Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects
Date
2022
Authors
Richter, Amelia
Sutherland, Darcy
Ebrahimikondori, Hossein
Babcock, Alana
Louie, Nathan
Li, Chenkai
Coombe, Lauren
Lin, Diana
Warren, René L.
Yanai, Anat
Journal Title
Journal ISSN
Volume Title
Publisher
Antibiotics
Abstract
Antimicrobial peptides (AMPs) are a diverse class of short, often cationic biological molecules that present promising opportunities in the development of new therapeutics to combat antimicrobial resistance. Newly developed in silico methods offer the ability to rapidly discover numerous novel AMPs with a variety of physiochemical properties. Herein, using the rAMPage AMP discovery pipeline, we bioinformatically identified 51 AMP candidates from amphibia and insect RNA-seq data and present their in-depth characterization. The studied AMPs demonstrate activity against a panel of bacterial pathogens and have undetected or low toxicity to red blood cells and human cultured cells. Amino acid sequence analysis revealed that 30 of these bioactive peptides belong to either the Brevinin-1, Brevinin-2, Nigrocin-2, or Apidaecin AMP families. Prediction of three-dimensional structures using ColabFold indicated an association between peptides predicted to adopt a helical structure and broad-spectrum antibacterial activity against the Gram-negative and Gram-positive species tested in our panel. These findings highlight the utility of associating the diverse sequences of novel AMPs with their estimated peptide structures in categorizing AMPs and predicting their antimicrobial activity.
Description
Opinions expressed in this document are those of the author and not necessarily those of the Governments of Canada and British Columbia. The Governments of Canada and British Columbia and their directors, agents, employees, or contractors will not be liable for any claims, damages, or losses of any kind whatsoever arising out of the use of, or reliance upon, this information.
Keywords
antimicrobial peptide, AMP discovery, structure prediction, antimicrobial resistance
Citation
Richter, A., Sutherland, D., Ebrahimikondori, H., Babcock, A., Louie, N., Li, C., Coombe, L., Lin, D., Rm, W., Yanai, A., Kotkoff, M., Helbing, C. C., Hof, F., Hoang, L., & Birol, İ. (2022). Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects. Antibiotics, 11(12), 1710. https://doi.org/10.3390/antibiotics11121710