A global metabolite profiling approach to identify protein-metabolite interactions

Understanding the biochemical functions of proteins is an important factor in elucidating their cellular and physiological functions. Due to the predominance of biopolymer interactions in biology, many methods have been designed to interrogate and identify biologically relevant interactions that proteins make to DNA, RNA, and other proteins. Complementary approaches that can elucidate binding interactions between proteins and small molecule metabolites will impact the understanding of protein-metabolite interactions and fill a need that is outside the scope of current methods. Here, we demonstrate the ability to identify natural protein-metabolite interactions from complex metabolite mixtures by combining a protein-mediated small molecule enrichment step with a global metabolite profiling platform.     

Genetic and genomic approaches to identify and study the targets of bioactive small molecules

Natural and synthetic bioactive small molecules form the backbone of modern therapeutics. These drugs primarily exert their effect by targeting cellular host or foreign proteins that are critical for the progression of disease. Therefore, a crucial step in the process of recognizing valuable new drug leads is identification of their protein targets; this is often a time consuming and difficult task. This report is intended to provide a comprehensive review of recent developments in genetic and genomic approaches to overcome the hurdle of discovering the protein targets of bioactive small molecules.     

Approaches to dihydrooxazine ring systems and application in the synthesis of bioactive natural products

This review describes selected approaches to the synthesis of 4H-5,6-dihydro-1,2-oxazines and application of these methods to the synthesis of natural products containing this heterocyclic ring system. The focus is on applications and on interesting aspects of chemistry related to this subclass of natural products, as well as newer methods for the synthesis of oxazines.     

An elastic network model to identify characteristic stress response genes

Exposing eukaryotic cells to a toxic compound and subsequent gene expression profiling may allow the prediction of selected toxic effects based on changes in gene expression. This objective is complicated by the observation that compounds with different modes of toxicity cause similar changes in gene expression and that a global stress response affects many genes. We developed an elastic network model of global stress response with nodes representing genes which are connected by edges of graded coexpression. The expression of only few genes have to be known to model the global stress response of all but a few atypical responder genes. Those required genes and the atypical response genes are shown to be good biomarker for tox predictions. In total, 138 experiments and 13 different compounds were used to train models for different toxicity classes. The deduced biomarkers were shown to be biologically plausible. A neural network was trained to predict the toxic effects of compounds from profiling experiments. On a validation data set of 189 experiments with 16 different compounds the accuracy of the predictions was assessed: 14 out of 16 compounds have been classified correctly. Derivation of model based biomarkers through the elastic network approach can naturally be extended to other areas beyond toxicology since subtle signals against a broad response background are common in biological studies.     

Metabolic diversity of lichen-forming ascomycetous fungi: culturing, polyketide and shikimate metabolite production, and PKS genes

Lichens are composite and symbiotic organisms. Biologically, they often have been interpreted as one organism (fungi and algae associated within a common thallus), but taxonomically as a life form of ascomycetous fungi; as the lichen-forming fungus or "mycobiont" has been, in most cases, classified as the dominant symbiotic partner. About 46% of the ascomycota are lichen-forming, however, about 2-3% of the lichen fungi are basidiomycota. Lichen-forming fungi produce a great variety of secondary metabolites, biosynthetically derived from the acetyl polymalonyl, mevalonic and shikimate pathways. Thus, secondary metabolites comprise a significant proportion of the lichen thallus dry weight (0.1-5% or even more). The majority of secondary lichen products are aromatic polyketides, and a number of them has been shown to exhibit marked biological activity.     

Ultrasound-assisted conversion of toxic beta-asarone into nontoxic bioactive phenylpropanoid: isoacoramone, a metabolite of Piper marginatum and Acorus tararinowii

Ultrasound-assisted synthesis of bioactive isoacoramone (1), a metabolite of Piper marginatum and Acorus tararinowii, has been achieved by oxidation of toxic beta-asarone (2) with potassium permanganate/copper sulphate/alumina into asaronaldehyde (3) followed by treatment with ethylmagnesium iodide to provide 1-(2,4,5-trimethoxy)phenyl-1-propanol (4) which upon further oxidation with potassium permanganate/copper sulphate afforded 1 in 64% yield (overall 32%). Toxicological evaluation of 1 reveals it to be nontoxic up to 60 mg/kg b.w.     

