Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Gas‐phase tautomerism in hydroxy azo dyes – from 4‐phenylazo‐1‐phenol to 4‐phenylazo‐anthracen‐1‐ol

The tautomeric constants of a series of azo dyes were estimated in the gas phase by using electron ionization mass spectrometry. It was shown that the relative amount of the keto tautomer increases from 4‐phenylazo‐1‐phenol to 4‐phenylazo‐anthracen‐1‐ol, thus confirming the quantum‐chemical predictions. The existence of the enol tautomer of 4‐phenylazo‐anthracen‐1‐ol is shown for the first time by mass spectrometry in the gas phase. This finding is supported by flash photolysis measurements in solution. Copyright © 2010 John Wiley & Sons, Ltd.     

Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylating agents and matrix-assisted laser desorption/ionization mass spectrometry

We describe a simple approach for the relative quantification of individual proteins within a mixture. The method is based on the differential labelling of the mixtures by use of a commercially available acrylamide and deuterium-labelled [2,3,3'-d(3)]-acrylamide to alkylate proteins prior to two-dimensional (2-D) gel electrophoresis. The tryptic digests of the separated proteins were subjected to reflector matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis and the relative peak heights of cysteine-containing peptides were used to quantify their precursor proteins. This approach was tested for the relative quantification of proteins within an artificial mixture of standard proteins and for proteins observed in a 2-D map of rat serum. A good correlation was found between the measured ratios derived from MALDI-TOF data and those theoretically calculated prior to 2-D analysis via known mixing ratios of the two alkylating reagents. The described procedure has proved to be effective for comparative measurements of protein abundances within the investigated mixtures.     

Titanium isopropoxide as efficient catalyst for the aza-Baylis-Hillman reaction. Selective formation of alpha-methylene-beta-amino acid derivatives

The direct formation of alpha-methylene-beta-amino acid derivatives is achieved using the aza version of the Baylis-Hillman protocol. The products are readily formed in a three-component one-pot reaction between arylaldehydes, sulfonamides, and alpha,beta-unsaturated carbonyl compounds. The reaction is efficiently catalyzed by titanium isopropoxide and 2-hydroxyquinuclidine in the presence of molecular sieves. The protocol allows for structural variation of the substrates, tolerating electron-poor and electron-rich arylaldehydes and various Michael acceptors.     

Peroxynitrite decomposition catalyst prevents apoptotic cell death in a human astrocytoma cell line incubated with supernatants of HIV-infected macrophages

Background  

Oxidative stress has shown to contribute in the mechanisms underlying apoptotic cell death occuring in AIDS-dementia complex. Here we investigated the role of peroxynitrite in apoptosis occurring in astroglial cells incubated with supernatants of HIV-infected human primary macrophages (M/M).     

Elliptic Equations with Degenerate Coercivity： Gradient Regularity

In this paper, we prove higher integrability results for the gradient of the solutions of some elliptic equations with degenerate coercivity whose prototype is where for example, a(x,u)=(1+|u|)^−θ with θ ∈ (0,1). We study the same problem for minima of functionals closely related to the previous equation.     

Femtosecond laser-induced damage of gold films

Single- and multi-shot ablation thresholds of gold films in the thickness range of 31-1400 nm were determined employing a Ti:sapphire laser delivering pulses of 28 fs duration, 793 nm center wavelength at 1 kHz repetition rate. The gold layers were deposited on BK7 glass by an electron beam evaporation process and characterized by atomic force microscopy and ellipsometry. A linear dependence of the ablation threshold fluence F_th on the layer thickness d was found for d ≤ 180 nm. If a film thickness of about 180 nm was reached, the damage threshold remained constant at its bulk value. For different numbers of pulses per spot (N-on-1), bulk damage thresholds of ∼0.7 J cm⁻² (1-on-1), 0.5 J cm⁻² (10-on-1), 0.4 J cm⁻² (100-on-1), 0.25 J cm⁻² (1000-on-1), and 0.2 J cm⁻² (10000-on-1) were obtained experimentally indicating an incubation behavior. A characteristic layer thickness of L_c ≈ 180 nm can be defined which is a measure for the heat penetration depth within the electron gas before electron-phonon relaxation occurs. L_c is by more than an order of magnitude larger than the optical absorption length of α⁻¹ ≈ 12 nm at 793 nm wavelength.