Affinity Reagents that Target a Specific Inactive Form of Protein Kinases

Chemistry and Biology

Volumn 17, Issue 2, 2010, Pages 195-206

  Ranjitkar, Pratistha ^a   Brock, Amanda M ^a   Maly, Dustin J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

CELLBIO; CHEMBIO; SIGNALING

Indexed keywords

4,4 DIFLUORO 4 BORA 3A,4A DIAZA S INDACENE; 4,4-DIFLUORO-4-BORA-3A,4A-DIAZA-S-INDACENE; BORON DERIVATIVE; LIGAND; PROTEIN KINASE; PROTEIN KINASE INHIBITOR;

ARTICLE; BINDING SITE; CELL LINE; CHEMISTRY; ENZYME ACTIVE SITE; HUMAN; KINETICS; METABOLISM; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

BINDING SITES; BORON COMPOUNDS; CATALYTIC DOMAIN; CELL LINE; HUMANS; KINETICS; LIGANDS; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 77049120764     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2010.01.008     Document Type: Article

References (43)

1. Angell R.M., Angell T.D., Bamborough P., Bamford M.J., Chung C.W., Cockerill S.G., Flack S.S., Jones K.L., Laine D.I., Longstaff T., et al. Biphenyl amide p38 kinase inhibitors 4: DFG-in and DFG-out binding modes. Bioorg. Med. Chem. Lett. 18 (2008) 4433-4437
2. Choi Y., Syeda F., Walker J.R., Finerty Jr. P.J., Cuerrier D., Wojciechowski A., Liu Q., Dhe-Paganon S., and Gray N.S. Discovery and structural analysis of Eph receptor tyrosine kinase inhibitors. Bioorg. Med. Chem. Lett. 19 (2009) 4467-4470
3. Cohen P. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem. Sci. 25 (2000) 596-601
4. Cohen P. Protein kinases-the major drug targets of the twenty-first century?. Nat. Rev. Drug Discov. 1 (2002) 309-315
5. Cumming J.G., McKenzie C.L., Bowden S.G., Campbell D., Masters D.J., Breed J., and Jewsbury P.J. Novel, potent and selective anilinoquinazoline and anilinopyrimidine inhibitors of p38 MAP kinase. Bioorg. Med. Chem. Lett. 14 (2004) 5389-5394
6. Dar A.C., Lopez M.S., and Shokat K.M. Small molecule recognition of c-Src via the Imatinib-binding conformation. Chem. Biol. 15 (2008) 1015-1022
7. DiMauro E.F., Newcomb J., Nunes J.J., Bemis J.E., Boucher C., Buchanan J.L., Buckner W.H., Cee V.J., Chai L., Deak H.L., et al. Discovery of aminoquinazolines as potent, orally bioavailable inhibitors of Lck: synthesis, SAR, and in vivo anti-inflammatory activity. J. Med. Chem. 49 (2006) 5671-5686
8. Engh R.A., and Bossemeyer D. The protein kinase activity modulation sites: mechanisms for cellular regulation - targets for therapeutic intervention. Adv. Enzyme Regul. 41 (2001) 121-149
9. Fabian M.A., Biggs III W.H., Treiber D.K., Atteridge C.E., Azimioara M.D., Benedetti M.G., Carter T.A., Ciceri P., Edeen P.T., Floyd M., et al. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol. 23 (2005) 329-336
10. Fedorov O., Marsden B., Pogacic V., Rellos P., Muller S., Bullock A.N., Schwaller J., Sundstrom M., and Knapp S. A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc. Natl. Acad. Sci. USA 104 (2007) 20523-20528
11. Han S., Mistry A., Chang J.S., Cunningham D., Griffor M., Bonnette P.C., Wang H., Chrunyk B.A., Aspnes G.E., Walker D.P., et al. Structural characterization of proline-rich tyrosine kinase 2 (PYK2) reveals a unique (DFG-out) conformation and enables inhibitor design. J. Biol. Chem. 284 (2009) 13193-13201
12. Hanks S.K., and Hunter T. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J. 9 (1995) 576-596
13. Hodous B.L., Geuns-Meyer S.D., Hughes P.E., Albrecht B.K., Bellon S., Bready J., Caenepeel S., Cee V.J., Chaffee S.C., Coxon A., et al. Evolution of a highly selective and potent 2-(pyridin-2-yl)-1,3,5-triazine Tie-2 kinase inhibitor. J. Med. Chem. 50 (2007) 611-626
14. Huang W.S., Zhu X., Wang Y., Azam M., Wen D., Sundaramoorthi R., Thomas R.M., Liu S., Banda G., Lentini S.P., et al. 9-(Arenethenyl)purines as dual Src/Abl kinase inhibitors targeting the inactive conformation: design, synthesis, and biological evaluation. J. Med. Chem. 52 (2009) 4743-4756
15. Huse M., and Kuriyan J. The conformational plasticity of protein kinases. Cell 109 (2002) 275-282
16. Iacob R.E., Pene-Dumitrescu T., Zhang J., Gray N.S., Smithgall T.E., and Engen J.R. Conformational disturbance in Abl kinase upon mutation and deregulation. Proc. Natl. Acad. Sci. USA 106 (2009) 1386-1391
17. Jacobs M.D., Caron P.R., and Hare B.J. Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex. Proteins 70 (2008) 1451-1460
18. Jeffrey P.D., Russo A.A., Polyak K., Gibbs E., Hurwitz J., Massague J., and Pavletich N.P. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature 376 (1995) 313-320
19. Kannan N., Taylor S.S., Zhai Y., Venter J.C., and Manning G. Structural and functional diversity of the microbial kinome. PLoS Biol. 5 (2007) e17
