Designing a diverse high-quality library for crystallography-based FBDD screening

Methods in Enzymology

Volumn 493, Issue , 2011, Pages 3-20

  Tounge, Brett A ^a   Parker, Michael H ^a  

^a JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; AMIDE; AMIDINE; AMINE; CARBOXYLIC ACID; CHEMICAL COMPOUND; PEPTIDE LIBRARY;

ALGORITHM; ARTICLE; BIOPHYSICS; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; FRAGMENT BASED DRUG DISCOVERY; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; MOLECULAR LIBRARY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SOLUBILITY; X RAY CRYSTALLOGRAPHY;

EID: 79952430797     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381274-2.00001-7     Document Type: Chapter

References (42)

1. C. Abad-Zapatero Ligand efficiency indices for effective drug discovery Expert Opin. Drug Discov. 2 2007 469 488 (Pubitemid 47073073)
2. Accelrys Pipeline Pilot, 7.5 2009 Accelrys, San Diego, CA
3. J. Barker, T. Hesterkamp, M. Schade, and M. Whittaker Fragment screening: Biochemical assays versus NMR Innov. Pharm. Technol. 23 2007 19 22 (Pubitemid 351210731)
4. N. Baurin, F. Aboul-Ela, X. Barril, B. Davis, M. Drysdale, B. Dymock, H. Finch, C. Fromont, C. Richardson, H. Simmonite, and R.E. Hubbard Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets J. Chem. Inf. Comput. Sci. 44 2004 2157 2166
5. S.D. Bembenek, B.A. Tounge, and C.H. Reynolds Ligand efficiency and fragment-based drug discovery Drug Discov. Today 14 2009 278 283
6. G.W. Bemis, and M.A. Murcko The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 39 1996 2887 2893 (Pubitemid 26251026)
7. G.W. Bemis, and M.A. Murcko Properties of known drugs. 2. Side chains J. Med. Chem. 42 1999 5095 5099 (Pubitemid 30020260)
8. J. Blaney, V. Nienaber, and S.K. Burley Fragment-based lead discovery and optimization using X-ray crystallography, computational chemistry, and high-throughput organic synthesis Meth. Princ. Med. Chem. 34 2006 215 248
9. N. Blomberg, D.A. Cosgrove, P.W. Kenny, and K. Kolmodin Design of compound libraries for fragment screening J. Comput. Aided Mol. Des. 23 2009 513 525
10. M. Brewer, O. Ichihara, C. Kirchhoff, M. Schade, and M. Whittaker Assembling a fragment library E. Zartler, M. Shapiro, Fragment-Based Drug Discovery: A Practical Approach 2008 John Wiley & Sons, Ltd United Kingdom 39 62
11. I.J. Chen, and R.E. Hubbard Lessons for fragment library design: Analysis of output from multiple screening campaigns J. Comput. Aided Mol. Des. 23 2009 603 620
12. G. Chessari, and A.J. Woodhead From fragment to clinical candidateA historical perspective Drug Discov. Today 14 2009 668 675
13. N. Colclough, A. Hunter, P.W. Kenny, R.S. Kittlety, L. Lobedan, K.Y. Tam, and M.A. Timms High throughput solubility determination with application to selection of compounds for fragment screening Bioorg. Med. Chem. 16 2008 6611 6616 (Pubitemid 351802211)
14. M. Congreve, R. Carr, C. Murray, and H. Jhoti A 'rule of three' for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877 (Pubitemid 37194496)
15. C. Dalvit NMR methods in fragment screening: Theory and a comparison with other biophysical techniques Drug Discov. Today 14 2009 1051 1057
16. U.H. Danielson Fragment library screening and lead characterization using SPR biosensors Curr. Top. Med. Chem. (Sharjah, United Arab Emirates) 9 2009 1725 1735
17. E. de Kloe Gerdien, D. Bailey, R. Leurs, and J.P. de Esch Iwan Transforming fragments into candidates: Small becomes big in medicinal chemistry Drug Discov. Today 14 2009 630 646
18. M. Fischer, and R.E. Hubbard Fragment-based ligand discovery Mol. Interv. 9 2009 22 30
