(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.
Dalia Barsyte-Lovejoy  1 ,  Fengling Li  2 ,  Menno J Oudhoff  3 ,  John H Tatlock  4 ,  Aiping Dong  2 ,  Hong Zeng  2 ,  Hong Wu  2 ,  Spencer A Freeman  5 ,  Matthieu Schapira  6 ,  Guillermo A Senisterra  2 ,  Ekaterina Kuznetsova  2 ,  Richard Marcellus  7 ,  Abdellah Allali-Hassani  2 ,  Steven Kennedy  2 ,  Jean-Philippe Lambert  8 ,  Amber L Couzens  8 ,  Ahmed Aman  7 ,  Anne-Claude Gingras  9 ,  Rima Al-Awar  10 ,  Paul V Fish  11 ,  Brian S Gerstenberger  12 ,  Lee Roberts  13 ,  Caroline L Benn  14 ,  Rachel L Grimley  14 ,  Mitchell J S Braam  3 ,  Fabio M V Rossi  15 ,  Marius Sudol  16 ,  Peter J Brown  2 ,  Mark E Bunnage  13 ,  Dafydd R Owen  13 ,  Colby Zaph  17 ,  Masoud Vedadi  18 ,  Cheryl H Arrowsmith  19
Affiliations
  • 1. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; [email protected] [email protected] [email protected].
  • 2. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
  • 3. Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
  • 4. Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, San Diego, CA 92121;
  • 5. Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
  • 6. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada M5S 1A8;
  • 7. Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
  • 8. Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada M5G 1X5;
  • 9. Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada M5G 1X5; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8;
  • 10. Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada M5S 1A8; Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
  • 11. Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Sandwich, Kent CT13 9NJ, United Kingdom;
  • 12. Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Groton, CT 06340;
  • 13. Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139;
  • 14. Neusentis Research Unit, Pfizer Worldwide Research and Development, Cambridge CB21 6GS, United Kingdom;
  • 15. Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
  • 16. Weis Center for Research, Geisinger Clinic, Danville, PA 17821;
  • 17. Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6T1Z3; and.
  • 18. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada M5S 1A8; [email protected] [email protected] [email protected].
  • 19. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON, Canada M5G 1L7 [email protected] [email protected] [email protected].
PMID: 25136132 DOI: 10.1073/pnas.1407358111
Abstract

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.
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