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Volumn 5, Issue JUN, 2014, Pages

Computational methods for analysis and inference of kinase/inhibitor relationships

Author keywords

Chemogenomics; Drug design and development; Kinase activity modulation; Kinase inhibitors; Kinase inhibitor inference

Indexed keywords

CYCLIN DEPENDENT KINASE 2; DASATINIB; G PROTEIN COUPLED RECEPTOR INHIBITOR; IMATINIB; PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE INHIBITOR; PROTEIN KINASE INHIBITOR; UNCLASSIFIED DRUG;

EID: 84906247317     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00196     Document Type: Short Survey
Times cited : (18)

References (41)
  • 1
    • 80755125565 scopus 로고    scopus 로고
    • Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity
    • doi: 10.1038/nbt.2017
    • Anastassiadis, T., Deacon, S. W., Devarajan, K., Ma, H., and Peterson, J. R. (2011). Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nat. Biotechnol. 29, 1039-1045. doi: 10.1038/nbt.2017
    • (2011) Nat. Biotechnol. , vol.29 , pp. 1039-1045
    • Anastassiadis, T.1    Deacon, S.W.2    Devarajan, K.3    Ma, H.4    Peterson, J.R.5
  • 2
    • 84858029492 scopus 로고    scopus 로고
    • Identification of binding specificity-determining features in protein families
    • doi: 10.1021/jm200979x
    • Anderson, P. C., De Sapio, V., Turner, K. B., Elmer, S. P., Roe, D. C., and Schoeniger, J. S. (2012). Identification of binding specificity-determining features in protein families. J. Med. Chem. 55, 1926-1939. doi: 10.1021/jm200979x
    • (2012) J. Med. Chem. , vol.55 , pp. 1926-1939
    • Anderson, P.C.1    De Sapio, V.2    Turner, K.B.3    Elmer, S.P.4    Roe, D.C.5    Schoeniger, J.S.6
  • 3
    • 36549040859 scopus 로고    scopus 로고
    • The selectivity of protein kinase inhibitors: a further update
    • doi: 10.1042/BJ20070797
    • Bain, J., Plater, L., Elliott, M., Shpiro, N., Hastie, C. J., McLauchlan, H. et al. (2007). The selectivity of protein kinase inhibitors: a further update. Biochem. J. 408, 297-315. doi: 10.1042/BJ20070797
    • (2007) Biochem. J. , vol.408 , pp. 297-315
    • Bain, J.1    Plater, L.2    Elliott, M.3    Shpiro, N.4    Hastie, C.J.5    McLauchlan, H.6
  • 4
    • 58149102549 scopus 로고    scopus 로고
    • Assessment of chemical coverage of kinome space and its implications for kinase drug discovery
    • doi: 10.1021/jm8011036
    • Bamborough, P., Drewry, D., Harper, G., Smith, G. K., and Schneider, K. (2008). Assessment of chemical coverage of kinome space and its implications for kinase drug discovery. J. Med. Chem. 51, 7898-7914. doi: 10.1021/jm8011036
    • (2008) J. Med. Chem. , vol.51 , pp. 7898-7914
    • Bamborough, P.1    Drewry, D.2    Harper, G.3    Smith, G.K.4    Schneider, K.5
  • 5
    • 84883470010 scopus 로고    scopus 로고
    • How community has shaped the Protein Data Bank
    • doi: 10.1016/j.str.2013.07.010
    • Berman, H. M., Kleywegt, G. J., Nakamura, H., and Markley, J. L. (2013). How community has shaped the Protein Data Bank. Structure 21, 1485-1491. doi: 10.1016/j.str.2013.07.010
    • (2013) Structure , vol.21 , pp. 1485-1491
    • Berman, H.M.1    Kleywegt, G.J.2    Nakamura, H.3    Markley, J.L.4
  • 6
    • 84879530245 scopus 로고    scopus 로고
    • Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome
    • doi: 10.1371/journal.pcbi.1003087
    • Bryant, D. H., Moll, M., Finn, P. W., and Kavraki, L. E. (2013). Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PLoS Comput. Biol. 9:e1003087. doi: 10.1371/journal.pcbi.1003087
    • (2013) PLoS Comput. Biol , vol.9
    • Bryant, D.H.1    Moll, M.2    Finn, P.W.3    Kavraki, L.E.4
  • 7
    • 78649946365 scopus 로고    scopus 로고
    • Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach
    • doi: 10.1021/mp1002976
