Chemical dimerizers and three-hybrid systems: Scanning the proteome for targets of organic small molecules

Chemistry and Biology

Volumn 11, Issue 5, 2004, Pages 599-608

  Kley, Nikolai ^a  

^a GPC Biotech Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AP 1510; DNA BINDING PROTEIN; DRUG DERIVATIVE; DRUG RECEPTOR; PROTEOME; RAPAMYCIN; TACROLIMUS;

ANIMAL; CHEMISTRY; DIMERIZATION; DRUG DESIGN; DRUG SCREENING; GENE EXPRESSION; GENETICS; INSTRUMENTATION; METABOLISM; PROTEIN MICROARRAY; REVIEW; SIGNAL TRANSDUCTION; TWO HYBRID SYSTEM;

ANIMALS; DIMERIZATION; DNA-BINDING PROTEINS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; GENE EXPRESSION; PROTEIN ARRAY ANALYSIS; PROTEOME; RECEPTORS, DRUG; SIGNAL TRANSDUCTION; SIROLIMUS; TACROLIMUS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 2642520581     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2003.09.017     Document Type: Review

References (78)

1. Schreiber S.L. Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem. 6:1998;1127-1152
2. Stockwell B.R. Frontiers in chemical genetics. Trends Biotechnol. 18:2000;449-455
3. Marton M.J., DeRisi J.L., Bennett H.A., Iyer V.R., Meyer M.R., Roberts C.J., Stoughton R., Burchard J., Slade D., Dai H., et al. Drug target validation and identification of secondary drug target effects using microarrays. Nat. Med. 4:1998;1293-1301
4. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126
5. Waring J.F., Ulrich R.G. The impact of genomics-based technologies on drug safety evaluation. Annu. Rev. Pharmacol. Toxicol. 40:2000;335-352
6. Ulrich R., Friend S.H. Toxicogenomics and drug discovery. will new technologies help us produce better drugs? Nat. Rev. Drug Discov. 1:2002;84-88
7. Hanash S. Disease proteomics. Nature. 422:2003;226-232
8. Lewis T.S., Hunt J.B., Aveline L.D., Jonscher K.R., Louie D.F., Yeh J.M., Nahreini T.S., Resing K.A., Ahn N.G. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol. Cell. 6:2000;1343-1354
9. Adam G.C., Sorensen E.J., Cravatt B.F. Chemical strategies for functional proteomics. Mol. Cell. Proteomics. 1:2002;781-790
10. Adam G.C., Sorensen E.J., Cravatt B.F. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat. Biotechnol. 20:2002;805-809
11. Frye S. Structure-activity relationship homology (SARAH). a conceptual framework for drug discovery in the genomic era Chem. Biol. 6:1999;R3-R7
12. Greenbaum D., Baruch A., Hayrapetian L., Darula Z., Burligmae A., Medzihradszky K.F., Bogyp M. Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics. 1:2002;60-68
13. Greenbaum D.C., Arnold W.D., Lu F., Hayrapetian L., Baruch A., Krumrine J., Toba S., Chehade K., Broemme D., Kuntz I.D., et al. Small molecule affinity fingerprinting. a tool for enzyme family subclassification, target identification, and inhibitor design Chem. Biol. 9:2002;1085-1094
14. Borodovsky A., Ovaa H., Kolli N., Gan-Erdene T., Wilkinson K.D., Ploegh H.L., Kessler D.M. Chemistry-based functional proteomics reveals novel members of the deubiquinating enzyme family. Chem. Biol. 9:2002;1149-1159
15. Bishop A.C., Ubersax J.A., Petsch D.T., Matheos D.P., Gray N.S., Blethrow J., Shimizu E., Tsien J.Z., Schultz P.G., Rose M.D., et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature. 407:2000;395-401
16. Phizicky E., Bastiaens P.I.H., Zhu H., Snyder M., Fields S. Protein analysis on a proteomic scale. Nature. 422:2003;208-215
17. Licitra E.J., Liu J.O. A three-hybrid system for detecting small ligand-protein receptor interactions. Proc. Natl. Acad. Sci. USA. 93:1996;12817-12821
18. Tanaka H., Ohshima N., Hidaka H. Isolation of cDNAs encoding cellular drug-binding proteins using a novel expression cloning procedure. drug-western Mol. Pharmacol. 55:1999;356-363
