Bioinformatic Guided Discovery and Characterization of New RiPP Natural Products

PROJECT SUMMARY
Ranging from penicillin to artemisinin, natural products have been essential in the discovery and
development of new drugs. To complement the traditional activity-guided isolation approaches, genome mining
techniques can enable an efficient and high throughput discovery pipeline by specifically targeting promising
organisms and gene clusters for detailed study. However, detailed understanding of a biosynthetic pathway is
typically needed, significantly constraining the search process. Therefore, alternative bioinformatic approaches
combined with detailed biochemical characterization and bioactivity studies will help expand our collective
understanding of bioactive secondary metabolites in nature and their value for human health.
The overall focus of the Chekan lab is to utilize enzyme-independent genome mining as a guide to enable
the discovery and detailed study of new types of bioactive natural products and biosynthetic pathways. This
proposal focuses on the ribosomally synthesized and post-translationally modified peptide (RiPP) family of
natural products. RiPPs are a ubiquitous family of natural products found across all domains of life and possess
a wide range of bioactivities, with antibiotic activity being particularly well represented. These natural products
all share a consistent biosynthetic logic, but can be generated from a wide variety of biosynthetic enzymes. In
order to discover completely new classes of RiPPs, we propose to exploit conserved biosynthetic and structural
features instead of specific enzymatic transformations. This will allow for rapid in silico identification of promising
biosynthetic gene clusters that generate never before isolated molecules. To fully study and characterize these
new pathways, a combination of biochemical and structural approaches will be employed. These results will give
important insights into the new biosynthetic enzymes, reveal their mechanisms, and assess their applicability for
engineering. Finally, this first project will reveal the bioactivity of the newly discovered natural products and their
mechanism of action. To complement this discovery element, a second project will seek to link peptidic natural
product families, for which no biosynthetic information is available, to their biosynthetic enzymes. This proposal
will also enable the training of both graduate students and postdocs, the next generation of scientists responsible
for advancing human health. Overall, the results of this proposal will not only lead to the discovery of new natural
products and enzymes, but will inform future genome mining based discovery studies and pathway engineering
efforts to identify promising drug leads.

Grant Number: 5R35GM147439-04
NIH Institute/Center: NIH
Principal Investigator: Jonathan Chekan