Ultrafast de novo docking combining pharmacophores and combinatorics

We report on a successful de novo design approach which relies on the combination of multi-million compound combinatorial docking under receptor-based pharmacophore constraints. Inspired by a rationale by A.R. Leach et al., we document on the unification of two steps into one for ligand assembly. In the original work, fragments known to bind in protein active sites were connected forming novel ligand compounds by means of generic skeleton linkers and following a combinatorial approach. In our approach, the knowledge of fragments binding to the protein has been expressed in terms of a receptor-based pharmacophore definition. The combinatorial linking step is performed in situ during docking, starting from combinatorial libraries. Three sample scenarios growing in size and complexity (combinatorial libraries of 1 million, 1.3 million, and 22.4 million compounds) have been created to illustrate the method. Docking could be accomplished between minutes and several hours depending on the outset; the results were throughout promising. Technically, a module compatibility between FlexX(C) and FlexX-Pharm has been established. The background is explained, and the crucial points from an information scientist's perspective are highlighted.     

Ethylene oligomerisation and polymerisation with nickel phosphanylenolates bearing electron-withdrawing substituents: Structure-reactivity relationships

Three SHOP-type catalysts, in which the C=C(O) double bond was substituted by electron-withdrawing substituents, [Ni{Ph2PC(R1)=C(R2)O}Ph(PPh3)] (2: R1,R2 = -C(Me)=NN(Ph)-; 3: R1 = CO2Et, R2 = Ph; 4: R1 = CO2Et, R2 = CF3), were assessed as ethylene-oligomerisation and -polymerisation catalysts and compared to Keim's complex, [Ni{Ph2PCH=C(Ph)O}Ph(PPh3)] (1). A rationale for the influence of the double-bond substituents of the P,O-chelate unit on the catalytic properties is proposed, on the basis of X-ray diffraction studies, spectroscopic data and DFT-B3 LYP calculations. Whatever their relative electron-withdrawing strength, the R1 and R2 substituents induce an increase in activity with respect to catalyst 1. For those systems in which the basicity of the oxygen atom is decreased relative to that of the phosphorus atom, the chain-propagation rate increases with respect to that for catalyst 1. Reduction of the basicity of the P relative to that of the O, however, induces higher chain-termination rates.     

Interaction of alpha-synuclein with divalent metal ions reveals key differences: a link between structure, binding specificity and fibrillation enhancement

The aggregation of alpha-synuclein (AS) is characteristic of Parkinson's disease and other neurodegenerative synucleinopathies. Interactions with metal ions affect dramatically the kinetics of fibrillation of AS in vitro and are proposed to play a potential role in vivo. We recently showed that Cu(II) binds at the N-terminus of AS with high affinity (K(d) approximately 0.1 microM) and accelerates its fibrillation. In this work we investigated the binding features of the divalent metal ions Fe(II), Mn(II), Co(II), and Ni(II), and their effects on AS aggregation. By exploiting the different paramagnetic properties of these metal ions, NMR spectroscopy provides detailed information about the protein-metal interactions at the atomic level. The divalent metal ions bind preferentially and with low affinity (millimolar) to the C-terminus of AS, the primary binding site being the (119)DPDNEA(124) motif, in which Asp121 acts as the main anchoring residue. Combined with backbone residual dipolar coupling measurements, these results suggest that metal binding is not driven exclusively by electrostatic interactions but is mostly determined by the residual structure of the C-terminus of AS. A comparative analysis with Cu(II) revealed a hierarchal effect of AS-metal(II) interactions on AS aggregation kinetics, dictated by structural factors corresponding to different protein domains. These findings reveal a strong link between the specificity of AS-metal(II) interactions and the enhancement of aggregation of AS in vitro. The elucidation of the structural basis of AS metal binding specificity is then required to elucidate the mechanism and clarify the role of metal-protein interactions in the etiology of Parkinson's disease.     

Analysis of lanthanide-induced NMR shifts of the Ce@C82 anion

The mapping of bond connectivity in the carbon cage of [Ce@C82]- and full assignment of the NMR lines were successfully achieved by means of 2D INADEQUATE NMR measurement. Paramagnetic NMR analysis shows that the Ce atom in [Ce@C82]- is located at an off-centered position adjacent to a hexagonal ring along the C2 axis of the C2v-C82 cage.     

