Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Rapid and simple method for determination of Nepsilon-(carboxymethyl)lysine and Nepsilon-(carboxyethyl)lysine in urine using gas chromatography/mass spectrometry

A new procedure was developed to determine in urine the concentrations of N(epsilon)-(carboxymethyl)lysine (CML) and N(epsilon)-(carboxyethyl)lysine (CEL), the major products of oxidative modification of glycated proteins, to assess levels of oxidative stress in physiological systems. The urine samples were acetonitrile-deproteinized, then derivatized by ethylchloroformate, and N(O,S)-ethoxycarbonyl ethyl esters of amino acids were analysed by isotope dilution gas chromatography/mass spectrometry. Recovery averaged 89%. Linearity was excellent (r = 0.998-0.999) in the 0.5-25 micromol/L range for CML and CEL. The limit of detection of this assay was 0.1 micromol/L (corresponding to 0.20 pmol of CML or CEL on column). Intra-day and inter-day precisions were likewise excellent, with relative standard deviations <4.63 and <6.15%, respectively. Accuracy of CML and CEL determination (15 micromol/L) was 2.9 and 5.9% of the estimated theoretical value. The time from obtaining the urine sample to determination of the concentration from the chromatographic peak was 80 min or less. This method is sensitive, reproducible, accurate, relatively cheap and very simple. It can be useful for laboratories involved in the diagnosis and monitoring of age-related chronic diseases.     

Design of a combined ozone/electron beam process for waste water and economic feasibility of the process

A design of a combined ozone/electron beam irradiation process for treating a 50 m³/h waste water stream from a molasses processing is discussed. Moreover, a cost evaluation of such a process in comparison to a conventional ozonation/biology treatment process has been performed to assess the potential of the irradiation process for technical use. Although the result of this comparison is not bad for the irradiation process an implementation into a full scale plant would not seem to be the thing to do in the present case.     

One‐pot synthesis of 1‐ and 5‐substituted 1H‐tetrazoles using 1,4‐dihydroxyanthraquinone–copper(II) supported on superparamagnetic Fe3O4@SiO2 magnetic porous nanospheres as a recyclable catalyst

An effective one‐pot, convenient process for the synthesis of 1‐ and 5‐substituted 1H‐tetrazoles from nitriles and amines is described using1,4‐dihydroxyanthraquinone–copper(II) supported on Fe₃O₄@SiO₂ magnetic porous nanospheres as a novel recyclable catalyst. The application of this catalyst allows the synthesis of a variety of tetrazoles in good to excellent yields. The preparation of the magnetic nanocatalyst with core–shell structure is presented by using nano‐Fe₃O₄ as the core, tetraethoxysilane as the silica source and poly(vinyl alcohol) as the surfactant, and then Fe₃O₄@SiO₂ was coated with 1,4‐dihydroxyanthraquinone–copper(II) nanoparticles. The new catalyst was characterized using Fourier transform infrared spectroscopy, X‐ray diffraction, transmission electron microscopy, field emission scanning electron microscopy, dynamic light scattering, thermogravimetric analysis, vibration sample magnetometry, X‐ray photoelectron spectroscopy, nitrogen adsorption–desorption isotherm analysis and inductively coupled plasma analysis. This new procedure offers several advantages such as short reaction times, excellent yields, operational simplicity, practicability and applicability to various substrates and absence of any tedious workup or purification. In addition, the excellent catalytic performance, thermal stability and separation of the catalyst make it a good heterogeneous system and a useful alternative to other heterogeneous catalysts. Also, the catalyst could be magnetically separated and reused six times without significant loss of catalytic activity. Copyright © 2016 John Wiley & Sons, Ltd.     

α‐ZrP/Uracil/Cu2+ nanoparticles as an efficient catalyst in the Morita‐Baylis‐Hillman reaction

A facile synthesis of uracil‐Cu²⁺ nanoparticles immobilized on alpha‐zirconium hydrogen phosphate (α‐ZrP), abbreviated as α‐ZrP/Uracil/Cu²⁺, was presented. This compound was synthesized by the thermal method and used as a reusable catalyst for the Morita‐Baylis‐Hillman reaction without any additives. First, (3‐ iodopropyl) trimethoxysilane as a linker is reacted with α‐ZrP support to give the α‐ZrP/IPTMOS. Addition of uracil and then the addition of copper (II) acetate to α‐ZrP/IPTMOS results in the production of selected catalyst. The Morita‐Baylis‐Hillman reaction catalyzed by α‐ZrP/Uracil/Cu^{2 +} demonstrated high product yield, short reaction time and a straightforward work‐up. The catalyst with enough outside surface was easily recovered using centrifugation and reused five times without a significant reduction in its activity.     

