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.

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.

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.

Halofantrine-phospholipid interactions: monolayer studies.

The antimalarial agent halofantrine penetrates dipalmitolylphosphatidylcholine (DPPC) monolayers resulting in an increase in surface pressure and an expansion in area occupied by the lipid components of the monolayer. This phenomenon is observed at concentrations (0.05-0.2 microm) of halofantrine that have no surface activity. Penetration increases with drug concentration and is greatest at low initial surface pressures of the monolayer. A critical surface pressure of the DPPC monolayer has been determined from constant area and constant pressure conditions. The magnitude of these values support the hypothesis that halofantrine readily penetrates the DPPC monolayers. The presence of cholesterol in the DPPC monolayer hampers penetration and a lower critical surface pressure is obtained under such conditions. Even then, a slower rate of penetration is observed only in monolayers maintained at high initial surface pressures (10, 15 mN/m), corresponding to the liquid condensed phase of the monolayer, and not at low surface pressures (2.5, 5.0 mN/m). These results help to give a better understanding of the dynamics of the halofantrine-phospholipid interaction as well as the pharmacodynamic character of the drug.

Study of synthesis and cardiovascular activity of some furoxan derivatives as potential NO-donors.

A series of hybrid molecules incorporating the furoxan and nicorandil moieties were designed as potential NO donors with cardiovascular and cerebrovascular activities. Thirty-six target molecules were successfully synthesized by conventional methods and characterized by infrared spectroscopy, 1H-NMR spectroscopy and high resolution mass spectra. The compounds were tested for their effects on KCl-induced contraction of rabbit thoracic aorta whose endothelium was denuded. Eight compounds were found to reduce KCl-induced contraction by more than 30% at 10 microM. All except one of these compounds are characterized by the presence of electron withdrawing groups in the phenyl ring attached via an amide or ester linkage to the furoxan moiety. The nature of the terminal carbonyl linkage (ester or amide) and the length or type of the alkyl chain bridging the two carbonyl functions have little effect on the activity. One of the active compounds, N-(4-methoxy-benzoyl)-N'-[3-methylfuroxanyl-4-carbonyl)piperazine (17i) was tested for hypotensive effects on anaesthesized rats at 1.5 mg/kg, and found to demonstrate a gradual and sustained hypotensive effect. The results suggest that the furoxan-nicorandil derivatives are a useful lead in the design of NO-donor compounds for hypertension.

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.

The antimalarial agent halofantrine perturbs phosphatidylcholine and phosphatidylethanolamine bilayers: a differential scanning calorimetric study.

The interaction of halofantrine with phosphatidylcholine and phosphatidylethanolamine bilayers has been investigated by differential scanning calorimetry. Halofantrine caused a broadening of the gel to liquid crystalline phase transition endotherm of the phosphatidylcholines. A decrease in the transition temperature Tm and enthalpy (delta H) of transition was also observed. This varied with the chain length of the phospholipid and was more pronounced with short chain members. Halofantrine-induced changes to the thermotropic characteristics of dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers suggested that the penetration of halofantrine into the bilayer was diminished in the presence of cholesterol. A more complex calorimetric profile was observed in the interaction of halofantrine with phosphatidylethanolamines and the results suggested that halofantrine did not disrupt the cooperativity of the phosphatidylethanolamine bilayers to the same extent as that observed with the phosphatidylcholines. Halofantrine caused significant perturbation of phospholipids and this property might have an important bearing on its pharmacodynamic effects.

Chiral resolution of atropine, homatropine and eight synthetic tropinyl and piperidinyl esters by capillary zone electrophoresis with cyclodextrin additives.

Chiral resolution of atropine, homatropine and eight synthetic tropinyl and piperidinyl esters were studied by capillary zone electrophoresis with cyclodextrin additives. Atropine and eight synthetic derivatives were successfully resolved by heptakis-(2,3,6-tri-O-methyl)-beta-cyclodextrin (TM-beta-CD) at concentrations ranging from 10 to 40 mM. Homatropine was baseline resolved by 10 mM beta-cyclodextrin and hydroxypropyl-beta-cyclodextrin (HP-beta-CD), respectively. The developed method was employed for the determination of atropine enantiomers in human serum.

