AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens

Li, C.; Sutherland, D.; Hammond, S. A.; Yang, C.; Taho, F.; Bergman, L.; Houston, S.; Warren, R. L.; Wong, T.; Hoang, L. M. N.; Cameron, C. E.; Helbing, C. C.; Birol, I.

doi:10.1101/2020.06.16.155705

bioRxiv · 10.1101/2020.06.16.155705

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens

Li, C.·Sutherland, D.·Hammond, S. A.·Yang, C.·Taho, F.·Bergman, L.·Houston, S.·Warren, R. L.·Wong, T.·Hoang, L. M. N.·Cameron, C. E.·Helbing, C. C.·Birol, I.

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Abstract

Antibiotic resistance is a growing global health concern prompting researchers to seek alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging therapeutic agents with promising utility in this domain and using in silico methods to discover novel AMPs is a strategy that is gaining interest. Such methods can filter through large volumes of candidate sequences and reduce lab screening costs. Here we introduce AMPlify, an attentive deep learning model for AMP prediction, and demonstrate its utility in prioritizing peptide sequences derived from the Rana [Lithobates] catesbeiana (bullfrog) genome. We tested the bioactivity of our predicted peptides against a panel of bacterial species, including representatives from the World Health Organizations "priority pathogens" list. Four of our novel AMPs were active against multiple species of bacteria, including a multi-drug resistant isolate of carbapenemase-producing Escherichia coli, demonstrating the utility of tools like AMPlify in our fight against antibiotic resistance.

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Li, C., Sutherland, D., Hammond, S. A., Yang, C., Taho, F., Bergman, L., Houston, S., Warren, R. L., Wong, T., Hoang, L. M. N., Cameron, C. E., Helbing, C. C., Birol, I.. 2020-06-17. AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. https://doi.org/10.1101/2020.06.16.155705

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