Discovery of Novel Bacterial DNA Gyrase Inhibitors

Authors

Eddy E. Alfonso Maqueira, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biochemistry

First Advisor's Name

Fenfei Leng

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Jeremy Chambers

Second Advisor's Committee Title

committee member

Third Advisor's Name

Yukching Tse Dinh

Third Advisor's Committee Title

committee member

Fourth Advisor's Name

Kalai Mathee-Narasimhan

Fourth Advisor's Committee Title

committee member

Keywords

DNA gyrase, DNA topoisomerase, gyrase inhibitor, supercoiling-dependent fluorescence quenching assay, high-throughput screening assay, gyrase poison, gallate-based DNA gyrase inhibitors

Date of Defense

3-29-2023

Abstract

Bacterial DNA gyrase is a type IIA DNA topoisomerase. Due to its essential role in DNA replication and transcription, this enzyme is a validated target for discovering and developing new antibiotics. DNA gyrase is the target of fluoroquinolones (FQs), one of the most effective and prescribed antibiotics in the world. However, the emergence of resistant bacterial strains to FQs and other antibiotics in the last decades has stimulated the search for non-FQ gyrase inhibitors with antimicrobial activities. Based on a supercoiling-dependent fluorescence quenching (SDFQ) method, a high-throughput screening (HTS) assay to identify inhibitors targeting bacterial DNA gyrase has been established. After screening the National Institutes of Health's Molecular Libraries Small Molecule Repository library containing 370,620 compounds using this SDFQ HTS method, 2891 new gyrase inhibitors were discovered. Subsequently, 235 compounds were acquired to analyze their inhibition activities against bacterial DNA gyrase using gel- and SDFQ-based DNA gyrase inhibition assays, in which 155 new bacterial DNA gyrase inhibitors with a wide structural diversity were identified. Several of them have potent antibacterial activities. These newly discovered gyrase inhibitors include several DNA gyrase poisons that stabilize the gyrase-DNA cleavage complexes and provide new chemical scaffolds for the design and synthesis of bacterial DNA gyrase inhibitors that may be used to combat multidrug-resistant bacterial pathogens.

In a second effort to discover novel bacterial DNA gyrase inhibitors, a pool of naturally occurred polyphenols was screened. It was discovered that digallic acid and several food additives based on gallic acid, such as dodecyl gallate, are potent DNA gyrase inhibitors. Interestingly, the IC₅₀ of these gallate derivatives against DNA gyrase is correlated with the length of the hydrocarbon chain connected to gallic acid. These new bacterial DNA gyrase inhibitors are ATP-competitive inhibitors of DNA gyrase. It was found that digallic acid and gallate derivatives also potently inhibit E. coli DNA topoisomerase IV. Furthermore, it was demonstrated that several gallate derivatives have strong antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). This study provides a solid foundation for the design and synthesis of gallate-based DNA gyrase inhibitors that may be used to combat antibacterial resistance.

Identifier

FIDC011083

ORCID

0000-0002-4395-8038

Previously Published In

Alfonso, E.E., et al., Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay. ACS Pharmacology & Translational Science, 2022. 5(10): p. 932-944.

Alfonso, E. E., Troche, R., Deng, Z., Annamalai, T., Chapagain, P., Tse-Dinh, Y. C., and Leng, F. (2022) Potent Inhibition of Bacterial DNA Gyrase by Digallic Acid and Other Gallate Derivatives, ChemMedChem 17, e202200301.

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Recommended Citation

Alfonso Maqueira, Eddy E., "Discovery of Novel Bacterial DNA Gyrase Inhibitors" (2023). FIU Electronic Theses and Dissertations. 5249.
https://digitalcommons.fiu.edu/etd/5249