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Volumn 11, Issue 11, 2015, Pages

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; DIAGNOSIS; DISEASES; DRUG THERAPY; ENZYMES; FREE ENERGY;

EID: 84949294800     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004578     Document Type: Article
Times cited : (57)

References (68)
  • 1
    • 0036635291 scopus 로고    scopus 로고
    • Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug
    • Capdeville R, Buchdunger E, Zimmermann J, Matter A, Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nat Rev Drug Discov. 2002;1(7):493–502. 12120256
    • (2002) Nat Rev Drug Discov , vol.1 , Issue.7 , pp. 493-502
    • Capdeville, R.1    Buchdunger, E.2    Zimmermann, J.3    Matter, A.4
  • 2
    • 33747154547 scopus 로고    scopus 로고
    • Evolving concepts in the management of chronic myeloid leukemia: recommendations from an expert panel on behalf of the European LeukemiaNet
    • Baccarani M, Saglio G, Goldman J, Hochhaus A, Simonsson B, Appelbaum F, et al. Evolving concepts in the management of chronic myeloid leukemia: recommendations from an expert panel on behalf of the European LeukemiaNet. Blood. 2006 Sep;108(6):1809–20. doi: 10.1182/blood-2006-02-005686 16709930
    • (2006) Blood , vol.108 , Issue.6 , pp. 1809-1820
    • Baccarani, M.1    Saglio, G.2    Goldman, J.3    Hochhaus, A.4    Simonsson, B.5    Appelbaum, F.6
  • 3
    • 84861850285 scopus 로고    scopus 로고
    • Very long-term follow-up results of imatinib mesylate therapy in chronic phase chronic myeloid leukemia after failure of interferon alpha therapy
    • Kantarjian H, O’Brien S, Garcia-Manero G, Faderl S, Ravandi F, Jabbour E, et al. Very long-term follow-up results of imatinib mesylate therapy in chronic phase chronic myeloid leukemia after failure of interferon alpha therapy. Cancer. 2012;118(12):3116–22. doi: 10.1002/cncr.26568 22370904
    • (2012) Cancer , vol.118 , Issue.12 , pp. 3116-3122
    • Kantarjian, H.1    O’Brien, S.2    Garcia-Manero, G.3    Faderl, S.4    Ravandi, F.5    Jabbour, E.6
  • 4
    • 0347132269 scopus 로고    scopus 로고
    • Regulation of the c-Abl and Bcr-Abl tyrosine kinases
    • Hantschel O, Superti-Furga G, Regulation of the c-Abl and Bcr-Abl tyrosine kinases. Nat Rev Mol Cell Biol. 2004 Jan;5(1):33–44. doi: 10.1038/nrm1280 14708008
    • (2004) Nat Rev Mol Cell Biol , vol.5 , Issue.1 , pp. 33-44
    • Hantschel, O.1    Superti-Furga, G.2
  • 5
    • 15944404601 scopus 로고    scopus 로고
    • The development of imatinib as a therapeutic agent for chronic myeloid leukemia
    • Deininger M, Buchdunger E, Druker BJ, The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood. 2005;105(7):2640–53. doi: 10.1182/blood-2004-08-3097 15618470
    • (2005) Blood , vol.105 , Issue.7 , pp. 2640-2653
    • Deininger, M.1    Buchdunger, E.2    Druker, B.J.3
  • 6
    • 79951913278 scopus 로고    scopus 로고
    • Mechanisms of drug resistance in kinases
    • Barouch-Bentov R, Sauer K, Mechanisms of drug resistance in kinases. Expert Opin Investig Drugs. 2011;20(2):153–208. doi: 10.1517/13543784.2011.546344 21235428
    • (2011) Expert Opin Investig Drugs , vol.20 , Issue.2 , pp. 153-208
    • Barouch-Bentov, R.1    Sauer, K.2
  • 7
    • 70149117469 scopus 로고    scopus 로고
    • Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations
    • Dixit A, Verkhivker GM, Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations. PLoS Comput Biol. 2009;5(8):e1000487. doi: 10.1371/journal.pcbi.1000487 19714203
    • (2009) PLoS Comput Biol , vol.5 , Issue.8
