Ligand-orientation based fragment selection in STD NMR screening

Journal of Medicinal Chemistry

Volumn 58, Issue 21, 2015, Pages 8739-8742

  Cala, Olivier ^a   Krimm, Isabelle ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOPURINE; 2 HYDROXYBIPHENYL; 3 QUINOLINECARBOXYLIC ACID; 7 AZAINDOLE; CARBOXYLIC ACID DERIVATIVE; GLYCOGEN PHOSPHORYLASE; INDOLE DERIVATIVE; LIGAND; PROTON; UNCLASSIFIED DRUG; MOLECULAR LIBRARY; PROTEIN; PROTEIN BINDING;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DRUG SCREENING; EPITOPE MAPPING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; SATURATION TRANSFER DIFFERENCE; ANIMAL; CHEMISTRY; DRUG DESIGN; HUMAN; METABOLISM; MOLECULAR LIBRARY; PHARMACOLOGY; PROCEDURES;

ANIMALS; BINDING SITES; DRUG DESIGN; HUMANS; LIGANDS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEINS; SMALL MOLECULE LIBRARIES;

EID: 84947475154     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/acs.jmedchem.5b01114     Document Type: Article

References (25)

1. Erlanson, D. Introduction to Fragment-Based Drug Discovery. In Fragment-Based Drug Discovery and X-Ray Crystallography; Topics in Current Chemistry; Davies, T. G., Hyvönen, M., Eds.; Springer: Berlin, Heidelberg, 2012; Vol. 317, pp 1-32.
2. Chen, H.; Zhou, X.; Wang, A.; Zheng, Y.; Gao, Y.; Zhou, J. Evolutions in Fragment-based Drug Design: The Deconstruction-reconstruction Approach Drug Discovery Today 2015, 20 (1) 105-113 10.1016/j.drudis.2014.09.015
3. Dalvit, C. NMR methods in fragment screening: theory and a comparison with other biophysical techniques Drug Discovery Today 2009, 14 (21-22) 1051-1057 10.1016/j.drudis.2009.07.013
4. Kim, H.-Y.; Wyss, D. NMR Screening in Fragment-Based Drug Design: A Practical Guide. In Chemical Biology; Methods in Molecular Biology; Hempel, J. E.; Williams, C. H.; Hong, C. C., Eds.; Springer: New York, 2015; Vol. 1263, pp 197-208.
5. Cala, O.; Guillière, F.; Krimm, I. NMR-based Analysis of Protein-ligand Interactions Anal. Bioanal. Chem. 2014, 406 (4) 943-956 10.1007/s00216-013-6931-0
6. Barile, E.; Pellecchia, M. NMR-Based Approaches for the Identification and Optimization of Inhibitors of Protein-Protein Interactions Chem. Rev. 2014, 114 (9) 4749-4763 10.1021/cr500043b
7. Goldflam, M.; Tarragó, T.; Gairí, M.; Giralt, E. NMR Studies of Protein-Ligand Interactions. In Protein NMR Techniques; Methods in Molecular Biology; Shekhtman, A.; Burz, D. S., Eds.; Humana Press: Totowa, NJ; 2012; Vol. 831, pp 233-259.
8. Harner, M. J.; Frank, A. O.; Fesik, S. W. Fragment-based drug discovery using NMR spectroscopy J. Biomol. NMR 2013, 56 (2) 65-75 10.1007/s10858-013-9740-z
9. Meyer, B.; Peters, T. NMR Spectroscopy Techniques for Screening and Identifying Ligand Binding to Protein Receptors Angew. Chem., Int. Ed. 2003, 42 (8) 864-890 10.1002/anie.200390233
10. Wang, Y.-S.; Liu, D.; Wyss, D. F. Competition STD NMR for the detection of high-affinity ligands and NMR-based screening Magn. Reson. Chem. 2004, 42 (6) 485-489 10.1002/mrc.1381
11. ͆ledź, P.; Abell, C.; Ciulli, A. Ligand-Observed NMR in Fragment-Based Approaches. In NMR of Biomolecules: Towards Mechanistic Systems Biology Bertini, I.; McGreevy, K. S.; Parigi, G., Eds.; Wiley-Blackwell: New York, 2012.
