A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.     

Total spontaneous resolution of chiral covalent networks from stereochemically labile metal complexes

Stereochemically labile copper and zinc complexes with the N,N'-dimethylethylenediamine ligand (dmeda) have been shown to be promising precursors for the total spontaneous resolution of chiral covalent networks. (N,N')-[Cu(NO3)2(dmeda)]infinity crystallises as a conglomerate and yields either enantiopure (R,R)-1 or enantiopure (S,S)-1. A mixed-valence copper(I/II) complex, [{Cu(II)Br2(dmeda)}3(Cu(I)Br)2]infinity (2), which crystallises as a pair of interpenetrating chiral (10,3)-a nets, is formed from CuBr, CuBr2 and dmeda. One net contains ligands with solely (R,R) configuration and exhibits helices with (P) configuration while the other has solely (S,S)-dmeda ligands and gives rise to a net in which the helices have (M) configuration. The whole crystalline arrangement is racemic, because the interpenetrating chiral nets are of opposite handedness. With zinc chloride (R,S)-[ZnCl(dmeda)2]2[ZnCl4] (3) is obtained, which is a network structure, although not chiral. Total spontaneous resolution of stereochemically labile metal complexes formed from achiral or racemic building blocks is suggested as a viable route for the preparation of covalent chiral networks. Once the absolute structure of the compound has been determined by X-ray crystallography, a quantitative determination of the enantiomeric excess of the bulk product can be undertaken by means of solid-state CD spectroscopy.     

Nonspecific interactions of a carboxylate-substituted PPE with proteins. A cautionary tale for biosensor applications

Two carboxylate-substituted, fluorescent (Phi = 0.08), water-soluble poly(p-phenyleneethynylene)s (PPE) and a water-soluble model compound were exposed to a series of proteins and bovine serum. While the anionic PPEs do not have any specific binding sites, they form stable complexes with histone, lysozyme, myoglobin, and hemoglobin. The complex formation was evidenced by fluorescence quenching. Bovine serum albumin does not quench the fluorescence of the PPEs but enhances it, probably due to its surfactant character. These results imply that the use of charged conjugated polymers as biosensors, while an attractive proposition, has to take into account strong nonspecific interactions between conjugated polymers and the host of proteins that is found in cells and complex biological fluids.     

Asymmetry of electron transmission through monolayers of helical polyalanine adsorbed on gold surfaces

Polyalanine derivatives containing cysteamine linker R-(Ala)14NH-(CH2)2-SH, where R is ferrocenecarbonyl or hydrogen, were synthesized and then used to form self-assembled monolayers on gold. The tilt angles and the packing density of the molecules within monolayer assemblies were determined by FTIR spectroscopy and scanning tunneling microscopy, respectively. Electrochemical properties of monolayer-modified electrodes were studied using cyclic voltammetry and impedance spectroscopy. Measurements of electron-transfer rates using electrochemical techniques and scanning tunneling spectroscopy revealed asymmetry dependent on the applied voltage. It is suggested that the observed electron-transfer behavior is connected with the electric field generated by the molecular dipole of the polyalanine helix.     

Synthesis,characterisation and ferric ion complexation studies of chelating probes for oxidative stress

The ferric ion binding characteristics of a novel chelating probe for detecting reactive oxygen and nitrogen species are reported. The probe comprises a polyaminocarboxylic acid chelator (EDTA) conjugated with aromatic amino acids. The probe (i) complexes redox-active and non-redox active metal ions and (ii) differentiates between different reactive oxygen/nitrogen species based upon the reaction products with same. The ferric ion binding characteristics were measured using species distribution and electronic absorption spectroscopic investigations. Over the physiological pH range a favoured one to one complex exists.     

