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Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting

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Abstract

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term “catalomics” defines an emerging ‘-omics’ field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.

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References

  1. Creighton TE (1993) Proteins: structure and molecular properties, 2nd edn. Freeman, New York

    Google Scholar 

  2. Hanash S (2003) Nature 422:226

    Article  CAS  Google Scholar 

  3. Drews J (2000) Science 287:1960

    Article  CAS  Google Scholar 

  4. Hu Y, Uttamchandani M, Yao SQ (2006) Comb Chem High Throughput Screen 9:203

    Article  CAS  Google Scholar 

  5. Chen GYJ, Uttamchandani M, Lue RY, Lesaicherre ML, Yao SQ (2003) Curr Top Med Chem 3:705; Chattopadhaya S, Yao SQ (2006) Enzyme assays on chips. In: Reymond JL (ed) Enzyme assays: high-throughput screening. Genetic selection and fingerprinting. Wiley; Panicker RC, Chattopadhaya S, Yao SQ (2006) Anal Chim Acta 56:76; Uttamchandani M, Wang J, Yao SQ (2006) Mol BioSyst 2:58

    Article  CAS  Google Scholar 

  6. Reymond JL (ed) (2006) Enzyme assays: high-throughput screening. Genetic selection and fingerprinting. Wiley

  7. Morís-Varas F, Shah A, Aikens J, Nadkarni NP, Rozzell JD, Demirjian DC (1999) Bioorg Med Chem 7:2183; Janes LE, Löwendahl AC, Kazlauskas RJ (1998) Chem Eur J 4:2325

    Article  Google Scholar 

  8. Goddard JP, Reymond JL (2004) Curr Opin Biotechnol 15:314; Goddard JP, Reymond JL (2004) Trends Biotechnol 22:363

    Article  CAS  Google Scholar 

  9. Klein G, Reymond JL (1998) Bioorg Med Chem Lett 8:1113

    Article  CAS  Google Scholar 

  10. Badalassi F, Wahler D, Klein G, Crotti P, Reymond JL (2000) Angew Chem Int Ed 39:4067

    Article  CAS  Google Scholar 

  11. González-García EM, Helaine V, Klein G, Schuermann M, Sprenger GA, Fessner WD, Reymond JL (2003) Chem Eur J 9:893

    Article  Google Scholar 

  12. Leroy E, Bensel N, Reymond JL (2003) Adv Syn Catal 345:859; Leroy E, Bensel N, Reymond JL (2003) Bioorg Med Chem Lett 13:2105

    Article  CAS  Google Scholar 

  13. Nyfeler E, Grognux J, Wahler D, Reymond JL (2003) Helv Chim Acta 86:2919

    Article  CAS  Google Scholar 

  14. González-García EM, Grognux J, Wahler D, Reymond JL (2003) Helv Chim Acta 86:2458

    Article  Google Scholar 

  15. Badalassi F, Nguyen HK, Crotti P, Reymond JL (2002) Helv Chim Acta 85:3090

    Article  CAS  Google Scholar 

  16. Sevestre A, Virgil H, Ghislain G, Christine M, Laurence H (2003) Tetrahedron lett 44:827

    Article  CAS  Google Scholar 

  17. Gutiérrez MC, Sleegers A, Simpson HD, Alphand V, Furstoss R (2003) Org Biomol Chem 1:3500

    Article  Google Scholar 

  18. Gao W, Xing B, Tsien RY, Rao J (2003) J Am Chem Soc 125:11146

    Article  CAS  Google Scholar 

  19. Matayoshi ED, Wang GT, Krafft GA, Erickson J (1990) Science 247:954

    Article  CAS  Google Scholar 

  20. Karvinen J, Laitala V, Makinen ML, Mulari O, Tamminen J, Hermonen J, Hurskainen P, Hemmila I (2004) Anal Chem 76:1429

    Article  CAS  Google Scholar 

  21. Vaknin A, Berg HC (2004) Proc Natl Acad Sci USA 101:17072

    Article  CAS  Google Scholar 

  22. Wichmann O, Wittbrodt J, Schultz C (2006) Angew Chem Int Ed 45:508; Farber SA, Pack M, Ho SY, Johnson ID, Wagner DS, Dosch R, Mullins MC, Hendrickson HS, Hendrickson EK, Halpern ME (2001) Science 292:1385

    Article  CAS  Google Scholar 

  23. Hailing PJ, Ulijn RV, Flitsch SL (2005) Curr Opin Biotechnol 16:385; St. Hilaire PM, Willert M Juliano MA, Juliano L, Meldal M (1999) J Comb Chem 1:509; Blum G, Mullins SR, Keren K, Fonovic M, Jedeszko C, Rice MJ, Sloane BF, Bogyo M (2005) Nat Chem Biol 1:203

