Molecular docking with ligand attached water molecules

A novel approach to incorporate water molecules in protein-ligand docking is proposed. In this method, the water molecules display the same flexibility during the docking simulation as the ligand. The method solvates the ligand with the maximum number of water molecules, and these are then retained or displaced depending on energy contributions during the docking simulation. Instead of being a static part of the receptor, each water molecule is a flexible on/off part of the ligand and is treated with the same flexibility as the ligand itself. To favor exclusion of the water molecules, a constant entropy penalty is added for each included water molecule. The method was evaluated using 12 structurally diverse protein-ligand complexes from the PDB, where several water molecules bridge the ligand and the protein. A considerable improvement in successful docking simulations was found when including flexible water molecules solvating hydrogen bonding groups of the ligand. The method has been implemented in the docking program Molegro Virtual Docker (MVD).     

Optical coherence tomography��current technology and applications in clinical and biomedical research

Optical coherence tomography (OCT) is a noninvasive imaging technique that provides real-time two- and three-dimensional images of scattering samples with micrometer resolution. By mapping the local reflectivity, OCT visualizes the morphology of the sample. In addition, functional properties such as birefringence, motion, or the distributions of certain substances can be detected with high spatial resolution. Its main field of application is biomedical imaging and diagnostics. In ophthalmology, OCT is accepted as a clinical standard for diagnosing and monitoring the treatment of a number of retinal diseases, and OCT is becoming an important instrument for clinical cardiology. New applications are emerging in various medical fields, such as early-stage cancer detection, surgical guidance, and the early diagnosis of musculoskeletal diseases. OCT has also proven its value as a tool for developmental biology. The number of companies involved in manufacturing OCT systems has increased substantially during the last few years (especially due to its success in opthalmology), and this technology can be expected to continue to spread into various fields of application.     

In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum

A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90?% of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex.     

Self-consistent modeling of entangled network strands and linear dangling structures in a single-strand mean-field slip-link model

Linear viscoelastic (LVE) measurements as well as non-linear elongation measurements have been performed on stoichiometrically imbalanced polymeric networks to gain insight into the structural influence on the rheological response (Jensen et al., Rheol Acta 49(1):1–13, 2010). In particular, we seek knowledge about the effect of dangling ends and soluble structures. To interpret our recent experimental results, we exploit a molecular model that can predict LVE data and non-linear stress–strain data. The slip-link model has proven to be a robust tool for both LVE and non-linear stress–strain predictions for linear chains (Khaliullin and Schieber, Phys Rev Lett 100(18):188302–188304, 2008, Macromolecules 42(19):7504–7517, 2009; Schieber, J Chem Phys 118(11):5162–5166, 2003), and it is thus used to analyze the experimental results. Initially, we consider a stoichiometrically balanced network, i.e., all strands in the ensemble are attached to the network in both ends. Next we add dangling strands to the network representing the stoichiometric imbalance, or imperfections during curing. By considering monodisperse network strands without dangling ends, we find that the relative low-frequency plateau, G₀/G_N⁰G_0/G_N^0, decreases linearly with the average number of entanglements. The decrease from G_N⁰G_N^0 to G ₀ is a result of monomer fluctuations between entanglements, which is similar to “longitudinal modes” in tube theory. It is found that the slope of G′ is dependent on the fraction of network strands and the structural distribution of the network. The power-law behavior of G ^″ is not yet captured quantitatively by the model, but our results suggest that it is a result of polydisperse dangling and soluble structures.     

Extraction of polycyclic aromatic hydrocarbons from smoked fish using pressurized liquid extraction with integrated fat removal

Quantification of polycyclic aromatic hydrocarbons (PAHs) in smoked fish products often requires multiple clean-up steps to remove fat and other compounds that may interfere with the chemical analysis. We present a novel pressurized liquid extraction (PLE) method that integrates exhaustive extraction with fat retention in one single analytical step. The PLE parameters: type of fat retainer, flush volume, solvent composition, fat-to-fat retainer ratio (FFR), and the dimensions of the extraction cells were the most important factors for obtaining fat-free extracts with high recoveries of PAHs. A 100 mL extraction cell filled with 18 g activated silica gel, dichloromethane:hexane (15:85, v/v) as extraction solvent, FFR of 0.025 and 100% flush volume was the best analytical setup for integrated extraction and fat retention.The one-step procedure provided a more rapid and cost-efficient alternative with minimization of waste generation compared to the standard reference method that is based on a multi-step procedure. Furthermore, the analytical quality of the two methods are comparable, while the new integrated approach for extraction and cleanup is less prone to analytical errors (random and systematic) because of fewer analytical steps.     

