Dicyanopyrazine studies. Part VII: Solid state absorption spectra and aggregation behavior of aminovinylpyrazine dyes containing a long chain alkyl group

The solid state absorption maxima of aminovinylpyrazine dyes containing long chain alkyl groups were changed drastically by the differences in their molecular stacking. The spectral shift from solution to the solid state was evaluated by the Δλ values, and the shift was correlated with substituent effects and their three dimensional molecular structures. Related dyes were synthesized by the nucleophilic substitution of 2,3-dichloro-5,6-dicyanopyrazine with various Fisher’s base type enamines having long alkyl chain groups.     

The predicted 3D structures of the human M1 muscarinic acetylcholine receptor with agonist or antagonist bound

The muscarinic acetylcholine G-protein-coupled receptors are implicated in diseases ranging from cognitive dysfunctions to smooth-muscle disorders. To provide a structural basis for drug design, we used the MembStruk computational method to predict the 3D structure of the human M1 muscarinic receptor. We validated this structure by using the HierDock method to predict the binding sites for three agonists and four antagonists. The intermolecular ligand-receptor contacts at the predicted binding sites agree well with deductions from available mutagenesis experiments, and the calculated relative binding energies correlate with measured binding affinities. The predicted binding site of all four antagonists is located between transmembrane (TM) helices 3, 4, 5, 6, and 7, whereas the three agonists prefer a site involving residues from TM3, TM6, and TM7. We find that Trp 157(4) contributes directly to antagonist binding, whereas Pro 159(4) provides an indirect conformational switch to position Trp 157(4) in the binding site (the number in parentheses indicates the TM helix). This explains the large decrease in ligand binding affinity and signaling efficacy by mutations of Trp 157(4) and Pro 159(4) not previously explained by homology models. We also found that Asp 105(3) and aromatic residues Tyr 381(6), Tyr 404(7), and Tyr 408(7) are critical for binding the quaternary ammonium head group of the ligand through cation-pi interactions. For ligands with a charged tertiary amine head group, we suggest that proton transfer from the ligand to Asp 105(3) occurs upon binding. Furthermore, we found that an extensive aromatic network involving Tyr 106(3), Trp 157(4), Phe 197(5), Trp 378(6), and Tyr 381(6) is important in stabilizing antagonist binding. For antagonists with two terminal phenyl rings, this aromatic network extends to Trp 164(4), Tyr 179(extracellular loop 2), and Phe 390(6) located at the extracellular end of the TMs. We find that Asn 382(6) forms hydrogen bonds with selected antagonists. Tyr381(6) and Ser 109(3) form hydrogen bonds with the ester moiety of acetylcholine, which binds in the gauche conformation.     

Chemical synthesis of a dual branched malto-decaose: a potential substrate for alpha-amylases

A convergent block strategy for general use in efficient synthesis of complex alpha-(1-->4)- and alpha-(1-->6)-malto-oligosaccharides is demonstrated with the first chemical synthesis of a malto-oligosaccharide, the decasaccharide 6,6'-bis(alpha-maltosyl)-maltohexaose, with two branch points. Using this chemically defined branched oligosaccharide as a substrate, the cleavage pattern of seven different alpha-amylases were investigated. Alpha-amylases from human saliva, porcine pancreas, barley alpha-amylase 2 and recombinant barley alpha-amylase 1 all hydrolysed the decasaccharide selectively. This resulted in a branched hexasaccharide and a branched tetrasaccharide. Alpha-amylases from Asperagillus oryzae, Bacillus licheniformis and Bacillus sp. cleaved the decasaccharide at two distinct sites, either producing two branched pentasaccharides, or a branched hexasaccharide and a branched tetrasaccharide. In addition, the enzymes were tested on the single-branched octasaccharide 6-alpha-maltosyl-maltohexaose, which was prepared from 6,6'-bis(alpha-maltosyl)-maltohexaose by treatment with malt limit dextrinase. A similar cleavage pattern to that found for the corresponding linear malto-oligosaccharide substrate was observed.     

