Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Initial value problem of the Whitham equations for the Camassa-Holm equation

We study the Whitham equations for the Camassa-Holm equation. The equations are neither strictly hyperbolic nor genuinely nonlinear. We are interested in the initial value problem of the Whitham equations. When the initial values are given by a step function, the Whitham solution is self-similar. When the initial values are given by a smooth function, the Whitham solution exists within a cusp in the x-t plane. On the boundary of the cusp, the Whitham solution matches the Burgers solution, which exists outside the cusp.     

Tissue-specific and neural activity-regulated expression of human BDNF gene in BAC transgenic mice

Background  

Brain-derived neurotrophic factor (BDNF) is a small secreted protein that has important roles in the developing and adult nervous system. Altered expression or changes in the regulation of the BDNF gene have been implicated in a variety of human nervous system disorders. Although regulation of the rodent BDNF gene has been extensively investigated, in vivo studies regarding the human BDNF gene are largely limited to postmortem analysis. Bacterial artificial chromosome (BAC) transgenic mice harboring the human BDNF gene and its regulatory flanking sequences constitute a useful tool for studying human BDNF gene regulation and for identification of therapeutic compounds modulating BDNF expression.     

Luminescence of ruthenium halide complexes containing a hemilabile phosphine pyrenyl ether ligand

A series of Ru(II) complexes, tcc-RuX2(POC4Pyr-P,O)2 (X = Cl (3), Br (4), I (5)), containing the hemilabile phosphine pyrenyl ether ligand 4-{2-(diphenylphosphino)phenoxy}butylpyrene (POC4Pyr (1)) are reported. The synthesis and spectroscopic properties of both the ligand, POC4pyr (1), and ligand oxide, P(=O)OC4pyr 2, and the solid-state structure of 1 are reported. Complexes 3-5 react rapidly with CO to give complexes ttt-RuX2(CO)2(POC4pyr-P)2 (X = Cl (6), Br (7), I (8)). No pyrene excimer emission is detected from 3-5; however, different intensities of excimer emission are observed for 6-8. The intensity of excimer emission decreases through the series, with 6 showing the most intense response. The emission is solely due to intramolecular pyrene excimers at low concentrations (< or =10(-4) M). Comparison of the UV-vis and steady-state fluorescence spectra shows overlap between the low energy d-d absorption of 7 and 8 with excimer emission (480 nm), suggesting nonradiative energy transfer may be occurring. Once excess CO is removed, complexes 6-8 isomerize to cis-dicarbonyl complexes cct-RuX2(CO)2(POC4Pyr-P)2 (X = Cl (9), Br (10), I (11)). The intensity of excimer emission from 9-11 increases with respect to the excimer emission observed for 6-8, with 9 showing a significant increase in excimer intensity.     

Mono(dinitrogen) and carbon monoxide adducts of bis(cyclopentadienyl) titanium sandwiches

The silyl-substituted titanocene complex, (eta5-C5Me4SiMe2Ph)2Ti, coordinates dinitrogen upon cooling to -35 degrees C to yield an unprecedented example of a mono(dinitrogen) complex of a substituted bis(cyclopentadienyl) titanium compound, (eta5-C5Me4SiMe2Ph)2Ti(N2). Analogous monocarbonyl derivatives, (eta5-C5Me4R)2Ti(CO) (R = SiMe3, SiMe2Ph, CHMe2), have been prepared by mixing the dicarbonyl compounds with the corresponding sandwiches. Both (eta5-C5Me4SiMe2Ph)2Ti(N2) and (eta5-C5Me4SiMe2Ph)2Ti(CO) have been characterized by X-ray diffraction, and mixed N2-CO titanocene complexes have also been observed by in situ IR spectroscopy.     

Anion separation by selective crystallization of metal-organic frameworks

A novel approach for the separation of anions from aqueous mixtures was demonstrated, which involves their selective crystallization with metal-organic frameworks (MOFs) containing urea functional groups. Self-assembly of Zn2+ with the N,N'-bis(m-pyridyl)urea (BPU) linker results in the formation of one-dimensional MOFs including various anions for charge balance, which interact to different extents with the zinc nodes and the urea hydrogen-bonding groups, depending on their coordinating abilities. Thus, Cl-, Br-, I-, and SO4(2-), in the presence of BPU and Zn2+, form MOFs from water, in which the anions coordinate the zinc and are hydrogen-bonded to the urea groups, whereas NO3- and ClO4- anions either do not form MOFs or form water-soluble discrete coordination complexes under the same conditions. X-ray diffraction, FTIR, and elemental analysis of the coordination polymers precipitated from aqueous mixtures containing equivalent amounts of these anions indicated total exclusion of the oxoanions and selective crystallization of the halides in the form of solid solutions with the general composition ZnCl(x)Br(y)I(z).BPU (x + y + z = 2), with an anti-Hofmeister selectivity. The concomitant inclusion of the halides in the same structural frameworks facilitates the rationalization of the observed selectivity on the basis of the diminishing interactions with the zinc and urea acidic centers in the MOFs when going from Cl- to I-, which correlates with decreasing anionic charge density in the same order. The overall crystal packing efficiency of the coordination frameworks, which ultimately determines their solubility, also plays an important role in the anion crystallization selectivity under thermodynamic equilibration.     

