Molecular dynamics and pharmacophore modelling studies of different subtype (ALK and EGFR (T790M)) inhibitors in NSCLC

Extensively validated 3D pharmacophore models for ALK (anaplastic lymphoma kinase) and EGFR (T790M) (epithelial growth factor receptor with acquired secondary mutation) were developed. The pharmacophore model for ALK (r² = 0.96, q² = 0.692) suggested that two hydrogen bond acceptors and three hydrophobic groups arranged in 3-D space are essential for the binding affinity of ALK inhibitors. Similarly, the pharmacophore model for EGFR (T790M) (r² = 0.92, q² = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). These pharmacophore models allowed searches for novel ALK and EGFR (T790M) dual inhibitors from multiconformer 3D databases (Asinex, Chembridge and Maybridge). Finally, the eight best hits were selected for molecular dynamics simulation, to study the stability of their complexes with both proteins and final binding orientations of these molecules. After molecular dynamics simulations, one hit has been predicted to possess good binding affinity for both ALK and EGFR (T790M), which can be further investigated for its experimental in-vitro/in-vivo activities.     

Exploration of antioxidant activity of newly synthesized azo flavones and its correlation with electrochemical parameters along with the study of their redox behaviour

A series of 7-hydroxy-2-aryl-3-(2-aryldiazenyl)-4H-chromen-4-one derivatives was synthesized in quantitative yields. Herein, we demonstrate the antioxidant potential of the synthesized substituted azo flavones using 1,1-diphenyl-2-picryl-hydrazyl assay method along with the evaluation of their redox behaviour by cyclic voltammetry. The synthesized compounds manifested good antioxidant potential as compared to standard antioxidant ascorbic acid, which especially pertains to the compounds having methoxy and hydroxyl groups. A good correlation between minimum inhibitory concentration (IC₅₀) and deduced electrochemical parameter, i.e., half peak oxidation potential (E _p/2) values, was established.     

Primary photophysical and photochemical processes for Pt(SCN)<Subscript>6</Subscript><Superscript>2–</Superscript> complex

Photosolvation of a Pt^IV hexathiocyanate complex Pt(SCN)₆ ^2– in water and ethanol was studied by steady-state photolysis, nanosecond laser flash photolysis, and ultrafast kinetic spectroscopy. Complexes Pt(SCN)₅(H₂O)^– and Pt(SCN)₅(C₂H₅OH)^– were found to be the only reaction products. The quantum yields of photosolvation are independent of the excitation wavelength, being equal to 0.25 and 0.5 for the solutions of the complex in water and ethanol, respectively. Photosolvation proceeds by the mechanism of heterolytic metal—ligand bond dissociation without involvement of redox processes. The characteristic time of formation of the end products for both solvents is about 10 ps. Three successive intermediates detected on the picosecond time scale were interpreted as Pt^IV complexes. The nature of the intermediates and possible mechanisms of photosolvation are discussed.     

<Emphasis Type="Italic">N</Emphasis>-Allyl-substituted aminomethylene-1,1-bisphosphonates in 1,3-dipolar cycloaddition reaction with aromatic nitrile <Emphasis Type="Italic">N</Emphasis>-oxides

A reaction of N-allyl-substituted aminomethylene-1,1-bisphosphonates with aromatic nitrile N-oxides was used to obtain new aminomethylenebisphosphonates with one or two 3-arylisoxazoline rings at the nitrogen atom. NMR spectroscopy studies showed that the bisphosphonates with two isoxazoline fragments in the molecule exist in solution as a mixture of two diastereomers.     

Foreword

Electrochemical behaviors of U⁴⁺ in LiCl–KCl–UF₄ eutectic and deposition of U metal were investigated. It was found that the presence of F^? has influence on the diffusion of U³⁺ and U⁴⁺ as comparing to data obtained in pure chloride molten salts. Electrochemical deposition of U was carried out by using pulse current electrolysis. Characterization results indicate that U metal was obtained at the cathode, implying U metal can be directly deposited from LiCl–KCl–UF₄ eutectic in this case and the extractive ratio is calculated to be 98%. Our results demonstrate feasible separation of U from LiCl–KCl–UF₄ molten salt by electrochemical method.     