Discovery of 3H-imidazo[4,5-b]pyridines as potent c-Met kinase inhibitors: design, synthesis, and biological evaluation

To identify novel c-Met inhibitors, sequences and crystal structures of the human kinome were analyzed to find interesting hinge binders that have been underexplored within the tyrosine kinase subfamily. Through this study, the imidazolopyridine ring was selected as a novel c-Met hinge-binding inhibitor scaffold. A series of derivatives was prepared, and the structure-activity relationships were studied. Among these, one compound in particular showed excellent activities in enzymatic and cellular assays, good in vitro metabolic stability, and favorable pharmacokinetic parameters. When administered orally, the compound inhibited tumor growth in an NIH-3T3/TPR-Met xenograft model and did not show adverse effects on body weight. The present work not only conceptually demonstrates a new route for designing novel kinase inhibitors by using known structural information of ligand-hinge interactions but also provides a series of imidazolopyridine derivatives as potent c-Met inhibitors.     

Peculiar sandwich-like π–π interaction regulating the nonplanarity of the model heme crystals

X-ray crystallographic analysis of bis(pyridine N-oxide) complexes of iron(III) porphyrinates has revealed that the two pyridine rings of the axial ligands correctly sandwich the porphyrin ring to induce the deformation of commonly observed S₄ saddled porphyrin ring.     

Oxidative Gold Catalysis Meets Photochemistry – Synthesis of Benzo[a]fluorenones from Diynes

Diynes bearing one terminal and one triarylmethyl‐substituted alkyne were converted into complex benzofluorenone derivatives via a one‐pot process involving a gold‐catalyzed step followed by a photocyclization/oxidation. In the first step an N‐oxide was used to position‐selectively generate an α‐oxo carbenoid at the terminal alkyne which after a regioselective 1,6‐carbene transfer along the tethered tritylalkyne and a subsequent aryl 1,2‐shift furnished tetraphenylethylene‐like derivatives. These intermediates were successfully transformed to fluorenones via oxidative photocyclization.

     

Sila-haloperidol, a silicon analogue of the dopamine (D2) receptor antagonist haloperidol: synthesis, pharmacological properties, and metabolic fate

Haloperidol (1 a), a dopamine (D(2)) receptor antagonist, is in clinical use as an antipsychotic agent. Carbon/silicon exchange (sila-substitution) at the 4-position of the piperidine ring of 1 a (R(3)COH --> R(3)SiOH) leads to sila-haloperidol (1 b). Sila-haloperidol was synthesized in a new multistep synthesis, starting from tetramethoxysilane and taking advantage of the properties of the 2,4,6-trimethoxyphenyl unit as a unique protecting group for silicon. The pharmacological profiles of the C/Si analogues 1 a and 1 b were studied in competitive receptor binding assays at D(1)-D(5), sigma(1), and sigma(2) receptors. Sila-haloperidol (1 b) exhibits significantly different receptor subtype selectivities from haloperidol (1 a) at both receptor families. The C/Si analogues 1 a and 1 b were also studied for 1) their physicochemical properties (log D, pK(a), solubility in HBSS buffer (pH 7.4)), 2) their permeability in a human Caco-2 model, 3) their pharmacokinetic profiles in human and rat liver microsomes, and 4) their inhibition of the five major cytochrome P450 isoforms. In addition, the major in vitro metabolites of sila-haloperidol (1 b) in human liver microsomes were identified using mass-spectrometric techniques. Due to the special chemical properties of silicon, the metabolic fates of the C/Si analogues 1 a and 1 b are totally different.     

Effects of oxygenates and moisture on adsorptive desulfurization of liquid fuels with Cu(I)Y zeolite

Oxygenates (i.e., ethanol and MTBE as required additives in gasoline) and moisture were found to have strong inhibiting effects on desulfurization by adsorption with zeolite. The effects of each individual molecule were studied quantitatively by using a model fuel (500 ppmw thiophene in 80% n-octane + 20% benzene). Cu(I)Y was used as the π-complexation sorbent. Ab initio molecular orbital calculations showed that the adsorption bond energies with Cu(I)Y were: 21.4 kcal/mol for thiophene; 31.0 kcal/mol for MTBE and 41.6 kcal/mol for ethanol. Separation or selectivity factors can be estimated from heats of adsorption, and the inhibiting effects were predicted to follow the order of the relative heats of adsorption: water > ethanol > MTBE > thiophene. The inhibiting effects were measured by the decreases in the desulfurization capacities of Cu(I)Y in the presence of each additive in the model fuel. The results were in agreement with the theoretical prediction. In addition, the desulfurization capacity was strongly dependent on the liquid hourly space velocity because of the diffusion limitation of thiophene in the zeolite crystals.     

