Efficient search of chemical space: navigating from fragments to structurally diverse chemotypes

J Med Chem. 2013 Nov 14;56(21):8879-91. doi: 10.1021/jm401309q. Epub 2013 Oct 31.

Abstract

We introduce a novel strategy to sample bioactive chemical space, which follows-up on hits from fragment campaigns without the need for a crystal structure. Our results strongly suggest that screening a few hundred or thousand fragments can substantially improve the selection of small-molecule screening subsets. By combining fragment-based screening with virtual fragment linking and HTS fingerprints, we have developed an effective strategy not only to expand from low-affinity hits to potent compounds but also to hop in chemical space to substantially novel chemotypes. In benchmark calculations, our approach accessed subsets of compounds that were substantially enriched in chemically diverse hit compounds for various activity classes. Overall, half of the hits in the screening collection were found by screening only 10% of the library. Furthermore, a prospective application led to the discovery of two structurally novel histone deacetylase 4 inhibitors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Discovery
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / pharmacology
  • Enzymes / metabolism
  • High-Throughput Screening Assays
  • Models, Molecular
  • Molecular Structure
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology
  • Structure-Activity Relationship

Substances

  • Enzyme Inhibitors
  • Enzymes
  • Small Molecule Libraries

Associated data

  • PDB/4C3F