Samuel Bertrand

Current approaches and challenges for the metabolite profiling of complex natural extracts.

Metabolite profiling is critical in many aspects of the life sciences, particularly natural product research. Obtaining precise information on the chemical composition of complex natural extracts (metabolomes) that are primarily obtained from plants or microorganisms is a challenging task that requires sophisticated, advanced analytical methods. In this respect, significant advances in hyphenated chromatographic techniques (LC-MS, GC-MS and LC-NMR in particular), as well as data mining and processing methods, have occurred over the last decade. Together, these tools, in combination with bioassay profiling methods, serve an important role in metabolomics for the purposes of both peak annotation and dereplication in natural product research. In this review, a survey of the techniques that are used for generic and comprehensive profiling of secondary metabolites in natural extracts is provided. The various approaches (chromatographic methods: LC-MS, GC-MS, and LC-NMR and direct spectroscopic methods: NMR and DIMS) are discussed with respect to their resolution and sensitivity for extract profiling. In addition the structural information that can be generated through these techniques or in combination, is compared in relation to the identification of metabolites in complex mixtures. Analytical strategies with applications to natural extracts and novel methods that have strong potential, regardless of how often they are used, are discussed with respect to their potential applications and future trends.

Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery

Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.

De Novo Production of Metabolites by Fungal Co-culture of Trichophyton rubrum and Bionectria ochroleuca

The co-cultivation of fungi has recently been described as a promising strategy to induce the production of novel metabolites through possible gene activation. A large screening of fungal co-cultures in solid media has identified an unusual long-distance growth inhibition between Trichophyton rubrum and Bionectria ochroleuca. To study metabolite induction in this particular fungal interaction, differential LC-MS-based metabolomics was performed on pure strain cultures and on their co-cultures. The comparison of the resulting fingerprints highlighted five de novo induced compounds, which were purified using software-oriented semipreparative HPLC-MS. One metabolite was successfully identified as 4″-hydroxysulfoxy-2,2″-dimethylthielavin P (a substituted trimer of 3,5-dimethylorsellinic acid). The nonsulfated form, as well as three other related compounds, were found in the pure strain culture of B. ochroleuca.

Detection of metabolite induction in fungal co-cultures on solid media by high-throughput differential ultra-high pressure liquid chromatography–time-of-flight mass spectrometry fingerprinting

Access to new biological sources is a key element of natural product research. A particularly large number of biologically active molecules have been found to originate from microorganisms. Very recently, the use of fungal co-culture to activate the silent genes involved in metabolite biosynthesis was found to be a successful method for the induction of new compounds. However, the detection and identification of the induced metabolites in the confrontation zone where fungi interact remain very challenging. To tackle this issue, a high-throughput UHPLC-TOF-MS-based metabolomic approach has been developed for the screening of fungal co-cultures in solid media at the petri dish level. The metabolites that were overexpressed because of fungal interactions were highlighted by comparing the LC-MS data obtained from the co-cultures and their corresponding mono-cultures. This comparison was achieved by subjecting automatically generated peak lists to statistical treatments. This strategy has been applied to more than 600 co-culture experiments that mainly involved fungal strains from the Fusarium genera, although experiments were also completed with a selection of several other filamentous fungi. This strategy was found to provide satisfactory repeatability and was used to detect the biomarkers of fungal induction in a large panel of filamentous fungi. This study demonstrates that co-culture results in consistent induction of potentially new metabolites.

Hydroxamate, a key pharmacophore exhibiting a wide range of biological activities

Naturally occurring hydroxamic acid derivatives are biosynthesized by microorganisms (siderophores) and plants (benzoxazinoids). Recent developments in drug discovery have highlighted the numerous biological and pharmacological properties that the hydroxamic acid function may possess, leading to therapeutic applications. These properties may be explained by its ability to chelate metals via the presence of two oxygen atoms. Their pharmacological activities can be divided into three groups. The first concerns the ability of these hydroxamic acid derivatives to scavenge metals (particularly iron), which leads to antioxidant, antimicrobial and metal detoxification activities. The latter is largely used to treat iron overload in patients. The second group of activities is related to their ability to inhibit metallo-enzymes, which gives them a wide range of pharmacological effects: antimicrobial, anti-inflammatory and antitumor. The third group is linked to the capacity of these compounds to generate nitric oxide, which confers hypotensive activity. However, hydroxamates exhibit relatively low stability in vivo, which can be overcome by the synthesis of appropriately designed analogs. For this purpose, many different strategies have been proposed. In this review, we compare and discuss the various synthetic pathways used to obtain the most complex of them, the N-substituted hydroxamic acids. We conclude that among numerous protocols reported so far, the direct N-substitution of hydroxamic acids, the acylation of the appropriate N-O derivative and the direct oxidation of the corresponding amide allow for the synthesis of a wide range of new biologically active compounds.

Acylated pregnane glycosides from Caralluma sinaica.

