Capillary bioreactors based on human purine nucleoside phosphorylase: A new approach for ligands identification and characterization

The enzyme purine nucleoside phosphorylase (PNP) is a target for the discovery of new lead compounds employed on the treatment severe T-cell mediated disorders. Within this context, the development of new, direct, and reliable methods for ligands screening is an important task. This paper describes the preparation of fused silica capillaries human PNP (HsPNP) immobilized enzyme reactor (IMER). The activity of the obtained IMER is monitored on line in a multidimensional liquid chromatography system, by the quantification of the product formed throughout the enzymatic reaction. The Km value for the immobilized enzyme was about twofold higher than that measured for the enzyme in solution (255 +/- 29.2 mu M and 133 +/- 114.9 mu M, respectively). A new fourth-generation immucillin derivative (DI4G: IC50 = 40.6 +/- 0.36 nM), previously identified and characterized in HsPNP free enzyme assays, was used to validate the IMER as a screening method for HsPNP ligands. The validated method was also used for mechanistic studies with this inhibitor. This new approach is a valuable tool to PNP ligand screening, since it directly measures the hypoxanthine released by inosine phosphorolysis, thus furnishing more reliable results than those one used in a coupled enzymatic spectrophotometric assay. (C) 2011 Elsevier B.V. All rights reserved.

Coal Seam Gas Water from Maramarua, New Zealand: Characterisation and Comparison to United States Analogues

Groundwater from Maramarua has been identified as coal seam gas (CSG) water by studying its composition, and comparing it against the geochemical signature from other CSG basins. CSG is natural gas that has been produced through thermogenic and biogenic processes in underground coal seams; CSG extraction requires the abstraction of significant amounts of CSG water. To date, no international literature has described coal seam gas water in New Zealand, however recent CSG exploration work has resulted in CSG water quality data from a coal seam in Maramarua, New Zealand. Water quality from this site closely follows the geochemical signature associated with United States CSG waters, and this has helped to characterise the type of water being abstracted. CSG water from this part of Maramarua has low calcium, magnesium, and sulphate concentrations but high sodium (334 mg/l), chloride (146 mg/l) and bicarbonate (435 mg/l) concentrations. In addition, this water has high pH (7.8) and alkalinity (360 mg/l as CaCO3), which is a direct consequence of carbonate dissolution and biogenic processes. Different analyte ratios ('source-rock deduction' method) have helped to identify the different formation processes responsible in shaping Maramarua CSG water

Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid analogues

The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O+·C2HO4-·2H2O, (I), and with adipic acid, bis­(4-car­bam­oylpiperidinium) adipate dihydrate, 2C6H13N2O+·C6H8O42-·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carb­oxy­lic acid O-HOcarboxyl hydrogen-bonding inter­actions, forming C(5) chain substructures which extend along a. The isonipecotamide cations also give parallel chain substructures through amide N-HO hydrogen bonds, the chains being linked across b and down c by alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N-HOcarboxyl hydrogen bonds, generating cyclic R43(10) and R32(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water mol­ecule. In the crystal structure, the two inversion-related cations are inter­linked through the two water mol­ecules, which act as acceptors in dual amide N-HOwater hydrogen bonds, to give a cyclic R42(8) association which is conjoined with an R44(12) motif. Further N-HOwater, water O-HOamide and piperidinium N-HOcarbox­yl hydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water mol­ecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide-amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazine) phenxyacetate, C4H10NO+ C8H7O3- (I), (4-fluorophenoxy)acetate, C4H10NO+ C8H6FO3- (II) and isomeric morpholinium (3,5-dichlorophenoxy)acetate (3,5-D) (III) and morpholinium (2,4-dichlorophenoxy)acetate (2,4-D), C4H10NO+ C8H5Cl2O3- (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation-anion N-H...O,O' R2/1(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N---H...O interaction is linear. In the structures of (I), (II) and (III), the second N-H...O(carboxyl) hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N-H...O hydrogen bonds [graph set R2/4(8)], giving a cyclic heterotetrameric structure.

Novel Functionalised Troger's Bases: Synthesis of a New Class of Troger's Base Analogues Containing Dicarboxyl Functionality

The synthesis of three new Troger's base analogues, each functionalized with two carboxyl groups, is described. Copyright.

Self-Assembly of Bile Steroid Analogues: Molecules, Fibers, and Networks

Structural and rheological features of a series of molecular hydrogels formed by synthetic bile salt analogues have been scrutinized. Among seven gelators, two are neutral compounds, while the others are cationic systems among which one is a tripodal steroid derivative. Despite the fact that the chemical structures are closely related, the variety of physical characteristics is extremely large in the structures of the connected fibers (either plain cylinders or ribbons), in the dynamical modes for stress relaxation of the associated SAFINs, in the scaling laws of the shear elasticity (typical of either cellular solids or fractal floc-like assemblies), in the micron-scale texture and the distribution of ordered domains (spherulites, crystallites) embedded in a random mesh, in the type of nodal zones (either crystalline-like, fiber entanglements, or bundles), in the evolution of the distribution and morphology of fibers and nodes, and in the sensitivity to added salt. SANS appears to be a suitable technique to infer all geometrical parameters defining the fibers, their interaction modes, and the volume fraction of nodes in a SAFIN. The tripodal system is particularly singular in the series and exhibits viscosity overshoots at the startup of shear flows, an “umbrella-like” molecular packing mode involving three molecules per cross section of fiber, and scattering correlation peaks revealing the ordering and overlap of 1d self-assembled polyelectrolyte species.

