NMR in peptide drug development

Methods in Molecular Biology

Volumn 494, Issue , 2008, Pages 87-113

  Westermann, Jan Christoph ^a   Craik, David J ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Binding mode; Binding site; Binding studies; Drug design; NMR; Screening; Solution structure

Indexed keywords

EID: 84934435200     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-419-3_6     Document Type: Review

References (83)

1. Fry, D. and Sun, H. (2006) Utilizing peptide structures as keys for unlocking challenging targets. Mini. Rev. Med. Chem. 6, 979-987.
2. Valente, A. P., Miyamoto, C. A. and Almeida, F. C. (2006) Implications of protein conformational diversity for binding and development of new biological active compounds. Curr. Med. Chem. 13, 3697-3703.
3. Craik, D. J. and Clark, R. J. (2005) Structure-based drug design and NMR-based screening. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine (Meyers R. A., ed.). 2nd ed.Wiley-VCH, Weinheim, pp. 517-605.
4. Fu, R. and Cross, T. A. (1999) Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure. Annu. Rev. Biophys. Biomol. Struct. 28, 235-268.
5. Guthrie, D. J. (1997) 1H nuclear magnetic resonance (NMR) in the elucidation of peptide structure. Methods Mol. Biol. 73, 163-184.
6. Wuthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley Interscience, New York.
7. Sillerud, L. O. and Larson, R. S. (2006) Nuclear magnetic resonance-based screening methods for drug discovery. Methods Mol. Biol. 316, 227-289.
8. Pellecchia, M. (2005) Solution nuclear magnetic resonance spectroscopy techniques for probing intermolecular interactions. Chem. Biol. 12, 961-971.
9. Homans, S.W. (2005) Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem 6, 1585-1591.
10. Homans, S. W. (2004) NMR spectroscopy tools for structure-aided drug design. Angew. Chem. Int. Ed. Engl. 43, 290-300.
11. Salvatella, X. and Giralt, E. (2003) NMR-based methods and strategies for drug discovery. Chem. Soc. Rev. 32, 365-372.
12. Meyer, B. and Peters, T. (2003) NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. 42, 864-890.
13. Fejzo, J., Lepre, C. and Xie, X. (2003) Application of NMR screening in drug discovery. Curr. Top. Med. Chem. 3, 81-97.
14. Coles, M., Heller, M. and Kessler, H. (2003) NMR-based screening technologies. Drug Discov. Today 8, 803-810.
15. Pellecchia, M., Sem, D. S. and Wuthrich, K. (2002) NMR in drug discovery. Nat. Rev. Drug. Discov. 1, 211-219.
16. Hajduk, P. J., Meadows, R. P. and Fesik, S.W. (1999) NMR-based screening in drug discovery. Q. Rev. Biophys. 32, 211-240.
17. Zartler, E. R. and Shapiro, M. J. (2006) Protein NMR-based screening in drug discovery. Curr. Pharm. Des. 12, 3963-3972.
18. Leone, M., Freeze, H. H., Chan, C. S. and Pellecchia, M. (2006) The Nuclear Overhauser Effect in the lead identification process. Curr. Drug Discov. Technol. 3, 91-100.
19. Zartler, E. R. and Shapiro, M. J. (2005) Fragonomics: fragment-based drug discovery. Curr. Opin. Chem. Biol. 9, 366-370.
20. Schade, M. and Oschkinat, H. (2005) NMR fragment screening: tackling proteinprotein interaction targets. Curr. Opin. Drug Discov. Devel. 8, 365-373.
21. Lepre, C. A., Moore, J. M. and Peng, J.W. (2004) Theory and applications of NMR-based screening in pharmaceutical research. Chem. Rev. 104, 3641-3676.
