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Screening a fragment cocktail library using ultrafiltration

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Abstract

Ultrafiltration provides a generic method to discover ligands for protein drug targets with millimolar to micromolar K d, the typical range of fragment-based drug discovery. This method was tailored to a 96-well format, and cocktails of fragment-sized molecules, with molecular masses between 150 and 300 Da, were screened against medical structural genomics target proteins. The validity of the method was confirmed through competitive binding assays in the presence of ligands known to bind the target proteins.

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References

  1. Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Science 274(5292):1531–1534

    Article  CAS  Google Scholar 

  2. Oprea TI, Davis AM, Teague SJ, Leeson PD (2001) J Chem Inf Comput Sci 41(5):1308–1315

    Article  CAS  Google Scholar 

  3. Carr R, Jhoti H (2002) Drug Discov Today 7(9):522–527

    Article  CAS  Google Scholar 

  4. Erlanson DA, McDowell RS, O'Brien T (2004) J Med Chem 4(14):3463–3482

    Article  Google Scholar 

  5. Hajduk PJ, Greer J (2007) Nat Rev Drug Discov 6(3):211–219

    Article  CAS  Google Scholar 

  6. Verlinde C, Fan EK, Shibata S, Zhang ZS, Sun ZH, Deng W, Ross J, Kim J, Xiao LR, Arakaki TL, Bosch J, Caruthers JM, Larson ET, LeTrong I, Napuli A, Kelley A, Mueller N, Zucker F, Van Voorhis WC, Buckner FS, Merritt EA, Hol WGJ (2009) Curr Top Med Chem 9(18):1678–1687

    Article  CAS  Google Scholar 

  7. Carr RAE, Congreve M, Murray CW, Rees DC (2005) Drug Discov Today 10(14):987–992

    Article  CAS  Google Scholar 

  8. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Adv Drug Del Rev 46(1–3):3–26

    Article  CAS  Google Scholar 

  9. Deng GJ, Sanyal G (2006) J Pharm Biomed Anal 40(3):528–538

    Article  CAS  Google Scholar 

  10. Wood WJL, Patterson AW, Tsuruoka H, Jain RK, Ellman JA (2005) J Am Chem Soc 127(44):15521–15527

    Article  CAS  Google Scholar 

  11. Makara GM, Athanasopoulos J (2005) Curr Opin Biotechnol 16(6):666–673

    CAS  Google Scholar 

  12. Vuignier K, Schappler J, Veuthey JL, Carrupt PA, Martel S (2010) Anal Bioanal Chem 398(1):53–66

    Article  CAS  Google Scholar 

  13. Murray CW, Carr MG, Callaghan O, Chessari G, Congreve M, Cowan S, Coyle JE, Downham R, Figueroa E, Frederickson M, Graham B, McMenamin R, O'Brien MA, Patel S, Phillips TR, Williams G, Woodhead AJ, Woolford AJA (2010) J Med Chem 53(16):5942–5955

    Article  CAS  Google Scholar 

  14. Hartshorn MJ, Murray CW, Cleasby A, Frederickson M, Tickle IJ, Jhoti H (2005) J Med Chem 48(2):403–413

    Article  CAS  Google Scholar 

  15. Mayer M, Meyer B (2001) J Am Chem Soc 123(25):6108–6117

    Article  CAS  Google Scholar 

  16. Hajduk PJ, Meadows RP, Fesik SW (1997) Science 278(5337):497

    Article  CAS  Google Scholar 

  17. Hajduk PJ, Meadows RP, Fesik SW (1999) Q Rev Biophys 32(3):211–240

    Article  CAS  Google Scholar 

  18. Hajduk PJ, Gomtsyan A, Didomenico S, Cowart M, Bayburt EK, Solomon L, Severin J, Smith R, Walter K, Holzman TF, Stewart A, McGaraughty S, Jarvis MF, Kowaluk EA, Fesik SW (2000) J Med Chem 43(25):4781–4786

