Natural products continue to inspire novel chemistry and biology. The enediynes represent one of the most fascinating families of natural products for their unprecedented molecular architecture and extraordinary biological activities. A great challenge is to develop innovative methods to discover new enediynes and produce them in sufficient quantities for chemical, biological, and clinical investigations. In this application, w propose to mine the genomes of the Actinomycetale collection at The Scripps Research Institute for new enediynes. Our hypotheses are: (i) genome survey of our strain collection for the enediyne polyketide synthase (PKS) gene cassettes will allow us to identify potential enediyne producers, (ii) genome sequencing of the potential producers for enediyne biosynthetic gene clusters will allow us to predict the structural novelty of the new enediynes, and (iii) genetic manipulation and fermentation optimization of the most promising strains will allow us to produce and isolate the new enediynes. We have completed a genome survey of 3,500 strains from our Actinomycetale collection and identified 92 strains (hits) that can be phylogenetically grouped into 48 clades according to the enediyne PKS cassettes. Genome sequencing of representative hits from 28 clades confirmed that each clade encodes distinct enediyne biosynthetic gene clusters.
The specific aims for this grant are: (i) genome sequencing of representative hits from all 48 clades to identify a total of 48 distinct enediyne gene clusters and prioritize the hits for enediyne discovery and (ii) genetic manipulation and fermentation optimization of the most promising hits to produce and isolate the new enediynes for structural characterization. Discovery of an enediyne is a significant event in natural products chemistry, biology, and drug discovery.
We aim at discovering 6-12 new enediynes from the 92 hits, nearly doubling the inventory of enediyne natural products known to date. The outcomes of this application include (i) fundamental contributions to genome mining and metabolic pathway engineering for natural product discovery and production, (ii) discovery of new enediyne natural products to inspire chemistry, biology, and medicine, and (iii) new insights into enediyne chemistry and biosynthetic machineries. The long-term goal of our research is to understand at a molecular level how microorganisms synthesize complex natural products and to exploit this knowledge to discover novel natural products and engineer their analogues for drug discovery.

Public Health Relevance

The enediyne natural products possess unprecedented molecular architecture and extraordinary cytotoxicity, making them one of the most fascinating families of natural products known to date. This project aims at discovering new enediyne natural products, by an innovative genome mining approach, from Actinomycetales, and producing them in sufficient quantities for structural elucidation to inspire new chemistry, biology, and medicine.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM115575-03
Application #
9402089
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Fabian, Miles
Project Start
2016-03-01
Project End
2019-12-31
Budget Start
2018-01-01
Budget End
2018-12-31
Support Year
3
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Scripps Florida
Department
Type
DUNS #
148230662
City
Jupiter
State
FL
Country
United States
Zip Code
33458
Rudolf, Jeffrey D; Chang, Chin-Yuan; Ma, Ming et al. (2017) Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 34:1141-1172
Annaval, Thibault; Rudolf, Jeffrey D; Chang, Chin-Yuan et al. (2017) Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis. ACS Omega 2:5159-5169
Rudolf, Jeffrey D; Yan, Xiaohui; Shen, Ben (2016) Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery. J Ind Microbiol Biotechnol 43:261-76
Yan, Xiaohui; Ge, Huiming; Huang, Tingting et al. (2016) Strain Prioritization and Genome Mining for Enediyne Natural Products. MBio 7:
Huang, Tingting; Chang, Chin-Yuan; Lohman, Jeremy R et al. (2016) Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. J Antibiot (Tokyo) 69:731-740
Shen, Ben (2015) A New Golden Age of Natural Products Drug Discovery. Cell 163:1297-300
Shen, Ben; Hindra; Yan, Xiaohui et al. (2015) Enediynes: Exploration of microbial genomics to discover new anticancer drug leads. Bioorg Med Chem Lett 25:9-15