Anomeric modification of carbohydrates using the Mitsunobu reaction.

The Mitsunobu reaction basically consists in the conversion of an alcohol into an ester under inversion of configuration, employing a carboxylic acid and a pair of two auxiliary reagents, mostly triphenylphosphine and a dialkyl azodicarboxylate. This reaction has been frequently used in carbohydrate chemistry for the modification of sugar hydroxy groups. Modification at the anomeric position, leading mainly to anomeric esters or glycosides, is of particular importance in the glycosciences.

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.

Both metabolism and transport are key elements defining the bioavailability and biological activity of molecules, i.e. their adverse and therapeutic effects.

In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window.

In this study, two probabilistic machine-learning algorithms were compared for in silico target prediction of bioactive molecules, namely the well-established Laplacian-modified Naïve Bayes classifier (NB) and the more recently introduced (to Cheminformatics) Parzen-Rosenblatt Window. Both classifiers were trained in conjunction with circular fingerprints on a large data set of bioactive compounds extracted from ChEMBL, covering 894 human protein targets with more than 155,000 ligand-protein pairs. This data set is also provided as a benchmark data set for future target prediction methods due to its size as well as the number of bioactivity classes it contains.

How do metabolites differ from their parent molecules and how are they excreted?

Understanding which physicochemical properties, or property distributions, are favorable for successful design and development of drugs, nutritional supplements, cosmetics, and agrochemicals is of great importance. In this study we have analyzed molecules from three distinct chemical spaces (i) approved drugs, (ii) human metabolites, and (iii) traditional Chinese medicine (TCM) to investigate four aspects determining the disposition of small organic molecules. First, we examined the physicochemical properties of these three classes of molecules and identified characteristic features resulting from their distinctive biological functions.

In vitro bioavailability of iron from the heme analogue sodium iron chlorophyllin.

The use of heme analogues from vegetable origin could provide an alternative iron source of potentially high bioavailability. Sodium iron chlorophyllin is a water-soluble semisynthetic chlorophyll derivative where the magnesium in the porphyrin ring has been substituted by iron. We have used an in vitro model that combines gastric and intestinal digestion followed by intestinal iron uptake in Caco-2 cells to determine the bioavailability of iron from sodium iron chlorophyllin.

Modeling of the relationship between dipeptide structure and dipeptide stability, permeability, and ACE inhibitory activity.

Selected di- and tripeptides exhibit angiotensin-I converting enzyme (ACE) inhibitory activity in vitro. However, the efficacy in vivo is most likely limited for most peptides due to low bioavailability. The purpose of this study was to identify descriptors of intestinal stability, permeability, and ACE inhibitory activity of dipeptides.

In vitro models for processes involved in intestinal absorption.

The abundance of different techniques and protocols available reflects the need for reliable in vitro methods to assess intestinal absorption of potentially bioactive compounds. Physicochemical assays try to pinpoint the molecular properties contributing to the absorption process. The end points of biologically based methods, such as cell cultures and excised tissues, account for all processes undergone by a molecule that traverses a 'living' biological membrane, a cell or tissue.

Comparison of in vitro assays of cellular toxicity in the human hepatic cell line HepG2.

Cytotoxicity testing allows determining whether a compound or extract contains significant quantities of biologically harmful chemicals. Cytotoxicity test methods are useful for screening because they serve to separate toxic from nontoxic materials, providing predictive evidence of compound safety. However, a wide range of assays measuring different aspects of cell death is available in the market, but it is difficult to determine which one(s) to use when evaluating a selection of compounds.

Chemical synthesis of uridine diphospho-D-xylose and UDP-L-arabinose.

Leloir transferases, like UDP-d-xylosyl transferase and arabinosyl transferase, utilize nucleoside diphosphate sugars to build up plant oligo- and polysaccharides. By the described, scalable three-step synthesis a simple route is described to arrive at the respective enzyme substrates, which are otherwise difficult to obtain.

Evaluation of similarity measures for searching the dictionary of natural products database.

Similarity searches using combinations of seven different similarity coefficients and six different representations have been carried out on the Dictionary of Natural Products database. The objective was to discover if any special methods of searching apply to this database, which is very different in nature from the many synthetic databases that have been the subject of previous studies of similarity searching. Search effectiveness was assessed by a recall analysis of the search outputs from sets of pharmacologically active target structures.

Epoxidation of C-branched glycals: unexpected stereochemical results and their theoretical rationale.

This paper describes the synthesis of C-3 methyl-branched glycosides by epoxidation of partially unblocked L-configured glycals. The stereochemical result depends on the orientation of the allylic hydroxyl group. A theoretical explanation is presented, based on the conformational preferences of the respective glycal half-chair conformations that were estimated by applying the BP density functional and a valence triple-zeta basis set.