Identification of direct target engagement biomarkers for kinase-targeted therapeutics

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Paweletz, Cloud P ^a   Andersen, Jannik N ^a   Pollock, Roy ^a   Nagashima, Kumiko ^a   Hayashi, Mansuo L ^a   Yu, Shangshuan U ^a   Guo, Hongbo ^a   Bobkova, Ekaterina V ^a   Xu, Zangwei ^a   Northrup, Alan ^a   Blume Jensen, Peter ^b   Hendrickson, Ronald C ^a   Chi, An ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

^b Metamark Genetics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1; PHOSPHOTRANSFERASE; PROTEIN SERINE THREONINE KINASE; PROTEIN TYROSINE KINASE INHIBITOR; PROTEIN KINASE INHIBITOR;

ARTICLE; AUTOPHOSPHORYLATION; CONTROLLED STUDY; DRUG TARGETING; MASS SPECTROMETRY; PHARMACODYNAMICS; PROTEIN DEPHOSPHORYLATION; PROTEIN PHOSPHORYLATION; QUANTITATIVE ANALYSIS; AMINO ACID SEQUENCE; BIOCATALYSIS; CELL LINE; DRUG EFFECT; HUMAN; METABOLISM; MOLECULAR GENETICS; PHOSPHORYLATION; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BIOCATALYSIS; BIOLOGICAL MARKERS; CELL LINE; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PHOSPHOTRANSFERASES; PROTEIN KINASE INHIBITORS; TANDEM MASS SPECTROMETRY;

EID: 80055025828     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026459     Document Type: Article

References (43)