20. 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., et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26 (2008) 127-132
21. Kornev A.P., Haste N.M., Taylor S.S., and Eyck L.F. Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proc. Natl. Acad. Sci. USA 103 (2006) 17783-17788
22. Liu Y., and Gray N.S. Rational design of inhibitors that bind to inactive kinase conformations. Nat. Chem. Biol. 2 (2006) 358-364
23. Manning G., Whyte D.B., Martinez R., Hunter T., and Sudarsanam S. The protein kinase complement of the human genome. Science 298 (2002) 1912-1934
24. Mol C.D., Dougan D.R., Schneider T.R., Skene R.J., Kraus M.L., Scheibe D.N., Snell G.P., Zou H., Sang B.C., and Wilson K.P. Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J. Biol. Chem. 279 (2004) 31655-31663
25. Nagar B., Bornmann W.G., Pellicena P., Schindler T., Veach D.R., Miller W.T., Clarkson B., and Kuriyan J. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res. 62 (2002) 4236-4243
26. O'Hare T., Shakespeare W.C., Zhu X., Eide C.A., Rivera V.M., Wang F., Adrian L.T., Zhou T., Huang W.S., Xu Q., et al. AP24534, a pan-BCR-ABL inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance. Cancer Cell 16 (2009) 401-412
27. Okram B., Nagle A., Adrian F.J., Lee C., Ren P., Wang X., Sim T., Xie Y., Wang X., Xia G., et al. A general strategy for creating "inactive-conformation" abl inhibitors. Chem. Biol. 13 (2006) 779-786
28. Pargellis C., Tong L., Churchill L., Cirillo P.F., Gilmore T., Graham A.G., Grob P.M., Hickey E.R., Moss N., Pav S., et al. Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat. Struct. Biol. 9 (2002) 268-272
29. Pellicena P., and Kuriyan J. Protein-protein interactions in the allosteric regulation of protein kinases. Curr. Opin. Struct. Biol. 16 (2006) 702-709
30. Perera B.G., and Maly D.J. Design, synthesis and characterization of "clickable" 4-anilinoquinazoline kinase inhibitors. Mol. Biosyst. 4 (2008) 542-550
31. Quintas-Cardama A., Kantarjian H., and Cortes J. Flying under the radar: the new wave of BCR-ABL inhibitors. Nat. Rev. Drug Discov. 6 (2007) 834-848
32. Schindler T., Bornmann W., Pellicena P., Miller W.T., Clarkson B., and Kuriyan J. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289 (2000) 1938-1942
33. Schroeder G.M., An Y.M., Cai Z.W., Chen X.T., Clark C., Cornelius L.A.M., Dai J., Gullo-Brown J., Gupta A., Henley B., et al. Discovery of N-(4-(2-Amino-3-chloropyridin-4-yloxy)-3-fluorophenyl)-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide (BMS-777607), a selective and orally efficacious inhibitor of the Met kinase superfamily. J. Med. Chem. 52 (2009) 1251-1254
34. Seeliger M.A., Nagar B., Frank F., Cao X., Henderson M.N., and Kuriyan J. c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure 15 (2007) 299-311
35. Seeliger M.A., Ranjitkar P., Kasap C., Shan Y., Shaw D.E., Shah N.P., Kuriyan J., and Maly D.J. Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res. 69 (2009) 2384-2392
36. Simard J.R., Getlik M., Grütter C., Pawar V., Wulfert S., Rabiller M., and Rauh D. Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors. J. Am. Chem. Soc. 131 (2009) 13286-13296
37. Simard J.R., Kluter S., Grütter C., Getlik M., Rabiller M., Rode H.B., and Rauh D. A new screening assay for allosteric inhibitors of cSrc. Nat. Chem. Biol. 5 (2009) 394-396
38. Sullivan J.E., Holdgate G.A., Campbell D., Timms D., Gerhardt S., Breed J., Breeze A.L., Bermingham A., Pauptit R.A., Norman R.A., et al. Prevention of MKK6-dependent activation by binding to p38alpha MAP kinase. Biochemistry 44 (2005) 16475-16490
39. Taylor S.S., Bubis J., Toner-Webb J., Saraswat L.D., First E.A., Buechler J.A., Knighton D.R., and Sowadski J. CAMP-dependent protein kinase: prototype for a family of enzymes. FASEB J. 2 (1988) 2677-2685
40. Wan P.T., Garnett M.J., Roe S.M., Lee S., Niculescu-Duvaz D., Good V.M., Jones C.M., Marshall C.J., Springer C.J., Barford D., and Marais R. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116 (2004) 855-867
41. Weisberg E., Manley P.W., Breitenstein W., Bruggen J., Cowan-Jacob S.W., Ray A., Huntly B., Fabbro D., Fendrich G., Hall-Meyers E., et al. Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell 7 (2005) 129-141
42. Wissing J., Jansch L., Nimtz M., Dieterich G., Hornberger R., Keri G., Wehland J., and Daub H. Proteomics analysis of protein kinases by target class-selective prefractionation and tandem mass spectrometry. Mol. Cell. Proteomics 6 (2007) 537-547
43. Wong L., Jennings P.A., and Adams J.A. Communication pathways between the nucleotide pocket and distal regulatory sites in protein kinases. Acc. Chem. Res. 37 (2004) 304-311