Overview of Probing Protein‐Ligand Interactions Using NMR

Clémentine Aguirre1, Olivier Cala1, Isabelle Krimm1

1 Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon, Villeurbanne
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 17.18
DOI:  10.1002/0471140864.ps1718s81
Online Posting Date:  August, 2015
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Nuclear magnetic resonance (NMR) is a powerful technique for the study and characterization of protein‐ligand interactions. In this unit we review both experiments where the NMR spectrum of the protein is observed (protein‐observed NMR experiments) and those where the NMR spectra of the ligand is observed (ligand‐observed NMR experiments) for the identification of binding partners, the measurement of protein‐ligand affinity, the design of molecules that are active against biological targets such as proteins, and the assessment of the binding modes of the ligands. Ligand‐observed methods discussed in this unit are Nuclear Overhauser Effect (NOE)—based approaches, with well‐known experiments such as the Saturation Transfer Difference, Water‐Ligand Observed via Gradient Spectroscopy (WaterLOGSY), and transferred—Nuclear Overhauser Effect Spectroscopy (tr‐NOESY) experiments, and also the INPHARMA experiment. Regarding protein‐observed experiments, this unit focuses on the use of chemical shift perturbations observed in protein‐NMR spectra upon ligand binding. Also discussed is how these chemical shift perturbations can be used for the analysis of protein‐ligand complexes, including fast structure determination when combined with docking. © 2015 by John Wiley & Sons, Inc.

Keywords: NMR; ligand; NOE; INPHARMA; WaterLOGSY; chemical shift perturbations; 3D structure

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Table of Contents

  • Introduction
  • Ligand‐Observed NMR Experiments
  • Protein‐Observed NMR Experiments: Chemical Shift Perturbations (CSPs)
  • Conclusion
  • Acknowledgements
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
  Aguirre, C., ten Brink, T., Cala, O., Guichou, J.‐F., and Krimm, I. 2014a. Protein‐ligand structure guided by backbone and side‐chain proton chemical shift perturbations. J. Biomol. NMR 60:147‐156.
  Aguirre, C., tenBrink, T., Guichou, J.‐F., Cala, O., and Krimm, I. 2014b. Comparing binding modes of analogous fragments using NMR in fragment‐based drug design: Application to PRDX5. PLoS One 9:e102300.
  Angulo, J. and Nieto, P.M. 2011. STD‐NMR: Application to transient interactions between biomolecules‐a quantitative approach. Eur. Biophys. J. 40:1357‐1369.
  Angulo, J., Enríquez‐Navas, P.M., and Nieto, P.M. 2010. Ligand‐receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: The binding isotherm of STD initial growth rates. Chemistry 16:7803‐7812.
  Arepalli, S.R., Glaudemans, C.P., Daves, G. Jr., Kovac, P., and Bax, A. 1995. Identification of protein‐mediated indirect NOE effects in a disaccharide‐Fab’ complex by transferred ROESY. J. Magn. Reson. B 106:195‐198.
  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.
  Bartoschek, S., Klabunde, T., Defossa, E., Dietrich, V., Stengelin, S., Griesinger, C., Carlomagno, T., Focken, I., and Wendt, K.U. 2010. Drug design for G‐protein‐coupled receptors by a ligand‐based NMR method. Angew. Chem. Int. Ed. Engl. 49:1426‐1429.
  Basilio, N., Martn‐Pastor, M., and Garca‐Ro, L. 2012. Insights into the structure of the supramolecular amphiphile formed by a sulfonated calix[6]arene and alkyltrimethylammonium surfactants. Langmuir 28:6561‐6568.
  Becattini, B., Culmsee, C., Leone, M., Zhai, D., Zhang, X., Crowell, K.J., Rega, M.F., Landshamer, S., Reed, J.C., Plesnila, N., and Pellecchia, M. 2006. Structure‐activity relationships by interligand NOE‐based design and synthesis of antiapoptotic compounds targeting Bid. Proc. Natl. Acad. Sci. U.S.A. 103:12602‐12606.
