Abstract
Cell-permeable small molecules that are capable of activating particular enzymes would be invaluable tools for studying protein function in complex cell-signaling cascades. But, is it feasible to identify compounds that allow chemical–biology researchers to activate specific enzymes in a cellular context? In this review, we describe some recent advances in achieving targeted enzyme activation with small molecules. In addition to surveying progress in the identification and targeting of enzymes that contain natural allosteric-activation sites, we focus on recently developed protein-engineering strategies that allow researchers to render an enzyme of interest “activatable” by a pre-chosen compound. Three distinct strategies for targeting an engineered enzyme are discussed: direct chemical “rescue” of an intentionally inactivated enzyme, activation of an enzyme by targeting a de novo small-molecule-binding site, and the generation of activatable enzymes via fusion of target enzymes to previously characterized small-molecule-binding domains.
Similar content being viewed by others
References
Koh JT, Zheng J (2007) The new biomimetic chemistry: artificial transcription factors. ACS Chem Biol 2:599–601
Rowe SP, Casey RJ, Brennan BB et al (2007) Transcriptional up-regulation in cells mediated by a small molecule. J Am Chem Soc 129:10654–10655
Lindsley JE, Rutter J (2006) Whence cometh the allosterome? Proc Natl Acad Sci USA 103:10533–10535
Hardy JA, Wells JA (2004) Searching for new allosteric sites in enzymes. Curr Opin Struct Biol 14:706–715
Matschinsky FM, Glaser B, Magnuson MA (1998) Pancreatic beta-cell glucokinase: closing the gap between theoretical concepts and experimental realities. Diabetes 47:307–315
de la Iglesia N, Mukhtar M, Seoane J et al (2000) The role of the regulatory protein of glucokinase in the glucose sensory mechanism of the hepatocyte. J Biol Chem 275:10597–10603
Chu CA, Fujimoto Y, Igawa K et al (2004) Rapid translocation of hepatic glucokinase in response to intraduodenal glucose infusion and changes in plasma glucose and insulin in conscious rats. Am J Physiol Gastrointest Liver Physiol 286:G627–G634
Grimsby J, Sarabu R, Corbett WL et al (2003) Allosteric activators of glucokinase: potential role in diabetes therapy. Science 301:370–373
Molnes J, Bjorkhaug L, Sovik O et al (2008) Catalytic activation of human glucokinase by substrate binding-residue contacts involved in the binding of D-glucose to the super-open form and conformational transitions. FEBS J 275:2467–2481
Coghlan M, Leighton B (2008) Glucokinase activators in diabetes management. Expert Opin Investig Drugs 17:145–167
Johnson TO, Humphries PS (2006) Glucokinase activators for the treatment of type 2 diabetes. Annu Rep Med Chem 41:141–154
Johnson D, Shepherd RM, Gill D et al (2007) Glucokinase activators: molecular tools for studying the physiology of insulin-secreting cells. Biochem Soc Trans 35:1208–1210
Futamura M, Hosaka H, Kadotani A et al (2006) An allosteric activator of glucokinase impairs the interaction of glucokinase and glucokinase regulatory protein and regulates glucose metabolism. J Biol Chem 281:37668–37674
Ralph EC, Thomson J, Almaden J et al (2008) Glucose modulation of glucokinase activation by small molecules. Biochemistry 47:5028–5036
Kamata K, Mitsuya M, Nishimura T et al (2004) Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure 12:429–438
Pang T, Zhang ZS, Gu M et al (2008) Small molecule antagonizes autoinhibition and activates AMP-activated protein kinase in cells. J Biol Chem 283:16051–16060
Mantelingu K, Kishore AH, Balasubramanyam K et al (2007) Activation of p300 histone acetyltransferase by small molecules altering enzyme structure: probed by surface-enhanced Raman spectroscopy. J Phys Chem B 111:4527–4534
Thakur CS, Jha BK, Dong BH et al (2007) Small-molecule activators of RNase L with broad-spectrum antiviral activity. Proc Natl Acad Sci USA 104:9585–9590
Howitz KT, Bitterman KJ, Cohen HY et al (2003) Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 425:191–196
Wood JG, Rogina B, Lavu S et al (2004) Sirtuin activators mimic caloric restriction and delay ageing in metazoans. Nature 430:686–689
Kaeberlein M, McDonagh T, Heltweg B et al (2005) Substrate-specific activation of sirtuins by resveratrol. J Biol Chem 280:17038–17045
Carter P, Wells JA (1987) Engineering enzyme specificity by substrate-assisted catalysis. Science 237:394–399
Peracchi A (2008) How (and why) to revive a dead enzyme: the power of chemical rescue. Curr Chem Biol 2:32–49
