Novel chemical space exploration via natural products

J Med Chem. 2009 Apr 9;52(7):1953-62. doi: 10.1021/jm801514w.


Natural products (NPs) are a rich source of novel compound classes and new drugs. In the present study we have used the chemical space navigation tool ChemGPS-NP to evaluate the chemical space occupancy by NPs and bioactive medicinal chemistry compounds from the database WOMBAT. The two sets differ notably in coverage of chemical space, and tangible leadlike NPs were found to cover regions of chemical space that lack representation in WOMBAT. Property based similarity calculations were performed to identify NP neighbors of approved drugs. Several of the NPs revealed by this method were confirmed to exhibit the same activity as their drug neighbors. The identification of leads from a NP starting point may prove a useful strategy for drug discovery in the search for novel leads with unique properties.

Publication types

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

MeSH terms

  • Biological Products* / chemistry
  • Computer Graphics
  • Databases, Factual
  • Drug Design
  • Drug Discovery / methods*
  • Molecular Structure
  • Pharmaceutical Preparations* / chemistry
  • Structure-Activity Relationship


  • Biological Products
  • Pharmaceutical Preparations