Identification of novel S-adenosyl-L-homocysteine hydrolase inhibitors through homology-model-based virtual screening, synthesis, and biological evaluation

The present study describes a successful application of computational approaches to identify novel Leishmania donovani (Ld) AdoHcyase inhibitors utilizing the differences for Ld AdoHcyase NAD(+) binding between human and Ld parasite. The development and validation of the three-dimensional (3D) structures of Ld AdoHcyase using the L. major AdoHcyase as template has been carried out. At the same time, cloning of the Ld AdoHcyase gene from clinical strains, its overexpression and purification have been performed. Further, the model was used in combined docking and molecular dynamics studies to validate the binding site of NAD in Ld. The hierarchical structure based virtual screening followed by the synthesis of five active hits and enzyme inhibition assay has resulted in the identification of novel Ld AdoHcyase inhibitors. The most potent inhibitor, compound 5, may serve as a "lead" for developing more potent Ld AdoHcy hydrolase inhibitors as potential antileishmanial agents.     

Analyte-driven switching of DNA charge transport: de novo creation of electronic sensors for an early lung cancer biomarker

A general approach is described for the de novo design and construction of aptamer-based electrochemical biosensors, for potentially any analyte of interest (ranging from small ligands to biological macromolecules). As a demonstration of the approach, we report the rapid development of a made-to-order electronic sensor for a newly reported early biomarker for lung cancer (CTAP III/NAP2). The steps include the in vitro selection and characterization of DNA aptamer sequences, design and biochemical testing of wholly DNA sensor constructs, and translation to a functional electrode-bound sensor format. The working principle of this distinct class of electronic biosensors is the enhancement of DNA-mediated charge transport in response to analyte binding. We first verify such analyte-responsive charge transport switching in solution, using biochemical methods; successful sensor variants were then immobilized on gold electrodes. We show that using these sensor-modified electrodes, CTAP III/NAP2 can be detected with both high specificity and sensitivity (K(d) ～1 nM) through a direct electrochemical reading. To investigate the underlying basis of analyte binding-induced conductivity switching, we carried out F?rster Resonance Energy Transfer (FRET) experiments. The FRET data establish that analyte binding-induced conductivity switching in these sensors results from very subtle structural/conformational changes, rather than large scale, global folding events. The implications of this finding are discussed with respect to possible charge transport switching mechanisms in electrode-bound sensors. Overall, the approach we describe here represents a unique design principle for aptamer-based electrochemical sensors; its application should enable rapid, on-demand access to a class of portable biosensors that offer robust, inexpensive, and operationally simplified alternatives to conventional antibody-based immunoassays.     

Solid-state nuclear magnetic resonance studies delineate the role of the protein in activation of both aromatic rings of thiamin

Knowledge of the state of ionization and tautomerization of heteroaromatic cofactors when enzyme-bound is essential for formulating a detailed stepwise mechanism via proton transfers, the most commonly observed contribution to enzyme catalysis. In the bifunctional coenzyme, thiamin diphosphate (ThDP), both aromatic rings participate in catalysis, the thiazolium ring as an electrophilic covalent catalyst and the 4'-aminopyrimidine as acid-base catalyst involving its 1',4'-iminopyrimidine tautomeric form. Two of four ionization and tautomeric states of ThDP are well characterized via circular dichroism spectral signatures on several ThDP superfamily members. Yet, the method is incapable of providing information about specific proton locations, which in principle may be accessible via NMR studies. To determine the precise ionization/tautomerization states of ThDP during various stages of the catalytic cycle, we report the first application of solid-state NMR spectroscopy to ThDP enzymes, whose large mass (160,000-250,000 Da) precludes solution NMR approaches. Three de novo synthesized analogues, [C2,C6'-(13)C(2)]ThDP, [C2-(13)C]ThDP, and [N4'-(15)N]ThDP used with three enzymes revealed that (a) binding to the enzymes activates both the 4'-aminopyrimidine (via pK(a) elevation) and the thiazolium rings (pK(a) suppression); (b) detection of a pre-decarboxylation intermediate analogue using [C2,C6'-(13)C(2)]ThDP, enables both confirmation of covalent bond formation and response in 4'-aminopyrimidine ring's tautomeric state to intermediate formation, supporting the mechanism we postulate; and (c) the chemical shift of bound [N4'-(15)N]ThDP provides plausible models for the participation of the 1',4'-iminopyrimidine tautomer in the mechanism. Unprecedented detail is achieved about proton positions on this bifunctional coenzyme on large enzymes in their active states.     

Stability of ruthenium nanoparticles synthesized by solvothermal method

One of the major obstacles to the synthesis of nanoparticles and nanocatalyst is the stability of particles. In the present study, polymer stabilized ruthenium nanoparticles were synthesized by solvothermal method using solutions of ruthenium chloride in ethylene glycol in presence of poly(N ‐vinyl‐2‐pyrrolidone) (PVP) as a stabilizing agent. Stability of nanoparticles was studied by varying different parameters e.g. PVP/RuCl₃ molar raio, RuCl₃ concentration, reaction temperature and time and expressed in terms of particle size and size distribution. Transmission electron microscope (TEM) analysis revealed the presence of metallic clusters with a uniform size of about 20‐65 nm. Dispersion destabilisation of colloidal nanoparticles was detected by Turbiscan. Polymer stabilized ruthenium nanoparticles were dispersed on γ‐alumina to prepare uniformly disperse Ru/γ‐Al₂O₃ catalyst by mechanical strirring and sonication. Inductively coupled plasma‐optical emission spectroscopy (ICP‐OES), X‐Ray powder diffraction (XRD), Transmission electron microscopy (TEM) and Thermo gravimetric analysis (TGA) were used to characterize the supported catalyst. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Joint replenishment of multi retailer with variable replenishment cycle under VMI

In the recent article, Darwish and Odah (2010) develop a scheme that allows for identical replenishment cycles for all the retailers, in the context of a single vendor supplying a group of retailers under VMI partnership. This paper proposes an alternative replenishment scheme allowing for different replenishment cycles for each retailer. An example has been shown to illustrate the cost savings under the proposed model.     

