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A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics

Nature Chemical Biology volume 10, pages 853–860 (2014)Cite this article

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Abstract

Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity. In ERK1/2, SCH772984 induces a so-far-unknown binding pocket that accommodates the piperazine-phenyl-pyrimidine decoration. This new binding pocket was created by an inactive conformation of the phosphate-binding loop and an outward tilt of helix αC. In contrast, structure determination of SCH772984 with the off-target haspin and JNK1 revealed two canonical but distinct type I binding modes. Notably, the new binding mode with ERK1/2 was associated with slow binding kinetics in vitro as well as in cell-based assay systems. The described binding mode of SCH772984 with ERK1/2 enables the design of a new type of specific kinase inhibitors with prolonged on-target activity.

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Figure 1: Illustrating inhibition modes of kinase inhibitors.
Figure 2: SCH772984 has a unique binding mode in ERK1/2.
Figure 3: Selectivity and off-target binding modes of SCH772984.
Figure 4: Slow kinetics of SCH772984 both in vitro and in cell-based systems.
Figure 5: Structural analysis of inhibitor interactions and mutagenesis of key residues that modulate binding kinetics.
Figure 6: Effects of ERK and PARP inhibitors on BRCA2-deficient cell survival.

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Acknowledgements

S.K. is supported by the Structural Genomics Consortium, a registered charity (number 1097737) that receives funds from AbbVie, Bayer, Boehringer Ingelheim, the Canada Foundation for Innovation, the Canadian Institutes for Health Research, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, the Novartis Research Foundation, the Ontario Ministry of Economic Development and Innovation, Pfizer, Takeda and the Wellcome Trust (092809/Z/10/Z). A.C. is supported by the European Union FP7 Grant No. 278568 'PRIMES' (Protein interaction machines in oncogenic EGF receptor signalling). Work in M.T.'s laboratory is supported by Cancer Research UK, the EMBO Young Investigator Program and The Royal Society, and E.T. is funded by a Medical Research Council PhD Studentship. We thank the staff at Diamond Light Source for assistance during data collection at the synchrotron and H. Lee (Seoul National University) for providing the sheep anti-BRCA2 antibody.

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Authors and Affiliations

  1. Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK

    Apirat Chaikuad & Stefan Knapp

  2. Telomere and Genome Stability Group, The Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Old Road Campus Research Building, Oxford, UK

    Eliana M C Tacconi, Jutta Zimmer & Madalena Tarsounas

  3. Department of Biological Chemistry and Molecular Pharmacology, Department of Cancer Biology, Harvard Medical School, Dana Farber Cancer Institute, Boston, Massachusetts, USA

    Yanke Liang & Nathanael S Gray

  4. Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA

    Stefan Knapp

  5. Nuffield Department of Medicine Research Building, Target Discovery Institute, University of Oxford, Oxford, UK

    Stefan Knapp

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  1. Apirat Chaikuad
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Contributions

A.C. purified all of the proteins and determined crystal structures and biophysical characterization. N.S.G. and Y.L. synthesized inhibitors and provided enzymatic screening data. E.M.C.T. and J.Z. developed cellular assays. A.C., M.T. and S.K. wrote the paper with assistance from all co-authors.

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Correspondence to Madalena Tarsounas or Stefan Knapp.

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Chaikuad, A., M C Tacconi, E., Zimmer, J. et al. A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics. Nat Chem Biol 10, 853–860 (2014). https://doi.org/10.1038/nchembio.1629

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