Selective, rapid and optically switchable regulation of protein function in live mammalian cells (original) (raw)

• Shogren-Knaak, M. A., Alaimo, P. J. & Shokat, K. M. Recent advantages in chemical approaches to the study of biological systems. Annu. Rev. Cell Dev. Biol. 17, 405–433 (2001).
  Article CAS Google Scholar
• Knight, Z. A. & Shokat, K. M. Chemical genetics: where genetics and pharmacology meet. Cell 128, 425–430 (2007).
  Article CAS Google Scholar
• Schreiber, S. L. Organic synthesis toward small-molecule probes and drugs. Proc. Natl Acad. Sci. USA 108, 6699–6702 (2011).
  Article CAS Google Scholar
• Belshaw, P. J., Schoepfer, J. G., Liu, K-Q., Morrison, K. L. & Schreiber, S. L. Rational design of orthogonal receptor–ligand combinations. Angew. Chem. Int. Ed. 34, 2129–2132 (1995).
  Article CAS Google Scholar
• Bishop, A. C. et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407, 395–401 (2000).
  Article CAS Google Scholar
• Zheng, H., Al-Ayoubi, A. & Eblen, S. T. MAP Kinase Signaling Protocols Vol. 661 (Springer, 2010).
  Google Scholar
• Erlanson, D. A., Wells, J. A. & Braisted, A. C. Tethering: fragment-based drug discovery. Annu. Rev. Biophys. Biomol. Struct. 33, 199–223 (2004).
  Article CAS Google Scholar
• Cravatt, B. F., Wright, A. T. & Kozarich, J. W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77, 383–414 (2008).
  Article CAS Google Scholar
• Takaoka, Y., Ojida, A. & Hamachi, I. Protein organic chemistry and applications for labeling and engineering in live-cell systems. Angew. Chem. Int. Ed. 52, 4088–4106 (2013).
  Article CAS Google Scholar
• Chen, Z., Jing, C., Gallagher, S. S., Sheetz, M. P. & Cornish, V. W. Second-generation covalent TMP-Tag for live cell imaging. J. Am. Chem. Soc. 134, 13692–13699 (2012).
  Article CAS Google Scholar
• Liu, Q. et al. Developing irreversible inhibitors of the protein kinase cysteinome. Chem. Biol. 20, 146–159 (2013).
  Article Google Scholar
• Blair, J. A. et al. Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nature Chem. Biol. 3, 229–238 (2007).
  Article CAS Google Scholar
• Volgraf, M. et al. Allosteric control of an ionotropic glutamate receptor with an optical switch. Nature Chem. Biol. 2, 47–52 (2006).
  Article CAS Google Scholar
• Fehrentz, T., Schönberger, M. & Trauner, D. Optochemical genetics. Angew. Chem. Int. Ed. 50, 12156–12182 (2011).
  Article CAS Google Scholar
• Szymański, W., Beierle, J. M., Kistemaker, H. A. V., Velema, W. A. & Feringa, B. L. Reversible photocontrol of biological systems by the incorporation of molecular photoswitches. Chem. Rev. 113, 6114–6178 (2013).
  Article Google Scholar
• Sletten, E. M. & Bertozzi, C. R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Ed. 48, 6974–6998 (2009).
  Article CAS Google Scholar
• Lang, K. & Chin, J. W. Bioorthogonal reactions for labeling proteins. ACS Chem. Biol. 9, 16–20 (2014).
  Article CAS Google Scholar
• Lang, K. & Chin, J. W. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem. Rev. 114, 4764–4806 (2014).
  Article CAS Google Scholar
• Lang, K. et al. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nature Chem. 4, 298–304 (2012).
  Article CAS Google Scholar
• Plass, T. et al. Amino acids for Diels–Alder reactions in living cells. Angew. Chem. Int. Ed. 51, 4166–4170 (2012).
  Article CAS Google Scholar
• Kaya, E. et al. A genetically encoded norbornene amino acid for the mild and selective modification of proteins in a copper free click reaction. Angew. Chem. Int. Ed. 51, 4466–4469 (2012).
  Article CAS Google Scholar
• Seitchik, J. L. et al. Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with _trans_-cyclooctenes. J. Am. Chem. Soc. 134, 2898–2901 (2012).
  Article CAS Google Scholar
• Lang, K. et al. Genetic encoding of bicyclononynes and _trans_-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels–Alder reactions. J. Am. Chem. Soc. 134, 10317–10320 (2012).
  Article CAS Google Scholar
• Elliott, T. S. et al. Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal. Nature Biotechnol. 32, 465–472 (2014).
  Article CAS Google Scholar
• Bianco, A., Townsley, F. M., Greiss, S., Lang, K. & Chin, J. W. Expanding the genetic code of Drosophila melanogaster. Nature Chem. Biol. 8, 748–750 (2012).
  Article CAS Google Scholar
• Krishnamurthy, V. M. et al. Carbonic anhydrase as a model for biophysical and physical–organic studies of proteins and protein–ligand binding. Chem. Rev. 108, 946–1051 (2008).
  Article CAS Google Scholar
• Vauquelin, G. Simplified models for heterobivalent ligand binding: when are they applicable and which are the factors that affect their target residence time. Naunyn-Schmiedeberg’s Arch. Pharmacol. 386, 949–962 (2013).