Calculation of absorption spectra for light-harvesting systems using non-Markovian approaches as well as modified Redfield theory

For an ensemble of B850 rings of the light-harvesting system LH2 of purple bacteria the linear absorption spectrum is calculated. Using different Markovian and non-Markovian, time-dependent and time-independent methods based on second-order perturbation theory in the coupling between the excitonic system and its surrounding environment as well as the modified Redfield theory, the influence of the shape of the spectral density on the linear absorption spectrum is demonstrated for single samples and in the ensemble average. For long bath correlation times non-Markovian effects clearly show up in the static absorption line shapes. Among the different spectral densities studied is one of the purple bacterium Rhodospirillum molischianum obtained by a molecular-dynamics simulation earlier. The effect of static disorder on its line shapes in the ensemble average is analyzed and the results of the present calculations are compared to experimental data.     

Immunoassay as an analytical tool in agricultural biotechnology

Immunoassays for biotechnology engineered proteins are used by AgBiotech companies at numerous points in product development and by feed and food suppliers for compliance and contractual purposes. Although AgBiotech companies use the technology during product development and seed production, other stakeholders from the food and feed supply chains, such as commodity, food, and feed companies, as well as third-party diagnostic testing companies, also rely on immunoassays for a number of purposes. The primary use of immunoassays is to verify the presence or absence of genetically modified (GM) material in a product or to quantify the amount of GM material present in a product. This article describes the fundamental elements of GM analysis using immunoassays and especially its application to the testing of grains. The 2 most commonly used formats are lateral flow devices (LFD) and plate-based enzyme-linked immunosorbent assays (ELISA). The main applications of both formats are discussed in general, and the benefits and drawbacks are discussed in detail. The document highlights the many areas to which attention must be paid in order to produce reliable test results. These include sample preparation, method validation, choice of appropriate reference materials, and biological and instrumental sources of error. The article also discusses issues related to the analysis of different matrixes and the effects they may have on the accuracy of the immunoassays.     

A general strategy for creating "inactive-conformation" abl inhibitors

Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.     

A ferrocenyl-bridged intramolecularly coordinated bis(diorganostannylene): Synthesis, molecular structure and reactivity of [4-t-Bu-2,6-{P(O)(O-i-Pr)2C6H2Sn}C5H4]2Fe

The intramolecularly coordinated heteroleptic stannylene [4-t-Bu-2,6-{P(O)(O-i-Pr)₂}₂C₆H₂]SnCl serves as synthon for the synthesis of the ferrocenyl-bridged bis(diorganostannylene) [4-t-Bu-2,6-{P(O)(O-i-Pr)₂}₂C₆H₂SnC₅H₄]₂Fe (1) which in turn reacts with W(CO)₆ and Cr(CO)₄(C₇H₈) to provide the corresponding transition metal complexes [4-t-Bu-2,6-{P(O)(O-i-Pr)₂}₂C₆H₂Sn{W(CO)₅}C₅H₄]₂Fe (2) and [4-t-Bu-2,6-{P(O)(O-i-Pr)₂}₂C₆H₂SnC₅H₄]₂Fe · Cr(CO)₄ (3), respectively. Reaction of compound 1 with sulphur and atmospheric moisture gave, under partial tin-carbon and oxygen-carbon bond cleavage, a tetranuclear organotin-oxothio cluster 5. All compounds were characterized by ¹H, ¹³C, ³¹P, and ¹¹⁹Sn NMR, and IR spectroscopy, as well as by single-crystal X-ray diffraction analysis. Compounds 1 and 3 were also investigated by Mössbauer spectroscopy. Cyclovoltametric studies reveal the influence of the organostannyl moieties on the redox-behaviour of compounds 1-3 in comparison with unsubstituted ferrocene.     

Electroanalytical applications of boron-doped diamond microelectrode arrays

The electrochemical characteristics of a novel all diamond fabricated boron-doped diamond microelectrode array (BDD-MEA) are critically appraised. The voltammetric response of simple electron transfer processes has been investigated and found to generate sigmoidal voltammetric curves. Furthermore, the device has been utilized for various analytical applications including, the direct detection of 4-nitrophenol over the concentration range 1.8-9.2 μM, manganese over the range 0.1-4.8 μM and the indirect determination of sulfide producing a limit of detection of 23 μM.     

Ruthenium tetraoxide oxidations of alkanes: DFT calculations of barrier heights and kinetic isotope effects

The oxidation of C-H and C-C bonds by metal-oxo compounds is of general interest. We studied the RuO4-mediated catalytic oxidation of several cycloalkanes such as adamantane and cis- and trans-decalin as well as methane. B3LYP/6-31G(d) calculations on the experimentally proposed (3+2) mechanism are in good agreement with known experimental results. Comparison of experimental and theoretical kinetic isotope effects confirms the proposed mechanism. Besides RuO4, we also looked at RuO4(OH)- as a potential active species to account for ruthenium tetraoxide oxidations under strong basic conditions.