Development of New Novel Bacterial Topoisomerase Inhibitors As Promising Antibiotics with a 5-Amino-1,3-Dioxane Linker Moiety DI
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Development of New Novel Bacterial Topoisomerase Inhibitors as Promising Antibiotics with a 5-Amino-1,3-dioxane Linker Moiety DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Linsen Li Graduate Program in Pharmaceutical Sciences The Ohio State University 2019 Dissertation Committee: Mark J Mitton-Fry, Ph.D., Advisor Karl A Werbovetz, Ph.D. Mireia Guerau-de-Arellano, Ph.D. James R Fuchs, Ph.D. Copyright by Linsen Li 2019 Abstract Multidrug-resistant bacteria (MDR) have become one of the greatest threats to human beings. Regardless of the mechanism of action involved, resistance has eventually developed after the clinical use of each class of antibiotics. Thus, new antibiotic classes with unprecedented mechanisms of action are in urgent demand. With a distinct mechanism of action, Novel Bacterial Topoisomerase Inhibitors (NBTIs) represent a promising new class of antibiotics. The recent development of NBTIs has been encouraging. Several NBTIs have processed to clinical trials, and one NBTI (Gepotidacin) has successfully completed Phase 2 clinical trials. However, the cardiac toxicity from the inhibition of hERG K+ channels is one of the major challenges in the discovery of NBTIs. In this work, a 5-amino-1,3-dioxane linker moiety was incorporated in new NBTIs to decrease hERG inhibition, which was demonstrated by comparison with several structure- matched pairs with other linker moieties. A variety of NBTIs with a 5-amino-1,3-dioxane linker have been synthesized and evaluated. Many of these newly synthesized NBTIs showed potent antibacterial activity, covering methicillin-resistant Staphylococcus aureus (MRSA) and fluoroquinolone-resistant strains. Some of these new NBTIs displayed dual inhibition against both DNA gyrase and topoisomerase IV of S. aureus, but they targeted DNA gyrase more potently than topoisomerase IV. These new NBTIs presented low toxicity to human cells and minimal inhibition of human topoisomerase IIα. Additionally, several new NBTIs revealed favorable hERG profiles. With promising preclinical ii attributes, some of these NBTIs have the potential to be evaluated in in vivo experiments and can serve as the starting point for further development of new NBTIs. iii Dedication This document is dedicated to my grandparents. iv Acknowledgements It’s like a formality to express thanks to the advisor in the dissertation of each doctoral student. However, I would like to give my sincere appreciation and admiration to my advisor, Dr. Mark Mitton-Fry. I joined the Mitton-Fry research group and became the first student in the lab in the summer of 2016. Then I found this mid-aged man very interesting. Dr. Mitton-Fry is always walking with his fast split steps, enjoying his time in front of his research hood. It’s very easy to tell his brilliant intelligence at most times, but he was even not able to set up an old iPhone, although he tried hard to learn from his young daughter. During the past years, his expertise, cautious and discreet attitude toward research, and passion for work have always inspired me tremendously. I feel very lucky to have Dr. Mitton-Fry as my advisor in my Ph.D. program. I’m grateful to the medicinal chemistry program in the College of Pharmacy for offering me the opportunity to study and work here with many great scholars from the whole world. I’m grateful to Dr. Chenglong Li as my research advisor for my first three years in the program. I learned many useful computational tools for drug discovery and got training in synthetic chemistry in Dr. Chenglong Li’s lab. I’m also grateful to Dr. James Fuchs, Dr. Karl Werbovetz and Dr. Mireia Guerau-de-Arellano for serving as my committee members. They have been always willing to help and have given me lots of beneficial suggestions. I would like to thank Dr. Craig McElroy for assistance with the research instruments. I’m also thankful to all my lab-mates in Dr. Mitton-Fry’s lab and Dr. Chenglong Li’s lab. These interesting people have created a joyful environment in the lab and helped a lot. v I would like to thank all my friends met in the Ohio State University. There are so many fantastic things around campus: the white bass and rainbow trout swimming under harmonious spring breeze, the soccer balls dribbling upon lush green lawn, the snowboard flipping from peak of white mountains, and so on. It was my friends that painted these fantastic things into my memory, which made my Ph.D. program a wonderful journey. I would like to thank my roommates in Nanjing University and intimate friends, Dr. Lichen Liu, Hao Li, Dr. Mufan Li and Jinping Liu. Regardless