Exploiting structural principles to design cyclin-dependent kinase inhibitors

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1754, Issue 1-2, 2005, Pages 58-64

  Noble, Martin ^a   Barrett, Paul ^a   Endicott, Jane ^a   Johnson, Louise ^a   McDonnell, Jim ^a   Robertson, Giles ^a   Zawaira, Alex ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

CDK; Cyclin dependent kinase inhibitor; Drug design; Peptide inhibitor; Protein dynamic; Protein:protein interaction

Indexed keywords

CYCLIN A; CYCLIN DEPENDENT KINASE 2; CYCLIN DEPENDENT KINASE INHIBITOR; PROTEIN KINASE;

CONFERENCE PAPER; DRUG DESIGN; DRUG STRUCTURE; DYNAMICS; FEASIBILITY STUDY; HYDROPHOBICITY; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS;

ANIMALS; ANTINEOPLASTIC AGENTS; CYCLIN-DEPENDENT KINASES; DRUG DESIGN; ENZYME INHIBITORS; HUMANS; MODELS, MOLECULAR; PROTEIN INTERACTION MAPPING; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 29144520253     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.08.019     Document Type: Conference Paper

References (61)

1. M. Malumbres, and A. Carnero Cell cycle deregulation: a common motif in cancer Prog. Cell Cycle Res. 5 2003 5 18
2. R. Donnellan, and R. Chetty Cyclin D1 and human neoplasia Mol. Pathol. 51 1998 1 7
3. R. Donnellan, and R. Chetty Cyclin E in human cancers FASEB J. 13 1999 773 780
4. C. Catzavelos, N. Bhattacharya, Y.C. Ung, J.A. Wilson, L. Roncari, C. Sandhu, P. Shaw, H. Yeger, I. Morava-Protzner, L. Kapusta, E. Franssen, K.I. Pritchard, and J.M. Slingerland Decreased levels of the cell-cycle inhibitor p27Kip1 protein: prognostic implications in primary breast cancer Nat. Med. 3 1997 227 230
5. Y.N. Chen, S.K. Sharma, T.M. Ramsey, L. Jiang, M.S. Martin, K. Baker, P.D. Adams, K.W. Bair, and W.G. Kaelin Jr. Selective killing of transformed cells by cyclin/cyclin-dependent kinase 2 antagonists Proc. Natl. Acad. Sci. U. S. A. 96 1999 4325 4329
6. M. Ljungman, and M.T. Paulsen The cyclin-dependent kinase inhibitor roscovitine inhibits RNA synthesis and triggers nuclear accumulation of p53 that is unmodified at Ser15 and Lys382 Mol. Pharmacol. 60 2001 785 789
7. S. Bach, M. Knockaert, J. Reinhardt, O. Lozach, S. Schmitt, B. Baratte, M. Koken, S.P. Coburn, L. Tang, T. Jiang, D.C. Liang, H. Galons, J.F. Dierick, L.A. Pinna, F. Meggio, F. Totzke, C. Schachtele, A.S. Lerman, A. Carnero, Y. Wan, N. Gray, and L. Meijer Roscovitine targets: protein kinases and pyridoxal kinase J. Biol. Chem. 280 2005 31208 31219
8. E.C. Busby, D.F. Leistritz, R.T. Abraham, L.M. Karnitz, and J.N. Sarkaria The radiosensitizing agent 7-hydroxystaurosporine (UCN-01) inhibits the DNA damage checkpoint kinase hChk1 Cancer Res. 60 2000 2108 2112
9. P.R. Graves, L. Yu, J.K. Schwarz, J. Gales, E.A. Sausville, P.M. O'Connor, and H. Piwnica-Worms The Chk1 protein kinase and the Cdc25C regulatory pathways are targets of the anticancer agent UCN-01 J. Biol. Chem. 275 2000 5600 5605
10. O. Tetsu, and F. McCormick Proliferation of cancer cells despite CDK2 inhibition Cancer Cells 3 2003 233 245
11. C. Berthet, E. Aleem, V. Coppola, L. Tessarollo, and P. Kaldis Cdk2 knockout mice are viable Curr. Biol. 13 2003 1775 1785
12. S. Ortega, I. Prieto, J. Odajima, A. Martin, P. Dubus, R. Sotillo, J.L. Barbero, M. Malumbres, and M. Barbacid Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice Nat. Genet. 35 2003 25 31
13. Y. Geng, Q. Yu, E. Sicinska, M. Das, J.E. Schneider, S. Bhattacharya, W.M. Rideout, R.T. Bronson, H. Gardner, and P. Sicinski Cyclin E ablation in the mouse Cell 114 2003 431 443
14. E. Aleem, H. Kiyokawa, and P. Kaldis Cdc2-cyclin E complexes regulate the G1/S phase transition Nat. Cell Biol. 7 2005 831 836
15. P.D. Adams, W.R. Sellers, S.K. Sharma, A.D. Wu, C.M. Nalin, and W.G. Kaelin Jr. Identification of a cyclin-cdk2 recognition motif present in substrates and p21-like cyclin-dependent kinase inhibitors Mol. Cell. Biol. 16 1996 6623 6633
