Advertisement

American Journal of Pharmacogenomics

, Volume 4, Issue 6, pp 371–381 | Cite as

Activity-Based Protein Profiling

Applications to Biomarker Discovery, In Vivo Imaging and Drug Discovery
  • Alicia B. Berger
  • Phillip M. Vitorino
  • Matthew BogyoEmail author
Technology

Abstract

The genomic revolution has created a wealth of information regarding the fundamental genetic code that defines the inner workings of a cell. However, it has become clear that analyzing genome sequences alone will not lead to new therapies to fight human disease. Rather, an understanding of protein function within the context of complex cellular networks will be required to facilitate the discovery of novel drug targets and, subsequently, new therapies directed against them.

The past ten years has seen a dramatic increase in technologies that allow large-scale, systems-based methods for analysis of global biological processes and disease states. In the field of proteomics, several well-established methods persist as a means to resolve and analyze complex mixtures of proteins derived from cells and tissues. However, the resolving power of these methods is often challenged by the diverse and dynamic nature of the proteome. The field of activity-based proteomics, or chemical proteomics, has been established in an attempt to focus proteomic efforts on subsets of physiologically important protein targets. This new approach to proteomics is centered around the use of small molecules termed activity-based probes (ABPs) as a means to tag, enrich, and isolate, distinct sets of proteins based on their enzymatic activity.

Chemical probes can be ‘tuned’ to react with defined enzymatic targets through the use of chemically reactive warhead groups, fused to selective binding elements that control their overall specificity. As a result, ABPs function as highly specific, mechanism-based reagents that provide a direct readout of enzymatic activity within complex proteomes. Modification of protein targets by an ABP facilitates their purification and isolation, thereby eliminating many of the confounding issues of dynamic range in protein abundance. In this review, we outline recent advances in the field of chemical proteomics. Specifically, we highlight how this technology can be applied to advance the fields of biomarker discovery, in vivo imaging, and small molecule screening and drug target discovery.

Keywords

Epidermal Growth Factor Receptor Cysteine Protease Fluorescence Resonance Energy Transfer Fatty Acid Amide Hydrolase Epidermal Growth Factor Receptor Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was funded by a National Technology Centers for Networks and Pathways grant, NIH grant U54 RR020843 (awarded to Dr Bogyo). Dr Berger was funded by NHGRI trainiing grant 5T32HG00044.

