Identification of gel-separated tumor marker proteins by mass spectrometry

Two-dimensional gel electrophoresis with subsequent analysis by mass spectrometry was applied to study differences in protein expression between benign and malignant solid tumors from human beast, lung and ovary cells. Cells from freshly resected clinical material were lysed and the extracts were subjected to isoelectric focusing with immobilized pH gradients followed by second-dimensional separation on 10-13% sodium dodecyl sulfate (SDS)/polyacrylamide gels. Polypeptides were identified using matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry after in-gel protein digestion. Some of the upregulated polypeptides in malignant cells are of potential importance as markers of tumor proliferation. Twenty such proteins were identified, ten constituting novel identifications and ten sequence verifications of previously gel-matched proteins. The proteins identified span a wide range of functions, but several cases of protein truncation were found. Truncated forms of cytokeratins 6D and 8, and of cathepsin D were identified. Truncated froms of these over-expressed proteins support the presence of proteolytic processing steps in tumor material. The protein processing and the difference between protein and mRNA abundancies in tumors of different malignancy and origin suggest that studies at the protein level are important for an understanding of tumor phenotypes.     

Purine and sugar chemistry on solid phase--100 years after the Emil Fischer's Chemistry Nobel Prize 1902

The Nobel Prize in Chemistry 1902 was given to Hermann Emil Fischer "in recognition of the extraordinary services he had rendered by his work on sugar and purine synthesis". This truly great chemist of all time named a group of bicyclic nitrogenous structures as purines, discovered the synthesis of glucose, fructose and mannose starting from glycerol, and further created the basis for glucoside-, amino acid-, and enzyme chemistry. To honour his discoveries, and to celebrate the 100 year since his Nobel Prize, we decided to write a short review article on the latest discoveries in the fields of purine/pyrimidine and sugar chemistry being performed on solid support. The review summarizes most of the material being published in the field since 1960, and ends by giving a picture of future directions for the field of drug discovery based on sugar and purine chemistry.     

Die Berechnung komplexer Absorptionsgleichgewichte ionogener Substanzen in wäßrigen Lösungsmitteln mit Hilfe eines Reaktionsmodells

The solubility of ionogen substances in water and aqueous ionic solutions is important for calculation of absorption processes. Aqueous solutions with complex reaction systems behave themselves extremely nonideal. In simple cases equilibria can be determined with the concept of nonideal thermodynamics. The model used in this work is based on ideal calculation of reaction equilibria and gas solubility. The model parameters (equilibrium constants andHenry constants) for the systems SO₂-H₂O,MEA-H₂S-H₂O,DEA-H₂S-H₂O andMEA-CO₂-H₂O are computed by regression of experimental data. Equilibrium reactions are selected according toBrinkley's method. The selection of the reacting species has decisive influence on the accuracy of the data fitting. Data regression is done numerically and leads to the formulation of nonlinear systems of equations, which have to be solved for each data point. This solutions are performed in an inner loop. By using the maximum-likelihood-principle the model parameters are optimized in the superior regression loop. Experimental data for the regression are the partial pressure and the total concentration of gas in the liquid phase. The used model is able to fit these data satisfactoryly. The model parameters, which are calculated from simultaneous data regression for different temperatures, ensure a simple correlation ofvan't Hoff. However, for similar reactions equilibria in different reaction systems, it is impossible to compute the same values for the equilibrium constants.     

Investigation of lipase-catalyzed Michael-type carbon–carbon bond formations

Conjugate additions of carbon nucleophiles to appropriate acceptor molecules were investigated with respect to the synthetic potential and stereochemistry of the products. Reactions of short-chain α,β-unsaturated ketones and mono-substituted nitroalkenes with CH-acidic carboxylic ester derivatives were catalyzed by various immobilized lipases. Using methyl nitroacetate complete conversion with methyl vinyl ketone and trans-β-nitrostyrene was obtained. The reactions proceeded without enantioselectivity. Evidence for enzyme catalysis is provided by the observation that after denaturation of Candida antarctica lipase B or inhibition no reaction took place. Docking studies with the chiral addition product methyl 2-methyl-2-nitro-5-oxohexanoate did not reveal any specific binding mode for this reaction product, which would have been the requirement for stereoselective additions. These results support the experimental findings that the conjugate addition takes place without enantiopreference.     

Fe(III)-coordination properties of neuromelanin components: 5,6-dihydroxyindole and 5,6-dihydroxyindole-2-carboxylic acid

The Fe(III)-coordination chemistry of neuromelanin building-block compounds, 5,6-dihydroxyindole (DHI), 5,6-dihydroxyindole-2-carboxylic acid (DHICA), and 5,6-dihydroxy-N-methyl-indole (Me-DHI), and the neurotransmitter dopamine were explored in aqueous solution by anaerobic pH-dependent spectrophotometric titrations. The Fe(III)-binding constants and pH-dependent speciation parallel those of catechol in that mono, bis, and tris FeLx species are present at concentrations dependent on the pH. The bis FeL2 dihydroxyindole species are favorable for L = DHI and DHICA under neutral to mildly acidic conditions. DHI and DHICA are stronger Fe(III) chelates than catechol, dopamine, and Me-DHI at pH values from 3 to 10. Oxidation studies reveal that iron accelerates the air oxidation of DHI and DHICA.     

Density matrix analysis, simulation, and measurements of electronic absorption and fluorescence spectra of spirobifluorenes

The linear absorption and fluorescence spectra as well as the oscillator strengths of 2,2',7,7'-tetraphenyl-9,9'-spirobifluorene (A), 2,2',7,7'-tetrakis(biphenyl-4-yl)-9,9'-spirobifluorene (B), and 2,2',7,7'-tetrakis(9,9'-spirobifluoren-2-yl)-9,9'-spirobifluorene (C) are calculated on the basis of the collective electronic oscillator (CEO) approach of Mukamel et al. (see, e.g., Chem. Rev. 2002, 102, 3171). The graphical visualization and quantitative characterization of CEO modes allows one to extract the real-space distribution of electronic excitations of the molecules under study. Effects of the lengthening and branching of the oligophenylene segments have been analyzed. The influence of the lowest excited (S1) vs ground-state (S0) geometry changes on the CEO modes is investigated and related to the geometry changes of the molecular parts. The obtained theoretical results are in good agreement with experimental trends observed in absorption and fluorescence data.     

Carbon-carbon bond formation in palladium(II)-catalyzed allylic oxidation: a novel oxidative carbocyclization of allene-substituted olefins

A new efficient palladium(II)-catalyzed oxidative carbocyclization has been developed. It was found that allene-substituted olefins 1 cyclized in the presence of 1 mol % Pd(O2CCF3)2 and p-benzoquinone (2 equiv) to give bicyclic ring systems 2 in good to excellent yields. The cyclization constitutes a new type of carbon-carbon bond forming reaction between an allene and an olefin under oxidative conditions.     

On Wong-Zakai approximation of stochastic differential equations

An approximation theorem of stochastic differential equations driven by semimartingales is proved, based on approximation of semimartingales by a sequence of processes with piecewise monotonic sample functions.