Design and synthesis of aryl ether inhibitors of the Bacillus anthracis enoyl-ACP reductase

The problem of increasing bacterial resistance to the current generation of antibiotics is well documented. Known resistant pathogens such as methicillin-resistant Staphylococcus aureus are becoming more prevalent, while the potential exists for developing drug-resistant pathogens for use as bioweapons, such as Bacillus anthracis. The biphenyl ether antibacterial agent, triclosan, exhibits broad-spectrum activity by targeting the fatty acid biosynthetic pathway through inhibition of enoyl-acyl carrier protein reductase (ENR) and provides a potential scaffold for the development of new, broad-spectrum antibiotics. We used a structure-based approach to develop novel aryl ether analogues of triclosan that target ENR, the product of the fabI gene, from B. anthracis (BaENR). Structure-based design methods were used for the expansion of the compound series including X-ray crystal structure determination, molecular docking, and QSAR methods. Structural modifications were made to both phenyl rings of the 2-phenoxyphenyl core. A number of compounds exhibited improved potency against BaENR and increased efficacy against both the Sterne strain of B. anthracis and the methicillin-resistant strain of S. aureus. X-ray crystal structures of BaENR in complex with triclosan and two other compounds help explain the improved efficacy of the new compounds and suggest future rounds of optimization that might be used to improve their potency.     

Monosaccharide Derivatives with Low‐Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine–Amide,Phenyl–Arginine,Sulfur–π, and Halogen Bond Interactions

The design of small and high‐affinity lectin inhibitors remains a major challenge because the natural ligand binding sites of lectin are often shallow and have polar character. Herein we report that derivatizing galactose with un‐natural structural elements that form multiple non‐natural lectin–ligand interactions (orthogonal multipolar fluorine–amide, phenyl–arginine, sulfur–π, and halogen bond) can provide inhibitors with extraordinary affinity (low nanomolar) for the model lectin, galectin‐3, which is more than five orders of magnitude higher than the parent galactose; moreover, is selective over other galectins.     

Formation mechanism of polyaniline self‐assembled needles and urchin‐like structures assisted by magnesium oxide

The polyaniline (PANI) morphological structure is strongly correlated with the preparation procedure, yielding diverse geometries such as nano‐tubes, belts, rods, fibres and particles. In this study, the synthesis of a novel PANI morphology of consisting of hollow needles and urchin‐like structures is presented and its formation mechanism is explained. The polymer was synthesized by chemical oxidative polymerization of aniline in the presence of magnesium oxide as a structural directing agent. The morphological study of the urchin‐like PANI was conducted using scanning electron microscopy and in situ monitoring of needle growth was done using optical microscopy. The structure and functional groups of these novel structures were characterized using Fourier transform infrared spectroscopy. Additionally, the formation mechanism is modelled based on the multi‐layer theory where a core–shell structure exists between the polymer (shell) and the magnesium oxide particles (core). © 2014 Society of Chemical Industry     

Supramolecular π–π assembly of a neutral [Cu(salen)] complex via the templating effect of an ionic inorganic complex Na2[Cu(mnt)2] forming a framework type material having well-defined channels

A classical ionic inorganic complex Na₂[Cu(mnt)₂] (mnt²⁻ = maleonitriledithiolate = 1,2-dicyanoethylenedithiolate), that acts as a template in assembling neutral [Cu(salen)] (salen = bis(salicylidene)ethylenediamine) complexes forming a framework type arrangement, is accommodated in the channel formed in the crystal structure of a new type of host–guest compound [Cu(salen)]₄ · Na₂[Cu(mnt)₂] (1). The non-covalent supramolecular interactions among [Cu(salen)] complexes and between [Cu(salen)] and [Cu(mnt)₂]²⁻ complexes in the crystal lattice of 1 result in weak antiferromagnetic coupling.     

On the way to selective PARP-2 inhibitors. Design, synthesis, and preliminary evaluation of a series of isoquinolinone derivatives

PARP-1 and PARP-2 are members of the family of poly(ADP-ribose)polymerases, which are involved in the maintenance of genomic integrity under conditions of genotoxic stimuli. The different roles of the two isoforms under pathophysiological conditions have not yet been fully clarified, and this is partially due to the lack of selective inhibitors. We report herein the synthesis and preliminary pharmacological evaluation of a large series of isoquinolinone derivatives as PARP-1/PARP-2 inhibitors. Among them, we identified the 5-benzoyloxyisoquinolin-1(2 H)-one derivative as the most selective PARP-2 inhibitor reported so far, with a PARP-2/PARP-1 selectivity index greater than 60.     

