KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms

Bioorthogonal metal-free click-ligation of cRGD-pentapeptide to alginate

Click reactions have become very common and powerful ligation techniques, of which 1,3-dipolar cycloadditions have most frequently been employed. Since metal-mediated cycloadditions are incompatible in biomedical applications due to toxicity issues associated with transition metals like copper, metal-free variants provide important alternatives. The metal-free conjugation process is studied in detail with special emphasis put on the reaction progress. This report unfolds the first aqueous metal-free "click" conjugation of a cyclic RGD-pentapeptide with the biomacromolecule alginate, creating a "smart" bioactive polymer with potential applications in biomedicine. © 2012 The Royal Society of Chemistry

JSBML: a flexible Java library for working with SBML

The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend

Oxidative azidations of phenols and ketones using iodine azide after release from an ion exchange resin

The oxidative oligoazidation of phenols and ketones using iodine azide (IN3) provided by its release from an ion exchange resin is reported. Preliminary mechanistic studies indicate a previously unknown reactivity of iodine azide toward phenols and ketones. © The Royal Society of Chemistry 2021

Photochemical Transformations with Iodine Azide after Release from an Ion-Exchange Resin

This report discloses the photochemical homolytic cleavage of iodine azide after its formation following release from polymer-bound bisazido iodate(I) anions. A series of radical reactions are reported including the 1,2-functionlization of alkenes and the unprecedented chemoselective oxidation of secondary alcohols in the presence of primary alcohols

Novel double functional protection of cephalostatin analogues using a gas-free chlorination method

Herewith, we report on a method that allows to simultaneously protect both the ∆14,15 bond and the carbonyl group of the symmetrical bis-steroidal diketone 2. We found that environmentally friendly and gas-free chlorination is ideally suited to achieve this goal. This method was discovered during our efforts to methoxylate 2 in a solution of dichloromethane and basic methanol in the presence of diacetoxy iodobenzene. Unexpectedly, the ∆14,15 bonds were chlorinated once as well as twice in a statistical manner. Interestingly, the singly dichlorinated desymmetrized product is an ideal precursor for conduction a series of position selective transformations. Importantly, the carbonyl group present in the nonchlorinated hemisphere can be selectively reduced, olefinated or oximated, while the other carbonyl group stays unaltered. A structurally related “monomeric” steroid derivative undergoes ∆14,15 chlorination and 11-position methoxylation under same conditions. These findings represent a powerful entry for preparing new nonsymmetrical cephalostatin derivatives. © 201

A practical synthesis of Rho-Kinase inhibitor Y-27632 and fluoro derivatives and their evaluation in human pluripotent stem cells

A practical synthesis of the Rho-Kinase inhibitor Y-27632 and two new fluoro derivatives was achieved in seven steps and with a good overall yield of 45% starting from commercially available (R)-1-phenylethylamine. Compared to Y-27632 the new fluoro derivatives showed reduced or no effect on hPSC vitality and expansion after dissociation in human pluripotent stem cells. © 2011 The Royal Society of Chemistry