19. A.K. Ghose, V.N. Viswanadhan, and J.J. Wendoloski Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragment methods: An analysis of AlogP and CLogP methods J. Phys. Chem. A 102 1998 3762 3772 (Pubitemid 128611348)
20. P.J. Hajduk, T. Gerfin, J.-M. Boehlen, M. Haeberli, D. Marek, and S.W. Fesik High-throughput nuclear magnetic resonance-based screening J. Med. Chem. 42 1999 2315 2317 (Pubitemid 29305164)
21. M.M. Hann, A.R. Leach, and G. Harper Molecular complexity and its impact on the probability of finding leads for drug discovery J. Chem. Inf. Comput. Sci. 41 2001 856 864
22. M.J. Hartshorn, C.W. Murray, A. Cleasby, M. Frederickson, I.J. Tickle, and H. Jhoti Fragment-based lead discovery using X-ray crystallography J. Med. Chem. 48 2005 403 413 (Pubitemid 40139783)
23. L. Hopkins Andrew, R. Groom Colin, and A. Alex Ligand efficiency: A useful metric for lead selection Drug Discov. Today 9 2004 430 431 (Pubitemid 38510559)
24. E. Jacoby, J. Davies, and M.J.J. Blommers Design of small molecule libraries for NMR screening and other applications in drug discovery Curr. Top. Med. Chem. (Hilversum, Netherlands) 3 2003 11 23
25. H. Jhoti Fragment-based drug discovery using rational design Ernst Schering Found. Symp. Proc. 3 2007 169 185
26. H. Jhoti, A. Cleasby, M. Verdonk, and G. Williams Fragment-based screening using X-ray crystallography and NMR spectroscopy Curr. Opin. Chem. Biol. 11 2007 485 493 (Pubitemid 47588996)
27. T. Liu, Y. Lin, X. Wen, and R.N. Jorissen BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 35 2007 D198 D201
28. M. Mayer, and B. Meyer Characterization of ligand binding by saturation transfer difference NMR spectroscopy Angew. Chem. Int. Ed. 38 1999 1784 1788 (Pubitemid 29290947)
29. K.A. Mercier, K. Germer, and R. Powers Design and characterization of a functional library for NMR screening against novel protein targets Comb. Chem. High Throughput Screening 9 2006 515 534 (Pubitemid 44156709)
30. C.W. Murray, and D.C. Rees The rise of fragment-based drug discovery Nat. Chem. 1 2009 187 192
31. J.W.M. Nissink Simple size-independent measure of ligand efficiency J. Chem. Inf. Model. 49 2009 1617 1622
32. M. Orita, K. Ohno, and T. Niimi Two golden ratio' indices in fragment-based drug discovery Drug Discov. Today 14 2009 321 328
33. M. Orita, M. Warizaya, Y. Amano, K. Ohno, and T. Niimi Advances in fragment-based drug discovery platforms Expert Opin. Drug Discov. 4 2009 1125 1144
34. S. Perspicace, D. Banner, J. Benz, F. Muller, D. Schlatter, and W. Huber Fragment-based screening using surface plasmon resonance technology J. Biomol. Screen. 14 2009 337 349
35. D. Rogers, and M. Hahn Extended-connectivity fingerprints J. Chem. Inf. Model. 50 2010 742 754
36. A. Schuffenhauer, S. Ruedisser, A.L. Marzinzik, W. Jahnke, M. Blommers, P. Selzer, and E. Jacoby Library design for fragment based screening Curr. Top. Med. Chem. (Sharjah, United Arab Emirates) 5 2005 751 762 (Pubitemid 41179715)
37. M.N. Schulz, and R.E. Hubbard Recent progress in fragment-based lead discovery Curr. Opin. Pharmacol. 9 2009 615 621
38. J. Spulino Fragment Screening Purely with Protein Crystallography. L. Kuo, Fragment Based Drug Design Tools, Practical Approaches, and Examples 2011 Elsevier San Diego 493
39. Symyx Solutions, Inc. Available Chemicals Directory 2007 Symyx Solutions, Inc, San Diego, CA
40. Symyx Solutions, Inc. Comprehensive Medicinal Chemistry 2007 Symyx Solutions, Inc, San Diego, CA
41. B.A. Tounge, and C.H. Reynolds Defining privileged reagents using subsimilarity comparison J. Chem. Inf. Comput. Sci. 44 2004 1810 1815
42. X. Wang, Q. Yang, and Q. You Fragment-based drug discovery Zhongguo Yaoke Daxue Xuebao 40 2009 289 296