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Volumn 73, Issue 1, 2008, Pages 11-18

Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors

Author keywords

Angiogenesis; Cancer; EphB4; Fragment based docking; High throughput screening; Tyrosine kinases

Indexed keywords

ADENOSINE TRIPHOSPHATE; ERYTHROPOIETIN PRODUCING HUMAN HEPATOCELLULAR CARCINOMA RECEPTOR TYROSINE KINASE B 4 INHIBITOR; PROTEIN TYROSINE KINASE INHIBITOR; UNCLASSIFIED DRUG;

EID: 50849118847     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22028     Document Type: Article
Times cited : (59)

References (43)
  • 2
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen WL. The many roles of computation in drug discovery. Science 2004;303:1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 6
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - a free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK. ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005;45:177-182.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 7
    • 2542631937 scopus 로고    scopus 로고
    • Virtual screening for inhibitors of human aldose reductase. Proteins: Struct Funct
    • Kraemer O, Hazemann I, Podjarny AD, Klebe G. Virtual screening for inhibitors of human aldose reductase. Proteins: Struct Funct Bioinformatics 2004;55:814-823.
    • (2004) Bioinformatics , vol.55 , pp. 814-823
    • Kraemer, O.1    Hazemann, I.2    Podjarny, A.D.3    Klebe, G.4
  • 8
    • 33745645832 scopus 로고    scopus 로고
    • Discovery of a nanomolar inhibitor of the human murine double minute 2 (MDM2)-p53 interaction through an integrated, virtual database screening strategy
    • Lu Y, Nikolovska-Coleska Z, Fang X, Gao W, Shangary S, Qiu S, Qin D, Wang S. Discovery of a nanomolar inhibitor of the human murine double minute 2 (MDM2)-p53 interaction through an integrated, virtual database screening strategy. J Med Chem 2006;49:3759-3762.
    • (2006) J Med Chem , vol.49 , pp. 3759-3762
    • Lu, Y.1    Nikolovska-Coleska, Z.2    Fang, X.3    Gao, W.4    Shangary, S.5    Qiu, S.6    Qin, D.7    Wang, S.8
  • 9
    • 33845511093 scopus 로고    scopus 로고
    • Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based highthroughput docking
    • Kolb P, Caflisch A. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based highthroughput docking. J Med Chem 2006;49:7384-7392.
    • (2006) J Med Chem , vol.49 , pp. 7384-7392
    • Kolb, P.1    Caflisch, A.2
  • 11
  • 12
    • 0034780805 scopus 로고    scopus 로고
    • Fragment-based flexible ligand docking by evolutionary optimization
    • Budin N, Majeux N, Caflisch A. Fragment-based flexible ligand docking by evolutionary optimization. Biol Chem 2001;382:1365-1372.
    • (2001) Biol Chem , vol.382 , pp. 1365-1372
    • Budin, N.1    Majeux, N.2    Caflisch, A.3
  • 13
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker A, Karplus M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins: Struct Funct Genet 1991;11:29-34.
    • (1991) Proteins: Struct Funct Genet , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 15
    • 1642288258 scopus 로고    scopus 로고
    • Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
    • Böhm HJ, Böhringer M, Bur D, Gmünder H, Huber W, Klaus W, Kostrewa D, Kühne H, Lübbers T, Meunier-Keller N, Müller F. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J Med Chem 2000;43:2664-2674.
    • (2000) J Med Chem , vol.43 , pp. 2664-2674
    • Böhm, H.J.1    Böhringer, M.2    Bur, D.3    Gmünder, H.4    Huber, W.5    Klaus, W.6    Kostrewa, D.7    Kühne, H.8    Lübbers, T.9    Meunier-Keller, N.10    Müller, F.11
  • 16
    • 0033026444 scopus 로고    scopus 로고
    • Strategies toward the design of novel and selective protein tyrosine kinase inhibitors