19. Sche P.P., McKenzie K.M., White J.D., Austin D.J. Display cloning. functional identification of natural product receptors using cDNA-phage display Chem. Biol. 6:1999;707-716
20. McPherson M., Yang Y., Hammond P.W., Kreider B.L. Drug receptor identification from multiple tissues using cellular-derived mRNA display libraries. Chem. Biol. 9:2002;691-698
21. Liu J., Farmer J.D. Jr., Lane W.S., Friedman J., Weissman I., Schreiber S.L. Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 66:1991;807-815
22. Heitman J., Movva N.R., Hall M.N. Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science. 253:1991;905-909
23. Brown E.J., Albers M.W., Shin T.B., Ichikawa K., Keith C.T., Lanes W.S., Schreiber S.L. A mammalian protein targeted by G1-arresting rapamycin-receptor complex. Nature. 369:1994;756-758
24. Sabatini D.M., Erdjument-Bormage H., Lui M., Tempst P., Snyder S.H. RAFT1. a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast tors Cell. 78:1994;35-43
25. Chiu I.M., Katz H., Berlin V. RAPT1, a mammalian homolog of yeast Tor, interacts with the FKBP12/rapamycin complex. Proc. Natl. Acad. Sci. USA. 91:1994;12574-12578
26. Rivera V.M., Clackson T., Natesan S., Pollock R., Amara J.F., Keenan T., Magari S.R., Philipps T., Courage N.L., Cerasoli F., et al. A humanized system for pharmacologic control of gene expression. Nat. Med. 2:1996;1028-1032
27. Ho S.N., Biggar S.R., Spencer D.M., Schreiber S.L., Crabtree G.R. Dimeric ligands define a role for transcriptional activation domains in reinitiation. Nature. 382:1997;822-826
28. Pollock R., Issner R., Zoller K., Natesan S., Rivera V.M., Clackson T. Delivery of a stringent dimerizer-regulated gene expression system in a single retroviral vector. Proc. Natl. Acad. Sci. USA. 97:2000;13221-13226
29. Clackson T. Regulated gene expression systems. Gene Ther. 7:2000;120-125
30. Pollock R., Clackson T. Dimerizer-regulated gene expression. Curr. Opin. Biotechnol. 13:2002;459-467
31. Spencer D.M., Wandless T.J., Schreiber S.L., Crabtree G.R. Controlling signal transduction with synthetic ligands. Science. 262:1993;1019-1024
32. Amara J.F., Clackson T., Rivera V.M., Guo T., Keenan T., Natesan S., Pollock R., Yang W., Courage N.L., Holt D.A., et al. A versatile synthetic dimerizer for the regulation of protein-protein interactions. Proc. Natl. Acad. Sci. USA. 94:1997;10618-10623
33. Belshaw P.J., Ho S.N., Crabtree G.R., Schreiber S.L. Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins. Proc. Natl. Acad. Sci. USA. 93:1996;4604-4607
34. Liberles S.D., Diver S.T., Austin D.J., Schreiber S.L. Inducible gene expression and protein translocation using nontoxic ligands identified by a mammalian three-hybrid screen. Proc. Natl. Acad. Sci. USA. 94:1997;7825-7830
35. Clackson T., Yang W., Rozamus L.W., Hatada M., Amara J.F., Rollins C.T., Stevenson L.F., Magari S.R., Wood S.A., Courage N.L., et al. Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity. Proc. Natl. Acad. Sci. USA. 95:1998;10437-10442
36. Belshaw P.J., Spencer D.M., Crabtree G.R., Screiber S.L. Controlling programmed cell death with a cyclophilin-cyclosporine-based chemical inducer of dimerization. Proc. Natl. Acad. Sci. USA. 93:1996;4604-4607
37. Holsinger L.J., Spencer D.M., Austin D.J., Schreiber S.L., Crabtree G.R. Signal transduction in T lymphocytes using a conditional allele of Sos. Proc. Natl. Acad. Sci. USA. 92:1995;9810-9814
38. Spencer D.M., Graef I., Austin D.J., Schreiber S.L., Crabtree G.R. A general strategy for producing conditional alleles of Src-like tyrosine kinases. Proc. Natl. Acad. Sci. USA. 92:1995;9805-9809
39. Luo Z., Tzivion G., Belshaw P.J., Vavvas D., Marshall M., Avruch J. Oligomerization activates c-Raf-1 through a Ras-dependent mechanism. Nature. 383:1996;181-185