    • Brylinski, M., and Skolnick, J. (2010). Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol. Pharm. 7, 2324-2333. doi: 10.1021/mp1002976
    • (2010) Mol. Pharm. , vol.7 , pp. 2324-2333
    • Brylinski, M.1    Skolnick, J.2
  • 8
    • 57649131066 scopus 로고    scopus 로고
    • Prediction of specificity-determining residues for small-molecule kinase inhibitors
    • doi: 10.1186/1471-2105-9-491
    • Caffrey, D. R., Lunney, E. A., and Moshinsky, D. J. (2008). Prediction of specificity-determining residues for small-molecule kinase inhibitors. BMC Bioinformatics 9:491. doi: 10.1186/1471-2105-9-491
    • (2008) BMC Bioinformatics , vol.9 , pp. 491
    • Caffrey, D.R.1    Lunney, E.A.2    Moshinsky, D.J.3
  • 9
    • 84881028324 scopus 로고    scopus 로고
    • Large-scale prediction of human kinase/inhibitor interactions using protein sequences and molecular topological structures
    • doi: 10.1016/j.aca.2013.07.003
    • Cao, D. S., Zhou, G. H., Liu, S., Zhang, L. X., Xu, Q. S., He, M. et al. (2013). Large-scale prediction of human kinase/inhibitor interactions using protein sequences and molecular topological structures. Anal. Chim. Acta 792, 10-18. doi: 10.1016/j.aca.2013.07.003
    • (2013) Anal. Chim. Acta , vol.792 , pp. 10-18
    • Cao, D.S.1    Zhou, G.H.2    Liu, S.3    Zhang, L.X.4    Xu, Q.S.5    He, M.6
  • 10
    • 84860295971 scopus 로고    scopus 로고
    • Small molecule kinase inhibitors as anti-cancer therapeutics
    • doi: 10.2174/138955712800493915
    • Chahrour, O., Cairns, D., and Omran, Z. (2012). Small molecule kinase inhibitors as anti-cancer therapeutics. Mini Rev. Med. Chem. 12, 399-411. doi: 10.2174/138955712800493915
    • (2012) Mini Rev. Med. Chem. , vol.12 , pp. 399-411
    • Chahrour, O.1    Cairns, D.2    Omran, Z.3
  • 11
    • 77954249073 scopus 로고    scopus 로고
    • SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties
    • doi: 10.1093/nar/gkq480
    • Chen, Y. F., Hsu, K. C., Lin, S. R., Wang, W. C., Huang, Y. C., and Yang, J. M. (2010). SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Res. 38, W424-W430. doi: 10.1093/nar/gkq480
    • (2010) Nucleic Acids Res. , vol.38
    • Chen, Y.F.1    Hsu, K.C.2    Lin, S.R.3    Wang, W.C.4    Huang, Y.C.5    Yang, J.M.6
  • 12
    • 84876517808 scopus 로고    scopus 로고
    • KIDFamMap: a database of kinase/inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms
    • doi: 10.1093/nar/gks1218
    • Chiu, Y. Y., Lin, C. T., Huang, J. W., Hsu, K. C., Tseng, J. H., You, S. R. et al. (2013). KIDFamMap: a database of kinase/inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. Nucleic Acids Res. 41, D430-D440. doi: 10.1093/nar/gks1218
    • (2013) Nucleic Acids Res. , vol.41
    • Chiu, Y.Y.1    Lin, C.T.2    Huang, J.W.3    Hsu, K.C.4    Tseng, J.H.5    You, S.R.6
  • 13
    • 12144249613 scopus 로고    scopus 로고
    • Interaction profiles of protein kinase/inhibitor complexes and their application to virtual screening
    • doi: 10.1021/jm049312t
    • Chuaqui, C., Deng, Z., and Singh, J. (2005). Interaction profiles of protein kinase/inhibitor complexes and their application to virtual screening. J. Med. Chem. 48, 121-133. doi: 10.1021/jm049312t
    • (2005) J. Med. Chem. , vol.48 , pp. 121-133
    • Chuaqui, C.1    Deng, Z.2    Singh, J.3
  • 14
  • 16
    • 38049155899 scopus 로고    scopus 로고
    • A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases
    • doi: 10.1073/pnas.0708800104
    • Fedorov, O., Marsden, B., Pogacic, V., Rellos, P., Müller, S., Bullock, A. N. et al. (2007). A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc. Natl. Acad. Sci. U.S.A. 104, 20523-20528. doi: 10.1073/pnas.0708800104
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 20523-20528
