Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Synthesis and characterization of Mo(6) chalcobromides and cyano-substituted compounds built from a novel [(Mo(6)Br(i)(6)Y(i)(2))L(a)(6)](n)()(-) discrete cluster unit (Y(i) = S or Se and L(a) = Br or CN)

The syntheses, crystal structures determined by single-crystal X-ray diffraction, and characterizations of new Mo(6) cluster chalcobromides and cyano-substituted compounds with 24 valence electrons per Mo(6) cluster (VEC = 24), are presented in this work. The structures of Cs(4)Mo(6)Br(12)S(2) and Cs(4)Mo(6)Br(12)Se(2) prepared by solid state routes are based on the novel [(Mo(6)Br(i)(6)Y(i)(2))Br(a)(6)](4)(-) (Y = S, Se) discrete units in which two chalcogen and six bromine ligands randomly occupy the inner positions, while the six apical ones are fully occupied by bromine atoms. The interaction of these two compounds with aqueous KCN solution results in apical ligand exchange giving the two first Mo(6) cyano-chalcohalides: Cs(0.4)K(0.6)(Et(4)N)(11)[(Mo(6)Br(6)S(2))(CN)(6)](3).16H(2)O and Cs(0.4)K(0.6)(Et(4)N)(11)[(Mo(6)Br(6)Se(2))(CN)(6)](3).16H(2)O. Their crystal structures, built from the original [(Mo(6)Br(i)(6)Y(i)(2))(CN)(a)(6)](4)(-) discrete units, will be compared to those of the two solid state precursors and other previously reported Mo(6) cluster compounds. Their redox properties and (77)Se NMR characterizations will be presented. Crystal data: Cs(4)Mo(6)Br(12)S(2), orthorhombic, Pbca (No. 61), a = 11.511(5) A, b = 18.772(5) A, c = 28.381 A (5), Z = 8; Cs(4)Mo(6)Br(12)Se(2), Pbca (No. 61), a = 11.6237(1) A, b = 18.9447(1) A, c = 28.4874(1) A, Z = 8; Cs(0.4)K(0.6)(Et(4)N)(11)[(Mo(6)Br(6)S(2))(CN)(6)](3).16H(2)O, Pm-3m (No. 221), a = 17.1969(4) A, Z = 1; Cs(0.4)K(0.6)(Et(4)N)(11)[(Mo(6)Br(6)Se(2))(CN)(6)](3).16H(2)O, Pm-3m (No. 221), a = 17.235(5) A, Z = 1.     

A Density Functional Theory Study on Electronic Structure and Second—order Nonlinear Optical Properties of Some Push—Pull Molecules

Time-dependent density-functional theory(TDDFT)has been applied to calculate the electronic structure and second-order nonlinear optical(NLO) properties of some organic molecules.The two-dimensional(2-D)charge transfer charateristics of calculated molecules were studied and compared with corresponding experimental results.All the theoretical results agree well with the measurement.For 2-D molecule with two-fold symmetry,the dominant charge transfer is off-diagonal,while for three-fold symmetry 2-D molecule,the dominant charge transfer is not only between branches and central group but also among branches.     

New benzyne approach to the synthesis of dehydroaporphines, 4,5-dioxoaporphines and aristolactams

A new strategy for the synthesis of some aporphinoid alkaloids is described. It is based on the intermolecular Diels-Alder cyclization between benzyne and an appropriate methylene isoquinoline derivative.     

Triplex and quadruplex DNA structures studied by electrospray mass spectrometry

DNA triplex and quadruplex structures have been successfully detected by electrospray ionization mass spectrometry (ESI-MS). Circular dichroism and UV-melting experiments show that these structures are stable in 150 mM ammonium acetate at pH 7 for the quadruplexes and pH 5.5 for the triplexes. The studied quadruplexes were the tetramer [d(TGGGGT)](4), the dimer [d(GGGGTTTTGGGG)](2), and the intramolecular folded strand dGGG(TTAGGG)(3), which is an analog of the human telomeric sequence. The absence of sodium contamination allowed demonstration of the specific inclusion of n - 1 ammonium cations in the quadruplex structures, where n is the number of consecutive G-tetrads. We also detected the complexes between the quadruplexes and the quadruplex-specific drug mesoporphyrin IX. MS/MS spectra of [d(TGGGGT)](4) and the complex with the drug are also reported. As the drug does not displace the ammonium cations, one can conclude that the drug binds at the exterior of the tetrads, and not between them. For the triplex structure the ESI-MS spectra show the detection of the specific triplex, at m/z values typically higher than those typically observed for duplex species. Upon MS/MS the antigene strand, which is bound into the major groove of the duplex, separates from the triplex. This is the same dissociation pathway as in solution. To our knowledge this is the first report of a triplex DNA structure by electrospray mass spectrometry.     

