The economic and social burden for the treatment of chronic and infectious diseases is enormous, >$300B. The emergence of drug resistant microbes, the diminishing supply of novel classes of antibiotics, and the dramatic reduction in discovery and development of anti-infective, anti-proliferation and anti-inflammation agents have further amplified public health concern. Fungi are prolific producers of anti-microbial secondary metabolites (SM) and since the turn of the century have provided 45% of bioactive molecules from all microbial sources. However, fungal SM pathways remain largely untapped due to difficulties in efficiently handling and expressing these SM pathways. This research proposal is to advance the science of functional SM metagenomics, to further advance our newly-developed fungal artificial chromosome (FAC) technology, precisely engineer and activate large intact silent SM pathways-containing FAC clones, and to discover novel natural products (NPs) for pharmaceutical and clinical development. Ongoing research at Intact Genomics, University of Wisconsin Madison and Northwestern University have orchestrated key technological breakthroughs that together resulted in the next generation fungal SM discovery platform. This discovery technology combined: 1) an improved methodology for the isolation and purification of high molecular weight genomic DNA from fungi; 2) a new E. coli-Aspergillus shuttle or FAC vector and an A. nidulans host for enhanced expression of cloned large DNAs; 3) a random shear BAC/FAC cloning method to produce unbiased very large insert sizes (>100 kb) for covering the entire set of intact SM biosynthetic gene clusters (BGCs) of a fungal genome (one FAC clone = one intact SM pathway); 4) precisely engineering and activating large intact silent SM gene clusters-FACs by Red/ET techniques and BGC-refactoring via yeast; and 5) a rapid and improved small molecule identification method through both function screening and chemical analysis. In Phase I and ongoing research, we have achieved phenomenal 50~60% compound hit rate by directly transferring fungal genome sequence through FACs first-time. We propose in this Phase II study to further increase the compound hit rate to about 90%. We will also engineer at least 50 silent SM pathways from 7 sequenced fungi (283 SM BGCs) which will be extensively screened for antimicrobial and anticancer agents and insecticides. We expect to uncover >40 novel chemical entities using this approach, and lead candidates with high potency against multiple- drug-resistance bacterial and fungal pathogens, anticancer and insecticide leads. These technologies represent an important advancement for the science of NP discovery in general. In addition, the FACs and compounds produced from this research are a valuable genomic resource that may be screened for other bioactive compounds: for example, antidepressants, antiviral, and anti-inflammatory activities.

Public Health Relevance

We are potentially losing the battle in the fight against both chronic and infectious diseases due to the alarming increasing number of chronic problems and multi-drug resistance microbes coupled with our inability to find drug leads with novel acting mechanisms; the loss of life and the burden of treatment is a significant public health threat to American citizens. The proposed research further develops a robust methodology advancing fungal artificial chromosome (FAC) technology and tools for drug discovery; this novel technology permits access to the majority of fungal cryptic biosynthetic gene clusters of natural products in a sequenced fungal genome with the aim to eventually activate all silent and cryptic pathways for pharmaceutical discovery. Our functional metagenomic approach will be used to identify and characterize novel anticancer, antibiotic, and insecticidial compounds to combat the threat of cancers, mosquitoes, and microbial pathogens.

National Institute of Health (NIH)
National Center for Complementary & Alternative Medicine (NCCAM)
Small Business Innovation Research Grants (SBIR) - Phase II (R44)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Hopp, Craig
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Intact Genomics, Inc.
Saint Louis
United States
Zip Code