MORPH: A new tool for ligand design

Journal of Chemical Information and Modeling

Volumn 50, Issue 6, 2010, Pages 1159-1164

  Beno, Brett R ^a   Langley, David R ^a  

^a BRISTOL MYERS SQUIBB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; AROMATIZATION; DRUG PRODUCTS; HYDROGEN BONDS; LIGANDS;

AROMATIC MOIETIES; COCRYSTAL STRUCTURE; CYCLIN-DEPENDENT KINASE; FUSED-RING SYSTEM; HYDROGEN BOND DONORS; NON-HYDROGEN ATOMS; THREE-DIMENSIONAL MODEL; TOXICITY PROPERTIES;

AROMATIC COMPOUNDS;

3 AMINOPYRAZOLE; 3-AMINOPYRAZOLE; CYCLIN A; CYCLIN DEPENDENT KINASE 2; LIGAND; PROTEIN KINASE INHIBITOR; PYRAZOLE DERIVATIVE; PYRIMIDINE DERIVATIVE;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; DRUG ANTAGONISM; DRUG DESIGN; METABOLISM; PROTEIN CONFORMATION;

ALGORITHMS; CYCLIN A; CYCLIN-DEPENDENT KINASE 2; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN KINASE INHIBITORS; PYRAZOLES; PYRIMIDINES; SOFTWARE;

EID: 77954044426     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9004964     Document Type: Article

References (28)