Scalar Dissipation Rate Transport in the Context of Large Eddy Simulations for Turbulent Premixed Flames with Non-Unity Lewis Number

The effects of global Lewis number Le on the statistical behaviour of the unclosed terms in the transport equation of the Favre-filtered scalar dissipation rate (SDR) Ñ _c have been analysed using a Direct Numerical Simulation (DNS) database of freely propagating statistically planer turbulent premixed flames with Le ranging from 0.34 to 1.2. The DNS data has been explicitly filtered to analyse the statistical behaviour of the unclosed terms in the SDR transport equation arising from turbulent transport T ₁, density variation due to heat release T ₂, scalar-turbulence interaction T ₃, reaction rate gradient T ₄, molecular dissipation (?D ₂) and diffusivity gradients f(D) in the context of Large Eddy Simulations (LES). It Le has significant effects on the magnitudes of T ₁, T ₂, T ₃, T ₄, (?D ₂) and f(D). Moreover, both qualitative and quantitative behaviours of the unclosed terms T ₁, T ₂, T ₃, T ₄, (?D ₂) and f(D) are found to be significantly affected by the LES filter width Δ, which have been explained based on a detailed scaling analysis. Both scaling analysis and DNS data suggest that T ₂, T ₃, T ₄, (?D ₂) and f(D) remain leading order contributors to the SDR \(\tilde {{N}}_{c} \) transport for LES. The scaling estimates of leading order contributors to the SDR \(\tilde {{N}}_{c} \) transport has been utilised to discuss the possibility of extending an existing SDR model for Reynolds Averaged Navier Stokes (RANS) simulation for SDR \(\tilde {{N}}_{c} \) closure in the context of LES of turbulent premixed combustion.     

Design of tunable asymmetric directional coupler filter using periodically segmented Ti:LiNbO3 waveguides

A tunable wavelength filter is designed using Ti:LiNbO₃ asymmetric directional coupler. One arm of the directional coupler is made of continuous waveguide while the other arm is periodic segmented. This segmentation reduces the lithographic steps and hence the fabrication cost required for such asymmetric coupler based filter. The propagation constant of periodical segmented and continuous waveguides are analysed using Effective-Index-based Matrix Method. The tunability is achieved using electro-optic property of LiNbO₃.     

Defect-dominated optical emission and enhanced ultraviolet photoconductivity properties of ZnO nanorods synthesized by simple and catalyst-free approach

We report on the defect-dominated light emission and ultraviolet (UV) photoconductivity characteristics of ZnO nanorods (NRs) fabricated using a facile, cost-effective, and catalyst-free thermal decomposition route under varying reaction temperatures. The morphological and structural studies reveal the formation of homogeneous quality nanorods in large scale at the highest reaction temperature of 600 ^°C. The luminescence feature of the nanorods is dominated by the defect related emission over the typical band edge emission. The variation of band-edge and native defect-related emission response of the samples has been correlated to the morphology and microstructure. In photoconductivity studies, the I–V characteristics of the ZnO NRs prepared at different reaction temperatures in dark and under UV illumination (λ=365 nm) follow the power law, i.e., IαV ^r . An enhanced ultraviolet photodetection has been observed in the nanorods fabricated at the highest reaction temperature of 600 ^°C. The sample prepared at highest reaction temperature of 600 ^°C exhibits UV photosensitivity value (photo-to-dark current ratio) of around 1.18×10³, which is much higher in magnitude compared to that of the samples prepared at lower reaction temperatures. The enhanced photoconductivity may be assigned to the development of uniformity and homogeneity of the nanorods. Further development of such ZnO nanostructures can form the basis of promising prototype luminescent and UV photodetecting devices.     

A posteriori testing of the flame surface density transport equation for LES

Flame Surface Density (FSD) models for Large Eddy Simulation (LES) are implemented and tested for a canonical configuration and a practical bluff body stabilised burner, comparing common algebraic closures with a transport equation closure in the context of turbulent premixed combustion. The transported method is expected to yield advantages over algebraic closures, as the equilibrium of subgrid production and destruction of FSD is no longer enforced and resolved processes of strain, propagation and curvature are explicitly accounted for. These advantages might have the potential to improve the ability to capture large-scale unsteady flame propagation in situations with combustion instabilities or situations where the flame encounters progressive wrinkling with time. The initial study of a propagating turbulent flame in wind-tunnel turbulence shows that the Algebraic Flame Surface Density (FSDA) method can predict an excessively wrinkled flame under fine grid conditions, potentially increasing the consumption rate of reactants to artificially higher levels. In contrast, the Flame Surface Density Transport (FSDT) closure predicts a smooth flame front and avoids the formation of artificial flame cusps when the grid is refined. Five FSDA models and the FSDT approach are then applied to the LES of the Volvo Rig. The predicted mean velocities are found to be relatively insensitive to the use of the FSDT and FSDA approaches, whereas temperature predictions exhibit appreciable differences for different formulations. The FSDT approach yields very similar temperature predictions to two of the tested FSDA models, quantitatively capturing the mean temperature. Grid refinement is found to improve the FSDT predictions of the mean flame spread. Overall, the paper demonstrates that the apparently complicated FSD transport equation approach can be implemented and applied to realistic, strongly wrinkled flames with good success, and opens up the field for further work to improve the models and the overall FSDT approach.