Tissue distribution of capilliposide B,capilliposide C and their bioactive metabolite in mice using liquid ‐tandem mass spectrometry

Lysimachia capillipes Hemsl (Primulaceae), a folk medicinal plant in China, showed significant anti‐tumor activities in vivo and in vitro . Capilliposide B (LC‐B) and capilliposide C (LC‐C) are the main bioactive components in this plant. To explore their tissue distribution, a reliable bioanalytical method for the quantification of LC‐B, LC‐C and their bioactive metabolite, capilliposide A (LC‐A), in mouse tissues was developed and validated. In this study, the tissue distribution profiles of the three compounds were examined after intravenous administration of pure LC‐B and oral administration of total saponins of L. capillipes Hemsl extract (LCE) for 10 days. Method validation was conducted over the curve range 10.0–5000 ng/mL for all three analytes in various tissue homogenates. The relative standard deviation of intra‐day and inter‐day precision of the QC samples was <14.7%, and the accuracy ranged from 85.9 to 114.0%. The results indicated that LC‐B was rapidly and widely distributed throughout the whole body except for muscle following intravenous administration of LC‐B. In addition, LC‐A was only in liver, intestine, lung and stomach. After oral administration of LCE, LC‐B and LC‐C were distributed into various tissues. The highest levels were observed in stomach and intestine.     

The detection of androstenedione abuse in sport: a mass spectrometry strategy to identify the 4‐hydroxyandrostenedione metabolite

Studies have shown that the administration of androstenedione (ADIONE) significantly increases the urinary ratio of testosterone glucuronide to epitestosterone glucuronide (T/E) – measured by gas chromatography/mass spectrometry (GC/MS) – in subjects with a normal (≈1) or naturally high (>1) initial values. However, the urinary T/E ratio has been shown not to increase in subjects with naturally low (<1) initial values. Such cases then rely on the detection of C₆‐hydroxylated metabolites shown to be indicative of ADIONE administration. While these markers may be measured in the routine GC/MS steroid profile, their relatively low urinary excretion limits the use of gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) to specifically confirm ADIONE administration based on depleted ¹³C content. A mass spectrometry strategy was used in this study to identify metabolites of ADIONE with the potential to provide compound‐specific detection. C₄‐hydroxylation was subsequently shown to be a major metabolic pathway following ADIONE administration, thereby resulting in urinary excretion of 4‐hydroxyandrostenedione (4OH‐ADIONE). Complementary analysis of 4OH‐ADIONE by GC/MS and GC/C/IRMS was used to confirm ADIONE administration. Copyright © 2008 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.     

The first total synthesis of a bioactive metabolite, a spirobenzofuran isolated from the fungi Acremonium sp. HKI 0230

The first total synthesis of a bioactive metabolite, isolated from the fungi Acremonium sp. HKI 0230, containing a cyclopentaspirobenzofuran carbon framework, employing an Ireland ester Claisen rearrangement and RCM reaction based strategy has been accomplished.     

Bowls,Hoops, and Saddles: Synthetic Approaches to Curved Aromatic Molecules

This review summarizes recent advances in the chemistry of curved aromatic molecules. By focusing on the key accomplishments of the last decade, we provide a general overview of synthetic methods capable of efficient induction of internal strain in π‐conjugated frameworks. The review is structured according to the topology change involved in the strain‐inducing reaction step (cyclizations, eliminations, ring expansions and contractions), and highlights the striking diversity of structures achievable with modern synthetic methodology.     

Electrochemistry of organic,bioactive compounds and biopolymers

Monatshefte für Chemie - Chemical Monthly -     

Approaches to hydration, old and new: Insights through Hofmeister effects

Hydration effects in colloidal interactions or problems involving electrolytes are usually taken care of by effective electrostatic potentials that subsume notions like hydrated ion size, Gurney potentials, soft and hard, chaotropic and cosmotropic ions, and inner and outer Helmholtz planes. Quantum fluctuation (dispersion) forces between ions and between ions and surfaces are missing from classical theories, at least not explicit in standard approaches to hydration. This paper outlines an evolving back-to-basics approach that allows these ion specific forces to be included in theories quantitatively. In this approach ab initio quantum mechanics is used to calculate dynamic polarisabilities of ions and to quantify bare ion radii. The ionic dispersion potentials between ions, and between ions and surfaces in water can then be given explicit analytic form from an extension of Lifshitz theory. They are included in the theory along with electrostatic potentials. In a first stage the primitive (continuum solvent) model provides a skeletal theory on which to build in hydration. Extension of the ab initio calculations to include “dressed” ions, i.e. water hydration shells for cosmotropic ions, quadrupolar and octupolar polarisability contributions and; for colloids, allowance for a surface hydration layer, permits quantification of Hofmeister effects and Gurney potentials. With these extensions, primary hydration forces (short range repulsion) arise due to an interplay between surface hydration layers and specific ion interactions. Apparent longer range “secondary hydration forces” are shown to be a consequence of ion-surface dispersion interactions and are not true “hydration forces”.     