    • Dixit, A.1    Verkhivker, G.M.2
  • 8
    • 80053590126 scopus 로고    scopus 로고
    • Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases
    • Dixit A, Verkhivker GM, Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS Comput Biol. 2011;7(10):e1002179. doi: 10.1371/journal.pcbi.1002179 21998569
    • (2011) PLoS Comput Biol , vol.7 , Issue.10
    • Dixit, A.1    Verkhivker, G.M.2
  • 9
    • 0035800507 scopus 로고    scopus 로고
    • Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification
    • Gorre ME, Mohammed M, Ellwood K, Hsu N, Paquette R, Rao PN, et al. Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science. 2001;293(5531):876–80. doi: 10.1126/science.1062538 11423618
    • (2001) Science , vol.293 , Issue.5531 , pp. 876-880
    • Gorre, M.E.1    Mohammed, M.2    Ellwood, K.3    Hsu, N.4    Paquette, R.5    Rao, P.N.6
  • 10
    • 40049099220 scopus 로고    scopus 로고
    • The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP
    • Yun CH, Mengwasser KE, Toms AV, Woo MS, Greulich H, Wong KK, et al. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. Proc Natl Acad Sci USA. 2008;105(6):2070–5. doi: 10.1073/pnas.0709662105 18227510
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.6 , pp. 2070-2075
    • Yun, C.H.1    Mengwasser, K.E.2    Toms, A.V.3    Woo, M.S.4    Greulich, H.5    Wong, K.K.6
  • 11
    • 53549104402 scopus 로고    scopus 로고
    • Activation of tyrosine kinases by mutation of the gatekeeper threonine
    • Azam M, Seeliger MA, Gray NS, Kuriyan J, Daley GQ, Activation of tyrosine kinases by mutation of the gatekeeper threonine. Nat Struct Mol Biol. 2008 Oct;15(10):1109–1118. doi: 10.1038/nsmb.1486 18794843
    • (2008) Nat Struct Mol Biol , vol.15 , Issue.10 , pp. 1109-1118
    • Azam, M.1    Seeliger, M.A.2    Gray, N.S.3    Kuriyan, J.4    Daley, G.Q.5
  • 12
    • 84879510153 scopus 로고    scopus 로고
    • Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase
    • Sutto L, Gervasio FL, Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. Proc Natl Acad Sci USA. 2013;110(26):10616–21. doi: 10.1073/pnas.1221953110 23754386
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.26 , pp. 10616-10621
    • Sutto, L.1    Gervasio, F.L.2
  • 13
    • 84928731157 scopus 로고    scopus 로고
    • The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study
    • Bunney TD, Wan S, Thiyagarajan N, Sutto L, Williams SV, Ashford P, et al. The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study. EBioMedicine. 2015 Mar;2(3):194–204. doi: 10.1016/j.ebiom.2015.02.009 26097890
    • (2015) EBioMedicine , vol.2 , Issue.3 , pp. 194-204
    • Bunney, T.D.1    Wan, S.2    Thiyagarajan, N.3    Sutto, L.4    Williams, S.V.5    Ashford, P.6
  • 14
    • 84923348238 scopus 로고    scopus 로고
    • Kinase dynamics. Using ancient protein kinases to unravel a modern cancer drug’s mechanism
    • Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, et al. Kinase dynamics. Using ancient protein kinases to unravel a modern cancer drug’s mechanism. Science. 2015 Feb;347(6224):882–886. doi: 10.1126/science.aaa1823 25700521
    • (2015) Science , vol.347 , Issue.6224 , pp. 882-886
    • Wilson, C.1    Agafonov, R.V.2    Hoemberger, M.3    Kutter, S.4    Zorba, A.5    Halpin, J.6
  • 15
    • 0001686739 scopus 로고    scopus 로고
    • 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
    • Shah NP, Nicoll JM, Nagar B, Gorre ME, Paquette RL, Kuriyan J, et al. 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. doi: 10.1016/S1535-6108(02)00096-X 12204532
