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.     

Radical Rearrangement Chemistry in Ultraviolet Photodissociation of Iodotyrosine Systems: Insights from Metastable Dissociation,Infrared Ion Spectroscopy,and Reaction Pathway Calculations

We report on the ultraviolet photodissociation (UVPD) chemistry of protonated tyrosine, iodotyrosine, and diiodotyrosine. Distonic loss of the iodine creates a high-energy radical at the aromatic ring that engages in hydrogen/proton rearrangement chemistry. Based on UVPD kinetics measurements, the appearance of this radical is coincident with the UV irradiation pulse (8 ns). Conversely, sequential UVPD product ions exhibit metastable decay on ca. 100 ns timescales. Infrared ion spectroscopy is capable of confirming putative structures of the rearrangement products as proton transfers from the imine and β-carbon hydrogens. Potential energy surfaces for the various reaction pathways indicate that the rearrangement chemistry is highly complex, compatible with a cascade of rearrangements, and that there is no preferred rearrangement pathway even in small molecular systems like these.

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Hydridosilazanes hydrolysis-condensation reactions studied by <Superscript>1</Superscript>H and <Superscript>29</Superscript>Si liquid NMR spectroscopy

Hydridosilazane compounds containing Si–N and Si–H bonds can be used as precursors of SiO_x materials. The hydrolysis-condensation reactions of tetramethyldisilazane, as a polyhydridosilazane model compound, were investigated by ¹H and ²⁹Si liquid NMR spectroscopy. These reactions were carried out at room temperature for up to 120 min in presence of water. The identified products are short linear siloxane species (hydride terminated polydimethylsiloxanes M^HD_xM^H) and cyclosiloxanes. Silicon hydride persistence in the reactional mixture suggested that silazane group is more sensitive to hydrolysis reaction than silicon hydride group. Moreover, additional experiments evidenced that the low steric hindrance of the silicon hydride influences the silazane hydrolysis kinetic. Hence the presence of ammonia released during silazane hydrolysis reaction was demonstrated to be a catalyst of the silicon hydride hydrolysis reaction.     

Sustainable Heck-Matsuda reaction with catalytic amounts of diazonium salts: an experimental and theoretical study

The palladium-catalyzed Heck-Matsuda reaction with a catalytic amount of an in-situ-generated diazonium salt proceeded under mild and sustainable conditions. The reaction proceeded at room temperature, under base-free conditions, and only generated tBuOH, H(2)O, and N(2) as by-products. Ortho-substituted diazonium salts were more-efficiently coupled to methyl acrylate than their corresponding para isomers, which required the addition of anisole as an additive. In support of these experimental data, we carried out theoretical studies to gain a deeper understanding of these reaction outcomes.     

Structural role of counterions adsorbed on self-assembled peptide nanotubes

Among noncovalent forces, electrostatic ones are the strongest and possess a rather long-range action. For these reasons, charges and counterions play a prominent role in self-assembly processes in water and therefore in many biological systems. However, the complexity of the biological media often hinders a detailed understanding of all the electrostatic-related events. In this context, we have studied the role of charges and counterions in the self-assembly of lanreotide, a cationic octapeptide. This peptide spontaneously forms monodisperse nanotubes (NTs) above a critical concentration when solubilized in pure water. Free from any screening buffer, we assessed the interactions between the different peptide oligomers and counterions in solutions, above and below the critical assembly concentration. Our results provide explanations for the selection of a dimeric building block instead of a monomeric one. Indeed, the apparent charge of the dimers is lower than that of the monomers because of strong chemisorption. This phenomenon has two consequences: (i) the dimer-dimer interaction is less repulsive than the monomer-monomer one and (ii) the lowered charge of the dimeric building block weakens the electrostatic repulsion from the positively charged NT walls. Moreover, additional counterion condensation (physisorption) occurs on the NT wall. We furthermore show that the counterions interacting with the NTs play a structural role as they tune the NTs diameter. We demonstrate by a simple model that counterions adsorption sites located on the inner face of the NT walls are responsible for this size control.     

Stöber silica particles as basis for redox modifications: particle shape, size, polydispersity, and porosity

The synthesis of Stöber silica particles as basis for redox modifications is optimized for desired properties, in particular diameter in a wide sub-micrometer range, spherical shape, monodispersity, the absence of porosity, and aggregation free isolability for characterization and later covalent modification. The materials are characterized by SEM, DLS, nitrogen sorption isotherms, helium as well as Gay-Lussac (water) pycnometry, and DRIFT spectroscopy. Particles with diameters between approximately 50 and 800 nm are obtained by varying the concentrations of the reagents and reactants, the type of solvent as well as the temperature. The use of high water concentrations and post-synthetic calcination at 600 °C results in silica particles that can be considered as nonporous with respect to the size of the active molecules to be immobilized. The effect of reaction temperature on size distribution is identified. Low polydispersity is achieved by performing the reaction in a temperature range in which a change in temperature has only a weak or no effect on the final particle diameter. Upon optimization of the sol–gel process, the shape of the particles is still spherical. The agreement between experimental and geometric data is within the expected precision of the characterization techniques.     

Redox grafting of diazotated anthraquinone as a means of forming thick conducting organic films

Thick conductive layers containing anthraquinone moieties are covalently immobilized on gold using redox grafting of the diazonium salt of anthraquinone (i.e., 9,10-dioxo-9,10-dihydroanthracene-1-diazonium tetrafluoroborate). This grafting procedure is based on using consecutive voltammetric sweeping and through this exploiting fast electron transfer reactions that are mediated by the anthraquinone redox moieties in the film. The fast film growth, which is followed by infrared reflection absorption spectroscopy, atomic force microscopy, X-ray photoelectron spectroscopy, ellipsometry, and coverage calculation, results in a mushroom-like structure. In addition to varying the number of sweeps, layer thickness control can easily be exerted through appropriate choice of the switching potential and sweep rate. It is shown that the grafting of the diazonium salt is essentially a diffusion-controlled process but also that desorption of physisorbed material during the sweeping process is essentially for avoiding blocking of the film due to clogging of the electrolyte channels in the film. In general, sweep rates higher than 0.5 V s(-1) are required if thick, porous, and conducting films should be formed.     

Identification of markers of thermal processing (“roasting”) in aqueous extracts of Coffea arabica L. seeds through NMR fingerprinting and chemometrics

Roasting of Coffea arabica L. seeds gives rise to chemical reactions that produce more than 800 compounds, some being responsible for the desired organoleptic properties for which the beverage called “coffee” is known. In the industry, the “roasting profile,” that is, the times and temperatures applied, is key to influence the composition of roasted coffee beans and the flavour of the beverage made from them. The impact of roasting on the chemical composition of coffee has been the subject of numerous studies, including by nuclear magnetic resonance (NMR) spectroscopy. However, the roasting equipment and profiles applied in these studies are often far from real industrial conditions. In this work, the effects of two critical technological parameters of the roasting process, namely, the “development time” (the period of time after the “first crack,” a characteristic noise due to seed disruption) and the final roasting temperature on coffee extracts, were investigated. Seeds were roasted at pilot scale according to 13 industrial roasting profiles and extracted in D₂O. The extracts were analysed by ¹H NMR experiments. The NMR spectra were compared using (a) quantitative analysis of main signals by successive orders of magnitude and (b) chemometric tools (principal component analysis, partial least squares and sparse-orthogonal partial least squares analysis). This allowed to identify compounds, which may serve as markers of roasting and showed that changes in chemical composition can be detected even for slight change in final temperature (~1°C) or in total roasting time (~25 s).