Quantitative methods for the analysis of protein phosphorylation in drug development

Expert Review of Proteomics

Volumn 1, Issue 3, 2004, Pages 327-341

  Olive, D Michael ^a  

^a LI COR Biosciences   (United States)

Author keywords

Pathway; Phosphorylation; Protein kinase; Signal transduction

Indexed keywords

BCR ABL PROTEIN; IMATINIB; PLATELET DERIVED GROWTH FACTOR RECEPTOR; PROTEIN KINASE; PROTEIN KINASE C KIT; PROTEIN KINASE INHIBITOR; SERINE; TYROSINE; UNCLASSIFIED DRUG; PHOSPHOPROTEIN; PROTEIN; PROTEIN KINASE B;

APOPTOSIS; CANCER CELL; CELL CYCLE PROGRESSION; CELL DIFFERENTIATION; CELL GROWTH; CELL METABOLISM; CELL MOTION; CHROMOSOME TRANSLOCATION; CHRONIC MYELOID LEUKEMIA; DERMATOFIBROSARCOMA PROTUBERANS; DRUG TARGETING; ENZYME ANALYSIS; ENZYME INHIBITION; GASTROINTESTINAL STROMAL TUMOR; GENE MUTATION; GENE SEQUENCE; HUMAN; ONCOGENE; PROTEIN PHOSPHORYLATION; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR GENE; ANIMAL; CHEMISTRY; DRUG DESIGN; DRUG EFFECT; GENETICS; METABOLISM; MUTATION; PHOSPHORYLATION;

ANIMALS; DRUG DESIGN; HUMANS; MUTATION; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEINS; PROTO-ONCOGENE PROTEINS C-AKT;

EID: 33646148263     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.1.3.327     Document Type: Review

References (69)