Caralluma sinaica is sold on local markets of Saudi Arabia for various health benefits however no phytochemical study has specifically been performed on this species. NMR and UHPLC-ESI-TOF-MS profilings of the ethanolic extract of the whole plant reveal a very complex phytochemical composition dominated by pregnanes. Detailed information on its constituents was obtained after isolation. Six pregnane glycosides were obtained and characterized based on the extensive spectroscopic analysis (including IR, ¹H NMR, ¹³C NMR and MS data), in addition to ten known compounds (seven pregnanes and three flavonoids). The compounds were identified as 12β-O-benzoyl-20-O-acetyl boucerin-3-O-6-deoxy-3-O-methyl-β-D-glucopyranosyl-(1-->4)-β-D-cymaropyranosyl-(1-->4)-β-D-cymaropyranoside, 12β-O-tigloyl-20-O-acetyl boucerin-3-O-β-D-glucopyranosyl-(1-->4)-β-D-cymaropyranoside, 12β-O-benzoyl-20-O-acetyl boucerin-3-O-β-D-glucopyranosyl-(1-->4)-β-D-digitalopyranosyl-(1-->4)-β-D-cymaropyranosyl-(1-->4)-β-D-cymaropyranoside, 12β-O-benzoyl-20-O-acetyl boucerin-3-O-β-D-glucopyranosyl-(1-->4)-hevetopyranosyl-(1-->4)-β-D-cymaropyranosyl-(1-->4)-β-D-cymaropyranoside, 12β-O-benzoyl-20-O-tigloyl boucerin-3-O-β-D-glucopyranosyl-(1-->4)-β-D-cymaropyranoside, 12β-20-O-dibenzoyl boucerin-3-O-β-D-glucopyranosyl-(1-->4)-β-D-cymaropyranosyl-(1-->4)-β-D-cymaropyranoside. Finally, the isolated compounds were evaluated for their quinone reductase induction.

Hydroxamate siderophores of Scedosporium apiospermum.

Scedosporium apiospermum is an emerging pathogen colonizing the airways of patients with cystic fibrosis and causing severe infections in immunocompromised hosts. In order to improve our knowledge on the pathogenic mechanisms of this fungus, we investigated the production of siderophores. Cultivation on CAS medium and specific assays for different classes of siderophores suggested the secretion of hydroxamates. A maximal production was obtained by cultivation of the fungus at alkaline pH in an iron-restricted liquid culture medium. Siderophores were then extracted from the culture filtrate by liquid/liquid extraction, and separated by reverse phase high performance liquid chromatography. Two siderophores, dimerumic acid and Nα-methyl coprogen B, were identified by electrospray ionization-mass spectrometry and MS–MS fragmentation. Finally, comparison of various strains suggested a higher production of Nα-methyl coprogen B by clinical isolates of respiratory origin. Studies are initiated in order to determine the potential usefulness of these siderophores as diagnostic markers of scedosporiosis.

Nα-methyl coprogen B, a potential marker of the airway colonization by Scedosporium apiospermum in patients with cystic fibrosis

Scedosporium apiospermum is an emerging pathogen colonizing the airways of patients with cystic fibrosis (CF). While usually responsible for chronic colonization without clinical signs, this fungus may cause severe and often lethal infections in lung transplant recipients. Early diagnosis of its airway colonization and appropriate treatment are required to eradicate the fungus when a lung transplantation is planned. Here we propose an alternative to mycological examination of sputum samples based on extraction of siderophores by chromatography on Amberlite XAD-4, followed by high performance liquid chromatography analysis of the siderophore extract. Improvement of the extraction procedure was performed in a fractional factorial design which revealed the importance of prior ammonium sulfate precipitation of the proteins, alkalinization of the obtained solution and stirring during extraction. In order to verify the specificity of N(α)-methyl coprogen B for S. apiospermum, the method was applied on culture supernatants of different filamentous fungi colonizing the airways of CF patients, including some aspergilli and Exophiala dermatitidis. N(α)-methyl coprogen B was detected exclusively for species of the S. apiospermum complex. Likewise, sputum samples from colonized and non-colonized CF patients were analyzed, and the siderophore was detected exclusively in three out of the five specimens which were found by culture to contain S. apiospermum. Together these results confirmed N(α)-methyl coprogen B as a marker of the airway colonization by species of the S. apiospermum complex.

Cancer chemopreventive diterpenes from Salvia corrugata

NMR and NP-HPLC-UV profiling of the exudate of Salvia corrugata revealed that its secondary metabolite composition was largely dominated by α-hydroxy-β-isopropyl-benzoquinone diterpenoids. Among them, four diterpenes not described previously were isolated and identified as fruticulin C (3), 7α-methoxy-19-acetoxy-royleanone (4), 7α,19-diacetoxy-royleanone (5), and 7-dehydroxy-conacytone (7). In addition, the known diterpenes fruticulin A (1), demethyl-fruticulin A (2) and 7α-O-methyl-conacytone (6) were also obtained. The isolated compounds were evaluated for their cancer chemopreventive activity by measuring quinone reductase induction activity and histone deacetylase inhibition. Three compounds (1, 2 and 5) showed promising activity.

HPLC Profiling with At-line Microdilution Assay for the Early Identification of Anti-fungal Compounds in Plants from French Polynesia

INTRODUCTION The search for anti-fungal compounds has maintained a scientific interest notably due to existing difficulties in the treatment of mycoses and their increasing occurrence in hospitals. OBJECTIVE Development of a simple method to rapidly identify anti-fungal compounds in crude plant extracts based on a HPLC microfractionation approach combined with an at-line anti-Candida assay. METHODS The scale of the semi-preparative HPLC microfractionation was adapted to fit the sensitivity of the Candida albicans anti-fungal in a 96-well microdilution assay. This format is also compatible for MS and NMR dereplication of the active compounds. RESULTS Based on the screening of 12 crude extracts of plants from French Polynesia, three plants, which displayed various levels of anti-fungal activities, were selected to assess the efficiency of the HPLC anti-fungal profiling and the scale necessary for microfractionation. The same anti-Candida assay was performed on the HPLC microfractions collected using a generic profiling method. Analysis of active microfractions by MS and NMR issued from the most active extract enabled an efficient dereplication of the compounds responsible for the anti-fungal activity. CONCLUSION A generic HPLC anti-fungal profiling method was developed which revealed that only 50 mg of crude extract were sufficient for a rapid identification of compound(s) responsible for the anti-Candida activity. This approach was illustrated by the study of Alphitonia zizyphoides, a plant traditionally used to treat dermatomycoses.