    • Fedorov, O.1    Marsden, B.2    Pogacic, V.3    Rellos, P.4    Müller, S.5    Bullock, A.N.6
  • 17
    • 77249164281 scopus 로고    scopus 로고
    • The (un)targeted cancer kinome
    • doi: 10.1038/nchembio.297
    • Fedorov, O., Muller, S., and Knapp, S. (2010). The (un)targeted cancer kinome. Nat. Chem. Biol. 6, 166-169. doi: 10.1038/nchembio.297
    • (2010) Nat. Chem. Biol. , vol.6 , pp. 166-169
    • Fedorov, O.1    Muller, S.2    Knapp, S.3
  • 18
    • 77955645488 scopus 로고    scopus 로고
    • Non-ATP competitive protein kinase inhibitors
    • doi: 10.2174/092986710791859333
    • Garuti, L., Roberti, M., and Bottegoni, G. (2010). Non-ATP competitive protein kinase inhibitors. Curr. Med. Chem. 17, 2804-2821. doi: 10.2174/092986710791859333
    • (2010) Curr. Med. Chem. , vol.17 , pp. 2804-2821
    • Garuti, L.1    Roberti, M.2    Bottegoni, G.3
  • 19
    • 84862192766 scopus 로고    scopus 로고
    • ChEMBL: a large-scale bioactivity database for drug discovery
    • doi: 10.1093/nar/gkr777
    • Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A. et al. (2012). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 40, D1100-D1107. doi: 10.1093/nar/gkr777
    • (2012) Nucleic Acids Res. , vol.40
    • Gaulton, A.1    Bellis, L.J.2    Bento, A.P.3    Chambers, J.4    Davies, M.5    Hersey, A.6
  • 20
    • 84871730931 scopus 로고    scopus 로고
    • Approaches to discover non-ATP site kinase inhibitors
    • doi: 10.1039/c2md20180a
    • Gavrin, L. K., and Saiah, E. (2013). Approaches to discover non-ATP site kinase inhibitors. Med. Chem. Commun . 4, 41-51. doi: 10.1039/c2md20180a
    • (2013) Med. Chem. Commun. , vol.4 , pp. 41-51
    • Gavrin, L.K.1    Saiah, E.2
  • 21
    • 42949150113 scopus 로고    scopus 로고
    • High-throughput kinase profiling as a platform for drug discovery
    • doi: 10.1038/nrd2541
    • Goldstein, D. M., Gray, N. S., and Zarrinkar, P. P. (2008). High-throughput kinase profiling as a platform for drug discovery. Nat. Rev. Drug Discov. 7, 391-397. doi: 10.1038/nrd2541
    • (2008) Nat. Rev. Drug Discov. , vol.7 , pp. 391-397
    • Goldstein, D.M.1    Gray, N.S.2    Zarrinkar, P.P.3
  • 22
    • 77950473958 scopus 로고    scopus 로고
    • Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis
    • doi: 10.1093/bioinformatics/btp650
    • Huang, D., Zhou, T., Lafleur, K., Nevado, C., and Caflisch, A. (2010). Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. Bioinformatics 26, 198-204. doi: 10.1093/bioinformatics/btp650
    • (2010) Bioinformatics , vol.26 , pp. 198-204
    • Huang, D.1    Zhou, T.2    Lafleur, K.3    Nevado, C.4    Caflisch, A.5
  • 24
    • 84901068489 scopus 로고    scopus 로고
    • K-Map: connecting kinases with therapeutics for drug repurposing and development
    • doi: 10.1186/1479-7364-7-20
    • Kim, J., Yoo, M., Kang, J., and Tan, A. C. (2013). K-Map: connecting kinases with therapeutics for drug repurposing and development. Hum. Genomics 7, 20. doi: 10.1186/1479-7364-7-20
    • (2013) Hum. Genomics , vol.7 , pp. 20
    • Kim, J.1    Yoo, M.2    Kang, J.3    Tan, A.C.4
  • 26
    • 77953665615 scopus 로고    scopus 로고
    • Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques
    • doi: 10.1186/1471-2105-11-339
    • Lapins, M., and Wikberg, J. E. (2010). Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. BMC Bioinformatics 11:339. doi: 10.1186/1471-2105-11-339
    • (2010) BMC Bioinformatics , vol.11 , pp. 339
    • Lapins, M.1    Wikberg, J.E.2
  • 27
    • 33745298429 scopus 로고    scopus 로고
    • Rational design of inhibitors that bind to inactive kinase conformations
    • doi: 10.1038/nchembio799
    • Liu, Y., and Gray, N. S. (2006). Rational design of inhibitors that bind to inactive kinase conformations. Nat. Chem. Biol. 2, 358-364. doi: 10.1038/nchembio799
