Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery

Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):12984-9. doi: 10.1073/pnas.1304045110. Epub 2013 Jul 19.


In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.

Keywords: drug design; hot spots; protein–ligand interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / antagonists & inhibitors*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Biophysics / methods
  • Calorimetry
  • Crystallography, X-Ray
  • Drug Discovery / methods*
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology*
  • Kinetics
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Structure
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / enzymology
  • Peptide Synthases / antagonists & inhibitors*
  • Peptide Synthases / chemistry
  • Peptide Synthases / metabolism
  • Protein Binding
  • Protein Structure, Tertiary
  • Protein Unfolding
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / metabolism
  • Small Molecule Libraries / pharmacology*
  • Temperature


  • Bacterial Proteins
  • Enzyme Inhibitors
  • Ligands
  • Small Molecule Libraries
  • Peptide Synthases
  • pantothenate synthetase

Associated data

  • PDB/4DDH
  • PDB/4DDK
  • PDB/4DDM
  • PDB/4EF6
  • PDB/4EFK
  • PDB/4FZJ
  • PDB/4G5F
  • PDB/4G5Y