DRBEM solution of biomagnetic fluid flow and heat transfer in cavities-CMMSE2016

In this paper, we investigate the fully developed, laminar, forced convection flow of an electrically non-conducting, viscous, biomagnetic fluid in the 2D cross-section (cavity) of a long impermeable pipe. The fluid is under the influence of a point magnetic source placed below the cavity. The dual reciprocity boundary element method (DRBEM) with constant and linear elements is used for solving the governing equations resulting from the Navier–Stokes and energy equations together with magnetization and buoyancy forces. The fundamental solution of Laplace equation is made use of converting differential equations to boundary integral equations by taking all the terms other than Laplacian as inhomogeneity in the Poisson’s equations for the velocity components, pressure and the temperature of the fluid. The unknown pressure boundary conditions are approximated through momentum equations by using finite difference approximation for the pressure gradients and DRBEM coordinate matrix for the other terms. All the space derivatives are also calculated by DRBEM coordinate matrix which is one of the main advantages of DRBEM. Pipe axis velocity is also computed. The effects of magnetization and the buoyancy force on the fluid with or without viscous dissipation term in the energy equation are investigated in square and lid-driven cavities for several values of magnetic (Mn) and Rayleigh (Ra) numbers. It is observed that the flow and heat transfer are significantly affected with increasing values of Mn and Ra. DRBEM gives small sized linear systems due to its boundary only nature at a considerably low computational expense.     

Investigation of Cold Atmospheric Plasma-Activated Water for the Dental Unit Waterline System Contamination and Safety Evaluation in Vitro

The disinfection of the inner surface of a medical device has long been a challenge for the central sterile supply departments. Dental unit waterline system (DUWLs) foster the attachment of microorganisms and development of biofilm, which lead to continuous contamination of the outlet water from dental units; this contamination may be responsible for a potential risk of infection due to the exposure of patients and medical staff. The present study investigated the disinfection effects of cold atmospheric plasma-activated water (CAPAW) on DUWLs using a model of 5-day-old Enterococcus faecalis biofilm. The results showed that the colony-forming unit was reduced from 10⁷ to 0 after 5 min of treatment. The physicochemical properties of CAPAW were evaluated, including the pH value, oxidation reduction potential, and NO radical. The results showed that the inactivation mechanisms were mainly triggered by the reactive oxygen/nitrogen species. Additionally, CAPAW had a metal corrosion rate same as that of deionized water. We conclude that CAPAW can be applied as an appropriate alternative disinfectant against biofilm contamination of DUWLs.     

Molecular Cloning and Characteristic Features of a Novel Extracellular Tyrosinase from <Emphasis Type="Italic">Aspergillus niger</Emphasis> PA2

Biofertilizers have been widely used in many countries for their benefit to soil biological and physicochemical properties. A new microbial biofertilizer containing Phanerochaete chrysosporium and Bacillus thuringiensis was prepared to decrease nicotine content in tobacco leaves by regulating soil nitrogen supply. Soil NO₃ ^?-N, NH₄ ⁺-N, nitrogen supply-related enzyme activities, and nitrogen accumulation in plant leaves throughout the growing period were investigated to explore the mechanism of nicotine reduction. The experimental results indicated that biofertilizer can reduce the nicotine content in tobacco leaves, with a maximum decrement of 16–18 % in mature upper leaves. In the meantime, the total nitrogen in mature lower and middle leaves increased with the application of biofertilizer, while an opposite result was observed in upper leaves. Protein concentration in leaves had similar fluctuation to that of total nitrogen in response to biofertilizer. NO₃ ^?-N content and nitrate reductase activity in biofertilizer-amended soil increased by 92.3 and 42.2 %, respectively, compared to those in the control, whereas the NH₄ ⁺-N and urease activity decreased by 37.8 and 29.3 %, respectively. Nitrogen uptake was improved in the early growing stage, but this phenomenon was not observed during the late growth period. Nicotine decrease is attributing to the adjustment of biofertilizer in soil nitrogen supply and its uptake in tobacco, which result in changes of nitrogen content as well as its distribution in tobacco leaves. The application of biofertilizer containing P. chrysosporium and B. thuringiensis can reduce the nicotine content and improve tobacco quality, which may provide some useful information for tobacco cultivation.     

Alkaline Protease Production from <Emphasis Type="Italic">Brevibacterium luteolum</Emphasis> (MTCC 5982) Under Solid-State Fermentation and Its Application for Sulfide-Free Unhairing of Cowhides

Enzyme-based unhairing in replacement of conventional lime sulfide system has been attempted as an alternative for tackling pollution. The exorbitant cost of enzyme and the need for stringent process control need to be addressed yet. This study developed a mechanism for regulated release of protease from cheaper agro-wastes, which overcomes the necessity for stringent process control along with total cost reduction. The maximum protease activity of 1193.77 U/g was obtained after 96 h of incubation with 15% inoculum of the actinomycete strain Brevibacterium luteolum (MTCC 5982) under solid-state fermentation (SSF). The medium after SSF was used for unhairing without the downstream processing to avoid the cost involved in enzyme extraction. This also helped in the regulated release of enzyme from bran to the process liquor for controlled unhairing and avoided the problem of grain-pitting. Unhairing process parameters were standardized as 20% enzyme offer, 40% Hide-Float ratio at 5 ± 1 rpm, and process pH of 9.0. The cost of production of 1000 kU of the protease was calculated as 0.44 USD. The techno-economic feasibility studies for setting up an SSF enzyme production plant showed a high return on investment of 15.58% with a payback period of 6.4 years.     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.