoxide. The activities of these compounds as long-acting contraceptive agents have been evaluated.

Long-acting contraceptive agents: norethisterone esters of arylcarboxylic acids.

The synthesis of esters of norethisterone (17 alpha-ethynyl-17 beta-hydroxy-estr-4-en-3-one) with acids containing a benzene ring is described, two methods of esterification being compared in terms of yield and convenience. The activities of these esters as long-acting contraceptive agents have been evaluated.

Long-acting contraceptive agents: levonorgestrel esters of unsaturated acids.

Esters of levonorgestrel (13 beta-ethyl-17 beta-ethynyl-17 beta-hydroxygon-4-en-3-one) with a variety of unsaturated carboxylic acids have been synthesized for evaluation as potential long-acting, injectable contraceptive agents.

PIP: This paper describes the synthesis of esters of levonorgestrel (13 beta-ethyl-17 beta-ethynyl-17 beta-hydroxygon-4-en-3-one) with a variety of unsaturated carboxylic acids for evaluation as potential longacting injectable contraceptive agents. 1-Cyclohexenylacetic acid was prepared by the hydrolysis of 1-cyclohexenylacetonitrile. The synthesis of E-penta-2,4-dienoic acid was achieved by the condensation of acrolein with malonic acid. Reformatsky reaction between crotonaldehyde and ethyl 2-bromopropionate followed by dehydration of the condensation product was used for the synthesis of E,E-2-methylhexa-2,4-dienoic acid. In the preparation of 5-methyl-2-furylacetic acid, 5-methylfurfural was subjected to condensation reaction with rhodanine followed by hydrolysis. The levonorgestrel esters were synthesized by reaction of the appropriate acid chloride with the thallim salt of levonorgestrel, which was obtained by use of thallous ethoxide. The esters prepared were levonorgestrel 1-cyclohexenylacetate; levonorgestrel 1-cyclopentenylacetate; levonorgestrel E-penta-2,4-dienoate; levonorgestrel E,E-2methylhexa-2,4-dienoate; levonorgestrel 5-methyl-2-furylethaoate; levonorgestrel 3-(5'-methyl-2'-furyl)propanoate; levonorgestrel 3-(5'-ethyl-2'-furyl)propanoate; leveonorgestrel 4-(5'-methyl-2'-furyl)butanoate; levonorgestrel E-non-2-en-4-ynoate; 1-cyclohexenylacetic acid; 1-cyclopentenylacetic acid; E-penta-2,4-dienoic acid; E,E-2-methylhexa-2,4-dienoic acid; 5-methyl-2-furylacetic acid; and E-non-2-en-4-ynoic acid.

Caffeine and nicotinamide enhances the aqueous solubility of the antimalarial agent halofantrine.

The aqueous solubility of the antimalarial agent halofantrine in phosphate buffers pH 5.9 and 7.0 (ionic strength 0.08) is increased by the addition of caffeine and nicotinamide. Solubility is increased to a greater extent in the presence of caffeine (12.5-125 mM) than nicotinamide (125 mM -2.0 M). The greatest increase in solubility was observed at pH 5.9 where the basal solubility of halofantrine rose from 0.91 to 435 microM when 125 mM caffeine was added. Phase solubility studies support the formation of a 1:1 complex between caffeine and halofantrine which is characterised by a K(1:1) constant of 2.75x10(3) M(-1) (pH 5.9). A less stable 1:1 complex is formed at pH 7.0 (K(1:1)=6.37x10(3) M(-1)). Differential scanning calorimetry of solid mixtures of caffeine and halofantrine showed the absence of the endotherms of the two drugs and the appearance of a distinct endotherm (with a smaller enthalpy) characteristic of the complex. An analysis of the 1H-NMR spectra of mixtures of caffeine and halofantrine revealed perturbations in the chemical shifts of the methyl group and proton at positions 4 and 8 of caffeine, and a change in splitting pattern of the H(9) proton of the phenanthrene ring in halofantrine.

M3/M1-Selective antimuscarinic tropinyl and piperidinyl esters.

The binding affinities of some tropinyl and piperidinyl esters for the submandibulary glands (M3/M1) and heart ventricle (M2) were determined from displacement experiments using 3H-labelled N-methylscopolamine as radioligand. The antimuscarinic activities of these esters were also evaluated on guinea pig bronchi. The esters inhibited the M3-mediated carbachol-induced contraction of the bronchial smooth muscle and a reasonable correlation was obtained between the binding affinities of the esters for the submandibulary glands (pKM3,M1) and their inhibitory activities (pIC50) on guinea pig bronchi. A promising compound, N-methylpiperidinyl cyclohexylphenylpropionate (NCPP) which combined good antimuscarinic activity (pA2=9.34) with a 20-fold selectivity at the M3/M1 receptors, was identified. Quantitative structure-activity relationships (QSAR) showed that the size of the ester was the main structural feature determining both binding affinity for the M3/M1 receptors and inhibitory activity on guinea pig bronchi. Esters with substituted acyl side chains (fewer hyperconjugable H atoms at the alpha-carbon) are generally associated with better activity and affinity.

Action of mefloquine on toad isolated rectus abdominis muscle.

