Ligand-Observed NMR in Fragment-Based Approaches

NMR of Biomolecules: Towards Mechanistic Systems Biology

Volumn , Issue , 2012, Pages 264-280

  Śledź, Pawel ^a   Abell, Chris ^a   Ciulli, Alessio ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Binding mode; Fragment based design; Interligand Overhauser effect; Ligand observed NMR; Relative affinity; Relaxation edited filter; Saturation transfer difference; WaterLOGSY

Indexed keywords

EID: 84885516643     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527644506.ch15     Document Type: Chapter

References (49)

1. Hajduk, P.J., Olejniczak, E.T., and Fesik, S.W. (1997) One-dimensional relaxation-and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J. Am. Chem. Soc., 119, 12257-12261.
2. London, R.E. (1999) Theoretical analysis of the inter-ligand Overhauser effect: a new approach for mapping structural relationships of macromolecular ligands. J. Magn. Reson., 141, 301-311.
3. Mayer,M. andMeyer, B. (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Edit., 38, 1784-1788.
4. Dalvit, C., Pevarello, P., Tato, M., Veronesi, M., Vulpetti, A., and Sundstrom, M. (2000) Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR, 18, 65-68.
5. Jahnke, W., Floersheim, P., Ostermeier, C., Zhang, X., Hemmig, R., Hurth, K., and Uzunov, D.P. (2002) NMR reporter screening for the detection of high-affinity ligands. Angew. Chem. Int. Ed., 41, 3420-3423.
6. Becattini, B., Culmsee, C., Leone, M., Zhai, D., Zhang, X., Crowell, K.J., Rega, M.F., Landshamer, S., Reed, J., Plesnila, N. et al. (2006) Structure-activity relationships by interligand NOE-based design and synthesis of antiapoptotic compounds targeting Bid. Proc. Natl. Acad. Sci. USA, 103, 12602-12606.
7. Ciulli, A. and Abell, C. (2007) Fragment-based approaches to enzyme inhibition. Curr. Opin. Biotechnol., 18, 489-496.
8. Pellecchia, M., Bertini, I., Cowburn, D., Dalvit, C.,Giralt, E., Jahnke,W., James, T.L., Homans, S.W., Kessler, H., Luchinat, C. et al. (2008) Perspectives on NMR in drug discovery: a technique comes of age. Nat. Rev. Drug Discov., 9, 738-745.
9. Barelier, S., Pons, J., Gehring, K., Lancelin, J.-M., and Krimm, I. (2010) Ligand specificity in fragment-based drug design. J. Med. Chem., 53, 5256-5266.
10. Sledz, P., Silvestre, H.L.,Hung, A.W., Ciulli, A., Blundell, T.L., and Abell, C. (2010) Optimization of the interligand Overhauser effect for fragment linking: application to inhibitor discovery against Mycobacterium tuberculosis pantothenate synthetase. J. Am. Chem. Soc., 132, 4544-4545.
11. Pellecchia, M., Becattini, B., Crowell, K.J., Fattorusso, R., Forino, M., Fragai, M., Jung, D., Mustelin, T., and Tautz, L. (2004) Expert Opin. Ther. Targets, 8, 597.
12. Segel, I.H. (1975) Enzyme Kinetics, John Wiley & Sons, Inc., New York.
13. Lepre, C.A., Moore, J.M., and Peng, J.W. (2004) Chem. Rev., 104, 3641.
14. Pellecchia, M., Bertini, I., Cowburn, D., Dalvit, C., Giralt, E., Jahnke, W., James, T.L., Homans, S.W., Kessler, H., Luchinat, C., Meyer, B., Oschkinat, H., Peng, J., Schwalbe, H., and Siegal, G. (2008). Nat. Rev. Drug Discov., 9, 738.
15. Hajduk, P.J., Olejniczak, E.T., and Fesik, S.W. (1997) J. Am. Chem. Soc., 119, 12257.
16. Mayer, M. and Meyer, B. (1999) Angew. Chem. Int. Ed., 38, 1784.
17. Dalvit, C., Pevarello, P., Tato, M., Veronesi, M., Vulpetti, A., and Sundstrom, M. (2000) J. Biomol. NMR, 18, 65.
