Lessons learnt from assembling screening libraries for drug discovery for neglected diseases

To enable the establishment of a drug discovery operation for neglected diseases, out of 2.3 million commercially available compounds 222 552 compounds were selected for an in silico library, 57 438 for a diverse general screening library, and 1 697 compounds for a focused kinase set. Compiling these libraries required a robust strategy for compound selection. Rules for unwanted groups were defined and selection criteria to enrich for lead-like compounds which facilitate straightforward structure-activity relationship exploration were established. Further, a literature and patent review was undertaken to extract key recognition elements of kinase inhibitors ("core fragments") to assemble a focused library for hit discovery for kinases. Computational and experimental characterisation of the general screening library revealed that the selected compounds 1) span a broad range of lead-like space, 2) show a high degree of structural integrity and purity, and 3) demonstrate appropriate solubility for the purposes of biochemical screening. The implications of this study for compound selection, especially in an academic environment with limited resources, are considered.     

Study of epoxy toughened by in situ formed rubber nanoparticles

The effect of rubber nanoparticles on mechanical properties and fracture toughness was investigated. Rubber nanoparticles of 2–3 nm were in situ synthesized in epoxy taking advantage of the reaction of an oligomer diamine with epoxy. The chemical reaction was verified by gel permeation chromatography (GPC) and ¹HNMR, and the microstructure was characterized by transmission electron microscope. The rubber nanoparticles caused much less Young's modulus deterioration but toughened epoxy to a similar degree in comparison with their peer liquid rubber that formed microscale particles during curing. Fifteen wt % of rubber nanoparticles increased fracture energy from 140 to 840 J/m² with Young's modulus loss from 2.85 to 2.49 GPa. The toughening mechanism might be the stress relaxation of the matrix epoxy leading to larger plastic work absorbed at the crack tip; there is no particle cavitation or deformation; neither crack deflection nor particle bridging were observed. The compound containing rubber nanoparticles demonstrates Newtonian liquid behavior with increasing shear rate; it shows lower initial viscosity at low shear rate than neat epoxy; this provides supplementary evidence to NMR and GPC result. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Thermochemical Reactions Between PZT and Ag/Pd Powders: Relevance to Cofiring of Multilayer Actuators

Mixtures of Ag_{1− x} Pd _x ( x =0.2, 0.3) and doped PZT ceramic powders have been heat treated in air and the resulting phase content has been analyzed by X-ray diffraction and transmission electron microscopy. Beginning around 400°C, a phase similar to PbPdO₂ is formed on the surface of the Ag_{1− x} Pd _x particles and subsequently decomposes at temperatures <700°C. Consequently, the remaining Ag_{1− x} Pd _x powder becomes significantly silver-rich while the reaction progresses. After decomposition the Pd appears to realloy and the initial Ag_{1− x} Pd _x composition is recovered. We show that the reaction is all but eliminated in a nitrogen atmosphere. The occurrence of this reaction was also investigated in PZT multilayer actuators cofired with Ag_0.7Pd_0.3 electrodes. Transmission electron microscope analysis revealed the presence of distinct crystallites at the electrode–ceramic interface, most likely nucleated from a PbO liquid phase arising from the decomposition of PbPdO₂.     

The influence of pH on particle packing in YSZ coatings electrophoretically deposited from a non-aqueous suspension

