Library design for fragment based screening

Current Topics in Medicinal Chemistry

Volumn 5, Issue 8, 2005, Pages 751-762

  Schuffenhauer, Ansgar ^a   Ruedisser, Simon ^a   Marzinzik, Andreas L ^a   Jahnke, Wolfgang ^a   Blommers, Marcel ^a   Selzer, Paul ^a   Jacoby, Edgar ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACETAMIDE DERIVATIVE; AMINE; FK 506 BINDING PROTEIN; NEW DRUG;

BINDING AFFINITY; BINDING SITE; BIOINFORMATICS; DRUG RESEARCH; DRUG STRUCTURE; DRUG SYNTHESIS; HIGH THROUGHPUT SCREENING; IC 50; MOLECULAR LIBRARY; NUCLEAR MAGNETIC RESONANCE; PREDICTION; PROBABILITY; PROTEIN BINDING; PROTEIN TARGETING; REVIEW; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS; VALIDATION PROCESS;

COMBINATORIAL CHEMISTRY TECHNIQUES; LIGANDS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; SENSITIVITY AND SPECIFICITY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 23844542148     PISSN: 15680266     EISSN: None     Source Type: Journal    
DOI: 10.2174/1568026054637700     Document Type: Review

References (52)

1. Ertl, P. Cheminformatics analysis of organic substituents: identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups. J. Chem. Inf. Comput. Sci., 2003, 43, 374-380.
2. Bohacek, R. S.; McMartin, C.; Guida, W. C. The art and practice of structure based drug design: a molecular modeling perspective. Med. Res. Rev., 1996, 16, 3-50.
3. Villar, H. O.; Koehler R. T. Comments on the design of chemical libraries for screening. Mol. Divers., 2000, 5, 13-24.
4. Harper, G.; Pickett, S. D.; Green D. V. S. Design of compound screening collection for use in high throughput screening. Comb. Chem. High Throughput Screen., 2004, 7, 63-70.
5. Hann, M. M.; Leach, A. R.; Harper, G. Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci., 2001, 41, 856-864.
6. Hann, M. M.; Oprea, T. I. Pursuing the leadlikeness concept in pharmaceutical research, Curr. Opin. Chem. Biol., 2004, 8, 225-263.
7. Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. USA, 1999, 96, 9997-10002.
8. Hopkins, A. L.; Groom C. R. Ligand efficiency: a useful metric for lead selection. Drug Discov. Today, 2004, 9, 430-431.
9. Lepre, C, A.; Moore, J. M,.; Peng, J. W. Theory and applications of NMR-based screening in pharmaceutical research. Chem. Rev., 2004, 104, 3641-3675.
10. Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Discovering high-affinity ligands for proteins: SAR by NMR. Science, 1996, 274, 1531-1534.
11. Fejzo, J.; Lepre, C. A.; Peng, J. W.; Bemis, G. W.; Murcko, M. A.; Moore, J. M. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem. Biol., 1999, 6, 755-769.
12. Fejzo, J.; Lepre, C.; Xie, X. Application of NMR screening in drug discovery. Curr. Top. Med. Chem., 2003, 3, 81-97.
13. Hartshorn, M.J.; Murray, C. W.; Cleasby, A.; Frederickson, M.; Tickle, I.J.; Jhoti, H. Fragment-based lead discovery using X-ray crystallography. J. Med. Chem., 2005, 48, 403-413.
14. Nienaber, V. L.; Ricardson P. L.; Klighofer, V.; Bouska, J. J.; Giranda, V. L.; Greer, J. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nature Biotech., 2000, 18, 1105-1108.
15. Swayze, E. E.; Jefferson, E. A.; Sannes-Lowery, K. A.; Blyn, L. B.; Risen, L. M.; Arakawa, S.; Osgood, S. A.; Hofstadler, S. A.; Griffey, R. H. SAR by MS: A ligand based technique for drug lead discovery against structured RNA targets. J. Med. Chem., 2002, 45, 3816-3819.
16. Sannes-Lowery, K. A.; Griffey, R. H.; Hofstadler, S. A. Measuring dissociation constants of RNA and aminoglycoside antibiotics by electrospray ionization mass spectrometry. Anal. Biochem., 2000, 280, 264-271.