The effects of mefloquine and quinine on acetylcholine-induced contractures of the toad rectus abdominis muscle have been investigated. Both drugs depressed acetylcholine-induced contractures in a dose-related and non-competitive manner. A partial reversal of the block was observed in the presence of 4-aminopyridine (10, 50 microM) and increased Ca2+ content (1.25x) of the Ringer solution. In both cases, the mefloquine-induced blockade was more readily reversed than that induced by quinine. Mefloquine and quinine at concentrations greater than 100 and 500 microM, respectively, also elicited a direct contractile response on the muscle. Quantitative differences in their contractile activity have been attributed to the greater lipid solubility and tissue binding affinity of mefloquine.

Investigation of the anti-acetylcholinesterase activities of the antimalarial agent, amodiaquine, and related compounds.

The antimalarial agent, amodiaquine, is a potent inhibitor of AChE (Ki = 1.50 x 10(-9) M, pH 7.4, 25 degrees C). Both the protonated diethylamino and phenolic hydroxyl functions of amodiaquine are necessary for interaction with AChE. This suggests that the inhibition of AChE by amodiaquine may involve binding of the protonated diethylamino and phenolic hydroxyl functions to the anionic and esteric sites of the enzyme respectively. The anti-AChE property of amodiaquine may be related in some way to the gastrointestinal and central nervous system disturbances frequently encountered when large doses of amodiaquine are used for the treatment of malaria.

Hydrophobicity and antifilarial activities of 4-aminoquinolines.

The apparent partition coefficients (Papp.) of eight 4-aminoquinolines in 1-octanol/pH 7.4 buffered solutions have been determined and correlated with their reported antifilarial activities. Antifilarial activity appears to be present only in those 4-aminoquinolines which have log Papp. values falling within a narrow range of 2.8 to 3.2.

Sulfatide-tenascin interaction mediates binding to the extracellular matrix and endocytic uptake of liposomes in glioma cells.

Tenascin-C is an extracellular matrix glycoprotein, whose expression is highly restricted in normal adult tissues, but markedly up-regulated in a range of tumors, and therefore serves as a potential receptor for targeted anticancer drug or gene delivery. We describe here a liposomal carrier system in which the targeting ligand is sulfatide. Experiments with tenascin-C-expressing glioma cells demonstrated that binding of liposomes to the extracellular matrix relied essentially on the sulfatide-tenascin-C interaction. Following binding to the extracellular matrix, the sulfatide-containing liposomes were internalized via both caveolae/lipid raft- and clathrin-dependent pathways, which would ensure direct cytoplasmic release of the cargoes carried in the liposomes. Such natural lipid-guided intracellular delivery targeting at the extracellular matrix glycoproteins of tumor cells thus opens a new direction for development of more effective anticancer chemotherapeutics in future.

Comparison of the effects of mefloquine and ryanodine on the directly stimulated rat hemidiaphragm preparation.

The effects of the antimalarial agent mefloquine on directly stimulated rat hemidiaphragm were investigated after nerve transmission had been blocked with alpha-bungarotoxin. Mefloquine (50 and 75 microM) caused contractures and diminished directly stimulated twitch responses. The mefloquine-induced contracture was significantly diminished in low Ca2+ Krebs-Henseleit solution and after pretreatment with phospholipase C. It was potentiated following an initial exposure to ryanodine. Mefloquine, as well as ryanodine, reduced the caffeine contractures obtained in low Ca2+ media. The results suggest that Ca(2+)-induced Ca2+ release, involving the action of mefloquine on some phospholipid component of the sarcolemma, appears to be important in the initiation of the contracture. The loss in caffeine response following pretreatment with mefloquine indicates that mefloquine also causes depletion of Ca2+ from sarcoplasmic reticulum stores.

Effects of mefloquine on the isolated chick biventer cervicis and rat phrenic nerve hemidiaphragm preparations.

The effects of the antimalarial agent mefloquine on skeletal muscle and its neurotransmission were investigated on the isolated chick biventer cervicis and rat phrenic nerve hemidiaphragm. At concentrations of 64, 128 and 257 microM, mefloquine reduced twitch contraction responses to nerve stimulation, and inhibited carbachol- and KCl-induced contractures of avian muscle. Qualitatively similar responses were observed for chloroquine (257 microM) and quinine (512 microM) but the inhibitory effects of mefloquine were more pronounced and less readily reversible. On the rat phrenic nerve hemidiaphragm, mefloquine (50, 75 and 100 microM) inhibited twitch contractions stimulated indirectly via the nerve. When nerve transmission has been blocked with alpha-bungarotoxin, mefloquine inhibited twitch responses obtained by direct stimulation of the hemidiaphragm. The present findings indicate that its prime action seems to be on muscle contractility, possibly by inhibiting excitation-contraction coupling.

Effects of mefloquine on the release of marker enzymes from the rat liver crude lysosomal fraction.

The effects of the antimalarial agent mefloquine on the release of marker enzymes, acid phosphatase and beta glucuronidase, from the rat liver lysosomes in a crude lysosomal preparation were investigated and compared with that of chloroquine whose membrane effects have been well-documented in the literature. At 10 microM, mefloquine decreased significantly the release of marker enzymes when compared to the control, but at the higher concentrations of 100 microM and 500 microM, it markedly accelerated the release of enzymes. This suggested that mefloquine exerted a concentration-dependent biphasic effect of membrane stabilization and labilization. In comparison, chloroquine diminished the release of enzymes over the concentration range of 10-500 microM, that is showing a membrane stabilizing effect similar to other reports. Since serum levels of 1.6-3.2 microM are reported after a weekly dose of mefloquine, the present results suggest that a predominant stabilization effect should prevail under these conditions. However, higher drug concentrations may result in labilization with undesirable consequences.