    • (2002) Cancer Cell , vol.2 , pp. 117-125
    • Shah, N.P.1    Nicoll, J.M.2    Nagar, B.3    Gorre, M.E.4    Paquette, R.L.5    Kuriyan, J.6
  • 16
    • 0037459344 scopus 로고    scopus 로고
    • Mechanisms of Autoinhibition and STI-571 / Imatinib Resistance Revealed by Mutagenesis of BCR-ABL
    • Azam M, Latek RR, Daley GQ, Mechanisms of Autoinhibition and STI-571 / Imatinib Resistance Revealed by Mutagenesis of BCR-ABL. Cell. 2003;112:831–843. doi: 10.1016/S0092-8674(03)00190-9 12654249
    • (2003) Cell , vol.112 , pp. 831-843
    • Azam, M.1    Latek, R.R.2    Daley, G.Q.3
  • 17
    • 33745164854 scopus 로고    scopus 로고
    • Activity of dual SRC-ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance
    • Azam M, Nardi V, Shakespeare WC, Metcalf CA, Bohacek RS, Wang Y, et al. Activity of dual SRC-ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance. Proc Natl Acad Sci USA. 2006;103(24):9244–9. doi: 10.1073/pnas.0600001103 16754879
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.24 , pp. 9244-9249
    • Azam, M.1    Nardi, V.2    Shakespeare, W.C.3    Metcalf, C.A.4    Bohacek, R.S.5    Wang, Y.6
  • 18
    • 33646742004 scopus 로고    scopus 로고
    • Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
    • Zheng W, Brooks BR, Thirumalai D, Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci USA. 2006;103(20):7664–9. doi: 10.1073/pnas.0510426103 16682636
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.20 , pp. 7664-7669
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 19
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R, Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 2000;9(1):10–9. doi: 10.1110/ps.9.1.10 10739242
    • (2000) Protein Sci , vol.9 , Issue.1 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 20
    • 84940081777 scopus 로고    scopus 로고
    • A dynamically coupled allosteric network underlies binding cooperativity in Src kinase
    • Foda ZH, Shan Y, Kim ET, Shaw DE, Seeliger MA, A dynamically coupled allosteric network underlies binding cooperativity in Src kinase. Nat Comm. 2015;6:5939. doi: 10.1038/ncomms6939
    • (2015) Nat Comm , vol.6 , pp. 5939
    • Foda, Z.H.1    Shan, Y.2    Kim, E.T.3    Shaw, D.E.4    Seeliger, M.A.5
  • 21
    • 33745298429 scopus 로고    scopus 로고
    • Rational design of inhibitors that bind to inactive kinase conformations
    • Liu Y, Gray NS, Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol. 2006;2(7):358–64. doi: 10.1038/nchembio799 16783341
    • (2006) Nat Chem Biol , vol.2 , Issue.7 , pp. 358-364
    • Liu, Y.1    Gray, N.S.2
  • 23
    • 58549114067 scopus 로고    scopus 로고
    • A conserved protonation-dependent switch controls drug binding in the Abl kinase
    • Shan Y, Seeliger MA, Eastwood MP, Frank F, Xu H, Jensen MO, et al. A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proc Natl Acad Sci USA. 2009;106(1):139–144. doi: 10.1073/pnas.0811223106 19109437
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.1 , pp. 139-144
    • Shan, Y.1    Seeliger, M.A.2    Eastwood, M.P.3    Frank, F.4    Xu, H.5    Jensen, M.O.6
  • 24
    • 0036682301 scopus 로고    scopus 로고
    • Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small Molecule Inhibitors PD173955 and Imatinib Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small
    • Nagar B, Bornmann WG, Pellicena P, Pd MI, Sti I, Schindler T, et al. Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small Molecule Inhibitors PD173955 and Imatinib Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small. Cancer. 2002;p. 4236–4243.
