REPLACE Strategy for Generating Non-ATP-Competitive Inhibitors of Cell Cycle Protein Kinases

Protein-Protein Interactions in Drug Discovery

Volumn 56, Issue , 2013, Pages 291-304

  Mcinnes, Campbell ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Cyclin groove; Cyclin dependent kinase; Non ATP competitive inhibitor; Polo box; Protein protein interaction; REPLACE strategy

Indexed keywords

HUMAN COMPUTER INTERACTION;

CYCLIN GROOVE; CYCLIN-DEPENDENT KINASE; NON-ATP-COMPETITIVE INHIBITOR; POLO-BOX; PROTEIN-PROTEIN INTERACTIONS; REPLACE STRATEGY;

ENZYME INHIBITION;

EID: 85016471958     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527648207.ch12     Document Type: Chapter

References (44)

1. Wang, S., Griffiths, G., Midgley, C.A., Barnett, A.L., Cooper, M., Grabarek, J., Ingram, L., Jackson,W., Kontopidis, G., McClue, S.J., McInnes, C., McLachlan, J., Meades, C., Mezna, M., Stuart, I., Thomas, M.P., Zheleva, D.I., Lane, D.P., Jackson, R. C., Glover, D.M., Blake, D.G., and Fischer, P.M. (2010) Discovery and characterization of 2-anilino-4-(thiazol-5-yl)pyrimidine transcriptional CDK inhibitors as anticancer agents. Chemistry & Biology, 17, 1111-1121.
2. Biondi, R.M. and Nebreda, A.R. (2003) Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. The Biochemical Journal, 372, 1-13.
3. Kirkland, L.O. and McInnes, C. (2009) Non-ATP-competitive protein kinase inhibitors as anti-tumor therapeutics. Biochemical Pharmacology, 77, 1561-1571.
4. McInnes, C., Andrews, M.J., Zheleva, D.I., Lane, D.P., and Fischer, P.M. (2003) Peptidomimetic design of CDK inhibitors targeting the recruitment site of the cyclin subunit. Current Medicinal Chemistry - Anti-Cancer Agents, 3, 57-69.
5. Zheleva, D.I., McInnes, C., Gavine, A.L., Zhelev, N.Z., Fischer, P.M., and Lane, D.P. (2002) Highly potent p21WAF1-derived peptide inhibitors of CDK-mediated pRb phosphorylation: delineation and structural insight into their interactions with cyclin A. The Journal of Peptide Research, 60, 257-270.
6. Sherr, C.J. (1996) Cancer cell cycles. Science, 274, 1672-1677.
7. Malumbres, M. and Barbacid, M. (2001) To cycle or not to cycle: a critical decision in cancer. Nature Reviews Cancer, 1, 222-231.
8. Mendoza, N., Severin, C., Marsters, J., and Wickramasinghe, D. (2004) Cyclin A antagonists kill tumor cells in vitro and in vivo. Proceedings of the American Association for Cancer Research, 45, Abs. 834.
9. Kontopidis, G., Andrews, M.J.I., McInnes, C., Cowan, A., Powers, H., Innes, L., Plater, A., Griffiths, G., Paterson, D., Zheleva, D. I., Lane, D.P., Green, S., Walkinshaw, M.D., and Fischer, P.M. (2003) Structural understanding of cyclin groove inhibition: complex crystal structures through ligand exchange. Presented at 5th International Conference on Molecular Structural Biology, Vienna.
10. Atkinson, G.E., Cowan, A., McInnes, C., Zheleva, D.I., Fischer, P.M., and Chan, W.C. (2002) Peptide inhibitors of CDK2- cyclin a that target the cyclin recruitmentsite: structural variants of the C-terminal Phe. Bioorganic & Medicinal Chemistry Letters, 12, 2501-2505.
11. Mendoza, N., Fong, S., Marsters, J., Koeppen, H., Schwall, R., and Wickramasinghe, D. (2003) Selective cyclin-dependent kinase 2/cyclin A antagonists that differ from ATP site inhibitors block tumor growth. Cancer Research, 63, 1020-1024.
12. Lowe, E.D., Tews, I., Cheng, K.Y., Brown, N.R., Gul, S., Noble, M.E.M., Gamblin, S.J., and Johnson, L.N. (2002) Specificity determinants of recruitment peptides bound to phospho-CDK2/cyclin A. Biochemistry, 41, 15625-15634.
