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Determining target engagement in living systems

Nature Chemical Biology volume 9, pages 200–205 (2013)Cite this article

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Chemical probes are critical tools for elucidating the biological functions of proteins and can lead to new medicines for treating disease. The pharmacological validation of protein function requires verification that chemical probes engage their intended targets in vivo. Here we discuss technologies, both established and emergent, for measuring target engagement in living systems and propose that determining this parameter should become standard practice for chemical probe and drug discovery programs.

Determining the biological functions of proteins requires selective tools to perturb their expression and/or activity in living systems. Molecular biology methods, such as targeted gene disruption and RNAi, are ubiquitous and fairly straightforward methods to achieve this goal. Small-molecule probes offer complementary and, in some ways, superior tools for interrogating proteins and pathways because they can provide greater spatiotemporal control over protein function and can perturb this parameter without concomitant changes in protein expression1. This latter feature, of course, also means that the effect of small molecules on protein function can rarely be inferred from simple protein abundance measurements such as western blotting. Alternative assays must be enlisted to confirm that a small molecule interacts with its intended protein target in a living system, a parameter that is referred to as target engagement.

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Figure 1: Approaches for measuring target engagement in cellular systems.
Figure 2: Approaches for measuring target engagement in model organisms.
Figure 3: Approaches for measuring target engagement in humans.

References

  1. Weiss, W.A., Taylor, S.S. & Shokat, K.M. Nat. Chem. Biol. 3, 739–744 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Grimwood, S. & Hartig, P.R. Pharmacol. Ther. 122, 281–301 (2009).

    CAS  PubMed  Google Scholar 

  3. Krishna, R., Herman, G. & Wagner, J.A. AAPS J. 10, 401–409 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Wong, D.F., Tauscher, J. & Grunder, G. Neuropsychopharmacology 34, 187–203 (2009).

    CAS  PubMed  Google Scholar 

  5. Matthews, P.M., Rabiner, E.A., Passchier, J. & Gunn, R.N. Br. J. Clin. Pharmacol. 73, 175–186 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Wagner, J.A. Annu. Rev. Pharmacol. Toxicol. 48, 631–651 (2008).

    CAS  PubMed  Google Scholar 

  7. Shelat, A.A. & Guy, R.K. Nat. Chem. Biol. 3, 442–446 (2007).

    CAS  PubMed  Google Scholar 

  8. Inglese, J. et al. Nat. Chem. Biol. 3, 466–479 (2007).

    CAS  PubMed  Google Scholar 

  9. Bigott-Hennkens, H.M., Dannoon, S., Lewis, M.R. & Jurisson, S.S. Q. J. Nucl. Med. Mol. Imaging 52, 245–253 (2008).

    CAS  PubMed  Google Scholar 

  10. Dormán, G. & Prestwich, G.D. Trends Biotechnol. 18, 64–77 (2000).

    PubMed  Google Scholar 

  11. Halvorsen, S.W. & Berg, D.K. J. Neurosci. 7, 2547–2555 (1987).

    CAS  PubMed  Google Scholar 

  12. Zhang, J., Yang, P.L. & Gray, N.S. Nat. Rev. Cancer 9, 28–39 (2009).

    PubMed  Google Scholar 

  13. Paweletz, C.P. et al. PLoS ONE 6, e26459 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Bantscheff, M. et al. Nat. Biotechnol. 25, 1035–1044 (2007).

    CAS  PubMed  Google Scholar 

  15. Cravatt, B.F., Wright, A.T. & Kozarich, J.W. Annu. Rev. Biochem. 77, 383–414 (2008).

    CAS  PubMed  Google Scholar 

  16. Nodwell, M.B. & Sieber, S.A. Top. Curr. Chem. 324, 1–41 (2012).

    CAS  PubMed  Google Scholar 

  17. Patricelli, M.P. et al. Chem. Biol. 18, 699–710 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kubota, K. et al. Nat. Biotechnol. 27, 933–940 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Stains, C.I. et al. Chem. Biol. 19, 210–217 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Bantscheff, M. et al. Nat. Biotechnol. 29, 255–265 (2011).

    CAS  PubMed  Google Scholar 

  21. Liu, Y., Patricelli, M.P. & Cravatt, B.F. Proc. Natl. Acad. Sci. USA 96, 14694–14699 (1999).

    CAS  PubMed  Google Scholar 

  22. Kato, D. et al. Nat. Chem. Biol. 1, 33–38 (2005).

    CAS  PubMed  Google Scholar 

  23. Hsu, K.L. et al. Nat. Chem. Biol. 8, 999–1007 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Cohen, M.S., Hadjivassiliou, H. & Taunton, J. Nat. Chem. Biol. 3, 156–160 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Edgington, L.E. et al. J. Am. Chem. Soc. 135, 174–182 (2013).