17. Salemme, F. R.; Weber, P. C. Application of calorimetric methods to drug discovery and the study of protein interactions. Curr. Opin. Struct. Biol., 2003, 13, 115-121.
18. Leavitt, S.; Freire, E. Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol., 2001, 11, 560-566.
19. Selzer, P.; Roth H. J.; Ertl, P.; Schuffenhauer A. Complex molecules - do they add value? Curr. Opin. Chem. Biol., 2005, 9, 1-7.
20. Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci., 2003, 43, 391-405.
21. Jacoby, E.; Davies, J.; Blommers, M. J. J. Design of small molecule libraries for NMR screening and other applications in drug discovery. Curr. Top. Med. Chem., 2003, 3, 11-23.
22. Hajduk, P. J.; Olejniczak, E. T.; Fesik, S. W. One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J. Am. Chem. Soc., 1997, 119, 12257-12261.
23. Dalvit, C.; Fogliatto, G.; Stewart, A.; Veronesi, M.; Stockman, B. WaterLOGSY as a method for primary NMR screening: practical aspects and range of applicability. J Biomol. NMR, 2001, 21, 349-359.
24. Boehm, H. J.; Boehringer, M.; Bur, D.; Gmuender, H.; Huber, W.; Klaus, W.; Kostrewa, D.; Kuehne, H.; Luebbers, T.; Meunier-Keller N.; Mueller, M. Novel inhibitors of DNA-gyrase: 3D structure based needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem., 2000, 43, 2664-2674.
25. Liu, G.; Huth J. R.; Olejnaniczak, E. T.; Mendoza, R.; DeVries, P.; Leitza, S.; Reilly, E. B.; Okasinski, G. F.; Fesik, S. W.; von Geldern, T. W. Novel p-arylthio cinnamides as antagonists of leukocyte function-associated antigen-1/intracellular adehion molecules-1 interaction. 2. mechanism of inhibition and structure based improvement of pharmaceutical properties. J. Med. Chem., 2001, 44, 1201-1210.
26. Hajduk, P. J.; Sheppard, G; Nettesheim D. G.; Olejniczak, E. T.; Shuker, S. B.; Meadows, R. P.; Steinman, D. H.; Caffera G. M.; Marcotte, P. A.; Severin, J.; Walter, K.; Smith, H.; Gubbins, E.; Simmer, R.; Holzman, T. F.; Morgan, D. W.; Davidsen, S. K.; Summers, J. B.; Fesik, S. W. Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J. Am. Chem. Soc., 1997, 119, 5818-5827.
27. Liu, G.; Xin, Z.; Liang, H.; Abad-Zapatero, C.; Hajduk, P. J.; Janowick, D. A.; Szczepankiewicz, B. G.; Pei. Z.; Hutchins, C. W.; Ballaron, S. J.; Stashko, M. A.; Lubben, T. H.; Berg, C. E.; Rondinone, C. M.; Trevillyan, J. M.; Jirousek, M. R. Selective protein tyrosine phosphatase 1B inhibitors: targeting the second phoshotyrosine binding site with non-carbocylic acid-containing ligands. J. Med. Chem., 2003, 46, 3437-3440.
28. Hajduk, P. J.; Dinges, J.; Schkeryantz, J. M.; Janowick, D.; Kaminski, M.; Tufano, M.; Augeri, D. J.; Petros, A.; Nienaber, V.; Zhong, P.; Hammond, R.; Coen, M.; Beutel, B.; Katz, L.; Fesik, S. W. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J. Med. Chem., 1999, 42, 3852-3859.
29. Hajduk, P. J.; Dinges, J.; Miknis, G. F.; Merlock, M.; Middleton, T.; Kempf, D. J.; Egan, D. A.; Walter, K. A.; Robins, T. S.; Shuker, S. B.; Holzman, T. F.; Fesik, S. W. NMR-based discovery of lead inhibitors that block DNA binding in the human papillomavirus E2 protein. J. Med. Chem., 1997, 40, 3144-3150.
30. Szezepankiewicz, B. G.; Liu, G.; Hajduk, P. J.; Abad-Zapatero, C.; Pei, Z.; Xin, Z.; Lubben, T. H.; Trevillyan, J. M.; Stashko, M. A.; Ballaron, S. J.; Liang, H.; Huang, F.; Hutchins, C. W.; Fesik, S. W.; Jirousek, M. R. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a fragment linking strategy. J. Am. Chem. Soc., 2003, 125, 4087-4096.
31. Murray, C. W.; Verdonk, M. L. The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J. Comput. -Aid. Mol. Design., 2002, 16, 741-753.
32. Rees, D. C.; Congreve, M.; Murray C. W.; Carr, R. Fragment based lead discovery. Nature Rev. Drug. Disc., 2004, 3, 550-672.