13. Kontopidis, G., Andrews, M.J., McInnes, C., Cowan, A., Powers, H., Innes, L., Plater, A., Griffiths, G., Paterson, D., Zheleva, D.I., Lane, D.P., Green, S., Walkinshaw, M.D., and Fischer, P.M. (2003) Insights 302j 12 REPLACE Strategy for Generating Non-ATP-Competitive Inhibitors of Cell Cycle Protein Kinases into cyclin groove recognition: complex crystal structures and inhibitor design through ligand exchange. Structure, 11, 1537-1546.
14. Castanedo, G., Clark, K., Wang, S., Tsui, V., Wong, M., Nicholas, J., Wickramasinghe, D., Marsters, J.C.Jr., and Sutherlin, D. (2006) CDK2/cyclin A inhibitors: targeting the cyclin A recruitment site with small molecules derived from peptide leads. Bioorganic & Medicinal Chemistry Letters, 16, 1716-1720.
15. Andrews, M.J.I., McInnes, C., Kontopidis, G., Innes, L., Cowan, A., Plater, A., and Fischer, P.M. (2004) Design, synthesis, biological activity and structural analysis of cyclic peptide inhibitors targeting the substrate recruitment site of cyclindependent kinase complexes. Organic & Biomolecular Chemistry, 2, 2735-2741.
16. Andrews, M.J., Kontopidis, G., McInnes, C., Plater, A., Innes, L., Cowan, A., Jewsbury, P., and Fischer, P.M. (2006) REPLACE: a strategy for iterative design of cyclin-binding groove inhibitors. ChemBioChem, 7, 1909-1915.
17. Carr, R.A., Congreve, M., Murray, C.W., and Rees, D.C. (2005) Fragment-based lead discovery: leads by design. Drug Discovery Today, 10, 987-992.
18. Premnath, P.N., Liu, S., Bolger, J., Kirkland, L., Perkins, T., and McInnes, C. (2012) Optimization of CDK/cyclin groove inhibitors through REPLACE mediated fragment assembly. Journal of Medicinal Chemistry, submitted.
19. Liu, S., Bolger, J.K., Kirkland, L.O., Premnath, P.N., and McInnes, C. (2010) Structural and functional analysis of cyclin D1 reveals p27 and substrate inhibitor binding requirements. ACS Chemical Biology, 5, 1169-1182.
20. Lee, K.S., Grenfell, T.Z., Yarm, F.R., and Erikson, R.L. (1998) Mutation of the polobox disrupts localization and mitotic functions of the mammalian polo kinase Plk. Proceedings of the National Academy of Sciences of the United States of America, 95, 9301-9306.
21. Lee, K.S., Song, S., and Erikson, R.L. (1999) The polo-box-dependent induction of ectopic septal structures by a mammalian polo kinase, Plk, in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 96, 14360-14365.
22. Yuan, J., Kramer, A., Eckerdt, F., Kaufmann, M., and Strebhardt, K. (2002) Efficient internalization of the polo-box of polo-like kinase 1 fused to an antennapedia peptide results in inhibition of cancer cell proliferation. Cancer Research, 62, 4186- 4190.
23. May, K.M., Reynolds, N., Cullen, C.F., Yanagida, M., and Ohkura, H. (2002) Polo boxes and Cut23 (Apc8) mediate an interaction between polo kinase and the anaphase-promoting complex for fission yeast mitosis. Journal of Cell Biology, 156, 23-28.
24. Nakajima, H., Toyoshima-Morimoto, F., Taniguchi, E., and Nishida, E. (2003) Identification of a consensus motif for Plk (Polo-like kinase) phosphorylation reveals Myt1 as a Plk1 substrate. Journal of Biological Chemistry, 278, 25277-25280.
25. Neef, R., Preisinger, C., Sutcliffe, J., Kopajtich, R., Nigg, E.A., Mayer, T.U., and Barr, F.A. (2003) Phosphorylation of mitotic kinesin-like protein 2 by polo-like kinase 1 is required for cytokinesis. Journal of Cell Biology, 162, 863-875.
26. Cheng, K.-Y., Lowe, E.D., Sinclair, J., Nigg, E.A., and Johnson, L.N. (2003) The crystal structure of the human polo-like kinase-1 polo box domain and its phospho-peptide complex. EMBO Journal, 22, 5757-5768.
27. Elia, A.E.H., Rellos, P., Haire, L.F., Chao, J.W., Ivins, F.J., Hoepker, K., Mohammad, D., Cantley, L.C., Smerdon, S.J., and Yaffe, M.B. (2003) The molecular basis for phosphodependent substrate targeting and regulation of Plks by the polo-box domain. Cell, 115, 83-95.
