title: (R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells.
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.
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; carrow@uhnres.utoronto.ca m.vedadi@utoronto.ca d.barsyte@utoronto.ca.
authors.forename: Dalia
authors.initials: D
authors.lastname: Barsyte-Lovejoy
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Fengling
authors.initials: F
authors.lastname: Li
authors.affiliation: Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
authors.forename: Menno J
authors.initials: MJ
authors.lastname: Oudhoff
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, San Diego, CA 92121;
authors.forename: John H
authors.initials: JH
authors.lastname: Tatlock
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Aiping
authors.initials: A
authors.lastname: Dong
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Hong
authors.initials: H
authors.lastname: Zeng
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Hong
authors.initials: H
authors.lastname: Wu
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
authors.forename: Spencer A
authors.initials: SA
authors.lastname: Freeman
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada M5S 1A8;
authors.forename: Matthieu
authors.initials: M
authors.lastname: Schapira
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Guillermo A
authors.initials: GA
authors.lastname: Senisterra
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Kuznetsova
authors.affiliation: Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors.forename: Richard
authors.initials: R
authors.lastname: Marcellus
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Abdellah
authors.initials: A
authors.lastname: Allali-Hassani
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Steven
authors.initials: S
authors.lastname: Kennedy
authors.affiliation: Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada M5G 1X5;
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Lambert
authors.affiliation: Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada M5G 1X5;
authors.forename: Amber L
authors.initials: AL
authors.lastname: Couzens
authors.affiliation: Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors.forename: Ahmed
authors.initials: A
authors.lastname: Aman
authors.affiliation: 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;
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gingras
authors.affiliation: 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;
authors.forename: Rima
authors.initials: R
authors.lastname: Al-Awar
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Sandwich, Kent CT13 9NJ, United Kingdom;
authors.forename: Paul V
authors.initials: PV
authors.lastname: Fish
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Groton, CT 06340;
authors.forename: Brian S
authors.initials: BS
authors.lastname: Gerstenberger
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139;
authors.forename: Lee
authors.initials: L
authors.lastname: Roberts
authors.affiliation: Neusentis Research Unit, Pfizer Worldwide Research and Development, Cambridge CB21 6GS, United Kingdom;
authors.forename: Caroline L
authors.initials: CL
authors.lastname: Benn
authors.affiliation: Neusentis Research Unit, Pfizer Worldwide Research and Development, Cambridge CB21 6GS, United Kingdom;
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Grimley
authors.affiliation: Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
authors.forename: Mitchell J S
authors.initials: MJ
authors.lastname: Braam
authors.affiliation: Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
authors.forename: Fabio M V
authors.initials: FM
authors.lastname: Rossi
authors.affiliation: Weis Center for Research, Geisinger Clinic, Danville, PA 17821;
authors.forename: Marius
authors.initials: M
authors.lastname: Sudol
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Brown
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139;
authors.forename: Mark E
authors.initials: ME
authors.lastname: Bunnage
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139;
authors.forename: Dafydd R
authors.initials: DR
authors.lastname: Owen
authors.affiliation: 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.
authors.forename: Colby
authors.initials: C
authors.lastname: Zaph
authors.affiliation: Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada M5S 1A8; carrow@uhnres.utoronto.ca m.vedadi@utoronto.ca d.barsyte@utoronto.ca.
authors.forename: Masoud
authors.initials: M
authors.lastname: Vedadi
authors.affiliation: 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 carrow@uhnres.utoronto.ca m.vedadi@utoronto.ca d.barsyte@utoronto.ca.
authors.forename: Cheryl H
authors.initials: CH
authors.lastname: Arrowsmith
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D004305:Dose-Response Relationship, Drug; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D044127:Epigenesis, Genetic / Q000187:drug effects*; D005347:Fibroblasts / Q000187:drug effects; D000090683:Hippo Signaling Pathway; D011495:Histone-Lysine N-Methyltransferase / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D008780:Methyltransferases / Q000037:antagonists & inhibitors / Q000378:metabolism; D009154:Mutation; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D017434:Protein Structure, Tertiary; D011759:Pyrrolidines / Q000737:chemistry / Q000494:pharmacology*; D015398:Signal Transduction / Q000187:drug effects*; D013329:Structure-Activity Relationship; D013449:Sulfonamides / Q000737:chemistry / Q000494:pharmacology*; D044005:Tetrahydroisoquinolines / Q000737:chemistry / Q000494:pharmacology*; D014157:Transcription Factors; D000091102:YAP-Signaling Proteins
chemical_list: C000592938:(R)-PFI-2; D048868:Adaptor Proteins, Signal Transducing; D004791:Enzyme Inhibitors; D010750:Phosphoproteins; D011759:Pyrrolidines; D013449:Sulfonamides; D044005:Tetrahydroisoquinolines; D014157:Transcription Factors; D000091102:YAP-Signaling Proteins; C088374:YAP1 protein, human; D008780:Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; C540312:SETD7 protein, human; D017346:Protein Serine-Threonine Kinases
keywords: chemical biology; chemical probe; epigenetics