Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity.

G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. Here, we utilize high-throughput, large-scale custom DNA G4 microarrays to analyze the G4-binding selectivity of BMVC. BMVC preferentially binds to the parallel MycG4 and selectively recognizes flanking sequences of parallel G4s, especially the 3'-flanking thymine. Importantly, the microarray results are confirmed by orthogonal NMR and fluorescence binding analyses. Our study demonstrates the potential of custom G4 microarrays as a platform to broadly and unbiasedly assess the binding selectivity of G4-interactive ligands, and to help understand the properties that govern molecular recognition.

In vitro cytotoxicity assessment of monocationic and dicationic pyridinium-based ionic liquids on HeLa, MCF-7, BGM and EA.hy926 cell lines.

Dicationic ionic liquids (ILs) generally possess higher thermal and electrochemical stability than the analogous monocationic ILs, which makes them more suitable for high-temperature applications as solvents for organic reactions, lubricants or stationary phase in gas chromatography. However, knowledge on dicationic IL cytotoxicity is still scarce. Here we explore the cytotoxicity of twelve mono- and dicationic pyridinium-based ILs on HeLa, MCF-7, BGM and EA.hy926 cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, cell cycle arrest assays, apoptosis experiments and orange staining were carried out. The results showed that dicationic ILs are generally less cytotoxic than their monocationic counterparts. In monocationic ILs, cytotoxicity was stronger when they contain long alkyl chains, because of their higher lipophilicity. However, the full effect of the length of the linkage alkyl chain of dicationic ILs on cytotoxicity is not clear probably because the chain is "trapped" between both cationic moieties. IL cytotoxicity is highly dependent on the cell type, and HeLa cells exposed to [C12Pyr]Br die via apoptosis. The present study increases our knowledge of IL cytotoxicity on human and monkey cells and clarifies the cell death mechanism. The results suggest that dicationic ILs offer the potential to replace some monocationic ILs because of their lower cytotoxicity.

Effects of chain rigidity on the adsorption of a polyelectrolyte chain on mixed lipid monolayer: a Monte Carlo study.

We apply Monte Carlo simulation to explore the adsorption of a positively charged polyelectrolyte on a lipid monolayer membrane, composed of electronically neutral, monovalent anionic and mulvitalent anionic phospholipids. We systematically assess the influence of various factors, including the intrinsic rigidity of the polyelectrolyte chain, the bead charge density of the polyelectrolyte, and the ionic strength of the saline solution, on the interfacial structural properties of the polyelectrolyte/monolayer complex. The enhancement of the polyelectrolyte chain intrinsic rigidity reduces the polyelectrolyte conformational entropy loss and the energy gains in electrostatic interaction, but elevates the segregated anionic lipid demixing entropy loss. This energy-entropy competition results in a nonmonotonic dependence of the polyelectrolyte/monolayer association strength on the degree of chain rigidity. The semiflexible polyelectrolyte, i.e., the one with an intermediate degree of chain rigidity, is shown to associate onto the ternary membane below a higher critical ionic concentration. In this ionic concentration regime, the semiflexible polyelectrolyte binds onto the monolayer more firmly than the pancake-like flexible one and exhibits a stretched conformation. When the chain is very rigid, the polyelectrolyte with bead charge density Zb = +1 exhibits a larger tail and tends to dissociate from the membrane, whereas the one with Zb = +2 can still bind onto the membrane in a bridge-like conformation. Our results imply that chain intrinsic rigidity serves as an efficient molecular factor for tailoring the adsorption/desorption transition and interfacial structure of the polyelectrolyte/monolayer complex.

Assessment of bromide-based ionic liquid toxicity toward aquatic organisms and QSAR analysis.

