Novel kinase inhibitors by reshuffling ligand functionalities across the human kinome

Journal of Chemical Information and Modeling

Volumn 52, Issue 12, 2012, Pages 3107-3115

  Vidović, Dušica ^a   Muskal, Steven M ^b   Schürer, Stephan C ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^b Eidogen Sertanty Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; ENZYME INHIBITION; KNOWLEDGE MANAGEMENT; LEAD COMPOUNDS;

CLINICAL DEVELOPMENT; COMPETITIVE BINDING; INTEGRATED WORKFLOW; KINASE INHIBITORS; MEDICINAL CHEMISTRY; RETROSPECTIVE ANALYSIS; STRUCTURAL SIMILARITY; THERAPEUTIC DRUGS;

LIGANDS;

ADENOSINE TRIPHOSPHATE; LIGAND; PROTEIN KINASE; PROTEIN KINASE INHIBITOR; PROTEOME;

ARTICLE; CHEMISTRY; DRUG ANTAGONISM; DRUG DESIGN; ENZYME SPECIFICITY; HUMAN; HUMAN GENOME; METABOLISM; MOLECULAR DOCKING; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ADENOSINE TRIPHOSPHATE; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; GENOME, HUMAN; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEOME; SUBSTRATE SPECIFICITY;

EID: 84871565042     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci3003842     Document Type: Article

References (38)

1. Cohen, P. Protein kinases-the major drug targets of the twenty-first century? Nat. Rev. Drug. Discov. 2002, 1, 309-315
2. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome Science 2002, 298, 1912-1934
3. Zhang, J.; Yang, P. L.; Gray, N. S. Targeting cancer with small molecule kinase inhibitors Nat. Rev. Cancer 2009, 9, 28-39
4. Fedorov, O.; Muller, S.; Knapp, S. The (un)targeted cancer kinome Nat. Chem. Biol. 2010, 6, 166-169
5. Lenihan, D. J. Tyrosine kinase inhibitors: can promising new therapy associated with cardiac toxicity strengthen the concept of teamwork? J. Clinical Oncol. 2008, 26, 5154-5
6. Joensuu, H.; Trent, J. C.; Reichardt, P. Practical management of tyrosine kinase inhibitor-associated side effects in GIST Cancer Treatment Reviews 2011, 37, 75-88
7. Zuccotto, F.; Ardini, E.; Casale, E.; Angiolini, M. Through the "gatekeeper door": exploiting the active kinase conformation J. Med. Chem. 2010, 53, 2681-2694
8. Liu, Y.; Gray, N. S. Rational design of inhibitors that bind to inactive kinase conformations Nat. Chem. Biol. 2006, 2, 358-364
9. Anastassiadis, T.; Deacon, S. W.; Devarajan, K.; Ma, H.; Peterson, J. R. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity Nat. Biotechnol. 2011, 29, 1039-1045
10. Davis, M. I.; Hunt, J. P.; Herrgard, S.; Ciceri, P.; Wodicka, L. M.; Pallares, G.; Hocker, M.; Treiber, D. K.; Zarrinkar, P. P. Comprehensive analysis of kinase inhibitor selectivity Nat. Biotechnol. 2011, 29, 1046-1051
11. Goldstein, D. M.; Gray, N. S.; Zarrinkar, P. P. High-throughput kinase profiling as a platform for drug discovery Nat. Rev. Drug. Discov. 2008, 7, 391-397
12. Karaman, M. W.; Herrgard, S.; Treiber, D. K.; Gallant, P.; Atteridge, C. E.; Campbell, B. T.; Chan, K. W.; Ciceri, P.; Davis, M. I.; Edeen, P. T.; Faraoni, R.; Floyd, M.; Hunt, J. P.; Lockhart, D. J.; Milanov, Z. V.; Morrison, M. J.; Pallares, G.; Patel, H. K.; Pritchard, S.; Wodicka, L. M.; Zarrinkar, P. P. A quantitative analysis of kinase inhibitor selectivity Nat. Biotechnol. 2008, 26, 127-132
13. Knight, Z. A.; Lin, H.; Shokat, K. M. Targeting the cancer kinome through polypharmacology Nat. Rev. Cancer 2010, 10, 130-137
14. Vidović, D.; Schürer, S. C. Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design J. Med. Chem. 2009, 52, 6649-59
15. Akritopoulou-Zanze, I.; Hajduk, P. J. Kinase-targeted libraries: the design and synthesis of novel, potent, and selective kinase inhibitors Drug Discov. Today 2009, 14, 291-297
16. 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
17. 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
18. Leach, A. R.; Hann, M. M. Molecular complexity and fragment-based drug discovery: ten years on Current Opin. Chem. Biol. 2011, 15, 489-96
19. Hoffer, L.; Renaud, J.-P.; Horvath, D. Fragment-Based Drug Design: Computational and Experimental State of the Art Comb. Chem. High Throughput Screening 2011, 14, 500-20
20. Vieth, M.; Erickson, J.; Wang, J.; Webster, Y.; Mader, M.; Higgs, R.; Watson, I. Kinase inhibitor data modeling and de novo inhibitor design with fragment approaches J. Med. Chem. 2009, 52, 6456-6466
21. 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, 2768-75
22. Target Informatics Platform (TIP); Eidogen-Sertanty, Inc. http://www.eidogen-sertanty.com/tip.php.
23. Altschup, S. F.; Gish, W.; Pennsylvania, T.; Park, U. Basic Local Alignment Search Tool 2Department of Computer Science J. Mol. Biol. 1990, 215, 403-410
24. Aronov, A. M.; McClain, B.; Moody, C. S.; Murcko, M. A. Kinase-likeness and kinase-privileged fragments: toward virtual polypharmacology J. Med. Chem. 2008, 51, 1214-1222
25. Schmitt, S.; Kuhn, D.; Klebe, G. A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology J. Mol. Biol. 2002, 323, 387-406
26. Eidogen Visualization Environment (EVE); Eidogen-Sertanty, Inc. http://www.eidogen-sertanty.com/eve.php.
27. Accelrys Pipeline Pilot 8.0; Accelrys, San Diego, CA; 2010.
28. ChemAxon JChem Software Suite; ChemAxon, Budapest, HU; 2011.
29. Open Eye Filter; OpenEye Scientific Software, Inc., Santa Fe, NM, 2011; http://www.eyesopen.com/filter.
30. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks J. Med. Chem. 1996, 39, 2887-2893
31. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
32. Flower, D. On the properties of bit string-based measures of chemical similarity J. Chem. Inf. Comp. Sci. 1998, 38, 379-386
33. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical similarity searching J. Chem. Inf. Comp. Sci. 1998, 38, 983-996
34. Kinase Knowledge Base (Q4 2009); Eidogen-Sertanty Inc., Oceanside, CA, USA, 2009.
35. LigPrep; Schrodinger LLC, Portland, OR, USA, 2011.
36. Glide; Schrodinger LLC, Portland, OR, USA, 2011.
37. Ligand Expo 2011. http://ligand-expo.rcsb.org/.
38. Tuccinardi, T.; Botta, M.; Giordano, A.; Martinelli, A. Protein Kinases: Docking and Homology Modeling Reliability J. Chem. Inf. Model. 2010, 50, 1432-1441