Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening

Biochemistry. 2019 Oct 22;58(42):4304-4316. doi: 10.1021/acs.biochem.9b00625. Epub 2019 Oct 11.


Fatty acid binding protein 5 (FABP5) is a promising target for development of inhibitors to help control pain and inflammation. In this work, computer-based docking (DOCK6 program) was employed to screen ∼2 M commercially available compounds to FABP5 based on an X-ray structure complexed with the small molecule inhibitor SBFI-26 previously identified by our group (also through virtual screening). The goal was discovery of additional chemotypes. The screen resulted in the purchase of 78 candidates, which led to the identification of a new inhibitor scaffold (STK-0) with micromolar affinity and apparent selectivity for FABP5 over FABP3. A second similarity-based screen resulted in three additional hits (STK-15, STK-21, STK-22) from which preliminary SAR could be derived. Notably, STK-15 showed comparable activity to the SBFI-26 reference under the same assay conditions (1.40 vs 0.86 μM). Additional molecular dynamics simulations, free energy calculations, and structural analysis (starting from DOCK-generated poses) revealed that R enantiomers (dihydropyrrole scaffold) of STK-15 and STK-22 have a more optimal composition of functional groups to facilitate additional H-bonds with Arg109 of FABP5. This observation suggests enantiomerically pure compounds could show enhanced activity. Overall, our study highlights the utility of using similarity-based screening methods to discover new inhibitor chemotypes, and the identified FABP5 hits provide a strong starting point for future efforts geared to improve activity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cell Survival / drug effects
  • Crystallization
  • Crystallography, X-Ray
  • Cyclobutanes / chemistry
  • Cyclobutanes / pharmacology
  • Dicarboxylic Acids / chemistry
  • Dicarboxylic Acids / pharmacology
  • Drug Evaluation, Preclinical / methods*
  • Fatty Acid Binding Protein 3 / antagonists & inhibitors
  • Fatty Acid Binding Protein 3 / chemistry
  • Fatty Acid-Binding Proteins / antagonists & inhibitors*
  • Fatty Acid-Binding Proteins / chemistry*
  • Human Umbilical Vein Endothelial Cells
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology*
  • User-Computer Interface


  • 1-naphthyl alpha-truxillate
  • Cyclobutanes
  • Dicarboxylic Acids
  • FABP3 protein, human
  • FABP5 protein, human
  • Fatty Acid Binding Protein 3
  • Fatty Acid-Binding Proteins
  • Ligands
  • Recombinant Proteins
  • Small Molecule Libraries