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.     

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.     

Infinitely Many Solutions of Nonlocal Kirchhoff-Type Equations via Perturbation Methods

Mathematical Notes - We study the multiplicity of weak solutions to the boundary-value problem $$\begin{alignedat}{2} - M\biggl(\iint_{\mathbb R^{2N}}|u(x)-u(y)|^2 K(x-y)\,d x\,d y\biggr)\mathscr...     

Broadening and Shift of the D1 and D2 Lines of Rb Atoms by Neon: Resolving Hyperfine Components in a Half-Wave Cell Using Double Differentiation with Respect to Frequency

Optics and Spectroscopy - A cell with a submicron thickness was used to measure the broadening and shift of the D1 and D2 lines of Rb atoms by neon. The resolution of hypefine components...     

Unbounded Solutions to Systems of Differential Equations at Resonance

Journal of Dynamics and Differential Equations - We deal with a weakly coupled system of ODEs of the type $$\begin{aligned} x_j'' + n_j^2 \,x_j + h_j(x_1,\ldots ,x_d) = p_j(t), \qquad...     

A tight Hermite–Hadamard inequality and a generic method for comparison between residuals of inequalities with convex functions

Periodica Mathematica Hungarica - We present a tight parametrical Hermite–Hadamard type inequality with probability measure, which yields a considerably closer upper bound for the mean value...     

On the Distributivity and Modularity Properties of the Lattice of Fitting Classes

Mathematical Notes - It is proved that the lattice of all Fitting classes of finite groups is not distributive, and conditions under which Fitting classes satisfy the distributive and modular laws...     

A Comparison of Neutron Identification Methods in Inorganic ZnS-based Scintillators

Physics of Atomic Nuclei - The paper presents a comparison of three neutrons identifying methods in scintillators based on ZnS with 6Li and 10B: charge integration method, pulse gradient analysis,...     

Quantitative Analysis of Al in Flour Products by Laser-Induced Breakdown Spectroscopy Combined with Partial Least Squares

Journal of Applied Spectroscopy - Based on partial least squares (PLS) analysis, the effects of different smoothing points and different preprocessing methods on the accuracy and precision of the...     

Growth of $${\text{N}}{{{\text{d}}}_{{{\text{1}}\; - \;y}}}{\text{Eu}}_{y}^{{{\text{2}} + }}{{{\text{F}}}_{{{\text{3}}\; - \;y}}}$$ Single Crystals with Tysonite-Type (LaF3) Structure and Investigation of the Concentration Dependence of Some Their Properties

Crystallography Reports - Nd1 – yEuyF3 – y crystals (y is the molar fraction of EuF2; 0 ≤ y ≤ 0.15) with a tysonite (LaF3) structure have...