Design,preparation and characterization of Cu/GA/Fe3O4@SiO2 nanoparticles as a catalyst for the synthesis of benzodiazepines and imidazoles

The synthesis and characterization of an efficient and reusable nanocatalyst, Cu/GA/Fe₃O₄@SiO₂, obtained by ultrasonic‐assisted grafting of guanidineacetic acid on modified Fe₃O₄@SiO₂ core–shell nanocomposite spheres and subsequent immobilization of Cu(II), are described. The catalyst was characterized by means of X‐ray diffraction, scanning and transmission electron microscopies, energy‐dispersive X‐ray spectroscopy, elemental analysis, thermogravimetric analysis, Fourier transform infrared spectroscopy, vibrating sample magnetometry and inductively coupled plasma optical emission spectrometry. The prepared nanocatalyst facilitated an efficient and straightforward friendly procedure for the synthesis of benzodiazepines and imidazoles in ethanol and under solvent‐free conditions, respectively. The nanocatalyst can be easily recovered using a magnet and reused several times without any significant loss of activity. Copyright © 2016 John Wiley & Sons, Ltd.     

Copper(I) oxide nanoparticles supported on magnetic casein as a bio‐supported and magnetically recoverable catalyst for aqueous click chemistry synthesis of 1,4‐disubstituted 1,2,3‐triazoles

Copper(I) oxide nanoparticles supported on magnetic casein (Cu₂O/Casein@Fe₃O₄NPs) has been synthesized as a bio‐supported catalyst and was characterized using powder X‐ray diffraction, transmission electron microscopy, energy dispersive X‐ray and Fourier transform infrared spectroscopies, thermogravimetric analysis and inductively coupled plasma optical emission spectrometry. The catalytic activity of the synthesized catalyst was investigated in one‐pot three‐component reactions of alkyl halides, sodium azide and alkynes to prepare 1,4‐disubstituted 1,2,3‐triazoles with high yields in water. The reaction work‐up is simple and the catalyst can be magnetically separated from the reaction medium and reused in subsequent reactions.     

Synthesis,characterization and application of alumina/ vanadium pentoxide nanocomposit by sol–gel method

In this work, we report the preparation of Al₂O₃/V₂O₅ nanocomposit using vanadium and aluminum nitrate by sol–gel method. Characterization of nanocomposit was carried out by powder X‐ray diffractometry (XRD), Fourier transform infrared (FT‐IR), scanning electron microscopy (SEM), Energy‐Dispersive X‐ray (EDX) and UV spectroscopy. Then, applicability of the synthesized nanocomposit was tested as a nanocatalyst for the synthesis of diindolyl oxindole derivatives, an important class of potentially bioactive compounds. The products were obtained in good to high yields from one‐pot three‐component condensation of isatin with indole. Also, this nanocatalyst has been reused several times, without observable loss of activity.     

Synthesis and properties of sulfur‐contained poly(silylene arylacetylene)s

Poly(silylene arylacetylene) (PSA) is a kind of poly(arylacetylene) silicon‐containing resins with excellent heat resistance and good mechanical performances. In this article, the sulfur atom is introduced into the main chain of the PSA molecule to obtain a sulfur‐containing poly(silylene arylacetylene), named S‐PSA. By Williamson and Sonogashira reactions, bis(4‐ethynylphenyl)sulfide and bis(4‐ethynylphenyl)sulfone were synthesized. Thereafter, through Grignard reagent way, the poly(silylene ethynylene phenylene sulfide phenylene ethynylene) (PSESE) and poly(silylene ethynylene phenylene sulfone phenylene ethynylene) (PSESO₂E) were synthesized from bis(4‐ethynylphenyl)sulfide, bis(4‐ethynylphenyl)sulfone, and methylphenyl dichlorosilane. Poly(silylene ethynylene phenylene sulfoxide phenylene ethynylene) (PSESOE) was synthesized by the oxidation of PSESE. The structures and properties of these resins were characterized and the mechanical properties of the T300 reinforced composites were tested. The results show that the novel S‐PSA resins have excellent heat resistance and good mechanical properties, and could be used as resin matrices for high‐performance composites in high‐tech fields. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 2324–2332     

Nickel(II) Schiff base complex supported on nano‐titanium dioxide: A novel straightforward route for preparation of supported Schiff base complexes applying 2,4‐toluenediisocyanate

For the first time, a novel, straightforward and inexpensive route for immobilization of metals in Schiff base complex form is reported applying 2,4‐toluenediisocyanate as a precursor of primary amine group. A nickel(II) Schiff base complex supported on nano‐TiO₂ was designed and synthesized as an effective heterogeneous nanocatalyst for organic reactions, and well characterized using various techniques such as Fourier transform infrared spectroscopy, field emission scanning electron microscopy, transmission electron microscopy, X‐ray diffraction, energy‐dispersive X‐ray analysis and thermogravimetric analysis. The catalytic efficiency of the complex was evaluated in selective oxidation of sulfide to sulfoxide by hydrogen peroxide as an oxidant under solvent‐free conditions at room temperature, which successfully resulted in high yield and high conversion of products. Effective factors including solvent type, oxidant and catalyst amount were also optimized. The catalyst shows outstanding reusability and could be impressively recovered for six consecutive cycles without significant change of its catalytic efficiency.