Cyclononitols: a flexible synthetic approach towards nine-membered carbasugar analogues

A novel, concise, stereocontrolled approach to nine-membered carbasugar analogues (cyclononitols) from a bicyclo[4.3.1]deca-2,4-dien-10-one scaffold, harbouring a `locked' cyclononane ring and latent functionalities, is described.

Infrared spectra of 1.3-dithiole-2-thione and its selenium analogues ând frequency assignment and molecular force constants

Infrared spectra of 1,3-dithiole-2-thione (DTT) and its four selenium analogues have been studied in the region 4000 to 20 cm�1. Assignment of all the fundamental frequencies was made by noting the band shifts on progressive selenation. Normal coordinate analysis procedures have been applied for both in-plane and out-of-plane vibrations to help the assignments. The Urey�Bradley force function supplemented with valence force constants for the out-of-plane vibrations was employed for coordinate calculations. A correlation of the infrared assignments of DTT with its different selenium analogues is accomplished. Further, the infrared assignments are compared with those of trithiocarbonate ion and its selenium analogues and other structurally related heterocyclic molecules.

Binding of polyphenols to plant cell wall analogues - Part 1: Anthocyanins

Anthocyanins are located within the vacuole of plant cells, and are released following cell rupture during eating or processing at which time they first come into contact with the plant cell wall. The extent of anthocyanin-cell wall interaction was investigated by monitoring the rate of anthocyanin depletion in the presence of pure cellulose or cellulose-pectin composites as cell wall models. It was found that anthocyanins interact with both cellulose and pectin over a two-stage process with initially (mins-hours) 13 similar to 18% of anthocyanins binding to cellulose or cellulose/pectincomposites. With prolonged exposure (days-weeks), a gradual increase in anthocyanin binding occurs, possibly due to anthocyanins stacking on top of a base layer. Binding of acylated and non-acylated anthocyanins followed a similar pattern with slightly more (5-10%) binding of the acylated forms. Composites with the highest pectin content had the greatest anthocyanin binding suggesting the existence of both ionic interactions (with pectin) and hydrophobic interactions (with cellulose) of anthocyanin with plant cell walls.

Binding of polyphenols to plant cell wall analogues - Part 2: Phenolic acids

Bacterial cellulose and cellulose-pectin composites were used as well-defined model plant cell wall (PCW) systems to study the interaction between phenolic acids (PA) derived from purple carrot juice concentrate (PCJC) and PCW components. Significant PA depletion from solution occurred, with pure cellulose initially (30 s-1 h) absorbing more than cellulose-pectin composites in the first hour (ca 20% cf 10-15%), but with all composites absorbing similar levels (ca 30%) after several days. Individual PAs bound to different relative extents with caffeic acid > chlorogenic acid > ferulic acid. Extrapolation of data for these model systems to carrot puree suggests that nutritionally-significant amounts of PAs could bind to cell walls, potentially restricting bioavailability in the small intestine and, as a consequence, delivering PAs to the large intestine for fermentation and metabolism by gut bacteria. (C) 2012 Elsevier Ltd. All rights reserved.

Theoretical studies on penicillins, penicillin sulphones and their 1-oxa-1-dethia and 1-carba-1-dethia analogues: binding specificities of transeptidases and penicillinases

Empirical potential energy calculations have been carried out to determine the preferred conformations of penicillins and penicillin sulphones and their 1-oxa-1-dethia and 1-carba-1-dethia analogues. With the exception of 1-oxa-1-dethia penicillins, all the other compounds favour C2 and the C3 puckered conformations of their five-membered rings. Replacement of C2 methyl groups by hydrogen atoms as in bisnorpenicillin V or oxidation of sulphur in position 1 as in sulphones, makes the C3 puckered form much less favourable. Addition of an amino-acyl group at the C6 atom, however, makes the C3 puckered form more favoured in penicillin G or V and in 1-carba-1-dethia penicillins. Through the replacement of the sulphur atom at position 1 by an oxygen atom or by a -CH2 group increases the non-planarity of the lactam peptide bond, it significantly affects the relative disposition of the C3 carboxyl group with respect to the β-lactam ring. These conformational differences have been correlated with the biological activities of these compounds. The present study suggests that the conformation of the bicyclic ring system may be more important for initial binding with the crosslinking enzyme(s) involved in the biosynthesis of bacterial cell-wall peptidoglycan and that the mode of binding is influenced by the nature of the side-group at the C6 atom. These studies predict, in agreement with experimental results, that the 1-oxa-1-dethia penicillin nulceus is an inhibitor of penicillianses. The study also suggests that the stereospecificities of the crosslinking enzyme(s) and penicillinases are very similar with regard to the nature of the side-group at the 6 atom and the confirmation of the bicyclic ring system. However, the confirmational requirement for the bicyclic ring system appears to be more specific in the former enzyme than in the latter.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.