    Article  Google Scholar 

  24. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Science 251:767

    Article  CAS  Google Scholar 

  25. http://www.affymetrix.com; Schena M, Shalon D, Davis RW, Brown PO, (1995) Science 270:467

    Google Scholar 

  26. MacBeath G, Koehler AN, Schreiber SL (1999) J Am Chem Soc 121:7967; MacBeath G, Schreiber SL (2000) Science 289:1760

    Article  CAS  Google Scholar 

  27. Joos TO, Schrenk M, Höpfl P, Kröger K, Chowdhury U, Stoll D, Schörner D, Durrr M, Herick K, Rupp S, Sohn K, Hämmerle H (2000) Electrophoresis 21:2641; Ge H (2000) Nucleic Acids Res 28:e3

    Article  CAS  Google Scholar 

  28. Vijayendran RA, Leckband DE (2001) Anal Chem 73:471

    Article  CAS  Google Scholar 

  29. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Science 293:2101

    Article  CAS  Google Scholar 

  30. Lesaicherre ML, Lue RYP, Chen GYJ, Zhu Q, Yao SQ (2002) J Am Chem Soc 124:8768; Lue RYP, Chen GYJ, Hu Y, Zhu Q, Yao SQ (2004) J Am Chem Soc 126:1055

    Article  CAS  Google Scholar 

  31. Hodneland CD, Lee YS, Min DH, Mrksich M (2002) Proc Natl Acad Sci USA 99:5048

    Article  CAS  Google Scholar 

  32. Kindermann N, George M, Johnsson N, Johnsson K (2003) J Am Chem Soc 125:7810

    Article  CAS  Google Scholar 

  33. Yin J, Liu F, Li X, Walsh CT (2004) J Am Chem Soc 126:7754

    Article  CAS  Google Scholar 

  34. Tan LP, Chen GYJ, Yao SQ (2004) Bioorg Med Chem Lett 14:5735; Tan LP, Lue RYP, Chen GYJ, Yao SQ (2004) Bioorg Med Chem Lett 14:6067

    Article  CAS  Google Scholar 

  35. Girish A, Sun H, Yeo SYD, Chen GYJ, Chua TK, Yao SQ (2005) Bioorg Med Chem Lett 15:2447

    Article  CAS  Google Scholar 

  36. Zhang K, Diehl MR, Tirell DA (2005) J Am Chem Soc 127:10136

    Article  CAS  Google Scholar 

  37. Watzke A, Köhn M, Rodriguez MR, Wacker R, Schröder, Breinbauer R, Kuhlmann J, Alexandrov K, Niemeyer CM, Goody RS, Waldmann H (2006) Angew Chem Int Ed 45:1408

    Article  CAS  Google Scholar 

  38. Kwon Y, Coleman MA, Camarero JA (2006) Angew Chem Intl Ed 45:1726

    Article  CAS  Google Scholar 

  39. Panicker RC, Huang X, Yao SQ (2004) Comb Chem High Throughput Screen 7:547; Schutkowski M, Reineke U, Reimer U (2005) ChemBioChem 6:513

    CAS  Google Scholar 

  40. Frank R (1992) Tetrahedron 48:9217

    Article  CAS  Google Scholar 

  41. Falsey JR, Renil R, Park S, Li S, Lam KS (2001) Bioconj Chem 12:346

    Article  CAS  Google Scholar 

  42. Houseman BT, Huh JH, Kron SJ, Mrksich M (2002) Nat Biotechnol 20:270; Houseman BT, Gawalt ES, Mrksich M (2003) Langmuir 19:1522

    Article  CAS  Google Scholar 

  43. Lesaicherre ML, Uttamchandani M, Chen GYJ, Yao SQ (2002) Bioorg Med Chem Lett 12:2079

    Article  CAS  Google Scholar 

  44. Lesaicherre ML, Uttamchandani M, Chen GYJ, Yao SQ (2002) Bioorg Med Chem Lett 12:2085; Uttamchandani M, Chan EWS, Chen GYJ, Yao SQ (2003) Bioorg Med Chem Lett 13:2997

    Article  CAS  Google Scholar 

  45. Schreiber SL (2005) Nat Chem Biol 1:64

    Article  CAS  Google Scholar 

  46. Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL (2002) Nature 416:653; Uttamchandani M, Walsh DP, Khersonsky SM, Huang X, Yao SQ, Chang YT (2004) J Comb Chem 6:862; Hergenrother PJ, Depew KM, Screiber SL (2000) J Am Chem Soc 122:7849; Seeman DB, Park SB, Koehler AN, Schreiber SL (2003) Angew Chem Intl Ed 42:2376