of the long distance apart each of us, our daily conversations gave me not only broad insight into chemistry, but also more comprehensive thoughts on the world. Finally, I would like to thank my family. It was their love and selfless support that made the completion of this thesis possible. vi Vita 2008 – 2012………………..B.S. Chemistry, Nanjing University 2012 – 2013………………..Research Assistant, Department of Chemistry, Tsinghua University 2013 – present …………….Graduate Teaching Associate, Graduate Research Associate, Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University Publications Li L, Okumu AA, Nolan S, English A, Vibhute S, Lu Y, Hervert-Thomas K, Seffernick JT, Azap L, Cole SL, Shinabarger D, Koeth LM, Lindert S, Yalowich JC, Wozniak DJ, Mitton-Fry MJ. 1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis 2019, 5, 1115-1128. Li L, Okumu AA, Nolan S, Li Z, Karmahapatra S, English A, Yalowich JC, Wozniak DJ, Mitton- Fry MJ. Synthesis and Anti-staphylococcal Activity of Novel Bacterial Topoisomerase Inhibitors with a 5-Amino-1,3-dioxane Linker Moiety. Bioorg Med Chem Lett 2018, 28, 2477-2480. Webb LM, Amici SA, Jablonski KA, Savardekar H, Panfil AR, Li L, Zhou W, Peine K, Karkhanis V, Bachelder EM, Ainslie KM, Green PL, Li C, Baiocchi RA, Guerau-de-Arellano M. PRMT5-Selective Inhibitors Suppress Inflammatory T Cell Responses and Experimental Autoimmune Encephalomyelitis. J Immunol 2017, 198, 1439-1451. vii Li L, Niu Z, Cai S, Zhi Y, Li H, Rong H, Liu L, Liu L, He W, Li Y. A PdAg bimetallic nanocatalyst for selective reductive amination of nitroarenes. Chem Commun 2013, 49, 6843-6845. Zhang Q, Cai S, Li L, Chen Y, Rong H, Niu Z, Liu J, He W, Li Y. Direct Syntheses of Styryl Ethers from Benzyl Alcohols via Ag Nanoparticle-Catalyzed Tandem Aerobic Oxidation. ACS Catalysis 2013, 3, 1681-1684. Li H, Li L, Li Y. The Electronic Structure and Geometric Structure of Nanoclusters as Catalytic Active Sites. Nanotechnology Reviews 2013, 2, 515-528. Fields of Study Major Field: Pharmacy (Pharmaceutical Sciences) viii Table of Contents Abstract ........................................................................................................................................... ii Dedication ...................................................................................................................................... iv Acknowledgements ......................................................................................................................... v Vita ................................................................................................................................................ vii List of Tables ................................................................................................................................ xiii List of Figures .............................................................................................................................. xiv List of Scheme .............................................................................................................................. xvi Chapter 1. Brief Overview of Antibiotics and Novel Bacterial Topoisomerase Inhibitors ............. 1 1.1 Introduction ........................................................................................................................... 1 1.2 Typical Classes of Antibiotics ............................................................................................... 1 1.2.1 Cell wall antibiotics ............................................................................................................ 2 1.2.1.1 β-lactam antibiotics ..................................................................................................... 3 1.2.1.1 Glycopeptide antibiotics .............................................................................................. 5 1.2.2 Bacterial ribosome antibiotics ............................................................................................ 7 1.2.2.1 Aminoglycoside antibiotics ......................................................................................... 8 1.2.2.2 Macrolide antibiotics ................................................................................................. 10 1.2.2.3 Tetracycline antibiotics ............................................................................................. 11 1.2.2.4 Oxazolidinone antibiotics .......................................................................................... 11 1.2.3 Cell membrane antibiotics ................................................................................................ 12 1.2.4 Folate biosynthesis antibiotics .........................................................................................