Application and utilization of chemoinformatics tools in lead generation and optimization

The process of Drug Discovery is a complex and high risk endeavor that requires focused attention on experimental hypotheses, the application of diverse sets of technologies and data to facilitate high quality decision-making. All is aimed at enhancing the quality of the chemical development candidate(s) through clinical evaluation and into the market. In support of the lead generation and optimization phases of this endeavor, high throughput technologies such as combinatorial/high throughput synthesis and high throughput and ultra-high throughput screening, have allowed the rapid analysis and generation of large number of compounds and data. Today, for every analog synthesized 100 or more data points can be collected and captured in various centralized databases. The analysis of thousands of compounds can very quickly become a daunting task. In this article we present the process we have developed for both analyzing and prioritizing large sets of data starting from diversity and focused uHTS in support of lead generation and secondary screens supporting lead optimization. We will describe how we use informatics and computational chemistry to focus our efforts on asking relevant questions about the desired attributes of a specific library, and subsequently in guiding the generation of more information-rich sets of analogs in support of both processes.     

Development of the Pictet-Spengler reaction catalyzed by AuCl3/AgOTf

Mild and efficient AuCl3/AgOTf-catalyzed Pictet-Spengler reactions were developed to afford in good yields a variety of tetrahydroisoquinoline and tetrahydro-beta-carboline ring systems, which constitute important motifs in biologically active natural and synthetic organic compounds.     

Gold electroless deposition into poly-3,4-ethylenedioxythiophene films

By electroless deposition of gold into poly-3,4-ethylenedioxythiophene (PEDOT) films, the composite films (PEDOT-Au) are synthesized. Their electrochemical properties are studied by cyclic voltammetric (CVA) method. It is shown that in contrast to the original PEDOT film, the CVA curves of composite PEDOT-Au films measured in the presence of chloride ions reveal additional redox peaks associated with the presence of gold particles. The loading of metal gold particles by its chemical deposition into the polymer film is quantitatively assessed using quartz crystal microbalance method. The film mass is shown to depend on the time of gold loading and its original concentration in solution. The gold particles are shown to be oxidized by a reaction of the first order with respect to chloride ions. Based on the results of voltammetric and microbalance methods, the formation of a poorly soluble gold oxidation product Au(I)Cl in chloride-containing solutions was inferred.     

Determination of chromium(VI) in the soil organic fraction

A procedure was developed for determining chromium(VI) in the soil organic fraction; it consisted of three steps: the preparation of a soil solution; the isolation and separation of chromium(VI) and chromium(III); and the determination of chromium(VI). Soil solutions were prepared by leaching soil samples with a Na₄P₂O₇ solution (the Rudd method). Chromium(VI) was extracted from the soil solution with a solution of sodium diethyldithiocarbamate in n-amyl alcohol; the conditions of the extraction and separation of chromium(VI) and chromium(III) were optimized. Chromium(VI) in solutions was determined after back extraction by spectrophotometry with diphenylcarbazide or by flame atomic absorption spectrometry. The procedure was validated using a reference soil sample, and the material balance of chromium in the systems under study was calculated.     

Potential applications of fluorhydroxyapatite as biomaterials in medicine

The present work was undertaken to investigate the bioactivity and cytotoxicity of fluorhydroxyapatite ceramics. The bioactivity was evaluated by in vitro testing in simulated body fluid (SBF), in which ion concentrations are almost identical with inorganic ion concentrations of human blood plasma. Pellets of FA, HA and FHA were immersed in SBF for 48 hours, 1 week and 4 weeks at 36.5°C. Changes of the surface microstructure of the samples were observed by scanning electron microscopy (SEM). 48 hours and one week immersion in SBF did not result in any substantial progress in bioactivity. After 4 weeks in SBF a new biologically active layer was created on the surface of the biomaterials. In addition, the embryonal mouse fibroblast cell line NIH-3T3 was used for a comparative study of basal cytotoxicity of FHA, HA and FA discs. The sensitivity of these cells for tested biomaterials was evaluated on the basis of two cytotoxic end points: cell proliferation and cell morphology. The basal cytotoxicity of FHA, FA and HA discs was measured by a direct contact method. After 24, 48 and 72 hours, the cell growth was evaluated by direct counting of non-affected cells and cells treated by biomaterials. After 72 hours of biomaterials treatment, about 25% inhibition of cell number and unchanged morphology was found.      