16. V.T. Skamnaki, D.J. Owen, M.E. Noble, E.D. Lowe, G. Lowe, N.G. Oikonomakos, and L.N. Johnson Catalytic mechanism of phosphorylase kinase probed by mutational studies Biochemistry 38 1999 14718 14730
17. M. Huse, and J. Kuriyan The conformational plasticity of protein kinases Cell 109 2002 275 282
18. L.N. Johnson, M.E. Noble, and D.J. Owen Active and inactive protein kinases: structural basis for regulation Cell 85 1996 149 158
19. J. Yang, P. Cron, V.M. Good, V. Thompson, B.A. Hemmings, and D. Barford Crystal structure of an activated Akt/protein kinase B ternary complex with GSK3-peptide and AMP-PNP Nat. Struct. Biol. 9 2002 940 944
20. S. Cox, E. Radzio-Andzelm, and S.S. Taylor Domain movements in protein kinases Curr. Opin. Struct. Biol. 4 1994 893 901
21. N. Narayana, S. Cox, X. Nguyen-huu, L.F. Ten Eyck, and S.S. Taylor A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility Structure 5 1997 921 935
22. M.H. Seifert, C.B. Breitenlechner, D. Bossemeyer, R. Huber, T.A. Holak, and R.A. Engh Phosphorylation and flexibility of cyclic-AMP-dependent protein kinase (PKA) using (31)P NMR spectroscopy Biochemistry 41 2002 5968 5977
23. I. Tsigelny, J.P. Greenberg, S. Cox, W.L. Nichols, S.S. Taylor, and L.F. Ten Eyck 600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase Biopolymers 50 1999 513 524
24. M.A. Young, S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 105 2001 115 126
25. C.P. Barrett, and M.E. Noble Molecular motions of human cyclin-dependent kinase 2 J. Biol. Chem. 280 2005 13993 14005
26. I. Bartova, M. Otyepka, Z. Kriz, and J. Koca Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop Protein Sci. 13 2004 1449 1457
27. S.K. Hanks, and T. Hunter Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification FASEB J. 9 1995 576 596
28. Y. Bourne, M.H. Watson, A.S. Arvai, S.L. Bernstein, S.I. Reed, and J.A. Tainer Crystal structure and mutational analysis of the Saccharomyces cerevisiae cell cycle regulatory protein Cks1: implications for domain swapping, anion binding and protein interactions Structure Fold Des. 8 2000 841 850
29. H. Song, N. Hanlon, N.R. Brown, M.E. Noble, L.N. Johnson, and D. Barford Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2 Mol. Cell 7 2001 615 626
30. K.L. Gould, S. Moreno, D.J. Owen, S. Sazer, and P. Nurse Phosphorylation at Thr167 is required for Schizosaccharomyces pombe p34cdc2 function EMBO J. 10 1991 3297 3309
31. R. Capdeville, E. Buchdunger, J. Zimmermann, and A. Matter Glivec (STI571, Imatinib), a rationally developed targeted anticancer drug Nat. Rev., Drug Discov. 1 2002 493 502
32. T. Schindler, W. Bornmann, P. Pellicena, W.T. Miller, B. Clarkson, and J. Kuriyan Structural mechanism for STI-571 inhibition of abelson tyrosine kinase Science 289 2000 1938 1942
33. S. Holton, A. Merckx, D. Burgess, C. Doerig, M. Noble, and J. Endicott Structures of P. falciparum PfPK5 test the CDK regulation paradigm and suggest mechanisms of small molecule inhibition Structure (Camb.) 11 2003 1329 1337
34. L. Prade, R.A. Engh, A. Girod, V. Kinzel, R. Huber, and D. Bossemeyer Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential Structure 5 1997 1627 1637
35. M.B. Lamers, A.A. Antson, R.E. Hubbard, R.K. Scott, and D.H. Williams Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporine J. Mol. Biol. 285 1999 713 725
36. C.N. Cavasotto, and R.A. Abagyan Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 337 2004 209 225
37. D. Wisniewski, C.L. Lambek, C. Liu, A. Strife, D.R. Veach, B. Nagar, M.A. Young, T. Schindler, W.G. Bornmann, J.R. Bertino, J. Kuriyan, and B. Clarkson Characterization of potent inhibitors of the Bcr-Abl and the c-kit receptor tyrosine kinases Cancer Res. 62 2002 4244 4255
38. M. Otyepka, Z. Kriz, and J. Koca Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations J. Biomol. Struct. Dyn. 20 2002 141 154
39. A.I. Archakov, V.M. Govorun, A.V. Dubanov, Y.D. Ivanov, A.V. Veselovsky, P. Lewi, and P. Janssen Protein-protein interactions as a target for drugs in proteomics Proteomics 3 2003 380 391
