Predicting inactive conformations of protein kinases using active structures: Conformational selection of Type-II inhibitors

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Xu, Min ^a   Yu, Lu ^a   Wan, Bo ^a   Yu, Long ^a   Huang, Qiang ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ABELSON KINASE; ABELSON KINASE 1; B RAF KINASE; B RAF KINASE 1; PROTEIN KINASE; PROTEIN KINASE 2 INHIBITOR; PROTEIN KINASE EPHA 3; PROTEIN KINASE INHIBITOR; PROTEIN KINASE KIT; PROTEIN KINASE LCK; PROTEIN KINASE MK14; PROTEIN KINASE SRC; UNCLASSIFIED DRUG; WATER;

AREA UNDER THE CURVE; ARTICLE; COMPUTER ANALYSIS; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; MOLECULAR DOCKING; PREDICTION; PROTEIN DATABASE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; DRUG EFFECT; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; ROTATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AREA UNDER CURVE; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEIN STRUCTURE, SECONDARY; ROTATION; THERMODYNAMICS; USER-COMPUTER INTERFACE; WATER;

EID: 79960817172     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022644     Document Type: Article

References (44)

1. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S, (2002) The protein kinase complement of the human genome. Science 298: 1912-1934.
2. Capra M, Nuciforo PG, Confalonieri S, Quarto M, Bianchi M, et al. (2006) Frequent alterations in the expression of serine/threonine kinases in human cancers. Cancer Res 66: 8147-8154.
3. Hunter T, (1998-1999) The role of tyrosine phosphorylation in cell growth and disease. Harvey Lect 94: 81-119.
4. Cohen P, (2002) Protein kinases-the major drug targets of the twenty-first century? Nat Rev Drug Discov 1: 309-315.
5. Imming P, Sinning C, Meyer A, (2006) Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 5: 821-834.
6. Vieth M, Sutherland JJ, Robertson DH, Campbell RM, (2005) Kinomics: Characterizing the therapeutically validated kinase space. Drug Discov Today 10: 839-846.
7. Seeliger MA, Nagar B, Frank F, Cao X, Henderson MN, et al. (2007) c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure 15: 299-311.
8. Knighton D, Zheng J, Ten Eyck L, Ashford V, Xuong N, et al. (1991) Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253: 407-414.
9. Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, et al. (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289: 1938-1942.
10. Levinson NM, Kuchment O, Shen K, Young MA, Koldobskiy M, et al. (2006) A Src-like inactive conformation in the Abl tyrosine kinase domain. PLoS Biol 4: e144.
11. Shan Y, Seeliger MA, Eastwood MP, Frank F, Xu H, et al. (2009) A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proc Natl Acad Sci U S A 106: 139-144.
12. De Bondt HL, Rosenblatt J, Jancarik J, Jones HD, Morgan DO, et al. (1993) Crystal structure of cyclin-dependent kinase 2. Nature 363: 595-602.
13. Xu W, Harrison SC, Eck MJ, (1997) Three-dimensional structure of the tyrosine kinase c-Src. Nature 385: 582-585.
14. Sicheri F, Moarefi I, Kuriyan J, (1997) Crystal structure of the Src family tyrosine kinase Hck. Nature 385: 602-609.
15. Noble MEM, Endicott JA, Johnson LN, (2004) Protein kinase inhibitors: Insights into drug design from structure. Science 303: 1800-1805.
16. Liu Y, Gray NS, (2006) Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2: 358-364.
17. Wood ER, Truesdale AT, McDonald OB, Yuan D, Hassell A, et al. (2004) A unique structure for epidermal growth factor receptor bound to GW572016 (lapatinib) relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Res 64: 6652-6659.
18. Ranjitkar P, Brock AM, Maly DJ, (2010) Affinity reagents that target a specific inactive form of protein kinases. Chemistry & Biology 17: 195-206.
19. Nagar B, Bornmann WG, Pellicena P, Schindler T, Veach DR, et al. (2002) Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res 62: 4236-4243.
20. Weisberg E, Manley PW, Breitenstein W, Brüggen J, Cowan-Jacob SW, et al. (2005) Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell 7: 129-141.
21. Mol CD, Fabbro D, Hosfield DJ, (2004) Structural insights into the conformational selectivity of STI-571 and related kinase inhibitors. Curr Opin Drug Discov Devel 7: 639-648.
22. Kantarjian H, Sawyers C, Hochhaus A, Guilhot F, Schiffer C, et al. (2002) Hematologic and cytogenetic responses to imatinib mesylate in chronic myelogenous leukemia. N Engl J Med 346: 645-652.
23. Nagar B, Hantschel O, Young MA, Scheffzek K, Veach D, et al. (2003) Structural basis for the autoinhibition of c-Abl kinase. Cell 112: 859-871.
24. Deininger M, Buchdunger E, Druker BJ, (2005) The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood 105: 2640-2653.
25. Vajpai N, Strauss A, Fendrich G, Cowan-Jacob S, Manley P, et al. (2008) Solution conformations and dynamics of Abl kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J Biol Chem 283: 18292-18302.
26. Okram B, Nagle A, Adrián FJ, Lee C, Ren P, et al. (2006) A general strategy for creating "inactive-conformation" Abl inhibitors. Chem Biol 13: 779-786.
27. Marsden BD, Knapp S, (2008) Doing more than just the structure-structural genomics in kinase drug discovery. CurrOpin Chem Biol 12: 40-45.
28. Kufareva I, Abagyan R, (2008) Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem 51: 7921-7932.
29. Das R, Baker D, (2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77: 363-382.
30. Yang S, Roux B, (2008) Src kinase conformational activation: Thermodynamics, pathways, and mechanisms. PLoS Comput Biol 4: e1000047.
31. Brady GP, Stouten PFW, (2000) Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-Aided Molecular Design 14: 383-401.
32. Huang B, Schroeder M, (2006) LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Structural Biology 6: 19.
33. Aleksandrov A, Simonson T, (2010) Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases. J Biol Chem 285: 13807-13815.
34. Jura N, Zhang X, Endres NF, Seeliger MA, Schindler T, et al. (2011) Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. Mol Cell 42: 9-22.
35. Zhang Y, Skolnick J, (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucl Acids Res 33: 2302-2309.
36. Huey R, Morris GM, Olson AJ, Goodsell DS, (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28: 1145-1152.
37. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19: 1639-1662.
38. Jenwitheesuk E, Samudrala R, (2003) Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Struct Biol 3: 2.
39. Jenwitheesuk E, Samudrala R, (2005) Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antivir Ther 10: 157-166.
40. Irwin JJ, Shoichet BK, (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45: 177-182.
41. Boehr DD, Nussinov R, Wright PE, (2009) The role of conformational ensembles in biomolecular recognition. Nat Chem Biol 5: 789-796.
42. Eswar N, Marti-Renom MA, Webb B, Madhusudhan MS, Eramian D, et al. (2006) Comparative protein structure modeling with MODELLER. Current Protocols in Bioinformatics: John Wiley & Sons, Inc pp. 5.6.1-5.6.30.
43. Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264.
44. Canutescu AA, Dunbrack RL Jr, (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci 12: 963-972.