Prokaryotic DNA gyrase is a type II topoisomerase that can introduce negative supercoils to the DNA substrates with the hydrolysis of ATP. Because DNA gyrase only exists in bacterial cells and is an essential enzyme to bacteria, it is possible to identify inhibitors targeting DNA gyrase without affecting host human enzymes. Additionally, DNA gyrase can form covalent enzyme-DNA complex intermediates. This property makes gyrase an excellent bactericidal target for developing antibiotics. Indeed, fluoroquinolones are among the most successful antibiotics targeted to DNA gyrase. Unfortunately, bacterial resistance to fluoroquinolones has emerged and makes the development of new, more effective antibiotics an urgent issue especially for Gram-negative bacterial infections. The long-term goal of the proposed research is to discover and develop new and effective antibiotics that are capable of treating infections of antibiotic resistance bacteria. The objectives of this application are to develop novel biochemical and cell-based assays to screen antimicrobial compounds targeting bacterial DNA gyrase, and screen the NCATS compound library to identify novel DNA gyrase inhibitors. The biochemical primary assay stems from the synthesis of a type of unique fluorescence- labeled DNA molecules that can be used to study DNA topology and topoisomerases by fluorescence resonance energy transfer (FRET). The cellular assay is based on one recently constructed E. coli strain FL#1181 that contains a pair of divergently coupled PgyrA and PT7A1/O4 promoters controlling the luc and lacZ genes at the attTn7 site of the E. coli chromosome (84 min of the chromosome). Since transcription-coupled DNA supercoiling (TCDS) provided by a strong IPTG-inducible promoter, such as the T7A1/O4 promoter (PT7A1/O4), is capable of potently inhibiting the divergently coupled, supercoiling-sensitive gyrA promoter (PgyrA), our hypothesis is that DNA gyrase inhibitors should greatly ?enhance? the expression of the firefly luciferase under the control of the divergently coupled, supercoiling-sensitive PgyrA. As a result, the luminescence generated from the firefly luciferase will be significantly increased. This unique property of TCDS can be effectively used to screen and identify antimicrobial compounds targeting bacterial DNA gyrase.
Three specific aims are:
Aim 1. Develop a novel in vitro biochemical assay to screen inhibitors targeting bacterial DNA gyrase.
Aim 2. Screen the NCATS compound collection to identify bacterial DNA gyrase inhibitors.
Aim 3. Validate hits and identify DNA gyrase poisons using a newly developed cell-based method targeting TCDS. This truely interdisciplinary and collaborative effort brings two labs together (Leng and Smith labs) and offers a novel solution to address an urgent world health problem, antimicrobial resistance. !

Public Health Relevance

Antibiotic resistance is one of the most serious health problems in the US and also in the world. The worst scenario is that, as WHO pointed out, ?Over the last 30 years, no major new types of antibiotics have been developed? to combat antibacterial resistance pathogens. The proposed research is to develop and utilize two novel high throughput screening assays to discover new types of antibiotics from the millions of compounds found in small molecule libraries that may target DNA gyrase and fight this urgent public health threat.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Exploratory/Developmental Grants (R21)
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Special Emphasis Panel (ZRG1)
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Xu, Zuoyu
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Florida International University
Schools of Arts and Sciences
United States
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Liu, Yingting; Hua, Zhi-Chun; Leng, Fenfei (2018) DNA Supercoiling Measurement in Bacteria. Methods Mol Biol 1703:63-73
Liu, Yingting; Berrido, Andrea M; Hua, Zi-Chun et al. (2017) Biochemical and biophysical properties of positively supercoiled DNA. Biophys Chem 230:68-73
Zhi, Xiaoduo; Dages, Samantha; Dages, Kelley et al. (2017) Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. J Biol Chem 292:14566-14575
Gu, Maxwell; Berrido, Andrea; Gonzalez, Walter G et al. (2016) Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases. Sci Rep 6:36006