A deep learning method for predicting the minimum inhibitory concentration of antimicrobial peptides against Escherichia coli using Multi-Branch-CNN and Attention

Jielu YAN, Bob ZHANG*, Mingliang ZHOU, François Xavier CAMPBELL-VALOIS, Shirley W.I. SIU*

*Corresponding author for this work

Research output: Journal PublicationsReview articleOther Review

2 Citations (Scopus)

Abstract

Antimicrobial peptides (AMPs) are a promising alternative to antibiotics to combat drug resistance in pathogenic bacteria. However, the development of AMPs with high potency and specificity remains a challenge, and new tools to evaluate antimicrobial activity are needed to accelerate the discovery process. Therefore, we proposed MBC-Attention, a combination of a multi-branch convolution neural network architecture and attention mechanisms to predict the experimental minimum inhibitory concentration of peptides against Escherichia coli. The optimal MBC-Attention model achieved an average Pearson correlation coefficient (PCC) of 0.775 and a root mean squared error (RMSE) of 0.533 (log μM) in three independent tests of randomly drawn sequences from the data set. This results in a 5–12% improvement in PCC and a 6–13% improvement in RMSE compared to 17 traditional machine learning models and 2 optimally tuned models using random forest and support vector machine. Ablation studies confirmed that the two proposed attention mechanisms, global attention and local attention, contributed largely to performance improvement. IMPORTANCE Antimicrobial peptides (AMPs) are potential candidates for replacing conventional antibiotics to combat drug resistance in pathogenic bacteria. Therefore, it is necessary to evaluate the antimicrobial activity of AMPs quantitatively. However, wet-lab experiments are labor-intensive and time-consuming. To accelerate the evaluation process, we develop a deep learning method called MBC-Attention to regress the experimental minimum inhibitory concentration of AMPs against Escherichia coli. The proposed model outperforms traditional machine learning methods. Data, scripts to reproduce experiments, and the final production models are available on GitHub.

Original languageEnglish
Number of pages18
JournalmSystems
Volume8
Issue number4
Early online date11 Jul 2023
DOIs
Publication statusPublished - Aug 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright © 2023 Yan et al.

Keywords

  • antimicrobial peptides
  • deep learning
  • drug discovery
  • minimum inhibitory concentrations
  • regression

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