Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues

A number of the structurally diverse chemical compounds with functional diketo acid (DKA) subunit(s) have been revealed by combined online and MoStBiodat 3D pharmacophore-guided ZINC and PubChem database screening. We used the structural data available from such screening to analyse the similarities of the compounds containing the DKA fragment. Generally, the analysis by principal component analysis and self-organizing neural network approaches reveals four families of compounds complying with the chemical constitution (aromatic, aliphatic) of the compounds. From a practical point of view, similar studies may reveal potential bioisosteres of known drugs, e.g. raltegravir/elvitegravir. In this context, it seems that mono-halogenated aryl substructures with para group show the closest similarity to these compounds, in contrast to structures where the aromatic ring is halogenated in both ortho- and para-locations.     

Pyrolysis/gas chromatography/mass spectrometry of asphaltene fractions

Two n-heptane-precipitated asphaltene samples, characterized by elemental analysis and nuclear magnetic resonance spectrometry, were fractionated according to relative molecular size by gel permeation chromatography (GPC). Both the whole asphaltene samples and their fractions were analysed by pyrolysis/gas chromatography/mass spectrometry. The data obtained from the pyrograms (average side-chain length, aromaticity index, sulphur compounds vs. aliphatic compounds, presence of SO₂ and CO₂) demonstrated that, in the case of asphaltenes, GPC fractionation results in the separation of different chemical structures ranging from lower molecular mass, highly aromatic and polar compounds to higher molecular mass, less polar and aromatic compounds.     

Correlation of para substituent carbon-13 chemical shifts in aromatic compounds using polar (inductive) and resonance constants which are identical for aliphatic and aromatic compounds

A correlation of para substituted ¹³C chemical shifts in aromatic compounds with substituent polar (inductive) and resonance constants σ* and σ^r of aliphatic compounds has been studied. It has been shown that the precision of the correlations obtained corresponds to that of the Swain-Lupton and Taft two-parameter equations, but the correlation equation used in this work seems to permit a more exact separation of the substituent effects of aromatic compounds into inductive and resonance contributions. Thus, σ* and σ^r substituent constants are universal parameters which can be used in a correlation analysis of the properties of both aliphatic and aromatic compounds.     

Synthesis,anticancer screening,and in silico ADME prediction of novel 2-pyridones as Pim inhibitors

A novel series of 26 substituted N-(2-ethylphenyl)-2-oxo-pyridine-3-carbonitriles have been designed and synthesized via one-pot synthesis of various aromatic aldehydes, different aromatic acetophenones, and 2-cyano-N-(2-ethylphenyl)acetamide 1 . Moreover, cytotoxicity of the target compounds was evaluated by NCI, which selected 14 compounds for one-dose screening. Among them, compound 21 was selected for five-dose screening, which confirmed its potency against most of cancer cell lines. This compound elicited selectivity profile against human cell line WI-38. Cell cycle analysis was carried out, revealed that compound 21 is an apoptosis inducer causing cell cycle arrest at G2/M. Further exploration on the mode of action by evaluating its effect against Pim-1, Pim-2, and Pim-3 demonstrated its inhibitory effect on Pim-1 and Pim-3 rather than Pim-2. Molecular docking showed that compound 21 binds with high affinity to the active site of Pim-1 enzyme through three hydrogen bonds and two arene-H bonds.     

Determination of traces of aromatic compounds in multicomponent mixtures by HRCGC

The possibilities and difficulties of trace analysis of highly complex organic mixtures has been demonstrated by the analysis of traces of numerous aromatic substances in an n-alkane matrix with a boiling point range of 151–270°C. Single column high resolution capillary gas chromatography (under optimized conditions) was performed after an off-line LC preseparation step which had been evaluated using a model mixture. Gas chromatographic quantitation of the 191 aromatic compounds identified was performed with an internal standard; following splitless injection and separation on a polydimethyl-siloxane column under temperature-programmed conditions the compounds were detected by flame ionization. The response factors of aromatic hydrocarbons at trace levels were verified and the precision and reproducibility both of the GC determination and the overall analysis, including preseparation, were studied. Percentage by weight of individual aromatic compounds (mainly alkylbenzenes, indanes, naphthalenes, and acenaphthenes) was in the range 10^?3 to 10^?6.     