Synthesis, crystal structure, magnetic properties, and electronic structure of the new ternary vanadate CuMnVO4

A new magnetic oxide, CuMnVO4, was prepared, and its crystal structure was determined by single-crystal X-ray diffraction. The magnetic properties of CuMnVO4 were characterized by magnetic susceptibility and specific heat measurements, and the spin exchange interactions of CuMnVO4 were analyzed on the basis of spin-polarized electronic band structure calculations. CuMnVO4 contains MnO4 chains made up of edge-sharing MnO6 octahedra containing high-spin Mn2+ cations. Our work shows that CuMnVO4 undergoes a three-dimensional antiferromagnetic transition at approximately 20 K. Both the intrachain and interchain spin exchanges are antiferromagnetic, and the interchain spin exchange is not negligible compared to the intrachain spin exchange.     

Isotropic hard core dumbell fluid: Equation of state

A monte-Carlo calculation has been made for 108 hard core dumbbells of the compressibility factor in the isotropic density range. These compressibility factors are compared to several approximate theories, and comments are made on the utility of these approximate theories.     

EPR evidence for 17O− on molybdenum oxide supported by silica-gel

The EPR spectrum of ¹⁷O^? on partially reduced molybdenum oxide supported on silica-gel has been observed following adsorption of N₂O at room temperature. The spectrum is chracterized by g_⊥=2.019 and g_|=2.002 with a_|¹⁷O^?=96±1 G and a_|⁹⁵MO,⁹⁷MO=7.5±0.5 G. The O ^?ion appears to undergo exchange with oxide ions at the surface.     

Studies on structure characterization of tryptophan melanin: Comparison between filament and curie-point pyrolysis gas chromatography/mass spectrometry

Structural studies of a synthetic melanin, obtained by means of performic acid oxidation of tryptophan, were carried out by pyrolysis gas chromatography/mass Spectrometry (Py-GC/MS). To identify the best pyrolysis conditions, both Curie-point pyrolysis and filament pyrolysis were employed and the effects of pyrolysis temperatures and times were studied. Using the first approach, various compounds were identified: toluene, ethylbenzene, styrene, indole, methylindole, ethylindole, phenol, cresol and ethylphenol. Using filament pyrolysis some interesting differences could be observed. Whereas toluene, ethylbenzene, phenol, cresol and methylindole were found, neither indole nor ethylindole was detected. Instead, new pyrolysis products were evident, such as methylpyrrole and indolin-2-one. Hence filament pyrolysis seems to activate different thermal decomposition pathways of the melanin under study. It is suggested that tryptophan melanin is a polymer containing indole and hydroxyindole derivatives as subunits.     

Characteristics of immunosorbents used as a new approach to selective solid-phase extraction in environmental analysis

Summary The trace-level determination of organic pollutants in complex matrices is difficult and often not reliable because theccurrent extraction procedures are non-selective. New extraction sorbents involving antigen-antibody interactions, called immunosorbents (ISs), have been synthesised in order to trap a group of structurally related pollutants. The IS capacity is always high for the analyte-antigen used to make the antibodies, but can be low for some related compounds. In this work, we show the relationship that exists between capacity, break-through volume and recovery of analytes because of the competition between the structurally related compounds for antibody sites. Breakthrough due to the overloading of the column should be avoided because calibration curves are no longer linear. The capacity of two ISs, one made for trapping the triazine pesticide group and the second for the phenylurea, group, have been optimised by selecting silica with 50 nm pore size. Calibration curves are linear for all the compounds in a mixture of ten phenylureas up to a concentration of 5 to 10 μg L⁻¹ for each compound when handling 50 mL water samples through a precolumn packed with 0.22 g of IS. Under these conditions, reliable quantitative results are obtained because calibration curves are similar when compounds are alone or in a mixture. Application to the clean-up of soil extracts illustrates the high selectivity and the high potential of these new sorbents in environmental analysis. Presented at the 21^st ISC held in Stuttgart, Germany, 15^th–20^th September, 1996