Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

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.

Accession codes


Protein Data Bank


  1. Krause, D.S. & Van Etten, R.A. Tyrosine kinases as targets for cancer therapy. N. Engl. J. Med. 353, 172–187 (2005).

    Article  CAS  Google Scholar 

  2. Sebolt-Leopold, J.S. & English, J.M. Mechanisms of drug inhibition of signalling molecules. Nature 441, 457–462 (2006).

    Article  CAS  Google Scholar 

  3. Shaw, R.J. & Cantley, L.C. Ras, PI(3)K and mTOR signalling controls tumour cell growth. Nature 441, 424–430 (2006).

    Article  CAS  Google Scholar 

  4. Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004).

    Article  CAS  Google Scholar 

  5. Samuels, Y. & Velculescu, V.E. Oncogenic mutations of PIK3CA in human cancers. Cell Cycle 3, 1221–1224 (2004).

    Article  CAS  Google Scholar 

  6. Li, J. et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275, 1943–1947 (1997).

    Article  CAS  Google Scholar 

  7. Knight, Z.A. & Shokat, K.M. Chemically targeting the PI3K family. Biochem. Soc. Trans. 35, 245–249 (2007).

    Article  CAS  Google Scholar 

  8. Maira, S.M. et al. Identification and characterization of NVP-BEZ235, a new orally available dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor with potent in vivo antitumor activity. Mol. Cancer Ther. 7, 1851–1863 (2008).

    Article  CAS  Google Scholar 

  9. Engelman, J.A. et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 316, 1039–1043 (2007).

    Article  CAS  Google Scholar 

  10. Sergina, N.V. et al. Escape from HER-family tyrosine kinase inhibitor therapy by the kinase-inactive HER3. Nature 445, 437–441 (2007).

    Article  CAS  Google Scholar 

  11. Haas-Kogan, D.A. et al. Epidermal growth factor receptor, protein kinase B/Akt, and glioma response to erlotinib. J. Natl. Cancer Inst. 97, 880–887 (2005).

    Article  CAS  Google Scholar 

  12. Mellinghoff, I.K. et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med. 353, 2012–2024 (2005).

    Article  CAS  Google Scholar 

  13. Fan, Q.W. et al. Combinatorial efficacy achieved through two-point blockade within a signaling pathway-a chemical genetic approach. Cancer Res. 63, 8930–8938 (2003).

    CAS  PubMed  Google Scholar 

  14. Wang, M.Y. et al. Mammalian target of rapamycin inhibition promotes response to epidermal growth factor receptor kinase inhibitors in PTEN-deficient and PTEN-intact glioblastoma cells. Cancer Res. 66, 7864–7869 (2006).

    Article  CAS  Google Scholar 

  15. Mohi, M.G. et al. Combination of rapamycin and protein tyrosine kinase (PTK) inhibitors for the treatment of leukemias caused by oncogenic PTKs. Proc. Natl. Acad. Sci. USA 101, 3130–3135 (2004).

    Article  CAS  Google Scholar 

  16. Fan, Q.W. et al. A dual phosphoinositide-3-kinase alpha/mTOR inhibitor cooperates with blockade of epidermal growth factor receptor in PTEN-mutant glioma. Cancer Res. 67, 7960–7965 (2007).

    Article  CAS  Google Scholar 

  17. Knight, Z.A. & Shokat, K.M. Features of selective kinase inhibitors. Chem. Biol. 12, 621–637 (2005).

    Article  CAS  Google Scholar 

  18. Knight, Z.A. et al. A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling. Cell 125, 733–747 (2006).

    Article  CAS  Google Scholar 

  19. Karaman, M.W. et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26, 127–132 (2008).

    Article  CAS  Google Scholar 

  20. Hopkins, A.L., Mason, J.S. & Overington, J.P. Can we rationally design promiscuous drugs? Curr. Opin. Struct. Biol. 16, 127–136 (2006).

    Article  CAS  Google Scholar 

  21. Scheeff, E.D. & Bourne, P.E. Structural evolution of the protein kinase-like superfamily. PLoS Comput. Biol. 1, e49 (2005).

    Article  Google Scholar 

  22. Walker, E.H., Perisic, O., Ried, C., Stephens, L. & Williams, R.L. Structural insights into phosphoinositide 3-kinase catalysis and signalling. Nature 402, 313–320 (1999).

    Article  CAS  Google Scholar 

  23. Walker, E.H. et al. Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine. Mol. Cell 6, 909–919 (2000).

    Article  CAS  Google Scholar 

  24. Liu, Y. et al. Wortmannin, a widely used phosphoinositide 3-kinase inhibitor, also potently inhibits mammalian polo-like kinase. Chem. Biol. 12, 99–107 (2005).

