Structure-based virtual screening of natural products as potential stearoyl-coenzyme a desaturase 1 (SCD1) inhibitors

Stearyl coenzyme A desaturase enzyme 1 (SCD1) is a key enzyme that catalyzes the conversion of saturated fatty acids (SFA) into monounsaturated fatty acids (MUFA) and plays a vital role in lipid metabolism of tumor cells. SCD1 is overexpressed in a variety of malignant tumors, and its related inhibitors showed significant anti-tumor activity in vitro and in vivo experiments, which is a new target for tumor therapy. The focus of this study is to identify novel SCD1 inhibitors from natural products through computer simulations. First, 176,602 compounds from natural product databases were virtually screened. By molecular dynamics (MD) simulations, the ligand-protein interactions of 5 compounds with high docking manifestation were analyzed accurately. Then, MM-GBSA and MM-PBMA methods were used to verify the results. Finally, ADMET prediction was performed for the 5 compounds. As a result, two natural products with potential inhibition towards SCD1 were identified, which had the excellent docking manifestation, binding mode within SCD1 pocket and stability during molecular dynamics simulation. This study provides a meaningful model for the development and optimization of new inhibitors and anti-tumor drugs targeting SCD1.     

Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation

The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. Therefore, there is increased interest in screening compounds that can inhibit influenza virus RNA polymerase. Three natural compounds were found by using molecular docking-based virtual screening, which could bind tightly within the polymerase acidic protein-polymerase basic protein 1 (PA-PB1) subunit of influenza virus polymerase. Firstly, their drug likeness properties were evaluated, which showed that the hepatotoxicity values of all the three compounds indicating they had less or no hepatotoxicity, and did not have the plasma protein biding (PPB) ability, the three compounds needed to be modified in some aspects, like bulky molecular size. The stability of the complexes of PA-hits was validated through molecular dynamics (MD) simulation, revealing compound 2 could form more stable complex with PA subunit. The torsional conformations of each rotatable bond of the ligands in PA subunit were also monitored, to investigate variation in the ligand properties during the simulation, compound 3 had fewer rotatable bonds, indicating that the molecule had stronger rigidity. The bar charts of protein–ligand contacts and contacts over the course of trajectory showed that four key residues (Glu623, Lys643, Asn703 and Trp706) of PA subunit that participated in hydrogen-bond, water bridge and hydrophobic interactions with the hit compounds. Finally, the binding free energy and contributed energies were calculated by using MM-GBSA method. Out of the three compounds, compound 1 showed the lowest total binding free energy. Among all the interactions, the contribution of the covalent binding and the van der Waals energy were more than other items, compound 1 formed more stable hydrogen bonds with the residues of PA subunit binding pocket. This study smoothed the path for the development of novel lead compounds with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of influenza, which provided a good basis for further research on novel and effective influenza virus PA-PB1 interaction inhibitors.     

Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution

The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET.     

Caseinolytic Proteins (Clp) in the Genus Klebsiella: Special Focus on ClpK

Caseinolytic proteins (Clp), which are present in both prokaryotes and eukaryotes, play a major role in cell protein quality control and survival of bacteria in harsh environmental conditions. Recently, a member of this protein family, ClpK was identified in a pathogenic strain of Klebsiella pneumoniae which was responsible for nosocomial infections. ClpK is linked to the thermal stress survival of this pathogen. The genome wide analysis of Clp proteins in Klebsiella spp. indicates that ClpK is present in only 34% of the investigated strains. This suggests that the uptake of the clpk gene is selective and may only be taken up by a pathogen that needs to survive harsh environmental conditions. In silico analyses and molecular dynamic simulations show that ClpK is mainly α-helical and is highly dynamic. ClpK was successfully expressed and purified to homogeneity using affinity and anion exchange chromatography. Biophysical characterization of ClpK showed that it is predominantly alpha-helical, and this is in agreement with in silico analysis of the protein structure. Furthermore, the purified protein is biologically active and hydrolyses ATP in a concentration- dependent manner.     

Antiferromagnetic-vortex dynamics driven by spin-polarized current in small thin disks

We investigate vortex configuration confined in antiferromagnetic thin disks. By virtue of sublattice mismatch at the disk borders, we propose a model that takes such a magnetostatic-like cost into account. The model predicts that onion-like configuration interpolates between curly and divergent vortex. Concerning its dynamics, it is shown that the vortex acquires oscillatory dynamics with well-defined amplitude and frequency that may be controlled on demand by an alternating spin-polarized current. These findings may be useful for the emerging field of antiferromagnetic topological spintronics, once vortex dynamics may be controlled by purely electronic means.     