Yttria stabilized zirconia (YSZ) coatings were produced from a YSZ suspension in acetylacetone (ACAC) using electrophoretic deposition (EPD) and then sintered with substrate constraint at 1200 and 1300 °C. Before EPD, the operational pH of the suspension was adjusted by addition of acetic acid or triethanolamine (TEA) base. The effect of suspension pH on the deposition of EPD coatings was studied with respect to the suspension stability, coating density and microstructure. Results showed that the zeta potential had a high positive value on both sides of the iso-electric point (IEP). This probably resulted from the adsorption of TEA, detected by Fourier transform infrared spectroscopy. Three alkalies with different molecular structures were compared and the effect of their molecule length on the interparticle repulsion was discussed. Based on this, particle interactions were estimated for different pH suspensions. The reduced particle coagulation increased the packing density of the EPD coatings from 38% at pH 7.4 to 53% at pH 8.4. Therefore, subsequent sintering of coatings was promoted. The sinterability was evaluated by micro-hardness and microstructure. After sintering at 1200 °C, coatings made in pH 8.4 suspensions obtained a hardness of 786 MPa and had fewer big pores than coatings fabricated in pH 7.4 suspensions that had a hardness of 457 MPa.     

Studies into the swelling of gelatine films using a scanning fluid dynamic gauge

Fluid dynamic gauging (FDG) has been developed to measure both the thickness and strength (cohesive or adhesive) of a range of fouling deposits, in situ and in real time. We report the development of a scanning FDG device (sFDG) with fully automated movement and deposit thickness measurement. Thickness-time profiles can be collected for several points on the surface over the course of a single experiment. sFDG is employed here to study the cleaning kinetics of model gelatine fouling layers when contacted with aqueous solutions at different pHs and temperatures, and with a commercial dishwasher formulation containing enzymes.Solution pH is an important parameter: above ～pH 10.6 the gelatine layers swell markedly, due to protonation of the amino acids proline and hydroxyproline, and subsequent charge repulsion within the gel. An unusual behaviour (discontinuity) is reported during swelling in the commercial formulation. It is proposed that hydration of the deposit and an extent of swelling (ratio of the final to the initial deposit thickness) of ～12 is necessary before the enzymes can promote deposit removal.     

Corrosion studies of rebar in contact with saturated solution produced by leaching of Portland Type-II cement: examining the effects of chloride,carbonation and an amorphous silica additive

This study examined the effects of silica addition on electrochemical behavior of rebar in native pH 12.5 saturated solutions prepared by leaching of Portland Type-II cement, and in solutions reduced by CO₂ to pH 9. Cyclic polarizations showed that at pH 12.5 the silica additive increased the threshold concentration required for pitting from 100 to 105mM, and from 0.3 mM to 0.5 mM at pH 9. Passivation kinetic exponents were consistently larger for solutions with either pH when silica was present. The silica additive provided the passive film with generally increased resistance and lower capacitance, as confirmed by electrochemical impedance spectroscopy. Charge carrier densities calculated from Mott-Schottky plots were on the order of 1020 (cm^-3), increasing significantly after the passive film breakdown. Raman spectroscopy of rebar samples immersed in saturated cement solutions showed films predominantly composed of iron oxyhydroxides with a new shoulder attributed to amorphous silica.     

The Engineering of Bacteria Bearing Azido‐Pseudaminic Acid‐Modified Flagella

Catch a tiger by the tail : We have demonstrated that by feeding nonmotile mutant C. jejuni bacteria with a neutral azide‐labelled pseudaminic acid precursor we can restore their ability to generate functional flagella. The presence of azido‐pseudaminic acid on the surface of the flagella provides a bio‐orthogonal chemical handle that can be used to modify the flagellar proteins.

     

Modeling the breakage stage in spheronization of cylindrical paste extrudates

Spheronization of cylindrical extrudates on a rotating friction plate involves breakage and rounding. Little attention has been given to the breakage stage and quantitative modeling of this process is scarce. Two simple models are compared with experimental data obtained for the early stages of spheronization of microcrystalline cellulose/water extrudates. Tests were conducted for different times (t), rotational speeds (ω), initial loadings, and on pyramidal friction plates with different dimensions. The first model, describing the number of pellets, validated ω³t as a characteristic time scale for the breakage stage. The kinetic parameters obtained by fitting showed a systematic dependence on plate dimensions expressed as a scaled gap width. The second model, a simple population balance, described the evolution of the number and length of pellets. The pseudo rate constants provided insights into the kinetics: extrudates tended to break near the middle, while breakage of smaller pellets was slowed down by more pellet–pellet collisions.     

