On sampling of fragment space

Journal of Medicinal Chemistry

Volumn 50, Issue 14, 2007, Pages 3214-3221

  Makara, Gergely M ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; DIPEPTIDYL PEPTIDASE IV INHIBITOR; INTEGRASE INHIBITOR; METABOTROPIC RECEPTOR 5; SULFONAMIDE; TETRAZOLE DERIVATIVE;

ARTICLE; DATA BASE; HIGH THROUGHPUT SCREENING; LIBRARY; PHARMACOPHORE; TECHNIQUE;

AMIDES; ANTIGENS, CD26; DRUG DESIGN; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; PROTEASE INHIBITORS;

EID: 34447538158     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0700316     Document Type: Article

References (31)

1. 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.
2. Congreve, M.; Carr, R.; Murray, C.; Jhoti, J. A 'Rule of Three' for Fragment-Based Lead Discovery? Drug Discovery Today 2003, 8, 876-877.
3. Hopkins, A. L.; Groom, C. R.; Alex, A. Ligand Efficiency: A Useful Metric for Lead Selection. Drug Discovery Today 2004, 9, 430-431.
4. Proudfoot, J. R. Drugs, Leads, and Drug-Likeness: An Analysis of Some Recently Launched Drugs Bioorg. Med. Chem. Lett. 2002, 12, 1647-1650.
5. Harper, G.; Pickett, S. D.; Green, D. V. S. Design of a Compound Screening Collection for Use in High Throughput Screening. Comb. Chem. High Throughput Screening 2004, 7, 63-70.
6. Hann, M. M.; Oprea, T. I. Pursuing the Leadlikeness Concept in Pharmaceutical Research. Curr. Opin. Chem. Biol. 2004, 8, 255-263.
7. Makara, G. M.; Athanasopoulos, J. Improving Success Rates for Lead Generation Using Affinity Binding Technologies. Curr. Opin. Biotechnol. 2005, 16, 666-673.
8. Carr, R. A. E.; Congreve, M.; Murray, C. W.; Rees, D. C. Fragment-Based Lead Discovery: Leads by Design. Drug Discovery Today 2005, 10, 987-992.
9. Sanders, W. J.; Nienaber, V. L.; Lerner, C. G.; McCall, J. O.; Merrick, S. M.; Swanson, S. J.; Harlan, J. E.; Stoll, V. S.; Stamper, G. F.; Betz, S. F.; Condroski, K. R.; Meadows, R. P.; Severin, J. M.; Walter, K. A.; Magdalinos, P.; Jakob, C. G.; Wagner, R.; Beutel, B. A. Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization. J. Med. Chem. 2004, 47, 1709-1718.
10. Hajduk, P.; Huth, J. R.; Fesik, S. W. Draggability Indices for Protein Targets Derived from NMR-Based Screening Data. J. Med. Chem. 2005, 48, 2518-2525.
11. Poon, S. F.; Eastman, B. W.; Chapman, D. W.; Chung, J.; Cramer, M.; Holtz, G.; Cosforda, N. D. P.; Smith, N. D. 3-[3-Fluoro-5-(5-pyridin-2-yl- 2H-tetrazol-2-yl)phenyl]-4-methylpyridine: A Highly Potent and Orally Bioavailable Metabotropic Glutamate Subtype 5 (mGlu5) Receptor Antagonist. Bioorg. Med. Chem. Lett. 2004, 14, 5477-5480.
12. Smith, N. D.; Poon, S. F.; Huang, D.; Green, M.; King, C.; Tehrani, L.; Roppe, J. R.; Chung, J.; Chapman, D. P.; Cramera, M.; Cosforda, N. D. P. Discovery of Highly Potent, Selective, Orally Bioavailable, Metabotropic Glutamate Subtype 5 (mGlu5) Receptor Antagonists Devoid of Cytochrome P450 1A2 Inhibitory Activity. Bioorg. Med. Chem. Lett. 2004, 14, 5481-5484.
13. Tondi, D.; Morandi, F.; Bonnet, R.; Costi, M. P.; Shoichet, B. K. Structure-Based Optimization of a Non-β-lactam Lead Results in Inhibitors That Do Not Up-Regulate β-Lactamase Expression in Cell Culture. J. Am. Chem. Soc. 2005, 127, 4632-4639.
14. Powers, R. A.; Morandi, F.; Shoichet, B. K. Structure-Based Discovery of a Novel, Noncovalent Inhibitor of AmpC β-Lactamase. Structure 2002, 10, 1013-1023.
15. Kim, D.; Wang, L.; Beconi, M.; Eiermann, G. J.; Fisher, M. H.; He, H.; Hickey, G. J.; Kowalchick, J. E.; Letting, B.; Lyons, K.; Marsilio, F.; McCann, M. E.; Patel, R. A.; Petrov, A.; Scapin, G.; Patel, S. B.; Roy, R. S.; Wu, J. K.; Wyvratt, M. J.; Zhang, B. B.; Zhu, L.; Thornberry, N. A.; Weber, A. E. (2R)-4-Oxo-4-[3-(Trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4, 3-a]pyrazin-7(8H)-yl]-1-(2,4,5-trifluorophenyl)butan-2-amine: A Potent, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes. J. Med. Chem. 2005; 48, 141-151.
