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.     

Formation of low-temperature deformation-induced segregations of nickel in Fe–Ni-based austenitic alloys

ABSTRACT

The authors present the results of an investigation in Fe–Ni-Cr austenitic alloys of the low-temperature deformation-induced segregations of nickel that form in the micro regions being (i) located close to grain- and subgrain boundaries and (ii) characteristic of the concentration and magnetic inhomogeneities indicated by the appearance of a dark diffraction contrast at the electron diffraction patterns taken from these regions typical (at the same time) of an enhanced value of Curie temperature. The observed effects were connected with the micro distortions caused by the local change of lattice parameter because of an increase in nickel concentration, as well as in the result of a magnetostriction dilatation. Using methods of the X-ray energy dispersive spectroscopy (XEDS) and atomic-probe body-section radiography (tomography – APT) has made it possible to determine the borders of those regions of austenite that were characteristic of an enhanced concentration of nickel in the fields of the localisation of a deformation-induced segregation of nickel in the vicinity of grain (subgrain) boundaries of austenitic alloys of the types Fe–13Cr–30Ni and Fe–37Ni–3Ti.     

Molecular dynamics study of cluster structure and rotational wave properties in solid-state nanostructures

Molecular dynamics simulation was performed to study the formation of cluster structure, interfaces, and surfaces with different curvature radii in a perfect nanocrystal passed through by a nonlinear wave. It is shown that this process is a type of nanostructure self-organization in response to an external energy flux with subsequent development of a strong rotational field.     

On the redox reactions between allyl radicals and NOx

NO_x mitigation is a central focus of combustion technologies with increasingly stringent emission regulations. NO_x can also enhance the autoignition of hydrocarbon fuels and can promote soot oxidation. The reaction between allyl radical (C₃H₅) and NO_x plays an important role in the oxidation kinetics of propene. In this work, we measured the absolute rate coefficients for the redox reaction between C₃H₅ and NO_x over the temperature range of 1000–1252 K and pressure range of 1.5–5.0 bar using a shock tube and UV laser absorption technique. We produced C₃H₅ by shock heating of C₃H₅I behind reflected shock waves. Using a Ti:Sapphire laser system with frequency quadrupling, we monitored the kinetics of C₃H₅ at 220 nm. Unlike low-temperature chemistry, the two target reactions, C₃H₅ + NO → products (R1) and C₃H₅ + NO₂ → products (R2), exhibited a strong positive temperature dependence for this radical-radical type reaction. However, these reactions did not show any pressure dependence over the pressure range of 1.5–5.0 bar, indicating that the measured rate coefficients are close to the high-pressure limit. The measured values of the rate coefficients resulted in the following Arrhenius expressions (in unit of cm³/molecule/s):$k_1\left({\mathrm{C}}_3{\mathrm{H}}_5+\text{NO}\right)=1.49\times {10}^{?10}\exp \left(?6083.6\frac{\mathrm{K}}{T}\right)\left(1017?1252K\right)$$k_2\left({\mathrm{C}}_3{\mathrm{H}}_5+\mathrm{N}{\mathrm{O}}_2\right)=1.71\times {10}^{?10}\exp \left(?3675.7\frac{\mathrm{K}}{T}\right)\left(1062?1250K\right)$To our knowledge, these are the first high-temperature measurements of allyl + NO_x reactions. The reported data will be highly useful in understanding the interaction of NO_x with resonantly stabilized radicals as well as the mutual sensitization effect of NO_x on hydrocarbon fuels.     

Differential Graded Bocses and A ∞ $A_{\infty }$ -Modules

Algebras and Representation Theory - We introduce and study the category of twisted modules over a triangular differential graded bocs. We show that in this category idempotents split, that it...     

Synthesis,characterization, and transport properties of Nafion-polypyrrole membrane for direct methanol fuel cell (DMFC) application

Journal of Solid State Electrochemistry - Due to their distinctive chemical, electronic, and environmental properties, polypyrrole is used as a blocking barrier for methanol leakage in direct...     

Chiral 7-Oxabicyclo[2.2.1]heptane Building Blocks for Prostanoids

Russian Journal of Organic Chemistry - Methyl (Z)-3-[(2R,3R,4S,5S)-5-(2-methoxy-2-oxoethyl)-3,4-(isopropylidenedioxy)tetrahydrofuran-2-yl]-prop-2-enoate was synthesized, and its intramolecular...     

Plasma Crystal in (3 + 1) Dimensions

JETP Letters - A quasi-two-dimensional plasma crystal in (3 + 1) dimensions has been experimentally observed for the first time; i.e., three spatial coordinates of each microparticles of the...     

Experimental and numerical analysis of cylindrical turbulators in a double pipe heat exchanger under turbulent flow conditions

In the present work, the use of cylindrical turbulators in a double pipe heat exchanger has been investigated. Cylindrical fin type of turbulators has been placed circumferentially separated by 90° on the outer side of an inner pipe at a regular pitch. Experimental studies were undertaken for different air flow rates in a turbulent regime whose Reynolds number range between 2500 and 10000. Heat transfer characteristics like Nu and friction factor have been experimentally determined. Parametric studies were conducted by changing the pitch and also the orientation of the turbulators. Nu and friction factor were found to increase as the pitch is reduced. A model with alternatively changed orientation outperformed others by exhibiting highest Nu and reduced friction factor.