Discovery of linear receptors for multiple dihydrogen phosphate ions using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry to discover a new series of linear hydrazone-based receptors that bind multiple dihydrogen phosphate ions. Through the use of a template-driven, selection-based approach to receptor synthesis, dynamic combinatorial chemistry allows for the identification of unexpected host structures and binding motifs. Notably, we observed the unprecedented selection of these linear receptors in preference to competing macrocyclic hosts. Furthermore, linear receptors containing up to nine building blocks and three different building blocks were amplified in the dynamic combinatorial library. The receptors were formed using a dihydrazide building block based on an amino acid-disubstituted ferrocene scaffold. A detailed study of the linear pentamer revealed that it forms a helical ditopic receptor that employs four acylhydrazone hydrogen-bond donor motifs to cooperatively bind two dihydrogen phosphate ions.     

Studies of Edge Effects with Shroud‐Modified Electrodes

Micron and submicron platinum electrodes with hydrophobically‐modified shrouds have been prepared. The steady state response to a number of electrochemical species have been evaluated with respect to the shroud coating. For submicron electrodes deviations in response were observed based on the shroud modification. These effects were not observed in larger electrodes, and may be due to the so‐called “edge effect” for small diameter electrodes.     

AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics

Target identification remains challenging for the field of chemical biology. We describe an integrative chemical genomic and proteomic approach combining the use of differentially active analogs of small molecule probes with stable isotope labeling by amino acids in cell culture-mediated affinity enrichment, followed by subsequent testing of candidate targets using RNA interference-mediated gene silencing. We applied this approach to characterizing the natural product K252a and its ability to potentiate neuregulin-1 (Nrg1)/ErbB4 (v-erb-a erythroblastic leukemia viral oncogene homolog 4)-dependent neurotrophic factor signaling and neuritogenesis. We show that AAK1 (adaptor-associated kinase 1) is a relevant target of K252a, and that the loss of?AAK1?alters ErbB4 trafficking and expression levels,?providing evidence for a previously unrecognized role for AAK1 in Nrg1-mediated neurotrophic?factor signaling. Similar strategies should lead to the discovery of novel targets for therapeutic development.     

Novel proresolving aspirin-triggered DHA pathway

Endogenous mechanisms in the resolution of acute inflammation are of interest because excessive inflammation underlies many pathologic abnormalities. We report an aspirin-triggered DHA metabolome that biosynthesizes a potent product in inflammatory exudates and human leukocytes, namely aspirin-triggered Neuroprotectin D1/Protectin D1 [AT-(NPD1/PD1)]. The complete stereochemistry of AT-(NPD1/PD1) proved to be 10R,17R-dihydroxydocosa-4Z,7Z,11E,13E,15Z,19Z-hexaenoic acid. The chirality of hydroxyl groups and geometry of the conjugated triene system essential for bioactivity were established by matching biological materials with stereochemically pure isomers prepared by organic synthesis. AT-(NPD1/PD1) reduced neutrophil (PMN) recruitment in murine peritonitis in a dose-dependent fashion whereby neither a Δ(15)-trans-isomer nor DHA was effective. With human cells, AT-(NPD1/PD1) decreased transendothelial PMN migration as well as enhanced efferocytosis of apoptotic human PMN by macrophages. These results indicate that AT-(NPD1/PD1) is a potent anti-inflammatory proresolving molecule.     

Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase

The pentadecaketide fredericamycin has the longest carbon chain backbone among polycyclic aromatic polyketide antibiotics whose biosynthetic genes have been sequenced. This backbone is synthesized by the bimodular fdm polyketide synthase (PKS). Here, we demonstrate that the bimodular fdm PKS as well as its elongation module alone synthesize undecaketides and dodecaketides. Thus, unlike other homologs, the fdm ketosynthase-chain length factor (KS-CLF) heterodimer does not exclusively control the backbone length of its natural product. Using sequence- and structure-based approaches, 48 CLF multiple mutants were engineered and analyzed. Unexpectedly, the I134F mutant was unable to turn over but could initiate and partially elongate the polyketide chain. This unprecedented mutant suggests that the KS-CLF heterodimer harbors an as yet uncharacterized chain termination mechanism. Together, our findings reveal fundamental mechanistic differences between the fdm PKS and its well-studied homologs.     

