The increasing prevalence of antibiotic-resistant strains of bacterial pathogens represents a major unmet medical need. Naturally occuring or intentionally engineered drug-resistance in biothreat agents is also a serious risk for biodefense. The development of new antibiotics against unexploited targets with novel mechanisms of action is a vital part of the solution to these problems because such antibiotics will not be affected by pre-existing resistance alleles. Two essential components of the DNA replication pathway, helicase and primase, which act early and catalyze a rate-limiting step in replication, are currently untargeted by antibacterials. The goal of this project is to discover new inhibitors of the helicase or primase activities in bacterial DNA replication and develop them into antibiotics for biodefense and clinical applications. In Phase I research, active B. anthracis helicase and primase were purified and used to develop high-throughput inhibitor screens that were applied to a library of >180,000 discrete small molecule compounds and purified natural products. Evaluation of the hits in confirmation and validation assays identified four novel helicase inhibitors with potency vs. both S. aureus and B. anthracis helicases and one new primase inhibitor. These compounds exhibited sufficient antibacterial activity (MIC =25 ?g/ml) and selectivity for bacteria (CC50/MIC =2) to warrant further optimization. The most potent (MIC ~3 ?g/ml) and selective (CC50/MIC >16) inhibitor shares the bicyclic ring of the clinically-proven aminocoumarin scaffold;however, it does not inhibit DNA gyrase or the binding of ATP to helicase. Instead, it displays a mixed mode of inhibition including a component of competitive inhibition with the DNA substrate (Ki = 8 ?M). The inhibitor selectively inhibits DNA synthesis in macromolecular synthesis assays and is rapidly bactericidal at 4x MIC. The antibacterial spectrum as well as the observation that some inhibitors are nearly equipotent against B. anthracis and S. aureus helicases suggest that inhibitors can be optimized as broad-spectrum agents active against a range of Gram-positive bacterial species. In Phase II, analogs of the coumarin-type priority hit series will be designed, synthesized, and evaluated to optimize lead compounds through a drug discovery program incorporating rational design (SAR) and structure- based design elements. Analog design will be driven by determinations of potency, mechanism of action, antibacterial spectrum, and selectivity. The most promising lead compounds will be evaluated for favorable ADME properties and examined for pharmacokinetic properties, toxicity, and efficacy in animals to generate in vivo validated pre-clinical candidates. In Phase III, a potent, safe, orally active helicase/primase inhibitor will be advanced into IND-enabling toxicology and safety pharmacology studies, and an IND will be filed.

Public Health Relevance

The increasing prevalence of antibiotic-resistant strains of bacterial pathogens is a concern both for biodefense and for combating ordinary infectious disease in the clinic. New antibiotics targeting previously unexploited bacterial functions will not be subject to most existing resistance mechanisms. The focused drug discovery and development effort of this proposal is aimed at optimizing novel inhibitors of DNA helicase and primase, which are vital for bacterial DNA replication. This research will provide new chemical classes of antibacterial therapeutics for biodefense and clinical applications.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Small Business Technology Transfer (STTR) Grants - Phase II (R42)
Project #
2R42AI064974-03
Application #
7671850
Study Section
Special Emphasis Panel (ZRG1-IDM-Q (10))
Program Officer
Xu, Zuoyu
Project Start
2009-09-01
Project End
2011-08-31
Budget Start
2009-09-01
Budget End
2010-08-31
Support Year
3
Fiscal Year
2009
Total Cost
$870,838
Indirect Cost
Name
Microbiotix, Inc
Department
Type
DUNS #
158864715
City
Worcester
State
MA
Country
United States
Zip Code
01605
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Li, Bing; Pai, Ramdas; Di, Ming et al. (2012) Coumarin-based inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicase: chemical optimization, biological evaluation, and antibacterial activities. J Med Chem 55:10896-908
Biswas-Fiss, Esther E; Kurpad, Deepa S; Joshi, Kinjalben et al. (2010) Interaction of extracellular domain 2 of the human retina-specific ATP-binding cassette transporter (ABCA4) with all-trans-retinal. J Biol Chem 285:19372-83
Aiello, Daniel; Barnes, Marjorie H; Biswas, Esther E et al. (2009) Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases. Bioorg Med Chem 17:4466-76
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Biswas, Subhasis B; Wydra, Eric; Biswas, Esther E (2009) Mechanisms of DNA binding and regulation of Bacillus anthracis DNA primase. Biochemistry 48:7373-82