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. Therefore, this review focuses on the use of the Mitsunobu reaction for modifications of sugar hemiacetals. Strikingly, unprotected sugars can often be converted regioselectively at the anomeric center, whereas in other cases, the other hydroxy groups in reducing sugars have to be protected to achieve good results in the Mitsunobu procedure. We have reviewed on the one hand the literature on anomeric esterification, including glycosyl phosphates, and on the other hand glycoside synthesis, including S- and N-glycosides. The mechanistic details of the Mitsunobu reaction are discussed as well as this is important to explain and predict the stereoselectivity of anomeric modifications under Mitsunobu conditions. Though the Mitsunobu reaction is often not the first choice for the anomeric modification of carbohydrates, this review shows the high value of the reaction in many different circumstances.

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. In addition to evaluating the methods, different performance measures were explored. This is not as straightforward as in binary classification settings, due to the number of classes, the possibility of multiple class memberships, and the need to translate model scores into "yes/no" predictions for assessing model performance. Both algorithms achieved a recall of correct targets that exceeds 80% in the top 1% of predictions. Performance depends significantly on the underlying diversity and size of a given class of bioactive compounds, with small classes and low structural similarity affecting both algorithms to different degrees. When tested on an external test set extracted from WOMBAT covering more than 500 targets by excluding all compounds with Tanimoto similarity above 0.8 to compounds from the ChEMBL data set, the current methodologies achieved a recall of 63.3% and 66.6% among the top 1% for Naïve Bayes and Parzen-Rosenblatt Window, respectively. While those numbers seem to indicate lower performance, they are also more realistic for settings where protein targets need to be established for novel chemical substances.

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. For example, human metabolites and TCM molecules can be larger and more hydrophobic than drugs, which makes them less likely to cross membranes. We then quantified the shifts in physicochemical property space induced by metabolism from a holistic perspective by analyzing a data set of several thousand experimentally observed metabolic trees. Results show how the metabolic system aims to retain nutrients/micronutrients while facilitating a rapid elimination of xenobiotics. In the third part we compared these global shifts with the contributions made by individual metabolic reactions. For better resolution, all reactions were classified into phase I and phase II biotransformations. Interestingly, not all metabolic reactions lead to more hydrophilic molecules. We were able to identify biotransformations leading to an increase of logP by more than one log unit, which could be used for the design of drugs with enhanced efficacy. The study closes with the analysis of the physicochemical properties of metabolites found in the bile, faeces, and urine. Metabolites in the bile can be large and are often negatively charged. Molecules with molecular weight >500 Da are rarely found in the urine, and most of these large molecules are charged phase II conjugates.

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. On top of fundamental physical processes (e.g., solubility, diffusion) such biological methods incorporate physiological responses such as active transport and metabolism. In this review, an account of in vitro methods for the assessment of molecular properties (lipophilicity, solubility, permeability) influencing intestinal absorption is given. Their advantages and limitations and the possibilities offered by this area of research are also evaluated. The combination of results from both classes of assays (physicochemical and biological) and integration with computational models will guide future developments in this field. Finally, possible future developments including stem cell research and multiple-end point assays are discussed.

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. The objective of this study was to compare different commercially available in vitro assays for cytotoxicity in HepG2 cells according to its sensitivity, reproducibility, simplicity, cost, and speed. The assays evaluated included Alamar Blue for the measurement of mitochondrial activity, ATPlite and ViaLight for the determination of cellular adenosine triphosphate (ATP), ToxiLight as an indicator of cellular necrosis, and Caspase-3 Fluorometric Assay, Apo-ONE Caspase-3/7 Homogeneous Assay, and Caspase-Glo for the determination of caspase-3/7 activity. All assays were performed using 4 compounds of previously reported cytotoxic activity: DMSO, butyric acid, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), and camptothecine. Overall, it was concluded that the best way to evaluate the potential cytotoxicity of a compound is to employ a battery of assays that focus on different aspects of cell death. In this case, the focus has been on ATP levels, cell necrosis, and capsase-3/7 activation. Many other kits are commercially available in the market for these and other aspects of necrosis and/or apoptosis. However, the use of ViaLight Plus, ToxiLight, and Caspase-3 Fluorometric Assay resulted in the most useful combination when working with HepG2 cells.

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

ABSTRACT: Both metabolism and transport are key elements defining the bioavailability and biological activity of molecules, i.e. their adverse and therapeutic effects. Structured and high quality experimental data stored in a suitable container, such as a relational database, facilitates easy computational processing and thus allows for high quality information/knowledge to be efficiently inferred by computational analyses. Our aim was to create a freely accessible database that would provide easy access to data describing interactions between proteins involved in transport and xenobiotic metabolism and their small molecule substrates and modulators. We present Metrabase, an integrated cheminformatics and bioinformatics resource containing curated data related to human transport and metabolism of chemical compounds. Its primary content includes over 11,500 interaction records involving nearly 3,500 small molecule substrates and modulators of transport proteins and, currently to a much smaller extent, cytochrome P450 enzymes. Data was manually extracted from the published literature and supplemented with data integrated from other available resources. Metrabase version 1.0 is freely available under a CC BY-SA 4.0 license at http://www-metrabase.ch.cam.ac.uk.

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.

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. Our results demonstrate that sodium iron chlorophyllin is stable under simulated gastrointestinal conditions and is able to deliver bioavailable iron to Caco-2 cells. Similar to the heme, the bioavailability of iron from sodium iron chlorophyllin is dependent on the food matrix, and it was inhibited by calcium. Potentially, sodium iron chlorophyllin could be used as an iron fortificant from vegetable origin with high bioavailability.

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. A total of 228 dipeptides were synthesized; intestinal stability was obtained by in vitro digestion, intestinal permeability using Caco-2 cells and ACE inhibitory activity by an in vitro assay. Databases were constructed to study the relationship between structure and activity, permeability, and stability. Quantitative structure-activity relationship (QSAR) modeling was performed based on computed models using partial least squares regression based on 400 molecular descriptors. QSAR modeling of dipeptide stability revealed high correlation coefficients (R > 0.65) for models based on Z and X scales. However, amino acid (AA) clustering showed the best results in describing stability of dipeptides. The N-terminal AA residues Asp, Gly, and Pro as well as the C-terminal residues Pro, Ser, Thr, and Asp stabilize dipeptides toward luminal enzymatic peptide hydrolysis. QSAR modeling did not reveal significant correlation models for intestinal permeability. 2D-fingerprint models were identified describing ACE inhibitory activity of dipeptides. The intestinal stability of 12 peptides was predicted. Peptides were synthesized and stability was confirmed in simulated digestion experiments. Based on the results, specific dipeptides can be designed to meet both stability and activity criteria. However, postabsorptive ACE inhibitory activities of dipeptides in vivo are most likely limited due to the very low intestinal permeability of dipeptides.

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. The different target sets produce exceptional but contradictory results for the Russell-Rao and Forbes coefficients, which have been shown to be due to a dependence on molecular size; these are the coefficients of choice in the case of large and small structures, respectively. Rankings from these results have been combined using a data fusion scheme and some small gains in performance were normally obtained by using substructural fingerprints and molecular holograms in combination with the Squared Euclidean or Tanimoto coefficients.