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.

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, antimuscarinic activity and quantitative structure-activity relationship (QSAR) of tropinyl and piperidinyl esters.

A series of tropinyl and piperidinyl esters was synthesized and evaluated for inhibitory activities on the endothelial muscarinic receptors of rat (M3) and rabbit (M2) aorta. Some of the esters (cyclohexylphenylglycolates and cyclohexylphenylpropionates) were found to be better antimuscarinic compounds than standard M2 and M3 inhibitors such as AFDX116 and 4-diphenylacetoxy-N-methylpiperidine (DAMP), with pKEC50 values in the range of 8-9. A few esters were found to be more selective M3 than M2 inhibitors, but these tended to have low activities. The hydrophobic, electronic and steric characteristics of these esters were correlated with antimuscarinic activity by using appropriate parameters representing hydrophobicity (HPLC capacity factor, log kw), size (molecular volume) and electronic character (Taft's polar substituent constant sigma * and 13C chemical shift difference delta delta). Finally, 92% of the M2-inhibitory activities of the esters could be accounted for by the size and electronic character sigma * of the side chain. In contrast, the M3-inhibitory activities of these esters were mainly attributed to the electronic nature (sigma *, delta delta) of the side chain, with good activity being associated with electron-withdrawing groups. Visualization of the comparative molecular field analysis (CoMFA) steric and electrostatic fields provided further confirmation of the structure-activity relationship (SAR) derived from traditional quantitative structure activity relationship (QSAR) approaches.

Thermodynamics of partitioning of the antimalarial drug mefloquine in phospholipid bilayers and bulk solvents.

The antimalarial drug mefloquine binds avidly to phospholipids in biomembranes. The thermodynamics of the partitioning process in dimyristoylphosphatidylcholine (DMPC) bilayers was investigated to give some insight into the drug-phospholipid interaction. Thermodynamic parameters for the partition equilibria were evaluated from the equilibrium partition coefficients measured as a function of temperature. Negative values of delta H and delta S were obtained for the transfer of mefloquine from the aqueous to the gel phase of the phospholipid. The partitioning is enthalpy controlled which suggests that mefloquine interacts strongly with the phospholipid phase. In contrast, the partitioning of mefloquine into the liquid crystalline phase of DMPC is entropy controlled which is typical of a hydrophobic interaction between mefloquine and the aqueous phase. The partitioning of mefloquine into the bulk solvents octanol and hexane were found to be enthalpy and entropy controlled, respectively. The enthalpy dominated partitioning of mefloquine into gel phase DMPC and octanol is attributed to the occurrence of hydrogen bonding and van der Waals interactions between solute and solvent. The flat shape of mefloquine may further aid its interaction with the orderly domains of the lipidic/organic phase. This is apparent from a comparison of the partitioning characteristics of another structurally related but conformationally different molecule, quinine into DMPC and octanol.

Effects of mefloquine on Ca2+ uptake and release by dog brain microsomes.

The effects of the antimalarial drug, mefloquine, on the uptake and release of Ca2+ by crude microsomes from dog brain were investigated using a spectrophotometric method. Mefloquine inhibited the inositol-1,4,5-phosphate (IP3)-induced Ca2+ release with an IC50 of 42 microM, but was a weaker inhibitor of the uptake of Ca2+ into the vesicles (IC50: 272 microM). These effects of mefloquine are in contrast to its actions on Ca2+ uptake and release by skeletal muscle microsomes, where its predominant effect was seen to be the inhibition of Ca2+ uptake into the vesicles. Mefloquine was found to be more potent than quinine as a specific inhibitor of Ca2+ release from IP3-sensitive stores in dog brain microsomes. The possibility of the drug affecting cellular IP3-linked signal transduction processes should be considered.

Effects of mefloquine on Ca2+ uptake by crude microsomes of rabbit skeletal muscle.