  Begley, D.W., Zheng, S., and Varani, G. 2010. Fragment‐based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Chem. Biol. Drug Des. 76:218‐233.
  Benie, A.J., Moser, R., Bäuml, E., Blaas, D., and Peters, T. 2003. Virus‐ligand interactions: Identification and characterization of ligand binding by NMR spectroscopy. J. Am. Chem. Soc. 125:14‐15.
  Bhunia, A., Bhattacharjya, S., and Chatterjee, S. 2012. Applications of saturation transfer difference NMR in biological systems. Drug Discov. Today 17:505‐513.
  Breukels, V., Konijnenberg, A., Nabuurs, S.M., Doreleijers, J.F., Kovalevskaya, N.V., and Vuister, G.W. 2011. Overview on the use of NMR to examine protein structure. Curr. Protoc. Protein Sci. 64:17.5.1‐17.5.44.
  Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse‐Kunstleve, R.W., Jiang, J.‐S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54:905‐921.
  Cala, O., Guillière, F., and Krimm, I. 2014. NMR‐based analysis of protein‐ligand interactions. Anal. Bioanal. Chem. 406:943‐956.
  Campos‐Olivas, R. 2011. NMR screening and hit validation in fragment based drug discovery. Curr. Top. Med. Chem. 11:43‐67.
  Carlomagno, T. 2012. NMR in natural products: Understanding conformation, configuration and receptor interactions. Nat. Prod. Rep. 29:536‐554.
  Chen, J., Zhang, Z., Stebbins, J.L., Zhang, X., Hoffman, R., Moore, A., and Pellecchia, M. 2007. A fragment‐based approach for the discovery of isoform‐specific p38alpha inhibitors. ACS Chem. Biol. 2:329‐336.
  Cioffi, M., Hunter, C.A., and Packer, M.J. 2008a. Influence of conformational flexibility on complexation‐induced changes in chemical shift in a neocarzinostatin protein‐ligand complex. J. Med. Chem. 51:4488‐4495.
  Cioffi, M., Hunter, C.A., Packer, M.J., and Spitaleri, A. 2008b. Determination of protein ligand binding modes using complexation‐induced changes in 1H NMR chemical shift. J. Med. Chem. 51:2512‐2517.
  Cioffi, M., Hunter, C.A., Packer, M.J., Pandya, M.J., and Williamson, M.P. 2009. Use of quantitative 1H NMR chemical shift changes for ligand docking into barnase. J. Biomol. NMR 43:11‐19.
  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 αIIbβ3 in native platelets than in liposomes. J. Am. Chem. Soc. 127:916‐919.
  Dalvit, C., Cottens, S., Ramage, P., and Hommel, U. 1999. Half‐filter experiments for assignment, structure determination and hydration analysis of unlabelled ligands bound to 13C/15N labelled proteins. J. Biomol. NMR 13:43‐50.
  Dalvit, C., Fogliatto, G., Stewart, A., Veronesi, M., and Stockman, B. 2001. WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability. J. Biomol. NMR 21:349‐359.
  Dalvit, C., Pevarello, P., Tatò, M., Veronesi, M., Vulpetti, A., and Sundström, M. 2000a. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR 18:65‐68.
  Dalvit, C., Pevarello, P., Tat, M., Veronesi, M., Vulpetti, A., and Sundstrm, M. 2000b. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR 18:65‐68.
  Dalvit, C., Fasolini, M., Flocco, M., Knapp, S., Pevarello, P., and Veronesi, M. 2002. NMR‐based screening with competition water‐ligand observed via gradient spectroscopy experiments: Detection of high‐affinity ligands. J. Med. Chem. 45:2610‐2614.
  DiMicco, J.A. and Zaretsky, D.V. 2005. The mysterious role of prostaglandin E2 in the medullary raphé: A hot topic or not? Am. J. Physiol. Regul. Integr. Comp. Physiol. 289:R1589‐R1591.
  Dominguez, C., Boelens, R., and Bonvin, A.M.J.J. 2003. HADDOCK: A protein‐protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125:1731‐1737.
  Erlanson, D.A. 2012. Introduction to fragment‐based drug discovery. Top. Curr. Chem. 317:1‐32.
  Fielding, L. 2007. NMR methods for the determination of protein‐ligand dissociation constants. Prog. Nucl. Magn. Res. Spectr. 51:219‐242.
  Frank, A.O., Feldkamp, M.D., Kennedy, J.P., Waterson, A.G., Pelz, N.F., Patrone, J.D., Vangamudi, B., Camper, D.V., Rossanese, O.W., Chazin, W.J., and Fesik, S.W. 2013. Discovery of a potent inhibitor of replication protein a protein‐protein interactions using a fragment‐linking approach. J. Med. Chem. 56:9242‐9250.
  Goldflam, M., Tarragó, T., Gairí, M., and Giralt, E. 2012. NMR studies of protein‐ligand interactions. Methods Mol. Biol. 831:233‐259.
  Gonzalez‐Ruiz, D. and Gohlke, H. 2009. Steering protein‐ligand docking with quantitative NMR chemical shift perturbations. J. Chem. Inf. Model. 49:2260‐2271.
  Gorczynski, M.J., Grembecka, J., Zhou, Y., Kong, Y., Roudaia, L., Douvas, M.G., Newman, M., Bielnicka, I., Baber, G., Corpora, T., Shi, J., Sridharan, M., Lilien, R., Donald, B.R., Speck, N.A., Brown, M.L., and Bushweller, J.H. 2007. Allosteric inhibition of the protein‐protein interaction between the leukemia‐associated proteins Runx1 and CBFβ. Chem. Biol. 14:1186‐1197.
  Haigh, C.W. and Mallion, R.B. 1979. Ring current theories in nuclear magnetic resonance. Prog. Nucl. Magn. Reson. Spectrosc. 13:303‐344.
  Han, B., Liu, Y., Ginzinger, S.W., and Wishart, D.S. 2011. SHIFTX2: Significantly improved protein chemical shift prediction. J. Biomol. NMR 50:43‐57.
  Harner, M.J., Frank, A.O., and Fesik, S.W. 2013. Fragment‐based drug discovery using NMR spectroscopy. J. Biomol. NMR 56:65‐75.
  Huey, R., Morris, G.M., Olson, A.J., and Goodsell, D.S. 2007. A semiempirical free energy force field with charge‐based desolvation. J. Comput. Chem. 28:1145‐1152.
  Hunter, C.A. and Packer, M.J. 1999. Complexation‐induced changes in 1H NMR chemical shift for supramolecular structure determination. Chem. Eur. J. 5:1891‐1897.
  Jayalakshmi, V. and Krishna, N.R. 2002. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand‐receptor complexes. J. Magn. Reson. 155:106‐118.
  Kodama, Y., Takeuchi, K., Shimba, N., Ishikawa, K., ichiro Suzuki, E., Shimada, I., and Takahashi, H. 2013. Rapid identification of ligand‐binding sites by using an assignment free NMR approach. J. Med. Chem. 56:9342‐9350.
  Kohlhoff, K.J., Robustelli, P., Cavalli, A., Salvatella, X., and Vendruscolo, M. 2009. Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J. Am. Chem. Soc. 131:13894‐13895.
  Korb, O., Stützle, T., and Exner, T.E. 2007. An ant colony optimization approach to flexible protein‐ligand docking. Swarm Intelligence 2:115‐134.
  Korb, O., Stützle, T., and Exner, T.E. 2009. Empirical scoring functions for advanced protein‐ligand docking with PLANTS. J. Chem. Inf. Model. 49:84‐96.
  Krimm, I. 2012. INPHARMA‐based identification of ligand binding site in fragment‐based drug design. MedChemComm 5:605‐610.
  Krimm, I., Lancelin, J.‐M., and Praly, J.‐P. 2012. Binding evaluation of fragment‐based scaffolds for probing allosteric enzymes. J. Med. Chem. 55:1287‐1295.
  Lehtivarjo, J., Hassinen, T., Korhonen, S.‐P., Peräkylä, M., and Laatikainen, R. 2009. 4D prediction of protein 1H chemical shifts. J. Biomol. NMR 45:413‐426.
  Li, D.‐W. and Brüschweiler, R. 2012. PPM: A side‐chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J. Biomol. NMR 54:257‐265.
  Li, D., DeRose, E.F., and London, R.E. 1999. The inter‐ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands. J. Biomol. NMR 15:71‐76.
  Ludwig, C. and Guenther, U.L. 2009. Ligand based NMR methods for drug discovery. Front. Biosci. (Landmark Ed.) 14:4565‐4574.
  Ludwig, C., Michiels, P.J.A., Wu, X., Kavanagh, K.L., Pilka, E., Jansson, A., Oppermann, U., and Gnther, U.L. 2008. SALMON: Solvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy. J. Med. Chem. 51:1‐3.
  Mari, S., Serrano‐Gómez, D., Cañada, F.J., Corbí, A.L., and Jiménez‐Barbero, J. 2005. 1D saturation transfer difference NMR experiments on living cells: The DCSIGN/oligomannose interaction. Angew. Chem. Int. Ed. Engl. 44:296‐298.
  Maurer, T. 2005. NMR studies of protein‐ligand interactions. Methods Mol. Biol. 305:197‐214.
  Mayer, M. and James, T.L. 2004. NMR‐based characterization of phenothiazines as a RNA binding scaffold. J. Am. Chem. Soc. 126:4453‐4460.
  Mayer, M. and Meyer, B. 1999. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. Engl. 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.
  McCoy, M.A. and Wyss, D.F. 2000. Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations. J. Biomol. NMR 18:189‐198.
  McCoy, M.A. and Wyss, D.F. 2002. Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations. J. Am. Chem. Soc. 124:11758‐11763.
  McCoy, M.A., Senior, M.M., and Wyss, D.F. 2005. Screening of protein kinases by ATP‐STD NMR spectroscopy. J. Am. Chem. Soc. 127:7978‐7979.
  Medek, A., Hajduk, P.J., Mack, J., and Fesik, S.W. 2000. The use of differential chemical shifts for determining the binding site location and orientation of protein‐bound ligands. J. Am. Chem. Soc. 122:1241‐1242.
  Meiler, J .2003. PROSHIFT: Protein chemical shift prediction using artificial neural networks. J. Biomol. NMR 26:25‐37.
  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 αIIbβ3. J. Med. Chem. 44:3059‐3065.
  Meyer, B. and Peters, T. 2003. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. Engl. 42:864‐890.
  Mooij, W.T. M., Hartshorn, M.J., Tickle, I.J., Sharff, A.J., Verdonk, M.L., and Jhoti, H. 2006. Automated protein‐ligand crystallography for structure‐based drug design. ChemMedChem 1:827‐838.
  Moseley, H.N., Curto, E.V., and Krishna, N.R. 1995. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of NOESY spectra of interacting systems; two‐dimensional transferred NOESY. J. Magn. Reson. B 108:243‐261.
  Murray, C.W., Erlanson, D.A., Hopkins, A.L., Keserü, G.M., Leeson, P.D., Rees, D.C., Reynolds, C.H., and Richmond, N.J. 2014. Validity of ligand efficiency metrics. ACS Med. Chem. Lett. 5:616‐618.
  Nagaraja, C. 2006. Heteronuclear saturation transfer difference (HSTD) experiment for detection of ligand binding to proteins. Chem. Phys. Lett. 420:340‐346.
  Neal, S., Nip, A.M., Zhang, H., and Wishart, D.S. 2003. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR 26:215‐240.
  Nielsen, J.T., Eghbalnia, H.R., and Nielsen, N.C. 2012. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field. Prog. Nucl. Magn. Reson. Spectrosc. 60:1‐28.
  Ono, K., Takeuchi, K., Ueda, H., Morita, Y., Tanimura, R., Shimada, I., and Takahashi, H. 2014. Structure‐based approach to improve a small‐molecule inhibitor by the use of a competitive peptide ligand. Angew. Chem. Int. Ed. Engl. 53:2597‐2601.
  Orts, J., Griesinger, C., and Carlomagno, T. 2009. The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method. J. Magn. Reson. 200:64‐73.
  Pereira, A., Pfeifer, T.A., Grigliatti, T.A., and Andersen, R.J. 2009. Functional cell‐based screening and saturation transfer double‐difference NMR have identified haplosamate A as a cannabinoid receptor agonist. Chem. Biol. 4:139‐144.
  Post, C.B. 2003. Exchange‐transferred noe spectroscopy and bound ligand structure determination. Curr. Opin. Struct. Biol. 13:581‐588.
  Rademacher, C., Krishna, N.R., Palcic, M., Parra, F., and Peters, T. 2008. NMR experiments reveal the molecular basis of receptor recognition by a calicivirus. J. Am. Chem. Soc. 130:3669‐3675.
  Rademacher, C., Guiard, J., Kitov, P.I., Fiege, B., Dalton, K.P., Parra, F., Bundle, D.R., and Peters, T. 2011. Targeting norovirus infection‐multivalent entry inhibitor design based on NMR experiments. Chemistry 17:7442‐7453.
  Räuber, C. and Berger, S. 2010. 13C‐NMR detection of STD spectra. Magn. Reson. Chem. 48:91‐93.
  Ravindranathan, S., Mallet, J.‐M., Sinay, P., and Bodenhausen, G. 2003. Transferred cross‐relaxation and cross‐correlation in NMR: Effects of intermediate exchange on the determination of the conformation of bound ligands. J. Magn. Reson. 163:199‐207.
  Reese, M., Snchez‐Pedregal, V.M., Kubicek, K., Meiler, J., Blommers, M.J. J., Griesinger, C., and Carlomagno, T. 2007. Structural basis of the activity of the microtubule‐stabilizing agent epothilone a studied by NMR spectroscopy in solution. Angew. Chem. Int. Ed. Engl. 46:1864‐1868.
  Rega, M.F., Wu, B., Wei, J., Zhang, Z., Cellitti, J.F., and Pellecchia, M. 2011. SAR by interligand nuclear overhauser effects (ILOEs) based discovery of acylsulfonamide compounds active against Bcl‐x(L) and Mcl‐1. J. Med. Chem. 54:6000‐6013.
  Riedinger, C., Endicott, J.A., Kemp, S.J., Smyth, L.A., Watson, A., Valeur, E., Golding, B.T., Griffin, R.J., Hardcastle, I.R., Noble, M.E., and McDonnell, J.M. 2008. Analysis of chemical shift changes reveals the binding modes of isoindolinone inhibitors of the MDM2 p53 interaction. J. Am. Chem. Soc. 130:16038‐16044.
  Sahakyan, A.B., Vranken, W.F., Cavalli, A., and Vendruscolo, M. 2011. Structure‐based prediction of methyl chemical shifts in proteins. J. Biomol. NMR 50:331‐346.
  Sánchez‐Pedregal, V.M., Reese, M., Meiler, J., Blommers, M.J. J., Griesinger, C., and Carlomagno, T. 2005. The INPHARMA method: Protein‐mediated interligand NOEs for pharmacophore mapping. Angew. Chem. Int. Ed. Engl. 44:4172‐4175.
  Schieborr, U., Vogtherr, M., Elshorst, B., Betz, M., Grimme, S., Pescatore, B., Langer, T., Saxena, K., and Schwalbe, H. 2005. How much NMR data is required to determine a protein‐ligand complex structure? Chembiochem 6:1891‐1898.
  Shen, Y. and Bax, A. 2007. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J. Biomol. NMR 38:289‐302.
  Shen, Y. and Bax, A. 2010. SPARTA+: A modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J. Biomol. NMR 48:13‐22.
  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.