18. Orts, J., Tuma, J., Reese, M., Grimm, S.K., Monecke, P., Bartoschek, S., Schiffer, A., Wendt, K.U., Griesinger, C., and Carlomagno, T. (2008) Angew. Chem. Int. Ed., 47, 7736.
19. London, R.E. (1999) J. Magn. Reson., 141, 301.
20. Li, D., DeRose, E.F., and London, R.E. (1999) J. Biomol. NMR, 15, 71.
21. Becattini, B., Culmsee, C., Leone, M., Zhai, D., Zhang, X., Crowell, K.J., Rega, M.F., Landshamer, S., Reed, J., Plesnila, N., and Pellecchia, M. (2006) Proc. Natl. Acad. Sci. USA, 103, 12602.
22. Ciulli, A. and Abell, C. (2007) Curr. Opin. Biotechnol., 18, 489.
23. Vanwetswinkel, S., Heetebrij, R.J., van Duynhoven, J., Hollander, J.G., Filippov, D.V., Hajduk, P., and Siegal, G. (2005) Chem. Biol., 12, 207.
24. Kobayashi, M., Retra, K., Figaroa, F., Hollander, J.G., Ab, E., Heetebrij, R.J., Irth, H., and Siegal, G. (2010) J. Biomol. Screen., 15, 978.
25. Fruh, V., Zhou, Y., Chen, D., Loch, C., Ab, E., Grinkova, Y.N., Verheij, H., Sligar, S.G., Bushweller, J.H., and Siegal, G. (2010) Chem. Biol., 17, 881.
26. Kövér, K.E.,Groves, P., Jiménez-Barbero, J., and Batta, G. (2007) J. Am. Chem. Soc., 129, 11579.
27. Fehér, K., Groves, P., Batta, G., Jiménez-Barbero, J., Muhle-Goll, C., and Kövér, K.E. (2008) J. Am. Chem. Soc., 130, 17148.
28. Mayer, M. and Meyer, B. (2001) J. Am. Chem. Soc., 123, 6108.
29. Meyer, B. and Peters, T. (2003) Angew. Chem. Int. Ed., 42, 864.
30. McGovern, S.L., Helfand, B.T., Feng, B., and Shoichet, B. (2003) J. Med. Chem., 46, 4265.
31. Ciulli, A., Williams, G., Smith, A., Blundell, T., and Abell, C. (2006) J. Med. Chem., 49, 4992.
32. Barelier, S., Pons, J., Gehring, K., Lancelin, J.-M., and Krimm, I. (2010) J. Med. Chem., 53, 5256.
33. Ciulli, A. and Abell, C. (2005) Biochem. Soc. Trans., 33, 767.
34. Jahnke, W., Rudisser, S., and Zurini, M. (2001) J. Am. Chem. Soc., 123, 3149.
35. Dalvit, C., Flocco, M., Knapp, S., Mostardini, M., Perego, R., Stockman, B.J., Veronesi, M., and Varasi, M. (2002) J. Am. Chem. Soc., 124, 7702.
36. Jahnke, W., Floersheim, P., Ostermeier, C., Zhang, X., Hemmig, R., Hurth, K., and Uzunov, D.P. (2002) Angew. Chem. Int. Ed., 41, 3420.
37. Zhang, X., Sänger, A., Hemmig, R., and Jahnke, W. (2009) Angew. Chem. Int. Ed., 48, 6691.
38. Lucas, L.H., Yan, J.L., Larive, C.K., Zartler, E.R., and Shapiro, M.J. (2003) Anal. Chem., 75, 627.
39. Catoire, L.J., Damian, M., Giusti, F., Martin, A., van Heijenoort, C., Popot, J.L., Guittet, E., and Baneres, J.L. (2010) J. Am. Chem. Soc., 132, 9049.
40. Henrichsen, D., Ernst, B., Magnani, J.L., Wang, W.T., Meyer, B., and Peters, T. (1999) Angew. Chem. Int. Ed., 38, 98.
41. Mayer, M. and Meyer, B. (2000) J. Med. Chem., 43, 2093.
42. Chen, J., Zhang, Z., Stebbins, J.L., Zhang, X., Hoffman, R., Moore, A., and Pellecchia, M. (2007) ACS Chem. Biol., 2, 329.
43. Sledz, P., Silvestre, H.L., Hung, A.W., Ciulli, A., Blundell, T.L., and Abell, C. (2010) J. Am. Chem. Soc., 132, 4544.
44. Sanchez-Pedregal, V.M., Reese, M., Meiler, J., Blommers, M.J., Griesinger, C., and Carlomagno, T. (2005) Angew. Chem. Int. Ed., 44, 4172.
45. Bartoschek, S., Klabunde, T., Defossa, E., Dietrich, V., Stengelin, S., Griesinger, C., Carlomagno, T., Focken, I., and Wendt, K.U. (2010) Angew. Chem. Int. Ed., 49, 1426.
46. Orts, J., Griesinger, C., and Carlomagno, T. (2009) J. Magn. Reson., 200, 64.
47. Piotto, M., Saudek, V., and Sklenar, V. (1992) J. Biomol. NMR, 2, 661.
48. Hwang, T.L. and Shaka, A.J. (1995) J. Magn. Reson. A, 112, 275.
49. Hung, A.W., Silvestre, H.L., Wen, S., Ciulli, A., Blundell, T., and Abell, C. (2009) Angew. Chem. Int. Ed., 48, 8452.