    Article  CAS  Google Scholar 

  47. Köhn M, Wacker R, Peters C, Schröder H, Soulère L, Breinbauer R, Niemeyer CM, Waldmann H (2003) Angew Chem Intl Ed 42:5830; Soellner MB, Dickson KA, Nilsson BL, Raines RT (2003) J Am Chem Soc 125:11790

    Article  Google Scholar 

  48. Wang J, Uttamchandani M, Sun H, Yao SQ (2006) QSAR Comb Sci (in press); Uttamchandani M, Walsh DP, Yao SQ, Chang YT (2005) Curr Opin Chem Biol 9:4

  49. Liu Y, Patricelli MP, Cravatt BF (1999) Proc Natl Acad Sci USA 96:14694

    Article  CAS  Google Scholar 

  50. Speer AE, Cravatt BF (2004) Chem Bio Chem 5:41

    Google Scholar 

  51. Jeffery DA, Bogyo M (2003) Curr Opin Biotechnol 14:87

    Article  CAS  Google Scholar 

  52. Lo LC, Pang TL, Kuo CH, Chiang YL, Wang HY, Lin JJ (2002) J Proteome Res 1:35

    Article  CAS  Google Scholar 

  53. Hagenstein, MC, Mussgnug JH, Lotte K, Plessow, R, Brockhinke A, Kruse O, Sewald N (2003) Angew Chem Int Ed 42:5635

    Article  CAS  Google Scholar 

  54. Liau ML, Panicker RC, Yao SQ (2003) Tetrahedron Lett 44:1043; Wang G, Uttamchandani M, Chen GYJ, Yao SQ (2003) Org Lett 5:737; Zhu Q, Huang X, Chen GYJ, Yao SQ (2003) Tetrahedron Lett 44:2669; Zhu Q, Girish A, Chattopadhaya S, Yao SQ (2004) Chem Commun 13:1512; Chan EWS, Chattopadhaya S, Panicker RC, Huang X, Yao SQ (2004) J Am Chem Soc 126:14435; Chattopadhaya S, Chan EWS, Yao SQ (2005) Tetrahedron Lett 46:4053

    Article  CAS  Google Scholar 

  55. Chen GYJ, Uttamchandani M, Zhu Q, Wang G, Yao SQ (2003) Chem Bio Chem 4:336

    CAS  Google Scholar 

  56. Eppinger J, Funeriu DP, Miyake M, Denizot L, Miyake J (2004) Angew Chem Int Ed 43:3806; Funeriu DP, Eppinger J, Denizot L, Miyake M, Miyake J (2005) Nat Biotechnol 23:622; Srinivasan R, Huang X, Ng SL, Yao SQ (2006) ChemBioChem 7:32

    Article  CAS  Google Scholar 

  57. Abecassis V, Pompon D, Truan G (2000) Nucleic Acids Res 28:e88; Toepert F, Knaute T, Guffler S, Pires JR, Matzdorf T, Oschkinat H, Schneider-Mergener J (2003) Angew Chem Int Ed 115:1168; Grognux J, Reymond JL (2004) ChemBioChem 5:826; Goddard JP, Reymond JL (2004) J Am Chem Soc 126:11116; Reymond JL, Wahler D, ChemBioChem (2002) 3:701; Maly DJ, Huang L, Ellman JA (2002) ChemBioChem 3:17

    Article  CAS  Google Scholar 

  58. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Synder M (2000) Nature Genet 26:283

    Article  CAS  Google Scholar 

  59. Schutkowski M, Reimer U, Panse S, Dong L, Lizcano JM, Alessi DR, Schneider-Mergener J (2004) Angew Chem Intl Ed 43:2671; Panse S, Dong L, Burian A, Carus R, Schutkowski M, Reimer U, Schneider-Mergener J (2004) Mol Divers 8:291; Lizcano JM, Deak M, Morrice N, Kieloch A, Hastie CJ, Dong L, Schutkowski M, Reimer U, Alessi DR (2002) J Biol Chem 271:27839

