Investigating Structural Properties of Antibacterial Peptides

Abstract

The race towards uncovering and developing novel antibiotics requires a multipronged, interdisciplinary approach. Highlighted in this thesis are biochemical and structural studies on peptides, small naturally occurring molecules that have innate bioactivities, such as antimicrobial characteristics. These include: faerocin MK, a potent anti-listerial molecule; teixobactin, a peptide with the ability to inhibit Gram-positive bacteria; tridecaptin A1, an inhibitor of Gram-negative bacteria; and microcin J25, a lasso peptide with activity against Gram-negative foodborne pathogens. Faerocin MK was uncovered after the genome sequencing of a newly discovered probiotic bacterium, Enterococcus faecium M3K31. The sequence encoding for faerocin MK contained two components: a structural gene and an immunity protein. Heterologous expression studies led to the production, isolation, and characterization of this new peptide. These studies showed that this peptide is active against Gram-positive organisms, with potent activity against Listeria spp., a genus of foodborne pathogens responsible for listeriosis. Teixobactin is a peptide isolated in 2015 and has gained much attention due to its potent activity against Gram-positive bacteria and unique structural features. With the use of analogues, the binding of teixobactin and its bacterial target, lipid II, a peptidoglycan precursor present within bacterial membranes, was investigated. Furthermore, the activity of teixobactin was expanded to reach Gram-negative organisms through synergistic assays with membrane-disrupting peptides. Tridecaptin A1 is part of a class of peptides which are potent against Gram-negative bacteria. They are known to bind to lipid II, the same peptidoglycan precursor targeted by teixobactin and a number of other antimicrobial peptides. In order to better understand the tridecaptin A1 mechanism of action, in particular its interaction with lipid II at the bacterial membrane surface, nuclear magnetic resonance experiments were employed. The structures of tridecaptin A1 and lipid II were studied in a new series of membrane-mimicking micelles. These micelle-forming dodecylphosphocholine compounds were synthesized, with heteroatom replacements at strategic positions, and structural data was compared amongst analogues. Microcin J25 is a lasso peptide from Escherichia coli active against Gram-negative, foodborne pathogens such as Salmonella species and E. coli. The unique structure of this class of peptides, wherein the C-terminal is threaded through an N-terminal macrocycle, confers on them desirable attributes such as thermal stability and protease resistance, along with potent innate activities against bacteria and viruses. The lasso shape has long been regarded as a valuable scaffold for pharmaceutical development, yet these peptides have thus far been accessed through biological means as a facile synthetic approach has not been developed. A method to synthesize this interlocked, stable structure was initiated, providing a potential facile means of accessing microcin J25 and other lasso peptides in the future.