22. Vogtherr, M. and Fiebig, K. (2003) NMR-based screening methods for lead discovery. In: Modern Methods of Drug Discovery (Hillisch, A. and Hilgenfeld, R., ed.). Birhäuser Verlag, Switzerland, pp. 183-202.
23. Jahnke, W., Florsheimer, A., Blommers, M. J., et al. (2003) Second-site NMR screening and linker design. Curr. Top. Med. Chem. 3, 69-80.
24. Wyss, D. F., McCoy, M. A. and Senior, M. M. (2002) NMR-based approaches for lead discovery. Curr. Opin. Drug. Discov. Devel. 5, 630-647.
25. Villar, H. O., Yan, J. and Hansen, M. R. (2004) Using NMR for ligand discovery and optimization. Curr. Opin. Chem. Biol. 8, 387-391.
26. Pellecchia, M., Becattini, B., Crowell, K. J., et al. (2004) NMR-based techniques in the hit identification and optimisation processes. Expert Opin. Ther. Targets 8, 597-611.
27. Lepre, C. A., Peng, J., Fejzo, J., et al. (2002) Applications of SHAPES screening in drug discovery. Comb. Chem. High Throughput Screen 5, 583-590.
28. Sun, C. and Hajduk, P. J. (2006) Nuclear magnetic resonance in target profiling and compound file enhancement. Curr. Opin. Drug Discov. Devel. 9, 463-470.
29. Sun, C., Huth, J. R. and Hajduk, P. J. (2005) NMR in pharmacokinetic and pharmacodynamic profiling. Chembiochem 6, 1592-1600.
30. Holzgrabe, U., Wawer, I. and Diehl, B. (1999) NMR Spectroscopy in Drug Development and Analysis. Wiley-VCH, Weinheim.
31. Craik, D. J. (1996)NMR in Drug Design. CRC, New York.
32. Hansdschumacher, R. E. and Armitage, I. M. (1989) NMR Methods for Elucidating Macromolecule-Ligand Interactions: An Approach to Drug Design. Pergamon Press, Oxford.
33. Shuker, S. B., Hajduk, P. J., Meadows, R. P. and Fesik, S. W. (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274, 1531-1534.
34. Reid, D. G., MacLachlan, L. K., Edwards, A. J., Hubbard, J. A. and Sweeney, P. J. (1997) Introduction to the NMR of proteins. In: Protein NMR Techniques (Reid D. G., ed.). Humana Press, Totowa, NJ, pp. 1-28.
35. Wishart, D. S., Sykes, B. D. and Richards, F. M. (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31, 1647-1651.
36. Wishart, D. S., Bigam, C. G., Holm, A., Hodges, R. S. and Sykes, B. D. (1995) 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J. Biomol. NMR 5, 67-81.
37. Karplus, M. (1963) Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85, 2870-2871.
38. Lautz, J., Kessler, H., Blaney, J. M., Scheek, R. M. and Van Gunsteren, W. F. (1989) Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A. Int. J. Pept. Protein. Res. 33, 281-288.
39. Ottiger, M., Zerbe, O., Guntert, P. and Wuthrich, K. (1997) The NMR solution conformation of unligated human cyclophilin A. J. Mol. Biol. 272, 64-81.
40. Weber, C., Wider, G., von Freyberg, B., et al. (1991) The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry 30, 6563-6574.
41. Palmer, A. G. (2004)NMR Characterization of the dynamics of biomacromolecules. Chem. Rev. 104, 3623-3640.
42. O'Sullivan, D. B., Jones, C. E., Abdelraheim, S. R., et al. (2007) NMR characterization of the pH 4 beta-intermediate of the prion protein: the N-terminal half of the protein remains unstructured and retains a high degree of flexibility. Biochem. J. 401, 533-540.
43. Renisio, J. G., Perez, J., Czisch, M., et al. (2002) Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama. Proteins 47, 546-555.
44. Feng, L., Orlando, R. and Prestegard, J. H. (2006) Amide proton back-exchange in deuterated peptides: applications to MS and NMR analyses. Anal. Chem. 78, 6885-6892.
