Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

The intramolecular hydrogen bond in ortho-hydroxy acetophenones

The crystal structures of two ortho-hydroxy ketones (5-chloro-2-hydroxyacetophenone (I K) and 3,5-dichloro-2-hydroxyacetophenone (II K)) have been determined with X-ray diffraction at 100 K. A comparison of steric effects on properties of pseudoaromatic hydrogen bonds in ortho-hydroxy acetophenone and ortho-hydroxy ketimines have been carried out with the application of crystallographic data.

Nuclear quadrupole resonance (NQR) spectra have been measured and interpreted.     

Temperature coefficient of NH chemical shifts of thioamides and amides in relation to structure

NH chemical shift temperature coefficients have been measured in a large series of N-substituted-3-piperidinethiopropionamides in which the NN distances are short but of varied length, as well as in a couple of the corresponding amides and in some simpler amides and thioamides. Geometries are calculated by means of ab initio DFT methods. The N-substituted-3-piperidinethiopropionamides show in most cases strong intramolecular N–HN hydrogen bonds according to IR spectra and ab initio calculations. For compounds with rather short NN distances the S=C–N–H moiety is non-planar. Dihedral angles as small as 160° are found. The NH chemical shift coefficients measured in non-polar solvents in all the N-substituted-3-piperidinethiopropionamides are more negative (−8 to −17 ppb/K) than in non-hydrogen bonded thioamides. For the latter in non-polar solvents like CDCl₃ and toluene the temperature coefficients are as small as −1 to −4 ppb/K. The large negative effects can be related not only to the non-planarity of the thioamide group in a way that the more pronounced the non-planarity the more negative the temperature coefficients, but also to strong hydrogen bonding and the fact that the acceptor is a nitrogen. For similar amides with non-planar amide groups and nitrogen acceptor large negative temperature coefficients are likewise seen. In polar solvents like DMF the effects in simple thioamides are uniform and close to −6 ppb/K, whereas in the more complex compound like 4p(t) the temperature coefficient is close to 0. An essential feature of measuring temperature coefficients of compounds without strong intramolecular hydrogen bonds in non-polar solvents and at low temperatures is to keep the concentration low enough to avoid dimerisation.     

Lipases,liposomes and lipid-prodrugs

Colloidal and interfacial phenomena lie at the core of drug formulation, drug delivery, as well as drug binding and action at diseased sites, e.g., in cancer therapy. We review a class of liposome-based drug-delivery systems whose design and functional properties are intimately controlled by the stability of sub-micron structures, lipid-bilayer interfaces, and interfacially activated enzymes that can be exploited to target and deliver drugs. Moreover these drugs can themselves be special lipid molecules in the form of lipid prodrugs that both form the liposomal carrier as well as the substrate for endogenously upregulated lipases that turn the prodrugs into potent drugs precisely at the diseased site.     

Triphenylene silanes for direct surface anchoring in binary mixed self-assembled monolayers

New triphenylene-based silanes 2-(ω-(chlorodimethylsilyl)-n-alkyl)-3,6,7,10,11-penta-m-alkoxytriphenylene 4 (Tm-Cn) with n = 8 or 9 and m = 7, 8, 9, 10, or 11 were synthesized, and their self-assembly behavior in the liquid state and at glass and silicon oxide surfaces was investigated. The mesomorphic properties of triphenylene silanes 4 (Tm-Cn) and their precursors 3 (Tm-Cn) were determined by differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and X-ray diffraction. From the small-angle X-ray scattering (SAXS) regime, a preferential discotic lamellar mesophase can be deduced, and wide-angle X-ray scattering (WAXS) highlights the liquid-like characteristics of the alkyl side chains. To transfer these bulk structural properties to thin films, self-assembled monolayers (SAMs) were obtained by adsorption from solution and characterized by water contact angle measurements, null ellipsometry, and atomic force microscopy (AFM). Employing the concentration as an additional degree of freedom, binary SAMs of 2-(ω-(chlorodimethylsilyl)-undecyl)-3,6,7,10,11-penta-decyloxytriphenylene 4 (T10-C11) were coassembled with chlorodecyldimethylsilane or chlorodimethyloctadecylsilane, and their capability as model systems for organic templating was evaluated. The structure of the resulting binary mixed SAMs was analyzed by water contact angle measurements, null ellipsometry, and X-ray reflectivity (XRR) in combination with theoretical modeling by a multidimensional Parratt algorithm and AFM. The composition dependence of film thickness and roughness can be explained by a microscopic model including the steric hindrance of the respective molecular constituents.     

Halodiazophosphonates, a new class of diazo compounds for the diastereoselective intermolecular Rh(II) catalyzed cyclopropanation

(Halodiazomethyl)phosphonates 2A-C have been generated by a one-pot procedure via a clean, efficient, and rapid deprotonation/electrophilic halogenation sequence from diethyl diazomethylphosphonate 1 (EDP). Subsequent intermolecular Rh(II)-catalyzed cyclopropanation afforded the corresponding halocyclopropylphosphonates 3-10 in moderate to high yields and high diastereomeric ratios. Catalyst loadings down to 0.1 mol % as well as clean and selective product formation were achieved.     

The effect of loading and particle size on the oxygen reaction in CGO impregnated Pt electrodes

Porous platinum electrodes impregnated with Gd _x Ce_1−x O_2−δ (CGO) are investigated to characterise how nano-sized CGO grains affect the oxygen reaction. Impedance measurements were performed at temperatures between 450 and 750 °C and at oxygen partial pressures of 0.2 and 5 × 10⁻⁵ bar for electrodes with various CGO loadings and electrodes annealed at various temperatures. The morphology was characterised by scanning electron microscopy and the CGO grain size was determined from X-ray diffraction peak broadening. The results showed that the polarisation resistance decreased with increasing CGO loading and increasing annealing temperature. CGO facilitates transport of oxygen ions thereby increasing the effective triple-phase boundary.     

