Machine Learning Platform to Discover Novel Growth Inhibitors of Neisseria gonorrhoeae

Pharm Res. 2020 Jul 13;37(7):141. doi: 10.1007/s11095-020-02876-y.


Purpose: To advance fundamental biological and translational research with the bacterium Neisseria gonorrhoeae through the prediction of novel small molecule growth inhibitors via naïve Bayesian modeling methodology.

Methods: Inspection and curation of data from the publicly available ChEMBL web site for small molecule growth inhibition data of the bacterium Neisseria gonorrhoeae resulted in a training set for the construction of machine learning models. A naïve Bayesian model for bacterial growth inhibition was utilized in a workflow to predict novel antibacterial agents against this bacterium of global health relevance from a commercial library of >105 drug-like small molecules. Follow-up efforts involved empirical assessment of the predictions and validation of the hits.

Results: Specifically, two small molecules were found that exhibited promising activity profiles and represent novel chemotypes for agents against N. gonorrrhoeae.

Conclusions: This represents, to the best of our knowledge, the first machine learning approach to successfully predict novel growth inhibitors of this bacterium. To assist the chemical tool and drug discovery fields, we have made our curated training set available as part of the Supplementary Material and the Bayesian model is accessible via the web. Graphical Abstract.

Keywords: Diversity; Naïve Bayesian classifier; Neisseria gonorrhoeae; machine learning model.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology*
  • Bayes Theorem
  • Databases, Chemical
  • Drug Discovery*
  • Gonorrhea / drug therapy*
  • Gonorrhea / microbiology
  • Machine Learning*
  • Microbial Sensitivity Tests
  • Molecular Structure
  • Neisseria gonorrhoeae / drug effects*
  • Neisseria gonorrhoeae / growth & development
  • Structure-Activity Relationship


  • Anti-Bacterial Agents