As microbial genome sequencing becomes more widespread, the capacity of microorganisms to produce natural products is coming into better view. This competing renewal surveys this capacity using the latest in computational and expression screening and targets specific sub-classes of natural products that emerge from a fundamentally new platform for discovery of natural products from the microbial world. Described here is the pursuit of specific set of natural products and their gene clusters which have emerged from a new approach that achieves large-scale pairing of biosynthetic gene clusters with their small molecules for discovery. From a library of 178 actinobacteria strains, a genome-enabled metabolomics approach was used (a.k.a., metabologenomics) to correctly identify natural products and correlate them with their biosynthetic gene clusters. The proposed research extends this method to examine unknown metabolites, tambromycin (Aim 1) and rimosamides (Aim 2), each with their respective clusters exhibiting unusual biosynthetic mechanisms and monomers, such as the new amino acid, tambroline (see Aim 1). In the first two aims, the precise structures, biosynthetic details and in the case of tambromycin-the protein binding target(s) of these new natural products will be studied and defined.
In Aim 3 a, a set of new gene cluster-compound pairs will be mined in silico for those that terminate in reductase domains, and therefore likely harbor electrophilic warheads from reductive off-loading from thiotemplate assembly lines.
Aim 3 b proposes an expansion of this gene-cluster focused approach to discovering new bioactive metabolites by targeted mining of metabologenomics data for other pharmacophores known to elicit bioactivity. The specific case of a new polyene antibiotic is put forth based on sequence data indicating the presence of multiple dehydrogenase domains within the biosynthetic cluster. Mining the microbial world with metabologenomics represents a major shift from past activities in this R01 grant (which led to 18 publications over the past granting period). With a set of new compounds and their biosynthetic gene clusters in hand, the investigators will pursue several of these in targeted mode. Beyond the direct impact of this proposal, the work provides a major path forward for an 'omics'-driven resurgence in natural products discovery. Such a resurgence promises a more deterministic path for structure- based discovery of natural products and to provide these structures at a rate not seen before in the field (a.k.a. high throughput discovery as described in recent literature). In essence, the proposed research will demonstrate the value of regularizing a microbial strain collection into a bona fide library of compounds, which are known to be expressed and possess particular sub-structures (e.g., an electrophilic warhead). These value propositions serve as motivating rationales to merge a new kind of discovery pipeline containing unique molecular structures with assays for bioactivity.

Public Health Relevance

The proposed research will significantly advance public health because it provides a new path for the large- scale discovery and development of new drugs for human disease. This goal will be achieved by using a multidisciplinary approach that combines contemporary methods of genomics, metabolomics and synthetic chemistry to elucidate and investigate natural molecules from bacteria, a proven source of medicines used in hospitals today.

Agency
National Institute of Health (NIH)
Institute
National Center for Complementary & Alternative Medicine (NCCAM)
Type
Research Project (R01)
Project #
5R01AT009143-14
Application #
9240599
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Hopp, Craig
Project Start
2016-04-01
Project End
2021-03-31
Budget Start
2017-04-01
Budget End
2018-03-31
Support Year
14
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Northwestern University at Chicago
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
160079455
City
Evanston
State
IL
Country
United States
Zip Code
60201
Parkinson, Elizabeth I; Tryon, James H; Goering, Anthony W et al. (2018) Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. ACS Chem Biol 13:1029-1037
Clevenger, Kenneth D; Ye, Rosa; Bok, Jin Woo et al. (2018) Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity. Biochemistry 57:3237-3243
Kenney, Grace E; Dassama, Laura M K; Pandelia, Maria-Eirini et al. (2018) The biosynthesis of methanobactin. Science 359:1411-1416
Fisher, Oriana S; Kenney, Grace E; Ross, Matthew O et al. (2018) Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nat Commun 9:4276
Robey, Matthew T; Ye, Rosa; Bok, Jin Woo et al. (2018) Identification of the First Diketomorpholine Biosynthetic Pathway Using FAC-MS Technology. ACS Chem Biol 13:1142-1147
Mullowney, Michael W; McClure, Ryan A; Robey, Matthew T et al. (2018) Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 35:847-878
Miley, Galen P; Rote, Jennifer C; Silverman, Richard B et al. (2018) Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization. Org Lett 20:2369-2373
Clevenger, Kenneth D; Bok, Jin Woo; Ye, Rosa et al. (2017) A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol 13:895-901
Clevenger, Kenneth D; Mascarenhas, Romila; Catlin, Daniel et al. (2017) Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ. ACS Chem Biol 12:643-647
Mascarenhas, Romila; Le, Hoang V; Clevenger, Kenneth D et al. (2017) Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry 56:4951-4961

Showing the most recent 10 out of 16 publications