1. Blume-Jensen P, Hunter T. Oncogenic kinase signaling. Nature 411, 353-365 (2001).
2. Pawson T, Nash P. Protein-protein interactions define specificity in signal transduction. Genes Dev. 14, 1027-1047 (2000).
3. Reed JC. Dysregulation of apoptosis in cancer. J. Clin. Oncol. 17, 2941-2953 (1999).
4. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 100, 57-70 (2000).
5. Petricoin EF, Liotta LA. Proteomic analysis at the bedside: early detection of cancer. Trends Biotechnol. 20, S30-S34 (2002).
6. Liotta L, Petricoin E. Molecular profiling of human cancer. Nature Rev. Genet. 1, 48-56 (2000).
7. Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
8. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nature Biotechnol. 18, 1257-1261 (2000).
9. Legrain P, Jestin JL, Schachter V. From the analysis of protein complexes to proteome-wide linkage maps. Curr. Opin. Biotechnol. 11, 402-407 (2000).
10. Liotta LA, Kohn EC. The microenvironment of the tumor-host interface. Nature 411, 375-379 (2001).
11. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912-1934 (2002).
12. Daucey J, Sausville EA. Issues and progress with protein kinase inhibitors for cancer treatment. Nature Rev. Drug Discov. 2, 296-313 (2003).
13. Futreal PA, Kasprzyk A, Birney E et al. Cancer and genomics. Nature 409, 850-852 (2001).
14. Druker BJ. Inhibition of the Bcr-Abl tyrosine kinase as a therapeutic strategy for CML. Oncogene 21, 8541-8546 (2002).
15. Joensuu H, Fletcher C, Dimitrijevic S et al. Management of malignant gastrointestinal stromal tumors. Lancet Oncol. 3, 655-664 (2002).
16. Rubin BP, Schuetze SM, Eary JF et al. Molecular targeting of platelet-derived growth factor B by imatinib mesylate in a patient with metastatic dermatofibrosarcoma protuberans. J. Clin. Oncol 20, 3586-3591 (2002).
17. Bogdanovic S, Langlands B. Protein kinases: technologies and opportunities for drug discovery. D & MD Reports (2003).
18. Gallardo G, Tabraue C, Quintana J et al. Regulation by ceramide of epidermal growth factor signal transduction and mitogenesis in cell lines overexpressing the growth factor receptor. Cell. Mol. Biol. 46, 1305-1312 (2000).
19. Eccles SA. Cell biology of lymphatic metastasis. The potential role of c-erbB oncogene signaling. Rec. Res. Cancer Res. 157, 41-54 (2000).
20. Ciardiello F, Tortora G. A novel approach in the treatment of cancer: targeting the epidermal growth factor receptor. Clin. Cancer Res. 7, 2958-2970 (2001).
21. Ciardiello F, Caputo R, Bianco R et al. Antitumor effect and potentiation of cytotoxic drug activity in human cancer cells by ZD-1839 (Iressa), an epidermal growth factor receptor-selective tyrosine kinase inhibitor. Clin. Cancer Res. 6, 2053-2063 (2000).
22. Milas L, Mason K, Hunter N et al. In vivo enhancement of tumor radioresponse by C225 anti-epidermal growth factor antibody. Clin. Cancer Res. 6, 701-708 (2000).
23. Huang SM, Harari PM. Modulation of radiation response after epidermal growth factor receptor blockade in squamous carcinomas: inhibition of damage repair, cell cycle kinetics, and tumor angiogenesis. Clin. Cancer Res. 6, 2166-2174 (2000).
24. Pruitt K, Der CJ. Ras and Rho regulation of the cell cycle and oncogenesis. Cancer Lett. 171, 1-10 (2001).
25. Pollack PM, Meltzer PS. Lucky draw in the gene raffle. Nature 417, 906-907 (2002).
26. Grunicke HH, Maly K. Role of GTPases and GTPase regulatory proteins in oncogenesis. Crit. Rev. Oncol. 4, 389-402 (1993).
27. Davies H, Bignell GR, Cox C et al. Mutations of the BRAF gene in human cancer. Nature 417, 949-954 (2002).
28. Kerkoff E, Rappo UR. Cell cycle targets of Ras/Raf signaling. Oncogene 17, 1459-1462 (1998).
29. Stanton VP, Cooper GM. Activation of human Raf transforming genes by deletion of normal amino-terminal coding sequences. Mol. Cell. Biol. 7, 1171-1179 (1987).
30. Kolch W, Heidecker G, Kochs G et al. Protein kinase C-α activates Raf-1 by direct phosphorylation. Nature 364, 249-252 (1993).
31. Cornwell MM, Smith DE. A signal transduction pathway for activation of the mdr1 promoter involves the protooncogene c-raf kinase. J. Biol. Chem. 268, 15347-15350 (1993).
32. Catling AD, Schaeffer HJ, Reuter CW, Reddy GR, Weber MJ. A proline rich sequence unique to MEK1 and MEK2 is required for raf binding and regulates MEK function. Mol. Cell. Biol. 15, 5214-5225 (1995).
33. Vivanco I, Sawyers CL. The phosphoinositol 3-kinase Akt pathway in human cancer. Nature Rev. Cancer 2, 489-501 (2002).
34. Cantley LC. The phosphoinositide 3-kinase pathway. Science 296, 1655-1657 (2002).
35. Lu Y, Zi X, Zhao Y, Mascarenhas D, Pollack M. Insulin-like growth factor-I signaling and resistance to trastuzamab (Herceptin). J. Natl Cancer Inst. 93, 1852-1857 (2001).
36. Chakravarti A, Loeffler JS, Dyson NJ. Insulin-like growth factor I mediates resistance to anti-epidermal growth factor therapy in primary human glioblastoma cells through continued activation of phosphoinositide 3-kinase signaling. Cancer Res. 62, 200-207 (2002).
37. Angeles TS, Lippy JS, Yang SX. Quantitative, high-throughput cell based assays for inhibitors of trkA receptor. Anal. Biochem. 278, 93-98 (2000).
38. Waddleton D, Ramachandran C, Wang Q. Development of a time-resolved fluorescent assay for measuring tyrosine-phosphorylated proteins in cells. Anal. Biochem. 309, 150-157 (2002).