Optimal pension fund management under multi-period risk minimization

In this paper, a multi-period stochastic optimization model for solving a problem of optimal selection of a pension fund by a pension plan member is presented. In our model, members of the pension plan are given a possibility to switch periodically between J types of funds with different risk profiles and so actively manage their risk exposure and expected return. Minimization of a multi-period average value-at-risk deviation measure under expected return constraint leads to a large-scale linear program. A theoretical framework and a solution for the case of the pension system of Slovak Republic are presented.     

Antihydrogen formation by autoresonant excitation of antiproton plasmas

In efforts to trap antihydrogen, a key problem is the vast disparity between the neutral trap energy scale ( $\sim\!50\,\upmu\mathrm{eV}$ ), and the energy scales associated with plasma confinement and space charge (~1 eV). In order to merge charged particle species for direct recombination, the larger energy scale must be overcome in a manner that minimizes the initial antihydrogen kinetic energy. This issue motivated the development of a novel injection technique utilizing the inherent nonlinear nature of particle oscillations in our traps. We demonstrated controllable excitation of the center-of-mass longitudinal motion of a thermal antiproton plasma using a swept-frequency autoresonant drive. When the plasma is cold, dense and highly collective in nature, we observe that the entire system behaves as a single-particle nonlinear oscillator, as predicted by a recent theory. In contrast, only a fraction of the antiprotons in a warm or tenuous plasma can be similarly excited. Antihydrogen was produced and trapped by using this technique to drive antiprotons into a positron plasma, thereby initiating atomic recombination. The nature of this injection overcomes some of the difficulties associated with matching the energies of the charged species used to produce antihydrogen.     

Size-extensive vibrational self-consistent field method

The vibrational self-consistent field (VSCF) method is a mean-field approach to solve the vibrational Schro?dinger equation and serves as a basis of vibrational perturbation and coupled-cluster methods. Together they account for anharmonic effects on vibrational transition frequencies and vibrationally averaged properties. This article reports the definition, programmable equations, and corresponding initial implementation of a diagrammatically size-extensive modification of VSCF, from which numerous terms with nonphysical size dependence in the original VSCF equations have been eliminated. When combined with a quartic force field (QFF), this compact and strictly size-extensive VSCF (XVSCF) method requires only quartic force constants of the ?(4)V/?Q(i)(2)?Q(j)(2) type, where V is the electronic energy and Q(i) is the ith normal coordinate. Consequently, the cost of a XVSCF calculation with a QFF increases only quadratically with the number of modes, while that of a VSCF calculation grows quartically. The effective (mean-field) potential of XVSCF felt by each mode is shown to be harmonic, making the XVSCF equations subject to a self-consistent analytical solution without matrix diagonalization or a basis-set expansion, which are necessary in VSCF. Even when the same set of force constants is used, XVSCF is nearly three orders of magnitude faster than VSCF implemented similarly. Yet, the results of XVSCF and VSCF are shown to approach each other as the molecular size is increased, implicating the inclusion of unnecessary, nonphysical terms in VSCF. The diagrams of the XVSCF energy expression and their evaluation rules are also proposed, underscoring their connected structures.     

Two-dimensionally extended porphyrin tapes: synthesis and shape-dependent two-photon absorption properties

We report the synthesis and characterization of L- and T-shaped porphyrin tapes as extensible structural motifs of two-dimensionally extended porphyrin tapes. The two-photon absorption (TPA) cross-section values (sigma((2))) for L- and T-shaped porphyrin tapes as well as those for linear trimeric and tetrameric porphyrin tapes were measured by an open-aperture Z-scan method at 2300 nm, a wavelength at which the one-photon absorption contribution is either zero or almost negligible. Under these conditions, the sigma((2)) values for the linear porphyrin tape trimer and tetramer were determined to be 18 500 and 41 200 GM, respectively. The sigma((2)) value for the L-shaped trimer was determined to be 8700 GM, which is only half that of the linear trimer, whereas the sigma((2)) value for the T-shaped tetramer was measured to be 35 700 GM. These results clearly indicate the dependence of the TPA cross-section on the molecular shape, which underscores the importance of directionality in the pi-conjugation pathway for the enhancement of TPA cross- section.