The development of new drugs will certainly benefit from an ever improving knowledge of the living beings chemistry. However, identification of drugable molecules within the immense biodiversity of forests, soils or oceans still requires considerable investments in technical equipments, time and human resources. An important part of this process is the quick identification of known substances in order to concentrate the efforts on the discovery of new ones. A range of "dereplication" procedures are currently emerging to meet this challenge as key strategies to improve the performance of natural product screening programs. Initially defined in 1990 as "a process of quickly identifying known chemotypes", dereplication is today a not so univocal concept and has evolved over the last years in different ways. The present review covers all dereplication-related sudies in natural product research from 1990 to 2014.Its writing brought to light five distinct dereplication workflows that can be characterized by the nature of starting materials, by the key analytical technique, and above all by the final objective. Dereplication can be used as an untargeted workflow for the rapid identification of the major compounds whatever their chemical class in a single sample or for the acceleration of bioactivity-guided fractionation procedures. In other cases dereplication is fully integrated in metabolomic studies for the untargeted chemical profiling of natural extract collections or for the targeted identification of a predetermined class of metabolites. Finally a quite distinct dereplication approach mainly based on gene-sequence analyses is frequently used for the taxonomic identification of microbial strains.

A large variety of phytochemicals commonly consumed with the human diet, influence health and may contribute to the prevention of diseases. However, it is still difficult to make nutritional recommendations for these bioactive compounds. Current studies of phytochemicals are generally focused on specific compounds and their effects on a limited number of markers. New approaches are needed to take into account both the diversity of phytochemicals found in the diet and the complexity of their biological effects. Recent progress in high-throughput analytical technologies and in bioinformatics now allows the simultaneous analysis of the hundreds or more metabolites constituting the metabolome in urine or plasma. These analyses give complex metabolic fingerprints characteristic of a given phenotype. The exploitation of the wealth of information it contains, in randomized controlled trials and cohort studies, should lead to the discovery of new markers of intake for phytochemicals and new markers of effects. In this paper, we briefly review the current methods used to evaluate intake of phytochemicals and their effects on health. We then describe the applications of metabolomics in this field. Recent metabolomics studies illustrate the potential of such a global approach to explore the complex relationships linking phytochemical intake and metabolism and health.

Elucidation of the relationships between genotype, diet, and health requires accurate dietary assessment. In intervention and epidemiological studies, dietary assessment usually relies on questionnaires, which are susceptible to recall bias. An alternative approach is to quantify biomarkers of intake in biofluids, but few such markers have been validated so far. Here we describe the use of metabolomics for the discovery of nutritional biomarkers, using citrus fruits as a case study. Three study designs were compared. Urinary metabolomes were profiled for volunteers that had (a) consumed an acute dose of orange or grapefruit juice, (b) consumed orange juice regularly for one month, and (c) reported high or low consumption of citrus products for a large cohort study. Some signals were found to reflect citrus consumption in all three studies. Proline betaine and flavanone glucuronides were identified as known biomarkers, but various other biomarkers were revealed. Further, many signals that increased after citrus intake in the acute study were not sensitive enough to discriminate high and low citrus consumers in the cohort study. We propose that urine profiling of cohort subjects stratified by consumption is an effective strategy for discovery of sensitive biomarkers of consumption for a wide range of foods.

These data confirm the value of certain urinary polyphenols as biomarkers of intake. A validation in populations is now needed to evaluate their specificity, sensitivity, and responsiveness to dose under free-living conditions.

