Our research interests concern the structural identification of secondary metabolites (natural “small molecules”) and the elucidation of their biological functions. We currently pursue three major projects, which employ three different approaches for linking small-molecule molecular structures with biological function or activity.

1. Structures and functions of small molecules in C. elegans

The goal of this project is to complement the highly developed genomics and proteomics of the important model organism Caenorhabditis elegans with a comprehensive structural and biological characterization of its secondary metabolome, which, surprisingly, has been explored only to a very limited extent. C. elegans, which is one of the first multicellular organisms with a completed genome sequence, is small enough for high-throughput operations, yet features a highly differentiated physiology, and it has become apparent that many of the biological pathways in C. elegans show strong analogies to corresponding pathways in higher animals. The key element of our efforts towards characterizing the C. elegans metabolome is the application of a new NMR spectroscopic technique we recently developed, which allows to detect and identify individual compounds as components in complex mixtures, such as unfractionated C. elegans metabolite mixtures. Over the past 8 months, we have made significant progress toward preparation of a C. elegans-derived secondary metabolite library, which we are subjecting to a systematic biological investigation using a variety of established screens both our laboratory at BTI, and through newly established collaborations with Paul Sternberg’s lab at Caltech and Arthur Edison’s group at UF Gainesville. These experiments will take advantage of the extensive mutant and RNAi libraries that cover almost the entire C. elegans genome.  A successful conclusion of these efforts will provide a partial structural and functional annotation of the C. elegans secondary metabolome, greatly enhancing our understanding of C. elegans biology, with many possible implications for understanding the biology of higher organisms.

Our current investigations are focused on small molecules and genes involved in the control of development and ageing, as well as sexual reproduction. C. elegans is a particularly important model for ageing and lifespan control, because under poor environmental conditions C. elegans larvae enter a seemingly “non-ageing” state of metabolic arrest, the so called “dauer” stage. Interestingly, entry and exit form the dauer stage is regulated by a small-molecule pheromone, several components of which were recently identified. Using a novel NMR-based approach for the analysis of complex small-molecule mixtures, we have recently identified several new compounds which appear to potently active as signaling molecules in the dauer pathway. Moreover, it appears that, in C. elegans adult worms, these compounds significantly increase stress tolerance and under some conditions dramatically increase lifespan.
In collaboration with the laboratories of Paul Sternberg and Arthur Edison, we have recently shown that the signaling compounds we identified in the dauer pathway also act as sex pheromones in C. elegans. The discovery that largely overlapping families of small molecules regulate both development (dauer) and reproduction provides a direct linkage between the corresponding molecular pathways. Characterization of these molecule’s receptors and their downstream targets will likely provide further insights in how developmental and reproductive pathways are connected. A manuscript describing these findings is currently under review in Nature.

2. Discovery-aimed metabolomics via NMR: new antibiotics from fungi

Fungi are among the most prolific sources of pharmacologically relevant natural products. However, only a fraction of the biosynthetic capabilities of fungi have been discovered, because expression of many, perhaps even most biosynthetic pathways depends strongly on environmental conditions, including the presence of specific elicitors derived from the presence of other organisms. The primary aim of this project is to elicit the biosynthesis new fungal antibiotics by exposing fungi to a variety of culturing protocols that include exposure to different kinds of bacterial or fungal stimuli. Antibiotic assays in combination with our recently developed methodology for the differential analysis of 2D NMR spectra should enable fast and efficient recognition of production of new and unusual chemotypes.  Our initial results have shown that fungal secondary metabolite expression patterns change dramatically as a result of exposure to bacterial stimuli, and that some of the additional compounds produced have strong antibacterial properties. Current experiments are directed at broadening the range of bacterial stimuli used in these experiments, and to acquire and establish a greater number of fungal species.  Fungi are being obtained through our collaborations with the group of Nancy Keller at University of Wisconsin, Madison, and Donna Gibson at the USDA on Cornell campus. In addition to evaluation of their antibiotic or antifungal properties in our own laboratories, all new compounds will be formatted for high-throughput screening at the National Institutes of Health (via P41 GM079571, see below) and the Investigator-Initiated Screening Program at the BROAD Institute.

3. Arthropod-inspired compound libraries for biological screening

Funded 09-01-2007 NIH P41 GM079571-01, PI Frank Schroeder

Natural products from terrestrial animals are generally underrepresented in screening collections. Our own research on the chemical ecology of arthropods has resulted in the identification of structurally unique compounds, most of which have not yet been subjected to broad biological screening because the amounts available from the respective arthropod sources are very limited. The goal of this project is to synthesize four small libraries of 20-30 compounds each, based upon four arthropod-derived lead structures (1-4). For the initial stages of this project, two groups of arthropod compounds have been selected, for which limited testing has indicated interesting activities: the sulfated nucleosides (i.e. 4), which show specific affinity to kainate receptors, and the azamacrolides (i.e. 1), which bind to imidazoline-1 receptors. The arthropod-inspired libraries will be formatted for broad biological screening at the NIH and the Investigator-Initiated Screening Program at the Broad Institute, Cambridge, MA