1. Paul SM, Mytelka DS, Dunwiddle CT, Munos BH, Lindborg SR, et al. (2010) How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov 9: 203-214.
2. Kola I, Landis J, (2004) Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 3: 711-715.
3. Collins I, Workman P, (2006) New approaches to molecular cancer therapeutics. Nat Chem Biol 2: 689-700.
4. Wagner JA, (2008) Strategic approach to fit-for-purpose biomarkers in drug development. Annu Rev Pharmacol Toxicol 48: 631-651.
5. Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, et al. (2010) Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2: 43ra55.
6. Dancey JE, Dobbin KK, Groshen S, Jessup JM, Hruszkewycz AH, et al. (2010) Guidelines for the development and incorporation of biomarker studies in early clinical trials of novel agents. Clin Cancer Res 16: 1745-1755.
7. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA, (2002) Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 1: 683-695.
8. Wulfkuhle JD, Edmiston KH, Liotta LA, Petricoin EF 3rd, (2006) Technology insight: pharmacoproteomics for cancer-promises of patient-tailored medicine using protein microarrays. Nat Clin Pract Oncol 3: 256-268.
9. Woodcock J, Woosley R, (2008) The FDA critical path initiative and its influence on new drug development. Annu Rev Med 59: 1-12.
10. Tan DS, Thomas GV, Garrett MD, Benerji U, de Bono JS, et al. (2009) Biomarker-driven early clinical trials in oncology: a paradigm shift in drug development. Cancer J 15: 406-420.
11. Phillips KA, Van Bebber S, Issa AM, (2006) Diagnostics and biomarker development: priming the pipeline. Nat Rev Drug Discov 5: 463-469.
12. Wagner JA, Williams SA, Webster CJ, (2007) Biomarkers and surrogate end points for fit-for-purpose development and regulatory evaluation of new drugs. Clin Pharmacol Ther 81: 104-107.
13. Hanks SK, Quinn AM, Hunter T, (1988) The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241: 42-52.
14. Songyang Z, Lu KP, Kwon YT, Tsai LH, Filhol O, et al. (1996) A structural basis for substrate specificities of protein Ser/Thr kinases: primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1. Mol Cell Biol 16: 6486-6493.
15. Nolen B, Taylor S, Ghosh G, (2004) Regulation of protein kinases; controlling activity through activation segment conformation. Mol Cell 15: 661-675.
16. Pan BS, Chan GK, Chenard M, Chi A, Davis LJ, et al. (2010) MK-2461, a novel multitargeted kinase inhibitor, preferentially inhibits the activated c-Met receptor. Cancer Res 70: 1524-1533.
17. Baselga J, (2001) The EGFR as a target for anticancer therapy-focus on cetuximab. Eur J Cancer 37 (Suppl 4): S16-22.
18. Hudis CA, (2007) Trastuzumab-mechanism of action and use in clinical practice. N Engl J Med 357: 39-51.
19. Lochhead PA, (2009) Protein kinase activation loop autophosphorylation in cis: overcoming a Catch-22 situation. Sci Signal 2: pe4.
20. Wang J, Wu JJ, Wang ZX, (2011) Mechanistic Studies of the Autoactivation of PAK2. A two-step model of cis initiation followed by trans amplification. Journal of Biol Chem 286: 2689-2695.
21. Nolen S, Taylor G, Ghosh G, (2004) Regulation of protein kinases controlling activity through activation segment conformation. Mol Cell 15: 661-675.
22. Nagashima K, Shumway SD, Sathyanarayanan S, Chen AH, Dolinski B, et al. (2011) Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor. J Biol Chem 286: 6433-6448.
23. Downward J, Parker P, Waterfield MD, (1984) Autophosphorylation sites on the epidermal growth factor receptor. Nature 311: 483-485.
24. Blume-Jensen P, Hunter T, (2001) Oncogenic kinase signaling. Nature 411: 355-365.
25. Hunter T, (2000) Signaling-2000 and beyond. Cell 100: 113-127.
26. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S, (2002) The protein kinase complement of the human genome. Science 298: 1912-1934.
27. Casamayor A, Morrice NA, Alessi DR, (1999) Phosphorylation of Ser-241 is essential for the activity of 3-phosphoinositide-dependent protein kinase-1: identification of five sites of phosphorylation in vivo. Biochem J 342: 287-292.
28. Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, et al. (2008) Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell 31: 438-448.
29. Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, et al. (2009) Large-scale proteomics analysis of the human kinome. Mol Cell Proteomics 8: 1751-1764.
30. Xu Z, Nagashima K, Sun D, Rush T, Northrup A, et al. (2009) Development of high-throughput TR-FRET and AlphaScreen assays for identification of potent inhibitors of PDK1. J Biomol Screen 14: 1257-1762.
31. Bobkova EV, Weber MJ, Xu Z, Zhang YL, Jung J, et al. (2010) Discovery of PDK1 kinase inhibitors with a novel mechanism of action by ultrahigh throughput screening. J Biol Chem 285: 18838-18846.
32. Xu D, Yao Y, Jiang X, Lu L, Dai W, (2010) Regulation of PTEN stability and activity by Plk3. J Biol Chem 285: 39935-39942.
33. Ellwood-Yenn K, Keilhack H, Kunii K, Dolinski B, Connor Y, et al. (2011) PDK1 attenuation fails to prevent tumor formation in PTEN-deficient transgenic mouse models. Cancer Res 71: 3052-3065.
34. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386.
35. Sarker D, Pacey S, Workman P, (2007) Use of pharmacokinetic/pharmacodynamic biomarkers to support rational cancer drug development. Biomark Med 1: 399-417.
36. Luo FR, Yang Z, Camuso A, Smykla R, McGlinchey K, et al. (2006) Dasatinib (BMS-354825) pharmacokinetics and pharmacodynamic biomarkers in animal models predict optimal clinical exposure. Clin Cancer Res 12: 7180-7186.
37. Gao X, Harris TK, (2006) Role of the PH domain in regulating in vitro autophosphorylation events required for reconstitution of PDK1 catalytic activity. Bioorg Chem 34: 200-223.
38. Sequist LV, Muzikansky A, Engelman JA, (2011) A New BATTLE in the Evolving War on Cancer. Cancer Discovery 1: 14-16.
39. Rifai N, Gillette MA, Carr SA, (2006) Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 24: 971-983.
40. Kuhn E, Addona T, Keshishian H, Burgess M, Mani DR et al, (2009) Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem 55: 1108-1117.
41. Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, et al. (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nature Biotechnol 29: 625-634.
42. Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, et al. (2011) A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nature Biotechnol 29: 635-643.
43. Paweletz CP, Wiener MC, Bondarenko AY, Yates NA, Song Q, et al. (2010) Application of an end-to-end biomarker discovery platform to identify target engagement markers in cerebrospinal fluid by high resolution differential mass spectrometry. J Proteome Res 9: 1392-1401.