Thesis advisor: Eranthie Weerapana / Antibiotic resistance of bacterial pathogens poses an increasing threat to the wellbeing of our society and urgently calls for new strategies for infection diagnosis and antibiotic discovery. The overuse and misuse of broad-spectrum antibiotics has contributed to the antibiotic resistance crisis. Additionally, treatment of infections with broad-spectrum antibiotics can cause disruption to the host gut microbiome. The development of narrow-spectrum antibiotics would be ideal to avoid unnecessary cultivation of antibiotic resistance and damage to the human microbiota. Bacteria present many mechanisms of resistance, including modulating their cell surface with amine functionalities. In an age where infections are no longer responding to typical antibiotic treatments, novel drugs that target the characteristics of antibiotic resistance would be beneficial to remedy these defiant infections. Herein, we describe the utility of iminoboronate formation to target the amine- presenting surface modifications on bacteria, particularly those that display antibiotic resistance. Specifically, multiple 2-acetylphenylboronic acid warheads were incorporated into a peptide scaffold to develop potent peptide probes of bacterial cells. Further, by engineering a phage display library presenting the 2-acetylphenylboronic acid moieties, we were able to perform peptide library screens against live bacterial cells to develop reversible covalent peptide probes of target strains of bacteria. These peptide probes, which were developed for clinical strains of Staphylococcus aureus and Acinetobacter baumannii which display resistance, can label the target bacterium at submicromolar concentrations in a highly specific manner and in complex biological milieu. We further show that the identified peptide probes can be readily converted to bactericidal agents that deliver generic toxins to kill the targeted bacterial strain with high specificity. It is conceivable that this phage display platform is applicable to a wide array of bacterial strains, paving the way to facile diagnosis and development of strain-specific antibiotics. Furthermore, it is intriguing to speculate that even higher potency binding could be accomplished with better designed phage libraries with dynamic covalent warheads. This work is currently underway in our laboratory. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Peptide recognition domains (PRD) bind to short linear motifs on their biological partners and are found in several cellular pathways including those found to be critical in tumorigenesis. In this study, I aimed to generate peptide probes against PRDs present on proteins involved in ovarian cancer. Using bioinformatics, I identified 66 potential PRDs present on these proteins. I then used peptide phage display to successfully generate peptides against 27 of the 66 domains. To validate my results, I performed an extensive literature review and structural analysis. For several cases, the phage-display derived binding preferences are similar to previously reported studies. However, for a subset of domains, I identified non-canonical binding preferences that have not been reported previously in literature. The binding preferences obtained in this study can be used to design intracellular probes for studying the role of these PRDs in biological pathways important in ovarian cancer.

Peptide recognition domains (PRD) bind to short linear motifs on their biological partners and are found in several cellular pathways including those found to be critical in tumorigenesis. In this study, I aimed to generate peptide probes against PRDs present on proteins involved in ovarian cancer. Using bioinformatics, I identified 66 potential PRDs present on these proteins. I then used peptide phage display to successfully generate peptides against 27 of the 66 domains. To validate my results, I performed an extensive literature review and structural analysis. For several cases, the phage-display derived binding preferences are similar to previously reported studies. However, for a subset of domains, I identified non-canonical binding preferences that have not been reported previously in literature. The binding preferences obtained in this study can be used to design intracellular probes for studying the role of these PRDs in biological pathways important in ovarian cancer.