The effects of the antimalarial agent, mefloquine, and its derivatives on Ca2+ uptake and release by crude microsomes from the rabbit skeletal muscle were investigated using a spectrophotometric method. These compounds diminished the rate of Ca2+ uptake and inhibited the Ca2+ pump ATPase activity of the microsomes. Except for quinine, they appear to have negligible effects on Ca2+ release channels. Of the compounds investigated, mefloquine had the most pronounced effect on Ca2+ uptake and was also the most potent (noncompetitive) inhibitor of Ca(2+)-ATPase (Ki: 53 microM). The ability of mefloquine to interfere with Ca2+ sequestration into the sarcoplasmic reticulum via inhibition of the Ca2+ pump ATPase, may explain some of its actions on the isolated skeletal muscle (relaxation, inhibition of twitch responses, diminution of caffeine contractures) observed in earlier studies. However, its contractile effects are less readily explained. The novel finding that mefloquine inhibits the Ca2+ pump ATPase of the skeletal muscle, suggests that it may have similar effects on the Ca(2+)-ATPases of other tissues.

Molecular geometry and physiochemical characteristics of selected anilinoquinolines, indolo[3,2-c]quinolines and tetrahydroindolo[3,2-d]benzazepines.

The molecular geometry, acid dissociation constants and partition coefficients of the anilinoquinoline (I), indolo[3,2-c]quinoline (II) and tetrahydroindolo[3,2-d] [1]benzazepine (III) ring systems have been determined using representative compounds: 7-chloro-4-(p-anisidino)quinoline (Ia), 3-chloro-8-methoxy-11H-indolo[3,2-c]-quinoline (IIa) and 3-chloro-9-methoxy-5,6,7,12-tetrahydroindolo[3,2-d] [1]benzazepine (IIIa). Ring systems II and III are cyclic analogues of I. The minimum energy conformation was determined by molecular mechanics. Compound IIa is the most planar and conformationally restricted, followed by IIIa and Ia. The acid dissociation constants (pKa) were determined by the solubility method. The ring nitrogen of Ia is most basic, followed by that of IIa and IIIa. The partition coefficient (log P) was determined between octanol and appropriate aqueous buffers by the shaken flask method. Hydrophobicity decreases in the order of Ia > IIa > IIIa. Factors contributing to the different molecular geometry, pKa and hydrophobicity of these related compounds are discussed. The present study may contribute to the design of better drugs with ring system I, II or III.

Pharmacological activity and structure-activity relationship of (+/-)-erythro-mefloquine and related compounds on the isolated mouse phrenic nerve diaphragm preparation.

The effects of the antimalarial agent, (+/-)-erythro-mefloquine and related compounds [(+/-)-threo-mefloquine, (+/-)-erythro-N-methylmefloquine and its N-oxide, quinine, WR 184806 and halofanthrine] on the isolated mouse phrenic nerve diaphragm preparation were investigated. Based on their pharmacological effects, these compounds may be divided into two groups. The group I compounds, comprising (+/)-erythro-mefloquine, (+/-)-threo-mefloquine and WR 184806, were found to exert a contractile effect on the muscle and also to inhibit the indirectly (nerve) stimulated and directly (muscle) stimulated (after alpha-bungarotoxin) twitch responses. The group II compounds, comprising the other compounds except halofanthrine, lacked a contractile effect on muscle but potentiated the directly stimulated twitch responses (after alpha-bungarotoxin). Halofanthrine did not elicit any response from the preparation. The minimum energy conformations of these compounds were determined using an interactive molecular modelling program which incorporates MMX force field for molecular mechanics calculations. Conformational analyses of the erythro and threo isomers of mefloquine hydrochloride were also undertaken using 1H-NMR. The 1H-NMR data supported the proposal made on the basis of MMX calculations that the erythro isomer exists in solution as one predominant conformer whereas the threo isomer is present in solution as a mixed population of two stable conformers. The structure-activity relationship of the compounds is discussed.