Most clinically-used antibiotics are bacterially-produced small molecules known as natural products, or their derivatives. However, natural products are not being featured in antibiotic discovery programs due to high rates of rediscovery and low rates of new molecule discovery. This proposal describes a new genomicsbased approach to natural product discovery that employs a combination of bioinformatics, microbial ecology, genetics, and chemistry to identify cryptic biosynthetic loci and stimulate them to produce their encoded natural products. All molecules identified will be characterized for antimicrobial activity.
Specific Aim 1. Use bioinformatics to identify biosynthetic gene clusters and predict their products. New bioinformatic tools will be developed to identify biosynthetic gene clusters in the genomes of actinomycetes and other microbes, and to predict structural elements of their small molecule products. These predictions will be leveraged toward antibiotic discovery by using them as the basis for efforts to stimulate the production of cryptic natural products, as described in Specific Aims 2 and 3:
Specific Aim 2. Stimulate the production of cryptic metabolites by simulating a multispecies environment. Most screens for new natural products have been performed with strains grown as pure cultures in nutrientrich growth media. A new screening format has recently been developed in which strains are grown as microcolonies on nutrient-poor growth media. This microcolony screening methodology will be used to identify cryptic natural products with antimicrobial activity.
Specific Aim 3. Stimulate the production of cryptic metabolites by genetically manipulating producers. Most natural product-encoding gene clusters are thought to be repressed under standard culture conditions. Using actinomycete strains whose biosynthetic gene clusters have been identified by the efforts described in Specific Aim 1, endogenous gene cluster promoters will be systematically replaced with a strong, inducible promoter, enabling the controlled synthesis and isolation of their small molecule products and the subsequent characterization of their antimicrobial activity. .

Public Health Relevance

While most clinically-used antibiotics are small molecules produced by bacteria, these molecules are rarely used in antibiotic discovery programs due to the difficulty of finding new molecules. This proposal describes a new genomics-based approach to natural product discovery increasing the supply of new antibiotic candidates to combat resistant pathogens.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZAI1-DDS-M)
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Harvard University
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de Wispelaere, Melissanne; Lian, Wenlong; Potisopon, Supanee et al. (2018) Inhibition of Flaviviruses by Targeting a Conserved Pocket on the Viral Envelope Protein. Cell Chem Biol 25:1006-1016.e8
Huang, Nai-Jia; Pishesha, Novalia; Mukherjee, Jean et al. (2017) Genetically engineered red cells expressing single domain camelid antibodies confer long-term protection against botulinum neurotoxin. Nat Commun 8:423
Mertins, Philipp; Przybylski, Dariusz; Yosef, Nir et al. (2017) An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. Cell Rep 19:2853-2866
Nair, Dhanalakshmi R; Chen, Ji; Monteiro, João M et al. (2017) A quinolinol-based small molecule with anti-MRSA activity that targets bacterial membrane and promotes fermentative metabolism. J Antibiot (Tokyo) 70:1009-1019
Choo, Min-Kyung; Sano, Yasuyo; Kim, Changhoon et al. (2017) TLR sensing of bacterial spore-associated RNA triggers host immune responses with detrimental effects. J Exp Med 214:1297-1311
de Wispelaere, Mélissanne; Carocci, Margot; Liang, Yanke et al. (2017) Discovery of host-targeted covalent inhibitors of dengue virus. Antiviral Res 139:171-179
Umetsu, Dale T (2017) Mechanisms by which obesity impacts upon asthma. Thorax 72:174-177
Zheng, Huiqing; Colvin, Christopher J; Johnson, Benjamin K et al. (2017) Inhibitors of Mycobacterium tuberculosis DosRST signaling and persistence. Nat Chem Biol 13:218-225
Coulson, Garry B; Johnson, Benjamin K; Zheng, Huiqing et al. (2017) Targeting Mycobacterium tuberculosis Sensitivity to Thiol Stress at Acidic pH Kills the Bacterium and Potentiates Antibiotics. Cell Chem Biol 24:993-1004.e4
Chiaraviglio, Lucius; Kang, Yoon-Suk; Kirby, James E (2016) High Throughput, Real-time, Dual-readout Testing of Intracellular Antimicrobial Activity and Eukaryotic Cell Cytotoxicity. J Vis Exp :

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