    • (2002) Cancer , pp. 4236-4243
    • Nagar, B.1    Bornmann, W.G.2    Pellicena, P.3    Pd, M.I.4    Sti, I.5    Schindler, T.6
  • 25
    • 78649340278 scopus 로고    scopus 로고
    • Article Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry
    • Wodicka LM, Ciceri P, Davis MI, Hunt JP, Floyd M, Salerno S, et al. Article Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry. Chem Biol. 2010;17(11):1241–1249. doi: 10.1016/j.chembiol.2010.09.010 21095574
    • (2010) Chem Biol , vol.17 , Issue.11 , pp. 1241-1249
    • Wodicka, L.M.1    Ciceri, P.2    Davis, M.I.3    Hunt, J.P.4    Floyd, M.5    Salerno, S.6
  • 26
    • 33847659183 scopus 로고    scopus 로고
    • c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
    • Seeliger Ma, Nagar B, Frank F, Cao X, Henderson MN, Kuriyan J, c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure. 2007;15(3):299–311. doi: 10.1016/j.str.2007.01.015 17355866
    • (2007) Structure , vol.15 , Issue.3 , pp. 299-311
    • Seeliger, M.1    Nagar, B.2    Frank, F.3    Cao, X.4    Henderson, M.N.5    Kuriyan, J.6
  • 27
    • 77951557992 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
    • Aleksandrov A, Simonson T, Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases. J Biol Chem. 2010 Apr;285(18):13807–13815. doi: 10.1074/jbc.M110.109660 20200154
    • (2010) J Biol Chem , vol.285 , Issue.18 , pp. 13807-13815
    • Aleksandrov, A.1    Simonson, T.2
  • 28
    • 84873135773 scopus 로고    scopus 로고
    • Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
    • Lin YL, Meng Y, Jiang W, Roux B, Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci USA. 2013 Jan;110(5):1664–1669. doi: 10.1073/pnas.1214330110 23319661
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.5 , pp. 1664-1669
    • Lin, Y.L.1    Meng, Y.2    Jiang, W.3    Roux, B.4
  • 29
    • 84856694630 scopus 로고    scopus 로고
    • The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation
    • Lovera S, Sutto L, Boubeva R, Scapozza L, Dölker N, Gervasio FL, The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation. J Am Chem Soc. 2012;134(5):2496–9. doi: 10.1021/ja210751t 22280319
    • (2012) J Am Chem Soc , vol.134 , Issue.5 , pp. 2496-2499
    • Lovera, S.1    Sutto, L.2    Boubeva, R.3    Scapozza, L.4    Dölker, N.5    Gervasio, F.L.6
  • 30
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL, Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779–815. doi: 10.1006/jmbi.1993.1626 8254673
    • (1993) J Mol Biol , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 31
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C, Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct Funct Bioinf. 2006;65:712–725. doi: 10.1002/prot.21123
    • (2006) Proteins: Struct Funct Bioinf , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 32
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the Amber ff99SB protein force field
    • Lindorff-larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010;78(8):1950–8. doi: 10.1002/prot.22711 20408171
    • (2010) Proteins , vol.78 , Issue.8 , pp. 1950-1958
    • Lindorff-larsen, K.1    Piana, S.2    Palmo, K.3    Maragakis, P.4    Klepeis, J.L.5    Dror, R.O.6
  • 33
    • 67649494492 scopus 로고    scopus 로고
    • Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
    • Best RB, Hummer G, Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B. 2009;113(26):9004–15. doi: 10.1021/jp901540t 19514729
    • (2009) J Phys Chem B , vol.113 , Issue.26 , pp. 9004-9015
    • Best, R.B.1    Hummer, G.2
  • 34
    • 33645858780 scopus 로고
    • Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