40. Pruschy M.N., Spencer D.M., Kapoor T.M., Miyake H., Crabtree G.R., Schreiber S.L. Mechanistic studies of a signaling pathway activated by the organic dimerizer FK1012. Chem. Biol. 1:1994;163-172
41. Yang J., Symes K., Mercola M., Schreiber S.L. Small-molecule control of insulin and PDGF receptor signaling and the role of membrane attachment. Curr. Biol. 8:1997;11-18
42. Blau C.A., Peterson K.R., Drachman J.G., Spencer D.M. A proliferation switch for genetically modified cells. Proc. Natl. Acad. Sci. USA. 94:1997;3076-3081
43. Stockwell B.R., Schreiber S.L. Probing the role of homomeric receptor interactions in TGF-beta signaling using small molecule dimerizers. Curr. Biol. 8:1998;761-770
44. Stockwell B.R., Schreiber S.L. TGF-beta signaling with small molecule FKBP12 antagonists that bind myristolated FKBP12-TGF-beta type I receptor fusion proteins. Chem. Biol. 5:1998;385-395
45. Pollock R., Giel M., Linher K., Clackson T. Regulation of endogenous expression with a small-molecule dimerizer. Nat. Biotechnol. 20:2002;729-733
46. Spencer D.M., Belshaw P.J., Chen L., Ho S.N., Randazzo F., Crabtree G.R., Schreiber S.L. Functional analysis of fas signaling in vivo using synthetic inducers of dimerization. Curr. Biol. 6:1996;839-847
47. Rollins C.T., Rivera V.M., Woolfson D.N., Keenan T., Hatada M., Adams S.E., Antrade L.J., Yaeger D., van Schravendijk M.R., Holt D.A., et al. A ligand-reversible dimerization system for controlling protein-protein interactions. Proc. Natl. Acad. Sci. USA. 97:2000;7096-7101
48. Rivera V.M., Wang X., Wardwell S., Courage N.L., Volchuk A., Keenan T., Holt D.A., Gilman M., Orci L., Cerasoli F., et al. Regulation of protein secretion through controlled aggregation in the endoplasmatic reticulum. Science. 287:2000;826-830
49. Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature. 340:1989;245-246
50. Chien C.T., Bartel P., Sternglanz R., Fields S. The two-hybrid system. a method to identify and clone genes for proteins that interact with a protein of interest Proc. Natl. Acad. Sci. USA. 88:1991;9578-9582
51. Sengupta D.J., Zhang B., Kraemer B., Pochart P., Fields S., Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA. 94:1996;8496-8501
52. Yang M., Wu Z., Fields S. Protein-peptide interactions analyzed with the yeast-two-hybrid system. Nucleic Acids Res. 23:1995;1152-1162
53. Visintin M., Tse E., Axelson H., Rabitts T.H., Cattaneo A. Selection of antibodies for intracellular function using a two-hybrid in vivo system. Proc. Natl. Acad. Sci. USA. 96:1999;11723-11728
54. Lee J.W., Choi H.S., Gyuris J., Brent R., Moore D.D. Two classes of proteins dependent on either the presence or absence of thyroid hormone for interaction with the thyroid hormone receptor. Mol. Endocrinol. 9:1995;243-254
55. Lee J.W., Moore D.D., Heyman R.A. A chimeric thyroid hormone receptor constitutively bound to DNA requires retinoid X receptor for hormone-dependent transcriptional activation in yeast. Mol. Endocrinol. 8:1994;1245-1252
56. Vidal M., Brachmann R.K., Fattaey A., Harlow E., Boeke J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and protein-DNA interactions. Proc. Natl. Acad. Sci. USA. 93:1996;10315-10326
57. Huang J., Schreiber S.L. A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanaodroplets. Proc. Natl. Acad. Sci. USA. 94:1997;13396-13401
58. Kato-Stankiewicz J., Hakimi I., Zhi G., Zhang J., Serebriskii I., Guo L., Edamatsu H., Koide H., Menon S., Eckl R., et al. Proc. Natl. Acad. Sci. USA. 99:2002;14398-14403
59. Henthorn D.C., Jaxa-Chamiec A.A., Meldrum E. A GAL4-based yeast three-hybrid system for the identification of small molecule-target protein interactions. Biochem. Pharmacol. 63:2002;1619-1628
