OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

Determination of isotopic thorium in biological samples by combined alpha-spectrometry and neutron activation analysis

The determination of isotopic thorium by alpha-spectrometric methods is a routine practice for bioassay and environmental measurement programs. Alpha-spectrometry has excellent detection limits (by mass) for all isotopes of thorium except²³²Th due to its extremely long half-life. This paper reports a pre-concentration neutron activation analysis (PCNAA) method for²³²Th that may be performed following alpha-spectrometry if a suitable source preparation material is utilized. Human tissues and other samples were spiked with²²⁹Th and the thorium was isolated from the sample using ion exchange chromatography. The thorium was then electrodeposited from a sulfate-based medium onto a vanadium planchet, counted by alpha-spectrometry, and then analyzed for²³²Th by neutron activation analysis. The radiochemical yield was determined from the alpha-spectrometric method. Detection limits for²³²Th by this PCNAA method are approximately 50 times lower than achieved by alphaspectrometry.     

A trigonal bipyramidal uranyl amido complex: synthesis and structural characterization of [Na(THF)2][UO2(N(SiMe3)2)3

The synthesis and structural characterization of a rare example of a uranyl complex possessing three equatorial ligands, [M(THF)2][UO2(N(SiMe3)2)3] (3a, M = Na; 3b, M = K), are described. The sodium salt 3a is prepared by protonolysis of [Na(THF)2]2[UO2(N(SiMe3)2)4], whereas the potassium salt 3b is obtained via a metathesis reaction of uranyl chloride UO2Cl2(THF)2 (4) with 3 equiv of K[N(SiMe3)2]. A single-crystal X-ray diffraction study of 3a revealed a trigonal-bipyramidal geometry about uranium, formed by two axial oxo and three equatorial amido ligands, with average U=O and U-N bond distances of 1.796(5) and 2.310(4) A, respectively. One of the oxo ligands is also coordinated to the sodium counterion. 1H NMR spectroscopic studies indicate that THF adds reversibly as a ligand to 3 to expand the trigonal bipyramidal geometry. The degree to which the coordination sphere in 3 is electronically satisfied with only three amido donors is suggested by (1) the reversible THF coordination, (2) a modest elongation in the bond distances for a five-coordinate U(VI) complex, and (3) the basicity of the oxo ligands as evidenced in the contact to Na. The vibrational spectra of the series of uranyl amido complexes [UO2(N(SiMe3)2)n]2-n (n = 2-4) are compared, to evaluate the effects on the axial U=O bonding as a function of increased electron density donated from the equatorial region. Raman spectroscopic measurements of the nu 1 symmetric O=U=O stretch show progressive axial bond weakening as the number of amido donors is increased. Crystal data for [Na(THF)2][UO2(N(SiMe3)2)3]: orthorhombic space group Pna2(1), a = 22.945(1) A, b = 15.2830(7) A, c = 12.6787(6) A, z = 4, R1 = 0.0309, wR2 = 0.0524.     

Identification of phage antibodies toward the Werner protein by selection on Western blots

A procedure was established for selecting phage antibodies (phage-abs) from phage-displayed antibody repertoires by panning against proteins, separated by sodium dodecyl phosphate-polyacrylamide gel electrophoresis (SDS-PAGE) and electroblotted onto nitrocellulose membranes (Western blots). This immobilization strategy is applicable for secondary rounds of panning in selections against semipurified proteins, and directs the selection toward antibodies suitable as immunochemical reagents in Western blots. In model experiments, enrichment factors as high as 1.9x10(5) were obtained in a single round of panning. Furthermore, we demonstrate the application of this approach by selection of phage-abs recognizing the human Werner protein, which is defective in a premature aging syndrome.     