Effect of proton donors on the intramolecular coordination C=O→Si–F in (acyloxymethyl)trifluorosilanes. Ab initio,DFT and FTIR study,QTAIM analysis

The intramolecular С=O→Si coordination in H‐complexes of (acetoxymethyl)trifluorosilane and (benzoyloxymethyl)trifluorosilane with proton donors HCl, PhOH, MeOH, and CHCl₃ was investigated by density functional theory and second‐order Møller‐Plesset perturbation theory (MP2) methods. Interrelation and mutual influence of the intramolecular coordination bond С=O→Si and intermolecular hydrogen bonds C=O···H and Si–F···H in H‐complexes was established using the AIM and NBO analyses. The С=O→Si coordination is weakened by the C=O···H hydrogen bonding but enhanced by the Si–F_ax···H hydrogen bonding. The structure of H‐complexes of (acetoxymethyl)trifluorosilane with proton donors in solution was determined by comparing the ν(C=O) and ν(Si–F) frequencies calculated using the conductor‐like polarizable continuum model and their experimental Fourier transform infrared values. Copyright © 2014 John Wiley & Sons, Ltd.     

Metal-metabolomics of microalga Chlorella sorokiniana growing in selenium- and iodine-enriched media

The microalga Chlorella sorokiniana has been used to accumulate selenium and iodine from culture media enriched with these elements as a first stage in the production of supplemented foods. The microalgal colony was grown in a conventional culture medium containing iodine (KI) at concentrations in the range of 150?C4000 ??g mL^?1. Similar experiments were performed with selenium (SeO ₄ ^2? ) at concentrations in the range of 20?C500 ??g mL^?1. The concentration of iodine and selenium in the culture medium was analytically monitored daily and the viability of the colony was checked by biomass concentration measurement and by evaluation of the total content of chlorophyll and carotenoids. In addition, photosynthetic activity and the number of cells were also monitored. Iodine accumulation in the algal biomass increased rapidly with time and reached a steady state after 4 h of exposure. With Se exposure the colony viability decreased, although the culture grew well with concentrations of the element of 50 ??g mL^?1 in the culture medium; this experiment produced Se-enrichment in the alga (3 ??g g^?1) within 100 h. Sequential extraction of an algal pellet was performed in order to separate Se compounds according to their affinity with the following solvents: hot water to recover low molecular mass Se species, enzymatic extraction with driselase for species associated with the cell wall, sodium dodecyl sulphate (SDS) for water insoluble selenoproteins and, finally, enzymolysis with lipase and pronase that release and fragment residual selenoproteinsproducing compounds with low molecular mass. Size-exclusion chromatography (SEC) coupled with an ICP-MS detector showed the preponderance of Se-containing molecules with low molecular mass, possibly seleno-amino acids. Only a peak of low intensity located at 10 min was observed in the SDS extract that could be associated with a protein with molecular mass of 67 kDa. Finally, analysis of the aqueous extract of alga by reverse-phase chromatography with inductively-coupled plasma mass-spectrometry (RPC-ICP-MS) detection revealed the presence of selenocysteine (SeCys₂), selenomethylselenocysteine (SeMetSeCys), selenomethionine (SeMet), and Se(VI), particularly the last two species.     

Urinary calculi — atypical source of information on mercury in human biomonitoring

Chemical analysis of various biological matrices is routinely used for assessment of human exposure to various toxic metals. In this work, 489 samples of urinary calculi originating from almost the whole of The Czech Republic, were collected and subjected to mineralogical and elemental analysis. This study was aimed at mercury, the content of which was determined using thermo-oxidation — cold vapor — atomic absorption spectrometry. The effects of mineralogical composition, sex, age and region were recorded in order to verify the applicability of urinary calculi for biomonitoring. Relationships with other minor and trace elements were also investigated. Association of mercury with whewellite mineral was observed as well as a remarkable relationship with selenium, confirming the role of selenium in mercury excretion. No statistically significant effect was observed on the mercury content in stones with regard to the sex or region. Median values in age groups follow a trend with the maximum median value 0.365 mg kg^?1 in the group of 41–50 year old donors, decreasing to 0.060 mg kg^?1 for the oldest group (81–92 years). Our results confirm that urinary calculi can be helpful in providing complementary information on human exposure to mercury and its excretion.

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