Basis for resistance to imatinib in 16 BCR-ABL mutants as determined using molecular dynamics

Recent Patents on Anti-Cancer Drug Discovery

Volumn 4, Issue 2, 2009, Pages 164-173

  Lee, Tai Sung ^a   Potts, Steven J ^b   Albitar, Maher ^c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b Aperio Technologies   (United States)

^c QUEST DIAGNOSTICS NICHOLS INSTITUTE   (United States)

Author keywords

BCR ABL; Imatinib resistance; MD simulation; Molecular dynamics simulation

Indexed keywords

BCR ABL PROTEIN; IMATINIB; ANTINEOPLASTIC AGENT; PIPERAZINE DERIVATIVE; PYRIMIDINE DERIVATIVE;

ARTICLE; CHRONIC MYELOID LEUKEMIA; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENERGY CONSUMPTION; GENE MUTATION; HUMAN; MOLECULAR DYNAMICS; PATENT; PRIORITY JOURNAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG RESISTANCE; MUTATION;

ANTINEOPLASTIC AGENTS; COMPUTER SIMULATION; DRUG RESISTANCE, NEOPLASM; FUSION PROTEINS, BCR-ABL; HUMANS; MODELS, MOLECULAR; MUTATION; PIPERAZINES; PYRIMIDINES;

EID: 68949116362     PISSN: 15748928     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489209788452867     Document Type: Article

References (60)

