Potent and Selective SETDB1 Covalent Negative Allosteric Modulator Reduces Methyltransferase Activity in Cells

Mélanie Uguen; Devan J. Shell; Madhushika Silva; Yu Deng; Fengling Li; Magdalena M. Szewczyk; Ka Yang; Yani Zhao; Michael A. Stashko; Jacqueline L. Norris-Drouin; Jarod M. Waybright; Serap Beldar; Justin M. Rectenwald; Angie L. Mordant; Thomas S. Webb; Laura E. Herring; C.H. Arrowsmith; Suzanne Z. Ackloo; Steven P. Gygi; Robert K. McGinty; Dalia Baršytė-Lovejoy; Pengda Liu; Levon Halabelian; Lindsey Ingerman James; Kenneth H. Pearce; Stephen V. Frye

doi:10.1038/s41467-025-57005-3

Molecular BiologyNature CommunicationsFeb 24, 2025

Peer-reviewed journal article

Potent and Selective SETDB1 Covalent Negative Allosteric Modulator Reduces Methyltransferase Activity in Cells

Mélanie Uguen iD, Devan J. Shell iD, Madhushika Silva iD, Yu Deng iD, Fengling Li iD, Magdalena M. Szewczyk iD, Ka Yang iD, Yani Zhao iD, Michael A. Stashko, Jacqueline L. Norris-Drouin iD, Jarod M. Waybright iD, Serap Beldar iD, Justin M. Rectenwald iD, Angie L. Mordant iD, Thomas S. Webb, Laura E. Herring iD, C.H. Arrowsmith iD, Suzanne Z. Ackloo iD, Steven P. Gygi iD, Robert K. McGinty iD, Dalia Baršytė-Lovejoy iD, Pengda Liu iD, Levon Halabelian iD, Lindsey Ingerman James iD, Kenneth H. Pearce iD, Stephen V. Frye iD

Abstract

A promising drug target, SETDB1, is a dual Kme reader and methyltransferase, which has been implicated in cancer and neurodegenerative disease progression. To help understand the role of the triple Tudor domain (3TD) of SETDB1, its Kme reader, we first identified a low micromolar small molecule ligand, UNC6535, which occupies simultaneously both the TD2 and TD3 reader binding sites. Further optimization led to the discovery of UNC10013, the first covalent 3TD ligand targeting Cys385 of SETDB1. UNC10013 is potent with a kinact/KI of 1.0 x 106 M-1s-1 and demonstrated proteome-wide selectivity. In cells, negative allosteric modulation of SETDB1-mediated Akt methylation was observed after treatment with UNC10013. Therefore, UNC10013 is a potent, selective and cell-active covalent ligand for the 3TD of SETDB1, demonstrating negative allosteric modulator properties and making it a promising tool to study the biological role of SETDB1 in disease progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/615363v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@6db8e2org.highwire.dtl.DTLVardef@1852ee3org.highwire.dtl.DTLVardef@c95bb6org.highwire.dtl.DTLVardef@1a43951_HPS_FORMAT_FIGEXP M_FIG C_FIG

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