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Volumn 4, Issue 12, 2009, Pages

Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl

Author keywords

[No Author keywords available]

Indexed keywords

ABELSON KINASE; ADENOSINE TRIPHOSPHATE; IMATINIB; STEM CELL FACTOR RECEPTOR; ION CHANNEL; LIGAND; PIPERAZINE DERIVATIVE; PROTEIN KINASE INHIBITOR; PYRIMIDINE DERIVATIVE;

EID: 77949525702     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008470     Document Type: Article
Times cited : (41)

References (50)
  • 2
    • 0036527429 scopus 로고    scopus 로고
    • Protein kinases - the major drug targets of the twenty-first century?
    • Cohen P (2002) Protein kinases - the major drug targets of the twenty-first century? Nat Rev Drug Discov 1: 309-315.
    • (2002) Nat Rev Drug Discov , vol.1 , pp. 309-315
    • Cohen, P.1
  • 3
    • 0037392444 scopus 로고    scopus 로고
    • Issues and progress with protein kinase inhibitors for cancer treatment
    • Dancey J, Sausville EA (2003) Issues and progress with protein kinase inhibitors for cancer treatment. Nat Rev Drug Discov 2: 296-313.
    • (2003) Nat Rev Drug Discov , vol.2 , pp. 296-313
    • Dancey, J.1    Sausville, E.A.2
  • 4
    • 1642323740 scopus 로고    scopus 로고
    • Protein kinase inhibitors: Insights into drug design from structure
    • Noble MEM, Endicott JA, Johnson LN (2004) Protein kinase inhibitors: Insights into drug design from structure. Science 303: 1800-1805.
    • (2004) Science , vol.303 , pp. 1800-1805
    • Noble, M.E.M.1    Endicott, J.A.2    Johnson, L.N.3
  • 5
    • 35748985280 scopus 로고    scopus 로고
    • Protein kinase inhibitors: Structural insights into selectivity
    • Thaimattam R, Banerjee R, Miglani R, Iqbal J (2007) Protein kinase inhibitors: Structural insights into selectivity. Curr Pharm Des 13: 2751-2765.
    • (2007) Curr Pharm Des , vol.13 , pp. 2751-2765
    • Thaimattam, R.1    Banerjee, R.2    Miglani, R.3    Iqbal, J.4
  • 6
    • 9244222261 scopus 로고    scopus 로고
    • Targeted cancer therapy
    • Sawyers C (2004) Targeted cancer therapy. Nature 432: 294-297.
    • (2004) Nature , vol.432 , pp. 294-297
    • Sawyers, C.1
  • 8
    • 27544479318 scopus 로고    scopus 로고
    • Role of tyrosine kinase inhibitors in cancer therapy
    • Arora A, Scholar EM (2005) Role of tyrosine kinase inhibitors in cancer therapy. J Pharmacol Exp Ther 315: 971-979.
    • (2005) J Pharmacol Exp Ther , vol.315 , pp. 971-979
    • Arora, A.1    Scholar, E.M.2
  • 9
    • 0032933797 scopus 로고    scopus 로고
    • c-Src, receptor tyrosine kinases, and human cancer
    • Biscardi JS, Tice DA, Parsons SJ (1999) c-Src, receptor tyrosine kinases, and human cancer. Adv Cancer Res 76: 61-199.
    • (1999) Adv Cancer Res , vol.76 , pp. 61-199
    • Biscardi, J.S.1    Tice, D.A.2    Parsons, S.J.3
  • 10
    • 12144289677 scopus 로고    scopus 로고
    • Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF
    • Wan PTC, Garnett MJ, Roe SM, Lee S, Niculescu-Duvaz D, et al. (2004) Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116: 855-867.
    • (2004) Cell , vol.116 , pp. 855-867
    • Wan, P.T.C.1    Garnett, M.J.2    Roe, S.M.3    Lee, S.4    Niculescu-Duvaz, D.5
  • 11
    • 21244500204 scopus 로고    scopus 로고
    • Inhibition of GSK-3b as a target for cardioprotection: The importance of timing, location, duration and degree of inhibition
    • Murphy E, Steenbergen C (2005) Inhibition of GSK-3b as a target for cardioprotection: the importance of timing, location, duration and degree of inhibition. Expert Opin Ther Targets 9: 447-456.
    • (2005) Expert Opin Ther Targets , vol.9 , pp. 447-456
    • Murphy, E.1    Steenbergen, C.2
  • 14
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinase
    • Morgan H, John K (2002) The conformational plasticity of protein kinase. Cell 109: 275-282.
    • (2002) Cell , vol.109 , pp. 275-282
    • Morgan, H.1    John, K.2
  • 15
    • 33745298429 scopus 로고    scopus 로고
    • Rational design of inhibitors that bind to inactive kinase conformations
    • Liu Y, Gray NS (2006) Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2: 358-364.
    • (2006) Nat Chem Biol , vol.2 , pp. 358-364
    • Liu, Y.1    Gray, N.S.2
  • 16
    • 33746258750 scopus 로고    scopus 로고
    • A general strategy for creating ''Inactive-conformation'' Abl inhibitors
    • Okram B, Nagle A, Adrian FJ, Lee C, Ren P, et al. (2006) A general strategy for creating ''Inactive-conformation'' Abl inhibitors. Chem Biol 13: 779-786.
    • (2006) Chem Biol , vol.13 , pp. 779-786
    • Okram, B.1    Nagle, A.2    Adrian, F.J.3    Lee, C.4    Ren, P.5
