Hybrid Screening Approach for Very Small Fragments: X-ray and Computational Screening on FKBP51

J Med Chem. 2020 Jun 11;63(11):5856-5864. doi: 10.1021/acs.jmedchem.0c00120. Epub 2020 Jun 3.


Fragment-based drug discovery (FBDD) permits efficient sampling of the vast chemical space for hit identification. Libraries are screened biophysically and fragment:protein co-structures are determined by X-ray crystallography. In parallel, computational methods can derive pharmacophore models or screen virtual libraries. We screened 15 very small fragments (VSFs) (HA ≤ 11) computationally, using site identification by ligand competitive saturation (SILCS), and experimentally, by X-ray crystallography, to map potential interaction sites on the FKBP51 FK1 domain. We identified three hot spots and obtained 6 X-ray co-structures, giving a hit rate of 40%. SILCS FragMaps overlapped with X-ray structures. The compounds had millimolar affinities as determined by 15N HSQC NMR. VSFs identified the same interactions as known FK1 binder and provide new chemical starting points. We propose a hybrid screening strategy starting with SILCS, followed by a pharmacophore-derived X-ray screen and 15N HSQC NMR based KD determination to rapidly identify hits and their binding poses.

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Humans
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Molecular Dynamics Simulation
  • Protein Domains
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / metabolism
  • Tacrolimus Binding Proteins / chemistry
  • Tacrolimus Binding Proteins / metabolism*


  • Ligands
  • Small Molecule Libraries
  • Tacrolimus Binding Proteins
  • tacrolimus binding protein 5