1. Chu, G.-H.; Saeui, C. T.; Worm, K.; Weaver, D. G.; Goodman, A. J.; Broadrup, R. L.; Cassel, J. A.; DeHaven, R. N.; La Buda, C. J.; Koblish, M.; Brogdon, B.; Smith, S.; Le Bourdonnec, B.; Dolle, R. E. Novel pyridine derivatives as potent and selective CB2 cannabinoid receptor agonists Bioorg. Med. Chem. Lett. 2009, 19, 5931-5935
2. Vasiliou, S.; Castaner, R.; Bolos, J. SNS-032-Cyclin-dependent kinase inhibitor oncolytic Drugs Future 2008, 33, 932-937
3. Pevarello, P.; Brasca, M. G.; Amici, R.; Orsini, P.; Traquandi, G.; Corti, L.; Piutti, C.; Sansonna, P.; Villa, M.; Pierce, B. S.; Pulici, M.; Giordano, P.; Martina, K.; Fritzen, E. L.; Nugent, R. A.; Casale, E.; Cameron, A.; Ciomei, M.; Roletto, F.; Isacchi, A.; Fogliatto, G.; Pesenti, E.; Pastori, W.; Marsiglio, A.; Leach, K. L.; Clare, P. M.; Fiorentini, F.; Varasi, M.; Vulpetti, A.; Warpehoski, M. A. 3-Aminopyrazole Inhibitors of CDK2/Cyclin A as Antitumor Agents. 1. Lead Finding J. Med. Chem. 2004, 47, 3367-3380
4. Pevarello, P.; Brasca, M. G.; Orsini, P.; Traquandi, G.; Longo, A.; Nesi, M.; Orzi, F.; Piutti, C.; Sansonna, P.; Varasi, M.; Cameron, A.; Vulpetti, A.; Roletto, F.; Alzani, R.; Ciomei, M.; Albanese, C.; Pastori, W.; Marsiglio, A.; Pesenti, E.; Fiorentini, F.; Bischoff, J. R.; Mercurio, C. 3-Aminopyrazole Inhibitors of CDK2/Cyclin A as Antitumor Agents. 2. Lead Optimization J. Med. Chem. 2005, 48, 2944-2956
5. Traxler, P.; Furet, P. Strategies toward the design of novel and selective protein tyrosine kinase inhibitors Pharmacol. Ther. 1999, 82, 195-206
6. Hamdouchi, C.; Zhong, B.; Mendoza, J.; Collins, E.; Jaramillo, C.; De Diego, J. E.; Robertson, D.; Spencer, C. D.; Anderson, B. D.; Watkins, S. A.; Zhang, F.; Brooks, H. B. Structure-based design of a new class of highly selective aminoimidazo[1,2-a]pyridine-based inhibitors of cyclin dependent kinases Bioorg. Med. Chem. Lett. 2005, 15, 1943-1947
7. Mjalli, A. M. M.; Grella, B. S.; Subramanian, G.; Arimilli, M. N.; Gopalaswamy, R.; Andrews, R. C.; Davis, S.; Guo, X.; Zhu, J. Preparation of benzazole derivatives as Aurora kinase inhibitors. PCT Int. Appl.; WO 07/095124, 2007.
8. Mauser, H.; Guba, W. Recent developments in de novo design and scaffold hopping Curr. Opin. Drug Discovery Dev. 2008, 11, 365-374
9. SYBYL-X, version 1.1; Tripos: St. Louis, MO, 2007; http://www.tripos.com/ index.php?family=modulesSimplePage,&page=comp-informatics. Accessed April 21, 2010.
10. Maestro, version 9.0; Schrödinger, LLC: New York, NY, 2009; http://www.schrodinger.com/products/14/12/. Accessed April 21, 2010.
11. Discovery Studio, version 2.5; Accelrys, Inc.: San Diego, CA, 2009; http://accelrys.com/products/discovery-studio/. Accessed April 21, 2010.
12. Maass, P.; Schulz-Gasch, T.; Stahl, M.; Rarey, M. Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations J. Chem. Inf. Model. 2007, 47, 390-399
13. Fontaine, F.; Cross, S.; Plasencia, G.; Pastor, M.; Zamora, I. SHOP a method for structure-based fragment and scaffold hopping ChemMedChem 2009, 4, 427-439
14. Bergmann, R.; Liljefors, T.; Sorensen, M. D.; Zamora, I. SHOP Receptor-Based Scaffold HOPping by GRID-Based Similarity Searches J. Chem. Inf. Model. 2009, 49, 658-669
15. Bergmann, R.; Linusson, A.; Zamora, I. SHOP Scaffold HOPping by GRID-Based Similarity Searches J. Med. Chem. 2007, 50, 2708-2717
16. Pierce, A. C.; Rao, G.; Bemis, G. W. BREED: Generating Novel Inhibitors through Hybridization of Known Ligands. Application to CDK2, P38, and HIV Protease J. Med. Chem. 2004, 47, 2768-2775
17. Python Programming Language; Python Software Foundation: Wolfeboro Falls, NH; http://www.python.org/. Accessed April 21, 2010.
18. OEChem, version 1.6.1; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2009; http://www.eyesopen.com/products/toolkits/oechem.html. Accessed April 21, 2010.
19. Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D. L.; Leland, B. A.; Laufer, J. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited J. Chem. Inf. Comput. Sci. 1992, 32, 244-55
20. Carroll, F. A. Perspectives on Structure and Mechanism in Organic Chemistry; Brooks/Cole Publishing Company: Pacific Grove, CA, 1998; pp 206 - 208.
21. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-42
22. Maestro, version 8.5; Schrödinger, LLC: New York, NY, 2009; http://www.schrodinger.com/products/14/12/. Accessed April 21, 2010.
23. Kim, K. S.; Kimball, S. D.; Misra, R. N.; Rawlins, D. B.; Hunt, J. T.; Xiao, H.-Y.; Lu, S.; Qian, L.; Han, W.-C.; Shan, W.; Mitt, T.; Cai, Z.-W.; Poss, M. A.; Zhu, H.; Sack, J. S.; Tokarski, J. S.; Chang, C. Y.; Pavletich, N.; Kamath, A.; Humphreys, W. G.; Marathe, P.; Bursuker, I.; Kellar, O. K. A.; Roongta, U.; Batorsky, R.; Mulheron, J. G.; Bol, D.; Fairchild, C. R.; Lee, F. Y.; Webster, K. R. Discovery of Aminothiazole Inhibitors of Cyclin-Dependent Kinase 2: Synthesis, X-ray Crystallographic Analysis, and Biological Activities J. Med. Chem. 2002, 45, 3905-3927
24. SciFinder, version 2007; Chemical Abstracts Service: Columbus, OH, 2007; http://www.cas.org/products/scifindr/index.html. Accessed April 21, 2010.
25. Richardson, C. M.; Williamson, D. S.; Parratt, M. J.; Borgognoni, J.; Cansfield, A. D.; Dokurno, P.; Francis, G. L.; Howes, R.; Moore, J. D.; Murray, J. B.; Robertson, A.; Surgenor, A. E.; Torrance, C. J. Triazolo[1,5-a] pyrimidines as novel CDK2 inhibitors: Protein structure-guided design and SAR Bioorg. Med. Chem. Lett. 2006, 16, 1353-1357
26. Williamson, D. S.; Parratt, M. J.; Bower, J. F.; Moore, J. D.; Richardson, C. M.; Dokurno, P.; Cansfield, A. D.; Francis, G. L.; Hebdon, R. J.; Howes, R.; Jackson, P. S.; Lockie, A. M.; Murray, J. B.; Nunns, C. L.; Powles, J.; Robertson, A.; Surgenor, A. E.; Torrance, C. J. Structure-guided design of pyrazolo[1,5-a]pyrimidines as inhibitors of human cyclin-dependent kinase 2 Bioorg. Med. Chem. Lett. 2005, 15, 863-867
27. Fischmann, T. O.; Hruza, A.; Duca, J. S.; Ramanathan, L.; Mayhood, T.; Windsor, W. T.; Le, H. V.; Guzi, T. J.; Dwyer, M. P.; Paruch, K.; Doll, R. J.; Lees, E.; Parry, D.; Seghezzi, W.; Madison, V. Structure-guided discovery of cyclin-dependent kinase inhibitors Biopolymers 2008, 89, 372-379
28. Ghose, A. K.; Herbertz, T.; Pippin, D. A.; Salvino, J. M.; Mallamo, J. P. Knowledge Based Prediction of Ligand Binding Modes and Rational Inhibitor Design for Kinase Drug Discovery J. Med. Chem. 2008, 51, 5149-5171