    • Jorgensen WL, Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J Am Chem Soc. 1981;103(2):335–340. doi: 10.1021/ja00392a016
    • (1981) J Am Chem Soc , vol.103 , Issue.2 , pp. 335-340
    • Jorgensen, W.L.1
  • 35
    • 67650099787 scopus 로고    scopus 로고
    • ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
    • Harvey MJ, Giupponi G, De Fabritiis G, ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. J Chem Theory Comput. 2009;5(6):1632–1639. doi: 10.1021/ct9000685
    • (2009) J Chem Theory Comput , vol.5 , Issue.6 , pp. 1632-1639
    • Harvey, M.J.1    Giupponi, G.2    De Fabritiis, G.3
  • 36
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
    • Bussi G, Gervasio FL, Laio A, Parrinello M, Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc. 2006;128(41):13435–41. doi: 10.1021/ja062463w 17031956
    • (2006) J Am Chem Soc , vol.128 , Issue.41 , pp. 13435-13441
    • Bussi, G.1    Gervasio, F.L.2    Laio, A.3    Parrinello, M.4
  • 37
    • 38349091489 scopus 로고    scopus 로고
    • Well-tempered metadynamics: A smoothly converging and tunable free-energy method
    • Barducci A, Bussi G, Parrinello M, Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Phys Rev Lett. 2008;100(2):020603. doi: 10.1103/PhysRevLett.100.020603 18232845
    • (2008) Phys Rev Lett , vol.100 , Issue.2 , pp. 020603
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 38
    • 77952404209 scopus 로고    scopus 로고
    • Enhanced Sampling in the Well-Tempered Ensemble
    • Bonomi M, Parrinello M, Enhanced Sampling in the Well-Tempered Ensemble. Phys Rev Lett. 2010;104(19):1–4. doi: 10.1103/PhysRevLett.104.190601
    • (2010) Phys Rev Lett , vol.104 , Issue.19 , pp. 1-4
    • Bonomi, M.1    Parrinello, M.2
  • 39
    • 84863650597 scopus 로고    scopus 로고
    • Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble
    • Deighan M, Bonomi M, Pfaendtner J, Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble. J Chem Theory Comput. 2012; 8(7):2189–2192. doi: 10.1021/ct300297t
    • (2012) J Chem Theory Comput , vol.8 , Issue.7 , pp. 2189-2192
    • Deighan, M.1    Bonomi, M.2    Pfaendtner, J.3
  • 40
    • 84908348822 scopus 로고    scopus 로고
    • The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion
    • Dölker N, Górna MW, Sutto L, Torralba AS, Superti-Furga G, Gervasio FL, The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion. PLoS Comput Biol. 2014;10(10):e1003863. doi: 10.1371/journal.pcbi.1003863 25299346
    • (2014) PLoS Comput Biol , vol.10 , Issue.10
    • Dölker, N.1    Górna, M.W.2    Sutto, L.3    Torralba, A.S.4    Superti-Furga, G.5    Gervasio, F.L.6
  • 41
    • 84928725331 scopus 로고    scopus 로고
    • The Effect of a Widespread Cancer-Causing Mutation on the Inactive to Active Dynamics of the B-Raf Kinase
    • Marino KA, Sutto L, Gervasio FL, The Effect of a Widespread Cancer-Causing Mutation on the Inactive to Active Dynamics of the B-Raf Kinase. J Am Chem Soc. 2015 Apr;137:5280–5283. doi: 10.1021/jacs.5b01421 25868080
    • (2015) J Am Chem Soc , vol.137 , pp. 5280-5283
    • Marino, K.A.1    Sutto, L.2    Gervasio, F.L.3
  • 42
    • 84907199037 scopus 로고    scopus 로고
    • Conformational Changes and Free Energies in a Proline Isomerase
    • Papaleo E, Sutto L, Gervasio FL, Lindorff-Larsen K, Conformational Changes and Free Energies in a Proline Isomerase. J Chem Theory Comput. 2014;10(9):4169–4174. doi: 10.1021/ct500536r
    • (2014) J Chem Theory Comput , vol.10 , Issue.9 , pp. 4169-4174
    • Papaleo, E.1    Sutto, L.2    Gervasio, F.L.3    Lindorff-Larsen, K.4
  • 43
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, Spoel DVD, Lindahl E, van Der Spoel D, Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4(3):435–447. doi: 10.1021/ct700301q
