Cubic phases in biosensing systems

Incorporation of membrane proteins with retained activity in artificial membranes for use in membrane-based sensors has attracted scientists for decades. This review briefly summarises general concepts on relevant cubic phases with and without incorporated proteins and provides some insight into the development of biosensors where bicontinuous cubic phases are used for incorporation of an enzyme. Some new data on impedance characterisation of a supported cubic phase are also shown. An efficient membrane-based electrochemical biosensor requires that the analyte has free access to the immobilised membrane protein and that regeneration of the catalysing enzyme is fast. Long-term stability of the system is also necessary for the biosensor to find applications outside the research laboratory. These basic concepts are discussed in the review along with presentation of those biosensing systems based on cubic phases that are reported in the literature.     

Synthesis of fluorescein-labelled O-mannosylated peptides as components for synthetic vaccines: comparison of two synthetic strategies

Mannose-binding proteins on the surface of antigen-presenting cells (APCs) are capable of recognizing and internalizing foreign agents in the early stages of immune response. These receptors offer a potential target for synthetic vaccines, especially vaccines designed to stimulate T cells. We set out to synthesize a series of fluorescein-labelled O-mannosylated peptides using manual solid phase peptide synthesis (SPPS) on pre-loaded Wang resin, in order to test their ability to bind mannose receptors on human APCs in vitro. A flexible and reliable method for the synthesis of fluorescein-labelled O-mannosylated glycopeptides was desired in order to study their lectin-binding properties using flow cell cytometry. Two synthetic strategies were investigated: incorporation of a fluorescein label into the peptide chain via a lysine side chain epsilon-amino group at the final stage of standard Fmoc solid phase peptide synthesis or attachment of the fluorescein label to the N(alpha)-amino group of a lysine with further incorporation of a mannosylated peptide unit through the side chain N(epsilon)-amino group. The latter strategy proved more effective in that it facilitated SPPS by positioning the growing mannosylated peptide chain further removed from the fluorescein label.     

Enzymatic in-capillary derivatization for glucose determination by electrophoresis with spectrophotometric detection

The following paper compares several procedures of in-capillary bienzymatic derivatization with regard to glucose determination with the use of glucose oxidase and horseradish peroxidase. The procedures discussed below include continuous contact in the capillary, plug-plug injection, and sequential injection with incubation in the capillary inlet. The reaction of hydrogen peroxide catalyzed by peroxidase was performed using two different substrates. The best results were achieved for nicotinamide adenine dinucleotide, reduced disodium salt (NADH) acting both as a chromogenic reagent and a substrate for peroxidase, while the method employed was sequential injection and incubation at the capillary inlet. The LOD was estimated to be 25 nM with a linear response up to 0.1 microM.     

Polyfunctionalized pyrrolidines by Ugi multicomponent reaction followed by palladium-mediated SN2' cyclizations

A 4-component Ugi reaction with a suitable isocyanide, followed by a novel secondary transformation involving a Pd(II)-mediated (R5 = H) or a Pd(0)-mediated (R5 = CO2Me) SN2' cyclization to give highly functionalized N-acyl-2-vinylpyrrolidines, is reported. The overall yields are usually good and in most cases the Pd(0)-catalyzed reaction gave the final product in almost quantitative yield.     

Multicoordinational excited state twisting of indan-1,3-dione derivatives

Excited state relaxation of indan-1,3-dione derivatives with different substituents attached to the phenyl ring and with the bridged amino group was investigated by means of the steady-state fluorescence and femtosecond time-resolved absorption pump–probe spectroscopy. Bridging of the amino group increases the fluorescence quantum yield and the excited state lifetime. Analysis of the results indicates that the phenyl ring twisting around a single central bond leads to the nonradiative state formation and to subsequent fast relaxation to the ground state. Double bond twisting takes place in molecules with the bridged amino group and causes a large Stokes shift and slightly slower excited state relaxation.     

