Design of Screening Collections for Successful Fragment-Based Lead Discovery

Methods in Molecular Biology

Volumn 685, Issue , 2011, Pages 219-240

  Na, James ^a   Hu, Qiyue ^a  

^a PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

computational filtering; Fragment based lead discovery; library design; NMR screening; screening collection

Indexed keywords

LIGAND;

ARTICLE; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG SCREENING; ENZYME SPECIFICITY; METABOLISM; METHODOLOGY; MOLECULAR LIBRARY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG EVALUATION, PRECLINICAL; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; SMALL MOLECULE LIBRARIES; SUBSTRATE SPECIFICITY;

EID: 79952200622     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-931-4_11     Document Type: Chapter

References (37)

1. Congreve, M., Chessari, C., Tisi, D., Woodhead, A. (2008) Recent advances in fragment-based drug discovery. J Med Chem 51, 3661–3680.
2. Hesterkamp, T., Whittaker, M. (2008) Fragment-based activity space: smaller is better. Curr Opin Chem Biol 12, 260–268.
3. Hajduk, P. J., Greer, J. (2007) A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 6, 211–219.
4. Albert, J. S., Blomberg, N., Breeze, A. L., Brown, A. J. H., Burrows, J. N., Edwards, P. D., Folmer, R. H. A., Geschwindner, S., Griffen, E. J., Kenny, P. W., Nowak, T., Olsson, L.-L., Sanganee, H., Shapiro, A. B. (2007) An integrated approach to fragment-based lead generation philosophy, strategy and case studies from AstraZeneca’s drug discovery programmes. Curr Top Med Chem 7, 1600–1629.
5. Shuker, S. B., Hajduk, P. J., Meadows, R. P., Fesik, S. W. (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274, 1531–1534.
6. de Kloe, G. E., Bailey, D., Leurs, R., de Esch, I. J. P. (2009) Transforming fragments into candidates: small becomes big in medicinal chemistry. Drug Discovery Today 14, 630–646.
7. Hann, M. M., Oprea, T. I. (2004) Pursuing the lead-likeness concept in pharma-ceutical research. Curr Opin Chem Biol, 8, 255–263
8. Blomberg, N., Cosgrove, D. A., Kenny, P. W., Kolmodin, K. (2009) Design of compound libraries for fragment screening. J Comput Aided Mol Des 23, 513–525.
9. Barker, J., Courtney, S., Hesterkamp, T., Ull-mann, D., Whittaker, M. (2005) Fragment screening by biochemical assay. Exp Opin Drug Discov 1, 225–236.
10. Schuffenhauer, A., Ruedisser, S., Marzinzik, A., Jahnke, W., Selzer, P., Jacoby, E. (2005) Library design for fragment based screening. Curr Top Med Chem 5, 751–762.
11. Fejzo, J., Lepre, C. A., Peng, J. W., Bemis, G. W., Ajay, Murcko, M. A., Moore, J. M. (1999) The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem Biol 6, 755–769.
12. Lepre, C. A. (2001) Library design for NMR-based screening. Drug Discov Today 6, 133–140.
13. Taskinen, J., Norinder, U. (2006) In silico predictions of solubility, Comprehen Med Chem II, edited by Taylor, J. B., Triggle, D. J. 5, 627–648.
14. Congreve, M., Carr, R., Murray, C., Jhoti, H. (2003) A ‘rule of three’ for fragment-based lead discovery. Drug Discov Today 8, 876–877.
15. Mayer, M., Meyer, B. (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 38, 1784–1788.
16. Wang, Y., Liu, D., Wyss, D. F. (2004) Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Magn Reson Chem 42, 485–489.
17. Dalvit, C., Pevarello, P., Tato, M., Vulpetti, A., Sundstrom, M. (2000) Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J Biomol NMR 18, 65–68.
18. Baurin, N., Aboul-Ela, F., Barril, X., Davis, B., Drysdale, M., Dymock, B., Finch, H., Fromont, C., Richardson, C., Simmonite, H., Hubbard, R. E. (2004) Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. J Chem Inf Comput Sci 44, 2157–2166.
