Optimizing TRPM4 inhibitors in the MHFP6 chemical space

Eur J Med Chem. 2019 Mar 15:166:167-177. doi: 10.1016/j.ejmech.2019.01.048. Epub 2019 Jan 24.


We recently reported 4-chloro-2-(2-chlorophenoxy)acetamido)benzoic acid (CBA) as the first potent inhibitor of TRPM4, a cation channel implicated in cardiac diseases and prostate cancer. Herein we report a structure-activity relationship (SAR) study of CBA resulting in two new potent analogs. To design and interpret our SAR we used interactive color-coded 3D-maps representing similarities between compounds calculated with MHFP6 (MinHash fingerprint up to six bonds), a new molecular fingerprint outperforming other fingerprints in benchmarking virtual screening studies. We further illustrate the general applicability of our method by visualizing the structural diversity of active compounds from benchmarking sets in relation to decoy molecules and to drugs. MHFP6 chemical space 3D-maps might be generally helpful in designing, interpreting and communicating the results of SAR studies. The modified WebMolCS is accessible at http://gdb.unibe.ch and the code is available at https://github.com/reymond-group/webMolCS for off-line use.

Keywords: Chemical space; Cheminformatics; Ion channels; Structure-activity relationships; Virtual screening.

MeSH terms

  • Benzoates / chemistry
  • Benzoates / pharmacology
  • Drug Design*
  • Drug Evaluation, Preclinical
  • HEK293 Cells
  • Humans
  • Models, Molecular
  • Molecular Conformation
  • Structure-Activity Relationship
  • TRPM Cation Channels / antagonists & inhibitors*


  • Benzoates
  • TRPM Cation Channels