Structure and catalytic activity of some soluble polyethylene glycol-peptide conjugates

Soluble catalysts for the Juliá-Colonna asymmetric epoxidation reaction have been constructed in three different ways, using NH₂-PEG-OMe as the support system: suitable solvents have been identified and it is shown that the degree of helicity of the conjugates correlates with the extent of conversion and (to a lesser extent) the enantioselectivity of epoxidation.     

QSAR modeling of in vitro inhibition of cytochrome P450 3A4

We report the QSAR modeling of cytochrome P450 3A4 (CYP3A4) enzyme inhibition using four large data sets of in vitro data. These data sets consist of marketed drugs and drug-like compounds all tested in four assays measuring the inhibition of the metabolism of four different substrates by the CYP3A4 enzyme. The four probe substrates are benzyloxycoumarin, testosterone, benzyloxyresorufin, and midazolam. We first show that using state-of-the-art QSAR modeling approaches applied to only one of these four data sets does not lead to predictive models that would be useful for in silico filtering of chemical libraries. We then present the development and the testing of a multiple pharmacophore hypothesis (MPH) that is formulated as a conceptual extension of the traditional QSAR approach to modeling the promiscuous binding of a large variety of drugs to CYP3A4. In the simplest form, the MPH approach takes advantage of the multiple substrate data sets and identifies the binding of test compounds as either proximal or distal relative to that of a given substrate. Application of the approach to the in silico filtering of test compounds for potential inhibitors of CYP3A4 is also presented. In addition to an improvement in the QSAR modeling for the inhibition of CYP3A4, the results from this modeling approach provide structural insights into the drug-enzyme interactions. The existence of multiple inhibition data sets in the BioPrint database motivates the original development of the concept of a multiple pharmacophore hypothesis and provides a unique opportunity for formulating alternative strategies of QSAR modeling of the inhibition of the in vitro metabolism of CYP3A4.     

Solid-phase synthesis of phenols and pyridinones via arylboronation/oxidation protocol using aryl bromides

A sequence of two known reactions, palladium catalyzed arylboronation of arybromide and subsequent oxidation of arylboronate with oxone, has been carried out to prepare functionalized phenols and pyridin-2(1H)-one which were later loaded on to resin for solid-phase synthesis. Using these resin-bound templates, a number of solid-phase methods were developed to generate libraries of substituted phenols and pyridin-2(1H)-one.     

Coordination "oligomers" in self-assembly reactions of some "tritopic" picolinic dihydrazone ligands-mononuclear, dinuclear, hexanuclear, heptanuclear, and nonanuclear examples

"Tritopic" picolinic dihydrazone ligands with tridentate coordination pockets are designed to produce homoleptic [3 x 3] nonanuclear square grid complexes on reaction with transition-metal salts, and many structurally documented examples have been obtained with Mn(II), Cu(II), and Zn(II) ions. However, other oligomeric complexes with smaller nuclearities have also been discovered and identified structurally in some reactions involving Fe(II), Co(II), Ni(II), and Cu(II), with certain tritopic ligands. This illustrates the dynamic nature of the metal-ligand interaction and the conformationally flexible nature of the ligands and points to the possible involvement of some of these species as intermediates in the [3 x 3] grid formation process. Examples of mononuclear, dinuclear, hexanuclear, heptanuclear, and nonanuclear species involving Fe(II), Co(II), Ni(II), and Cu(II) salts with a series of potentially heptadentate picolinic dihydrazone ligands with pyrazine, pyrimidine, and pyridine end groups are described in the present study. Iron and cobalt complexation reactions are complicated by redox processes, which lead to mixed-oxidation-state Co(II)/Co(III) systems when starting with Co(II) salts, and reduction of Fe(III) to Fe(II) when starting with Fe(III). Magnetic exchange within the polynuclear structural frameworks is discussed and related to the structural features.     