Studies on Mechanochemistry: Solid Coordination Compounds from Primary Aromatic Amines and Cobalt(II) Chloride Hexahydrate

Cobalt(II) chloride hexahydrate and primary aromatic amines were reacted by co‐grinding in 1:2 metal salt to ligand ratio under solvent‐free environment at room temperature. Out of 16 solid state reactions, seven cobalt‐amine complexes could be established as solid coordination compounds by elemental analysis, TGA, IR, PXRD, magnetic susceptibility etc., in addition to visual observation of the color change of reaction mixture. Based on investigation of reaction and analysis of products, conclusions with outlook could be made as follows: On top of the —NH₂ group on primary aromatic amines an additional substituent group should better be at para or meta positions and not at ortho position in order to realize the solid coordination compounds. On the other hand, an electron withdrawing substituent or an extra aromatic ring is negative towards formation of the solid coordination compounds. The solid coordination Co(II)‐compounds are labile in solution.     

Volatile and key odourant compounds of Turkish Berberis crataegina fruit using GC-MS-Olfactometry

This research was conducted to identify the aroma and aroma-active compounds of Berberis crataegina for the first time. Volatile profile of B. crataegina was obtained using the purge and trap extraction method with dichloromethane. Gas chromatography was coupled to mass spectrometry (GC–MS) allowed the quantitative and qualitative detection of 22 compounds in the sample. Aldehydes were the main chemical group in the sample and followed by aromatic alcohols and lactone. Aroma extract dilution analysis was implemented for the specification of key odourants of B. crataegina. In total, eight key odourants were detected in the extract of the sample, using GC–MS–Olfactometry and aldehydes were the leading chemical group. The key odourants, found to be contributing to the overall aroma in B. crataegina, were nonanal (FD = 1024; green, flowery), hexanal (FD = 512; green) and linalool (FD = 256; flowery, rose) because of high FD factors.     

Characterization of the high molecular mass chlorinated matter in spent bleach liquors (SBL): 3—Mass spectrometric interpretation of aromatic degradation products in SBL

The aromatic content of the high molecular matter in pulp mill bleachery effluents has been characterized after chemical degradation in the laboratory followed by derivatization and gas chromatographic/mass spectrometric analysis. Aromatic molecules with carboxy, hydroxy, methoxy and chloro substituents were separated and identified by recording their computer-reconstructed ion current chromatograms. About 70 aromatic carboxylic acids were tentatively identified as degradation products. Aromatic compounds with hydroxy groups were derivatized to trideuteromethoxy groups in order to distinguish them by mass spectrometry from compounds with naturally occurring methoxy groups. Single and double hydrogen atom transfer between methyl ester and methoxy groups were observed in some molecules and given special attention when they occurred ortho to each other. A methoxy group substituted ortho to a methyl carboxylate resulted in an unusual fragmentation.     

QSAR-based toxicity classification and prediction for single and mixed aromatic compounds

Quantitative structure-activity relationships (QSARs) based on the octanol/water partition coefficient were employed to predict acute toxicities of 36 substituted aromatic compounds and their mixtures. In this study, the model developed by Verhaar et al. was modified and used to calculate octanol/water partition coefficients of chemical mixtures. To validate the model, acute toxicities of these chemicals were measured to Vibrio fischeri in terms of EC⁵⁰. The results indicated that the obtained QSAR models could be used to predict toxicities of samples consisting of these substituted aromatic compounds, individually or in combinations. The obtained equations were proved to be robust enough by using the leave-one-out test method. By classifying these chemicals into two groups, polar and non-polar, the toxicities of chemical mixtures within each group can be predicted accurately from their calculated partition coefficients.     

Uncatalyzed polymerization of bistriazolinediones with electron-rich aromatic compounds via electrophilic aromatic substitution

The reaction of 4-substituted-1,2,4-triazoline-3,5-diones(4R-TD's), i.e., MeTD(4-methyl substituted) and PhTD(4-Phenyl substituted) with electron rich aromatic compounds were investigated. N,N-Dimethylaniline undergoes reaction instantaneously with MeTD and PhTD. Electrophilic aromatic substitution occurred at room temperature at the para position without use of any catalyst. N,N,N′,N′-tetramethyl-m-phenylenediamine (TMPDA) undergoes reaction with 2 mol of PhTD and MeTD which lead to the formation of 2:1 adducts in high yields. These compounds were fully characterized by IR, ¹³C-NMR, ¹H-NMR and elemental analysis and were used as model compounds. The reaction of bistriazolinediones with TMPDA was performed in dimethylformamid at room temperature. The reactions are exothermic, fast, and gave novel polymer structures via electrophilic aromatic substitution. Some physical properties and structural characterization of these new polymers have been studied, and will be reported.     