References

  1. 1.
    Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science 2001 Feb 16; 291: 1304–51PubMedCrossRefGoogle Scholar
  2. 2.
    Corthals GL, Wasinger VC, Hochstrasser DF, et al. The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000 Apr; 21: 1104–15PubMedCrossRefGoogle Scholar
  3. 3.
    Patton WF. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 2000 Apr; 21: 1123–44PubMedCrossRefGoogle Scholar
  4. 4.
    Santoni V, Molloy M, Rabilloud T. Membrane proteins and proteomics: un amour impossible? Electrophoresis 2000 Apr; 21: 1054–70PubMedCrossRefGoogle Scholar
  5. 5.
    Gygi SP, Corthals GL, Zhang Y, et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 2000 Aug 15; 97: 9390–5PubMedCrossRefGoogle Scholar
  6. 6.
    Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999 Oct; 17: 994–9PubMedCrossRefGoogle Scholar
  7. 7.
    Zhou H, Ranish JA, Watts JD, et al. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol 2002 May; 20: 512–5PubMedCrossRefGoogle Scholar
  8. 8.
    Goshe MB, Smith RD. Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 2003 Feb; 14: 101–9PubMedCrossRefGoogle Scholar
  9. 9.
    Petricoin EF, Liotta LA. SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr Opin Biotechnol 2004 Feb; 15: 24–30PubMedCrossRefGoogle Scholar
  10. 10.
    Jeffery DA, Bogyo M. Chemical proteomics and its application to drug discovery. Curr Opin Biotechnol 2003 Feb; 14: 87–95PubMedCrossRefGoogle Scholar
  11. 11.
    Speers AE, Cravatt BF. Chemical strategies for activity-based proteomics. Chembiochem 2004 Jan 3; 5: 41–7PubMedCrossRefGoogle Scholar
  12. 12.
    Adam GC, Cravatt BF, Sorensen EJ. Profiling the specific reactivity of the proteome with non-directed activity-based probes. Chem Biol 2001 Jan; 8: 81–95PubMedCrossRefGoogle Scholar
  13. 13.
    Adam GC, Sorensen EJ, Cravatt BF. Chemical strategies for functional proteomics. Mol Cell Proteomics 2002 Oct; 1: 781–90PubMedCrossRefGoogle Scholar
  14. 14.
    Greenbaum D, Medzihradszky KF, Burlingame A, et al. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem Biol 2000 Aug; 7: 569–81PubMedCrossRefGoogle Scholar
  15. 15.
    Greenbaum D, Baruch A, Hayrapetian L, et al. Chemical approaches for functionally probing the proteome. Mol Cell Proteomics 2002 Jan; 1: 60–8PubMedCrossRefGoogle Scholar
  16. 16.
    Mason RW, Bartholomew LT, Hardwick BS. The use of benzyloxy-carbonyl[125I]iodotyrosylalanyldiazomethane as a probe for active cysteine proteinases in human tissues. Biochem J 1989 Nov 1; 263: 945–9PubMedGoogle Scholar
  17. 17.
    Shi GP, Munger JS, Meara JP, et al. Molecular cloning and expression of human alveolar macrophage cathepsin S, an elastinolytic cysteine protease. J Biol Chem 1992; 267(11): 7258–62PubMedGoogle Scholar
  18. 18.
    Bogyo M, Verhelst S, Bellingard-Dubouchaud V, et al. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. Chem Biol 2000 Jan; 7: 27–38PubMedCrossRefGoogle Scholar
  19. 19.
    Schaschke N, Assfalg-Machleidt I, Lassleben T, et al. Epoxysuccinyl peptide-derived affinity labels for cathepsin B. FEBS Lett 2000; 482(1–2): 91–6PubMedCrossRefGoogle Scholar
  20. 20.
    Borodovsky A, Kessler BM, Casagrande R, et al. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J 2001; 20(18): 5187–96PubMedCrossRefGoogle Scholar
  21. 21.
    Mikolajczyk J, Boatright KM, Stennicke HR, et al. Sequential autolytic processing activates the zymogen of Arg-gingipain. J Biol Chem 2003; 278(12): 10458–64PubMedCrossRefGoogle Scholar
  22. 22.
    Liu Y, Patricelli MP, Cravatt BF. Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci U S A 1999 Dec 21; 96: 14694–9PubMedCrossRefGoogle Scholar
  23. 23.
    Patricelli MP, Giang DK, Stamp LM, et al. Direct visualization of serine hydrolase activities in complex proteomes using fluorescent active site-directed probes. Proteomics 2001 Sep; 1: 1067–71PubMedCrossRefGoogle Scholar
  24. 24.
    Kidd D, Liu Y, Cravatt BF. Profiling serine hydrolase activities in complex proteomes. Biochemistry 2001; 40(13): 4005–15PubMedCrossRefGoogle Scholar
  25. 25.
    Meng L, Kwok BH, Sin N, et al. Eponemycin exerts its antitumor effect through the inhibition of proteasome function. Cancer Res 1999; 59(12): 2798–801PubMedGoogle Scholar
  26. 26.
    Saghatelian A, Jessani N, Joseph A, et al. Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci U S A 2004 Jul 6; 101: 10000–5PubMedCrossRefGoogle Scholar
  27. 27.
    Kumar S, Zhou B, Liang F, et al. Activity-based probes for protein tyrosine phosphatases. Proc Natl Acad Sci U S A 2004 May 25; 101: 7943–8PubMedCrossRefGoogle Scholar