    Article  CAS  Google Scholar 

  19. Vanwetswinkel S, Heetebrij RJ, van Duynhoven J, Hollander JG, Filippov DV, Hajduk PJ, Siegal G (2005) Chem Biol 12(2):207–216

    Article  CAS  Google Scholar 

  20. Frostell-Karlsson A, Remaeus A, Roos H, Andersson K, Borg P, Hamalainen M, Karlsson R (2000) J Med Chem 43(10):1986–1992

    Article  CAS  Google Scholar 

  21. Rich RL, Day YSN, Morton TA, Myszka DG (2001) Anal Biochem 296(2):197–207

    Article  CAS  Google Scholar 

  22. Navratilova I, Hopkins AL (2010) ACS Med Chem Lett 1(1):44–48

    Article  CAS  Google Scholar 

  23. Ciulli A, Williams G, Smith AG, Blundell TL, Abell C (2006) J Med Chem 49(16):4992–5000

    Article  CAS  Google Scholar 

  24. Flarakos J, Morand KL, Vouros P (2005) Anal Chem 77(5):1345–1353

    Article  CAS  Google Scholar 

  25. Wieboldt R, Zweigenbaum J, Henion J (1997) Anal Chem 69(9):1683–1691

    Article  CAS  Google Scholar 

  26. Chen CJ, Chen S, Woodbury CP, Venton DL (1998) Anal Biochem 261(2):164–182

    Article  CAS  Google Scholar 

  27. Johnson BM, Nikolic D, van Breemen RB (2002) Mass Spectrom Rev 21(2):76–86

    Article  CAS  Google Scholar 

  28. Kamchonwongpaisan S, Vanichtanankul J, Tarnchompoo B, Yuvaniyama J, Taweechai S, Yuthavong Y (2005) Anal Chem 77(5):1222–1227

    Article  CAS  Google Scholar 

  29. Nerli B, Romanini D, Pico G (1997) Chem Biol Interact 104(2–3):179–202

    Article  CAS  Google Scholar 

  30. Comess KM, Schurdak ME, Voorbach MJ, Coen M, Trumbull JD, Yang H, Gao L, Tang H, Cheng X, Lerner CG, McCall O, Burns DJ, Beutel BA (2006) J Biomol Screen 11(7):743–754

    Article  CAS  Google Scholar 

  31. van Breemen RB, Huang CR, Nikolic D, Woodbury CP, Zhao YZ, Venton DL (1997) Anal Chem 69(11):2159–2164

    Article  Google Scholar 

  32. Liu H, Delgado M, Forman LJ, Eggers CM, Montoya JL (1993) J Chromatogr Biomed Appl 616(1):105–115

    Article  CAS  Google Scholar 

  33. Minke WE, Roach C, Hol WGJ, Verlinde C (1999) Biochemistry (Mosc) 38(18):5684–5692

    Article  CAS  Google Scholar 

  34. Deng JP, Davies DR, Wisedchaisri G, Wu MT, Hol WGJ, Mehlin C (2004) Acta Crystallogr Sect D Biol Crystallogr 60:203–204