The toxicities of 24 bromide-based ionic liquids (Br-ILs) towards Vibrio fischeri (V. fischeri) and Daphnia magna (D. magna) were determined. These Br-ILs are composed of a bromide ion and a generic cation (i.e., pyrrolidinium, piperidinium, pyridinium or imidazolium) with different alkyl side chains. QSAR models with relatively high correlation coefficients, R(2), of 0.954 and 0.895 were developed for V. fischeri and D. magna. The model for V. fischeri indicated that the Br-IL toxicity towards V. fischeri was negatively correlated with the energy of the lowest unoccupied molecular orbitals (ELUMO) which reflects the electron affinities (EAs) and positively correlated with the volumes of Br-IL cations. For the D. magna model, the Br-IL toxicity was positively correlated with the dipole moment (µ) and negatively correlated with the total energy (TE) that is highly correlated with the molecular volume (V). For Br-ILs with the same cation ring, the toxicity increased as the length of the alkyl chains increased. For the same alkyl chain length, the toxicity order for V. fischeri was pyridinium>imidazolium>piperidinium>pyrrolidinium, except for those containing octyl side chains, while the toxicity ranking for D. magna was imidazolium~pyridinium>piperidinium>pyrrolidinium.

In situ assessment of effects of the bromide- and fluoride-incorporating adhesive systems on biofilm and secondary caries.

AIM: This in situ study assessed the effects of adhesive systems containing or not fluoride and/or the antibacterial monomer 12-methacryloyloxydodecylpyridinium bromide (MDPB) on the microbiological composition of dental biofilm and enamel demineralization. MATERIALS AND METHODS: During two phases of 14 days, ten volunteers wore intraoral palatal appliances containing two slabs of human enamel according to a double-blind, crossover design. The slabs were randomly restored using a composite resin and one of the following adhesive systems: All-Bond SE(TM) (self-etch, fluoride/MDPB free adhesive, AB) and Clearfl Protect Bond (self-etch containing fluoride and MDPB adhesive, CB). The biofilm formed on the slabs was analyzed with regard to total and mutans streptococci and lactobacilli counts. Demineralization represented by integrated area of hardness × lesion depth Delta S ( ΔS) was determined on enamel by analysis of cross-sectional microhardness, at 20 and 70 µm from the restoration margin. Data were analyzed by ANOVA. RESULTS: No statistically significant difference was found either in enamel demineralization or in the microbiological composition of dental biofilm. CONCLUSION: All adhesive systems containing or not fluoride and/or MDPB tested were unable to inhibit secondary caries in the in situ model used in the present research.

In vitro and in vivo genotoxicity assessment of HI-6 dimethanesulfonate/oxime.

Organophosphate compounds, which induce organophosphate poisoning, were originally used as pesticides. But this type of product has also been used as warfare nerve agent like sarin, soman, Russian VX, or tabun. HI-6-dimethanesulfonate is a salt of the oxime HI-6 used in the treatment of nerve-agent poisoning. It is known to be the best re-activator component of inactivated acetyl cholinesterase. HI-6-dimethanesulfonate has shown a higher level of solubility with similar potency to reactivate acetyl cholinesterase and a similar pharmacokinetics profile compared with HI-6 dichloride. HI-6 dimethanesulfonate was tested for its mutagenic and genotoxic potential by use of the standard ICH S2R (1) battery for the evaluation of pharmaceuticals. HI-6-dimethanesulfonate was mutagenic in the Ames test only in the presence of metabolic activation. In the mutation assay at the Tk locus in L5178Y mouse-lymphoma cells, HI-6-dimethanesulfonate showed mutagenic activity both with and without metabolic activation, with a significant increase in small colonies. The effects were in favour of a clastogenic activity. It was concluded that the compound was mutagenic and possibly clastogenic in vitro. In contrast, the in vivo micronucleus test in rat bone-marrow did not demonstrate any genotoxic activity and the Comet assay performed in rat liver did not show any statistically or biologically significant increases in DNA strand-breaks. The results of both in vivo studies performed on two different organs with two endpoints are sufficient to conclude the absence of a genotoxic hazard in vivo and to consider that there is no genotoxic concern in humans for HI-6-dimethanesulfonate.