    • (2008) J Chem Theory Comput , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Spoel, D.V.D.3    Lindahl, E.4    van Der Spoel, D.5
  • 44
    • 69349100797 scopus 로고    scopus 로고
    • PLUMED: a portable plugin for free-energy calculations with molecular dynamics
    • Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, et al. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Comp Phys Comm. 2009;180:1961–1972. doi: 10.1016/j.cpc.2009.05.011
    • (2009) Comp Phys Comm , vol.180 , pp. 1961-1972
    • Bonomi, M.1    Branduardi, D.2    Bussi, G.3    Camilloni, C.4    Provasi, D.5    Raiteri, P.6
  • 45
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M, Canonical sampling through velocity rescaling. J Chem Phys. 2007;126:14101. doi: 10.1063/1.2408420
    • (2007) J Chem Phys , vol.126 , pp. 14101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 46
    • 84907327659 scopus 로고    scopus 로고
    • A time-independent free energy estimator for metadynamics
    • Tiwary P, Parrinello M, A time-independent free energy estimator for metadynamics. J Phys Chem B. 2015 Jan;119(3):736–742. doi: 10.1021/jp504920s 25046020
    • (2015) J Phys Chem B , vol.119 , Issue.3 , pp. 736-742
    • Tiwary, P.1    Parrinello, M.2
  • 47
    • 33846946504 scopus 로고    scopus 로고
    • From A to B in free energy space
    • Branduardi D, Gervasio FL, Parrinello M, From A to B in free energy space. J Chem Phys. 2007 Feb;126(5):054103. doi: 10.1063/1.2432340 17302470
    • (2007) J Chem Phys , vol.126 , Issue.5 , pp. 054103
    • Branduardi, D.1    Gervasio, F.L.2    Parrinello, M.3
  • 48
    • 84929174775 scopus 로고    scopus 로고
    • Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics
    • Jo S, Chipot C, Roux B, Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. J Chem Theory Comput. 2015;11(5):2234–2244. doi: 10.1021/ct501034w
    • (2015) J Chem Theory Comput , vol.11 , Issue.5 , pp. 2234-2244
    • Jo, S.1    Chipot, C.2    Roux, B.3
  • 50
    • 84872241513 scopus 로고    scopus 로고
    • New insights in protein kinase conformational dynamics
    • Saladino G, Gervasio FL, New insights in protein kinase conformational dynamics. Curr Tomp Med Chem. 2012 Sep;12(17):1889–1895. doi: 10.2174/156802612804547407
    • (2012) Curr Tomp Med Chem , vol.12 , Issue.17 , pp. 1889-1895
    • Saladino, G.1    Gervasio, F.L.2
  • 51
    • 84923072401 scopus 로고    scopus 로고
    • Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms
    • Cavalli A, Spitaleri A, Saladino G, Gervasio FL, Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms. Acc Chem Res. 2015 Feb;48(2):277–285. doi: 10.1021/ar500356n 25496113
    • (2015) Acc Chem Res , vol.48 , Issue.2 , pp. 277-285
    • Cavalli, A.1    Spitaleri, A.2    Saladino, G.3    Gervasio, F.L.4
  • 52
    • 65249103495 scopus 로고    scopus 로고
    • Exploring Complex Protein-Ligand Recognition Mechanisms with Coarse Metadynamics
    • Masetti M, Cavalli A, Recanatini M, Gervasio FL, Exploring Complex Protein-Ligand Recognition Mechanisms with Coarse Metadynamics. The journal of physical chemistry B. 2009;113(14):4807–4816. doi: 10.1021/jp803936q 19298042
    • (2009) The journal of physical chemistry B , vol.113 , Issue.14 , pp. 4807-4816
    • Masetti, M.1    Cavalli, A.2    Recanatini, M.3    Gervasio, F.L.4
  • 53
    • 84855392245 scopus 로고    scopus 로고
    • Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib
    • Campos-Olivas R, Marenchino M, Scapozza L, Gervasio FL, Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib. Biomol NMR Assign. 2011 Oct;5(2):221–4. doi: 10.1007/s12104-011-9304-7 21523440
    • (2011) Biomol NMR Assign , vol.5 , Issue.2 , pp. 221-224
    • Campos-Olivas, R.1    Marenchino, M.2    Scapozza, L.3    Gervasio, F.L.4
  • 54
    • 10744232328 scopus 로고    scopus 로고
    • 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
    • Branford S, Rudzki Z, Walsh S, Parkinson I, Grigg A, Szer J, 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 Jul;102(1):276–83. doi: 10.1182/blood-2002-09-2896 12623848
    • (2003) Blood , vol.102 , Issue.1 , pp. 276-283
    • Branford, S.1    Rudzki, Z.2    Walsh, S.3    Parkinson, I.4    Grigg, A.5    Szer, J.6
  • 55
    • 0033816156 scopus 로고    scopus 로고
    • Abl protein-tyrosine kinase inhibitor STI571 inhibits in vitro signal transduction mediated by c-kit and platelet-derived growth factor receptors
    • Buchdunger E, Cioffi CL, Law N, Stover D, Ohno-Jones S, Druker BJ, et al. Abl protein-tyrosine kinase inhibitor STI571 inhibits in vitro signal transduction mediated by c-kit and platelet-derived growth factor receptors. J Pharmacol Exp Ther. 2000;295(1):139–45. 10991971
    • (2000) J Pharmacol Exp Ther , vol.295 , Issue.1 , pp. 139-145
    • Buchdunger, E.1    Cioffi, C.L.2    Law, N.3    Stover, D.4    Ohno-Jones, S.5    Druker, B.J.6
  • 56
    • 0035979656 scopus 로고    scopus 로고
    • Bcr-Abl inhibition as a modality of CML therapeutics
    • Buchdunger E, Matter A, Druker BJ, Bcr-Abl inhibition as a modality of CML therapeutics. Biochim Biophys Acta. 2001;1551(1):M11–8. 11553417
    • (2001) Biochim Biophys Acta , vol.1551 , Issue.1 , pp. M8-M11
    • Buchdunger, E.1    Matter, A.2    Druker, B.J.3
  • 57
    • 0031026055 scopus 로고    scopus 로고
    • Potent and selective inhibitors of the Abl-kinase: phenylamino-pyrimidine (PAP) derivatives
    • Zimmermann J, Buchdunger E, Mett H, Meyer T, Lydon NB, Potent and selective inhibitors of the Abl-kinase: phenylamino-pyrimidine (PAP) derivatives. Bioorg Med Chem Lett. 1997;7(2):187–192. doi: 10.1016/S0960-894X(96)00601-4
    • (1997) Bioorg Med Chem Lett , vol.7 , Issue.2 , pp. 187-192
    • Zimmermann, J.1    Buchdunger, E.2    Mett, H.3    Meyer, T.4    Lydon, N.B.5
  • 58
    • 0034665713 scopus 로고    scopus 로고
    • Structural mechanism for STI-571 inhibition of abelson tyrosine kinase
    • Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, Kuriyan J, Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science (80-). 2000;289(5486):1938–42. doi: 10.1126/science.289.5486.1938
    • (2000) Science (80-) , vol.289 , Issue.5486 , pp. 1938-1942
    • Schindler, T.1    Bornmann, W.2    Pellicena, P.3    Miller, W.T.4    Clarkson, B.5    Kuriyan, J.6
  • 59
    • 33749325184 scopus 로고    scopus 로고
    • Comparison of imatinib mesylate, dasatinib (BMS-354825), and nilotinib (AMN107) in an N-ethyl-N-nitrosourea (ENU)–based mutagenesis screen: high efficacy of drug combinations
    • Bradeen HA, Eide CA, O’Hare T, Johnson KJ, Willis SG, Lee FY, et al. Comparison of imatinib mesylate, dasatinib (BMS-354825), and nilotinib (AMN107) in an N-ethyl-N-nitrosourea (ENU)–based mutagenesis screen: high efficacy of drug combinations. Blood. 2006;108(7):2332–2338. doi: 10.1182/blood-2006-02-004580 16772610
    • (2006) Blood , vol.108 , Issue.7 , pp. 2332-2338
    • Bradeen, H.A.1    Eide, C.A.2    O’Hare, T.3    Johnson, K.J.4    Willis, S.G.5    Lee, F.Y.6
  • 60
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young Ma, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J, Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 2001;105(1):115–26. doi: 10.1016/S0092-8674(01)00301-4 11301007
    • (2001) Cell , vol.105 , Issue.1 , pp. 115-126
    • Young, M.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 61