Structural,electronic, magnetic properties and critical behavior of the equiatomic quaternary Heusler alloy CoFeTiSn

In this article, we study the exchange coupling interactions of the equiatomic quaternary Heusler alloy CoFeTiSn, using the two methods: Monte Carlo simulations and the ab-initio method. In a first step, we use the ab-initio calculations to investigate the structural, the electronic and the magnetic properties of this alloy under the GGA method. The analysis of the energy dependence on the lattice parameter a (Å) of the equiatomic quaternary Heusler alloy CoFeTiSn, is discussed for different atomic configurations. The ferromagnetic configuration is found to be the more stable one, with an optimal lattice parameter value 6.00 Å. On the other hand, the electronic structure results show that the compound CoFeTiSn exhibits a half-metallic character and a spin polarization of 100% at the Fermi-level. The total magnetic moment of this alloy is found to be equal to 2.00 μ_B which follows the Slater Pauling rule. Our results support the half-metallic behavior of the studied material. In order to complete this study, we reported the dependence of the critical transition temperature as a function of the parameter α of the equiatomic quaternary Heusler alloy CoFeTiSn. We showed that the critical temperature increases almost linearly with an increase of the values of the parameter α.     

Tensile properties of microtubules: A study by nonlinear molecular structural mechanics modelling

A nonlinear molecular structural mechanics (MSM) model is proposed in this paper for studying the tensile properties of microtubules (MTs). In the nonlinear MSM models, the interactions between tubulin monomers in MTs are treated as nonlinear axial and torsional springs, whose stiffness coefficients are extracted from all-atom molecular dynamics simulations. The Young's modulus and fracture properties of MTs under tension extracted from the present nonlinear MSM models are found to agree well with the existing simulation and experiment results, which shows the efficiency and accuracy of the proposed nonlinear MSM models. In addition, the nonlinear MSM models are also extended to investigate the tensile properties including Young's modulus and fracture strain of MTs possessing lattice defects. The results obtained from nonlinear MSM models are utilized to develop a predictive equation for quickly predicting the tensile properties of MTs with different lattice defect levels.     

Mechanistic model for the dielectric spectrum of a simple dielectric material

ABSTRACT

In this paper, we perform molecular dynamics simulations of a dielectric fluidic material composed of permanent molecular dipoles. The dielectric spectrum features two peaks at lower frequencies than the system phonon frequency. The primary peak is observed at all temperatures studied and shifts toward lower frequencies as the temperature decreases. During this shift, the secondary peak emerges with a higher peak frequency than the primary peak. The secondary peak amplitude increases as the temperature decreases. Both peaks are dependent on the wavevector; in the small wavevector regime, the primary peak is shifted to higher frequencies as the wavevector squared and the secondary peak amplitude increases as the wavevector increases, but shows no shift in frequency. From the polarisation balance equation, we propose a model for the dielectric spectrum. This captures the spectrum features, and we conjecture that the primary peak is due to dipole moment correlations (Debye-type) and the secondary peak is due to the correlation between the dipole moment and a microscopic local field.     

Dynamics of a Predator-Prey Model with Allee Effect and Herd Behavior

This paper deals with dynamics of a predator-prey model with Allee effect and herd behavior. We first study the stability of non-negative constant solutions for such system. We also establish the existence of Hopf bifurcation solutions for such predator-prey model. The stability and bifurcation direction of Hopf bifurcation solution in the case of spatial homogeneity are further discussed. At the same time, several examples are given by MATLAB. Finally, the numerical simulations of the system are carried out through MATLAB, which intuitively verifies and supplements the theoretical analysis results.     

Nonequilibrium Time Reversibility with Maps and Walks

Time-reversible dynamical simulations of nonequilibrium systems exemplify both Loschmidt’s and Zermélo’s paradoxes. That is, computational time-reversible simulations invariably produce solutions consistent with the irreversible Second Law of Thermodynamics (Loschmidt’s) as well as periodic in the time (Zermélo’s, illustrating Poincaré recurrence). Understanding these paradoxical aspects of time-reversible systems is enhanced here by studying the simplest pair of such model systems. The first is time-reversible, but nevertheless dissipative and periodic, the piecewise-linear compressible Baker Map. The fractal properties of that two-dimensional map are mirrored by an even simpler example, the one-dimensional random walk, confined to the unit interval. As a further puzzle the two models yield ambiguities in determining the fractals’ information dimensions. These puzzles, including the classical paradoxes, are reviewed and explored here.