    • Traxler P, Furet P. Strategies toward the design of novel and selective protein tyrosine kinase inhibitors. Pharmacol Ther 1999;82:195-206.
    • (1999) Pharmacol Ther , vol.82 , pp. 195-206
    • Traxler, P.1    Furet, P.2
  • 17
    • 0042510626 scopus 로고    scopus 로고
    • Identification of a new chemical class of potent angiogenesis inhibitors based on conformational considerations and database searching
    • Furet P, Bold G, Hofmann F, Manley P, Meyer T, Altmann KH. Identification of a new chemical class of potent angiogenesis inhibitors based on conformational considerations and database searching. Bioorg Med Chem Lett 2003;13:2967-2971.
    • (2003) Bioorg Med Chem Lett , vol.13 , pp. 2967-2971
    • Furet, P.1    Bold, G.2    Hofmann, F.3    Manley, P.4    Meyer, T.5    Altmann, K.H.6
  • 19
    • 33845668264 scopus 로고    scopus 로고
    • Design and effective synthesis of novel templates, 3,7-diphenyl-4-amino-thieno and furo-[3,2-c]pyridines as protein kinase inhibitors and in vitro evaluation targeting angiogenetic kinases
    • Miyazaki Y, Nakano M, Sato H, Truesdale AT, Stuart JD, Nartey EN, Hightower KE, Kane-Carson L. Design and effective synthesis of novel templates, 3,7-diphenyl-4-amino-thieno and furo-[3,2-c]pyridines as protein kinase inhibitors and in vitro evaluation targeting angiogenetic kinases. Bioorg Med Chem Lett 2007;17:250-254.
    • (2007) Bioorg Med Chem Lett , vol.17 , pp. 250-254
    • Miyazaki, Y.1    Nakano, M.2    Sato, H.3    Truesdale, A.T.4    Stuart, J.D.5    Nartey, E.N.6    Hightower, K.E.7    Kane-Carson, L.8
  • 21
    • 33846899405 scopus 로고    scopus 로고
    • Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitors
    • Liao JL. Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitors. J Med Chem 2007;50:409-424.
    • (2007) J Med Chem , vol.50 , pp. 409-424
    • Liao, J.L.1
  • 23
    • 50849125284 scopus 로고    scopus 로고
    • Foggia P. The VFLib Graph Matching Library, version 2.0
    • Foggia P. The VFLib Graph Matching Library, version 2.0. http://amalfi.dis.unina.it/graph/db/vflib-2.0/doc/vflib.html
  • 24
    • 0035929146 scopus 로고    scopus 로고
    • Structural basis for autoinhibition of the EphB2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region
    • Wybenga-Groot LE, Baskin B, Ong SH, Tong J, Pawson T, Sicheri F. Structural basis for autoinhibition of the EphB2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region. Cell 2001;106:745-757.
    • (2001) Cell , vol.106 , pp. 745-757
    • Wybenga-Groot, L.E.1    Baskin, B.2    Ong, S.H.3    Tong, J.4    Pawson, T.5    Sicheri, F.6
  • 25
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 26
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 29
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 30
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4:187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4:187-217.
  • 31
    • 84986505827 scopus 로고
    • Validation of the general purpose QUANTA 3.2/CHARMm force field
    • Momany FA, Rone R. Validation of the general purpose QUANTA 3.2/CHARMm force field. J Comput Chem 1992;13:888-900.
    • (1992) J Comput Chem , vol.13 , pp. 888-900
    • Momany, F.A.1    Rone, R.2
  • 32
    • 0346951125 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. I. Application to neutral molecules as models for polypeptides
    • No K, Grant J, Scheraga H. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. I. Application to neutral molecules as models for polypeptides. J Phys Chem 1990;94:4732-4739.
    • (1990) J Phys Chem , vol.94 , pp. 4732-4739
    • No, K.1    Grant, J.2    Scheraga, H.3
  • 33
    • 33751553791 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. II. Application to ionic and aromatic molecules as models for polypeptides