    Article  CAS  Google Scholar 

  25. Stauffer, F., Maira, S.M., Furet, P. & Garcia-Echeverria, C. Imidazo[4,5-c]quinolines as inhibitors of the PI3K/PKB-pathway. Bioorg. Med. Chem. Lett. 18, 1027–1030 (2008).

    Article  CAS  Google Scholar 

  26. Hanke, J.H. et al. Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. Study of Lck- and FynT-dependent T cell activation. J. Biol. Chem. 271, 695–701 (1996).

    Article  CAS  Google Scholar 

  27. Liu, Y. et al. Structural basis for selective inhibition of Src family kinases by PP1. Chem. Biol. 6, 671–678 (1999).

    Article  CAS  Google Scholar 

  28. Schindler, T. et al. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. Mol. Cell 3, 639–648 (1999).

    Article  CAS  Google Scholar 

  29. Sarbassov, D.D., Guertin, D.A., Ali, S.M. & Sabatini, D.M. Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex. Science 307, 1098–1101 (2005).

    Article  CAS  Google Scholar 

  30. Ishii, N. et al. Frequent co-alterations of TP53, p16/CDKN2A, p14ARF, PTEN tumor suppressor genes in human glioma cell lines. Brain Pathol. 9, 469–479 (1999).

    Article  CAS  Google Scholar 

  31. Fan, Q.W. et al. A dual PI3 kinase/mTOR inhibitor reveals emergent efficacy in glioma. Cancer Cell 9, 341–349 (2006).

    Article  CAS  Google Scholar 

  32. Samuels, Y. et al. Mutant PIK3CA promotes cell growth and invasion of human cancer cells. Cancer Cell 7, 561–573 (2005).

    Article  CAS  Google Scholar 

  33. Carlomagno, F. et al. BAY 43–9006 inhibition of oncogenic RET mutants. J. Natl. Cancer Inst. 98, 326–334 (2006).

    Article  CAS  Google Scholar 

  34. Carlomagno, F. et al. Point mutation of the RET proto-oncogene in the TT human medullary thyroid carcinoma cell line. Biochem. Biophys. Res. Commun. 207, 1022–1028 (1995).

    Article  CAS  Google Scholar 

  35. Gupta-Abramson, V. et al. Phase II trial of sorafenib in advanced thyroid cancer. J. Clin. Oncol. (in the press).

  36. Graupera, M. et al. Angiogenesis selectively requires the p110alpha isoform of PI3K to control endothelial cell migration. Nature 453, 662–666 (2008).

    Article  CAS  Google Scholar 

  37. Guba, M. et al. Rapamycin inhibits primary and metastatic tumor growth by antiangiogenesis: involvement of vascular endothelial growth factor. Nat. Med. 8, 128–135 (2002).

    Article  CAS  Google Scholar 

  38. de Klein, A. et al. A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. Nature 300, 765–767 (1982).

    Article  CAS  Google Scholar 

  39. Shah, N.P. et al. Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia. Cancer Cell 2, 117–125 (2002).

    Article  CAS  Google Scholar 

  40. Gorre, M.E. et al. Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science 293, 876–880 (2001).

    Article  CAS  Google Scholar 

  41. Sawyers, C.L. Cancer: mixing cocktails. Nature 449, 993–996 (2007).

    Article  CAS  Google Scholar 

  42. Stommel, J.M. et al. Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies. Science 318, 287–290 (2007).

    Article  CAS  Google Scholar 

  43. Schindler, T. et al. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289, 1938–1942 (2000).

    Article  CAS  Google Scholar 

  44. Liu, Y. & Gray, N.S. Rational design of inhibitors that bind to inactive kinase conformations. Nat. Chem. Biol. 2, 358–364 (2006).

    Article  CAS  Google Scholar 

  45. Dudley, D.T., Pang, L., Decker, S.J., Bridges, A.J. & Saltiel, A.R. A synthetic inhibitor of the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA 92, 7686–7689 (1995).

    Article  CAS  Google Scholar 

  46. Fry, D.W. et al. Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor. Proc. Natl. Acad. Sci. USA 95, 12022–12027 (1998).

    Article  CAS  Google Scholar 

  47. Cohen, M.S., Zhang, C., Shokat, K.M. & Taunton, J. Structural bioinformatics-based design of selective, irreversible kinase inhibitors. Science 308, 1318–1321 (2005).

    Article  CAS  Google Scholar 

Download references


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).

Author information

Authors and Affiliations



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.

Corresponding author

Correspondence to Kevan M Shokat.

Ethics declarations

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)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing