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References
Fry, D. and Sun, H. (2006) Utilizing peptide structures as keys for unlocking challenging targets. Mini. Rev. Med. Chem. 6, 979–987.
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.
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.
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.
Guthrie, D. J. (1997) 1H nuclear magnetic resonance (NMR) in the elucidation of peptide structure. Methods Mol. Biol. 73, 163–184.
Wuthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley Interscience, New York.
Sillerud, L. O. and Larson, R. S. (2006) Nuclear magnetic resonance-based screening methods for drug discovery. Methods Mol. Biol. 316, 227–289.
Pellecchia, M. (2005) Solution nuclear magnetic resonance spectroscopy techniques for probing intermolecular interactions. Chem. Biol. 12, 961–971.
Homans, S. W. (2005) Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem 6, 1585–1591.
Homans, S. W. (2004) NMR spectroscopy tools for structure-aided drug design. Angew. Chem. Int. Ed. Engl. 43, 290–300.
Salvatella, X. and Giralt, E. (2003) NMR-based methods and strategies for drug discovery. Chem. Soc. Rev. 32, 365–372.
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.
Fejzo, J., Lepre, C. and Xie, X. (2003) Application of NMR screening in drug discovery. Curr. Top. Med. Chem. 3, 81–97.
Coles, M., Heller, M. and Kessler, H. (2003) NMR-based screening technologies. Drug Discov. Today 8, 803–810.
Pellecchia, M., Sem, D. S. and Wuthrich, K. (2002) NMR in drug discovery. Nat. Rev. Drug. Discov. 1, 211–219.
Hajduk, P. J., Meadows, R. P. and Fesik, S. W. (1999) NMR-based screening in drug discovery. Q. Rev. Biophys. 32, 211–240.
Zartler, E. R. and Shapiro, M. J. (2006) Protein NMR-based screening in drug discovery. Curr. Pharm. Des. 12, 3963–3972.
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.
Zartler, E. R. and Shapiro, M. J. (2005) Fragonomics: fragment-based drug discovery. Curr. Opin. Chem. Biol. 9, 366–370.
Schade, M. and Oschkinat, H. (2005) NMR fragment screening: tackling protein-protein interaction targets. Curr. Opin. Drug Discov. Devel. 8, 365–373.
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.
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.
Jahnke, W., Florsheimer, A., Blommers, M. J., et al. (2003) Second-site NMR screening and linker design. Curr. Top. Med. Chem. 3, 69–80.
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.
Villar, H. O., Yan, J. and Hansen, M. R. (2004) Using NMR for ligand discovery and optimization. Curr. Opin. Chem. Biol. 8, 387–391.
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.
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.
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.
Sun, C., Huth, J. R. and Hajduk, P. J. (2005) NMR in pharmacokinetic and pharmacodynamic profiling. Chembiochem 6, 1592–1600.
Holzgrabe, U., Wawer, I. and Diehl, B. (1999) NMR Spectroscopy in Drug Development and Analysis. Wiley-VCH, Weinheim.
Craik, D. J. (1996) NMR in Drug Design. CRC, New York.
Hansdschumacher, R. E. and Armitage, I. M. (1989) NMR Methods for Elucidating Macromolecule-Ligand Interactions: An Approach to Drug Design. Pergamon Press, Oxford.
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.
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.
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.
Wishart, D. S., Bigam, C. G., Holm, A., Hodges, R. S. and Sykes, B. D. (1995) 1H, 13C and 15 N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J. Biomol. NMR 5, 67–81.
Karplus, M. (1963) Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85, 2870–2871.
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.
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.
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.
Palmer, A. G. (2004) NMR Characterization of the dynamics of biomacromolecules. Chem. Rev. 104, 3623–3640.
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.
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.
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.
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.
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.
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.
Englander, S. W., Downer, N. W. and Teitelbaum, H. (1972) Hydrogen exchange. Annu. Rev. Biochem. 41, 903–924.
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.
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.
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.
Petros, A. M., Dinges, J., Augeri, D. J., et al. (2006) Discovery of a potent inhibitor of the antiapoptotic protein Bcl-xL from NMR and parallel synthesis. J. Med. Chem. 49, 656–663.
Basus, V. J. (1989) Proton nuclear magnetic resonance assignments. Methods Enzymol. 177, 132–149.
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.
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.
Livett, B. G., Gayler, K. R. and Khalil, Z. (2004) Drugs from the sea: conopeptides as potential therapeutics. Curr. Med. Chem. 11, 1715–1723.
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.
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.
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.
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.
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.
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.
Mayer, M. and Meyer, B. (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chemie Int. Ed. 38, 1784–1788.
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.
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.
Carr, H. Y. and Purcell, E. M. (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Physical Rev. 94, 630–638.
Meiboom, S. and Gill, D. (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev. Sci. Instrum. 29, 688–691.
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.
Foster, M. P., McElroy, C. A. and Amero, C. D. (2007) Solution NMR of large molecules and assemblies. Biochemistry 46, 331–340.
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.
Grace, C. R. R. and Riek, R. (2003) Pseudomultidimensional NMR by spin-state selective off-resonance decoupling. J. Am. Chem. Soc. 125, 16104–16113.
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.
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.
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.
Meyer, B., Weimar, T. and Peters, T. (1997) Screening mixtures for biological activity by NMR. Eur. J. Biochem. 246, 705–709.
Mayer, M. and Meyer, B. (2000) Mapping the active site of angiotensin-converting enzyme by transferred NOE spectroscopy. J. Med. Chem. 43, 2093–2099.
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.
Aumailley, M., Gurrath, M., Muller, G., Calvete, J., Timpl, R. and Kessler, H. (1991) Arg-Gly-Asp constrained within cyclic pentapeptides. Strong and selective inhibitors of cell adhesion to vitronectin and laminin fragment P1. FEBS Lett. 291, 50–54.
Chatterjee, C. and Mukhopadhyay, C. (2005) Interaction and structural study of kinin peptide bradykinin and ganglioside monosialylated 1 micelle. Biopolymers 78,197–205.
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.
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.
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.
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.
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Westermann, JC., Craik, D.J. (2008). NMR in Peptide Drug Development. In: Otvos, L. (eds) Peptide-Based Drug Design. Methods In Molecular Biology™, vol 494. Humana Press. https://doi.org/10.1007/978-1-59745-419-3_6
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