Quantitative determination of fucoidan using polyion-sensitive membrane electrodes

The use of polyanion and polycation-sensitive membrane electrodes to detect five different preparations of fucoidan is described. Unlike linear polyanionic molecules previously measured with polymer membrane-based electrochemical sensors, fucoidans from marine brown algae are all highly branched, sulfated polysaccharides with varying charge densities and structures, depending on the species of seaweed, method of extraction used and extent of purification. When tridodecylmethylammonium (TDMA) was used as the ion-exchanger, a large, non-equilibrium EMF response was observed over a concentration range of 0.5–50 μg mL⁻¹ fucoidan. Fucoidan was also measured by titration with polycationic protamine, using a dinonylnaphthalene sulfonate (DNNS)-doped membrane electrode as the potentiometric endpoint detector. Potentiometric titration was used to determine the binding ratio between protamine and fucoidan at the neutralization endpoint for each fucoidan preparation. This binding ratio was then used to successfully determine the fucoidan content of commercially available nutritional supplements. Fucoidan was also measured in undiluted blood serum, demonstrating that this method may be applicable for measuring fucoidan for clinical applications.     

Nanostructure of silver metal produced photocatalytically in TiO2 films and the mechanism of the resulting photochromic behavior

The optical activity of composite films created by the photocatalytic reduction of silver or gold ions in TiO(2) upon irradiation by UV light has up to now been discussed in terms of the formation and light-induced destruction of distinct nanoparticles molded inside the porous nanocrystalline film. We present results from classical light scattering calculations and a logical analysis of experimental observations to add detail to the mechanism. As opposed to large, solid metal nanoparticles, coatings and small particles in heterogeneous external dielectric environments account for observations such as the broad optical spectrum and multiwavelength photochromic responses. For some steps of the photochromic process, we propose that visible light permits an equilibrium promoting the growth of small metal features or suspended particles. We use a new expression for the restricted path length in our size-dependent broadening corrections of metal shells and discuss this briefly. We conclude by discussing the consequence of plasmon absorption in the proximity of the electronically active TiO(2) surrounding matrix, leading to mass transfer and shape change of the metal and photochromic properties of the film.     

UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation

A new approach to obtain fragmentation information in liquid chromatography/mass spectrometry (LC/MS) studies of small molecules in complex mixtures is presented using simultaneous acquisition of exact mass at high and low collision energy, MS(E). LC/MS-TOF and LC/MS/MS-TOF are powerful tools for the analysis of complex mixtures, especially those for biological fluids allowing the elucidation of elemental composition and fragmentation information. In this example the composition of rat urine was studied using this new approach, allowing the structures of several endogenous components to be confirmed in one analytical run by the simultaneous acquisition of exact mass precursor and fragment ion data. The spectral data obtained using this new approach are comparable to those obtained by conventional LC/MS/MS as exemplified by the identification of endogenous metabolites present in rat urine.     

A convenient preparation of heteroaryl sulfonamides and sulfonyl fluorides from heteroaryl thiols

Heteroaromatic thiols may be oxidized to the sulfonyl chloride at low temperature (-25 degrees C) by using 3.3 equiv of aqueous sodium hypochlorite. The reaction is rapid, avoids the use of chlorine gas, and succeeds with substrates that have previously been found to afford little or none of the sulfonamide product with other procedures. The method allows the preparation of the sulfonyl fluorides, which are stable enough to be purified and stored, making them potentially useful monomers in parallel chemistry efforts.     

Carbon Dots (C‐dots) from Cow Manure with Impressive Subcellular Selectivity Tuned by Simple Chemical Modification

Improved cellular selectivity for nucleoli staining was achieved by simple chemical modification of carbon dots (C‐dots) synthesized from waste carbon sources such as cow manure (or from glucose). The C‐dots were characterized and functionalized (amine‐passivated) with ethylenediamine, affording amide bonds that resulted in bright green fluorescence. The new modified C‐dots were successfully applied as selective live‐cell fluorescence imaging probes with impressive subcellular selectivity and the ability to selectively stain nucleoli in breast cancer cell lineages (MCF‐7). The C‐dots were also tested in four other cellular models and showed the same cellular selection in live‐cell imaging experiments.     

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.