Calculating similarities between biological activities in the MDL Drug Data Report database

There are a number of licensed databases that assign biological activities to druglike compounds. The MDL Drug Data Report (MDDR), compiled from the patent literature, is a popular example. It contains several hundred distinct activities, some of which are therapeutic areas (e.g., Antihypertensive) and some of which are related to specific enzymes or receptors (e.g., ACE inhibitor). There are several data mining applications where it would be useful to calculate a similarity between any two activities. Two distinct activity labels can have a significant similarity for a number of reasons: two activities can be nearly synonymous (e.g., CCK B antagonist vs Gastrin antagonist), one activity may be a subset of another (e.g., Dopamine (D2) agonist vs Dopamine agonist), or an activity can be the mechanism by which another activity works (e.g., ACE inhibitor vs Antihypertensive), etc. In an ideal world, similarities for two activities could be calculated simply by comparing the compounds they have in common, but in hand-curated databases such as the MDDR the assignment of activities to compounds are inevitably inconsistent and incomplete. We propose a number of methods of calculating activity-activity similarities that hopefully compensate for errors in hand-curation. Two of these, TIMI and trend vector, show promise. Soft clustering of the activities using a union of similarity methods shows a reasonable association of therapeutic areas with their mechanisms.     

QUENCHING OF METHYLCYCLOHEXANE FLUORESCENCE BY METHANOL*

We measured the fluorescence emission spectrum and intensity decays of methylcyclohexane (MCH) when excited by simultaneous absorption of two photons at 298 nm. The steady-state intensities and lifetimes were both decreased by methanol, which was found to be an efficient quencher of MCH fluorescence. Methanol quenching of MCH is clearly dynamic, but the exact mechanism of quenching is unclear. Dynamic quenching of MCH was also observed by water and n-propanol. These results suggest that alkane fluorescence from biopolymers, if observable, will only occur from regions of the macromolecules that are not exposed to water.     

Separation of Trp-Arg and Arg-Trp using G-quartet-forming DNA oligonucleotides in open-tubular capillary electrochromatography

DNA oligonucleotides that form intramolecular G-quartet structures were investigated as stationary phase reagents for separation of mixtures of the isomeric dipeptides Trp-Arg and Arg-Trp in open-tubular capillary electrochromatography (OTCEC). The oligonucleotides included a thrombin-binding aptamer that forms a biplanar G-quartet structure and an oligonucleotide that forms a 4-plane G-quartet structure. Fluorescence, circular dichroism and UV-visible absorbance spectroscopies were used in batch solution studies to indicate interactions between the dipeptides and the biplanar G-quartet structure. Results for OTCEC separations were compared with results obtained for capillary zone electrophoresis separations on a bare capillary. Temperature studies suggest that resolution is improved when the G-quartet structure is partially destabilized, but control experiments in which potassium chloride was not included in the mobile phase indicate that the G-quartet structure nevertheless plays a role in the separations.     

The oscillation frequency of a quartz resonator in contact with liquid

A simple relationship is derived which expresses the change in oscillation frequency of a quartz crystal in contact with a fluid in terms of material parameters of the fluid and the quartz. The relationship is Δf = ?f^{$\text{3}\text{2}$}₀(η_L?_L/πμ_Q?_Q)^{$\text{1}\text{2}$}, where f₀ is the oscillation frequency of the free (dry) crystal, η_L and ?_L are the absolute viscosity and density of the liquid, respectively, and μ_Q and ?_Q are the elastic modulus and density of the quartz. This relation is obtained from a simple physical model which couples the shear wave in the quartz to a damped shear wave in the fluid. Quantitative comparisons with two test cases, aqueous solutions of glucose and ethanol at various concentrations, demonstrate the accuracy of this model.     