Trypanosoma brucei is a parasitic protist that undergoes a complex life cycle during transmission from its mammalian host (bloodstream forms) to the midgut of its insect vector (procyclic form). In both parasitic forms, most glycolytic steps take place within specialized peroxisomes, called glycosomes. Here, we studied metabolic adaptations in procyclic trypanosome mutants affected in their maintenance of the glycosomal redox balance. T. brucei can theoretically use three strategies to maintain the glycosomal NAD ؉ /NADH balance as follows: (i) the glycosomal succinic fermentation branch; (ii) the glycerol 3-phosphate (Gly-3-P)/dihydroxyacetone phosphate (DHAP) shuttle that transfers reducing equivalents to the mitochondrion; and (iii) the glycosomal glycerol production pathway. We showed a hierarchy in the use of these glycosomal NADH-consuming pathways by determining metabolic perturbations and adaptations in single and double mutant cell lines using a combination of NMR, ion chromatography-MS/MS, and HPLC approaches. Although functional, the Gly-3-P/DHAP shuttle is primarily used when the preferred succinate fermentation pathway is abolished in the ⌬pepck knock-out mutant cell line. In the absence of these two pathways (⌬pepck/ RNAi FAD-GPDH.i mutant), glycerol production is used but with a 16-fold reduced glycolytic flux. In addition, the ⌬pepck mutant cell line shows a 3.3-fold reduced glycolytic flux compensated by an increase of proline metabolism. The inability of the ⌬pepck mutant to maintain a high glycolytic flux demonstrates that the Gly-3-P/DHAP shuttle is not adapted to the procyclic trypanosome context. In contrast, this shuttle was shown earlier to be the only way used by the bloodstream forms of T. brucei to sustain their high glycolytic flux.

Because of their highly complex metabolite profile, the chemical characterization of bioactive natural extracts usually requires time-consuming multistep purification procedures to achieve the structural elucidation of pure individual metabolites. The aim of the present work was to develop a dereplication strategy for the identification of natural metabolites directly within mixtures. Exploiting the polarity range of metabolites, the principle was to rapidly fractionate a multigram quantity of a crude extract by centrifugal partition extraction (CPE). The obtained fractions of simplified chemical composition were subsequently analyzed by (13)C NMR. After automatic collection and alignment of (13)C signals across spectra, hierarchical clustering analysis (HCA) was performed for pattern recognition. As a result, strong correlations between (13)C signals of a single structure within the mixtures of the fraction series were visualized as chemical shift clusters. Each cluster was finally assigned to a molecular structure with the help of a locally built (13)C NMR chemical shift database. The proof of principle of this strategy was achieved on a simple model mixture of commercially available plant secondary metabolites and then applied to a bark extract of the African tree Anogeissus leiocarpus Guill. & Perr. (Combretaceae). Starting from 5 g of this genuine extract, the fraction series was generated by CPE in only 95 min. (13)C NMR analyses of all fractions followed by pattern recognition of (13)C chemical shifts resulted in the unambiguous identification of seven major compounds, namely, sericoside, trachelosperogenin E, ellagic acid, an epimer mixture of (+)-gallocatechin and (-)-epigallocatechin, 3,3'-di-O-methylellagic acid 4'-O-xylopyranoside, and 3,4,3'-tri-O-methylflavellagic acid 4'-O-glucopyranoside.

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Plant resistance to phytopathogenic microorganisms mainly relies on the activation of an innate immune response usually launched after recognition by the plant cells of microbe-associated molecular patterns. The plant hormones, salicylic acid (SA), jasmonic acid, and ethylene have emerged as key players in the signaling networks involved in plant immunity. Rhamnolipids (RLs) are glycolipids produced by bacteria and are involved in surface motility and biofilm development. Here we report that RLs trigger an immune response in Arabidopsis (Arabidopsis thaliana) characterized by signaling molecules accumulation and defense gene activation. This immune response participates to resistance against the hemibiotrophic bacterium Pseudomonas syringae pv tomato, the biotrophic oomycete Hyaloperonospora arabidopsidis, and the necrotrophic fungus Botrytis cinerea. We show that RL-mediated resistance involves different signaling pathways that depend on the type of pathogen. Ethylene is involved in RL-induced resistance to H. arabidopsidis and to P. syringae pv tomato whereas jasmonic acid is essential for the resistance to B. cinerea. SA participates to the restriction of all pathogens. We also show evidence that SA-dependent plant defenses are potentiated by RLs following challenge by B. cinerea or P. syringae pv tomato. These results highlight a central role for SA in RL-mediated resistance. In addition to the activation of plant defense responses, antimicrobial properties of RLs are thought to participate in the protection against the fungus and the oomycete. Our data highlight the intricate mechanisms involved in plant protection triggered by a new type of molecule that can be perceived by plant cells and that can also act directly onto pathogens.