Synthesis of spirane-bridged rigidified oxalkyl cyclopentadienyl ligands

Methods for the preparation of constrained spirane-bridged oxalkyl indenyl ligands are described. The cis,cis-α,α′-spirane derivatives were synthesised in several steps from spiro[4.4]nonane-1,6-dione. Carbylation was achieved by Wittig methenylation. A subsequent stereoselective hydroboration by 9-BBN followed by peroxide treatment furnished the corresponding cis-methanol. Further manipulations provided the cis-carboxylic ester, which in a double Grignard reaction with α,α′-dichloro-o-xylene, furnished the corresponding indenyl derivative. The final products were cis,cis-α-(2-indenyl)-α′-(methoxy or methoxymethyl)spiro[4.4]nonanes.     

Can decarbonylation of acyl radicals be overcome in radical addition reactions? En route to a solution employing N-acyl oxazolidinones and SmI2/H2O

The application of acyl radicals in radical addition reactions in the absence of a CO atmosphere is generally limited to aryl or alpha-unsubstituted alkyl acyl radicals due to competing decarbonylations where the rate constant for this degradation process surpasses 104 s-1. In this work, a potential solution to avoid the problem of decarbonylations is presented employing N-acyl oxazolidinones which are reduced to acyl radical equivalents in the presence of samarium diiodide and water. In the company of an acrylamide, acrylate, or acrylonitrile, the product from a formal acyl radical addition is obtained in yields up to 87%. Examples are given where the decarbonylation rate constants even exceed 108 s-1. It is proposed that the reaction proceeds via a ketyl-like intermediate.     

Direct Access to α,α‐Difluoroacylated Arenes by Palladium‐Catalyzed Carbonylation of (Hetero)Aryl Boronic Acid Derivatives

A palladium‐catalyzed carbonylative coupling of (hetero)aryl boronates or boronic acid salts with carbon monoxide and α‐bromo‐α,α‐difluoroamides and bromo‐α,α‐difluoroesters is described herein. The method is useful for the synthesis of a diverse selection of (hetero)aryl α,α‐difluoro‐β‐ketoamides and α,α‐difluoro‐β‐ketoesters, which are useful building blocks for the generation of functionalized difluoroacylated and difluoroalkyl arenes. The method could be further extended to a one‐pot protocol for the formation of difluoroacetophenones.     

A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models

Thiamin diphosphate (ThDP) is the biologically active form of vitamin B1 and an essential cofactor for a number of enzymes. The effect of solvent polarity on the tautomeric equilibria of ThDP using three model systems of the 4'-aminopyrimidine ring is studied by density functional theory calculations (B3LYP/6-311+G(d,p)//B3LYP/6-31G(d)) in the gas phase and selected solvents (cyclohexane, ether, dichloroethane, and water). Solvation effects are investigated using three different schemes: implicit solvation by a continuum model, explicit solvation by inclusion of three water molecules mimicking the first solvation shell of the enzymatic environment, and by a mixed implicit/explicit solvation model. The 4'-aminopyrimidine tautomer is more stable than the 1',4'-iminopyrimidine tautomer in all solvation schemes employed; however, the trend for the stabilities of the 1',4'-iminopyrimidine tautomer in the solvents depends on the specific ThDP-model. Formation of the catalytic important ylide for ThDP-dependent enzymes by deprotonation of ThDP(C2) is also investigated by localization of transition states for two possible pathways. Only the less stable tautomer, 1',4'-iminopyrimidine ThDP, is able to form the catalytic active ylide. Generation of the ylide through a direct intramolecular proton transfer from ThDP(C2) to the ThDP(N4') nitrogen lone pair is favored by 6 kcal/mol in the gas phase, as compared to a water-mediated ylide generation. However, inclusion of a dielectric medium reduces this difference dramatically. Furthermore, inclusion of two water molecules to model the apoenzymatic environment lowers the activation energies of both direct and water-mediated ylide generation.