Structural basis for thrombin activation of a protease-activated receptor: inhibition of intramolecular liganding

Protease-activated G protein-coupled receptors (PAR1-4) are tethered-ligand receptors that are activated by proteolytic cleavage of the extracellular domain (exodomain) of the receptor. PAR1, the prototypic member of the PAR family, is the high-affinity thrombin receptor of platelets and vascular endothelium and plays a critical role in blood coagulation, thrombosis, and inflammation. Here, we describe the solution structure of the thrombin-cleaved exodomain of PAR1. The side chains of a hydrophobic hirudin-like (Hir) sequence and adjacent anionic motif project into solution. Docking of the exodomain Hir sequence to exosite I of thrombin reveals that the tethered ligand in the cleaved exodomain bends away from thrombin, leaving its active site available to another large macromolecular substrate. The N-terminal ligand is longer than anticipated and forms an intramolecular complex with a region located in the C terminus of the exodomain. Mutational analysis confirmed that this C-terminal region is a ligand binding site for both intra- and intermolecular ligands. A lipidated-ligand binding site peptide was found to be an effective inhibitor of thrombin-induced platelet aggregation.     

Optimization Condition for Thin-Layer Identification of Bronzes after Anodic Sampling

JPC – Journal of Planar Chromatography – Modern TLC - Qualitative identification of Cu, Sn, Pb, Ni, and Fe in Cu-alloys is presented. The method involves anodic sampling of alloys,...     

Topochemical modification of cotton fibres with carboxymethyl cellulose

Adsorption of carboxymethyl cellulose (CMC) as a method to introduce charged (ionizable) groups onto cellulose cotton fibre surfaces was investigated. The method was based on application of a previously published method used for wood fibres. The amount of adsorbed ionizable groups was determined indirectly by analysis of CMC in solution by the phenol–sulphuric acid method and directly by conductometric titration of the fibres. Results from the two methods correlated well. The molecular weight and purity of the CMC had an influence on its adsorption onto cotton; high molecular weight CMC was preferentially adsorbed. The adsorbed charge correlated linearly with the amount of CMC adsorbed. The total charge of the cotton fibres could be increased by more than 50% by adsorption of CMC. It is expected that this modification procedure can be used in a wide spectrum of practical applications. Lidija Fras Zemljič and Karin Stana-Kleinschek are the members of the European Polysaccharide Network of Excellence (EPNOE).     

Researches on thiazolobenzodiazepines: Behavior of tetrahydro‐1,5‐benzodiazepinethiones with aromatic α‐haloketones

A number of 1‐substituted 4H,5H,6H‐[1,3]thiazolo[3,2‐a][1,5]benzodiazepinium‐11‐bromides and S‐(2‐oxo‐2‐phenyl‐X‐(p)‐ethyl)‐3‐(2‐methyl‐1H‐benzimidazol‐1‐yl) propane (or butane) thioate hydrobromides were obtained by direct reaction of the 5‐acetyl(or formyl, or anilinocarbonyl)‐substituted tetrahydro‐1,5‐benzodiazepine‐2‐thiones with aromatic α‐bromoketones. 2‐[(1‐Acetyl‐2(or 3)‐methyl‐2,3‐dihydro‐1H‐1,5‐benzodiazepin‐4‐yl) sulfanyl]‐1‐phenylethanones as intermediates of the formation of thiazolo [3,2‐a][1,5]benzodiazepine and N‐substituted 2‐methyl‐1H‐benzimidazole derivatives have been synthesized. Semiempirical AM1 calculations of a mechanism and energetic parameters for the heptatomic nucleus rearrangement to benzimidazole ring are presented. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:72–81, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20414     

Water-oil core-shell droplets for electrowetting-based digital microfluidic devices

Digital microfluidics based on electrowetting-on-dielectric (EWOD) has recently emerged as one of the most promising technologies to realize integrated and highly flexible lab-on-a-chip systems. In such EWOD-based digital microfluidic devices, the aqueous droplets have traditionally been manipulated either directly in air or in an immiscible fluid such as silicone oil. However, both transporting mediums have important limitations and neither offers the flexibility required to fulfil the needs of several applications. In this paper, we report on an alternative mode of operation for EWOD-based devices in which droplets enclosed in a thin layer of oil are manipulated in air. We demonstrate the possibility to perform on-chip the fundamental fluidic operations by using such water-oil core-shell droplets and compare systematically the results with the traditional approach where the aqueous droplets are manipulated directly in air or oil. We show that the core-shell configuration combines several advantages of both the air and oil mediums. In particular, this configuration not only reduces the operation voltage of EWOD-based devices but also leads to higher transport velocities when compared with the manipulation of droplets directly in air or oil.     