    Article  Google Scholar 

  35. Pickens JC, Merritt EA, Ahn M, Verlinde C, Hol WGJ, Fan EK (2002) Chem Biol 9(2):215–224

    Article  CAS  Google Scholar 

  36. Yamada Y, Merrill AH, McCormick DB (1990) Arch Biochem Biophys 278(1):125–130

    Article  CAS  Google Scholar 

  37. Efimov I, Kuusk V, Zhang XP, McIntire WS (1998) Biochemistry (Mosc) 37(27):9716–9723

    Article  CAS  Google Scholar 

  38. Bauer S, Kemter K, Bacher A, Huber R, Fischer M, Steinbacher S (2003) J Mol Biol 326(5):1463–1473

    Article  CAS  Google Scholar 

  39. Karthikeyan S, Zhou QX, Osterman AL, Zhang H (2003) Biochemistry (Mosc) 42(43):12532–12538

    Article  CAS  Google Scholar 

  40. Li X, Chang YH (1995) Proc Natl Acad Sci USA 92(26):12357–12361

    Article  CAS  Google Scholar 

  41. Lowther WT, Zhang Y, Sampson PB, Honek JF, Matthews BW (1999) Biochemistry (Mosc) 38(45):14810–14819

    Article  CAS  Google Scholar 

  42. Kawai M, BaMaung NY, Fidanze SD, Erickson SA, Tedrow JS, Sanders WJ, Vasudevan A, Park C, Hutchins C, Comess KM, Kalvin D, Wang J, Zhang Q, Lou P, Tucker-Garcia L, Bouska J, Bell RL, Lesniewski R, Henkin J, Sheppard GS (2006) Bioorg Med Chem Lett 16(13):3574–3577

    Article  CAS  Google Scholar 

  43. Lu JP, Chai SC, Ye QZ (2010) J Med Chem 53(3):1329–1337

    Article  CAS  Google Scholar 

  44. Altmeyer MA, Marschner A, Schiffmann R, Klein CD (2010) Bioorg Med Chem Lett 20(14):4038–4044

    Article  CAS  Google Scholar 

  45. Crowther GJ, Napuli AJ, Thomas AP, Chung DJ, Kovzun KV, Leibly DJ, Castaneda LJ, Bhandari J, Damman CJ, Hui R, Hol WGJ, Buckner FS, Verlinde C, Zhang ZS, Fan EK, Van Voorhis WC (2009) J Biomol Screen 14(6):700–707

    Article  CAS  Google Scholar 

  46. Fan E, Baker D, Fields S, Gelb MH, Buckner FS, van Voorhis WC, Phizicky E, Dumont M, Mehlin C, Grayhack E, Sullivan M, Verlinde C, DeTitta G, Meldrum DR, Merritt EA, Earnest T, Soltis M, Zucker F, Myler PJ, Schoenfeld L, Kim D, Worthey L, LaCount D, Vignali M, Li J, Mondal S, Massey A, Carroll B, Gulde S, Luft J, DeSoto L, Holl M, Caruthers J, Bosch J, Robien M, Arakaki T, Holmes M, Le Trong I, Hol WGJ (2008) Methods Mol Biol 426:497

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Eric T. Larson for his critical review of the manuscript. This work was supported by National Institutes of Health grants P50GM64655 (SGPP), P01AI067921 (MSGPP), and AI34501.

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Authors and Affiliations

  1. Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA

    Sayaka Shibata, Zhongsheng Zhang, Konstantin V. Korotkov, Jaclyn Delarosa, Jennifer Ross, Frank H. Zucker, Ethan A. Merritt, Christophe L. M. J. Verlinde, Wim G. J. Hol & Erkang Fan

  2. Department of Medicine, University of Washington, Seattle, WA, 98195, USA

    Alberto Napuli, Angela M. Kelley, Natasha Mueller, Frederick S. Buckner & Wesley C. Van Voorhis

  3. Department of Chemistry, University of Washington, Seattle, WA, 98195, USA

    Sayaka Shibata

  4. University of Washington, Box 357742, Seattle, WA, 98195, USA

    Erkang Fan

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  1. Sayaka Shibata
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  2. Zhongsheng Zhang
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  3. Konstantin V. Korotkov
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  4. Jaclyn Delarosa
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  5. Alberto Napuli
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  7. Natasha Mueller
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  8. Jennifer Ross
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  11. Ethan A. Merritt
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  12. Christophe L. M. J. Verlinde
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  14. Wim G. J. Hol
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  15. Erkang Fan
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Correspondence to Erkang Fan.

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Shibata, S., Zhang, Z., Korotkov, K.V. et al. Screening a fragment cocktail library using ultrafiltration. Anal Bioanal Chem 401, 1585–1591 (2011). https://doi.org/10.1007/s00216-011-5225-7

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  • DOI: https://doi.org/10.1007/s00216-011-5225-7

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