QSAR models for the reactivation of sarin inhibited acetylcholinesterase by quaternary pyridinium oximes based on Monte Carlo method.

Monte Carlo method has been used as a computational tool for building QSAR models for the reactivation of sarin inhibited acetylcholinesterase (AChE) by quaternary pyridinium oximes. Simplified molecular input line entry system (SMILES) together with hydrogen-suppressed graph (HSG) was used to represent molecular structure. Total number of considered oximes was 46 and activity was defined as logarithm of the AChE reactivation percentage by oximes with concentration of 0.001 M. One-variable models have been calculated with CORAL software for one data split into training, calibration and test set. Computational experiments indicated that this approach can satisfactorily predict the desired endpoint. Best QSAR model had the following statistical parameters: for training set r2=0.7096, s=0.177, MAE=0.148; calibration set: r2=0.6759, s=0.330, MAE=0.271 and test set: r2=0.8620, s=0.182, MAE=0.150. Structural indicators (SMILES based molecular fragments) for the increase and the decrease of the stated activity are defined. Using defined structural alerts computer aided design of new oxime derivatives with desired activity is presented.

Kinetic assessment of N-methyl-2-methoxypyridinium species as phosphonate anion methylating agents.

Organophosphate nerve agents and pesticides are potent inhibitors of acetylcholinesterase (AChE). Although oxime nucleophiles can reactivate the AChE-phosphyl adduct, the adduct undergoes a reaction called aging. No compounds have been described that reactivate the aged-AChE adduct. A family of 2-methoxypyridinium species which reverse aging in a model system is presented. A kinetic study of this system, which includes an SAR analysis, demonstrates that the reaction is highly tunable based on the ring substituents.

Assessment of bactericidal effects of quaternary ammonium-based antibacterial monomers in combination with colloidal platinum nanoparticles.

Pretreatment of dentin using colloidal platinum nanoparticles (CPtN) can enhance the bond strength of dentin adhesives. However, the combination of CPtN, which is negatively charged, with cationic monomer-containing adhesive may reduce the antibacterial activity of the original material. Thus, the purpose of this study was to assess the effect of CPtN on the bactericidal activity of two cationic antibacterial monomers, 12-methacryloyloxydodecylpyridinium bromide (MDPB) and methacryloxylethyl cetyl dimethyl ammonium chloride (DMAE-CB). The rapid killing effects of the two monomers against planktonic or attached Streptococcus mutans in the presence or absence of CPtN were examined by viable cell counts. The measurement of minimum inhibitory and bactericidal concentrations demonstrated that CPtN up to 2.5 mM has no antibacterial activity. In the absence of CPtN, rapid killing of both planktonic and attached Streptococcus mutans were achieved by the two cationic monomers. Combination with 0.1 mM CPtN did not reduce the bactericidal effects of the two monomers, indicating that CPtN may be used as a pretreatment with antibacterial adhesives.

Assessment of acetylcholinesterase activity using indoxylacetate and comparison with the standard Ellman's method.

Assay of acetylcholinesterase (AChE) activity plays an important role in diagnostic, detection of pesticides and nerve agents, in vitro characterization of toxins and drugs including potential treatments for Alzheimer's disease. These experiments were done in order to determine whether indoxylacetate could be an adequate chromogenic reactant for AChE assay evaluation. Moreover, the results were compared to the standard Ellman's method. We calculated Michaelis constant Km (2.06 × 10(-4) mol/L for acetylthiocholine and 3.21 × 10(-3) mol/L for indoxylacetate) maximum reaction velocity V(max) (4.97 × 10(-7) kat for acetylcholine and 7.71 × 10(-8) kat for indoxylacetate) for electric eel AChE. In a second part, inhibition values were plotted for paraoxon, and reactivation efficacy was measured for some standard oxime reactivators: obidoxime, pralidoxime (2-PAM) and HI-6. Though indoxylacetate is split with lower turnover rate, this compound appears as a very attractive reactant since it does not show any chemical reactivity with oxime antidots and thiol used for the Ellman's method. Thus it can be advantageously used for accurate measurement of AChE activity. Suitability of assay for butyrylcholinesterase activity assessment is also discussed.