39. Kolb AJ, Burke, JW, Mathis G. Homogenous time resolved fluorescent method for drug discovery. In: High Throughput Screening. Devlin JP (Ed.), Marcel Dekker, NY, USA, 345-359 (1997).
40. Glickman JF, Wu X, Mercuri R et al. Comparison of AlphaScreen, TR-FRET, and TRF as assay methods for FXR nuclear receptors. J. Biomol. Screen. 7, 3-10 (2002).
41. Zhang JH, Ching TDY, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high-throughput screening assays. J. Biomol. Screen. 4, 67-73 (1999).
42. Burke TJ, Loniello KR, Beebe JA et al. Development and application of fluorescence polarization assays in drug discovery. Comb. Chem. High Throughput Screen. 6, 183-194 (2003).
43. Turek TC, Small EC, Bryant RW et al. Development and validation of a competitive AKT serine/threonine kinase fluorescence polarization assay using product-specific antiphospho-serine antibody. Anal. Biochem. 299, 45-53 (2001).
44. Banks P, Gosselin M, Prystay L. Impact of red-shifted dye label for high throughput fluorescence polarization assays of G-protein coupled receptors. J. Biomol. Screen. 5, 329-334 (2000).
45. Banks P, Gosselin M, Prystay L. Fluorescence polarization assays for high throughput screening of G-protein coupled receptors. J. Biomol. Screen. 5, 159-167 (2000).
46. Fowler A, Swift D, Longman E et al. An evaluation of fluorescence polarization and lifetime discriminated polarization for high-throughput screening of serine/threonine kinases. Anal. Biochem. 308, 223-231 (2002).
47. Vedvik KL, Eliason HC, Hoffman RL et al. Overcoming compound interference in fluorescent polarization-based kinase assays using far-red tracers. Assay Drug Devel. 2, 193-203 (2004).
48. Beasley JR, Dunn DA, Walker TL et al. Evaluation of compound interference in immobilized metal ion affinity-based fluorescence polarization detection with a four million member compound collection. Assay Drug Devel. 1, 455-459 (2003).
49. Turek-Etienne TC, Kober TP, Stafford JM et al. Development of a fluorescence polarization AKT serine/threonine kinase assay using an immobilized metal ion affinity-based technology. Assay Drug Devel. 1, 545-553 (2003).
50. Gaudet EA, Huang KS, Zhang Y et al. A homogenous fluorescence polarization assay adaptable for a range of protein serine/threonine and tyrosine kinases. J. Biomol. Screen. 8, 164-175 (2003).
51. Lu Z, Yin Z, James L et al. Development of a fluorescence polarization bead-based coupled assay to target different activity/conformation states of a protein kinase. J. Biomol. Screen. 9, 309-321 (2004).
52. Loomans EEMG, van Doornmalen AM, Wat JWY et al. High throughput screening with immobilized metal ion affinity-based fluorescence polarization detection, a homogenous assay for protein kinases. Assay Drug Devel. 1, 445-453 (2003).
53. 3+ affinity chromatography. Anal. Biochem. 154, 250-254 (1986).
54. McCauley TJ, Stanaitis ML, Savage MD, Onken J, Millis SZ. IQ technology: development of a universal homogenous method for high-throughput screening of kinase and phosphatase activity. JAMA 8, 36-40 (2003).
55. Morgan AG, McCauley TJ, Stanaitis ML, Mathrubutham M, Millis SZ. Development and validation of a fluorescence technology for both primary and secondary screening of kinases that facilitates compound selectivity and site-specific inhibitor determination. Assay Drug Devel. 2, 171-181 (2004).
56. Xia W, Rininsland F, Wittenburg SK et al. Applications of fluorescent polymer superquenching to high-throughput screening assays for protein kinases. Assay Drug Devel. 2, 183-192 (2004).
57. Cohen CB, Chin-Dixon E, Jeong S et al. A microchip-based enzyme assay for protein kinase A. Anal. Biochem. 273, 89-97 (1999).
58. Dunne J, Reardon H, Trinh V et al. Comparison of on-chip and off-chip microfluidics kinase assay formats. Assay Drug Devel. 2, 121-129 (2004).
59. Chen H, Olive DM. Quantitative measurement of the activation of signaling pathways using two-color infrared fluorescent western blotting and cell-based assays. Proc. IBC Protein Kinases Meet. 7(March), (2002).
60. Russello S. Assessing cellular protein phosphorylation: high-throughput drug development technologies. Assay Drug Devel. 2, 225-235 (2004).
61. Wong SK. A 384-well cell-based phospho-ERK assay for dopamine D2 and D3 receptors. Anal. Biochem. (In Press).
62. Luttrell LM. Activation and targeting of mitogen-activated protein kinases by G-protein coupled receptors. Can. J. Physiol. Pharmacol. 80, 375-382 (2002).
63. Wong SK. G-protein selectivity is regulated by multiple intracellular regions of GPCRs. Neurosignals 12, 1-12 (2003).
64. Perez OD, Nolan GP. Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nature Biotechnol. 20, 155-162 (2002).
65. Sills MA, Weiss D, Pham Q et al. Comparison of assay technologies for tyrosine kinase assay generates different results in high-throughput screening. J. Biomol. Screen. 7, 191-214 (2002).
66. Biotech 2003 Report. Burrill and Company. 66-115 (2003).
67. Pelech S. Tracking cell signaling protein expression and phosphorylation by innovative proteomic solutions. Curr. Pharma. Biotechnol. 5, 69-77 (2004).
68. Luker G D, Sharma V, Pica CM et al. Noninvasive imaging of protein-protein interactions in living animals. Proc. Natl Acad. Sci. USA 99, 6961-6966 (2002)
69. Murakoshi H, Iino R, Kobayashi T et al. Single molecule imaging analysis of RAS activation in living cells. Proc. Natl Acad. Sci. USA 101, 7317-7322 (2004).