Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles

Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18787-92. doi: 10.1073/pnas.1012741107. Epub 2010 Oct 18.


Using a diverse collection of small molecules generated from a variety of sources, we measured protein-binding activities of each individual compound against each of 100 diverse (sequence-unrelated) proteins using small-molecule microarrays. We also analyzed structural features, including complexity, of the small molecules. We found that compounds from different sources (commercial, academic, natural) have different protein-binding behaviors and that these behaviors correlate with general trends in stereochemical and shape descriptors for these compound collections. Increasing the content of sp(3)-hybridized and stereogenic atoms relative to compounds from commercial sources, which comprise the majority of current screening collections, improved binding selectivity and frequency. The results suggest structural features that synthetic chemists can target when synthesizing screening collections for biological discovery. Because binding proteins selectively can be a key feature of high-value probes and drugs, synthesizing compounds having features identified in this study may result in improved performance of screening collections.

Publication types

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

MeSH terms

  • Drug Discovery
  • Models, Theoretical*
  • Protein Array Analysis / methods*
  • Protein Binding
  • Proteins / chemistry*


  • Proteins