Antitumour tiazofurin analogues embedded with an amide moiety at the C-2′ position

Synthesis of four new tiazofurin analogues has been accomplished starting from d-glucose. The key step of the synthesis was the three-step cascade that enabled an efficient hydrogen sulfide mediated one-pot conversion of 2-azido-3-O-acyl-ribofuranosyl cyanides to the corresponding 2-alkylamido ribofuranosyl thiocarboxamides. The resulting key intermediates were first converted to protected tiazofurin derivatives by cyclocondensation with ethyl bromopyruvate, and finally to target C-nucleosides by treatment with ammonia in methanol. In vitro cytotoxicities of tiazofurin analogues against a number of human tumour cell lines were recorded and compared with those observed for the parent molecule (tiazofurin), as well as the commercial antitumour agent doxorubicin (DOX). Analogues 2b-d have shown a potent in vitro cytotoxic activity against human myelogenous leukaemia K562. Among solid tumour cell lines, HT29 was sensitive only to 2d, while HeLa cells were sensitive to 2a, 2b and 2d. Only analogue 2a was highly cytotoxic against MCF-7 cells. No tiazofurin analogue exhibits any significant cytotoxicity towards normal foetal lung MRC-5 cells. Downregulation of Bcl-2, activation of caspase-3 and presence of cleavage product of PARP suggest that the cytotoxic effects of tiazofurin analogues 2a-d in K562 might be mediated by apoptosis in a caspase-dependent way. On the contrary, tiazofurin did not induce apoptosis of K562 cells, which suggests a different mechanism of action, most probably through the inhibition of IMPDH. Flow cytometry and Western blot analysis data agreed well with the results of MTT assay, and enabled identification of analogue 2c as the most promising antitumour agent that preferentially target cancer cells over normal cells and thus represents a new lead for further optimization.     

2-Substituted thiazole-4-carboxamide derivatives as tiazofurin mimics: synthesis and in vitro antitumour activity

Tiazofurin analogues bearing a 5-hydroxymethyl-2-methyl-tetrahydrofuro[2,3-d][1,3]dioxol-6-ol moiety as a sugar mimic (2 and 3), and two novel thiazole-based acyclo-C-nucleosides 4 and 16 have been synthesized in multistep sequences starting from d-xylose (compounds 2 and 3) or from d-arabinose (compounds 4 and 16). All synthesized analogues showed potent in vitro antitumour activities against a panel of human tumour cell lines. Flow cytometry data suggest that cytotoxic effects of analogues 2–4 and 16 in the culture of K562 cells might be mediated by apoptosis. It was also found that these analogues induced changes in cell cycle distribution of K562 cells. Results of western blot analysis (upregulation of Bax and downregulation of Bcl-2, activation of caspase-3 and the presence of a PARP cleavage product) suggest that tiazofurin mimics (2–4 and 16) in K562 cells induced apoptosis in a caspase-dependent way.     

Explicit–implicit mapping approach to nonlinear blind separation of sparse nonnegative dependent sources from a single mixture: pure component extraction from nonlinear mixture mass spectra

The nonlinear, nonnegative single‐mixture blind source separation problem consists of decomposing observed nonlinearly mixed multicomponent signal into nonnegative dependent component (source) signals. The problem is difficult and is a special case of the underdetermined blind source separation problem. However, it is practically relevant for the contemporary metabolic profiling of biological samples when only one sample is available for acquiring mass spectra; afterwards, the pure components are extracted. Herein, we present a method for the blind separation of nonnegative dependent sources from a single, nonlinear mixture. First, an explicit feature map is used to map a single mixture into a pseudo multi‐mixture. Second, an empirical kernel map is used for implicit mapping of a pseudo multi‐mixture into a high‐dimensional reproducible kernel Hilbert space. Under sparse probabilistic conditions that were previously imposed on sources, the single‐mixture nonlinear problem is converted into an equivalent linear, multiple‐mixture problem that consists of the original sources and their higher‐order monomials. These monomials are suppressed by robust principal component analysis and hard, soft, and trimmed thresholding. Sparseness‐constrained nonnegative matrix factorizations in reproducible kernel Hilbert space yield sets of separated components. Afterwards, separated components are annotated with the pure components from the library using the maximal correlation criterion. The proposed method is depicted with a numerical example that is related to the extraction of eight dependent components from one nonlinear mixture. The method is further demonstrated on three nonlinear chemical reactions of peptide synthesis in which 25, 19, and 28 dependent analytes are extracted from one nonlinear mixture mass spectra. The goal application of the proposed method is, in combination with other separation techniques, mass spectrometry‐based non‐targeted metabolic profiling, such as biomarker identification studies. Copyright © 2015 John Wiley & Sons, Ltd.