    • (2006) Nat. Chem. Biol. , vol.2 , pp. 358-364
    • Liu, Y.1    Gray, N.S.2
  • 28
    • 0036708537 scopus 로고    scopus 로고
    • Selecting screening candidates for kinase and G protein-coupled receptor targets using neural networks
    • doi: 10.1021/ci020267c
    • Manallack, D. T., Pitt, W. R., Gancia, E., Montana, J. G., Livingstone, D. J., Ford, M. G. et al. (2002). Selecting screening candidates for kinase and G protein-coupled receptor targets using neural networks. J. Chem. Inf. Comput. Sci. 42, 1256-1262. doi: 10.1021/ci020267c
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 1256-1262
    • Manallack, D.T.1    Pitt, W.R.2    Gancia, E.3    Montana, J.G.4    Livingstone, D.J.5    Ford, M.G.6
  • 29
    • 27544446579 scopus 로고    scopus 로고
    • Promiscuous drugs compared to selective drugs (promiscuity can be a virtue)
    • doi: 10.1186/1472-6904-5-3
    • Mencher, S. K., and Wang, L. G. (2005). Promiscuous drugs compared to selective drugs (promiscuity can be a virtue). BMC Clin. Pharmacol. 5:3. doi: 10.1186/1472-6904-5-3
    • (2005) BMC Clin. Pharmacol , vol.5 , pp. 3
    • Mencher, S.K.1    Wang, L.G.2
  • 31
    • 79960936435 scopus 로고    scopus 로고
    • High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors
    • doi: 10.1016/j.chembiol.2011.05.010
    • Miduturu, C. V., Deng, X., Kwiatkowski, N., Yang, W., Brault, L., Filippakopoulos, P. et al. (2011). High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors. Chem. Biol. 18, 868-879. doi: 10.1016/j.chembiol.2011.05.010
    • (2011) Chem. Biol. , vol.18 , pp. 868-879
    • Miduturu, C.V.1    Deng, X.2    Kwiatkowski, N.3    Yang, W.4    Brault, L.5    Filippakopoulos, P.6
  • 32
    • 84862018569 scopus 로고    scopus 로고
    • Dissecting kinase profiling data to predict activity and understand cross-reactivity of kinase inhibitors
    • doi: 10.1021/ci200607f
    • Niijima, S., Shiraishi, A., and Okuno, Y. (2012). Dissecting kinase profiling data to predict activity and understand cross-reactivity of kinase inhibitors. J. Chem. Inf. Model. 52, 901-912. doi: 10.1021/ci200607f
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 901-912
    • Niijima, S.1    Shiraishi, A.2    Okuno, Y.3
  • 33
    • 84977556624 scopus 로고    scopus 로고
    • Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases
    • doi: 10.1186/1758-2946-5-49
    • Paricharak, S., Klenka, T., Augustin, M., Patel, U. A., and Bender, A. (2013). Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases. J. Cheminform. 5, 49. doi: 10.1186/1758-2946-5-49
    • (2013) J. Cheminform. , vol.5 , pp. 49
    • Paricharak, S.1    Klenka, T.2    Augustin, M.3    Patel, U.A.4    Bender, A.5
  • 34
    • 78651107624 scopus 로고    scopus 로고
    • Trends in kinase selectivity: insights for target class-focused library screening
    • doi: 10.1021/jm101195a
    • Posy, S. L., Hermsmeier, M. A., Vaccaro, W., Ott, K. H., Todderud, G., Lippy, J. S. et al. (2011). Trends in kinase selectivity: insights for target class-focused library screening. J. Med. Chem. 54, 54-66. doi: 10.1021/jm101195a
    • (2011) J. Med. Chem. , vol.54 , pp. 54-66
    • Posy, S.L.1    Hermsmeier, M.A.2    Vaccaro, W.3    Ott, K.H.4    Todderud, G.5    Lippy, J.S.6
  • 36
    • 84873024709 scopus 로고    scopus 로고
    • Kinome-wide activity modeling from diverse public high-quality data sets
    • doi: 10.1021/ci300403k
    • Schürer, S. C., and Muskal, S. M. (2013). Kinome-wide activity modeling from diverse public high-quality data sets. J. Chem. Inf. Model. 53, 27-38. doi: 10.1021/ci300403k
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 27-38
    • Schürer, S.C.1    Muskal, S.M.2
  • 37
    • 84878884695 scopus 로고    scopus 로고
    • What general conclusions can we draw from kinase profiling data sets?