Magnetic Circular Dichroism of the Long‐Wavelength π‐π* Transitions in Nitrogen‐Containing Heteroconjugated Aromatic Compounds and in Selected Ruthenium Complexes

The long‐wavelength magnetic circular dichroism (MCD) spectra of some nitrogen‐containing heteroconjugated aromatic compounds have been recorded and interpreted on the basis of quantum‐chemical model calculations. In particular, the dependence of the MCD bands on the positions of the N‐atoms inside the aromatic rings and on substituents has been investigated. Some of the compounds considered form Ru²⁺ complexes. The influence of complexation on the long‐wavelength π‐π* bands of the ligands has also been recorded and discussed.     

Dehydrogenation of the NH−NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia

A novel strategy for the dehydrogenation of the NH−NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH₃) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.     

Methodology for Bioassay-Directed Fractionation Studies of Air Particulate Material and Other Complex Environmental Matrices

Abstract

A normal phase HPLC methodology using a semi-preparative polyaminocyano column in conjunction with a selection of short-term genotoxicity assays has been developed for bioassay-directed fractionation studies of complex environmental mixtures. To illustrate the effectiveness of this methodology, an organic extract prepared from respirable air particulate samples collected in Hamilton, Canada was separated into a non-polar aromatic fraction and a polar aromatic fraction using a combination of alumina and Sephadex LH20 chromatography. These fractions were evaluated for their genotoxic potential using the Salmonella/microsome (Ames) assay with six different strains of Salmonella.

The non-polar aromatic fraction was analyzed by normal phase HPLC and the eluent was collected in one-minute subfractions; these subtractions were bioassayed in three different Salmonella strains (YG1021 -S9, YG1024 -S9 and YG1029 +S9) to afford three different mutation profiles of this sample. Some subfractions which exhibited high mutagenic responses were subjected to further chemical analyses using GC/MS in order to identify those compounds responsible for the genotoxic responses. The nitroarene compounds 2-nitrofluoranthene, 1-nitropyrene and 2-nitropyrene and higher molecular weight polycyclic aromatic hydrocarbons such as benzo[a]pyrene and indeno[l,2,3-cd]pyrene were identified and quantified in some of the biologically active subfractions. The normal phase gradient conditions afforded very reproducible retention times for a series of polycyclic aromatic standards with a broad range of compound polarities. In addition, polycyclic aromatic hydrocarbons (PAH) were observed to elute from the normal phase HPLC column in a series of peaks; successive peaks contained PAH of increasing molecular weight while any individual peak was shown to contain PAH of the same molecular weight.     

Volatile Constituents of Achillea ligustica All. by HS-SPME/GC/GC-MS. Comparison with Essential Oils Obtained by Hydrodistillation from Corsica and Sardinia

The volatile components extracted from the headspace (HS) of Achillea ligustica All. samples and their separated organs using solid phase microextraction (SPME) were investigated by gas chromatography and gas chromatography-mass spectrometry. Fiftyseven compounds were identified, the main components were camphor (14.2–29.8%), artemisia ketone (0.3–26.7%), santolina alcohol (0.5–9.4%), camphene (3.0–9.0%) and trans-sabinyl acetate (1.6–5.5%). Moreover, the chemical composition of Corsican and Sardinian A. ligustica oils obtained from flowers and leafy stems harvested in four regions of both islands, were investigated. Two collective oils of A. ligustica were also investigated, comparison between both oils as well as from data literature were reported. A comparison of hydrodistillation and HS-SPME extraction of volatile components in term of isolation time, plant-consuming and chemical composition was discussed. HS-SPME technique was clearly fast in contrast to hydrodistillation (90 min/300 min). HS extraction was performed with a much smaller amount of plant than hydrodistillation. Although the aromatic profiles of HS-fractions and oils showed several quantitative differences HS-SPME can be applied to routine control analysis of aromatic and medicinal plants.

     

HPLC post column derivatization of aromatic amines usingN-methyl-9-chloroacridinium triflate

An HPLC post column chemical derivatization procedure based on the interaction between an acridinium triflate and amines to form highly colored derivatives on-line is described for the determination of aromatic amines. Benzocaine and butesin, local anesthetic agents that contain the aromatic amine group, were used as model compounds. Reversed-phase HPLC conditions were developed for both the separation of analytes and the reaction between analytes and the acridinium triflate in the system. Three-dimensional knitted teflon shape coils and the internal diameter and length of the coils were important parameters in reducing band broadening and background noise.N-Methyl-9-chloroacridinium triflate was shown to be applicable to the determination of primary aromatic amines, selected secondary aromatic amines, hydrazides, and hydrazines. Application of the on-line chemical derivatization procedure to the analysis of pharmaceutical dosage forms containing procainamide (primary aromatic amine), isoniazid (hydrazide), and hydralazine (hydrazine) is also described.     

