Chemiluminescent probe for the in vitro detection of protease activity

A strategy involving the use of a self-immolative linker has been investigated for the chemiluminescent sensing of proteases. The reactive linker enabled the release of a 1,2-dioxetane light precursor. As a proof of principle, caspase-3, a key peptidase involved in apoptosis has been targeted. An in vitro assay has been carried out and proved the decomposition of the linker and the selectivity for caspase-3.     

Alternative to consensus scoring--a new approach toward the qualitative combination of docking algorithms

Since the development of the first docking algorithm in the early 1980s a variety of different docking approaches and tools has been created in order to solve the docking problem. Subsequent studies have shown that the docking performance of most tools strongly depends on the considered target. Thus it is hard to choose the best algorithm in the situation at hand. The docking tools FlexX and AutoDock are among the most popular programs for docking flexible ligands into target proteins. Their analysis, comparison, and combination are the topics of this study. In contrast to standard consensus scoring techniques which integrate different scoring algorithms usually only by their rank, we focus on a more general approach. Our new combined docking workflow-AutoxX-unifies the interaction models of AutoDock and FlexX rather than combining the scores afterward which allows interpretability of the results. The performance of FlexX, AutoDock, and the combined algorithm AutoxX was evaluated on the basis of a test set of 204 structures from the Protein Data Bank (PDB). AutoDock and FlexX show a highly diverse redocking accuracy at the different complexes which assures again the usefulness of taking several docking algorithms into account. With the combined docking the number of complexes reproduced below an rmsd of 2.5 A could be raised by 10. AutoxX had a strong positive effect on several targets. The highest performance increase could be found when redocking 20 protein-ligand complexes of alpha-thrombin, plasmepsin, neuraminidase, and d-xylose isomerase. A decrease was found for gamma-chymotrypsin. The results show that--applied to the right target-AutoxX can improve the docking performance compared to AutoDock and FlexX alone.     

A food freshness sensor using the multistate response from analyte-induced aggregation of a cross-reactive poly(thiophene)

A single cross-reactive conjugated polymer generates a multidimensional response capable of identifying and differentiating between 22 structurally similar and biologically relevant amines with 97% accuracy in a highly competitive aqueous environment. Statistical analysis on an array of wavelengths was used to assess the viability of this approach. In a separate investigation, the multidimensional response from a single cross-responsive poly(thiophene) has been analyzed using a different ratiometric method to quantify the amount of biogenic amine present in a fish matrix, thereby evaluating the quality of the food.     

Cross sections for low-energy electron scattering from adenine in the condensed phase

Measurements of the vibrational and electronic excitation of a sub-monolayer up to a monolayer film of adenine were performed with a high resolution electron energy-loss (HREEL) spectrometer. The integral cross sections (over the half-space angle) for excitation of the normal vibrational modes of the ground electronic state and electronically excited states are calculated from the measured reflectivity EEL spectra. Most cross sections for vibrational excitation are of the order of 10(-17) cm(2), the largest being the out-of-plane wagging of the amino-group and the six-member ring deformations. A wide resonance feature appears in the incident energy dependence of the vibrational cross sections at 3-5 eV, while a weak shoulder is present in this dependence for combined ring deformations and bending of hydrogen atoms. For the five excited electronic states, at 4.7, 5.0, 5.5, 6.1 and 6.6 eV, the cross sections are of the order of 10(-18) cm(2), except in the case of the state at the energy of 6.1 eV, for which it is two to three times higher.     

Designed evolution of artificial metalloenzymes: protein catalysts made to order

Artificial metalloenzymes based on biotin-streptavidin technology, a "fusion" of chemistry and biology, illustrate how asymmetric catalysts can be improved and evolved using chemogenetic approaches.     

Unexpected formation of aryl ketones by palladium-catalyzed coupling of aryl bromides with vinylic acetates

A palladium-catalyzed coupling reaction of aryl bromides with vinylic acetates in the presence of tributyltin methoxide has been described. Unexpected formation of aryl ketones was obtained. Preliminary mechanistic studies indicated that the reaction proceeded by the addition of the aryl moiety in the coordination sphere of palladium to a ketene.     

Synthesis of pyridine-based polyaminocarboxylic ligands bearing a thioalkyl anchor

A bicyclic tetraazatriacetic chelating agent containing a thioalkyl pendant group was prepared. Four synthetic routes have been investigated via a Mitsunobu reaction from 2,4-[bishydroxymethyl]-3-hydroxy-pyridine 1. Deprotection of trityl thioether compound 5c led to ligand 6c in 22% overall yield from the starting 3-hydroxypyridine.