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.     

Conversion of rhenium alkylidyne complexes that contain unsupported metal-metal double bonds into relatives that contain μ-alkylidyne ligands

Photolysis of compounds of the type [Re(CCMe₂R)(OR′)₂] (R = Me or Ph; OR′ = O′Bu, OCMe₂(CF₃), or OCMe(CF₃)₂) in benzene with a medium pressure mercury lamp yields compounds of the type [Re(OR′)₂]₂(μ-CCMe₂R)₂ in an intramolecular and irreversible manner. [Re(CCMe₂R)(OR′)₂]₂ and [Re(OR′)₂]₂(μ-CCMe₂R)₂ (OR′ = O′Bu or OCMe₂(CF₃)₂) both react with excess carbon monoxide in several solvents to afford the dimers [Re(OR′)₂(CO)]₂(μ-CCMe₂R)₂ quantitatively. An X-ray study of [Re(O^tBu)₂(CO)]₂ (μ-C^tBu)₂ shows it to consist of two distorted trigonal bipyramids connected by two symmetrically bridging neopentylidyne ligands. The unbridged dimers of general formula [Re(CCMe₂R)(OR′)₂]₂ do not react readily with simple substrates such as phosphines, olefins, or acetylenes, although [Re(CCMe₂R)(O^tBu)₂]₂ can be oxidized by iodine to yield Re(CCMe₂R)(O^tBu)₂I₂ in good yield. In contrast, {Re[OCMe(CF₃)₂]₂}₂(μ-C^tBu)₂ reacts with one equivalent of phenylacetylene to give a species in which one of the two bridging alkylidyne ligands is retained.     

Asymmetric synthesis of functionalized trans-2,6-disubstituted piperidines with N-sulfinyl delta-amino beta-ketoesters. Synthesis of (-)-lasubine I

[reaction: see text] The hydroxy-directed reduction of 1,2-dehydropiperidines with the "ate" complex of DIBAL-H and n-BuLi affords functionalized trans-2,6-disubstituted piperidines. This methodology was employed in the asymmetric synthesis of the quinolizidine alkaloid (-)-lasubine I.     

INVESTIGATION OF THE ATRP OF n-BUTYL METHACRYLATE USING THE Cu（I）／N,N,N＇ N＂ N＂-PENTAMETHYLDIETHYLENETRIAMINE CATALYST SYSTEM

The polymerization of n-butyl methacrylate was investigated using the Atom Transfer Radical Polymerization technique with CuBr and CuCl/N,N,N‘,N“,N“-pentamethyldiethylenetriamine catalytic systems. Various combinations of catalyst systems and initiators were utilized in order to optimize the polymerization conditions and to obtain well-defined polymers (i.e. controlled molecular weights and low polydispersities). It has been found that the optimal initiator for this system is a chlorine-based initiator, when the catalyst used is a Cu(I) salt in conjunction with the N,N,N‘,N“,N“-pentamethyldiethylenetriamine ligand. Bromine-based initiators tend to result in large amounts of initial termination, leading to polymers with less than ideal chain end functionality, even if CuCI is used as the Cu(I) species to invoke the halogen exchange. Additionally, the effects of the polymerization temperature, copper(I) species and the initiator structure were determined.     

Shell-cross-linked vesicles synthesized from block copolymers of Poly(D,L-lactide) and Poly(N-isopropyl acrylamide) as thermoresponsive nanocontainers

A polylactide (D,L-PLA) macroRAFT agent was prepared by utilizing a hydroxyl-functional trithiocarbonate as a coinitiator for the ring-opening polymerization. The length of the resultant polymer was controlled by the concentration of the coinitiator leading to the formation of two PLA polymers with M(n) = 12500 g mol(-)(1) (PDI = 1.46) and M(n) = 20500 g mol(-)(1) (PDI = 1.38) each with omega-trithiocarbonate functionality. Chain extension of PLA via the RAFT (free radical) polymerization of N-isopropyl acrylamide (NIPAAm) resulted in the formation of amphiphilic block copolymers with the PNIPAAm block increasing in size with conversion. TEM measurements of the aggregates obtained by self-organization of the block copolymers in aqueous solutions indicated the formation of vesicles. The sizes of these aggregates were influenced by the ratio of both blocks and the molecular weight of each block. The lower critical solution temperature (LCST) of the block copolymer was largely unaffected by the size of each block. UV turbidity measurements indicated a higher LCST for the block copolymers than for the corresponding PNIPAAm homopolymers. Stabilization of the vesicles was attained by a cross-linking chain extension of the PNIPAAm block using hexamethylene diacrylate. As the trithiocarbonate group was located between the PLA and PNIPAAm blocks, the chain extension resulted in a cross-linked layer between the core and corona of the vesicles.     