40. D.C. Fry, S.D. Emerson, S. Palme, B.T. Vu, C.M. Liu, and F. Podlaski NMR structure of a complex between MDM2 and a small molecule inhibitor J. Biomol. NMR 30 2004 163 173
41. I.R. Hardcastle, S.U. Ahmed, H. Atkins, A.H. Calvert, N.J. Curtin, G. Farnie, B.T. Golding, R.J. Griffin, S. Guyenne, C. Hutton, P. Kallblad, S.J. Kemp, M.S. Kitching, D.R. Newell, S. Norbedo, J.S. Northen, R.J. Reid, K. Saravanan, H.M. Willems, and J. Lunec Isoindolinone-based inhibitors of the MDM2-p53 protein-protein interaction Bioorg. Med. Chem. Lett. 15 2005 1515 1520
42. L.T. Vassilev, B.T. Vu, B. Graves, D. Carvajal, F. Podlaski, Z. Filipovic, N. Kong, U. Kammlott, C. Lukacs, C. Klein, N. Fotouhi, and E.A. Liu In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 Science 303 2004 844 848
43. H. Nakajima, Y.B. Kim, H. Terano, M. Yoshida, and S. Horinouchi FR901228, a potent antitumor antibiotic, is a novel histone deacetylase inhibitor Exp. Cell Res. 241 1998 126 133
44. R. Furumai, A. Matsuyama, N. Kobashi, K.H. Lee, M. Nishiyama, H. Nakajima, A. Tanaka, Y. Komatsu, N. Nishino, M. Yoshida, and S. Horinouchi FK228 (depsipeptide) as a natural prodrug that inhibits class I histone deacetylases Cancer Res. 62 2002 4916 4921
45. J.M. Healy, O. Murayama, T. Maeda, K. Yoshino, K. Sekiguchi, and M. Kikuchi Peptide ligands for integrin alpha v beta 3 selected from random phage display libraries Biochemistry 34 1995 3948 3955
46. A. Wlodawer, and J. Vondrasek Inhibitors of HIV-1 protease: a major success of structure-assisted drug design Annu. Rev. Biophys. Biomol. Struct. 27 1998 249 284
47. S. Jones, and J.M. Thornton Searching for functional sites in protein structures Curr. Opin. Chem. Biol. 8 2004 3 7
48. W.S. Valdar, and J.M. Thornton Conservation helps to identify biologically relevant crystal contacts J. Mol. Biol. 313 2001 399 416
49. W.S. Valdar, and J.M. Thornton Protein-protein interfaces: analysis of amino acid conservation in homodimers Proteins 42 2001 108 1024
50. O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
51. P. Aloy, E. Querol, F.X. Aviles, and M.J. Sternberg Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking J. Mol. Biol. 311 2001 395 408
52. S. Jones, and J.M. Thornton Principles of protein-protein interactions Proc. Natl. Acad. Sci. U. S. A. 93 1996 13 20
53. L. Lo Conte, C. Chothia, and J. Janin The atomic structure of protein-protein recognition sites J. Mol. Biol. 285 1999 2177 2198
54. P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857
55. D.J. Owen, Y. Vallis, M.E. Noble, J.B. Hunter, T.R. Dafforn, P.R. Evans, and H.T. McMahon A structural explanation for the binding of multiple ligands by the alpha-adaptin appendage domain Cell 97 1999 805 815
56. R. Hoessel, S. Leclerc, J.A. Endicott, M.E. Nobel, A. Lawrie, P. Tunnah, M. Leost, E. Damiens, D. Marie, D. Marko, E. Niederberger, W. Tang, G. Eisenbrand, and L. Meijer Indirubin, the active constituent of a Chinese antileukaemia medicine, inhibits cyclin-dependent kinases Nat. Cell Biol. 1 1999 60 67
57. N.R. Brown, M.E. Noble, J.A. Endicott, E.F. Garman, S. Wakatsuki, E. Mitchell, B. Rasmussen, T. Hunt, and L.N. Johnson The crystal structure of cyclin A Structure 3 1995 1235 1247
58. P.D. Jeffrey, A.A. Russo, K. Polyak, E. Gibbs, J. Hurwitz, J. Massague, and N.P. Pavletich Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex Nature 376 1995 313 320
59. A.A. Russo, P.D. Jeffrey, A.K. Patten, J. Massague, and N.P. Pavletich Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex Nature 382 1996 325 331
60. M.J. Andrews, C. McInnes, G. Kontopidis, L. Innes, A. Cowan, A. Plater, and P.M. Fischer Design, synthesis, biological activity and structural analysis of cyclic peptide inhibitors targeting the substrate recruitment site of cyclin-dependent kinase complexes Org. Biomol. Chem. 2 2004 2735 2741
61. N. Kannan, and A.F. Neuwald Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha Protein Sci. 13 2004 2059 2077