Anionic polymerization and copolymerization of p-bromostyrene

Monodispersed poly(4-bromostyrenes) (PBs) and their block copolymers with styrene, isoprene, and 3-methylbutene were prepared and characterized by GPC and NMR. Polystyryl and α-methylstyryl carbanions act as effective initiators of the anionic polymerization of Bs in THF. The undersirable side reactions, due to thermally or photochemically induced decomposition of the bromostyryl carbanions, PBs^?, may be eliminated by conducting the reaction at ?78°C and in the dark. Under such conditions, the rate constant of propagation, k_p (?78°), is 1.5 × 10³ M^?1 s^?1. Radical anions, \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm Bs}^{\mathop - \limits_ \cdot} $\end{document}, formed as result of electron transfer from sodium naphthalenide to Bs, may eject spontaneously bromine ions. This step and reactions involving the respective phenyl radicals compete at ?78°C with the addition steps leading to polymer formation. Electron affinity of Bs seems to be much higher than that of styrene or isoprene, and PBs^? carbanions do not add to the latter monomers. Addition of Bs to polyisoprenyl carbanions leads to formation of the BsIBs block copolymers. BsIBs, prepared in THF, may be converted by preferential hydrogenation of the 1–2 adducts into block copolymers of Bs with poly(2-methylbutene) and isoprenyl segments. The effectiveness of Bs as a flame retarding constituent of polymeric systems seems to be much more pronounced when it is incorporated in a “block” than in a random fashion. A considerably larger fraction of PBs is required to achieve the same LOI value when the respective homopolymers are blended. Spatial distribution of the easily charred microdomains in the block copolymers is believed to be responsible for this phenomenon.     

Pressure-induced hydration at 0.6 GPa in a synthetic gallosilicate zeolite

The onset of pressure-induced hydration and volume expansion is lowered to 0.6 GPa via the increased flexibility of the host lattice using isomorphous substitution of Al by larger Ga in a sodium aluminosilicate natrolite.     

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.     

Heterocyclic amines. A convenient synthesis of 3,5-diamino-1,2,4-triazine derivatives

A facile synthesis of 3, 5-diamino-1, 2,4-triazines (I) via condensations in acidic media of acylnitriles with aminoguanidine and subsequent base-catalyzed cyclization of the resulting acylnitrile amidinohydrazones (IV) is described.     

Nitrotyrosine-modified proteins and oxidative stress induced by diesel exhaust particles

Protein tyrosine nitration is a post-translational modification that occurs under conditions of oxidative stress and may play a role in the pathogenesis of diseases such as asthma. Through their ability to generate reactive oxygen species in macrophages and epithelial cells, particulate pollutants, such as diesel exhaust particles (DEPs), may lead to a worsening of the asthmatic condition. In this study, we looked for evidence of oxidative modification of proteins in RAW 264.7 cell line treated with DEP chemicals. We show that the induction of oxidative stress is accompanied by 53 newly expressed proteins which are suppressed by a thiol antioxidant, N-acetylcysteine. These include antioxidant enzymes, pro-inflammatory components, and products of intermediary metabolism. In addition, inducible nitric oxide synthase (iNOS) was identified as a biologically relevant oxidative stress protein that is induced concurrent with increased NO production and protein tyrosine-nitration in DEP-exposed RAW 264.7 cells. Utilizing two-dimensional gel electrophoresis, anti-nitrotyrosine immunoblotting, and mass spectrometry led to the identification of an additional ten nitrotyrosine modified proteins, including oxidative stress proteins involved in intermediary metabolism (e.g., GAPDH and enolase), antioxidant defense (e.g., MnSOD) and inhibition of proteosomal activity (e.g., Hsp 90alpha). These oxidative proteins may serve as markers for oxidative stress generation in vivo.     

Photometrische Bestimmung von Nitrat und Nitrit in Schwefels?ure mit Brucin

Zusammenfassung Bei der Wahl einer geeigneten analytischen Methode für die Nitrat- und Nitritbestimmung in konzentrierter Schwefelsäure sind die bisher bekannten Verfahren [1,3–12] wegen ihrer ungenügenden Empfindlichkeit oder wegen Schwierigkeiten bei der Probeaufbereitung auszuschließen. Wir haben daher für diesen Zweck eine einfache und zuverlässige Modifikation unserer Brucinmethode [2] ausgearbeitet, wobei eine noch größere Empfindlichkeit der Nitratbestimmung erreicht wurde. Bei geeigneter Acidität kann die Brucin-methode auch für die selektive Nitritbestimmung verwendet werden. Das hier beschriebene Verfahren ersetzt eine analoge Modifikation [5], die wegen ihrer methodischen Unrichtigkeit unzureichend ist.

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Photometric determination of nitrate and nitrite in sulphuric acid using brucine

A modified brucine method is recommended as a result of a detailed study of the reaction conditions. By suitable selection of acidity and tempering period two ranges of sensitivity have been obtained for the nitrate determination (0–5 and 0.1 bis 0.5 g NO₃ ^–-N/g H₂SO₄, resp.). At low concentrations of sulphuric acid nitrite may be determined in presence of nitrate by the same brucine method. Maximum errors are ±0.02 resp. ±0.05 g NO₃ ^–-N and ±0.05 NO₂ ^–-N.