45. Morris, K. F., Gao, X. and Wong, T. C. (2004) The interactions of the HIV gp41 fusion peptides with zwitterionic membrane mimics determined by NMR spectroscopy. Biochim. Biophys. Acta 1667, 67-81.
46. D'Amelio, N., Bonvin, A. M., Czisch, M., Barker, P. and Kaptein, R. (2002) The C terminus of apocytochrome b562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state. Biochemistry 41, 5505-5514.
47. Liepinsh, E., Otting, G. and Wuthrich, K. (1992) NMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins. J. Biomol. NMR 2, 447-465.
48. Englander, S. W., Downer, N. W. and Teitelbaum, H. (1972) Hydrogen exchange. Annu. Rev. Biochem. 41, 903-924.
49. Claasen, B., Axmann, M., Meinecke, R. and Meyer, B. (2005) Direct observation of ligand binding to membrane proteins in living cells by a saturation transfer double difference (STDD) NMR spectroscopy method shows a significantly higher affinity of integrin α(IIb)β3 in native platelets than in liposomes. J. Am. Chem. Soc. 127, 916-919.
50. Meinecke, R. and Meyer, B. (2001) Determination of the binding specificity of an integral membrane protein by saturation transfer difference NMR: RGD peptide ligands binding to integrin alphaIIbbeta3. J. Med. Chem. 44, 3059-3065.
51. Kisselev, O. G., Kao, J., Ponder, J. W., Fann, Y. C., Gautam, N. and Marshall, G. R. (1998) Light-activated rhodopsin induces structural binding motif in G protein α subunit. Proc. Natl. Acad. Sci. 95, 4270-4275.
52. Petros, A. M., Dinges, J., Augeri, D. J., et al. (2006) Discovery of a potent inhibitor of the antiapoptotic protein Bcl-x¡sub¿L¡/ sub¿ from NMR and parallel synthesis. J. Med. Chem. 49, 656-663.
53. Basus, V. J. (1989) Proton nuclear magnetic resonance assignments. Methods Enzymol. 177, 132-149.
54. Seavey, B. R., Farr, E. A., Westler, W. M. and Markley, J. L. (1991) A relational database for sequence-specific protein NMR data. J. Biomol. NMR 1, 217-236.
55. Gayler, K., Sandall, D., Greening, D., et al. (2005) Molecular prospecting for drugs from the sea. Isolating therapeutic peptides and proteins from cone snail venom. IEEE Eng. Med. Biol. Mag. 24, 79-84.
56. Livett, B. G., Gayler, K. R. and Khalil, Z. (2004) Drugs from the sea: conopeptides as potential therapeutics. Curr. Med. Chem. 11, 1715-1723.
57. Sandall, D. W., Satkunanathan, N., Keays, D. A., et al. (2003) A novel α-conotoxin identified by gene sequencing is active in suppressing the vascular response to selective stimulation of sensory nerves in vivo. Biochemistry 42, 6904-6911.
58. Clark, R. J., Fischer, H., Nevin, S. T., Adams, D. J. and Craik, D. J. (2006) The synthesis, structural characterization, and receptor specificity of the α-conotoxin Vc1.1. J. Biol. Chem. 281, 23254-23263.
59. Hajduk, P. J., Augeri, D. J., Mack, J., et al. (2000) NMR-based screening of proteins containing 13C-labeled methyl groups. J. Am. Chem. Soc. 122, 7898-7904.
60. Bothner-By, A. A., Stephens, R. L., Lee, J., Warren, C. D. and Jeanloz, R.W. (1984) Structure determination of a tetrasaccharide: transient nuclear Overhauser effects in the rotating frame. J. Am. Chem. Soc. 106, 811-813.
61. Johnson, M. A. and Pinto, B. M. (2004) NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions. Carbohydr. Res. 339, 907-928.
62. Johnson, M. A., Rotondo, A. and Pinto, B. M. (2002) NMR studies of the antibody-bound conformation of a carbohydrate-mimetic peptide. Biochemistry 41, 2149-2157.