  Article CAS Google Scholar
• Gargano, J. M., Ngo, T., Kim, J. Y., Acheson, D. W. K. & Lees, W. J. Multivalent inhibition of AB5 toxins. J. Am. Chem. Soc. 123, 12909–12910 (2001).
  Article CAS Google Scholar
• Krishnamurthy, V. M., Semetey, V., Bracher, P. J., Shen, N. & Whitesides, G. M. Dependence of effective molarity on linker length for an intramolecular protein–ligand system. J. Am. Chem. Soc. 129, 1312–1320 (2007).
  Article CAS Google Scholar
• Hilger, R. A., Scheulen, M. E. & Strumberg, D. The Ras-Raf-MEK-ERK pathway in the treatment of cancer. Oncol. Res. Treat. 25, 511–518 (2002).
  Article CAS Google Scholar
• Sebolt-Leopold, J. S. & Herrera, R. Targeting the mitogen-activated protein kinase cascade to treat cancer. Nature Rev. Cancer 4, 937–947 (2004).
  Article CAS Google Scholar
• Solit, D. B. et al. BRAF mutation predicts sensitivity to MEK inhibition. Nature 439, 358–362 (2006).
  Article CAS Google Scholar
• Brott, B. K. et al. Mek2 is a kinase related to Mek1 and Ts differentially expressed in murine tissues. Cell Growth Differ. 4, 921–929 (1993).
  CAS PubMed Google Scholar
• Giroux, S. et al. Embryonic death of Mek1-deficient mice reveals a role for this kinase in angiogenesis in the labyrinthine region of the placenta. Curr. Biol. 9, 369–376 (1999).
  Article CAS Google Scholar
• Ussar, S. & Voss, T. MEK1 and MEK2, different regulators of the G1/S transition. J. Biol. Chem. 279, 43861–43869 (2004).
  Article CAS Google Scholar
• Zhao, Y. & Adjei, A. A. The clinical development of MEK inhibitors. Nature Rev. Clin. Oncol. 11, 385–400 (2014).
  Article CAS Google Scholar
• Tecle, H. et al. Beyond the MEK-pocket: can current MEK kinase inhibitors be utilized to synthesize novel type III NCKIs? Does the MEK-pocket exist in kinases other than MEK? Bioorg. Med. Chem. Lett. 19, 226–229 (2009).
  Article CAS Google Scholar
• Rice, K. D. et al. Novel carboxamide-based allosteric MEK inhibitors: discovery and optimization efforts toward XL518 (GDC-0973). ACS Med. Chem. Lett. 3, 416–421 (2012).
  Article CAS Google Scholar
• Yao, J. Z. et al. Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition. J. Am. Chem. Soc. 134, 3720–3728 (2012).
  Article CAS Google Scholar
• Barrett, S. D., Biwersi, C., Kaufman, M., Tecle, H. & Warmus, J. S. Oxygenated esters of 4-iodo phenylamino benzhydroxamic acid. International patent WO 02/06213 (2002).
• Hamon, F., Djedaini-Pilard, F., Barbot, F. & Len, C. Azobenzenes—synthesis and carbohydrate applications. Tetrahedron 65, 10105–10123 (2009).
  Article CAS Google Scholar
• Renner, C. & Moroder, L. Azobenzene as conformational switch in model peptides. ChemBioChem 7, 868–878 (2006).
  Article CAS Google Scholar
• Beharry, A. A., Wong, L., Tropepe, V. & Woolley, G. A. Fluorescence imaging of azobenzene photoswitching in vivo. Angew. Chem. Int. Ed. 50, 1325–1327 (2011).
  Article CAS Google Scholar
• Tang, P. C. et al. Pyrrole substituted 2-indolinone protein kinase inhibitors. US patent 6,573,293 (2003).
• Gajiwala, K. S. et al. KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Proc. Natl Acad. Sci. USA 106, 1542–1547 (2009).
  Article CAS Google Scholar
• Palacios, E. H. & Weiss, A. Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation. Oncogene 23, 7990–8000 (2004).
  Article CAS Google Scholar
• James, J. R. & Vale, R. D. Biophysical mechanism of T-cell receptor triggering in a reconstituted system. Nature 487, 64–69 (2012).
  Article CAS Google Scholar
• Au-Yeung, B. B. et al. The structure, regulation, and function of ZAP-70. Immunol. Rev. 228, 41–57 (2009).
  Article CAS Google Scholar
• Schmied, W. H., Elsässer, S. J., Uttamapinant, C. & Chin, J. W. Efficient multisite unnatural amino acid incorporation in mammalian cells via optimized pyrrolysyl tRNA synthetase/tRNA expression and engineered eRF1. J. Am. Chem. Soc. 136, 15577–15583 (2014).
  Article CAS Google Scholar
• Sander, J. D. & Joung, J. K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nature Biotechnol. 32, 347–355 (2014).
  Article CAS Google Scholar
• Mansour, S. et al. Transformation of mammalian cells by constitutively active MAP kinase kinase. Science 265, 966–970 (1994).
  Article CAS Google Scholar