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Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases

Nature Chemical Biology volume 4, pages 691–699 (2008)Cite this article

Abstract

The clinical success of multitargeted kinase inhibitors has stimulated efforts to identify promiscuous drugs with optimal selectivity profiles. It remains unclear to what extent such drugs can be rationally designed, particularly for combinations of targets that are structurally divergent. Here we report the systematic discovery of molecules that potently inhibit both tyrosine kinases and phosphatidylinositol-3-OH kinases, two protein families that are among the most intensely pursued cancer drug targets. Through iterative chemical synthesis, X-ray crystallography and kinome-level biochemical profiling, we identified compounds that inhibit a spectrum of new target combinations in these two families. Crystal structures revealed that the dual selectivity of these molecules is controlled by a hydrophobic pocket conserved in both enzyme classes and accessible through a rotatable bond in the drug skeleton. We show that one compound, PP121, blocks the proliferation of tumor cells by direct inhibition of oncogenic tyrosine kinases and phosphatidylinositol-3-OH kinases. These molecules demonstrate the feasibility of accessing a chemical space that intersects two families of oncogenes.

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Figure 1: Structural and sequence comparison of tyrosine kinases and PI(3)Ks.
Figure 2: Biochemical target selectivity of pyrazolopyrimidine inhibitors.
Figure 3: Crystal structures of S1 and S2 bound to human p110γ.
Figure 4: Structural comparison of pyrazolopyrimidine binding to tyrosine kinases and PI(3)Ks.
Figure 5: PP121 directly inhibits p110α/mTOR.
Figure 6: PP121 directly inhibits Src.
Figure 7: PP121 directly inhibits Ret.
Figure 8: PP121 redundantly targets Bcr-Abl and PI(3)K/mTOR in CML cells.

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Acknowledgements

We thank W.A. Weiss (University of California, San Francisco) for providing glioblastoma cells, W.M. Korn (University of California, San Francisco) for providing Seg1 cells, N. Shah (University of California, San Francisco) for providing BaF3 Bcr-Abl and BaF3 Bcr-Abl T315I cells, and D. Hanahan (University of California, San Francisco) for βTC3 cells. We thank P.J. Alaimo (Seattle University) for synthetic intermediates that were used to prepare several compounds, and J.L. Garrison for helpful comments on the text. This work was supported by the Sandler Program in Asthma Research and US National Institutes of Health grant AI44009. Mass spectrometry was made possible by US National Institutes of Health shared resource grants NCRR RR015804 and NCRR RR001614. B.G. has a Ramon y Cajal fellowship from the Ministerio de Educación y Ciencia in Spain and received funding from Comunidad Autonoma de Madrid-CSIC (CCG07-CSIC/GEN-2232).

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Author notes

  1. Beatriz Gonzalez & Zachary A Knight

    Present address: Present addresses: Instituto de Química-Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain (B.G.) and The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA (Z.A.K.).,

Authors and Affiliations

  1. Program in Chemistry and Chemical Biology, University of California, San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Beth Apsel & Morri E Feldman

  2. Department of Chemistry, University of California, Berkeley, Berkeley, 94720, California, USA

    Jimmy A Blair & Kevan M Shokat

  3. MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

    Beatriz Gonzalez & Roger L Williams

  4. Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Tamim M Nazif, Kevan M Shokat & Zachary A Knight

  5. Invitrogen Corporation, 501 Charmany Drive, Madison, 53719, Wisconsin, USA

    Brian Aizenstein & Randy Hoffman

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Contributions

B. Apsel and Z.A.K. synthesized the molecules, determined their IC50 values and performed cell proliferation assays. Z.A.K. performed the western blots. B. Apsel performed flow cytometry, angiogenesis and imaging assays. B.G. and R.L.W. determined the PI(3)K cocrystal structures. B. Apsel and J.A.B. determined the Src cocrystal structures. T.M.N. performed the HUVEC blots. B. Aizenstein and R.H. performed the Invitrogen SelectScreen. M.E.F. assisted with data analysis. Z.A.K. designed the experiments and wrote the paper, with input from B. Apsel and K.M.S.

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Correspondence to Kevan M Shokat.

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Competing interests

K.M.S., B. Apsel and Z.A.K. are joint inventors on UC Regents-owned patent applications covering these molecules, which have been licensed to Intellikine. K.M.S. and Z.A.K. hold stock in and are consultants to Intellikine. B. Aizenstein and R.H. are employees of Invitrogen Corporation.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–3 and Supplementary Methods (PDF 1249 kb)

Supplementary Movie 1

Conformational changes in Src associated with PP121 binding. (MOV 9080 kb)

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Apsel, B., Blair, J., Gonzalez, B. et al. Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases. Nat Chem Biol 4, 691–699 (2008). https://doi.org/10.1038/nchembio.117

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