Continuously emerging new and hard-to-treat microbes, and the growing incidence of multi-drug resistant infections pose formidable challenges to human health. Innovative approaches are urgently needed to speed up the discovery of new anti-infectives.
Our aim i s to achieve a paradigm shift in antimicrobial drug discovery by finding next generation anti-infectives that prevent disease by blocking pathogen adaptation to host physiology. To this end we propose using whole live animals for high throughput screening of small molecules. We have developed infection models in the nematode Caenorhabditis elegans that can be used to identify drugs that cure otherwise lethal infections. High throughput screening of nematodes in 384-well plates is followed by secondary screening in a more highly evolved model host, the fruit fly Drosophila melanogaster, increasing the likelihood of isolating drugs that will work in humans. Our approach is applicable to many different classes of microorganisms, including bacteria, viruses, fungi and parasites. It has several advantages over traditional drug discovery: (i) In addition to identifying conventional antibiotics, it will uncover entirely new classes of anti-infectives that only exhibit in vivo activity. Examples are "virulence blockers" and "immune escape blockers". (ii) Our approach is unbiased and requires no prior knowledge of potential drug targets or pathways. (iii) It bypasses the current bottleneck of toxicity/efficacy testing by automatically eliminating toxic compounds (because they would kill the nematodes), yielding quality hits with in vivo activity. (iv) It will identify compounds that prevent or mitigate microbial resistance development, or can be combined with antibiotic therapy, thereby increasing antibiotic efficacy. We predict that our approach can identify compounds that inhibit diverse aspects of virulence: (i) adhesion and colonization, (ii) epithelial barrier disruption, (iii) deep tissue invasion, (iv) biofilm formation, (v) avoidance of immune recognition, and (vi) modulation of immune signaling. Some of the molecular mechanisms underlying these processes are conserved across bacterial species. To establish proof-of-principle, we seek funding for discovering new anti-infectives against Pseudomonas aeruginosa, one of several gram-negative bacteria that have recently emerged in a multi-drug resistant form for which efficient antibiotics are either limited or not available. We plan to screen a large number of chemical compounds (250,000) to maximize the discovery of new classes of anti-infectives. Promising compounds will undergo characterization, efficacy testing in other gram-negative bacteria (Klebsiella, Acinetobacter, Enterobacter) and testing in mouse models of infection. For highly promising candidates we will attempt molecular target identification.

Public Health Relevance

Microbes that cause disease are becoming resistant to antibiotics faster than we can find new ones, making many common infections untreatable and life threatening. The goal of our project is to find a way to identify a new generation of antibiotics. Rather than simply preventing bacteria from growing, these new sophisticated drugs will prevent disease by interfering with a microbe's ability to interact with the human body.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-A (51))
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Xu, Zuoyu
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Massachusetts General Hospital
United States
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Pellegrino, Mark W; Nargund, Amrita M; Kirienko, Natalia V et al. (2014) Mitochondrial UPR-regulated innate immunity provides resistance to pathogen infection. Nature 516:414-7
Conery, Annie L; Larkins-Ford, Jonah; Ausubel, Frederick M et al. (2014) High-throughput screening for novel anti-infectives using a C. elegans pathogenesis model. Curr Protoc Chem Biol 6:25-37
Pukkila-Worley, Read; Feinbaum, Rhonda L; McEwan, Deborah L et al. (2014) The evolutionarily conserved mediator subunit MDT-15/MED15 links protective innate immune responses and xenobiotic detoxification. PLoS Pathog 10:e1004143
Haller, Samantha; Limmer, Stefanie; Ferrandon, Dominique (2014) Assessing Pseudomonas virulence with a nonmammalian host: Drosophila melanogaster. Methods Mol Biol 1149:723-40
Djonovic, Slavica; Urbach, Jonathan M; Drenkard, Eliana et al. (2013) Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants. PLoS Pathog 9:e1003217
Cezairliyan, Brent; Vinayavekhin, Nawaporn; Grenfell-Lee, Daniel et al. (2013) Identification of Pseudomonas aeruginosa phenazines that kill Caenorhabditis elegans. PLoS Pathog 9:e1003101
Kirienko, Natalia V; Kirienko, Daniel R; Larkins-Ford, Jonah et al. (2013) Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. Cell Host Microbe 13:406-16
Pukkila-Worley, Read; Ausubel, Frederick M (2012) Immune defense mechanisms in the Caenorhabditis elegans intestinal epithelium. Curr Opin Immunol 24:3-9
Wahlby, Carolina; Kamentsky, Lee; Liu, Zihan H et al. (2012) An image analysis toolbox for high-throughput C. elegans assays. Nat Methods 9:714-6
McEwan, Deborah L; Kirienko, Natalia V; Ausubel, Frederick M (2012) Host translational inhibition by Pseudomonas aeruginosa Exotoxin A Triggers an immune response in Caenorhabditis elegans. Cell Host Microbe 11:364-74

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