Nonlinear mechanical response of high density polyethylene. Part I: Experimental investigation and model evaluation

The nonlinear behavior of high density polyethylene (HDPE) is investigated for samples cut from thick-walled HDPE pipe. Extensive experimental work has been performed to characterize the non-linear time-dependent response of the material tested under uniaxial compression. Tests were conducted under conditions of constant strain rate, creep, stress relaxation, constant loading rate, abrupt change of strain rate, creep-recovery, cyclic strain rate, and various combinations of these loading conditions. Creep and stress relaxation response after strain reversal and the effect of the transient response on the following stress-strain behavior is examined. Permanent strains for the test specimens and their dependence on loading histories are investigated. Specimens cut at various orientations from the pipe are used to quantify the small amounts of local anisotropy in the pipe specimen. The experimental work has been used to develop both nonlinear viscoelastic (NVE) and viscoplastic (VP) constitutive models in a companion paper. Both the test results and the corresponding model predictions are reported in this paper. It is found that the VP model reproduces the nonlinear viscoelastic-viscoplastic behavior of HDPE very well provided that the current strain is not below the maximum strain imposed (there is no strain reversal). The NVE model predicts the material behavior reasonably well for some loading conditions, but inadequately for others.     

Structural Requirements of Jasmonates and Mimics for Nicotine Induction inNicotiana sylvestris

Jasmonic acid (JA) is strongly implicated in the long-distance signal transduction cascade increasing nicotine synthesis in the roots of plants after leaf wounding. In order to explore the structural requirements of the inducing signal, we examined jasmonates, mimics, and a biosynthetic precursor for nicotine-inducing activity (NIA). We examine the importance of the keto group on the five-membered ring and the double bond in then-pentenyl chain by comparing the NIA of methyl jasmonate (MJ) with that of cucurbic acid, 1,3-dithiolane-MJ, 1,3-dioxolane-MJ, methyl dihydrojasmonate (DHMJ), 1,3-dioxolane-DHMJ, 1-oxo-indan-4-carboxylic acid ILE-methyl ester, and 1-hydroxyl-indan-4-carboxylic acid ILE-methyl ester. We found that: 1,3-dioxolane MJ, cucurbic acid, and 1,3-dioxolane DHMJ were less active than MJ and that the isoleucine (ILE) conjugates of 1-oxo- and l-hydroxyindanon-4-carboxylic acid had the same NIA as MJ. The activities of these indanon amino acid conjugates may be due to the structural similarity of their keto or hydroxyl groups on the five-membered ring to MJ or to the keto-enolized MJ. These results support the hypothesis that the enolization of the keto group during or prior to its interaction with the putative JA receptor is required for activity. We explore the importance of the esterification of the carboxyl functional group by comparing the NIAs of cucurbic acid and cucurbic acid methyl ester, l-oxo-indan-4-carboxylic acid, 1-oxo-indan-4-carboxylic acid methyl ester, and l-oxo-indan-4-carboxylic acid ILE-methyl ester. In all cases, the esters were more active than the free acids. We compared the NIA of MJ of different epimeric composition (8% and 20% 3R,7S-MJ); 12-oxophytodienoic acid (12-oxo-PDA) methyl ester, an important precursor of JA; and coronatine (a well-known phytotoxin and putative structural mimic of 12-oxo-PDA).We found that: (1) the epimeric composition of MJ did not affect its NIA; (2) 12-oxo-PDA methyl ester had lower NIA than MJ; and (3) coronatine significantly inhibited plant growth but did not increase nicotine biosynthesis. In summary, JA, rather than its biosynthetic precursor, 12-oxo-PDA, is likely the endogenous signal inNicotiana sylvestris, and the keto functional group on the five-membered ring and the double bond in then-pentenyl side chain are crucial components of JA for NIA.