12. Scott, D. E.; Ehebauer, M. T.; Pukala, T.; Marsh, M.; Blundell, T. L.; Venkitaraman, A. R.; Abell, C.; Hyvönen, M. Using a fragment-based approach to target protein-protein interactions ChemBioChem 2013, 14 (3) 332-42 10.1002/cbic.201200521
13. Silvestre, H. L.; Blundell, T. L.; Abell, C.; Ciulli, A. Integrated Biophysical approach to fragment screening and validation for fragment-based lead discovery Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (32) 12984-12989 10.1073/pnas.1304045110
14. Mayer, M.; Meyer, B. 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. 2001, 123 (25) 6108-6117 10.1021/ja0100120
15. Angulo, J.; Nieto, P. M. STD-NMR: application to transient interactions between biomolecules-a quantitative approach Eur. Biophys. J. 2011, 40 (12) 1357-1369 10.1007/s00249-011-0749-5
16. Dias, D. M.; Van Molle, I.; Baud, M. G. J.; Galdeano, C.; Geraldes, C. F. G. C.; Ciulli, A. Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions? ACS Med. Chem. Lett. 2014, 5 (1) 23-28 10.1021/ml400296c
17. Aguirre, C.; ten Brink, T.; Guichou, J.-F.; Cala, O.; Krimm, I. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5 PLoS One 2014, 9 (7) e102300 10.1371/journal.pone.0102300
18. Pilger, J.; Mazur, A.; Monecke, P.; Schreuder, H.; Elshorst, B.; Bartoschek, S.; Langer, T.; Schiffer, A.; Krimm, I.; Wegstroth, M.; Lee, D.; Hessler, G.; Wendt, K.-U.; Becker, S.; Griesinger, C. A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles Angew. Chem., Int. Ed. 2015, 54 (22) 6511-6515 10.1002/anie.201500671
19. Gaboriaud-Kolar, N.; Skaltsounis, A.-L. Glycogen phosphorylase inhibitors: a patent review (2008-2012) Expert Opin. Ther. Pat. 2013, 23 (8) 1017-1032 10.1517/13543776.2013.794790
20. Krimm, I.; Lancelin, J.-M.; Praly, J.-P. Binding Evaluation of Fragment-Based Scaffolds for Probing Allosteric Enzymes J. Med. Chem. 2012, 55 (3) 1287-1295 10.1021/jm201439b
21. Barelier, S.; Linard, D.; Pons, J.; Clippe, A.; Knoops, B.; Lancelin, J.-M.; Krimm, I. Discovery of fragment molecules that bind the human peroxiredoxin 5 active site PLoS One 2010, 5 (3) e9744 10.1371/journal.pone.0009744
22. Yan, J.; Kline, A. D.; Mo, H.; Shapiro, M. J.; Zartler, E. R. The effect of relaxation on the epitope mapping by saturation transfer difference NMR J. Magn. Reson. 2003, 163 (2) 270-276 10.1016/S1090-7807(03)00106-X
23. Kemper, S.; Patel, M. K.; Errey, J. C.; Davis, B. G.; Jones, J. A.; Claridge, T. D. Group epitope mapping considering relaxation of the ligand (GEM-CRL): including longitudinal relaxation rates in the analysis of saturation transfer difference (STD) experiments J. Magn. Reson. 2010, 203 (1) 1-10 10.1016/j.jmr.2009.11.015
24. Vom, A.; Headey, S.; Wang, G.; Capuano, B.; Yuriev, E.; Scanlon, M. J.; Simpson, J. S. Detection and Prevention of Aggregation-based False Positives in STD-NMR-based Fragment Screening Aust. J. Chem. 2013, 66 (12) 1518-1524 10.1071/CH13286
25. Congreve, M.; Carr, C.; Murray, C.; Jhoti, H. A 'rule of three' for fragment-based lead discovery? Drug Discovery Today 2003, 8 (19) 876-877 10.1016/S1359-6446(03)02831-9