    CAS  PubMed  Google Scholar 

  26. Krysiak, J.M. et al. Angew. Chem. Int. Edn. Engl. 51, 7035–7040 (2012).

    CAS  Google Scholar 

  27. Verdoes, M. et al. Chem. Biol. 19, 619–628 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Rostovtsev, V.V., Green, J.G., Fokin, V.V. & Sharpless, K.B. Angew. Chem. Int. Edn. Engl. 41, 2596–2599 (2002).

    CAS  Google Scholar 

  29. Saxon, E. & Bertozzi, C.R. Science 287, 2007–2010 (2000).

    CAS  PubMed  Google Scholar 

  30. Bachovchin, D.A. et al. Proc. Natl. Acad. Sci. USA 108, 6811–6816 (2011).

    CAS  PubMed  Google Scholar 

  31. Geurink, P.P., Prely, L.M., van der Marel, G.A., Bischoff, R. & Overkleeft, H.S. Top. Curr. Chem. 324, 85–113 (2012).

    CAS  PubMed  Google Scholar 

  32. Salisbury, C.M. & Cravatt, B.F. Proc. Natl. Acad. Sci. USA 104, 1171–1176 (2007).

    CAS  PubMed  Google Scholar 

  33. Bradner, J.E. et al. Nat. Chem. Biol. 6, 238–243 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Tagore, D.M. et al. Nat. Chem. Biol. 5, 23–25 (2009).

    CAS  PubMed  Google Scholar 

  35. Gross, R.W. & Han, X. Chem. Biol. 18, 284–291 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Need, A.B., McKinzie, J.H., Mitch, C.H., Statnick, M.A. & Phebus, L.A. Life Sci. 81, 1389–1396 (2007).

    CAS  PubMed  Google Scholar 

  37. Lancelot, S. & Zimmer, L. Trends Pharmacol. Sci. 31, 411–417 (2010).

    CAS  PubMed  Google Scholar 

  38. Long, J.Z. et al. Nat. Chem. Biol. 5, 37–44 (2009).

    CAS  PubMed  Google Scholar 

  39. Ahn, K. et al. Chem. Biol. 16, 411–420 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Edgington, L.E., Verdoes, M. & Bogyo, M. Curr. Opin. Chem. Biol. 15, 798–805 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Edgington, L.E. et al. Nat. Med. 15, 967–973 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Choi, H.G. et al. ACS Med. Chem. Lett. 3, 658–662 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Adibekian, A. et al. J. Am. Chem. Soc. 134, 10345–10348 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Ashworth, S. et al. J. Nucl. Med. 51, 1021–1029 (2010).

    CAS  PubMed  Google Scholar 

  45. Yokoi, F. et al. Neuropsychopharmacology 27, 248–259 (2002).

    CAS  PubMed  Google Scholar 

  46. Erondu, N. et al. Cell Metab. 4, 275–282 (2006).

    CAS  PubMed  Google Scholar 

  47. Adams, J. Cancer Cell 5, 417–421 (2004).

    CAS  PubMed  Google Scholar 

  48. Arastu-Kapur, S. et al. Clin. Cancer Res. 17, 2734–2743 (2011).

    CAS  PubMed  Google Scholar 

  49. Carmi, C., Mor, M., Petronini, P.G. & Alfieri, R.R. Biochem. Pharmacol. 84, 1388–1399 (2012).

    CAS  PubMed  Google Scholar 

  50. Advani, R.H. et al. J. Clin. Oncol. 31, 88–94 (2013).

    CAS  PubMed  Google Scholar 

  51. Honigberg, L.A. et al. Proc. Natl. Acad. Sci. USA 107, 13075–13080 (2010).

    CAS  PubMed  Google Scholar 

  52. Ledford, H. Nature 483, 519 (2012).

    CAS  PubMed  Google Scholar 

  53. Apsel, B. et al. Nat. Chem. Biol. 4, 691–699 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Skaddan, M.B. et al. Nucl. Med. Biol. 39, 1058–1067 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Das Thakur, M. et al. Nature 494, 251–255 (2013).

    CAS  PubMed  Google Scholar 

  56. Wacker, S.A., Houghtaling, B.R., Elemento, O. & Kapoor, T.M. Nat. Chem. Biol. 8, 235–237 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Suwaki, N. et al. Sci. Transl. Med. 3, 85ra47 (2011).

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We are grateful for the support of the US National Institutes of Health (CA087660, CA132630, DA033760 and DA032541) and the Skaggs Institute for Chemical Biology.

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Authors and Affiliations

  1. Gabriel M. Simon is at Abide Therapeutics, San Diego, California, USA.,

    Gabriel M Simon

  2. Micah J. Niphakis and Benjamin F. Cravatt are at the Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA.,

    Micah J Niphakis & Benjamin F Cravatt

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Correspondence to Benjamin F Cravatt.

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Simon, G., Niphakis, M. & Cravatt, B. Determining target engagement in living systems. Nat Chem Biol 9, 200–205 (2013). https://doi.org/10.1038/nchembio.1211

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