Chemo-enzymatic synthesis of 4-methylumbelliferyl beta-(1-->4)-D-xylooligosides: new substrates for beta-D-xylanase assays

Transglycosylation catalyzed by a beta-D-xylosidase from Aspergillus sp. was used to synthesize a set of 4-methylumbelliferyl (MU) beta-1-->4-D-xylooligosides having the common structure [beta-D-Xyl-(1-->4)]2-5-beta-D-Xyl-MU. MU xylobioside synthesized chemically by the condensation of protected MU beta-D-xylopyranoside with ethyl 2,3,4-tri-O-acetyl-1-thio-beta-D-xylopyranoside was used as a substrate for transglycosylation with the beta-D-xylosidase from Aspergillus sp. to produce higher MU xylooligosides. The structures of oligosaccharides obtained were established by 1H and 13C NMR spectroscopy and electrospray tandem mass spectrometry. MU beta-D-xylooligosides synthesized were tested as fluorogenic substrates for the GH-10 family beta-D-xylanase from Aspergillus orizae and the GH-11 family beta-D-xylanase I from Trichoderma reesei. Both xylanases released the aglycone from MU xylobioside and the corresponding trioside. With substrates having d.p. 4 and 5, the enzymes manifested endolytic activities, splitting off MU, MUX, and MUX2 primarily.     

Conformational equilibria and photoinduced tautomerization in 2-(2′-pyridyl)pyrrole

Depending on the polarity and protic abilities of the solvent, 2-(2′-pyridyl)pyrrole can exist in either syn or anti rotameric forms. In nonpolar solvents, intramolecular excited state single proton transfer is observed, manifested by the appearance of low-energy tautomeric emission. The solvent-assisted excited state double proton transfer reaction is also detected. DFT calculations confirm low barriers for both single and double proton transfer processes in the lowest excited singlet state and show different character of the tautomerization in both cases: in the intramolecular reaction, mutual approach of two nitrogen atoms plays an important role.     

Synthesis of fused purinoquinazolines. Three new heterocyclic ring systems

The Ullmann reaction of 8-aminotheophylline or 8-aminocaffeine with 2-chlorobenzoic acid and of 8-bromotheophylline with ethyl-2-aminobenzoate afforded derivatives of three new heterocyclic systems: purino[7,8-α]quinazoline-5,9,11(6H,8H,10H)-trione, purino[8,9-b]quinazoline-2,4,11(1H,3H,5H)-trione and purino[8,7-b]quinazoline-2,4,6(1H,3H,11H)-trione, respectively.     

Study of the winter and summer changes of the air composition in the church of Szalowa, Poland, related to conservation

The St. Michael Archangel’s Church in Szalowa, Poland, was selected for closer investigation with respect to the indoor/outdoor air exchange and its influence on the air quality and work arts preservation. Chemical composition, size and abundance of particulate matter and concentration of gases NO₂, SO₂, O₃ inside and outside the church were determined. To study seasonal variation of the weather condition (temperature, inversion level, wind direction) and the influence of seasonal sources of the air pollution (like heating of the nearby houses), samples were collected in winter and summer time. It was stated that suspended particulate matter inside the wooden church has in general an outdoor source. Several groups of particles were distinguished such as the organic ones, soil dust, nitrates and sulphates. In case of organic and soil dust particles, the concentration inside was higher than outside. From the results, in comparison to literature data, one can conclude that accumulation of particulate suspended matter in the church is more intense than in other types of buildings. Gaseous pollutants were detected but their concentration was negligible.     

Detection and quantification of cocoa butter equivalents in cocoa butter and plain chocolate by gas liquid chromatography of triacylglycerols

The development and in-house testing of a method for the detection and quantification of cocoa butter equivalents in cocoa butter and plain chocolate is described. A database consisting of the triacylglycerol profile of 74 genuine cocoa butter and 75 cocoa butter equivalent samples obtained by high-resolution capillary gas liquid chromatography was created, using a certified cocoa butter reference material (IRMM-801) for calibration purposes. Based on these data, a large number of cocoa butter/cocoa butter equivalent mixtures were arithmetically simulated. By subjecting the data set to various statistical tools, reliable models for both detection (univariate regression model) and quantification (multivariate model) were elaborated. Validation data sets consisting of a large number of samples (n = 4050 for detection, n = 1050 for quantification) were used to test the models. Excluding pure illipé fat samples from the data set, the detection limit was determined between 1 and 3% foreign fat in cocoa butter. Recalculated for a chocolate with a fat content of 30%, these figures are equal to 0.3-0.9% cocoa butter equivalent. For quantification, the average error for prediction was estimated to be 1.1% cocoa butter equivalent in cocoa butter, without prior knowledge of the materials used in the blend corresponding to 0.3% in chocolate (fat content 30%). The advantage of the approach is that by using IRMM-801 for calibration, the established mathematical decision rules can be transferred to every testing laboratory.