Document Type


Date of Degree

Spring 2013

Degree Name

PhD (Doctor of Philosophy)

Degree In


First Advisor

Kerns, Robert J.

First Committee Member

Jin, Zhendong

Second Committee Member

Doorn, Jonathan

Third Committee Member

Spies, Ashley

Fourth Committee Member

Pigge, Christopher


Fluoroquinolones are broad spectrum antibiotics that have been in use for nearly 50 years. These agents are used to treat a variety of bacterial infections from simple urinary tract infections to tuberculosis. The protein targets of fluoroquinolones are bacterial type II topoisomerases. Fluoroquinolones inhibit the function of these topoisomerases by intercalating in the nick site of the DNA and forming an interaction with helix-4 of the enzyme through a magnesium-water bridge. The binding of a fluoroquinolone stabilizes the DNA-topoisomerase-fluoroquinolone ternary complex. Helix-4 is where some of the most important fluoroquinolone resistance mutations occur.

While the fluoroquinolone class of antibiotics has been successful at treating a variety of infections over the past few decades, a number of problems exist. These problems include the inability of many fluoroquinolones to kill non-growing cells, the emergence of fluoroquinolone resistant mutants, and adverse side effects of this antibiotic class. Thus, various aspects of fluoroquinolone structure and activity are explored in this study.

The first topic explored is the question of what structural features are necessary for a fluoroquinolone to be able to kill bacteria in the presence and absence of the protein synthesis inhibitor, chloramphenicol (to mimic a dormant, non-growing state of the bacteria). Previous studies have shown that steric bulk at the C-8 position (especially a methoxy group) is necessary to support the ability of a fluoroquinolone to kill non-growing cells. In this study, the N-1 position of a series of C-8 methoxy fluoroquinolones was explored to gain an understanding of what substituents at the N-1 position of C-8 methoxy fluoroquinolones support the ability to rapidly kill bacteria in the presence of a protein synthesis inhibitor.

In a second study the N-1 position is further explored, but with different goals. A recent crystal structure of a fluoroquinolone bound in the ternary complex with topoisomerase IV and DNA has revealed that the N-1 position of the fluoroquinolone is near in space to the catalytic tyrosine residue. It was reasoned that new interactions can be made with active site tyrosine residue through the N-1 position of the fluoroquinolone core. A number of N-1 fluoroquinolone derivatives were designed, synthesized, and evaluated for their ability to inhibit the DNA supercoiling activity of DNA gyrase, as well as the poisoning ability of the fluoroquinolones. The advantages of targeting the catalytic tyrosine residue are that this amino acid cannot be mutated without loss of enzyme function, and that by forming a new binding contact to the enzyme, activity can be maintained against helix-4 mutants.

Finally, in a step toward the goal of mitigating the tendon related side effects of fluoroquinolones (thought to be due to Ca2+ coordination), the metal binding domain of the fluoroquinolone was altered. These fluoroquinolones were tested for their ability to inhibit and poison DNA gyrase.

From the studies described, we have learned that the N-1 position is very sensitive to modification, that novel binding contacts to bacterial topoisomerases can be made through the N-1 position, and that modifying the metal binding domain of fluoroquinolones can lead to retention of activity against DNA gyrase. These accomplishments all push the fluoroquinolone field ahead by introducing a novel binding interaction to optimize (with the goal of creating a fluoroquinolone that is active against current fluoroquinolone resistant mutants) and by showing that fluoroquinolone activity can be retained even when the metal binding domain is altered, thus moving us closer to the goal of reducing tendon-related side effects.


Fluoroquinolone, Gyrase, Topoisomerase


xviii, 144 pages


Includes bibliographical references (pages 142-144).


Copyright © 2013 Tyrell Robert Towle