Kinetic and regiospecific interrogation of covalent intermediates in the nonribosomal peptide synthesis of yersiniabactin

For interrogation of enzyme-bound intermediates in nonribosomal peptide synthetases (NRPSs), mass spectrometry is used to read out the kinetics and substrate specificity of this medicinally important class of enzymes. The protein HMWP2 (230 kDa) catalyzes 11 chemical reactions, four of which could be resolved by fast quench approaches combined with mass spectrometry. The rate of complex intermediate accumulation at the PCP1 active site was observed to occur with a rate of 19 s(-1), with the rate of cysteine acylation faster than that of intermediate translocation. Use of alternative substrates for salicylic acid (at the ArCP carrier domain) and l-cysteine (at the PCP1 carrier domain) revealed a high penalty for omission of the salicyl alcohol. For some substrates, large discrepancies were found between prior adenylation assays and the current MS-based readouts. Indirect evidence for condensation via a thiolate attack (vs an amino group) was also accumulated. This is the first report to correlate the percent occupancy of multiple active sites in parallel with kinetic and structural resolution of intermediates and provides new evidence of interdomain and intermodule communication within thiotemplate assembly lines.     

Measurement of the Rates of Diffusion of Halomethanes into Polymer Films Using ATR-FTIR Spectroscopy

Polymer-modified attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and FEWS (fibre-optic evanescent wave) spectroscopy have been very successful to date for sensitive detection of organic pollutants in water utilising the mid-infrared (MIR) region of the electromagnetic spectrum (4000-400 cm^?1). This sensing approach involves the use of different polymer films for preconcentration with optimisation of the sensor related to the rate of diffusion of solvent molecules into these polymer films. Compounds such as chloroform, bromoform, bromodichloromethane and dibromochloromethane which are collectively referred to as trihalomethanes (THMs) were analysed in this work. A gaseous phase experimental design was used and from experimental data the rate of diffusion of each of the halomethanes was quantified based on a Fickian type diffusion model. Individual diffusion coefficient values were found to be in the range 3.38 E-10 ± 0.01 E-10 to 4.72 E-08 ± 0.42 E-08 cm² s^?1. Multicomponent effects were observed for mixtures of compounds diffusing into polyisobutylene and ethylene-propylene copolymer.     

Plate-based diversity subset screening: an efficient paradigm for high throughput screening of a large screening file

The screening files of many large companies, including Pfizer, have grown considerably due to internal chemistry efforts, company mergers and acquisitions, external contracted synthesis, or compound purchase schemes. In order to screen the targets of interest in a cost-effective fashion, we devised an easy-to-assemble, plate-based diversity subset (PBDS) that represents almost the entire computed chemical space of the screening file whilst comprising only a fraction of the plates in the collection. In order to create this file, we developed new design principles for the quality assessment of screening plates: the Rule of 40 (Ro40) and a plate selection process that insured excellent coverage of both library chemistry and legacy chemistry space. This paper describes the rationale, design, construction, and performance of the PBDS, that has evolved into the standard paradigm for singleton (one compound per well) high-throughput screening in Pfizer since its introduction in 2006.     

Growth spiral activity and step velocities on a crystal surface

The normal growth rates and slopes of the dominant growth spirals on a crystal face were measured using a novel application of interferometry and atomic force microscopy. The dislocations responsible for the spirals were also observed directly. In this way it was shown that the velocities of similar steps on growth spirals of different activity, growing simultaneously on the same crystal face, were the same, and hence independent of the growth spirals to which they belonged. With this information the relative activities of the spirals were quantified and discussed in terms of hollow dislocation cores and the back-stress effect.     