16. Jensen, B. F.; Vind, C.; B. S.; Padkjaer, S. B.; Brockhoff, P. B.; Refsgaard, H. H. F. In Silico Prediction of Cytochrome P450 2D6 and 3A4 Inhibition Using Gaussian Kernel Weighted k-Nearest Neighbor and Extended Connectivity Fingerprints, Including Structural Fragment Analysis of Inhibitors versus Noninhibitors. J. Med. Chem. 2007, 50, 501-511.
17. Godden, J. W.; Stahura, F. L.; Bajorath, J. Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds. J. Chem. Inf. Model. 2005, 45, 1812-1819.
18. Makara, G. M. Measuring Molecular Similarity and Diversity: Total Pharmacophore Diversity. J. Med. Chem. 2001, 44, 3563-3571.
19. Jain, A. N. Morphological Similarity: A 3D Molecular Similarity Method Correlated with Protein-Ligand Recognition. J. Comput.-Aided Mol. Design 2000, 14, 199-213.
20. Wiedeman, P. E.; Trevillyan, J. M. Dipeptidyl Peptidase IV Inhibitors for Type 2 Diabetes and Metabolic Syndrome. Drug Discovery Today: Ther. Strategies 2005, 2, 143-149.
21. Peters, J.; Weber, S.; Kritter, S.; Weiss, P.; Wallier, M. B.; Hennig, M.; Kuhn, B.; Loeffler, B.-M. Aminomethylpyrimidines as Novel DPP-IV Inhibitors: A 105-fold Activity Increase by Optimization of Aromatic Substituents. Bioorg. Med. Chem Lett. 2004, 14, 1491-1493.
22. Nordhoff, S.; Cerezo-Galvez, S.; Feurer, A.; Hill, O.; Matassa, V. G.; Metz, G.; Rummey, C.; Thiemann, M.; Edwards, P. J. The Reversed Binding of β-Phenethylamine Inhibitors of DPP-IV: X-ray Structures and Properties of Novel Fragment and Elaborated Inhibitors. Tetrahedron Lett. 2006, 16, 1744-1748.
23. Ward, R. A.; Perkins, T. D. J.; Stafford, J. Structure-Based Virtual Screening for Low Molecular Weight Chemical Starting Points for Dipeptidyl Peptidase IV Inhibitors. J. Med. Chem. 2005, 48, 6991-6996.
24. Xu, J.; Ok, H. O.; Gonzalez, E. J.; Colwell, L. F.; Habulihaz, B.; He, H.; Leiting, B.; Lyons, K. A.; Marsilio, F.; Patel, R. A.; Wu, J. K.; Thornberry, N. A.; Weber, A. E.; Parmee, E. R. Discovery of Potent and Selective β-Homophenylalanine Based Dipeptidyl Peptidase Inhibitors. Bioorg. Med. Chem Lett. 2004, 14, 4759-4762.
25. McClure, K. F.; Abramov, Y. A.; Laird, E. R.; Barberia, J. T.; Cai, W.; Carty, T. J.; Cortina, S. R.; Danley, D. E.; Dipesa, A. J.; Donahue, K. M.; Dombroski, M. A.; Elliott, N. C.; Gabel, C. A.; Han, S.; Hynes, T. R.; LeMotte, P. K.; Mansour, M. N.; Marr, E. S.; Letavic, M. A.; Pandit, J.; Ripin, D. B.; Sweeney, F. J.; Tan, D.; Tao, Y. Theoretical and Experimental Design of Atypical Kinase Inhibitors: Application to p38 MAP Kinase. J. Med. Chem. 2005, 48, 5728-5737.
26. Hajduk, P. H. Fragment-based Drug Design: How Big Is Too Big? J. Med. Chem. 2006, 49, 6972-6976.
27. Babaoglu, K.; Shoichet, B. K. Deconstructing Fragment-Based Inhibitor Discovery. Nature Chem. Biol. 2006, 2, 720-723.
28. Hajduk, P. H. Puzzling through Fragment-Based Drug Design. Nature Chem. Biol. 2006, 2, 658-659.
29. Olson, S.; Aster, S. D.; Brown, K.; Carbin, L.; Graham, D. W.; Hermanowski-Vosatka, A.; LeGrand, C. B.; Mundt, S. S.; Robbins, M. A.; Schaeffer, J. M.; Slossberg, L. H.; Szymonifka, M. J.; Thieringer, R.; Wright, S. D.; Balkovec, J. M. Adamantyl Triazoles as Selective Inhibitors of 11β-Hydroxysteroid Dehydrogenase Type 1. Bioorg. Med. Chem. Lett. 2005, 15, 4357-4362.
30. Omodei-Sale, A.; Consonni, P.; Galliani, G. A New Class of Nonhormonal Pregnancy-Terminating Agents. Synthesis and Contragestational Activity of 3,5-Diaryl-s-triazoles. J. Med. Chem. 1983, 26, 1187-1192.
31. Tetko, I. V.; Tanchuk, V. Y.; Kasheva, T. N.; Villa, A. E. P. Estimation of Aqueous Solubility of Chemical Compounds Using E-State Indices. J. Chem. Inf. Comput. Sci. 2001, 41, 1488-1493.