J Bacteriol Virol.  2017 Dec;47(4):179-188. 10.4167/jbv.2017.47.4.179.

Discovery of a New DNA Gyrase A Inhibitor, 4-[(1-methyl-6-nitroquinolin-1-ium-4-yl)amino]-N-[4-[(1-methylpyridin-1-ium-4-yl)amino]phenyl]benzamide

• Seo I
• Suh SI
• Suh MH
• Baek WK

• KMID: 2399977
• DOI: http://doi.org/10.4167/jbv.2017.47.4.179

Abstract

Escherichia coli (E. coli) is a clinically important causative organism that can lead to urinary tract infections. Quinolone antibiotics are among the first-line treatments for urinary tract infections. However, the frequency of resistance to quinolone in E. coli has been increasing. Therefore, new antimicrobial agents that can be used for treatment in lieu of quinolone antibiotics are needed. In this study, thirty-six compounds with higher scores in a virtual screening based on the three-dimensional structure of E. coli DNA gyrase were selected for in vitro antimicrobial activity testing. An in vitro test confirmed the antimicrobial activity of 4-[(1-methyl-6-nitroquinolin-1-ium-4-yl)amino]-N-[4-[(1-methylpyridin-1-ium-4-yl)amino]phenyl]benzamide (ZINC18057104) against E. coli among the 36 compounds. The minimum inhibitory concentration (MIC) of ZINC18057104 against E. coli ATCC® 25922â„¢ was 2 μg/ml, and the MICâ‚…â‚€ and MIC₉₀ for the 72 quinolone-resistant E. coli clinical isolates were 4 and 64 μg/ml, respectively. ZINC18057104, which has a quinoline structure which is similar to the quinolone antibiotics, is predicted to exhibit antimicrobial activity in quinolone-resistant E. coli because it has different molecular interactions with the DNA gyrase than that of existing quinolone antibiotics.

Keyword

Escherichia coli; DNA gyrase; Anti-bacterial agents; Drug discovery; ZINC18057104

MeSH Terms

Anti-Bacterial Agents
Anti-Infective Agents
DNA Gyrase*
DNA*
Drug Discovery
Escherichia coli
In Vitro Techniques
Mass Screening
Microbial Sensitivity Tests
Urinary Tract Infections
Anti-Bacterial Agents
Anti-Infective Agents
DNA
DNA Gyrase

Figure

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  Figure 1. The molecular structures of Escherichia coli DNA gyrase. (A) Secondary and tertiary structures of the GyrA homodimer. (B) DNA-gate region of the GyrA homodimer. (C) Hydrophobicity of the DNA-gate region (hydrophobic, red; hydrophilic, white). (D) Cubic box for the virtual screening centered at the DNA-gate region. Green, red, blue, white, and yellow spheres represent carbon, oxygen, nitrogen, hydrogen, and sulfur atoms, respectively.

• 

  Figure 2. Minimum inhibitory concentration (MIC) of ZINC18057104 against Escherichia coli. A broth microdilution test was done according to Clinical and Laboratory Standards Institute's recommendations, using the cation-adjusted Müller-Hinton broth. E. coli ATCC®25922 TM was used for the test. Turbidity was measured after 20 hours of treatment of ZINC18057104, and then the viability of the E. coli was confirmed again by a resazurin reduction assay. Conc.: concentration. Ctrl: control without inoculation.

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  Figure 3. ZINC18057104 and its molecular interaction with E. coli DNA gyrase A.(A-B) Chemical structure of ZINC18057104 (C-D) Three-dimensional structure of the E. coli DNA gyrase ZINC18057104 complex. E Hydrophobicity of the ZINC18057104 binding site (hydrophobic, red; hydrophilic, white). (F) Molecular interaction (yellow dotted lines) between the E. coli DNA gyrase (purple) and ZINC18057104.

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  Figure 4. Toxicity analyses of ZINC18057104 against Caenorhabditis elegans and human glioblastoma cells. (A) Cox proportional hazards survival analysis of C. elegans treated with ZIN18057104 at different concentrations. Conca: concentration (μg/ml). HRb: hazard ratio (95% confidence interval). (B) Percent viable human cells [measured as average fluorescence intensity ratio (test agent relative to Dimethyl sulfoxide)] for cytotoxicity analysis of ZINC18057104 at 0.0625, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, and 32 μg/ml against U-87MG and U-251MG cells using the resazurin reduction assay. Dimethyl sulfoxide was used as a negative control to determine a baseline measurement for the cytotoxic impact of each concentration. CC50 is the concentration at which 50% cell survival is obtained. DMSO: dimethyl sulfoxide.

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