메뉴 건너뛰기




Volumn 45, Issue 6, 2005, Pages 1854-1863

Investigation of DNA-binding properties of an aminoglycoside-polyamine library using Quantitative Structure-Activity Relationship (QSAR) models

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DATA ACQUISITION; DERIVATIVES; DNA; HYDROGEN BONDS; MOLECULAR STRUCTURE;

EID: 28944444772     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050082g     Document Type: Conference Paper
Times cited : (23)

References (44)
  • 1
    • 0345688128 scopus 로고    scopus 로고
    • A perspective of polyamine metabolism
    • Wallace, H. M.; Fraser, A. V.; Hughes, A. A perspective of polyamine metabolism. Biochem. J. 2003, 376, No. 1, 1-14.
    • (2003) Biochem. J. , vol.376 , Issue.1 , pp. 1-14
    • Wallace, H.M.1    Fraser, A.V.2    Hughes, A.3
  • 2
    • 0029980119 scopus 로고    scopus 로고
    • Polyamine-induced compaction and aggregation of DNA-a major factor in radioprotection of chromatin under physiological conditions
    • Newton, G. L.; Aguilera, J. A.; Ward, J. F.; Fahey, R. C. Polyamine-induced compaction and aggregation of DNA-a major factor in radioprotection of chromatin under physiological conditions. Radiat. Res. 1996, 145, No. 6, 776-780.
    • (1996) Radiat. Res. , vol.145 , Issue.6 , pp. 776-780
    • Newton, G.L.1    Aguilera, J.A.2    Ward, J.F.3    Fahey, R.C.4
  • 3
    • 0026446108 scopus 로고
    • Spermine and spermidine protection of plasmid DNA against single-strand breaks induced by singlet oxygen
    • Khan, A. U.; Mascio, P. D.; Medeiros, M. H. G.; Wilson, T. Spermine and Spermidine Protection of Plasmid DNA Against Single-Strand Breaks Induced by Singlet Oxygen. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 11428-11430.
    • (1992) Proc. Natl. Acad. Sci. U.S.A , vol.89 , pp. 11428-11430
    • Khan, A.U.1    Mascio, P.D.2    Medeiros, M.H.G.3    Wilson, T.4
  • 5
    • 0037418252 scopus 로고    scopus 로고
    • Polyamines protect Escherichia coli cells from the toxic effect of oxygen
    • Chattopadhyay, M. K.; Tabor, C. W.; Tabor, H. Polyamines protect Escherichia coli cells from the toxic effect of oxygen. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 2261-2265.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 2261-2265
    • Chattopadhyay, M.K.1    Tabor, C.W.2    Tabor, H.3
  • 6
    • 0029064780 scopus 로고
    • Suppression of c-myc oncogene expression by a polyamine-complexed triplex forming oligonucleotide in MCF-7 breast cancer cells
    • Thomas, T. J.; Faaland, C. A.; Gallo, M. A.; Thomas, T. Suppression of c-myc oncogene expression by a polyamine-complexed triplex forming oligonucleotide in MCF-7 breast cancer cells. Nucleic Acids Res. 1995, 23, 3594-3599.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3594-3599
    • Thomas, T.J.1    Faaland, C.A.2    Gallo, M.A.3    Thomas, T.4
  • 7
    • 0042229373 scopus 로고    scopus 로고
    • Development of polyamine analogues as cancer therapeutic agents
    • Thomas, T.; Balabhadrapathruni, S.; Gallo, M. A.; Thomas, T. J. Development of polyamine analogues as cancer therapeutic agents. Oncol. Res. 2002, 13, No. 3, 123-135.
    • (2002) Oncol. Res. , vol.13 , Issue.3 , pp. 123-135
    • Thomas, T.1    Balabhadrapathruni, S.2    Gallo, M.A.3    Thomas, T.J.4
  • 8
    • 0041430877 scopus 로고    scopus 로고
    • A review of polyamines and cancer
    • Criss, W. E. A review of polyamines and cancer. Turk. J. Med. Sci. 2003, 33, No. 4, 195-205.
    • (2003) Turk. J. Med. Sci. , vol.33 , Issue.4 , pp. 195-205
    • Criss, W.E.1
  • 9
    • 0023664206 scopus 로고
