.................................................................................................................................................. ii Acknowledgements ................................................................................................................................. v Preface .................................................................................................................................................. vii Table of contents .................................................................................................................................. viii Abbreviations ........................................................................................................................................ xv Co-authorship form .............................................................................................................................. xix Chapter 1: Introduction ............................................................................................................ 1 1.1 Antibiotics ..................................................................................................................................... 2 1.2 Biofilms: formation, pathogenicity and health consequences ....................................................... 5 1.2.1 Biofilm resistance mechanisms .............................................................................................. 8 1.3 Antimicrobial Peptides (AMP) ..................................................................................................... 9 1.3.1 Classification of antimicrobial peptides ............................................................................... 10 1.3.2 Mode of action of AMPs ...................................................................................................... 15 1.3.2.1 Bacterial cell wall architecture ...................................................................................... 15 1.3.2.1.1 Gram-positive cell wall .......................................................................................... 16 1.3.2.1.2 Gram-negative cell wall ......................................................................................... 17 1.3.2.2 Selectivity of AMPs to bacterial cells ........................................................................... 20 1.3.2.3 Shai-Matsuzaki-Huang (SMH) model .......................................................................... 21 1.3.2.4 Inhibitory activity of AMPs against biofilms ................................................................ 23 1.4 Therapeutic limitations of AMPs ................................................................................................ 25 1.5 Improving AMP stability through peptide modification ............................................................. 27 1.5.1 Unnatural amino acid incorporation..................................................................................... 28 1.5.2 Cyclisation ........................................................................................................................... 29 1.5.3 Nand C-terminal modification ........................................................................................... 31 1.6 Improving AMP stability using lipidation .................................................................................. 32 1.6.1 Classes of lipopeptides ......................................................................................................... 33 1.6.1.1 Daptomycin ................................................................................................................... 36 1.6.1.1.1 Mode of action ....................................................................................................... 38 1.6.1.1.2 Structure-activity relationship (SAR) studies ........................................................ 39 1.6.1.2 Polymyxin ..................................................................................................................... 40 1.6.1.2.1 Anti-biofilm activity of polymyxins ...................................................................... 42 1.6.1.2.2 Mode of action ....................................................................................................... 43