title: Substrate- and cofactor-independent inhibition of histone demethylase KDM4C.
abstract: Inhibition of histone demethylases has within recent years advanced into a new strategy for treating cancer and other diseases. Targeting specific histone demethylases can be challenging, as the active sites of KDM1A-B and KDM4A-D histone demethylases are highly conserved. Most inhibitors developed up-to-date target either the cofactor- or substrate-binding sites of these enzymes, resulting in a lack of selectivity and off-target effects. This study describes the discovery of the first peptide-based inhibitors of KDM4 histone demethylases that do not share the histone peptide sequence or inhibit through substrate competition. Through screening of DNA-encoded peptide libraries against KDM1 and -4 histone demethylases by phage display, two cyclic peptides targeting the histone demethylase KDM4C were identified and developed as inhibitors by amino acid replacement, truncation, and chemical modifications. Hydrogen/deuterium exchange mass spectrometry revealed that the peptide-based inhibitors target KDM4C through substrate-independent interactions located on the surface remote from the active site within less conserved regions of KDM4C. The sites discovered in this study provide a new approach of targeting KDM4C through substrate- and cofactor-independent interactions and may be further explored to develop potent selective inhibitors and biological probes for the KDM4 family.
authors.affiliation: Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, ‡Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Leurs
authors.forename: Brian
authors.initials: B
authors.lastname: Lohse
authors.forename: Kasper D
authors.initials: KD
authors.lastname: Rand
authors.forename: Shonoi
authors.initials: S
authors.lastname: Ming
authors.forename: Erik S
authors.initials: ES
authors.lastname: Riise
authors.forename: Philip A
authors.initials: PA
authors.lastname: Cole
authors.forename: Jesper L
authors.initials: JL
authors.lastname: Kristensen
authors.forename: Rasmus P
authors.initials: RP
authors.lastname: Clausen
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D002460:Cell Line / Q000187:drug effects; D003067:Coenzymes; D041961:Deuterium Exchange Measurement; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D057166:High-Throughput Screening Assays / Q000379:methods; D056466:Histone Demethylases / Q000037:antagonists & inhibitors / Q000378:metabolism; D006801:Humans; D020128:Inhibitory Concentration 50; D056484:Jumonji Domain-Containing Histone Demethylases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D008969:Molecular Sequence Data; D019151:Peptide Library
chemical_list: D003067:Coenzymes; D004791:Enzyme Inhibitors; C413655:KDM4C protein, human; D019151:Peptide Library; D056466:Histone Demethylases; D056484:Jumonji Domain-Containing Histone Demethylases; C495195:KDM1A protein, human; C494424:KDM4A protein, human