Marletta MA (2006) Raising enzymes from the dead and the secrets they can tell. ACS Chem Biol 1:73–74
Manning G, Whyte DB, Martinez R et al (2002) The protein kinase complement of the human genome. Science 298:1912–1934
Williams DM, Wang DX, Cole PA (2000) Chemical rescue of a mutant protein-tyrosine kinase. J Biol Chem 275:38127–38130
Lowry WE, Huang JY, Ma YC et al (2002) Csk, a critical link of G protein signals to actin cytoskeletal reorganization. Dev Cell 2:733–744
Madhusoodanan KS, Guo DG, McGarrigle DK et al (2006) Csk mediates G-protein-coupled lysophosphatidic acid receptor-induced inhibition of membrane-bound guanylyl cyclase activity. Biochemistry 45:3396–3403
Iguchi K, Usui S, Ishida R et al (2002) Imidazole-induced cell death, associated with intracellular acidification, caspase-3 activation, DFF-45 cleavage, but not oligonucleosomal DNA fragmentation. Apoptosis 7:519–525
Qiao YF, Molina H, Pandey A et al (2006) Chemical rescue of a mutant enzyme in living cells. Science 311:1293–1297
Yeatman TJ (2004) A renaissance for Src. Nat Rev Cancer 4:470–480
Hanke JH, Gardner JP, Dow RL et al (1996) Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. J Biol Chem 271:695–701
Erster O, Eisenstein M, Liscovitch M (2007) Ligand interaction scan: a general method for engineering ligand-sensitive protein alleles. Nat Methods 4:393–395
Griffin BA, Adams SR, Tsien RY (1998) Specific covalent labeling of recombinant protein molecules inside live cells. Science 281:269–272
Adams SR, Campbell RE, Gross LA et al (2002) New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J Am Chem Soc 124:6063–6076
Gaietta G, Deerinck TJ, Adams SR et al (2002) Multicolor and electron microscopic imaging of connexin trafficking. Science 296:503–507
Hoffmann C, Gaietta G, Bunemann M et al (2005) A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat Methods 2:171–176
Ju W, Morishita W, Tsui J et al (2004) Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors. Nat Neurosci 7:244–253
Zhang XY, Bishop AC (2007) Site-specific incorporation of allosteric-inhibition sites in a protein tyrosine phosphatase. J Am Chem Soc 129:3812–3813
Pollock R, Clackson T (2002) Dimerizer-regulated gene expression. Curr Opin Biotechnol 13:459–467
Walsh DP, Chang YT (2006) Chemical genetics. Chem Rev 106:2476–2530
Bishop A, Buzko O, Heyeck-Dumas S et al (2000) Unnatural ligands for engineered proteins: new tools for chemical genetics. Annu Rev Biophys Biomol Struct 29:577–606
Schreiber SL (1998) Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg Med Chem 6:1127–1152
Spencer DM, Graef I, Austin DJ et al (1995) A general strategy for producing conditional alleles of Src-like tyrosine kinases. Proc Natl Acad Sci USA 92:9805–9809
Li B, Desai SA, MacCorkle-Chosnek RA et al (2002) A novel conditional Akt ‘survival switch’ reversibly protects cells from apoptosis. Gene Ther 9:233–244
MacCorkle RA, Freeman KW, Spencer DM (1998) Synthetic activation of caspases: artificial death switches. Proc Natl Acad Sci USA 95:3655–3660
Smith KM, Van Etten RA (2001) Activation of c-Abl kinase activity and transformation by a chemical inducer of dimerization. J Biol Chem 276:24372–24379
Freeman KW, Gangula RD, Welm BE et al (2003) Conditional activation of fibroblast growth factor receptor (FGFR) 1, but not FGFR2, in prostate cancer cells leads to increased osteopontin induction, extracellular signal-regulated kinase activation, and in vivo proliferation. Cancer Res 63:6237–6243
Muthuswamy SK, Gilman M, Brugge JS (1999) Controlled dimerization of ErbB receptors provides evidence for differential signaling by homo- and heterodimers. Mol Cell Biol 19:6845–6857
Jin LQ, Asano H, Blau CA (1998) Stimulating cell proliferation through the pharmacologic activation of c-kit. Blood 91:890–897
Yang JX, Symes K, Mercola M et al (1998) Small-molecule control of insulin and PDGF receptor signaling and the role of membrane attachment. Curr Biol 8:11–18
Pratt MR, Schwartz EC, Muir TW (2007) Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt. Proc Natl Acad Sci USA 104:11209–11214
Xu W, Doshi A, Lei M et al (1999) Crystal structures of c-Src reveal features of its autoinhibitory mechanism. Mol Cell 3:629–638
Acknowledgments
The authors thank the National Institutes of Health (1 R15 GM071388-01A1) and Research Corporation (CC6372) for research support.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bishop, A.C., Chen, V.L. Brought to life: targeted activation of enzyme function with small molecules. J Chem Biol 2, 1–9 (2009). https://doi.org/10.1007/s12154-008-0012-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12154-008-0012-4