  28. 28.
    Zhu Q, Huang X, Chen GYJ, et al. Activity based fluorescent probes that target phosphatases. Tetrahedron Lett 2003; 44: 2669–72CrossRefGoogle Scholar
  29. 29.
    Adam GC, Sorensen EJ, Cravatt BF. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat Biotechnol 2002 Aug; 20: 805–9PubMedGoogle Scholar
  30. 30.
    Thornberry NA, Peterson EP, Zhao JJ, et al. Inactivation of interleukin-1 beta converting enzyme by peptide (acyloxy)methyl ketones. Biochemistry 1994 Apr 5; (33): 3934–40CrossRefGoogle Scholar
  31. 31.
    Hawthorne S, Hamilton R, Walker BJ, et al. Utilization of biotinylated diphenyl phosphonates for disclosure of serine proteases. Anal Biochem 2004 Mar 15; 326: 273–5PubMedCrossRefGoogle Scholar
  32. 32.
    Zhu Q, Girish A, Chattopadhaya S, et al. Developing novel activity-based fluorescent probes that target different classes of proteases. Chem Commun (Camb) 2004 Jul; 7(13): 1512–3CrossRefGoogle Scholar
  33. 33.
    Greenbaum DC, Arnold WD, Lu F, et al. Small molecule affinity fingerprinting: a tool for enzyme family subclassification, target identification, and inhibitor design. Chem Biol 2002 Oct; 9: 1085–94PubMedCrossRefGoogle Scholar
  34. 34.
    Uhlmann F, Wernic D, Poupart MA, et al. Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast. Cell 2000 Oct 27; 103: 375–86PubMedCrossRefGoogle Scholar
  35. 35.
    Salvesen GS. Caspases and apoptosis. Essays Biochem 2002; 38: 9–19PubMedGoogle Scholar
  36. 36.
    Lecaille F, Kaleta J, Bromme D. Human and parasitic papain-like cysteine proteases: their role in physiology and pathology and recent developments in inhibitor design. Chem Rev 2002 Dec; 102: 4459–88PubMedCrossRefGoogle Scholar
  37. 37.
    Faleiro L, Kobayashi R, Fearnhead H, et al. Multiple species of CPP32 and Mch2 are the major active caspases present in apoptotic cells. EMBO J 1997 May 1; 16: 2271–81PubMedCrossRefGoogle Scholar
  38. 38.
    Mason RW, Wilcox D, Wikstrom P, et al. The identification of active forms of cysteine proteinases in Kirsten-virus-transformed mouse fibroblasts by use of a specific radiolabelled inhibitor. Biochem J 1989 Jan 1; 257: 125–9PubMedGoogle Scholar
  39. 39.
    Joyce JA, Baruch A, Chehade K, et al. Cathepsin cysteine proteases are effectors of invasive growth and angiogenesis during multistage tumorigenesis. Cancer Cell 2004 May; 5: 443–53PubMedCrossRefGoogle Scholar
  40. 40.
    Baruch A, Greenbaum D, Levy ET, et al. Defining a link between gap junction communication, proteolysis, and cataract formation. J Biol Chem 2001 Aug 3; 276: 28999–9006PubMedCrossRefGoogle Scholar
  41. 41.
    Yasothornsrikul S, Greenbaum D, Medzihradszky KF, et al. CathepsinL in secretory vesicles functions as a prohormone-processing enzyme for production of the enkephalin peptide neurotransmitter. Proc Natl Acad Sci USA 2003 Aug 5; 100: 9590–5PubMedCrossRefGoogle Scholar
  42. 42.
    Greenbaum DC, Baruch A, Grainger M, et al. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science 2002 Dec 6; 298: 2002–6PubMedCrossRefGoogle Scholar
  43. 43.
    Oleksy A, Golonka E, Banbula A, et al. Growth phase-dependent production of a cell wall-associated elastinolytic cysteine proteinase by Staphylococcus epidermidis. Biol Chem 2004 Jun; 385: 525–35PubMedCrossRefGoogle Scholar
  44. 44.
    van der Hoorn RA, Leeuwenburgh MA, Bogyo M, et al. Activity profiling of papain-like cysteine proteases in plants. Plant Physiol 2004 Jul; 135: 1170–8PubMedCrossRefGoogle Scholar
  45. 45.
    Boatright KM, Renatus M, Scott FL, et al. A unified model for apical caspase activation. Mol Cell 2003 Feb; 11: 529–41PubMedCrossRefGoogle Scholar
  46. 46.
    Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001 Feb 15; 409: 860–921PubMedCrossRefGoogle Scholar
  47. 47.
    Jessani N, Liu Y, Humphrey M, et al. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc Natl Acad Sci U S A 2002 Aug 6; 99: 10335–40PubMedCrossRefGoogle Scholar
  48. 48.
    Overall CM, Lopez-Otin C. Strategies for MMP inhibition in cancer: innovations for the post-trial era. Nat Rev Cancer 2002 Sep; 2: 657–72PubMedCrossRefGoogle Scholar
  49. 49.
    Puente XS, Sanchez LM, Overall CM, et al. Human and mouse proteases: a comparative genomic approach. Nat Rev Genet 2003 Jul; 4: 544–58PubMedCrossRefGoogle Scholar
  50. 50.
    Chang C, Werb Z. The many faces of metalloproteases: cell growth, invasion, angiogenesis and metastasis. Trends Cell Biol 2001 Nov; 11: S37–43PubMedGoogle Scholar
  51. 51.
    Turner AJ, Isaac RE, Coates D. The neprilysin (NEP) family of zinc metalloendopeptidases: genomics and function. Bioessays 2001 Mar; 23: 261–9PubMedCrossRefGoogle Scholar