Viability of yeast cells in well controlled propagating and standing ultrasonic plane waves

Recent studies have shown that there is no loss of cell viability when the cells are subjected to ultrasonic standing wave fields in acoustic cell retention systems. These systems are characterised by waves that spatially vary in pressure amplitude in the direction of sound propagation. In this work an anechoic 'one-dimensional' sonication chamber has been developed that produces propagating waves, which differ from standing waves in that the pressure amplitude remains constant as the wave travels in a medium with negligible attenuation. The viability of yeast cell suspensions as a function of treatment time was investigated during exposure to both standing and propagating wave fields with frequencies slightly above 2 MHz. The influence of 12% (vol/vol) of ethanol in water on the spatial arrangement of the cells in suspension was also studied. Changes in yeast cell morphology caused by the different types of suspension media and the ultrasonic treatment were examined by transmission electron microscopy (TEM). The agglomeration of yeast cells within the pressure nodal planes appears to minimise damaging effects due to ultrasonic fields.     

The structure of Cu{100}-p(2 × 6)-2mg-Sn studied by DFT and LEED

Low Energy Electron Diffraction (LEED) and Density Functional Theory (DFT) have been used to analyse the structure of Cu{100}-p(2 × 6)-2mg-Sn at room temperature. In this work we found that the favoured geometry for this 0.33 ML Cu{100}-Sn phase is a combination of an overlayer structure and a surface alloy; two Sn atoms are alloyed in to the first copper layer and the other two Sn atoms adsorb at off symmetry hollow sites. In order to relieve the stress in the alloyed layer, the alloyed Sn atoms are buckled 0.59/0.45 ± 0.2 Å (DFT/LEED) above the centre of mass of the first layer copper atoms.     

Surface complexation of DNA with insoluble monolayers. Influence of divalent counterions

DNA interacts with insoluble monolayers made of cationic amphiphiles as well as with monolayers of zwitterionic lipids in the presence of divalent ions. Binding to dioctadecyldimethylammonium bromide (DODAB) or distearoyl-sn-glycero-3-phosphocholine (DSPC) monolayers in the presence of calcium is accompanied by monolayer expansion. For the positively charged DODAB monolayer, this causes a decrease of surface potential, while an increase is observed for the DSPC monolayers. Binding to dipalmitoyl-sn-glycero-3-phosphocholine preserves most of the liquid expanded-liquid condensed coexistence region. The liquid condensed domains adopt an elongated morphology in the presence of DNA, especially in the presence of calcium. The interaction of DNA with phospholipid monolayers is ion specific: the presence of calcium leads to a stronger interaction than magnesium and barium. These results were confirmed by bulk complexation studies.     

The development of novel organically modified sol-gel media for use with ATR/FTIR sensing

The ability to prepare and develop novel pre-concentration media by the sol-gel process, and their integration with mid-infrared transparent waveguides has been demonstrated. This research approach resulted in a mid-infrared sensing methodology in which the properties (porosity, functionality, polarity, etc.) of the recognition layer could be tailored by variation of the sol-gel precursors and processing conditions. Cross-linker type and concentration notably influenced p-xylene absorption and diffusion rate. Unreacted silanol groups appeared to be the dominant factor in the hydrophobicity of sol-gel layers. Variation of sol-gel precursors and thermal treatment altered both film cross-link density and polarity, as demonstrated by variation in the rate of analyte diffusion and equilibrium analyte concentration. The use of a novel 1 : 1 PTMOS : DPDMS material as pre-concentration medium in this analytical sensing approach was validated through the determination of p-nitrochlorobenzene in an aqueous environment. The response demonstrated linearity between 0-30 mg L(-1) with a correlation coefficient of 0.989 and a limit of detection of 0.7 mg L(-1). Sensing times for p-nitrochlorobenzene were also reduced from several hours to 24 minutes, without loss of measurement accuracy or sensitivity, by a 10 degrees C increase in the sensing temperature and the use of a predictive Fickian model previously developed by this research group.     

Synthesis of conformationally constrained 5,6,7, 8-Tetrahydroimidazo[1,5-a]pyridine inhibitors of farnesyltransferase

[reaction: see text] Synthesis of the 8-amino-5,6,7,8-tetrahydroimidazo[1,5-a]pyridine ring system was accomplished by intramolecular cyclization of an iminium ion, derived from condensation of an amine and a substituted gamma-(1-imidazolyl)butyraldehyde. The reaction was used to produce conformationally restricted farnesyltransferase inhibitor analogues which exhibit improved in vivo metabolic stability.