Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds

John R. Horton, Xu Liu, Molly Gale, Lizhen Wu, John R. Shanks, Xing Zhang, Philip J. Webber, Joshua S.K. Bell, Stephen C. Kales, Bryan T. Mott, Ganesha Rai, Daniel J. Jansen, Mark J. Henderson, Daniel J. Urban, Matthew D. Hall, Anton Simeonov, David J. Maloney, Margaret A. Johns, Haian Fu, Ajit JadhavPaula M. Vertino, Qin Yan, Xiaodong Cheng

Research output: Contribution to journalArticlepeer-review

76 Scopus citations

Abstract

The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.

Original languageEnglish (US)
Pages (from-to)769-781
Number of pages13
JournalCell Chemical Biology
Volume23
Issue number7
DOIs
StatePublished - Jul 21 2016
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmacology
  • Drug Discovery
  • Clinical Biochemistry

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