    • 75749146563 scopus 로고    scopus 로고
    • Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors
    • Zhang J, Adrián FJ, Jahnke W, Cowan-Jacob SW, Li AG, Iacob RE, et al. Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature. 2010 Jan;463(7280):501–6. doi: 10.1038/nature08675 20072125
    • (2010) Nature , vol.463 , Issue.7280 , pp. 501-506
    • Zhang, J.1    Adrián, F.J.2    Jahnke, W.3    Cowan-Jacob, S.W.4    Li, A.G.5    Iacob, R.E.6
  • 62
    • 65549152514 scopus 로고    scopus 로고
    • Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations
    • Seeliger Ma, Ranjitkar P, Kasap C, Shan Y, Shaw DE, Shah NP, et al. Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res. 2009;69(6):2384–92. doi: 10.1158/0008-5472.CAN-08-3953 19276351
    • (2009) Cancer Res , vol.69 , Issue.6 , pp. 2384-2392
    • Seeliger, M.1    Ranjitkar, P.2    Kasap, C.3    Shan, Y.4    Shaw, D.E.5    Shah, N.P.6
  • 63
    • 84860870716 scopus 로고    scopus 로고
    • Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization
    • Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, Dror RO, et al. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell. 2012;149(4):860–870. doi: 10.1016/j.cell.2012.02.063 22579287
    • (2012) Cell , vol.149 , Issue.4 , pp. 860-870
    • Shan, Y.1    Eastwood, M.P.2    Zhang, X.3    Kim, E.T.4    Arkhipov, A.5    Dror, R.O.6
  • 64
    • 84891836984 scopus 로고    scopus 로고
    • Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
    • Meng Y, Roux B, Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop. J Mol Biol. 2014;426:423–435. doi: 10.1016/j.jmb.2013.10.001 24103328
    • (2014) J Mol Biol , vol.426 , pp. 423-435
    • Meng, Y.1    Roux, B.2
  • 65
    • 68849105058 scopus 로고    scopus 로고
    • Double EGFR mutants containing rare EGFR mutant types show reduced in vitro response to gefitinib compared with common activating missense mutations
    • Tam IYS, Leung ELH, Tin VPC, Chua DTT, Sihoe ADL, Cheng LC, et al. Double EGFR mutants containing rare EGFR mutant types show reduced in vitro response to gefitinib compared with common activating missense mutations. Mol Cancer Ther. 2009;8(8):2142–51. doi: 10.1158/1535-7163.MCT-08-1219 19671738
    • (2009) Mol Cancer Ther , vol.8 , Issue.8 , pp. 2142-2151
    • Tam, I.Y.S.1    Leung, E.L.H.2    Tin, V.P.C.3    Chua, D.T.T.4    Sihoe, A.D.L.5    Cheng, L.C.6
  • 66
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita O, Onuchic JN, Wolynes PG, Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA. 2003;100(22):12570–12575. doi: 10.1073/pnas.2135471100 14566052
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.22 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 67
    • 84876902448 scopus 로고    scopus 로고
    • Transitions to catalytically inactive conformations in EGFR kinase
    • Shan Y, Arkhipov a, Kim ET, Pan aC, Shaw DE, Transitions to catalytically inactive conformations in EGFR kinase. Proc Natl Acad Sci USA. 2013;110(18): 7270–7275. doi: 10.1073/pnas.1220843110 23576739
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.18 , pp. 7270-7275
    • Shan, Y.1    Arkhipov, A.2    Kim, E.T.3    Pan, C.4    Shaw, D.E.5
  • 68
    • 77949525702 scopus 로고    scopus 로고
    • Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl
    • Yang LJ, Zou J, Xie HZ, Li LL, Wei YQ, Yang SY, Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl. PLoS ONE. 2009;4(12):e8470. doi: 10.1371/journal.pone.0008470 20041122
    • (2009) PLoS ONE , vol.4 , Issue.12
    • Yang, L.J.1    Zou, J.2    Xie, H.Z.3    Li, L.L.4    Wei, Y.Q.5    Yang, S.Y.6


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