Electrochemical testing of composite electrodes of (La1?x Sr x ) s MnO3 and doped ceria in NO-containing atmosphere

The possibility of using electrochemical cells for removal of NO _x from an exhaust gas with excess O₂ has been examined. (La_1−x Sr _x ) _s MnO₃ (LSM) and ceria doped with Pr or Gd were selected as electrode materials and investigated in three-electrode cells. The electrodes were characterised electrochemically with electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV), and the gas composition monitored while the electrodes were polarised. The electrodes of (La_0.5Sr_0.5)_0.99MnO₃ (LSM50) and Ce_0.8Pr_0.2O_2−δ exhibit higher current densities in 0.1% NO in Ar than in air at 300 to 400 °C during CV. This indicates some apparent selectivity towards NO compared to O₂. The electrodes can remove NO, when polarised to at least −0.6 V vs. Pt/Air at 600 °C, and EIS measurements under polarisation indicate that the kinetics of the electrodes change, when the electrode potential gets below −0.6 V vs. Pt/Air.     

Synthesis of Benz[a]azulenes Substituted at the Benzo Ring

It is shown that the thermal electrocyclic ring-closure reaction of 1,2-di[(E)-prop-1-enyl]benzene to yield 2,3-dimethylnaphthalene (cf. Scheme 1) [10] can successfully be applied also to the synthesis of benz[a]azulenes (cf. Schemes 2 and 3). Starting materials are methyl 4,6,8-trimethylazulen-2-yl ketone ( 6 ) and the corresponding 2-carbaldehyde 5 , which, in a Horner-Emmons reaction, are transformed into the (azulen-2-yl)-acrylates (E)- 8 and (E)- 7 , respectively. Vilsmeier formylation of these compounds, followed by the Horner-Emmons reaction leads to the formation of the bisacrylates (E,E)- 11 and (E,E)- 12 , respectively. In an alternative reaction, (E)- 8 , on treatment with dimethyl acetylenedicarboxylate (ADM) in the presence of [RuH₂(PPh₃)₄], can be transformed into the methoxycarbonyl-substituted bisacrylates (E,E)- and (E,Z)- 17 . All three bisacrylates, on heating at 180–190° in p-cymene, undergo cyclization to yield the corresponding dihydrobenz[a]azulenes 13 , 14 , and 18 , respectively, which could easily be dehydrogenated on heating in the presence of Pd/C. The new benz[a]azulenes 15 , 16 , and 19 are fully characterized.     

Formation of Heptaleno[1,2-c]furans and Heptaleno[1,2-c]furanones

The dehydrogenation reaction of the heptalene-4,5-dimethanols 4a and 4d , which do not undergo the double-bond-shift (DBS) process at ambient temperature, with basic MnO₂ in CH₂Cl₂ at room temperature, leads to the formation of the corresponding heptaleno[1,2-c]furans 6a and 6d , respectively, as well as to the corresponding heptaleno[1,2-c]furan-3-ones 7a and 7d , respectively (cf. Scheme 2 and 8). The formation of both product types necessarily involves a DBS process (cf. Scheme 7). The dehydrogenation reaction of the DBS isomer of 4a , i.e., 5a , with MnO₂ in CH₂Cl₂ at room temperature results, in addition to 6a and 7a , in the formation of the heptaleno[1,2-c]-furan-1-one 8a and, in small amounts, of the heptalene-4,5-dicarbaldehyde 9a (cf. Scheme 3). The benzo[a]heptalene-6,7-dimethanol 4c with a fixed position of the C?C bonds of the heptalene skeleton, on dehydrogenation with MnO₂ in CH₂Cl₂, gives only the corresponding furanone 11b (Scheme 4). By [²H₂]-labelling of the methanol function at C(7), it could be shown that the furanone formation takes place at the stage of the corresponding lactol [3-²H₂]- 15b (cf. Scheme 6). Heptalene-1,2-dimethanols 4c and 4e , which are, at room temperature, in thermal equilibrium with their corresponding DBS forms 5c and 5e , respectively, are dehydrogenated by MnO₂ in CH₂Cl₂ to give the corresponding heptaleno[1,2-c]furans 6c and 6e as well as the heptaleno[1,2-c]furan-3-ones 7c and 7e and, again, in small amounts, the heptaleno[1,2-c]furan-1-ones 8c and 8e , respectively (cf. Scheme 8). Therefore, it seems that the heptalene-1,2-dimethanols are responsible for the formation of the furan-1-ones (cf. Scheme 7). The methylenation of the furan-3-ones 7a and 7e with Tebbe's reagent leads to the formation of the 3-methyl-substituted heptaleno[1,2-c]furans 23a and 23e , respectively (cf. Scheme 9). The heptaleno[1,2-c]furans 6a, 6d , and 23a can be resolved into their antipodes on a Chiralcel OD column. The (P)-configuration is assigned to the heptaleno[1,2-c]furans showing a negative Cotton effect at ca. 320 nm in the CD spectrum in hexane (cf. Figs. 3–5 as well as Table 7). The (P)-configuration of (–)- 6a is correlated with the established (P)-configuration of the dimethanol (–)- 5a via dehydrogenation with MnO₂. The degree of twisting of the heptalene skeleton of 6 and 23 is determined by the Me-substitution pattern (cf. Table 9). The larger the heptalene gauche torsion angles are, the more hypsochromically shifted is the heptalene absorption band above 300 nm (cf. Table 7 and 8, as well as Figs. 6–9).