Synthesis, fluorescence and photoisomerization studies of azobenzene-functionalized poly(alkyl aryl ether) dendrimers

A series of azobenzene-functionalized poly(alkyl aryl ether) dendrimers have been synthesized and their photochemical and photophysical properties in solution and as thin films have been investigated. Although the photochemical behavior of the azodendrimers in solution indicated that the azobenzene units behave independently, very similar to the constituent monomer azobenzene unit, the properties of thin solid films of the dendrimers were distinctly different. The azodendrimers, AzoG1, AzoG2, and AzoG3 were observed to form stable supercooled glasses, which showed long-wavelength absorption and red emission characteristics of J-aggregates of the azobenzene chromophores. Reversible photoinduced isomerization of the azodendrimers in the glassy state is described.     

A rapid LC-MS-MS method for the determination of nicotine and cotinine in serum and saliva samples from smokers: validation and comparison with a radioimmunoassay method

The development and validation of a rapid liquid chromatography (LC)-tandem mass spectrometry (MS-MS) method for determination of nicotine and cotinine in smokers' serum is described. The method is based on solid-phase extraction in a 96-well plate format and requires only 100 microL of serum. Using normal-phase chromatography, both analytes elute in less than 1 min, which permits high sample throughput applications. The calibrated range is 2-100 ng/mL nicotine and 20-1,000 ng/mL cotinine. For known samples, recovery is 95-116% for nicotine and 93-94% for cotinine. The method is extended to rat serum and human saliva (cotinine only) using partial validation techniques. When compared with an existing radioimmunoassay method in our laboratory, the LC-MS-MS method gives improved accuracy, precision, and sample throughput.     

Capillary-channeled polymer fibers as stationary phases in liquid chromatography separations

A method utilizing capillary-channeled polymer (C-CP) fibers as stationary phases in high-performance liquid chromatographic separations has been investigated. Polymeric fibers of differing backbones (polypropylene and polyester) having nominal diameters of approximately 50 and approximately 35 microm and a channeled structure on their periphery were packed into stainless steel tubing (305 x 4.6 mm I.D.) for use in reversed-phase separations of various mixtures. The fibers have eight channels running continuously along the axis which exhibit very high surface activity. As such, solvent transport is affected through the channels through wicking action. Bundles of 1000-3000 fibers are loaded co-linearly into the tubing, providing flow channels extending the entire length of the columns. As a result, backing pressures are significantly lowered (approximately 50% reduction) in comparison to packed-sphere columns. In addition, the capital costs of the fiber material (< US$0.25 per column) are very attractive. Flow-rates of up to 5 ml/min can be used to achieve near baseline separation of related compounds in reasonable run times, indicating very fast mobile phase mass transfer (C-terms). The polymer stationary phases demonstrate high selectivity for a wide variety of analytes with gradient elution employed successfully in many instances. Specifically, separations of three polyaromatic hydrocarbons (benzo[a]pyrene, chrysene, pyrene), mixtures of both organic and inorganic lead compounds [chlorotriethyllead, chlorotriphenyllead, lead nitrate, lead(II) phthalocyanine], and a lipid standard of triglycerides were accomplished on the polymeric stationary phases. Other species of biological interest, including groups of aliphatic and aromatic amino acids have also been effectively separated. The reversed-phase nature of the fiber surfaces is supported through atomic force microscopy measurements using hydrophilic and hydrophobic functionalized polystyrene beads as the probe tips. Separations of the various analytes demonstrate the feasibility of utilizing C-CP fibers as stationary phases in reversed-phase LC. It is envisioned that columns of this nature would be particularly useful in prep-scale separations as well as for immobilization matrices for organic constituents in aqueous environments.     

Synthesis of the fungal natural product (−)-xylariamide A

The first synthesis of the fungal natural product (−)-xylariamide A 1 is reported. N,O-Bis(trimethylsilyl)acetamide induced coupling of d-tyrosine with (E)-but-2-enedioic acid 2,5-dioxo-pyrrolidin-1-yl ester methyl ester 5 produced the dechloro natural product 6, which was subsequently monochlorinated using oxone and KCl to yield synthetic 1. (−)-Xylariamide A 1, (+)-xylariamide A 2 and (−)-dechloroxylariamide A 6 displayed no cytotoxic or antimicrobial activity.     

Mass spectrometry of transition-metal π-complexes. III—a study of an iron-coordinated tautomer of phenol

A study of the fragmentation of the \documentclass{article}\pagestyle{empty}\begin{document}$ \left[{\left({{\rm C}_{\rm 6} {\rm H}_{\rm 6} {\rm O}} \right){\rm Fe}} \right]_{}^{_.^ + } $\end{document} ion formed from two different precursors suggests that the ions adopt different structures over that part of the energy distribution giving rise to decomposition in the ion source.