Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders

J Mol Biol. 2017 Aug 4;429(16):2556-2570. doi: 10.1016/j.jmb.2017.06.016. Epub 2017 Jun 30.


Fragment-based drug discovery is an increasingly popular method to identify novel small-molecule drug candidates. One of the limitations of the approach is the difficulty of accurately characterizing weak binding events. This work reports a combination of X-ray diffraction, surface plasmon resonance experiments and molecular dynamics simulations for the characterization of binders to different isoforms of the cyclophilin (Cyp) protein family. Although several Cyp inhibitors have been reported in the literature, it has proven challenging to achieve high binding selectivity for different isoforms of this protein family. The present studies have led to the identification of several structurally novel fragments that bind to diverse Cyp isoforms in distinct pockets with low millimolar dissociation constants. A detailed comparison of the merits and drawbacks of the experimental and computational techniques is presented, and emerging strategies for designing ligands with enhanced isoform specificity are described.

Keywords: PPIases; cyclophilin inhibitors; fragment-based drug discovery; free energy calculations; protein–ligand X-ray crystallography.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cyclophilins / antagonists & inhibitors*
  • Cyclophilins / metabolism*
  • Drug Discovery / methods*
  • Limit of Detection*
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Isoforms / antagonists & inhibitors
  • Protein Isoforms / metabolism
  • Surface Plasmon Resonance / methods
  • X-Ray Diffraction / methods


  • Protein Isoforms
  • Cyclophilins