63. Mayer, M. and Meyer, B. (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chemie Int. Ed. 38, 1784-1788.
64. Mayer, M. and Meyer, B. (2001) Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J. Am. Chem. Soc. 123, 6108-6117.
65. Vold, R. L., Waugh, J. S., Klein, M. P. and Phelps, D. E. (1968) Measurement of spin relaxation in complex systems. J. Chem. Phys. 48, 3831-3832.
66. Carr, H. Y. and Purcell, E. M. (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Physical Rev. 94, 630-638.
67. Meiboom, S. and Gill, D. (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev. Sci. Instrum. 29, 688-691.
68. Stejskal, E. O. and Tanner, J. E. (1965) Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient. J. Chem. Phys. 42, 288-292.
69. Foster, M. P., McElroy, C. A. and Amero, C. D. (2007) Solution NMR of large molecules and assemblies. Biochemistry 46, 331-340.
70. Keeler, C., Dannies, P. S. and Hodsdon, M. E. (2003) The tertiary structure and backbone dynamics of human prolactin. J. Mol. Biol. 328, 1105-1121.
71. Grace, C. R. R. and Riek, R. (2003) Pseudomultidimensional NMR by spin-state selective off-resonance decoupling. J. Am. Chem. Soc. 125, 16104-16113.
72. Pervushin, K., Riek, R., Wider, G. and Wuthrich, K. (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. 94, 12366-12371.
73. Arimoto, R., Kisselev, O. G., Makara, G. M. and Marshall, G. R. (2001) Rhodopsin-transducin interface: studies with conformationally constrained peptides. Biophys. J. 81, 3285-3293.
74. Tugarinov, V., Zvi, A., Levy, R. and Anglister, J. (1999) A cis proline turn linking two beta-hairpin strands in the solution structure of an antibody-bound HIV-1IIIB V3 peptide. Nat. Struct. Biol. 6, 331-335.
75. Meyer, B., Weimar, T. and Peters, T. (1997) Screening mixtures for biological activity by NMR. Eur. J. Biochem. 246, 705-709.
76. Mayer, M. and Meyer, B. (2000) Mapping the active site of angiotensin-converting enzyme by transferred NOE spectroscopy. J. Med. Chem. 43, 2093-2099.
77. D'Souza, S. E., Ginsberg, M. H. and Plow, E. F. (1991) Arginyl-glycyl-aspartic acid (RGD): a cell adhesion motif. Trends Biochem. Sci. 16, 246-250.
78. Aumailley, M., Gurrath, M., Muller, G., Calvete, J., Timpl, R. and Kessler, H. (1991) Arg-Gly-Asp constrainedwithin cyclic pentapeptides. Strong and selective inhibitors of cell adhesion to vitronectin and laminin fragment P1. FEBS Lett. 291, 50-54.
79. Chatterjee, C. and Mukhopadhyay, C. (2005) Interaction and structural study of kinin peptide bradykinin and ganglioside monosialylated 1 micelle. Biopolymers 78, 197-205.
80. Stuart, A. C., Gottesman, M. E. and Palmer, A. G., 3rd (2003) The N-terminus is unstructured, but not dynamically disordered, in the complex between HK022 Nun protein and λ-phage BoxB RNA hairpin. FEBS Lett. 553, 95-98.
81. Stamos, J., Eigenbrot, C., Nakamura, G. R., et al. (2004) Convergent recognition of the IgE binding site on the high-affinity IgE receptor. Structure 12, 1289-1301.
82. Garman, S. C., Wurzburg, B. A., Tarchevskaya, S. S., Kinet, J. P. and Jardetzky, T. S. (2000) Structure of the Fc fragment of human IgE bound to its high-affinity receptor Fc epsilonRI α. Nature 406, 259-266.
83. Nakamura, G.R., Reynolds, M.E., Chen, Y.M., Starovasnik, M.A. and Lowman, H.B. (2002) Stable "zeta" peptides that act as potent antagonists of the high-affinity IgE receptor. Proc. Natl. Acad. Sci. USA 99, 1303-1308.