Molecular recognition probes of solvation thermodynamics in solvent mixtures

High-throughput UV-Vis experiments using four molecular recognition-based probes, made by the combination of two hydrogen bond acceptors, tri-n-butylphosphine oxide and N,N'-bis(2-ethylhexyl)acetamide, and two hydrogen bond donors, 4-phenylazophenol and 4-nitrophenol, were performed. The association constants for the 1 : 1 H-bond interaction involved in each probe system were measured in mixtures of a polar and non-polar solvent, di-n-hexyl ether and n-octane, respectively. Similar behaviour was observed for all four systems. When the concentration of the polar solvent was low, the association constant was identical to that observed in pure n-octane. However, once the concentration of the polar solvent exceeded a threshold, the association constant decreased linearly with the concentration of di-n-hexyl ether. Selective solvation in mixtures can be understood based on the competition between the multiple competing equilibria in the system. In this case, solvation thermodynamics are dominated by competition of the ether for solvation of H-bond donors. For the more polar solute, 4-nitrophenol, the selective solvation starts at lower concentrations of the polar solvent compared with the less polar solute, 4-phenylazophenol. Thus the speciation and hence the properties of systems containing multiple solutes and multiple solvents can be estimated from the H-bond properties and the concentrations of the individual functional groups.     

Organometallic reactivity: the role of metal-ligand bond energies from a computational perspective

The association and dissociation of ligands plays a vital role in determining the reactivity of organometallic catalysts. Computational studies with density functional theory often fail to reproduce experimental metal-ligand bond energies, but recently functionals which better capture dispersion effects have been developed. Here we explore their application and discuss future challenges for computational studies of organometallic catalysis.     

Enantio- and diastereoselective synthesis of (E)-1,5-syn-diols: application to the synthesis of the C(23)-C(40) fragment of tetrafibricin

A highly stereoselective synthesis of (E)-1,5-syn-diols 6 is described. The kinetically controlled hydroboration of allenyltrifluoroborate 8 with Soderquist borane 2 provides the (Z)-allylic trifluoroborate 9, which undergoes sequential allylboration with two different aldehydes to provide (E)-1,5-syn-diols 6 in 72-98% yields with >95% ee and >20:1 dr. Application of this method to the synthesis of the tetrafibricin C(23)-C(40) fragment 19 is described.     

Triacylglycerol profiling of microalgae strains for biofuel feedstock by liquid chromatography-high-resolution mass spectrometry

Biofuels from photosynthetic microalgae are quickly gaining interest as a viable carbon-neutral energy source. Typically, characterization of algal feedstock involves breaking down triacylglycerols (TAG) and other intact lipids, followed by derivatization of the fatty acids to fatty acid methyl esters prior to analysis by gas chromatography (GC). However, knowledge of the intact lipid profile could offer significant advantages for discovery stage biofuel research such as the selection of an algal strain or the optimization of growth and extraction conditions. Herein, lipid extracts from microalgae were directly analyzed by ultra-high pressure liquid chromatography–mass spectrometry (UHPLC-MS) using a benchtop Orbitrap mass spectrometer. Phospholipids, glycolipids, and TAGs were analyzed in the same chromatographic run, using a combination of accurate mass and diagnostic fragment ions for identification. Using this approach, greater than 100 unique TAGs were identified over the six algal strains studied and TAG profiles were obtained to assess their potential for biofuel applications. Under the growth conditions employed, Botryococcus braunii and Scenedesmus obliquus yielded the most comprehensive TAG profile with a high abundance of TAGs containing oleic acid.     

Computational chemistry and molecular simulations of phosphoric acid

Quantum mechanics (QM) calculations, molecular dynamics (MD) simulations using the condensed‐phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field, and the atom‐centered density matrix propagation (ADMP) approach have been used to investigate properties of phosphoric acid (PA). QM using B3LYP/6‐31++G(d,p) density functional theory were used to calculate gas‐phase proton affinities and interaction energies of PA and its derivatives. Detailed single coordinate driving, followed by quadratic synchronous transit optimization was used to determine energy barriers for different proton transfer (PT) pathways. Determined energy barrier heights in ascending order are (unit: kJ/mol): H₃O⁺→H₃PO₄ (0); H₄P₂O₇→H₃PO₄ (2.61); H₃PO₄→H₂PO (5.31); H₄PO→H₃PO₄ (～7.33); H₃PO₄→H₄P₂O₇/H₃PO₄→H₃PO₄ (15.99); H₄P₂O₇→H₂O (28.61); H₃PO₄→H₂O (47.14). The COMPASS force field was used to study condensed‐phase properties of PA. Good agreement between experimental data and MD results including density, radial distribution functions, and self‐diffusion coefficient at different temperatures provides validation of the COMPASS force field for PA. Finally, preliminary ADMP studies on a cluster of three PA molecules shows that the ADMP approach can reasonably describe the PT and self‐dissociation processes in PA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011