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Targeting the disordered C terminus of PTP1B with an allosteric inhibitor

Nature Chemical Biology volume 10, pages 558–566 (2014)Cite this article

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Abstract

PTP1B, a validated therapeutic target for diabetes and obesity, has a critical positive role in HER2 signaling in breast tumorigenesis. Efforts to develop therapeutic inhibitors of PTP1B have been frustrated by the chemical properties of the active site. We define a new mechanism of allosteric inhibition that targets the C-terminal, noncatalytic segment of PTP1B. We present what is to our knowledge the first ensemble structure of PTP1B containing this intrinsically disordered segment, within which we identified a binding site for the small-molecule inhibitor MSI-1436. We demonstrate binding to a second site close to the catalytic domain, with cooperative effects between the two sites locking PTP1B in an inactive state. MSI-1436 antagonized HER2 signaling, inhibited tumorigenesis in xenografts and abrogated metastasis in the NDL2 mouse model of breast cancer, validating inhibition of PTP1B as a therapeutic strategy in breast cancer. This new approach to inhibition of PTP1B emphasizes the potential of disordered segments of proteins as specific binding sites for therapeutic small molecules.

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Figure 1: MSI-1436 was a noncompetitive inhibitor of PTP1B.
Figure 2: MSI-1436 induced a conformational change in PTP1B.
Figure 3: PTP1B residues 300–393 were flexible and predominantly disordered.
Figure 4: PTP1B residues were perturbed upon MSI-1436 binding.
Figure 5: Effect of mutations in the C terminus of PTP1B on inhibition by MSI-1436.
Figure 6: Effect of the allosteric inhibitor of PTP1B, MSI-1436, in cell and animal models of HER2-positive breast cancer.

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Acknowledgements

This research was supported by US National Institutes of Health (NIH) grants CA53840 and GM55989 and the Cold Spring Harbor Laboratory Cancer Centre Support Grant CA45508 to N.K.T.; by NIH grants GM100910 and GM098482, American Diabetes Association grant 1-14-ACN-31 and a Brown University Research Seed Fund grant by the Vice President for Research to W.P.; and by financial support from the French Agence Nationale de la Recherche (ANR) through ANR JCJC ProteinDisorder to M.R.J. and ANR MALZ TAUSTRUCT to M.B. J.K. is a fellow of the IDPbyNMR Marie Curie action of the European Commission (contract no 264257).

The 800-MHz NMR data were recorded at Brandeis University; the instrument was purchased with support from NIH S10-RR017269. NMR data (500 MHz and 850 MHz) were recorded in the Brown University Structural Biology Facility, which is generously supported by Brown University. N.K.T. is also grateful for support from the following foundations; The Gladowsky Breast Cancer Foundation, The Don Monti Memorial Research Foundation, Hansen Memorial Foundation, West Islip Breast Cancer Coalition for Long Island, Glen Cove CARES, Find a Cure Today (FACT), Constance Silveri, Robertson Research Fund and the Masthead Cove Yacht Club Carol Marcincuk Fund. PTP1B inhibitor MSI-1436 was provided by Ohr Pharmaceuticals and Genaera Corporation.

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  1. Bin Xue

    Present address: Present address: Department of Molecular and Cell Biology, University of California–Berkeley, Berkeley, California, USA.,

Authors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

    Navasona Krishnan, Bin Xue, Sai Dipikaa Akshinthala, Carla-Maria Gauss, Senthil K Muthuswamy & Nicholas K Tonks

  2. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA

    Dorothy Koveal & Rebecca Page

  3. Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA

    Daniel H Miller & Wolfgang Peti

  4. Department of Chemistry, Brown University, Providence, Rhode Island, USA

    Daniel H Miller & Wolfgang Peti

  5. Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Grenoble, France

    Jaka Kragelj, Malene Ringkjøbing Jensen & Martin Blackledge

  6. Department of Medical Biophysics, Ontario Cancer Institute, Campbell Family Institute for Breast Cancer Research, University of Toronto, Toronto, Canada

    Senthil K Muthuswamy

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Contributions

N.K. performed the biochemical characterization of PTP1B inhibition by MSI-1436 and tested the effects of the inhibitor in cell and animal models; D.K., D.H.M., J.K., M.R.J., R.P., M.B. and W.P. designed, performed and analyzed NMR-based structural work. C.M.G. performed the homology modeling, molecular docking and dynamics simulation. B.X., S.D.A. and S.K.M. helped with the breast cancer studies. N.K., W.P. and N.K.T. analyzed the data and wrote the manuscript, which was reviewed by all authors. N.K.T. directed the study.

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Correspondence to Nicholas K Tonks.

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Competing interests

A company called DepYmed Inc. was founded on 3 March 2014 with the primary purpose of taking MSI-1436 into the clinic in patients with HER2-positive breast cancer. It is owned equally by Ohr Pharmaceuticals and Cold Spring Harbor Laboratory. Authors N.K. and N.K.T. are entitled to a share based on the conditions of the Invention Agreement signed by all of the scientists at Cold Spring Harbor Laboratory.

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Krishnan, N., Koveal, D., Miller, D. et al. Targeting the disordered C terminus of PTP1B with an allosteric inhibitor. Nat Chem Biol 10, 558–566 (2014). https://doi.org/10.1038/nchembio.1528

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