Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches

ACS Chem Biol. 2009 Jun 19;4(6):473-83. doi: 10.1021/cb9000102.


As part of our effort to inhibit bacterial fatty acid biosynthesis through the recently validated target biotin carboxylase, we employed a unique combination of two emergent lead discovery strategies. We used both de novo fragment-based drug discovery and virtual screening, which employs 3D shape and electrostatic property similarity searching. We screened a collection of unbiased low-molecular-weight molecules and identified a structurally diverse collection of weak-binding but ligand-efficient fragments as potential building blocks for biotin carboxylase ATP-competitive inhibitors. Through iterative cycles of structure-based drug design relying on successive fragment costructures, we improved the potency of the initial hits by up to 3000-fold while maintaining their ligand-efficiency and desirable physicochemical properties. In one example, hit-expansion efforts resulted in a series of amino-oxazoles with antibacterial activity. These results successfully demonstrate that virtual screening approaches can substantially augment fragment-based screening approaches to identify novel antibacterial agents.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology*
  • Binding Sites
  • Carbon-Nitrogen Ligases / antagonists & inhibitors*
  • Carbon-Nitrogen Ligases / metabolism
  • Combinatorial Chemistry Techniques
  • Drug Discovery / methods*
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • Ligands
  • Microbial Sensitivity Tests
  • Molecular Weight
  • Structure-Activity Relationship


  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Ligands
  • Carbon-Nitrogen Ligases
  • biotin carboxylase

Associated data

  • PDB/2W6M
  • PDB/2W6N
  • PDB/2W6O
  • PDB/2W6P
  • PDB/2W6Q
  • PDB/2W6Z
  • PDB/2W70
  • PDB/2W71