    • No K, Grant J, Jhon M, Scheraga H. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. II. Application to ionic and aromatic molecules as models for polypeptides. J Phys Chem 1990;94:4740-4746.
    • (1990) J Phys Chem , vol.94 , pp. 4740-4746
    • No, K.1    Grant, J.2    Jhon, M.3    Scheraga, H.4
  • 34
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss D, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.3    Thornton, J.M.4
  • 35
    • 7444257387 scopus 로고    scopus 로고
    • Efficient evaluation of binding free energy
    • Huang D, Caflisch A. Efficient evaluation of binding free energy. J Med Chem 2004;47:5791-5797.
    • (2004) J Med Chem , vol.47 , pp. 5791-5797
    • Huang, D.1    Caflisch, A.2
  • 36
    • 41649096077 scopus 로고    scopus 로고
    • Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model
    • Kolb P, Huang D, Dey F, Caflisch A. Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. J Med Chem 2008;51:1179-1188.
    • (2008) J Med Chem , vol.51 , pp. 1179-1188
    • Kolb, P.1    Huang, D.2    Dey, F.3    Caflisch, A.4
  • 37
    • 20444427212 scopus 로고    scopus 로고
    • Virtual screening of 4-anilinoquinazoline analogues as EGFR kinase inhibitors: Importance of hydrogen bonds in the evaluation of poses and scoring functions
    • Aparna V, Rambabu G, Panigrahi SK, Sarma JARP, Desiraju GR. Virtual screening of 4-anilinoquinazoline analogues as EGFR kinase inhibitors: importance of hydrogen bonds in the evaluation of poses and scoring functions. J Chem Inf Model 2005;45:725-738.
    • (2005) J Chem Inf Model , vol.45 , pp. 725-738
    • Aparna, V.1    Rambabu, G.2    Panigrahi, S.K.3    Sarma, J.A.R.P.4    Desiraju, G.R.5
  • 38
    • 0019617042 scopus 로고
    • The specific velocity plot - a graphical method for determining inhibition parameters for both linear and hyperbolic enzyme-inhibitors
    • Baici A. The specific velocity plot - a graphical method for determining inhibition parameters for both linear and hyperbolic enzyme-inhibitors. Eur J Biochem 1981;119:9-14.
    • (1981) Eur J Biochem , vol.119 , pp. 9-14
    • Baici, A.1
  • 39
    • 0346850785 scopus 로고    scopus 로고
    • EphB4 signaling is capable of mediating ephrinb2-induced inhibition of cell migration
    • Sturz A, Bader B, Thierauch KH, Glienke J. EphB4 signaling is capable of mediating ephrinb2-induced inhibition of cell migration. Biochem Biophys Res Comm 2004;313:80-88.
    • (2004) Biochem Biophys Res Comm , vol.313 , pp. 80-88
    • Sturz, A.1    Bader, B.2    Thierauch, K.H.3    Glienke, J.4
  • 40
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: A useful metric for lead selection
    • Hopkins AL, Groom CR, Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov Today 2004;9:430-431.
    • (2004) Drug Discov Today , vol.9 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2    Alex, A.3
  • 41
    • 0029134581 scopus 로고    scopus 로고
    • Probing molecular interactions with homogeneous techniques based on rare earth cryptates and fluorescence energy transfer
    • Mathis G. Probing molecular interactions with homogeneous techniques based on rare earth cryptates and fluorescence energy transfer. Clin Chem 2003;41:1391-1397.
    • (2003) Clin Chem , vol.41 , pp. 1391-1397
    • Mathis, G.1
  • 42
    • 33745188660 scopus 로고    scopus 로고
    • Screening in a spirit haunted world
    • Shoichet BK. Screening in a spirit haunted world. Drug Discov Today 2006;11:607-615.
    • (2006) Drug Discov Today , vol.11 , pp. 607-615
    • Shoichet, B.K.1
  • 43
    • 33751076241 scopus 로고    scopus 로고
    • Deconstructing fragment-based inhibitor discovery
    • Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2006;2:720-723.
    • (2006) Nat Chem Biol , vol.2 , pp. 720-723
    • Babaoglu, K.1    Shoichet, B.K.2


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