Detection of Asp371, Phe375, and Tyr376 Influence on GD-95-10 Lipase Using Alanine Scanning Mutagenesis

GD-95-10 and GD-95-20 lipases are modified GD-95 lipase variants, which lack 10 and 20 C-terminal amino acids, respectively. Previous analysis showed that GD-95-10 lipase has higher activity than GD-95 lipase, while GD-95-20 lipase almost completely loses its activity. Analysis in silico suggested three conservative amino acids at region between 369 and 378 amino acids which can be relevant to the activity of GD-95-10 lipase. These amino acids have direct contacts with residues involved in substrate binding, stabilization of the serine loop or form oxyanion hole. In this work, the role of Asp371, Phe375, and Tyr376 on activity, functionality, and structure of GD-95-10 lipase was analyzed by Ala scanning mutagenesis. We showed that even a single mutation can impact the main structure and activity of Geobacillus lipases. Our experiments provide new knowledge about lipases from thermophilic Geobacillus bacteria and are important for protein engineering and synthetic biology. These enzymes and their engineering can be basis for future biocatalysts applied in production of biofuel or other industrial esters.     

Complexation copper(II) or magnesium ions with d-glucuronic acid – potentiometric,spectral and theoretical studies

Results of potentiometric and spectral studies have shown that in d-glucuronic acid (GluA) with Cu²⁺ or Mg²⁺ systems, the complexes ML and ML(OH)_x are formed. Overall stability constants (log β) and equilibrium constants (log K_e) were calculated for all complex forms. The mode of coordination for each form was concluded on the basis of spectral values, Vis, EPR, and chemical shifts in the ¹³C NMR. According to spectral analysis, Cu(GluA) exists in two possible forms, which confirm the occurrence of the coordination dichotomy in the system. The main center of interactions in the hydroxyl complexes Cu(GluA)(OH)_x and MgGluA are oxygens from the carboxyl group. Differences in the coordination mode in the copper(II) and magnesium systems at low pH were observed.     

Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches

In continuation of our recent studies on the quality of conformational models generated with CATALYST and OMEGA we present a large-scale survey focusing on the impact of conformational model quality and several screening parameters on pharmacophore-based and shape-based virtual high throughput screening (vHTS). Therefore, we collected known active compounds of CDK2, p38 MAPK, PPAR-gamma, and factor Xa and built a set of druglike decoys using ilib:diverse. Subsequently, we generated 3D structures using CORINA and also calculated conformational models for all compounds using CAESAR, CATALYST FAST, and OMEGA. A widespread set of 103 structure-based pharmacophore models was developed with LigandScout for virtual screening with CATALYST. The performance of both database search modes (FAST and BEST flexible database search) as well as the fit value calculation procedures (FAST and BEST fit) available in CATALYST were analyzed in terms of their ability to discriminate between active and inactive compounds and in terms of efficiency. Moreover, these results are put in direct comparison to the performance of the shape-based virtual screening platform ROCS. Our results prove that high enrichment rates are not necessarily in conflict with efficient vHTS settings: In most of the experiments, we obtained the highest yield of actives in the hit list when parameter sets for the fastest search algorithm were used.     

Evaluation of GSH adducts of adrenaline in biological samples

The sustained high release of catecholamines to circulation is a deleterious condition that may induce toxicity, which seems to be partially related to the products formed by oxidation of catecholamines that can be further conjugated with glutathione (GSH). The aim of the present study was to develop a method for the determination of GSH adducts of adrenaline in biological samples. Two position isomers of the glutathion-S-yl-adrenaline were synthesized and characterized by HPLC using diode array, coulometric and mass detectors. A method for the extraction of these adducts from human plasma was also developed, based on adsorption to activated alumina, which showed adequate recoveries and proved to be crucial in removing interferences from plasma. The selectivity, precision and linearity of the method were all within the accepted values for these parameters. Furthermore, the sensitivity of this method allows the detection of adduct amounts that are within the range of the expected concentrations for these adducts under certain pathophysiological conditions and/or drug treatments. In conclusion, the development of this method allows the direct analysis of GSH adducts of adrenaline in human plasma, providing a valuable tool for the study of the catecholamine oxidation process and its related toxicity.