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.     

Copper corrosion in buffered and non-buffered synthetic seawater: a comparative study

The electrochemical behaviour of copper in neutral buffered and non-buffered synthetic seawater and in pure chloride solutions has been studied by cyclic voltammetry, weight loss measurements, open circuit potential and scanning electron microscopy (SEM). Values of the repassivation potentials of Cu in non-buffered and buffered synthetic seawater, at 50 mV s^–1, were 0.12 and 0.46 V vs. SCE, respectively. The sharpness, heights and location of the different peaks as well as their charges were shown to be influenced by the composition of the solution, buffering conditions, deoxygenation, polarization potential and time. High chloride concentrations lead to higher oxidation charges. The anodic and the cathodic charges were shown to increase as the chloride concentration increases. The open circuit potential transients of copper in non-deoxygenated, non-buffered synthetic seawater indicate pitting from the beginning of the exposure, while in buffered solutions the pitting appeared only after a quite long exposure period, i.e. after 40 days. Corrosion rates of Cu samples after 3 months of immersion were higher in solutions of pure chloride (0.5 M) than in synthetic seawater. After six months the differences were even more noticeable. SEM images have showed a somewhat higher density of pits on copper samples immersed in the chloride solution (0.5 M), in comparison with those in synthetic seawater.     

Removal of oxygen from silicon by electron beam melting

Small amounts of multicrystalline silicon were melted in an electron beam furnace in different experimental conditions in order to investigate the oxygen evaporation behavior during the electron beam melting (EBM) process. The oxygen content level before and after EBM was determined by secondary ion mass spectroscopy. The oxygen content was reduced from 6.177 to 1.629 ppmw when silicon was melted completely at 15 kW with removal efficiency up to 73.6 %. After that, it decreased continually to <0.0517 ppmw when the refining time exceeded 600 s with a removal efficiency of more than 99.08 %. During the melting process, the evaporation rate of silicon is 1.10 × 10^?5 kg/s. The loss of silicon could be reduced up to 1.7 % during oxygen removal process to a desirable figure, indicating EBM is an effective method to remove oxygen from silicon and decrease the loss of silicon.     

Synthesis,anti‐migration and burning rate catalytic mechanism of ferrocene‐based compounds

One of the most important components of solid rocket propellant is the burning rate catalysts (BRC) which enhance burning rate of solid composite propellant. Low‐pressure exponents and stable burning rate are the key features of an excellent solid propellant. Addition of BRC to the propellant results in the increase of burning rate of the propellant and decrease in pressure exponents. Among all BRC, ferrocene‐based BRC have attracted much attention because of their better microscopic homogeneities in distribution, ignitability of the propellants and good compatibility with organic binder. However, the main barrier for the development and practical applications of ferrocene‐based BRC is their migration property. This article reviews the field and highlights recent progress. Copyright © 2014 John Wiley & Sons, Ltd.     

The asymptotic D-state to S-state ratio of triton

At low energies, an effective field theory (EFT) with only contact interactions as well as three-body forces allow a detailed analysis of renormalization in a non-perturbative context and uncovers novel asymptotic behaviour. Triton as a three-body system, based on the EFT have been previously shown to provide representative binding energies, charge radii, S-wave scattering amplitude and asymptotic normalization constants for the ³H bound state system. Herein, EFT predictions of the asymptotic D-state to S-state ratio of triton are calculated to more fully evaluate the adequacy of the EFT model. Manifestly model-independent calculations can be carried out to high orders, leading to high precision.     

Solvent‐assisted anionic ring opening polymerization of glycidol: Toward medium and high molecular weight hyperbranched polyglycerols

Hyperbranched polyglycerols (HPGs) are globular structures with a large number of functionalizable hydroxyl groups and have excellent in vitro and in vivo biocompatibility profiles comparable to polyethylene glycol. This work introduces a facile method for the synthesis of medium molecular weights (M_ws) (50–300 kDa) HPGs, which has been difficult to synthesize with low polydispersity, with the assistance of solvents by ring opening polymerization. The influence of different solvents (1,4‐dioxane, tetrahydropyran (THP), ethylene glycol diethyl ether (EGDE) and decane), solvent to glycidol ratio, concentration of glycidol and the time of polymerization on M_w and polydispersity of HPGs has been studied. The M_w and polydispersity of HPGs are significantly affected by the nature of the polymerization phase (homogeneous or heterogeneous) and chemical structure of the solvent. The differences in the solvation of the potassium cations and change in the nucleophilicity of the alkoxide anion in various solvents may be responsible for the changes in M_w and PDI of the HPG. The M_w of the HPG decreases in the order 1,4‐dioxane > THP > EGDE >decane. The microstructure, solution and thermal properties of the HPG do not depend on the nature of solvent. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2614–2621     

Offline estimation of 2D crystal lattice parameters by processing the electron diffraction image

Electron diffraction provides useful information about the internal composition of materials and has been in the use of material scientists for more than fifty years. In order to extract useful information from offline diffraction images, they are manually analyzed by using some photometric technique. Manual analysis is however a cumbersome, laborious and difficult task. To reduce the labors of material scientists one can employ image processing techniques to perform automated analysis, due to the well established popularity and clear evidence of widely used image processing techniques. In this work an image processing technique is being proposed for the extraction of 2D unit cell information from diffraction images on one hand and finding the 2D point group contained by the lattices on the other. The technique employs a morphological shrinking operation to find the center of each spot in the underlying preprocessed diffraction image. This is followed by the extraction of eight points with reference to the spot produced by the transmitted electron beam. The resultant nine points, i.e. the extracted eight plus the reference spot generated by the transmitted electron beam, are then subjected to symmetry operations, rotation symmetry and mirror symmetry, in polar coordinate system, to classify the point group of the lattice produced by the electron diffraction. One of the difficult task, even in manual analysis, is to ascertain the exact spot where the transmitted electron beam hit the sample at the time of realization of the image. This has been accurately and intuitively done by employing the notion that the transmitted spot must have greater number of pixels, with the highest gray value, among the diffracted spots. The proposed strategy has been applied to a sample set of various images and the results shows that the technique is efficient in determining the unit cell in 2D and classify the point group with good accuracy.     

Penultimate Approximations in Statistics of Extremes and Reliability of Large Coherent Systems

In reliability theory any coherent system can be represented as either a series-parallel or a parallel-series system. Its lifetime can thus be written as the minimum of maxima or the maximum of minima. For large-scale coherent systems it is sensible to assume that the number of system components goes to infinity. Then, the possible non-degenerate extreme value laws either for maxima or for minima are eligible candidates for the system reliability or at least for the finding of adequate lower and upper bounds for the reliability. The identification of the possible limit laws for the system reliability of homogeneous series-parallel (or parallel-series) systems has already been done under different frameworks. However, it is well-known that in most situations such non-degenerate limit laws are better approximated by an adequate penultimate distribution. Dealing with regular and homogeneous parallel-series systems, we assess both theoretically and through Monte-Carlo simulations the gain in accuracy when a penultimate approximation is used instead of the ultimate one.