Discovery of N6-phenyl-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine derivatives as novel CK1 inhibitors using common-feature pharmacophore model based virtual screening and hit-to-lead optimization

European Journal of Medicinal Chemistry

Volumn 56, Issue , 2012, Pages 30-38

  Yang, Ling Ling ^a,b   Li, Guo Bo ^a   Yan, Heng Xiu ^a   Sun, Qi Zheng ^a   Ma, Shuang ^a   Ji, Pan ^a   Wang, Ze Rong ^a   Feng, Shan ^a   Zou, Jun ^a   Yang, Sheng Yong ^a  

^a SICHUAN UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

Cancer; Casein kinase 1; Central nervous system disorders; Lead optimization; Pharmacophore; Virtual screening

Indexed keywords

1 [3 (3 AMINO 1H PYRAZOLO[3,4 D]PYRIMIDIN 6 YLAMINO)PHENYL] 3 (3 CHLORO 4 FLUOROPHENYL)UREA; CASEIN KINASE 1 INHIBITOR; CASEIN KINASE I; DIAMINE DERIVATIVE; N6 (4 CHLOROPHENYL) 1H PYRAZOLO[3,4 D]PYRIMIDINE 3,6 DIAMINE; N6 PHENYL 1H PYRAZOLO[3,4 D]PYRIMIDINE 3,6 DIAMINE; PYRAZOLE DERIVATIVE; PYRIMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; DRUG POTENCY; DRUG SCREENING; DRUG SELECTIVITY; DRUG SYNTHESIS; ENZYME INHIBITION; IC 50; MOLECULAR DOCKING; PHARMACOPHORE; VIRTUAL REALITY;

CASEIN KINASE I; DIAMINES; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN KINASE INHIBITORS; PYRIMIDINES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84865553393     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.08.007     Document Type: Article

References (35)