  52. 52.
    Garcia-Echeverria C, Traxler P, Evans DB. ATP site-directed competitive and irreversible inhibitors of protein kinases. Med Res Rev 2000 Jan; 20: 28–57PubMedCrossRefGoogle Scholar
  53. 53.
    Colman RF. Affinity labeling of purine nucleotide sites in proteins. Annu Rev Biochem 1983; 52: 67–91PubMedCrossRefGoogle Scholar
  54. 54.
    Wymann MP, Bulgarelli-Leva G, Zvelebil MJ, et al. Wortmannin inactivates phosphoinositide 3-kinase by covalent modification of Lys-802, a residue involved in the phosphate transfer reaction. Mol Cell Biol 1996 Apr; 16: 1722–33PubMedGoogle Scholar
  55. 55.
    Mustelin T, Feng GS, Bottini N, et al. Protein tyrosine phosphatases. Front Biosci 2002 Jan 1; 7: d85–142PubMedCrossRefGoogle Scholar
  56. 56.
    Ross DT, Scherf U, Eisen MB, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000 Mar; 24: 227–35PubMedCrossRefGoogle Scholar
  57. 57.
    Konecny G, Untch M, Pihan A, et al. Association of urokinase-type plasminogen activator and its inhibitor with disease progression and prognosis in ovarian cancer. Clin Cancer Res 2001 Jun; 7: 1743–9PubMedGoogle Scholar
  58. 58.
    Kanitakis J, Narvaez D, Claudy A. Differential expression of the CD10 antigen (neutral endopeptidase) in primary versus metastatic malignant melanomas of the skin. Melanoma Res 2002 Jun; 12: 241–4PubMedCrossRefGoogle Scholar
  59. 59.
    Galardy RE, Grobelny D, Foellmer HG, et al. Inhibition of angiogenesis by the matrix metalloprotease inhibitor N-[R-2-(hydroxamidocarbonymethyl)-4-methylpentanoyl)]L-tryptophan methylamide. Cancer Res 1994 Sep 1; 54: 4715–8PubMedGoogle Scholar
  60. 60.
    Grobelny D, Poncz L, Galardy RE. Inhibition of human skin fibroblast collagenase, thermolysin, and Pseudomonas aeruginosa elastase by peptide hydroxamic acids. Biochemistry 1992 Aug 11; 31: 7152–4PubMedCrossRefGoogle Scholar
  61. 61.
    Solorzano CC, Ksontini R, Pruitt JH, et al. A matrix metalloproteinase inhibitor prevents processing of tumor necrosis factor alpha (TNF alpha) and abrogates endotoxin-induced lethality. Shock 1997 Jun; 7: 427–31PubMedCrossRefGoogle Scholar
  62. 62.
    Baruch A, Jeffery DA, Bogyo M. Enzyme activity: it’s all about image. Trends Cell Biol 2004 Jan; 14: 29–35PubMedCrossRefGoogle Scholar
  63. 63.
    Gurtu V, Kain SR, Zhang G. Fluorometric and colorimetric detection of caspase activity associated with apoptosis. Anal Biochem 1997 Aug 15; 251: 98–102PubMedCrossRefGoogle Scholar
  64. 64.
    Packard BZ, Toptygin DD, Komoriya A, et al. Design of profluorescent protease substrates guided by exciton theory. Methods Enzymol 1997; 278: 15–23PubMedCrossRefGoogle Scholar
  65. 65.
    Komoriya A, Packard BZ, Brown MJ, et al. Assessment of caspase activities in intact apoptotic thymocytes using cell-permeable fluorogenic caspase substrates. J Exp Med 2000 Jun 5; 191: 1819–28PubMedCrossRefGoogle Scholar
  66. 66.
    Hirata H, Takahashi A, Kobayashi S, et al. Caspases are activated in a branched protease cascade and control distinct downstream processes in Fas-induced apoptosis. J Exp Med 1998 Feb 16; 187: 587–600PubMedCrossRefGoogle Scholar
  67. 67.
    Speers AE, Adam GC, Cravatt BF. Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne[3 + 2] cycloaddition. J Am Chem Soc 2003 Apr 23; 125: 4686–7PubMedCrossRefGoogle Scholar
  68. 68.
    Speers AE, Cravatt BF. Profiling enzyme activities in vivo using click chemistry methods. Chem Biol 2004 Apr; 11: 535–46PubMedCrossRefGoogle Scholar
  69. 69.
    Ovaa H, van Swieten PF, Kessler BM, et al. Chemistry in living cells: detection of active proteasomes by a two-step labeling strategy. Angew Chem Int Ed Engl 2003 Aug 11; 42: 3626–9PubMedCrossRefGoogle Scholar
  70. 70.
    Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov 2002 Sep; 1: 727–30PubMedCrossRefGoogle Scholar
  71. 71.
    Drews J. Drug discovery: a historical perspective. Science 2000 Mar 17; 287: 1960–4PubMedCrossRefGoogle Scholar
  72. 72.
    Sordella R, Bell DW, Haber DA, et al. Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways. Science 2004; 305: 1163–7PubMedCrossRefGoogle Scholar
  73. 73.
    Leung D, Hardouin C, Boger DL, et al. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat Biotechnol 2003 Jun; 21: 687–91PubMedCrossRefGoogle Scholar

Copyright information

© Adis Data Information BV 2004

Authors and Affiliations

  • Alicia B. Berger
    • 1
  • Phillip M. Vitorino
    • 1
  • Matthew Bogyo
    • 1
    Email author
  1. 1.Department of PathologyStanford University School of MedicineStanfordUSA

Personalised recommendations