Inhibition of Golgi mannosidase II with mannostatin A analogues: synthesis, biological evaluation, and structure-activity relationship studies

Mannostatin and aminocyclopentitetrol analogues with various substitutions at the amino function were synthesized. These compounds were tested as inhibitors of human Golgi and lysosomal alpha-mannosidases. Modification of the amine of mannostatin had only marginal effects, whereas similar modifications of aminocyclopentitetrol led to significantly improved inhibitors. Ab initio calculations and molecular docking studies were employed to rationalize the results. It was found that mannostatin and aminocyclopentitretrol could bind to Golgi alpha-mannosidase II in a similar mode to that of the known inhibitor swainsonine. However, due to the flexibility of the five-membered rings of these compounds, additional low-energy binding modes could be adopted. These binding modes may be relevant for the improved activities of the benzyl-substituted compounds. The thiomethyl moiety of mannostatin was predicted to make favorable hydrophobic interactions with Arg228 and Tyr727 that would possibly account for its greater inhibitory activity.     

Studies on the surface properties and the adhesion to metal of polyethylene coatings modified with primary aromatic amines

The surface free energy and acid–base characteristics of polyethylene coatings formed on steel in the presence of primary aromatic amines (PAAs) were investigated. PAAs were shown to interact with steel by a donor–acceptor mechanism. An increase in the coating adhesion is realized through chemical and physical bond formation between an adhesive and a substrate with the help of the PAA. The free surface energy of the contact‐to‐metal side of these coatings modified with PAA was shown to grow in parallel with the increase in adhesion. The results correlate with the data on polyethylene surface wetting with nonionic surfactants. Acid–base interactions were found to exert primary control over polyethylene's adhesion to steel. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 388–397, 2001     

Low energy ion‐solid interactions and chemistry effects in a series of pyrochlores

The effect of chemistry on low energy recoil events was investigated at 10 K for each type of atom in pyrochlores, using molecular dynamics simulation. Contour plots of the threshold displacement energy (E_d) in Gd₂Zr₂O₇ have been produced along more than 80 directions for each individual species. The E_d surface for each type of atom in Gd₂Zr₂O₇ is highly anisotropic; E_d of Zr exhibits the largest degree of anisotropy, while that of O_8b exhibits the smallest. The recommended values of E_d in Gd₂Zr₂O₇ based on the observed minima are 56, 94 and 25 eV, respectively, for Gd, Zr, and O. The influence of cation radius on E_d in pyrochlores A₂B₂O₇ (with A‐site ranging from Lu³⁺ to La³⁺ and B‐site ranging from Ti⁴⁺ to Ce⁴⁺) was also investigated along three directions [100], [110], and [111]. The E_d in pyrochlores strongly depended on the atom type, atom mass, knock‐on direction, and lattice position. The defects produced after low energy displacement events included cation antisite defects, cation Frenkel pairs, anion Frenkel pairs, various vacancies, and interstitials. Ce doping in pyrochlores may affect the radiation response, because it resulted in drastic changes in cation and anion displacement energies and formation of an unusual type of anti‐site defect. This work demonstrates links between E_d and amorphization resistance.     

Highly potent and specific GSK-3beta inhibitors that block tau phosphorylation and decrease alpha-synuclein protein expression in a cellular model of Parkinson's disease

Research by Klein and co-workers suggests that the inhibition of GSK-3beta by small molecules may offer an important strategy in the treatment of a number of central nervous system (CNS) disorders including Alzheimer's disease, Parkinson's disease, and bipolar disorders. Based on results from kinase-screening assays that identified a staurosporine analogue as a modest inhibitor of GSK-3beta, a series of 3-indolyl-4-indazolylmaleimides was prepared for study in both enzymatic and cell-based assays. Most strikingly, whereas we identified ligands having poor to high potency for GSK-3beta inhibition, only ligands with a Ki value of less than 8 nM, namely maleimides 18 and 22, were found to inhibit Tau phosphorylation at a GSK-3beta-specific site (Ser 396/404). Accordingly, maleimides 18 and 22 may protect neuronal cells against cell death by decreasing the level of alpha-Syn protein expression. We conclude that the GSK-3beta inhibitors described herein offer promise in defending cells against MPP+-induced neurotoxicity and that such compounds will be valuable to explore in animal models of Parkinson's disease as well as in other Tau-related neurodegenerative disease states.