Selective complexation of N-alkylpyridinium salts: binding of NAD+ in water.

A new class of receptor molecules is presented that is highly selective for N-alkylpyridinium ions and electron-poor aromatics. Its key feature is the combination of a well-preorganized molecular clip with an electron-rich inner cavity and strategically placed, flanking bis-phosphonate monoester anions. This shape and arrangement of binding sites attracts predominantly flat electron-poor aromatics in water, binds them mainly by pi-cation, pi-pi, CH-pi, and hydrophobic interactions, and leads to their highly efficient desolvation. NAD(+) and NADP, the important cofactors of many redox enzymes, are recognized by the new receptor molecule, which embraces the catalytically active nicotinamide site and the adenine unit. Even nucleosides such as adenosine are likewise drawn into the clip's cavity. Complex formation and structures were examined by one- and two-dimensional NMR spectroscopy, Job plot analyses, and isothermal titration microcalorimetric (ITC) measurements, as well as quantum chemical calculations of (1)H NMR shifts. The new receptor molecule is a promising tool for controlling enzymatic oxidation processes and for DNA chemistry.

Assessment of the contributions of CYP3A4 and CYP3A5 in the metabolism of the antipsychotic agent haloperidol to its potentially neurotoxic pyridinium metabolite and effect of antidepressants on the bioactivation pathway.

As a plausible explanation for the large interindividual variability in the pharmacokinetics of the neuroleptic agent haloperidol, the contributions of CYP3A isozymes (CYP3A4 and the polymorphic CYP3A5) predominantly involved in haloperidol bioactivation to the neurotoxic pyridinium species 4-(4-Chlorophenyl)-1-[4-(4-fluorophenyl)-4-oxobutyl]-pyridinium (HPP(+)) were assessed in human liver microsomes and heterologously expressed enzymes. Based on recent reports on drug-drug interactions between haloperidol and antidepressants including selective serotonin reuptake inhibitors, the inhibitory effects of antidepressants on the CYP3A4/5-mediated haloperidol bioactivation were also evaluated. HPP(+) formation followed Michaelis-Menten kinetics in microsomes, recombinant CYP3A4, and CYP3A5 with K(m) values of 24.4 +/- 8.9 microM, 18.3 +/- 4.9 microM, and 200.2 +/- 47.6 microM, respectively, and V(max) values of 157.6 +/- 13.2 pmol/min/mg of protein, 10.4 +/- 0.6 pmol/min/pmol P450, and 5.16 +/- 0.6 pmol/min/pmol P450, respectively. The similarity in K(m) values between human liver microsomal and recombinant CYP3A4 incubations suggests that polymorphic CYP3A5 may not be an important genetic contributor to the interindividual variability in CYP3A-mediated haloperidol clearance pathways. Besides HPP(+), a novel 4-fluorophenyl-ring-hydroxylated metabolite of haloperidol in microsomes/CYP3A enzymes was also detected. Its formation was consistent with previous reports on the detection of O-sulfate and -glucuronide conjugates of a fluorophenyl ring-hydroxylated metabolite of haloperidol in human urine. Finally, all antidepressants except buspirone inhibited the CYP3A4/5-catalyzed oxidation of haloperidol to HPP(+) in a concentration-dependent manner. Based on the estimated IC(50) values for inhibition of HPP(+) formation in microsomes, the antidepressants were ranked in the following order: fluoxetine, nefazodone, norfluoxetine, trazodone, and fluvoxamine. These inhibition results suggest that clinically observed drug-drug interactions between haloperidol and antidepressants may arise via the attenuation of CYP3A4/5-mediated 4-(4-chlorophenyl)-1-[4-(4-fluorophenyl)-4-oxobutyl]-4-piperidinol biotransformation pathways.