Highly selective inhibition of histone demethylases by de novo macrocyclic peptides

Akane Kawamura; Martin Münzel; Tatsuya Kojima; Clarence Yapp; Bhaskar Bhushan; Yuki Goto; Anthony Tumber; Takayuki Katoh; Oliver N F King; Toby Passioura; Louise J Walport; Stephanie B Hatch; Sarah Madden; Susanne Müller; Paul E Brennan; Rasheduzzaman Chowdhury; Richard J Hopkinson; Hiroaki Suga; Christopher J Schofield

doi:10.1038/ncomms14773

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides

Akane Kawamura, Martin Münzel, Tatsuya Kojima, Clarence Yapp, Bhaskar Bhushan, Yuki Goto, Anthony Tumber, Takayuki Katoh, Oliver N F King, Toby Passioura, Louise J Walport, Stephanie B Hatch, Sarah Madden, Susanne Müller, Paul E Brennan, Rasheduzzaman Chowdhury, Richard J Hopkinson, Hiroaki Suga, Christopher J Schofield

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

124 Citations (SciVal)

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.

Original language	English
Pages (from-to)	14773
Journal	Nature Communications
Volume	8
DOIs	https://doi.org/10.1038/ncomms14773
Publication status	Published - 6 Apr 2017

Keywords

Crystallography, X-Ray
Enzyme Inhibitors/pharmacology
Humans
Inhibitory Concentration 50
Jumonji Domain-Containing Histone Demethylases/antagonists & inhibitors
Mass Spectrometry
Peptides, Cyclic/pharmacology
Proteolysis
Structure-Activity Relationship
Substrate Specificity

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Kawamura, A., Münzel, M., Kojima, T., Yapp, C., Bhushan, B., Goto, Y., Tumber, A., Katoh, T., King, O. N. F., Passioura, T., Walport, L. J., Hatch, S. B., Madden, S., Müller, S., Brennan, P. E., Chowdhury, R., Hopkinson, R. J., Suga, H., & Schofield, C. J. (2017). Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nature Communications, 8, 14773. https://doi.org/10.1038/ncomms14773

Kawamura, A, Münzel, M, Kojima, T, Yapp, C, Bhushan, B, Goto, Y, Tumber, A, Katoh, T, King, ONF, Passioura, T, Walport, LJ, Hatch, SB, Madden, S, Müller, S, Brennan, PE, Chowdhury, R, Hopkinson, RJ, Suga, H & Schofield, CJ 2017, 'Highly selective inhibition of histone demethylases by de novo macrocyclic peptides', Nature Communications, vol. 8, pp. 14773. https://doi.org/10.1038/ncomms14773

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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.",

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AU - Kawamura, Akane

AU - Münzel, Martin

AU - Kojima, Tatsuya

AU - Yapp, Clarence

AU - Bhushan, Bhaskar

AU - Goto, Yuki

AU - Tumber, Anthony

AU - Katoh, Takayuki

AU - King, Oliver N F

AU - Passioura, Toby

AU - Walport, Louise J

AU - Hatch, Stephanie B

AU - Madden, Sarah

AU - Müller, Susanne

AU - Brennan, Paul E

AU - Chowdhury, Rasheduzzaman

AU - Hopkinson, Richard J

AU - Suga, Hiroaki

AU - Schofield, Christopher J

PY - 2017/4/6

Y1 - 2017/4/6

N2 - 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.

AB - 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.

KW - Crystallography, X-Ray

KW - Enzyme Inhibitors/pharmacology

KW - Humans

KW - Inhibitory Concentration 50

KW - Jumonji Domain-Containing Histone Demethylases/antagonists & inhibitors

KW - Mass Spectrometry

KW - Peptides, Cyclic/pharmacology

KW - Proteolysis

KW - Structure-Activity Relationship

KW - Substrate Specificity

U2 - 10.1038/ncomms14773

DO - 10.1038/ncomms14773

M3 - Article

C2 - 28382930

SN - 2041-1723

VL - 8

SP - 14773

JO - Nature Communications

JF - Nature Communications

ER -

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides

Abstract

Keywords

UN SDGs

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