Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

High-throughput screening of fuel cell electrocatalysts

The drawbacks of our earlier report of preparing fuel cell catalyst arrays by borohydride reduction of inkjet prepared arrays of metal salts are discussed along with the need for inclusion of state-of-the-art metrics in all array screening. An alternative method for screening of hydrogen/air cathode catalysts, direct methanol fuel cell (DMFC) anode catalysts, and catalyst loading studies is provided. State-of-the-art Johnson Matthey catalysts were used in control experiments to demonstrate the utility of the array fuel cell for high throughput screening of fuel cell catalysts in the 3-4 mg/cm² range. This report lays out hard learned rules for high throughput screening and demonstrates that the array fuel cell can be used for very precise screening of libraries of membrane electrode assembly (MEA) components without the pitfalls discussed in the introduction.     

Standardization of BSE rapid test performances and experiences gathered during the implementation of large-scale testing

The accumulation of pathological prion protein is used as a diagnostic marker for transmissible spongiform encephalopathies. According to European Union (EU) regulations cattle older than 30 months of age (Germany, France, Italy, and Spain by national law >24 months) and slaughtered for human consumption must be tested by using rapid tests for bovine spongiform encephalopathy (BSE). Likewise fallen stock and clinically affected animals must be tested. This article gives a short overview of the incidence of BSE in Europe. The diagnostic hierarchy, i.e., the officially approved methodology for the confirmation of suspect rapid test cases, and the organization of the numerous laboratories involved in this large-scale testing for BSE are described. Special emphasis is given to necessary quality control measures currently in place for BSE rapid testing laboratories and to measures intended to assure a consistent performance of the commercially available rapid test kits.Presented at BERM-9—Ninth International Symposium on Biological and Environmental Reference Materials, 15–19 June 2003, Berlin, Germany.     

Identification of new catalysts for the asymmetric reduction of imines into chiral amines with polymethylhydrosiloxane using high-throughput screening

The use of high-throughput techniques allowed the rapid identification of new catalysts for the enantioselective reduction of imines using polymethylhydrosiloxane (PMHS) as a reducing agent. By a simple modification of the chiral ligand structure that came out of the screening, the enantioselectivity of the reduction was increased from 40% ee to 60% ee.     

6s and 8d state self-energy for hydrogen-like ions and new results on the self-energy screening

We use a recently published method for the renormalization of the self-energy to calculate the self-energy of 6s and 8d levels to all orders in Zα. We demonstrate the accuracy of the method and its potential for high-n, low-Z applications. We also show that this method is perfectly suited for the evaluation of the two-electron self-energy (self-energy screening). For the first time, evaluation of the screening of the 1s electron by a second one in either the 1s,2s, 2p_1/2 or 2p_3/2 shells has been performed, for 30 ⩽ Z ⩽92. This revised version was published online in July 2006 with corrections to the Cover Date.     

Structural and electrical properties of crystalline (1−x)Ta2O5−xTiO2 thin films fabricated by metalorganic decomposition

Polycrystalline (1−x)Ta₂O₅−xTiO₂ thin films were formed on Si by metalorganic decomposition (MOD) and annealed at various temperatures. As-deposited films were in the amorphous state and were completely transformed to crystalline after annealing above 600 °C. During crystallization, a thin interfacial SiO₂ layer was formed at the (1−x)Ta₂O₅−xTiO₂/Si interface. Thin films with 0.92Ta₂O₅–0.08TiO₂ composition exhibited superior insulating properties. The measured dielectric constant and dissipation factor at 1 MHz were 9 and 0.015, respectively, for films annealed at 900 °C. The interface trap density was 2.5×10¹¹ cm⁻² eV⁻¹, and flatband voltage was −0.38 V. A charge storage density of 22.8 fC/μm² was obtained at an applied electric field of 3 MV/cm. The leakage current density was lower than 4×10⁻⁹ A/cm² up to an applied electric field of 6 MV/cm.     

Two-Dimensional Coulomb Systems on a Surface of Constant Negative Curvature

We study the equilibrium statistical mechanics of classical two-dimensional Coulomb systems living on a pseudosphere (an infinite surface of constant negative curvature). The Coulomb potential created by one point charge exists and goes to zero at infinity. The pressure can be expanded as a series in integer powers of the density (the virial expansion). The correlation functions have a thermodynamic limit, and remarkably that limit is the same one for the Coulomb interaction and some other interaction law. However, special care is needed for defining a thermodynamic limit of the free energy density. There are sum rules expressing the property of perfect screening. These generic properties can be checked on the Debye–Hückel approximation, and on two exactly solvable models, the one-component plasma and the two-component plasma, at some special temperature.     

Debye screening for two-dimensional Coulomb systems at high temperatures

The grand canonical ensemble of a two-dimensional Coulomb system with±1 charges is proved to have screening phenomena in its high-temperature region. The Coulomb potential in a finite region is assumed to be (–)^–1, where is the Laplacian with zero boundary conditions on. The hard-core condition is not assumed. The model is set up by separating (–)^–1 into a shortrange part and a long-range part depending on a parameter. The self-energies are subtracted only for the short-range part and therefore a choice of is a choice of subtraction of self-energies. The method of proof is in general the same as that of Brydges-Federbush Debye screening, except that here a modification for the short-range part of the potentials is needed.     

A Method for Clustering and Screening of Long-dimensional Chemical Data Based on Fingerprints and Similarity Measurements

A method for the treatment of long-dimensional chemical data arrays is presented in this work with the aim of maximising classification models. The method is based on the construction of fingerprints and the subsequent generation of a similarity matrix. The similarity calculation has been modified through a scaling process to take into account different significance shown by the variables. The method was applied to spectral measurements of wines and several aspects were studied, namely: threshold considered in the construction of fingerprints and patterns, weighting factor used for scaling, normalisation method, etc. The application of both Principal Components Analysis and Soft-Independent Modelling of Class Analogies to the similarity matrices gave better classifications of the information than those obtained using original data.