19. Hajduk, P. J., Huth, J., Tse, C. (2005) Predicting protein druggability. Drug Discov Today 10, 1675–1682.
20. Lau, W. F., Hepworth, D., Magee, T. V., Du, J., Bakken, G. A., Miller, M. D., Hendsch, Z. S., Thanabal, V., Kolodziej, S. A., Xing, L., Hu, Q., Narasimhan, L. S., Love, R., Charlton, M. E., Hughes, S., Van Hoorn, W., Mills, J. E., Withka, J. M. (2010) Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics. J Comput-Aided Mol Des. Manuscript in preparation.
21. Hu, Q., Yan, J., Withka, J. M., Sahasrabudhe, P., Moore, C., Na, J., Narasimhan, L. S. (2009) Computational analysis on NMR screenings of the Pfizer Fragment Initiative collection. 238th ACS National Meeting, Washington, DC, United States.
22. Hopkins, A. L., Groom, C. R., Alex, A. (2004) A useful metric for lead selection. Drug Disc Today 9, 430–431.
23. Huuskonen, J., Rantanen, J., Livingstone, D. (2000) Prediction of aqueous solubility for a diverse set of organic compounds based on atom-type electrotopological state indices. Eur J Med Chem 35, 1081–1088.
24. Chemical Computing Group Inc., Montreal, H3A 2R7 Canada.
25. Baurin, N., Baker, R., Richardson, C., Chen, I., Foloppe, N., Potter, A., Jordan, A., Roughley, S., Parratt, M., Greaney, P., Morley, D., Hubbard, R. E. (2004) Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds. J Chem Inf Comput Sci 44, 643–651.
26. Siegal, G., Ab, E., Schultz, J. (2007) Integration of fragment screening and library design. Drug Discov Today 12, 1032–1039
27. Chen, I., Hubbard, R. E. (2009) Lessons for fragment library design: analysis of output from multiple screening campaigns. J Comput Aided Mol Des 23, 603–620.
28. Hubbard, R. E., Davis, B., Chen, I., Drysdale, M. (2007) The SeeDs approach: integrating fragments into drug discovery. Curr Top Med Chem 7, 1568–1581.
29. Meiboom, S., Gill, D. (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 29, 688–691.
30. Hajduk, P. J., Huth, J. R., Fesik, S. (2005) Druggability indices for protein targets. J Med Chem 48, 2518–2525.
31. Halgren, T. A. (2009) Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 49, 377–389.
32. Ruppert, J., Welch, W., Jain, A. N. (1997) Automatic identification and representation of protein binding sites for molecular docking. Prot Sci 6, 524–533.
33. Brewer, M., Ichihara, O., Kirchhoff, C., Schade, M., Whittaker, M. (2008) Assembling a fragment library. Fragment-Based Drug Discovery: A Practical Approach, in (Zartler, E., Shapiro, M. J. eds.), pp. 39–62.
34. Hartshorn, M. J., Murray, C. W., Cleasby, A., Frederickson, M., Tickle, I. J., Jhoti, H. (2005) Fragment-based lead discovery using X-ray crystallography. J Med Chem 48, 403–413.
35. Card, G.L., Blasdel, L., England, B. P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S., Schlessinger, J., Zhang, K. Y. J. (2005) A family of phosphodiesterase inhibitors discovered by cocrys-tallography and scaffold-based drug design. Nat Biotechnol 23, 201–207.
36. Blaney, J., Nienaber, V., Burley, S. K. (2006) Fragment-based lead discovery and optimization using X-ray crystallography, computational chemistry, and highthrough-put organic synthesis, Fragment-Based Approaches in Drug Discovery, in (Jahnke, W., Erlanson, D. A., Mannhold, R., Kubinyi, H., and Folkers, G., eds.), pp. 215–248.
37. Erlanson, D.A., Ballinger, M. D., Wells, J. A. (2006) Tethering, Fragment-Based Approaches in Drug Discovery, in (Jahnke, W., Erlanson, D. A., Mannhold, R., Kubinyi, H., and Folkers, G., eds.), pp. 285–312.