(R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells

Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12853-8. doi: 10.1073/pnas.1407358111. Epub 2014 Aug 18.


SET domain containing (lysine methyltransferase) 7 (SETD7) is implicated in multiple signaling and disease related pathways with a broad diversity of reported substrates. Here, we report the discovery of (R)-PFI-2-a first-in-class, potent (Ki (app) = 0.33 nM), selective, and cell-active inhibitor of the methyltransferase activity of human SETD7-and its 500-fold less active enantiomer, (S)-PFI-2. (R)-PFI-2 exhibits an unusual cofactor-dependent and substrate-competitive inhibitory mechanism by occupying the substrate peptide binding groove of SETD7, including the catalytic lysine-binding channel, and by making direct contact with the donor methyl group of the cofactor, S-adenosylmethionine. Chemoproteomics experiments using a biotinylated derivative of (R)-PFI-2 demonstrated dose-dependent competition for binding to endogenous SETD7 in MCF7 cells pretreated with (R)-PFI-2. In murine embryonic fibroblasts, (R)-PFI-2 treatment phenocopied the effects of Setd7 deficiency on Hippo pathway signaling, via modulation of the transcriptional coactivator Yes-associated protein (YAP) and regulation of YAP target genes. In confluent MCF7 cells, (R)-PFI-2 rapidly altered YAP localization, suggesting continuous and dynamic regulation of YAP by the methyltransferase activity of SETD7. These data establish (R)-PFI-2 and related compounds as a valuable tool-kit for the study of the diverse roles of SETD7 in cells and further validate protein methyltransferases as a druggable target class.

Keywords: chemical biology; chemical probe; epigenetics.

Publication types

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

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism
  • Dose-Response Relationship, Drug
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • Epigenesis, Genetic / drug effects*
  • Fibroblasts / drug effects
  • Hippo Signaling Pathway
  • Histone-Lysine N-Methyltransferase / antagonists & inhibitors*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism*
  • Humans
  • MCF-7 Cells
  • Methyltransferases / antagonists & inhibitors
  • Methyltransferases / metabolism
  • Mutation
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Protein Serine-Threonine Kinases / genetics
  • Protein Structure, Tertiary
  • Pyrrolidines / chemistry
  • Pyrrolidines / pharmacology*
  • Signal Transduction / drug effects*
  • Structure-Activity Relationship
  • Sulfonamides / chemistry
  • Sulfonamides / pharmacology*
  • Tetrahydroisoquinolines / chemistry
  • Tetrahydroisoquinolines / pharmacology*
  • Transcription Factors
  • YAP-Signaling Proteins


  • (R)-PFI-2
  • Adaptor Proteins, Signal Transducing
  • Enzyme Inhibitors
  • Phosphoproteins
  • Pyrrolidines
  • Sulfonamides
  • Tetrahydroisoquinolines
  • Transcription Factors
  • YAP-Signaling Proteins
  • YAP1 protein, human
  • Methyltransferases
  • Histone-Lysine N-Methyltransferase
  • SETD7 protein, human
  • Protein Serine-Threonine Kinases

Associated data

  • PDB/4JLG