A comprehensive docking study on the selectivity of binding of aromatic compounds to proteins

Generally, computer-aided drug design is focused on screening of ligand molecules for a single protein target. The screening of several proteins for a ligand is a relatively new application of molecular docking. In the present study, complexes from the Brookhaven Protein Databank were used to investigate a docking approach of protein screening. Automated molecular docking calculations were applied to reproduce 44 protein-aromatic ligand complexes (31 different proteins and 39 different ligand molecules) of the databank. All ligands were docked to all different protein targets in altogether 12090 docking runs. Based on the results of the extensive docking simulations, two relative measures, the molecular interaction fingerprint (MIF) and the molecular affinity fingerprint (MAF), were introduced to describe the selectivity of aromatic ligands to different proteins. MIF and MAF patterns are in agreement with fragment and similarity considerations. Limitations and future extension of our approach are discussed.     

Isomerization of substituted tricyclic 4,5-dihydropyrazoles

Summary The acid and base catalyzed isomerization of some tricyclic 2-pyrazolines with N-Carbamoyl-,N-thiocarbamoyl-and N-phenyl substituents was investigated. Starting fromcis ortrans 3-H, 3a-H diastereomers, equilibrium mixtures ofcis andtrans diastereomers were prepared which were separated and subsequently studied by¹H NMR and¹³C NMR spectroscopy. A mechanism for the isomerization of the pyrazolines is suggested, supported by a deuterium exchange at C-3a.

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Isomerisierung von einigen substituierten 4,5-Dihydropyrazolen

Zusammenfassung Die Isomerisierung einiger tricyclischer 2-Pyrazoline mit N-Carbamoyl-, N-Thiocarbamoyl-und N-Phenyl-substituenten unter saurer und basischer Katalyse wurde untersucht. Ausgehend von dencis odertrans 3-H,3a-H-Diastereomeren wurdencis- undtrans Gleichgewichtsgemische gewonnen, die getrennt und durch¹H- und¹³C-NMR-Spektroskopie untersucht wurden. Ein Mechanismus für die Isomerisierung von Pyrazolinen wird vorgeschlagen, der durch den Deuteriumaustausch in Position 3a-C unterstützt wird.

     

Comparative study on separation of diastereomers by HPLC

Summary Reversed (RP-HPLC) and normal phase chromatographic (NP-HPLC) separations have been developed for diastereomers ofN-acyl-1-methyl-1,2,3,4-tetrahydo-β-carbolines which are acylated derivatives of simple natural β-carboline alkaloids. Separations of derivatives having different acyl moieties in theO,O-diacyl-tartaric acid ester subtituent differed remarkably. Little or no resolution in either NP-HPLC or RP-HPLC could be achieved with the diacetyl-tartrate derivative. Base-line separation by RP-HPLC but no separation by NP-HPLC was possible with the bulkier and more apolar dipivaloyl derivative. Retention order of the bis-benzoylated diastereomers was reversed and separation time increased dramatically by RP-HPLC. Good separation of the medium polarity, but rigid,N-camphanyl derivative by NP-HPLC has been achieved, whereas RP-HPLC could not be used for separation of these diastereomers. Separability of different diastereomers was highly dependent on polarity and rigidity of the derivatizingN-acyl moieties. Conformational analysis by molecular mechanics and comparison of the lowest energy conformational states of the diastereomers was applied to rationalise separation-retention behaviour of stereoisomers by RP-HPLC. Presented at Balaton Symposium '01 on High-Performance Separation Methods, Siófok, Hungary, September 2–4, 2001     

Analysis of cyanobacterial toxins (anatoxin-a, cylindrospermopsin, microcystin-LR) by capillary electrophoresis

Capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) were applied to the simultaneous separation of cyanobacterial toxins (anatoxin-a, microcystin-LR, cylindrospermopsin). The analytical performance data of both methods, optimized for the three toxins, were similar with a precision of migration times smaller than 0.8 RSD% and a detection limit in the range of 1-4 microg/mL, using spectrophotometric detection at 230 nm. Both methods were applied to an analysis of cyanotoxins in water bloom samples and crude cyanobacterial extracts. The results obtained indicate that, for complex matrices, the sequential application of CZE and MEKC is necessary. It is recommended to use both CE techniques for the analysis of the same sample in order to confirm the results by an orthogonal approach.     