    Article  CAS  Google Scholar 

  60. Martin K, Steinberg TH, Cooley LA, Gee KR, Beechem JM, Patton WF (2003) Proteomics 3:1244

    Article  CAS  Google Scholar 

  61. Salisbury CM, Maly DJ, Ellman JA (2002) J Am Chem Soc 124:14868

    Article  CAS  Google Scholar 

  62. Harris JL, Backes BJ, Leonetti F, Mahrus S, Ellman JA, Craik CS (2000) Proc Natl Acad Sci USA 97:7754

    Article  CAS  Google Scholar 

  63. Zhu Q, Uttamchandani M, Li D, Lesaicherre ML, Yao SQ (2003) Org Lett 5:1257

    Article  CAS  Google Scholar 

  64. Kiyonaka S, Sada K, Yoshimura I, Shinkai S, Kato N, Hamachi I (2004) Nature Mat 3:58

    Article  CAS  Google Scholar 

  65. Gosalia DN, Salisbury CM, Maly DJ, Ellman JA, Diamond SL (2005) Proteomics 5:1292; Gosalia DN, Salisbury CM, Ellman JA, Diamond SL (2005) Mol Cell Proteomics 4:626

    Article  CAS  Google Scholar 

  66. Shin I, Cho JW, Boo DW (2004) Comb Chem High Throughput Screen 7:565

    CAS  Google Scholar 

  67. Fukui S, Feizi T, Galustian C, Lawson AM, Chai W (2002) Nature Biotechnol 20:1011–1017; Wang D, Liu S, Trummer BJ, Deng C, Weng A (2002) Nature Biotechnol 20:275–281

    Article  CAS  Google Scholar 

  68. Houseman BT, Mrksich M (2002) Chem Bio 9:443

    Article  CAS  Google Scholar 

  69. Park S, Lee MR, Pyo SJ, Shin I (2004) J Am Chem Soc 126:4812

    Article  CAS  Google Scholar 

  70. Gosalia DN, Diamond SL (2003) Proc Natl Acad Sci USA 100:8721

    Article  CAS  Google Scholar 

  71. Uttamchandani M, Huang X, Chen GYJ, Yao SQ (2005) Bioorg Med Chem Lett 15:2135

    Article  CAS  Google Scholar 

  72. Wang J, Uttamchandani M, Yao SQ (2006) Chem Commun 717

  73. Muralidhar R, Kodadek T (2005) Proc Natl Acad Sci USA 102:12672

    Article  Google Scholar 

  74. Winssinger N, Harris JL, Backes BJ, Schultz PG (2001) Angew Chem Intl Ed 40:3152; Winssinger N, Ficarro S, Schultz PG, Harris JL (2002) Proc Natl Acad Sci USA 99:11139

    Article  CAS  Google Scholar 

  75. Winssinger N, Damoiseaux R, Tully DC, Geierstanger BH, Burdick K, Harris JL (2004) Chem Biol 11:1351; Harris J, Mason DE, Li J, Burdick KW, Backes BJ, Chen T, Shipway A, van Heeke G, Gough L, Ghaemmaghami A, Shakib F, Debaene F, Winssinger N (2004) Chem Biol 11:1361

    Article  CAS  Google Scholar 

  76. Hu Y, Chen GYJ, Yao SQ (2005) Angew Chem Int Ed 44:1048

    Article  CAS  Google Scholar 

  77. Ziauddin J, Sabatini DM (2001) Nature 411:107

    Article  CAS  Google Scholar 

  78. Bailey SN, Sabatini DM, Stockwell BR (2004) Proc Natl Acad Sci USA 101:16144

    Article  CAS  Google Scholar 

  79. Lee MY, Park CB, Dordick JB, Clark DS (2005) Proc Natl Acad Sci USA 102:983

    Article  CAS  Google Scholar 

  80. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Synder M (2004) Science 306:482

    Article  CAS  Google Scholar 

  81. Jeol GY, Stephanopoulos (2004) Science 304:428

    Article  Google Scholar 

  82. Su J, Bringer MR, Ismagilov RF, Mrksich M (2005) J Am Chem Soc 127:7280

    Article  CAS  Google Scholar 

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Acknowledgements

Funding support was provided by the National University of Singapore (NUS) and the Agency for Science, Technology and Research (A*STAR) of Singapore.

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Authors and Affiliations

  1. Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore

    Hongyan Sun, Jun Wang & Shao Q. Yao

  2. Department of Biological Sciences, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore

    Souvik Chattopadhaya & Shao Q. Yao

  3. Medicinal Chemistry Program of the Office of Life Sciences, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore

    Shao Q. Yao

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  1. Hongyan Sun
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  2. Souvik Chattopadhaya
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  3. Jun Wang
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  4. Shao Q. Yao
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Correspondence to Shao Q. Yao.

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Sun, H., Chattopadhaya, S., Wang, J. et al. Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting. Anal Bioanal Chem 386, 416–426 (2006). https://doi.org/10.1007/s00216-006-0511-5

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