1. U. Knippschild, A. Gocht, S. Wolff, N. Huber, J. Lohler, and M. Stoter The casein kinase 1 family: participation in multiple cellular processes in eukaryotes Cell. Signal. 17 2005 675 689
2. O. Marin, V.H. Bustos, L. Cesaro, F. Meggio, M.A. Pagano, M. Antonelli, C.C. Allende, L.A. Pinna, and J.E. Allende A noncanonical sequence phosphorylated by casein kinase 1 in beta-catenin may play a role in casein kinase 1 targeting of important signaling proteins Proc. Natl. Acad. Sci. U. S. A. 100 2003 10193 10200
3. J.K. Cheong, and D.M. Virshup Casein kinase 1: complexity in the family Int. J. Biochem. Cell. Biol. 43 2011 465 469
4. D.P. Hanger, H.L. Byers, S. Wray, K.Y. Leung, M.J. Saxton, A. Seereeram, C.H. Reynolds, M.A. Ward, and B.H. Anderton Novel phosphorylation sites in tau from Alzheimer brain support a role for casein kinase 1 in disease pathogenesis J. Biol. Chem. 282 2007 23645 23654
5. D.I. Perez, C. Gil, and A. Martinez Protein kinases CK1 and CK2 as new targets for neurodegenerative diseases Med. Res. Rev. 31 2011 924 954
6. N.P. Shanware, J.A. Hutchinson, S.H. Kim, L. Zhan, M.J. Bowler, and R.S. Tibbetts Casein kinase 1-dependent phosphorylation of familial advanced sleep phase syndrome-associated residues controls PERIOD 2 stability J. Biol. Chem. 286 2011 12766 12774
7. S. Luz, P. Kongsuphol, A.I. Mendes, F. Romeiras, M. Sousa, R. Schreiber, P. Matos, P. Jordan, A. Mehta, M.D. Amaral, K. Kunzelmann, and C.M. Farinha Contribution of casein kinase 2 and spleen tyrosine kinase to CFTR trafficking and protein kinase A-induced activity Mol. Cell. Biol. 31 2011 4392 4404
8. U. Knippschild, S. Wolff, G. Giamas, C. Brockschmidt, M. Wittau, P.U. Wurl, T. Eismann, and M. Stoter The role of the casein kinase 1 (CK1) family in different signaling pathways linked to cancer development Onkologie 28 2005 508 514
9. P. Gribbon, and A. Sewing Fluorescence readouts in HTS: no gain without pain? Drug Discov. Today 8 2003 1035 1043
10. D.B. Kitchen, H. Decornez, J.R. Furr, and J. Bajorath Docking and scoring in virtual screening for drug discovery: methods and applications Nat. Rev. Drug Discov. 3 2004 935 949
11. P.D. Lyne Structure-based virtual screening: an overview Drug Discov. Today 7 2002 1047 1055
12. G. Klebe Virtual ligand screening: strategies, perspectives and limitations Drug Discov. Today 11 2006 580 594
13. H. Eckert, and J. Bajorath Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches Drug Discov. Today 12 2007 225 233
14. P. Gedeck, and R.A. Lewis Exploiting QSAR models in lead optimization Curr. Opin. Drug Discov. Dev. 11 2008 569 575
15. N. Brown, and R.A. Lewis Exploiting QSAR methods in lead optimization Curr. Opin. Drug Discov. Dev. 9 2006 419 424
16. P.R. Murumkar, V.P. Zambre, and M.R. Yadav Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors J. Comput. Aided. Mol. Des. 24 2010 143 156
17. S.Y. Yang Pharmacophore modeling and applications in drug discovery: challenges and recent advances Drug Discov. Today 15 2010 444 450
18. G.B. Li, L.L. Yang, S. Feng, J.P. Zhou, Q. Huang, H.Z. Xie, L.L. Li, and S.Y. Yang Discovery of novel mGluR1 antagonists: a multistep virtual screening approach based on an SVM model and a pharmacophore hypothesis significantly increases the hit rate and enrichment factor Bioorg. Med. Chem. Lett. 21 2011 1736 1740
19. S. Thangapandian, S. John, S. Sakkiah, and K.W. Lee Potential virtual lead identification in the discovery of renin inhibitors: application of ligand and structure-based pharmacophore modeling approaches Eur. J. Med. Chem. 46 2011 2469 2476
20. P. Purushottamachar, J.B. Patel, L.K. Gediya, O.O. Clement, and V.C. Njar First chemical feature-based pharmacophore modeling of potent retinoidal retinoic acid metabolism blocking agents (RAMBAs): identification of novel RAMBA scaffolds Eur. J. Med. Chem. 47 2012 412 423
21. J. Zou, H.Z. Xie, S.Y. Yang, J.J. Chen, J.X. Ren, and Y.Q. Wei Towards more accurate pharmacophore modeling: multicomplex-based comprehensive pharmacophore map and most-frequent-feature pharmacophore model of CDK2 J. Mol. Graph. Model. 27 2008 430 438
22. R.M. Xu, G. Carmel, J. Kuret, and X. Cheng Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors Proc. Natl. Acad. Sci. U. S. A. 93 1996 6308 6313
23. N. Mashhoon, A.J. DeMaggio, V. Tereshko, S.C. Bergmeier, M. Egli, M.F. Hoekstra, and J. Kuret Crystal structure of a conformation-selective casein kinase-1 inhibitor J. Biol. Chem. 275 2000 20052 20060
24. F. Lovering, S. Kirincich, W. Wang, K. Combs, L. Resnick, J.E. Sabalski, J. Butera, J. Liu, K. Parris, and J.B. Telliez Identification and SAR of squarate inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2) Bioorg. Med. Chem. 17 2009 3342 3351
25. G. Rena, J. Bain, M. Elliott, and P. Cohen D4476, a cell-permeant inhibitor of CK1, suppresses the site-specific phosphorylation and nuclear exclusion of FOXO1a EMBO Rep. 5 2004 60 65
26. N. Oumata, K. Bettayeb, Y. Ferandin, L. Demange, A. Lopez-Giral, M.L. Goddard, V. Myrianthopoulos, E. Mikros, M. Flajolet, P. Greengard, L. Meijer, and H. Galons Roscovitine-derived, dual-specificity inhibitors of cyclin-dependent kinases and casein kinases 1 J. Med. Chem. 51 2008 5229 5242
27. G.P. Sapkota, L. Cummings, F.S. Newell, C. Armstrong, J. Bain, M. Frodin, M. Grauert, M. Hoffmann, G. Schnapp, M. Steegmaier, P. Cohen, and D.R. Alessi BI-D1870 is a specific inhibitor of the p90 RSK (ribosomal S6 kinase) isoforms in vitro and in vivo Biochem. J. 401 2007 29 38
28. K.M. Walton, K. Fisher, D. Rubitski, M. Marconi, Q.J. Meng, M. Sladek, J. Adams, M. Bass, R. Chandrasekaran, T. Butler, M. Griffor, F. Rajamohan, M. Serpa, Y. Chen, M. Claffey, M. Hastings, A. Loudon, E. Maywood, J. Ohren, A. Doran, and T.T. Wager Selective inhibition of casein kinase 1 epsilon minimally alters circadian clock period J. Pharmacol. Exp. Ther. 330 2009 430 439
29. Z. Zhou, A.K. Felts, R.A. Friesner, and R.M. Levy Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets J. Chem. Inf. Model. 47 2007 1599 1608
30. N. Huang, B.K. Shoichet, and J.J. Irwin Benchmarking sets for molecular docking J. Med. Chem. 49 2006 6789 6801
31. J.J. Irwin, and B.K. Shoichet ZINC-a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182
32. Y. Liu, and N.S. Gray Rational design of inhibitors that bind to inactive kinase conformations Nat. Chem. Biol. 2 2006 358 364
33. B. Okram, A. Nagle, F.J. Adrian, C. Lee, P. Ren, X. Wang, T. Sim, Y. Xie, G. Xia, G. Spraggon, M. Warmuth, Y. Liu, and N.S. Gray A general strategy for creating "inactive-conformation" abl inhibitors Chem. Biol. 13 2006 779 786
34. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748
35. Millipore Inc. KinaseProfiler Servce http://www.millipore.com/life- sciences/flx4/ld-kinases.