Dehydrogenation of the NH−NH Bond Triggered by Potassium tert‐Butoxide in Liquid Ammonia

A novel strategy for the dehydrogenation of the NH−NH bond is disclosed using potassium tert ‐butoxide (t BuOK) in liquid ammonia (NH₃) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one‐pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.     

Investigation of collision‐induced dissociations involving odd‐electron ion formation under positive electrospray ionization conditions using accurate mass

Collision induced dissociation (CID) has been extensively used for structure elucidation. CID in the electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) modes has been found to generate mostly even‐electron fragment ions while it has been occasionally reported to form odd‐electron free radical ions. However, the structural requirements and the fragmentation mechanisms for free‐radical CIDs have not been well characterized in the literature. For this purpose, we studied a series of aromatic and non‐aromatic compounds such as sulfonamides, N‐aryl amides, tert‐butyl‐substituted aromatic compounds, aryl alkyl ethers, and O‐alkyl aryl oximes using the LTQ? and LTQ Orbitrap? linear ion trap mass spectrometers. The accurate measurement of the fragment ion masses established the unambiguous assignment of the fragment structures resulting from the test compounds. Our results showed that free radical fragmentation is structure dependent and is to a large extent correlated with the neighboring groups in the structures that stabilize the newly formed free radical ions. Copyright © 2010 John Wiley & Sons, Ltd.     

Hydroxy and methoxy substituted N 1,N 4-diarylidene-S-methylthiosemicarbazone iron(III) and nickel(II) complexes

Template reactions of 2,4-dihydroxy-, 2,5-dihydroxy-, 2-hydroxy-3-methoxy- and 2-hydroxy-4-methoxy-benzaldehyde with methoxy- and hydroxy-substituted salicylaldehyde S-methylthiosemicarbazones in the presence of NiCl₂ and FeCl₃ resulted in the corresponding hydroxy- and methoxy-substituted N¹,N⁴-diarylidene-S-methylthiosemi-carbazone complexes. Characterization of the compounds, [Fe(L)Cl] and [Ni(L)], was accomplished by means of elemental analysis, conductivity and magnetic measurements, i.r. and ¹H-n.m.r. spectra. A systematic trend has been observed for the chemical shift values of the aromatic protons in the spectra of complexes.     

Investigation of substituent effects of chalcones by 13C n.m.r. spectroscopy

¹³C chemical shifts for 23 para- and meta-substituted chalcones of the types 1 and 2 have been determined. The aromatic shieldings are compared with previous results for other aromatic derivatives. Correlations of the ¹³C chemical shifts of vinyl carbons and carbonyl carbons as well as ring carbons with Hammett σ parameters, π electron densities and the reactivity parameters of Swain and Lupton provide a consistent picture of electronic effects transmitted through the carbon framework of the compounds studied.     

Comparative chemical analysis of commercial creosotes and solvent refined coal-II materials by high resolution gas chromatography

The chemical composition of a commercially available creosote was compared to a direct coal liquefaction product, i.e., solvent refined coal-II fuel oil blend (SRC-II FOB) using high resolution gas chromatography (HRGC). In addition, hydrogenated products of these materials were studied. Samples were fractionated by chemical class on neutral alumina. Those fractions previously shown to be the most mutagenic and tumorigenic in laboratory bioassays of coal-derived materials were analyzed and compared by HRGC and gas chromatography/mass spectrometry (GC/MS). Individual components were tentatively identified and quantitated. Although similar chemical components were present in the creosote and SRC-II FOB fractions studied, the creosotes had higher concentrations of heavy molecular weight materials and a lower ratio of alkylated to parent polycyclic aromatic compounds than the coal liquefaction products. The creosote samples also had a significantly higher concentration of components which eluted in the polycyclic aromatic hydrocarbon (PAH) chemical class fraction. Amino-substituted PAH were present in both nonhydrogenated coal liquid and creosote materials. The creosote and SRC-II FOB crudes and nitrogen-containing polycyclic aromatic compound (NPAC) chemical class fractions expressed similar microbial mutagenicity. Based on chemical analysis data, the predicted tumorigenic potency of the creosote in laboratory bioassay systems would be equivalent to or greater than the SRC-II FOB.