  • 18
    • 2942542387 scopus 로고    scopus 로고
    • Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase
    • Mol CD, Dougan DR, Schneider TR, Skene RJ, Kraus ML, et al. (2004) Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J Biol Chem 279: 31655-31663.
    • (2004) J Biol Chem , vol.279 , pp. 31655-31663
    • Mol, C.D.1    Dougan, D.R.2    Schneider, T.R.3    Skene, R.J.4    Kraus, M.L.5
  • 20
    • 44949190466 scopus 로고    scopus 로고
    • Detailed conformational dynamics of juxtamembrane region and activation loop in c- Kit kinase activation process
    • Zou J, Wang YD, Ma FX, Xiang ML, Shi B, et al. (2008) Detailed conformational dynamics of juxtamembrane region and activation loop in c- Kit kinase activation process. Proteins 72: 323-332.
    • (2008) Proteins , vol.72 , pp. 323-332
    • Zou, J.1    Wang, Y.D.2    Ma, F.X.3    Xiang, M.L.4    Shi, B.5
  • 21
    • 0030378980 scopus 로고    scopus 로고
    • SMD: Visual steering of molecular dynamics for protein design
    • Leech J, Prins J, Hermans J (1996) SMD: Visual steering of molecular dynamics for protein design. IEEE Comput Sci Eng 3: 38-45.
    • (1996) IEEE Comput Sci Eng , vol.3 , pp. 38-45
    • Leech, J.1    Prins, J.2    Hermans, J.3
  • 22
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11: 224-230.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 23
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmuller H, Heymann B, Tavan P (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271: 997-999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmuller, H.1    Heymann, B.2    Tavan, P.3
  • 24
    • 62449268980 scopus 로고    scopus 로고
    • Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter
    • Gua Y, Shrivastava IH, Amara SG, Bahar I (2009) Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proc Natl Acad Sci U S A 106: 2589-2594.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 2589-2594
    • Gua, Y.1    Shrivastava, I.H.2    Amara, S.G.3    Bahar, I.4
  • 25
    • 51849109110 scopus 로고    scopus 로고
    • Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach
    • Martinez L, Polikarpov I, Skaf MS (2008) Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach. J Phys Chem B 112: 10741-10751.
    • (2008) J Phys Chem B , vol.112 , pp. 10741-10751
    • Martinez, L.1    Polikarpov, I.2    Skaf, M.S.3
  • 26
    • 30444446327 scopus 로고    scopus 로고
    • Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands
    • Martinez L, Webb P, Polikarpov I, Skaf MS (2006) Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands. J Med Chem 49: 23-26.
    • (2006) J Med Chem , vol.49 , pp. 23-26
    • Martinez, L.1    Webb, P.2    Polikarpov, I.3    Skaf, M.S.4
  • 27
    • 46349088224 scopus 로고    scopus 로고
    • Ligand dissociation from estrogen receptor Is mediated by receptor dimerization: Evidence from molecular dynamics simulations
    • Sonoda MT, Martinez L, Webb P, Skaf MS, Polikarpov I (2008) Ligand dissociation from estrogen receptor Is mediated by receptor dimerization: evidence from molecular dynamics simulations. Mol Endocrinol 22: 1565-1578.
    • (2008) Mol Endocrinol , vol.22 , pp. 1565-1578
    • Sonoda, M.T.1    Martinez, L.2    Webb, P.3    Skaf, M.S.4    Polikarpov, I.5
  • 28
    • 41049092350 scopus 로고    scopus 로고
    • Ligand- escape pathways from the ligand-binding domain of PPARg receptor as probed by molecular dynamics simulations
    • Genest D, Garnier N, Arrault A, Marot C, Morin-Allory L, et al. (2008) Ligand- escape pathways from the ligand-binding domain of PPARg receptor as probed by molecular dynamics simulations. Eur Biophys J 37: 369-379.
    • (2008) Eur Biophys J , vol.37 , pp. 369-379
    • Genest, D.1    Garnier, N.2    Arrault, A.3    Marot, C.4    Morin-Allory, L.5
  • 29
    • 33751218931 scopus 로고    scopus 로고
    • Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics
    • Carlsson P, Burendahl S, Nilsson L (2006) Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. Biophys J 91: 3151-3161.
    • (2006) Biophys J , vol.91 , pp. 3151-3161
    • Carlsson, P.1    Burendahl, S.2    Nilsson, L.3
  • 30
    • 66749085629 scopus 로고    scopus 로고
    • Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions
    • Huang H, Ozkirimli E, Post CB (2009) Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions. J Chem Theory Comput 5: 1304-1314.
    • (2009) J Chem Theory Comput , vol.5 , pp. 1304-1314
    • Huang, H.1    Ozkirimli, E.2    Post, C.B.3
  • 32
    • 0035810148 scopus 로고    scopus 로고
    • Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor
    • Joensuu H, Roberts PJ, Sarlomo-Rikala M, Andersson LC, Tervahartiala P, et al. (2001) Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor. N Engl J Med 344: 1052-1056.
    • (2001) N Engl J Med , vol.344 , pp. 1052-1056
    • Joensuu, H.1    Roberts, P.J.2    Sarlomo-Rikala, M.3    Andersson, L.C.4    Tervahartiala, P.5
  • 33
    • 0035960428 scopus 로고    scopus 로고
    • Safety and efficacy of imatinib (ST1571) in metastatic gastrointestinal stromal tumours: A phase I study
    • van Oosterom AT, Judson I, Verweij J, Stroobants S, di Paola ED, et al. (2001) Safety and efficacy of imatinib (ST1571) in metastatic gastrointestinal stromal tumours: a phase I study. Lancet 358: 1421-1423.
    • (2001) Lancet , vol.358 , pp. 1421-1423
    • van Oosterom, A.T.1    Judson, I.2    Verweij, J.3    Stroobants, S.4    di Paola, E.D.5
  • 34
    • 0344626926 scopus 로고    scopus 로고
    • Structural basis for the autoinhibition of c-Abl tyrosine kinase
    • Nagar B, Hantschel O, Young MA, Scheffzek K, Veach D, et al. (2003) Structural basis for the autoinhibition of c-Abl tyrosine kinase. Cell 112: 859-871.
    • (2003) Cell , vol.112 , pp. 859-871
    • Nagar, B.1    Hantschel, O.2    Young, M.A.3    Scheffzek, K.4    Veach, D.5
  • 35
    • 2942594298 scopus 로고    scopus 로고
    • Juxtamembrane autoinhibition in receptor tyrosine kinases
    • Hubbard SR (2004) Juxtamembrane autoinhibition in receptor tyrosine kinases. Nat Rev Mol Cell Biol 5: 464-470.
    • (2004) Nat Rev Mol Cell Biol , vol.5 , pp. 464-470
    • Hubbard, S.R.1
  • 36
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78: 2690-2693.
    • (1997) Phys Rev Lett , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 37
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • Liphardt J, Dumont S, Smith SB, Tinoco I, Bustamante C (2002) Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science 296: 1832-1835.
    • (2002) Science , vol.296 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco, I.4    Bustamante, C.5
  • 38
    • 0027794972 scopus 로고
    • Targeted molecular dynamics simulation of conformational change-application to the t↔r transition in insulin
    • Schlitter J, Engels M, Kruger P, Jacoby E, Wollmer A (1993) Targeted molecular dynamics simulation of conformational change-application to the t↔ transition in insulin. Mol Simul 10: 291-308.
    • (1993) Mol Simul , vol.10 , pp. 291-308
    • Schlitter, J.1    Engels, M.2    Kruger, P.3    Jacoby, E.4    Wollmer, A.5
  • 39
    • 0028455053 scopus 로고
    • Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
    • Schlitter J, Engels M, Kruger P (1994) Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graphics 12: 84-89.
    • (1994) J Mol Graphics , vol.12 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Kruger, P.3
  • 40
    • 0001160648 scopus 로고    scopus 로고
    • Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
    • Marchi M, Ballone P (1999) Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems. J Chem Phys 110: 3697-3702.
    • (1999) J Chem Phys , vol.110 , pp. 3697-3702
    • Marchi, M.1    Ballone, P.2
  • 41
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
    • Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol 288: 441-459.
    • (1999) J Mol Biol , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 43
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • Mackerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.4    Evanseck, J.D.5
  • 44
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov D, Roux B (1994) Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J Chem Phys 100: 9050-9063.
    • (1994) J Chem Phys , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 47
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation - the langevin piston method
    • Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant-pressure molecular-dynamics simulation - the langevin piston method. J Chem Phys 103: 4613-4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 48
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J-P R, G C, HJC B
    • J-P R, G C, HJC B (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
  • 49
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • S M PAK
    • S M, PA K (1992) SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13: 952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
  • 50
    • 33846823909 scopus 로고
    • Particle mesh ewald - an n.log(n) method for ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh ewald - an n.log(n) method for ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


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