Molecular docking and ligand specificity in fragment-based inhibitor discovery

Nat Chem Biol. 2009 May;5(5):358-64. doi: 10.1038/nchembio.155. Epub 2009 Mar 22.

Abstract

Fragment screens have successfully identified new scaffolds in drug discovery, often with relatively high hit rates (5%) using small screening libraries (1,000-10,000 compounds). This raises two questions: would other noteworthy chemotypes be found were one to screen all commercially available fragments (>300,000), and does the success rate imply low specificity of fragments? We used molecular docking to screen large libraries of fragments against CTX-M beta-lactamase. We identified ten millimolar-range inhibitors from the 69 compounds tested. The docking poses corresponded closely to the crystallographic structures subsequently determined. Notably, these initial low-affinity hits showed little specificity between CTX-M and an unrelated beta-lactamase, AmpC, which is unusual among beta-lactamase inhibitors. This is consistent with the idea that the high hit rates among fragments correlate to a low initial specificity. As the inhibitors were progressed, both specificity and affinity rose together, yielding to our knowledge the first micromolar-range noncovalent inhibitors against a class A beta-lactamase.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Drug Discovery*
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Ligands
  • Models, Molecular
  • Molecular Structure
  • beta-Lactamase Inhibitors

Substances

  • Enzyme Inhibitors
  • Ligands
  • beta-Lactamase Inhibitors

Associated data

  • PDB/3G2Y
  • PDB/3G2Z
  • PDB/3G30
  • PDB/3G31
  • PDB/3G32
  • PDB/3G34
  • PDB/3G35
  • PubChem-Substance/57287690
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