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The Lipopeptide Antibiotic Daptomycin: Its Interaction With Calcium And Membranes And The Effects Of Membrane Lipid Composition On Its Activity by Robert Mackay Taylor A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Chemistry Waterloo, Ontario, Canada, 2018 ©Robert Mackay Taylor 2018 Examining Committee Membership The following served on the Examining Committee for this thesis. The decision of the Examining Committee is by majority vote. External Examiner Dr. Richard M. Epand, PhD. Professor Emeritus, McMaster University Biochemistry and Biomedical Sciences Supervisor Dr. Scott D. Taylor, PhD. Professor, University of Waterloo Chemistry Internal Member Dr. Michael Palmer, PhD. M.D., Dr. habil Associate Professor, University of Waterloo Chemistry Internal-external Member Dr. Zoya Leonenko, PhD. Professor, University of Waterloo Physics and Astronomy Other Member(s) Dr. Thorsten Dieckmann, PhD. Associate Professor, University of Waterloo Associate Chair (Graduate Studies and Research) Chemistry Dr. John Honek, PhD. Professor, University of Waterloo Chemistry ii Author’s Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. iii Abstract Daptomycin (Dap) is a calcium-dependent cyclic lipodepsipeptide antibiotic used clinically to treat infections with pathogenic Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). It targets the cell membrane, which must contain phosphatidylglycerol (PG) for activity. Although Dap was discovered over 30 years ago, its mechanism of action is still debated among researchers. Many action mechanisms have been proposed for Dap. The mechanism that has garnered the most attention involves Dap oligomerization in the cell membrane resulting in the formation of cation-selective pores, which lead to membrane depolarization and cell death. To further investigate this proposed mechanism of action, I here studied the interaction of Dap with calcium, the activity and pore-forming abilities of a Dap dimer, and the effects of membrane lipid composition on Dap-membrane interactions and pore formation. The stoichiometry of calcium to Dap in the presence of liposomes and how calcium concentration affects Dap oligomerization and membrane insertion was investigated using fluorescence spectroscopy and isothermal titration calorimetry. It was shown that Dap interacts with liposomes in two sequential calcium-binding events. The binding of the first calcium ion is suggested to cause oligomer formation of Dap in the membrane. The binding of a second calcium ion is suggested to cause a deeper insertion of this oligomer, followed, potentially, by translocation into the inner leaflet, ultimately forming a functional pore. The effect of Dap pre-oligomerization on antibacterial activity was studied via the synthesis and characterization of a Dap dimer. The dimer was prepared by connecting the N-termini of two Dap monomers via an octadecanedioate linker. It was anticipated that the dimer would decrease the entropic cost associated with oligomer formation. This would promote oligomer formation, thereby enhancing its activity. In contrast to expectation, the activity of the dimer was greatly reduced on vegetative cells yet was able to form cation-selective pores in liposomes. On bacterial L-forms, which lack a cell wall, dimer activity was close to that of the monomer. This suggests that the dimer was unable to cross the cell wall of vegetative cells, thus highlighting the role of the cell wall in Dap resistance. The effect of lipid acyl chain composition on Dap’s ability to interact with, oligomerize, and form pores in membranes was examined. Dap was found to insert into and form oligomers on phosphatidylcholine (PC)/PG liposomes containing either dimyristoyl (DMPC/DMPG), dioleyl iv (DOPC/DOPG) or dipalmitoleoyl (POPC/POPG) acyl chains. DMPC/DMPG lipids were found to support pore formation, while DOPC/DOPG and POPC/POPG lipids did not support pore formation. Only 1-5% of an added oleoyl chained lipid, regardless of head group, was necessary to prevent pore formation in liposomes containing dimyristoyl acyl chains. Permeabilization was regained when the molar concentration of Dap surpassed the molar concentration of the dioleoyl chained lipid present. This indicates a near-stoichiometric dose-response interaction of a dioleoyl chained lipid, DOPC, to Dap. The reason for the reduced permeabilization of Dap on DOPC/DOPG lipids was further investigated. Experiments indicated that the acyl chain unsaturation of dioleoyl chained lipids alone is not sufficient for the inhibitory effect of DOPC/DOPG lipids on Dap; thus, the greater length of oleoyl relative to myristoyl acyl groups appears to be important. Moreover, the inhibitory effect cannot be overcome by extending the N-terminal acyl residue of Dap itself. Overall, the findings in this thesis provide substantial new detail on the mode of action of Dap. They also shed light on mechanisms of bacterial resistance to Dap, and they help to reconcile some of the conflicting findings on Dap activity that were obtained with model membranes differing in lipid composition. v Acknowledgements I wish to express my deepest gratitude and appreciation to my supervisor Dr. Scott D. Taylor and mentor and committee member Dr. Michael Palmer. From day one of this journey, Dr. Scott Taylor has demonstrated the focus and drive needed in research. His constant guidance, support and discussions throughout my degree have been extremely appreciated. Although on paper Dr. Michael Palmer is a committee member of mine, I will always treat him as a supervisor to me. Dr. Palmer is an exceptionally intelligent person, in regards to research, science as a whole and the world outside the lab. I will always be eternally grateful for his support, humbleness, constant reassurance and guidance throughout my time here. Both Dr. Taylor and Dr. Palmer are curious gentlemen that are pushing science and the world of Daptomycin forward. I will always be eternally grateful for being a part of each of their labs. I wish to express gratitude to my committee members, Dr. Thorsten Dieckmann and Dr. John Honek, for their guidance and discussions throughout this degree. I would like to thank my external examiner, Dr. Richard Epand, and my internal-external examiner, Dr. Zoya Leonenko for their acceptance to read and edit this thesis and for their valuable comments and suggestions. Thank you to my family for their endless support and help throughout my career at the University of Waterloo. Thank you to my significant other, Victoria. She has and always will be there for me and love me through it all. Her support and love for me helped me get through when times were tough. Thank you to Dr. John Honek and Anton van der Ven for being the mentors I needed during my undergraduate studies. Their mentorship lead me to a path in research. Their guidance, understanding and fun-loving attitude made me understand the joys and hard work required of research. Thank you to my peers throughout my studies within Dr. Michael Palmer’s and Dr. Scott Taylor’s laboratories, namely (in no particular order): David Beriashvili, Braden Kralt, Brad Scott, Dr. Chuda Lohani, Dr. Tiahua Zhang, Jacob Soley, Michael Noden, Eric Brefo-Mensah, Bowen Zheng. vi Dedication To my loved ones… vii Table of Contents Examining Committee Membership .................................................................................... ii Author’s Declaration ........................................................................................................... iii Abstract ................................................................................................................................ iv Acknowledgements ............................................................................................................. vi Dedication ........................................................................................................................... vii Table of Contents .............................................................................................................. viii List of Figures ..................................................................................................................... xii List of Tables ....................................................................................................................... xv List of Abbreviations ......................................................................................................... xvi Chapter 1 Introduction ......................................................................................................... 1 1.1 Antibiotics .................................................................................................................... 2 1.2 Mechanisms of Action and Resistance of Antibiotics ............................................. 5 1.2.1 Cell Wall ................................................................................................................. 5 1.2.2 Protein Synthesis .................................................................................................... 7 1.2.3 DNA/RNA ............................................................................................................... 8 1.2.4 Cell Membranes

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