33. Erlanson, D. A.; McDowell, R. S.; O'Brien, T. Fragment-based drug discovery. J. Med. Chem., 2004, 47, 3463-3482.
34. Baurin. N.; Aboul-Ela, F.; Barril, X.; Davis, B.; Drysdale, M. Dymock, B.; Finch, H.; Fromont, C.; Richardson, C.; Simmonite, H.; Hubbard, R. E. Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. J. Chem. Inf. Comput. Sci., 2004, 44, 2157-2166.
35. Lepre, C. A. Strategies for NMR screening and library design. In BioNMR in Drug Research Zerbe, Oliver Ed., Vol 16 of series Methods and Principles in Medicinal Chemistry Wiley-VCH, Weinheim, 2003; pp. 391-415.
36. Congreve, M.; Carr R.; Murray, C.; Jhoti, H. A 'rule of three' for fragment base discovery. Drug Disc. Today, 2003, 8, 876-877.
37. Lipinski, C. A.; Lomabrdo, F.; Dominy, B. W.; Feeny, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev., 1997, 23, 3-35.
38. Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks. J. Med. Chem., 1996, 39, 1887-1893.
39. Jahnke, W.; Flörsheimer, A.; Blommers, M. J.; Paris C. G.; Heim, J.; Nalin, C. M.; Perez, L.B. Second-site NMR screening and linker design. Curr. Top. Med. Chem., 2003, 3, 69-80.
40. Vangrevelinghe, E.; Ruedisser, S. manuscript in preparation.
41. Wang, X.; Choe, Y.; Craik, C. S.; Ellman J. A. Design and synthesis of novel Inhibitors of gelatinase b. Bioorg. Med. Chem. Lett., 2002, 12, 2201-2204.
42. Lewis, W.G.; Green, L.G.; Grynszpan, F.; Radic, Z.; Carlier, P. R.; Taylor. P.; Finn, M. G.; Sharpless, K. B. Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks. Angew. Chem. Int. Ed. Engl., 2002, 41, 1053-1057.
43. Maly, D. J.; Choong, I. C.; Ellman, J. A. Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src inhibitors. Proc. Natl. Acad. Sci., 2000, 97, 2419-2424.
44. Rishton, G. M. Nonleadlikeness and leadlikeness in biochemical screening. Drug Discov. Today, 2003, 8, 86-96.
45. Huth, J. R.; Mendoza, R.; Olejniczak, E. T.; Johnson, R. W.; Cothron, D. A.; Liu, Y.; Lerner, C. G.; Chen, J.; Hajduk, P. J. ALARM NMR: A rapid and robust experimental methods to detect reactive false positives in biochemical screens. J. Am. Chem. Soc., 2005, 127, 217-224.
46. Andrews, K. M.; Cramer R. D. Toward general methods of targeted library design: Topomer shape similarity searching with diverse structures as queries. J. Med. Chem., 2000, 43, 1723-1740.
47. Ghose, A.K.; Viswanadhan, V.N.; Wendolowski, J.J. Prediction of hydrophobic (Lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods. J. Phys. Chem., 1998, 102, 3762-3772.
48. Hajduk, P. J.; Huth, J. R.; Fesik, S. W. Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem., 2005, 48, 2518-2525.
49. Schuffenhauer, A.; Popov, M.; Schopfer, U.; Acklin, P.; Stanek, J.; Jacoby, E. Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections. Comb. Chem. High Throughput Screen., 2004, 7, 771-781.
50. Liebschuetz, J. W.; Jones, S. D.; Morgan, P. D.; Murray, C. W.; Rimmer, A. D.; Roscoe, J. M. E.; Waszkowskowycz, B.; Welsh, P. M.. Wylie, W. A.; Young, S. C.; Martin, H.; Mahler, J.; Brady, L.; Wilkinson, K. PRO_SELECT: Combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors. J. Med. Chem., 2002, 45, 1221-1232.
51. Lewell, X.Q.; Judd, D.; Watson, S.; Hann, M. RECAP-retrosynthetic combinatorial analysis procedure: A powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci., 1998, 38, 511-522.
52. Hajduk, P. J.; Gomtsyan, A.; Didomenico S.; Cowart, M.; Bayburt, E. K.; Solomon, L.; Severin, J.; Smith, R.; Walter, K.; Holzman, T. F.; Stewart, A.; McGaraughty, S.; Jarvis, M. F.; Kowaluk, E. A.; Fesik, S. W. Design of adenosine kinase inhibitors from NMW-based screening of fragments. J. Med Chem., 2000, 43, 4781-4786.