60. Lin H., Abida W., Sauer R., Cornish V.W. Dexamethasone-methotrexate. an efficient chemical induced of protein dimerization in vivo J. Am. Chem. Soc. 122:2000;4247-4248
61. Abida W.M., Crater B.T., Althoff E., Lin H., Cornish V.W. Receptor-dependence of the transcription read-out in a small-molecule three-hybrid system. Chembiochem. 3:2002;887-895
62. Baker K., Sengupta D., Salazar-Jimenez G., Cornish V.W. An optimized dexamethasone-methotrexate yeast 3-hybrid system for high throughput screening of small molecule-protein interactions. Anal. Biochem. 315:2003;134-137
63. Baccanari D., Daluge S., King R. Inhibition of dihydrofolate reductase. effect of reduced nicotinamide adenine dinucleotide phosphate on the selectivity and affinity of diaminobenzylpyrimidines Biochemistry. 21:1982;5068-5075
64. Baccanari D., Joyner S. Dihydrofolate reductase hysteresis and its effect of inhibitor binding analyses. Biochemistry. 20:1981;1710-1716
65. Cayley P., Dunn S., King R. Kinetics of substrate, coenzyme, and inhibitor binding to Escherichia coli dihydrofolate reductase. Biochemistry. 20:1981;874-879
66. Appleman J., Prendergast N., Delcamp T., Freishman J., Blakley R. Kinetics of the formation and isomerization of methotrexate complexes of recombinant human dihydrofolate reductase. J. Biol. Chem. 263:1988;10304-10313
67. Appleman J., Howell E., Kraut J., Kuhl M., Blakley R.L. Role of aspartate 27 in the binding of methotrexate to dihydrofolate reductase from Escherichia coli. J. Biol. Chem. 263:1988;9187-9198
68. Knockaert M., Gray N., Damiens E., Chang Y.-T., Grellier P., Grant K., Fergusson D., Mottram J., Soete M., Dubremetz J.-F., et al. Intracellular targets of cyclin-dependent kinase inhibitors. identification by affinity chromatography using immmobilised inhibitors Chem. Biol. 7:2000;411-422
69. Johnsson N., Varshavsky A. Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. USA. 91:1994;10340-10344
70. Rojo-Niersbach E., Morley D., Heck S., Lehming N. A new method for the selection of protein-protein interactions in mammalian cells. Biochem. J. 348:2000;585-590
71. Remy I., Michnick S.W. Clonal selection and in vivo quantitation of protein interactions with protein fragment complementation assays. Proc. Natl. Acad. Sci. USA. 96:1999;5394-5399
72. Galarneau A., Primeau M., Trudeau L.E., Michnick S.W. Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat. Biotechnol. 20:2002;619-622
73. Wehrman T., Kleaveland B., Her J.H., Balint R.F., Blau H.M. Protein-protein interactions monitored in mammalian cells via complementation of beta-lactamase enzyme fragments. Proc. Natl. Acad. Sci. USA. 99:2002;3469-3474
74. Eyckerman S., Verhee A., der Heyden J.V., Lemmens I., Ostade X.V., Vandekerckhove J., Tavernier J. Design and application of a cytokine-receptor- based interaction trap. Nat. Cell Biol. 3:2001;1114-1119
75. Koide K., Finkelstein J.M., Ball Z., Verdine G.L. A synthetic library of cell-permeable molecules. J. Am. Chem. Soc. 123:2001;398-408
76. Baker K., Bleczinski C., Lin H., Salazar-Jimenez G., Sengupta D., Krane S., Cornish V.W. Chemical complementation. a reaction-independent genetic assay for enzyme catalysis Proc. Natl. Acad. Sci. USA. 99:2002;16537-16542
77. Firestine S.M., Salinas F., Nixon A.E., Baker S.J., Benkovic S.J. Using anAraC-based three-hybrid system to detect biocatalysts in vivo. Nat. Biotechnol. 18:2000;544-547
78. Becker F., Murthi K., Smith C., Come J., Costa-Roldan N., Kaufmann C., Hanke U., Degenhart C., Baumann S., Wallner W., et al. A three-hybrid approach to scanning the proteome for targets of small molecule kinase inhibitors. Chem. Biol. 11:2004;211-223