  Siebert, H.‐C., Lü, S.‐Y., Frank, M., Kramer, J., Wechselberger, R., Joosten, J., André, S., Rittenhouse‐Olson, K., Roy, R., von der Lieth, C.‐W., Kaptein, R., Vliegenthart, J.F. G., Heck, A.J. R., and Gabius, H.‐J. 2002. Analysis of protein‐carbohydrate interaction at the lower size limit of the protein part (15‐mer peptide) by NMR spectroscopy, electrospray ionization mass spectrometry, and molecular modeling. Biochemistry 41:9707‐9717.
  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.
  Sousa, S.F., Ribeiro, A.J. M., Coimbra, J.T. S., Neves, R.P. P., Martins, S.A., Moorthy, N.S. H.N., Fernandes, P.A., and Ramos, M.J. 2013. Protein‐ligand docking in the new millennium—a retrospective of 10 years in the field. Curr. Med. Chem. 20:2296‐2314.
  Stark, J. and Powers, R. 2008. Rapid protein‐ligand costructures using chemical shift perturbations. J. Am. Chem. Soc. 130:535‐545.
  Szczepina, M.G., Bleile, D.W., and Pinto, B.M. 2011. Investigation of the binding of a carbohydrate‐mimetic peptide to its complementary anticarbohydrate antibody by STD NMR spectroscopy and molecular‐dynamics simulations. Chemistry 17:11446‐11455.
  Szczepina, M.G., Zheng, R.B., Completo, G.C., Lowary, T.L., and Pinto, B.M. 2009. STD‐NMR studies suggest that two acceptor substrates for GlfT2, a bifunctional galactofuranosyltransferase required for the biosynthesis of Mycobacterium tuberculosis arabinogalactan, compete for the same binding site. Chembiochem 10:2052‐2059.
  Ten Brink, T., Aguirre, C., Exner, T.E., and Krimm, I. 2014. Performance of protein‐ligand docking with simulated chemical shift perturbations. J. Chem. Inf. Model. 55:275‐283.
  Valkov, E., Sharpe, T., Marsh, M., Greive, S., and Hyvönen, M. 2012. Targeting protein‐protein interactions and fragment‐based drug discovery. Top. Curr. Chem. 317:145‐179.
  Wagstaff, J.L., Taylor, S.L., and Howard, M.J. 2013. Recent developments and applications of saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy. Mol. Biosyst. 9:571‐577.
  Wang, Y.‐S., Liu, D., and Wyss, D.F. 2004. Competition STD NMR for the detection of high‐affinity ligands and NMR‐based screening. Magn. Res. Chem.42:485‐489.
  Williamson, M.P. 2013. Using chemical shift perturbation to characterise ligand binding. Prog. Nucl. Magn. Reson. Spectrosc. 73:1‐16.
  Wishart, D.S. 2011. Interpreting protein chemical shift data. Prog. Nucl. Magn. Reson. Spectrosc. 58:62‐87.
  Wyss, D.F., Arasappan, A., Senior, M.M., Wang, Y.‐S., Beyer, B.M., Njoroge, F.G., and McCoy, M.A. 2004. Non‐peptidic small‐molecule inhibitors of the single‐chain hepatitis C virus NS3 protease/NS4A cofactor complex discovered by structure‐based NMR screening. J. Med. Chem. 47:2486‐2498.
  Xu, X.P. and Case, D.A. 2001. Automated prediction of 13Cβ and 13C′ chemical shifts in proteins using a density functional database. J. Biomol. NMR 21:321‐333.
  Xu, X.‐P. and Case, D.A. 2002. Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408‐423.
  Yuan, Y., Wen, X., Sanders, D.A. R., and Pinto, B.M. 2005. Exploring the mechanism of binding of UDP‐galactopyranose to UDP‐galactopyranose mutase by STD‐NMR spectroscopy and molecular modeling. Biochemistry 44:14080‐14089.
  Zeng, J., Zhou, P., and Donald, B.R. 2013. HASH: A program to accurately predict protein Hα shifts from neighboring backbone shifts. J. Biomol. NMR 55:105‐118.
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