Pre-trained molecular representations enable antimicrobial discovery

The rise in antimicrobial resistance poses a worldwide threat, reducing the efficacy of common antibiotics. Determining the antimicrobial activity of new chemical compounds through experimental methods is still a time-consuming and costly endeavor. Compound-centric deep learning models hold the promise to speed up this search and prioritization process. Here, we introduce a lightweight computational strategy for antimicrobial discovery that builds on MolE(Molecular representation through redundancy reduced Embedding), a deep learning framework that leverages unlabeled chemical structures to learn task-independent molecular representations. By combining MolE representation learning with experimentally validated compound-bacteria activity data, we design a general predictive model that enables assessing compounds with respect to their antimicrobial potential. The model correctly identified recent growth-inhibitory compounds that are structurally distinct from current antibiotics and discovered de novo three human-targeted drugs as Staphylococcus aureus growth inhibitors which we experimentally confirmed. Our framework offers a viable cost-effective strategy to accelerate antibiotics discovery.