Comparative analysis of the underground parts ofGentiana species by HPLC with diode-array and mass spectrometric detection

Summary The aim of this work was to compare the chemical composition of the underground parts (roots and rhizomes) ofGentiana cruciata L.,Gentiana pneumonanthe L., andGentiana asclepiadea L.— the three gentians native to Hungary—with that of the widely used stomachicGentiana lutea L., to determine which of the three Hungarian species could be used as a substitute forGentiana lutea in pharmaceutical preparations. The four gentians were compared by means of RPHPLC with diode-array detection (DAD) and electrospray ionization-mass spectrometric detection (ESI-MSD). The quantities of the lead compounds, the secoiridoid-glycosides, in 220 samples of the underground parts of gentians originating from several locations in Hungary, were determined by a more economical RPHPLC-DAD method. The occurrence of the characteristic compounds investigated—bitter principles and xanthones—in the underground parts of the speciesGentiana asclepiadea L. suggest it might be a potential replacement forGentiana lutea L. in pharmaceutical products. Presented at Balaton Symposium '01 on High-Performance Separation Methods, Siófok, Hungary, September 2–4, 2001     

EPR study of free radicals in a main chain thermotropic polymer

Free radicals were generated in a rigid rod-like copolymer via mechanical route and by gamma radiation. The (EPR) method was used for studying free radicals formed at 123 K. The spectra of free radicals observed and the influence of molecular motions on the transport of radical centers in the fracture surface layer are discussed.     

Effects of different alkali metal ions on the cationization of poly(ethylene glycol)s in matrix-assisted laser desorption/ionization mass spectrometry: a new selectivity parameter

The cationization of poly(ethylene glycol)s, PEG 4000 and PEG 6000, under matrix-assisted laser desorption/ionization conditions was studied by using different concentration ratios of the sodium ion, as the reference ion, and another alkali metal ion (Li(+), K(+), Rb(+), Cs(+)). A linear correlation was found between the intensity ratio of the sodiated PEGs and PEGs cationized with alkali metal ions versus the initial concentration ratio of sodium and alkali metal ions. The slopes of these straight lines are proposed as a novel selectivity ratio for the ionization process. The intensity distribution of the cationized PEGs was also investigated. It was found that the cationized oligomers follow Poisson statistics. The M(n) and M(w) values were also evaluated. An explanation for the observed effects is given.     

Nitrogen bridgehead compounds. Part 35. Structures of α-formyl-2,3-polymethylene-3,4-dihydroquinazolin-4-ones

The structures of the title compounds bearing a five-, six- or seven-membered A ring have been investigated by uv and ¹H and ¹³C nmr spectroscopy. The imine-enol-enamine (I-II-III) tautomerism of these compounds depends greatly on the ring size. A significant solvent-dependence is observed only for the five-membered-ring compounds 1 and 2 , which in ethanolic solution exist predominantly in the imine form I, and in chloroform solution in the enol form II. The compounds with a six-membered A ring, 3 and 4 , are mainly in the enamine form III. On protonation, 3 and 4 change into the E and Z isomeric mixture of the enol tautomer II. The seven-membered-ring compound 5 is a mixture of the imine I and the enamine III tautomers.     

Adventages and limits on usage of thermal methods in complex systems

In order to increase the nutrition value of bread, one of the most commonly used foodstuff all over the world, different additives are used in bread processing. In this paper we describe the thermal changes in bread and that of with 0.5% crude soybean lecithin additive. Their thermal stability has been investigated by TG, DSC and EGD methods. The thermal changes were also followed of soy products, lecithin and lysine, ingredients used as bread additives in order to check if they may suffer any thermal degradation during the baking process. The data obtained can be of use only for qualitative conclusions. According to the obtained data at the usual bread baking temperature only the additives in crust may partly decompose while in the crumb, at lower temperatures the additives, due to baking, are not damaged. The thermal methods give a possibility for rapid estimation of processes induced by heat effects in additives during the baking, and they are suitable to detect the changes during the bread-making procedure. However, they are neither suitable to provide any quantitative data on these changes nor facts affecting the nutrition value and of the bread.     

Transition Metal Complexes with Pyrazole-based Ligands. Part 12. Characterisation and thermal decomposition of CuCl2 complexes with di- and trisubstituted pyrazoles

The synthesis of copper(II) chloride complexes with 3,5-dimethylpyrazole, 1-carboxamidine-3,5-dimethylpyrazole, 5-amino-4-carboxamide-1-phenylpyrazole and 4-acetyl-3-amino-5-methylpyrazole is described. The compounds are characterized by elemental analysis, FT-IR spectroscopy, thermal methods, magnetic moment and molar conductivity measurements. Thermal decomposition of the dichloro-(3,5-dimethylpyrazole)-copper(II) complex results in an unstable intermediate with a stochiometric composition. The decomposition of the other compounds is continuous. This revised version was published online in August 2006 with corrections to the Cover Date.