Speciation and biosynthetic variation in four dictyoceratid sponges and their cyanobacterial symbiont, Oscillatoria spongeliae

Four species of marine sponges (Phylum Porifera, Order Dictyoceratida), which contain the filamentous cyanobacterial symbiont Oscillatoria spongeliae, were collected from four locations in Palau. The halogenated natural products associated with the symbiont were characterized from each sample, revealing that each species contained either chlorinated peptides, brominated diphenyl ethers, or no halogenated compounds. Analysis of the host sponges and the symbionts indicated that each species of sponge contained a distinct strain of morphologically similar cyanobacteria. Although cospeciation may be present in this group, we have identified that at least one host switching event has occurred in this symbiosis. Only the strain of O. spongeliae in the sponge containing the chlorinated compounds possessed genes involved in the biosynthesis of chlorinated leucine precursors, indicating that the chemical variation observed in these animals has a genetic foundation.     

Approaches to polymer superlattice and molecular device

Approaches to polymer superlattice and molecular devices are shown, demonstrating with functional molecule material by incorporation of a functional molecule into the conducting polymer, conjugating copolymer superlattice by a novel potential programmed electro polymerization, ultrahigh anisotropic conductive LB heterolayers, and porphyrin arrays connected with conducting molecular wire and insulating molecular wire. These results show a practical method to fabricate ultimate functional materials such as molecular device which is the smallest functional material, and quantum functional material which creates a novel nature.     

Enantioselective synthesis of (3R,4E)-19-methylicos-4-en-1-yn-3-ol,a bioactive metabolite of the marine sponge Cribrochalina vasculum

The first stereoselective synthesis of (3R,4E)-19-methylicos-4-en-1-yn-3-ol, an immunosuppressive and antitumoral metabolite isolated from the Caribbean sponge Cribrochalina vasculum, has been achieved and its stereostructure has been confirmed. The key step of the synthesis involves a borane-mediated reduction of the parent (E)-19-methyl-1-trimethylsilylicos-4-en-1-yn-3-one in the presence of a chiral oxazaborolidine.     

Leucascandrolide A,a New Type of Macrolide: The first powerfully bioactive metabolite of calcareous sponges (Leucascandra caveolata,a new genus from the coral sea)

Leucascandrolide A ((+)- 1 ), a doubly O-bridged 18-membered macrolide of a new type, i.e., showing little C₁-branching vs. extensive 1,3-dioxygenation and a peculiar side chain, was isolated from a calcareous sponge of a new genus, Leucascandra caveolata BOROJEVIC and KLAUTAU from the Coral Sea. Transesterification of (+)- 1 gave the methyl ester 3 , derived from the side chain, and the 5-hydroxy derivative (+)- 2 , derived from the macrolide portion and with the natural configuration at C(5) (axial). Mosher's MTPA esters 4 and 5 obtained from (+)- 2 showed scattered Δδ = (δ(S) ? δ(R)) data. However, inversion of the configuration at C(5) led, via ketone (+)- 6 , to the less encumbered 5-equatorial hydroxy derivative (+)- 7 , whose MTPA esters 8 and 9 gave consistent Δδ data, allowing the assignment of the absolute configuration of (+)- 7 , and hence of (+)- 1 . The structural novelty of (+)- 1 and its powerful antifungal and cytotoxic activities are likely to renew interest in calcareous sponges, previously limited to scarcely biologically active 2-aminoimidazoles.     

A novel approach to tag and identify geranylgeranylated proteins

A recently developed proteomic strategy, the “GG‐azide”‐labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido‐geranylgeranyl analog and chemoselective derivatization of azido‐geranylgeranyl‐modified proteins by the “click” chemistry, using a tetramethylrhodamine‐alkyne. The resulting conjugated proteins can be separated by 1‐D or 2‐D and pH fractionation, and detected by fluorescence imaging. This method is compatible with downstream LC‐MS/MS analysis. Proteomic analysis of conjugated proteins by this approach identified several known geranylgeranylated proteins as well as Rap2c, a novel member of the Ras family. Furthermore, prenylation of progerin in mouse embryonic fibroblast cells was examined using this approach, demonstrating that this strategy can be used to study prenylation of specific proteins. The “GG‐azide”‐labeling approach provides a new tool for the detection and proteomic analysis of geranylgeranylated proteins, and it can readily be extended to other post‐translational modifications.     

Stereoselective syntheses of the bioactive polypropionates aureothin, N-acetylaureothamine, and aureonitrile

[reaction: see text] Concise total syntheses of the bioactive polypropionates aureothin, N-acetylaureothamine, and aureonitrile are described.     

Design, synthesis, and validation of rigid linkers for bioactive peptides

Rigid linkers of variable length were synthesized and used to connect two NDP-α-MSH ligands. The linkers were incorporated by solid-phase synthesis. Biological evaluations indicate that there is virtually no effect of these linkers on ligand binding to the human melanocortin 4 receptor.