Environmental Response

Devise powerful strategies to explore and interpret the molecular language used by bacteria to respond to environmental and ecological cues

Natural products and compounds inspired by these scaffolds represent nearly half of all currently available drugs and 75% of treatments for infectious disease. Natural products also provide critical tools to investigate myriad biological questions, including those being pursued by my research group (ACS Chem. Biol20105, 639-653). Despite this fact, natural product discovery efforts have declined in the last several decades because of the technical difficulties associated with isolation and structural elucidation of minute quantities of complex molecular scaffolds. Thus, new methods that facilitate compound separation and the discovery and characterization of low abundant molecules have the potential to dramatically expedite exploration of the confluence of natural product and antibiotic space. 

We are developing a chemoselective isolation strategy to enable enrichment of subsets of natural products from complex mixtures. Unlike traditional discovery methods that separate molecules by their physicochemical properties such as size or solubility, our approach facilitates separation based upon functional group composition. To accomplish this goal, we utilize a reversible tagging strategy that covalently captures small molecules, enabling their chemoselective enrichment, followed by release of the unaltered chemical structures. These “capture and release” tags, called reversible enrichment tags, purify specific classes of natural products from complex biological preparations (Figure 5). Following enrichment, compounds are liberated using conditions that do not interfere with the structural integrity of the molecules or subsequent bioassays. To date we have generated methods for the enrichment of hydroxyl-, phenoxyl- and carboxylic acid-containing compounds (Chem. Sci. 20112, 760-764; Org. Lett201113, 5652-5655;J. Org. Chem201378, 7349-7355;Tetrahedron201470, 4191-4196; Bioorg. Med. Chem. Lett201525, 4767-4769). These studies also afford fundamental knowledge about the use of reversible, chemoselective transformations (Mol. BioSyst20128, 2484-2493).

To expedite the identification of natural products residing in unexplored chemical space, we have also developed an approach that integrates several powerful mass spectrometry (MS, MS^2) and informatics platforms (XCMS, molecular networking) to pinpoint and prioritize unknowns (Curr. Opin. Chem. Biol. 201524, 104-111; Anal. Chem201526, 1899-902). The combined use of these tools facilitated the discovery of metabolites from the extensively studied Actinomycete, Streptomyces coelicolor M145. 

We identified a suite of 15 tri-hydroxamate, amphiphilic siderophores (Figure 6ACS Chem. Biol. 20138, 2009-2016; J. Am Soc. Mass Spectrom. 201526, 1899-1902). Compounds in this class have primarily been observed in marine microorganisms making their detection in the soil-dwelling S. coelicolor M145 significant. The identified molecules are part of a small list of secondary metabolites that have been discovered since sequencing of S. coelicolor M145 revealed that it possessed numerous putative secondary metabolite-producing gene clusters with no known metabolites. Thus, these siderophores illustrate the unexplored metabolic potential of both well-studied and new organisms that can be uncovered with our sensitive and robust approach. 

What types of methods will you learn/use on this project?

Organic synthesis, solid-phase synthesis, mass spectrometry, informatics, structure elucidation (NMR, MS, etc.), high-throughput screening and bioassay development.

nat prod central dogma
siderophore

Accurate mass fragmentation (MS2) data obtained from ferrioxamine B and three representative compounds. (a) Structure of ferrioxamine B (1) and three amphiphilic ferrioxamine family members, C13 with saturated acyl tail (2), C12 with monounsaturated acyl tail (3), and C14 with monohydoxylated acyl tail (4). (b) Fragmentation spectrum of ferrioxamine B is identical to known data and exhibits characteristic losses of m/z = 17, 118, and 200. (c) The characteristic fragmentation pattern was seen in the unknowns, suggesting that they possess the ferrioxamine core.