Models to predict solubility in ternary solvents based on sub-binary experimental data

The capability of the extended forms, of two well established cosolvency models, i.e. the combined nearly ideal binary solvent/Redlich-Kister equation and the modified Wilson model, used to predict the solute solubility in non-aqueous ternary solvent mixtures is presented. These predictions are based on the measured solubilities of anthracene in binary solvent mixtures. As a result the values of average percent deviations were less than 2% for the anthracene solubility in ternary mixtures. This work was also extended to other cosolvency models, ie. the extended Hildebrand solubility approach and the mixture response surface method, which are also commonly used for correlating solubility data in ternary solvents. The accuracy of the models is compared with each other and also with a published solubility model for ternary mixtures. The results illustrate that all models produced comparable accuracy.     

Liquid chromatographic determination of sulindac and metabolites in serum

An improved liquid chromatographic procedure is described for the quantitative determination of sulindac, sulindac sulfone, and sulindac sulfide from serum. The procedure makes use of acetonitrile extraction of the compounds of interest from acidified serum samples. Under these conditions extraction efficiencies in the 85 percent range are obtained for each of the compounds. The liquid chromatographic separation of the compounds of interest and the internal standard (indomethacin) is accomplished in an isocratic elution procedure using a nitrile (CN) stationary phase. The HPLC separation procedure is completed in less than 10 minutes, giving excellent resolution and peak shape.     

Electronic structures of some olefins and their radical cations

CNDO/2 calculations of the electronic properties of the series of isomeric butenes and pentenes yield ionization potentials which reproduce the observed trends. These are interpreted in terms of the charge distribution effects of the alkyl groups.

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Zusammenfassung CNDO/2 Rechnungen für die Butan- und Penten-Isomeren ergeben die richtigen Trends für die Ionisierungspotentiale. Sie werden im Zusammenhang mit der Änderung der Ladungsverteilung infolge Methylsubstitution diskutiert.

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Résumé Des calculs CNDO/2 des propriétés électroniques des séries d'isomères du butène et du pentène fournissent des potentiels d'ionisation qui reproduisent les tendances observées. Les distributions de charge calculées pour les molécules sont utilisées pour interpréter les propriétés observées en termes d'effet du substituant alkyle.

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Presented in part at the Eighth Theoretical Chemistry Symposium held at the Batelle Institute, Geneva, Switzerland; March 26–30, 1972.     

The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials

The natural atomic orbital/point (NAO-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.     

Neutron captue prompt gamma-ray activation analysis at the NIST Cold Neutron Research Facility

An instrument for neutron capture prompt gamma-ray activation analysis (PGAA) has been constructed as part of the Cold Neutron Research Facility at the 20 MW National Institute of Standards and Technology Research Reactor. The neutron fluence rate (thermal equivalent) is 1.5·10⁸ n ·cm^–2·s^–1, with negligible fast neutrons and gamma-rays. With compact geometry and hydrogen-free construction, the sensitivity is sevenfold better than an existing thermal instrument. Hydrogen background is thirtyfold lower.     

Template-directed self-assembly of 10-microm-sized hexagonal plates

This article presents a strategy for the fabrication of ordered microstructures using concepts of design inspired by molecular self-assembly and template-directed synthesis. The self-assembling components are 4-microm-thick hexagonal metal plates having sides 10 microm in length ("hexagons"), and each template consists of a 4-microm-thick circular metal plate surrounding a central cavity, the perimeter of which is complementary in shape to the external edges of a two-dimensional, close-packed array of hexagons. The hexagons and templates (collectively, "pieces") were fabricated via standard procedures and patterned into hydrophobic and hydrophilic regions using self-assembled monolayers (SAMs). Templated self-assembly occurs in water through capillary interactions between thin films of a nonpolar liquid adhesive coating the hydrophobic faces of the pieces. The hexagons tile the cavities enclosed by the templates, and the boundaries of the cavities determine the sizes and shapes of the assemblies. Curing the adhesive with ultraviolet light furnishes mechanically stable arrays having well-defined morphologies. By allowing control over the structures of the resulting aggregates, this work represents a step toward the development of practical methods for microfabrication based on self-assembly.