Ultra-large library docking for discovering new chemotypes

Nature. 2019 Feb;566(7743):224-229. doi: 10.1038/s41586-019-0917-9. Epub 2019 Feb 6.


Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible. Here we investigate structure-based docking of 170 million make-on-demand compounds from 130 well-characterized reactions. The resulting library is diverse, representing over 10.7 million scaffolds that are otherwise unavailable. For each compound in the library, docking against AmpC β-lactamase (AmpC) and the D4 dopamine receptor were simulated. From the top-ranking molecules, 44 and 549 compounds were synthesized and tested for interactions with AmpC and the D4 dopamine receptor, respectively. We found a phenolate inhibitor of AmpC, which revealed a group of inhibitors without known precedent. This molecule was optimized to 77 nM, which places it among the most potent non-covalent AmpC inhibitors known. Crystal structures of this and other AmpC inhibitors confirmed the docking predictions. Against the D4 dopamine receptor, hit rates fell almost monotonically with docking score, and a hit-rate versus score curve predicted that the library contained 453,000 ligands for the D4 dopamine receptor. Of 81 new chemotypes discovered, 30 showed submicromolar activity, including a 180-pM subtype-selective agonist of the D4 dopamine receptor.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry
  • Crystallography, X-Ray
  • Dopamine Agonists / chemistry*
  • Dopamine Agonists / isolation & purification*
  • Humans
  • Ligands
  • Machine Learning
  • Molecular Docking Simulation / methods*
  • Observation
  • Receptors, Dopamine D4 / agonists
  • Receptors, Dopamine D4 / chemistry
  • Receptors, Dopamine D4 / metabolism
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / isolation & purification*
  • beta-Lactamase Inhibitors / chemistry*
  • beta-Lactamase Inhibitors / isolation & purification*
  • beta-Lactamases / chemistry


  • Bacterial Proteins
  • Dopamine Agonists
  • Ligands
  • Small Molecule Libraries
  • beta-Lactamase Inhibitors
  • Receptors, Dopamine D4
  • AmpC beta-lactamases
  • beta-Lactamases