FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Oriented polymer dispersed discotic liquid crystals

Polymer dispersed discotic liquid crystals (PDDLCs) were prepared using the hexa-n-octanoate of rufigallol (RHO) and three polymer matrices: polystyrene (PS), poly(methyl methacrylate) (PMMA) and poly(ethyl methacrylate) (PEMA). The molecular orientation of RHO in stretched PDDLC films was characterized by means of infrared dichroism. It was found that the stretching of films that contain RHO in both the columnar D1 and crystalline phase can effectively align columns of RHO along the stretching direction, with the short axes of the rigid cores lying in the plane of the film. By contrast with stretched polymer dispersed nematic liquid crystals, no orientation of RHO is induced for films stretched with RHO in the isotropic phase, followed by rapid cooling to room temperature. However, if stretched films are cooled under strain into the columnar D1 phase, orientation of RHO can develop with time.     

UiO-66 and hcp UiO-66 Catalysts Synthesized from Ionic Liquids as Linker Precursors

Using ionic liquids (ILs) as linker precursors, the well-known metal-organic framework (MOF) UiO-66 (Universitetet i Oslo) and the recently reported MOF hcp UiO-66 (hexagonal closed packed) have been successfully synthesized and characterized. The advantage of the applied novel synthesis approach is an economically and environmentally benign work-up procedure, due to the better solubility of the IL. Additionally, the reactivity of the terephthalate anions is increased compared to terephthalic acid, resulting in faster MOF formation with an increased amount of defects in the MOF structure. In order to explore to the influence of defects on the catalytic performance, the cyclisation of citronellal to isopulegol was employed as test reaction. The activity of hcp UiO-66 and fcc UiO-66 (face centered cubic) is improved compared to other MOF or zeolite based catalysts, while the selectivity is similar.     

Discovery of Homobivalent Bitopic Ligands of the Cannabinoid CB2 Receptor**

Single chemical entities with potential to simultaneously interact with two binding sites are emerging strategies in medicinal chemistry. We have designed, synthesized and functionally characterized the first bitopic ligands for the CB₂ receptor. These compounds selectively target CB₂ versus CB₁ receptors. Their binding mode was studied by molecular dynamic simulations and site-directed mutagenesis.     

PAH metabolism in the earthworm Eisenia fetida – identification of phase II metabolites of phenanthrene and pyrene

Polycyclic aromatic hydrocarbons (PAHs) are soil contaminants. Because of their high lipophilicity, PAHs are associated with the organic matter in the soil. Transformation of PAHs generates polar metabolites and the interaction with organic matter in the soil changes. The polar PAH metabolites are persistent, highly water-soluble and potentially leachable from the soil; the understanding of transformation of PAHs to polar metabolites in the responsible organisms is of great importance. Here, we present a study of transformation of the PAHs pyrene and phenanthrene, by the common earthworm Eisenia fetida. The study showed that E. fetida in hydroponic culture was able to transform PAHs to conjugated phase II metabolites. We detected phenanthrene and pyrene metabolites with single- and multiple-phase II-conjugated groups. Sulphate conjugates were excreted to experiment water, and glucuronide and glucoside conjugates and metabolites with several hydroxylations and multiple conjugations were detected in worm tissue. The results demonstrate that earthworms are able to transform PAHs to water-soluble phase II metabolites, which can be excreted to the surrounding environment.     

Determination of pharmaceuticals, iodinated contrast media and musk fragrances in sludge by LC/tandem MS and GC/MS

Analytical methods have been developed that allow for the determination of antiphlogistics, lipid regulators, the antiepileptic carbamazepine, cytostatic agents, the psychiatric drug diazepam and iodinated contrast media (ICM) as well as two major polycyclic musk fragrances HHCB (galaxolide) and AHTN (tonalide) in activated and digested sludge. The procedures consist of ultrasonic solvent extraction (USE) using methanol/acetone or pressurized liquid extraction (PLE) using 100% methanol. Clean-up was performed with C18ec material and silica gel followed by LC tandem MS (electrospray or atmospheric pressure chemical ionization) detection for pharmaceuticals and iodinated contrast media as well as GC/MS in the SIM mode for musk fragrances. Absolute recoveries from spiked activated sludge in general ranged from 88+/-4 to 119+/-20% for ICM and were 78+/-15 and 87+/-10% for the AHTN and HHCB, respectively. For the pharmaceuticals, absolute recoveries in activated sludge ranged between 43 and 78%. Subsequently, compensation of losses was carried out by using surrogate standards (acidic pharmaceuticals: fenoprop, neutral pharmaceuticals: dihydro-carbamazepine, musk fragrances: AHTN-D3). With one exception the recoveries were also adequate in digested sludge ranging from 43% to 120%.     

3,5-Bis(2-hydroxyphenyl)-1<Emphasis Type="Italic">H</Emphasis>-1,2,4-triazole based ligands — protonation and metal complex formation

3,5-Bis(2-hydroxyphenyl)-1H-1,2,4-triazole (H₂L^a) and 4-[3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazol-1-yl]benzoic acid (H₃L^b) have been prepared, and crystal structure of the intermediate 2-(2-hydroxyphenyl)-4H-1,3-benzoxazin-4-one has been determined. Temperature dependent ¹H NMR spectroscopic measurements of H₂L^a indicated dynamic behavior with the equilibrium between the two asymmetric tautomers. For H₃L^b, pD-dependent ¹H NMR spectroscopic measurements showed small but characteristic shifts in the range of 0 ≤ pD ≤ 1, indicative of a triazole nitrogen atom protonation; the corresponding pK _a of 0.98 ± 0.04 was determined by spectrophotometric titrations. (H₂O, 26°C, 1 M KCl/HCl). Formation of [Fe^III(L^a)]⁺ (pH 2.5) and [Fe^III(L^a)₂]⁻ (pH > 6) was verified by UV-Vis spectroscopy. Complex formation of H₃L^b with Al³⁺ and VO²⁺ was investigated by ¹H NMR spectroscopic titration and cyclic voltammetry, respectively. Single crystals of the phenoxo bridged [V^VO(HL^b)(EtO)]₂·2EtOH were characterized by X-ray structural analysis. Dedicated to Professor Milan Melník on the occasion of his 70th birthday