title: Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
abstract: The JmjC histone demethylases (KDMs) are linked to tumour cell proliferation and are current cancer targets; however, very few highly selective inhibitors for these are available. Here we report cyclic peptide inhibitors of the KDM4A-C with selectivity over other KDMs/2OG oxygenases, including closely related KDM4D/E isoforms. Crystal structures and biochemical analyses of one of the inhibitors (CP2) with KDM4A reveals that CP2 binds differently to, but competes with, histone substrates in the active site. Substitution of the active site binding arginine of CP2 to N-ɛ-trimethyl-lysine or methylated arginine results in cyclic peptide substrates, indicating that KDM4s may act on non-histone substrates. Targeted modifications to CP2 based on crystallographic and mass spectrometry analyses results in variants with greater proteolytic robustness. Peptide dosing in cells manifests KDM4A target stabilization. Although further development is required to optimize cellular activity, the results reveal the feasibility of highly selective non-metal chelating, substrate-competitive inhibitors of the JmjC KDMs.
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.|Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
authors.forename: Akane
authors.identifier: 0000-0003-1169-5082
authors.initials: A
authors.lastname: Kawamura
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Münzel
authors.affiliation: Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Kojima
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.|Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
authors.forename: Clarence
authors.initials: C
authors.lastname: Yapp
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.|Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Bhushan
authors.affiliation: Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Goto
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.|Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
authors.forename: Anthony
authors.initials: A
authors.lastname: Tumber
authors.affiliation: Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Katoh
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Oliver N F
authors.initials: ON
authors.lastname: King
authors.affiliation: Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.
authors.forename: Toby
authors.initials: T
authors.lastname: Passioura
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Louise J
authors.identifier: 0000-0002-3795-8365
authors.initials: LJ
authors.lastname: Walport
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.|Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
authors.forename: Stephanie B
authors.initials: SB
authors.lastname: Hatch
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Sarah
authors.identifier: 0000-0001-6858-7651
authors.initials: S
authors.lastname: Madden
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.|Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
authors.forename: Susanne
authors.initials: S
authors.lastname: Müller
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.|Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
authors.forename: Paul E
authors.initials: PE
authors.lastname: Brennan
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Rasheduzzaman
authors.identifier: 0000-0002-8058-6149
authors.initials: R
authors.lastname: Chowdhury
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Hopkinson
authors.affiliation: Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.|JST, CREST, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Suga
authors.affiliation: Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Schofield
mesh_terms: D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D006801:Humans; D020128:Inhibitory Concentration 50; D056484:Jumonji Domain-Containing Histone Demethylases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D013058:Mass Spectrometry; D010456:Peptides, Cyclic / Q000494:pharmacology*; D059748:Proteolysis; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D004791:Enzyme Inhibitors; D010456:Peptides, Cyclic; D056484:Jumonji Domain-Containing Histone Demethylases