28. Leung, G.C., Hudson, J.W., Kozarova, A., Davidson, A., Dennis, J.W., and Sicheri, F. (2002) The Sak polo-box comprises a structural domain sufficient for mitotic subcellular localization. Nature Structural Biology, 9, 719-724.
29. Pawson, T. and Scott, J.D. (1997) Signaling through scaffold, anchoring, and adaptor proteins. Science, 278, 2075-2080.
30. Sawyer, T.K., Bohacek, R.S., Dalgarno, D.C., Eyermann, C.J., Kawahata, N., Metcalf, C.A.3rd, Shakespeare, W.C., Sundaramoorthi, R., Wang, Y., and Yang, M.G. (2002) SRC homology-2 inhibitors: peptidomimetic and nonpeptide. Mini- Reviews in Medicinal Chemistry, 2, 475-488.
31. Fischer, P.M. (2004) The design of drug candidate molecules as selective inhibitors of therapeutically relevant kinases. Current Medicinal Chemistry, 11, 1563-1583.
32. Bahassi, E.M., Conn, C.W., Myer, D.L., Hennigan, R.F., McGowan, C.H., Sanchez, Y., and Stambrook, P.J. (2002) Mammalian Polo-like kinase 3 (Plk3) is a multifunctional protein involved in stress response pathways. Oncogene, 21, 6633-6640.
33. Xie, S., Wu, H., Wang, Q., Cogswell, J.P., Husain, I., Conn, C., Stambrook, P., Jhanwar-Uniyal, M., and Dai,W. (2001) Plk3 functionally links DNA damage to cell cycle arrest and apoptosis at least in part via the p53 pathway. Journal of Biological Chemistry, 276, 43305-43312.
34. Yun, S.M., Moulaei, T., Lim, D., Bang, J.K., Park, J.E., Shenoy, S.R., Liu, F., Kang, Y.H., Liao, C., Soung, N.K., Lee, S., Yoon, D.Y., Lim, Y., Lee, D.H., Otaka, A., Appella, E., McMahon, J.B., Nicklaus, M.C., Burke, T.R.Jr., Yaffe, M.B., Wlodawer, A., and Lee, K.S. (2009) Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1. Nature Structural & Molecular Biology, 16, 876-882.
35. Lee, H.J., Hwang, H.I., and Jang, Y.J. (2010) Mitotic DNA damage response: Polo-like kinase-1 is dephosphorylated through ATM-Chk1 pathway. Cell Cycle, 9, 2389-2398.
36. van Vugt, M.A. and Medema, R.H. (2004) Checkpoint adaptation and recovery: back with Polo after the break. Cell Cycle, 3, 1383-1386.
37. Smits, V.A.J., Klompmaker, R., Arnaud, L., Rijksen, G., Nigg, E.A., and Medema, R.H. (2000) Polo-like kinase-1 is a target of the DNA damage checkpoint. Nature Cell Biology, 2, 672-676.
38. van Vugt, M.A., Smits, V.A., Klompmaker, R., and Medema, R.H. (2001) Inhibition of polo-like kinase-1 by DNA damage occurs in an ATM- or ATR-dependent fashion. Journal of Biological Chemistry, 276, 41656- 41660.
39. Reindl,W., Yuan, J., Kramer, A., Strebhardt, K., and Berg, T. (2008) Inhibition of polo-like kinase 1 by blocking polo-box domain-dependent PPIs. Chemistry & Biology, 15, 459-466.
40. Reindl,W., Yuan, J., Kramer, A., Strebhardt, K., and Berg, T. (2009) A panspecific inhibitor of the polo-box domains of polo-like kinases arrests cancer cells in mitosis. ChemBioChem, 10, 1145-1148.
41. Watanabe, N., Sekine, T., Takagi, M., Iwasaki, J., Imamoto, N., Kawasaki, H., and Osada, H. (2009) Deficiency in chromosome congression by the inhibition of Plk1 polo box domain-dependent recognition. The Journal of Biological Chemistry, 284, 2344-2353.
42. McInnes, C., Estes, K., Yang, Z., Farag, D.B., Johnson, P., Lazo, J., and Wyatt, M.D. (2012) Targeting sub-cellular localization through the polo-box domain: non-ATPcompetitive Inhibitors recapitulate a PLK1phenotype. Molecular Cancer Therapeutics, 11, 1683-1692.
43. Garcia-Alvarez, B., de Carcer, G., Ibanez, S., Bragado-Nilsson, E., and Montoya, G. (2007) Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization. Proceedings of the National Academy of Sciences of the United States of America, 104, 3107-3112.
44. Li, Q., Huang, Y., Xiao, N., Murray, V., Chen, J., and Wang, J. (2008) Real time investigation of protein folding, structure, and dynamics in living cells. Methods in Cell Biology, 90, 287-325.