Alana Babcock

Topic

Optimization of antimicrobial peptides against avian pathogens

Department of Chemistry

Date & location

• Wednesday, August 5, 2026
• 1:30 P.M.
• Elliott Building, Room 226

Examining Committee

Supervisory Committee

• Dr. Fraser Hof, Department of Chemistry, University of Victoria (Co-Supervisor)
• Dr. Caren Helbing, Department of Biochemistry and Microbiology, UVic (Co-Supervisor)
• Dr. Jeremy Wulff, Department of Chemistry, UVic (Member)

External Examiner

• Dr. Juergen Ehlting, Department of Biology, UVic

Chair of Oral Examination

• Dr. Aditya Mojumdar, Department of Biochemistry and Microbiology, UVic

Abstract

Antimicrobial resistance (AMR) is an emerging global crisis exacerbated by the overuse and misuse of antibiotics. Antibiotic use practices in the agricultural industry are a known contributor to AMR. Antimicrobial stewardship guidelines implemented to reduce AMR in the Canadian poultry industry have had unintended consequences for both production and flock health. Alternative veterinary antimicrobials are needed to protect animal health and ensure food security, without exacerbating the AMR crisis. The work presented in this thesis aims to expand the arsenal of effective antimicrobials for use in the poultry industry by developing antimicrobial peptides (AMPs). AMPs are short peptides endogenous to all classes of life and act through diverse and generalized mechanisms of action to either inhibit bacterial cell growth, cause cell death or modulate the host immune system to aid in pathogen clearance. While AMPs show promise, their translation from research to industry has been limited by their cost of development, as many AMPs have poor bioavailability and stability in vivo. We addressed these limitations by leveraging artificial intelligence for AMP optimization. We built upon the previously reported AMPlify AMP discovery deep learning model to produce AMPs with retained or improved bioactivity, and more favourable properties for therapeutic applications. The artificial intelligence-directed ‘AMP Enhancement’ tool, was developed as an extension to the AMPlify pipeline to identify key sites for K/R point mutations and N-/C-terminal truncations in previously validated AMPs. As a final step, a subset of the AMPs with promising physicochemical properties were manually selected for targeted synthetic modifications to assess their ability to further enhance both activity and therapeutic potential. This AMP optimization pipeline was validated using two previously identified AMPlify AMPs RaCa2 and RaCa7. The resulting dataset of 102 unique AMP sequences (56 from RaCa7 and 45 from RaCa2) was evaluated by antimicrobial susceptibility testing (AST) using Escherichia coli 25922 (EC), avian pathogenic E. coli 317 (APEC), Staphylococcus aureus 29213 (SA), and a BCCDC clinical isolate of Salmonella enterica serovar Enteritidis (CDCSE) along with a hemolysis assay (HC50). Many of the mutated and truncated derivative AMPs had improved potency compared to the WT AMPs. C-terminal amidation synthetic modification proved to be a highly effective synthetic modification to improve AMP activity. To expand upon this finding, we used AMPlify and rAMPage computational pipelines to identify 120 putative AMPs for pairwise comparison of their activity in either their C-terminal amide or C-terminal carboxylate formThe AMPs were evaluated for activity against pathogens important in the poultry industry and public health: avian pathogenic Escherichia coli (APEC), Escherichia coli 25922 (EC), Salmonella enterica serovar Enteritidis 4931 (SE), avian Salmonella enterica serovar Enteritidis LS101 (ASE) and Staphylococcus aureus 29213 (SA). There were 72 AMP pairs (144 unique AMPs) with activity (MIC ≤ 128 μg/mL) in either their C-terminal carboxylate form, C-terminal amide form or both. Of these AMPs, C-terminal amidation significantly increased AMP activity in 51.4% of AMPs against EC, 51.4% against APEC, 44.4% against SE, 36.1% against ASE, and 33.3% against SA. We successfully identified several peptides with high activity (MIC ≤ 4 μg/ml), and selectivity against EC (9), APEC (4), SE (3), and SA (13). The present work also provides actionable physicochemical information for incorporation into AMP discovery pipelines. The influence of the C-terminus, length, charge, secondary structure, and hydrophobicity of the active AMP pairs was investigated, using direct comparison and multiple linear regression (MLR). AMPs with longer lengths, positive charges of +1 to +5, and hydrophobic characteristics were all associated with increased antimicrobial activity. Several AMPs identified in this thesis are candidates for further testing as poultry therapeutics. The present work also provides actionable physicochemical information for incorporation into AMP discovery pipelines, augmenting the identification of AMPs as antibiotic alternatives from multiple genomic resources.