    • doi: 10.1016/j.bbapap.2012.12.023
    • Sutherland, J. J., Gao, C., Cahya, S., and Vieth, M. (2013). What general conclusions can we draw from kinase profiling data sets? Biochim. Biophys. Acta 1834, 1425-1433. doi: 10.1016/j.bbapap.2012.12.023
    • (2013) Biochim. Biophys. Acta , vol.1834 , pp. 1425-1433
    • Sutherland, J.J.1    Gao, C.2    Cahya, S.3    Vieth, M.4
  • 38
    • 84896960173 scopus 로고    scopus 로고
    • Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis
    • doi: 10.1021/ci400709d
    • Tang, J., Szwajda, A., Shakyawar, S., Xu, T., Hintsanen, P., Wennerberg, K. et al. (2014). Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J. Chem. Inf. Model. 54, 735-743. doi: 10.1021/ci400709d
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 735-743
    • Tang, J.1    Szwajda, A.2    Shakyawar, S.3    Xu, T.4    Hintsanen, P.5    Wennerberg, K.6
  • 39
    • 1542358841 scopus 로고    scopus 로고
    • Kinomics-structural biology and chemogenomics of kinase inhibitors and targets
    • doi: 10.1016/j.bbapap.2003.11.028
    • Vieth, M., Higgs, R. E., Robertson, D. H., Shapiro, M., Gragg, E. A., and Hemmerle, H. (2004). Kinomics-structural biology and chemogenomics of kinase inhibitors and targets. Biochim. Biophys. Acta 1697, 243-257. doi: 10.1016/j.bbapap.2003.11.028
    • (2004) Biochim. Biophys. Acta , vol.1697 , pp. 243-257
    • Vieth, M.1    Higgs, R.E.2    Robertson, D.H.3    Shapiro, M.4    Gragg, E.A.5    Hemmerle, H.6
  • 40
    • 4143122120 scopus 로고    scopus 로고
    • Classification of kinase inhibitors using a Bayesian model
    • doi: 10.1021/jm0303195
    • Xia, X., Maliski, E. G., Gallant, P., and Rogers, D. (2004). Classification of kinase inhibitors using a Bayesian model. J. Med. Chem. 47, 4463-4470. doi: 10.1021/jm0303195
    • (2004) J. Med. Chem. , vol.47 , pp. 4463-4470
    • Xia, X.1    Maliski, E.G.2    Gallant, P.3    Rogers, D.4
  • 41
    • 79952345084 scopus 로고    scopus 로고
    • Analysis of multiple compound-protein interactions reveals novel bioactive molecules
    • doi: 10.1038/msb.2011.5
    • Yabuuchi, H., Niijima, S., Takematsu, H., Ida, T., Hirokawa, T., Hara, T. et al. (2011). Analysis of multiple compound-protein interactions reveals novel bioactive molecules. Mol. Syst. Biol. 7, 472. doi: 10.1038/msb.2011.5
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 472
    • Yabuuchi, H.1    Niijima, S.2    Takematsu, H.3    Ida, T.4    Hirokawa, T.5    Hara, T.6


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