1. Kurzrock R, Gutterman J, Talpaz M. The molecular genetics of Philadelphia chromosome-positive leukemias. N Engl J Med 1988; 319: 990-998.
2. Faderl S. The biology of chronic myeloid leukemia. N Engl J Med 1999; 341: 164-172.
3. Deininger MW, Goldman JM, Melo JV. The molecular biology of chronic myeloid leukemia. Blood 2000; 96: 3343-3356.
4. Goldman JM, Druker BJ. Chronic myeloid leukemia: Current treatment options. Blood 2001; 98: 2039-2042.
5. Druker BJ, O'Brien SG, Cortes J, Radich J. Chronic myelogenous leukemia. Hematology (Am Soc Hematol Educ Program) 2002: 111-135.
6. Elefanty AG, Hariharan IK, Cory S. Bcr-abl, the hallmark of chronic myeloid leukaemia in man, induces multiple haemopoietic neoplasms in mice. EMBO J 1990; 9: 1069-1078.
7. Heisterkamp N. Acute leukemia in bcr/abl transgenic mice. Nature 1990; 344: 251-253.
8. Ren R. Mechanisms of Bcr-Abl in the pathogenesis of chronic myelogenous leukaemia. Nat Rev Cancer 2005; 5: 172-183.
9. Manley PW. Imatinib: A selective tyrosine kinase inhibitor. Eur J Cancer 2002; 38: S19-S27.
10. Deininger MW, Goldman JM, Lydon N, Melo JV. The tyrosine kinase inhibitor CGP57148B selectively inhibits the growth of BCR-ABL-positive cells. Blood 1997; 90: 3691-3698.
11. Holtz MS. Imatinib mesylate (STI571) inhibits growth of primitive malignant progenitors in chronic myelogenous leukemia through reversal of abnormally increased proliferation. Blood 2002; 99: 3792-3800.
12. Roche-Lestienne C. Several types of mutations of the ABL gene can be found in chronic myeloid leukemia patients resistant to STI571, and they can pre-exist to the onset of treatment. Blood 2002; 100: 1014-1018.
13. Weisberg E, Griffin JD. Resistance to imatinib (Glivec): Update on clinical mechanisms. Drug Resist Updat 2003; 6: 231-238.
14. Branford S, Rudzki Z, Walsh S, et al. Detection of BCR-ABL mutations in patients with CML treated with imatinib is virtually always accompanied by clinical resistance, and mutations in the ATP phosphate-binding loop (P-loop) are associated with a poor prognosis. Blood 2003; 102: 276-283.
15. Shah NP. Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia. Cancer cell 2002; 2: 117-125.
16. Yoshida C, Melo JV. Biology of chronic myeloid leukemia and possible therapeutic approaches to imatinib-resistant disease. Int J Hematol 2004; 79: 420-433.
17. Von Bubnoff N, Schneller F, Peschel C, Duyster J. BCR-ABL gene mutations in relation to clinical resistance of Philadelphia-chromosome-positive leukaemia to STI571: A prospective study. Lancet 2002; 359: 487-491.
18. Cowan-Jacob SW, Fendrich G, Floersheimer A, et al. Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallographica Section D 2007; 63: 80-93.
19. Azam M, Latek RR, Daley GQ. Mechanisms of autoinhibition and STI-571/ Imatinib resistance revealed by mutagenesis of BCRABL. Cell 2003; 112: 831-843.
20. Shah NP. Overriding imatinib resistance with a novel ABL kinase inhibitor. Science 2004; 305: 399-401.
21. Weisberg E, Manley PW, Cowan-Jacob SW, Hochhaus A, Griffin JD. Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia. Nat Rev Cancer 2007; 7: 345-356.
22. Manley PW, Cowan-Jacob SW, Mestan J. Advances in the structural biology, design and clinical development of Bcr-Abl Kinase inhibitors for the treatment of chronic myeloid leukaemia. Biochim Biophys Acta 2005; 1754: 3-13.
23. Schindler T, Bornmann W, Pellicena P, et al. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 2000; 289: 1938-1942.
24. Gorre ME, Sawyers CL. Molecular mechanisms of resistance to STI571 in chronic myeloid leukemia. Curr Opin Hematol 2002; 9: 303-307.
25. Nagar B, Bornmann WG, Pellicena P, et al. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res 2002; 62: 4236-4243.
26. Nagar B, Hantschel O, Young MA, et al. Structural basis for the autoinhibition of c-Abl tyrosine kinase. Cell 2003; 112: 859-871.
27. Corbin AS, Buchdunger E, Pascal F, Druker BJ. Analysis of the structural basis of specificity of inhibition of the Abl kinase by STI571. J Biol Chem 2002; 277: 32214-32219.
28. Nimmanapalli R, Bhalla K. Mechanisms of resistance to imatinib mesylate in Bcr-Abl-positive leukemias. Curr Opin Oncol 2002; 14: 616-620.
29. Gambacorti-Passerini CB, Gunby RH, Piazza R, et al. Molecular mechanisms of resistance to imatinib in Philadelphia-chromosomepositive leukaemias. Lancet Oncol 2003; 4: 75-85.
30. Nardi V, Azam M, Daley GQ. Mechanisms and implications of imatinib resistance mutations in BCR-ABL. Curr Opin Hematol 2004; 11: 35-43.
31. Verkhivker GM. In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures. Biopolymers 2007; 85: 333-348.
32. Karplus M, Kuriyan J. Chemical theory and computation special feature: Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005; 102: 6679-6685.
33. Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc 1999; 121: 8133-8143.
34. Pricl S, Fermeglia M, Ferrone M, Tamborini E. T315I-mutated Bcr-Abl in chronic myeloid leukemia and imatinib: Insights from a computational study. Mol Cancer Ther 2005; 4: 1167-1174.
35. Lee T-S, Potts SJ, Kantarjian H, et al. Molecular basis explanation of imatinib resistance of Bcr-Abl due to T315I and P-loop mutations from molecular dynamics simulations. Cancer 2008; 112: 1744-1753.
36. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926-935.
37. Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph 1996;14: 33-38.
38. Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT 2004.
39. Bayly CI, Cieplak P, Cornell W, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem 1993; 97: 10269-10280.
40. MacKerell J, Brooks B, Brooks I, et al. CHARMM: The energy function and its parameterization with an overview of the program. Encycl Comput Chem 1998; 1: Sect 271-277.
41. Brooks BR, Bruccoleri RE, Olafson BD, et al. Charmm: A program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983; 4: 187-217.
42. Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26: 1781-1802.
43. Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 1980; 72: 2384-2393.
44. Nose S, Klein ML. Constant pressure molecular dynamics for molecular systems. Mol Phys 1983; 50: 1055-1076.
45. Hoover WG. Canonical dynamics: Equilibration phase-space distributions. Phys Rev A 1985; 31: 1695-1697.
46. Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys 1995; 103: 8577-8593.
47. Allen MP, Tildesley DJ. Computer simulation of liquids. Oxford: Oxford University Press 1987.
48. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-Alkanes. J Comput Phys 1977; 23: 327-341.
49. Nicolini FE, Corm S, Le QH, Roche-Lestienne C, Preudhomme C. The prognosis impact of BCR-ABL P-loop mutations: Worse or not worse? Leukemia 2007; 21: 193-194.
50. Azam M, Daley GQ. Anticipating clinical resistance to target-directed agents: The BCR-ABL paradigm. Mol Diagn Ther 2006; 10: 67-76.
51. Nolen B, Taylor S, Ghosh G. Regulation of protein kinases: Controlling activity through activation segment conformation. Mol Cell 2004; 15: 661-675.
52. Nagar B. Structural basis for the autoinhibition of c-Abl tyrosine kinase. Cell 2003; 112: 859-871.
53. Nagar B. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res 2002; 62: 4236-4243.
54. Weisberg E, Manley P, Mestan J, et al. AMN107 (nilotinib): A novel and selective inhibitor of BCR-ABL. Br J Cancer 2006; 94: 1765-1769.
55. von Bubnoff N, Manley PW, Mestan J, et al. Bcr-Abl resistance screening predicts a limited spectrum of point mutations to be associated with clinical resistance to the Abl kinase inhibitor nilotinib (AMN107). Blood 2006; 108: 1328-1333.
56. Levinson NM, Kuchment O, Shen K, et al. A Src-Like inactive conformation in the Abl tyrosine kinase domain. PLoS Biol 2006; 4: e144.
57. O'Hare T, Eide CA, Deininger MWN. Bcr-Abl kinase domain mutations, drug resistance, and the road to a cure for chronic myeloid leukemia. Blood 2007; 110: 2242-2249.
58. Haura, E. B.: WO2008089135A2 (2008).
59. Cai, X., Qian, C., Gould, S., Zhai, H.: WO2008033746A2 (2008).
60. Huang, F., Clark, E. A., Wang, X.-D.: WO2008086342A2 (2008).