Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects
Published in Antibiotics, 2022
Recommended citation: Richter, A., Sutherland, D., Ebrahimikondori, H., Babock, A., Louie, N., Li, C., Coombe, L., Lin, D., Warren, R.L., Yanai, A., Kotkoff, M., Helbing, C.C., Hof, F., Hoang, L.M.N., & Birol, I. (2022). "Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects." Antibiotics 11(12):1710. https://doi.org/10.3390/antibiotics11121710
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.