    • Aggregation of DNA by analogues of spermidine; enzymatic and structural studies
    • Srivenugopal, K. S.; Wemmer, D. E.; Morris, D. R. Aggregation of DNA by analogues of spermidine; enzymatic and structural studies. Nucleic Acids Res. 1987, 15, 2563-2580.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 2563-2580
    • Srivenugopal, K.S.1    Wemmer, D.E.2    Morris, D.R.3
  • 10
    • 0017326868 scopus 로고
    • Polyamine induced aggregation of DNA
    • Osland, A; Kleppe, K. Polyamine induced aggregation of DNA. Nucleic Acids Res. 1977, 4, 685-695.
    • (1977) Nucleic Acids Res. , vol.4 , pp. 685-695
    • Osland, A.1    Kleppe, K.2
  • 12
    • 0029975925 scopus 로고    scopus 로고
    • DNA aggregation induced by polyamines and cobalthexamine
    • Pelta, J.; Livolant, F.; Sikorav, J. L. DNA aggregation Induced by Polyamines and Cobalthexamine. J. Biol. Chem. 1996, 277, No. 10, 5656-5662.
    • (1996) J. Biol. Chem. , vol.277 , Issue.10 , pp. 5656-5662
    • Pelta, J.1    Livolant, F.2    Sikorav, J.L.3
  • 13
    • 0023230920 scopus 로고
    • The interaction of spermine and pentamines with DNA
    • Basu, H. S.; Marton, L. J. The interaction of spermine and pentamines with DNA. Biochem. J. 1987, 244, No. 1, 243-246.
    • (1987) Biochem. J. , vol.244 , Issue.1 , pp. 243-246
    • Basu, H.S.1    Marton, L.J.2
  • 14
    • 0032819358 scopus 로고    scopus 로고
    • SpermineInduced aggregation of DNA, nucleosome and chromatin
    • Raspaud, E.; Chaperon, I.; Leforestier, A.; Livolant, F. SpermineInduced Aggregation of DNA, Nucleosome and Chromatin. Biophys. J. 1999, 77, No. 3, 1547-1555.
    • (1999) Biophys. J. , vol.77 , Issue.3 , pp. 1547-1555
    • Raspaud, E.1    Chaperon, I.2    Leforestier, A.3    Livolant, F.4
  • 15
    • 0034284109 scopus 로고    scopus 로고
    • Structural basis of polyamine-DNA recognition: Spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy
    • Deng, H.; Bloomfield, V. A.; Benevides, J. M.; Thomas, G. J., Jr. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res. 2000, 28, No. 17, 3379-3385.
    • (2000) Nucleic Acids Res. , vol.28 , Issue.17 , pp. 3379-3385
    • Deng, H.1    Bloomfield, V.A.2    Benevides, J.M.3    Thomas Jr., G.J.4
  • 16
    • 0033596851 scopus 로고    scopus 로고
    • Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-, double-, and triple-stranded DNA
    • Saminathan, M.; Antony, T.; Shirahata, A.; Sigal, L H.; Thomas, T.; Thomas, T. J. Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-, double-, and triple-stranded DNA. Biochemistry 1999, 38, No. 12, 3821-3830.
    • (1999) Biochemistry , vol.38 , Issue.12 , pp. 3821-3830
    • Saminathan, M.1    Antony, T.2    Shirahata, A.3    Sigal, L.H.4    Thomas, T.5    Thomas, T.J.6
  • 17
    • 0035856537 scopus 로고    scopus 로고
    • DNA condensation of polyamines: A laser light scattering study of structural effects
    • Vijayanathan, V.; Thomas, T.; Sriharata, A.; Thomas, T. J. DNA condensation of polyamines: A laser light Scattering Study of Structural Effects. Biochemistry 2001, 40, No. 45, 13644-13651.
    • (2001) Biochemistry , vol.40 , Issue.45 , pp. 13644-13651
    • Vijayanathan, V.1    Thomas, T.2    Sriharata, A.3    Thomas, T.J.4
  • 18
    • 0034214275 scopus 로고    scopus 로고
    • Rapid and sensitive ethidium fluorescence quenching assay of polyamine conjugate-DNA interactions for the analysis of lipoplex formation in gene therapy
    • Geall, A. J.; Blagbrough, I. S. Rapid and sensitive ethidium fluorescence quenching assay of polyamine conjugate-DNA interactions for the analysis of lipoplex formation in gene therapy. J. Pharm. Biomed. Anal. 2000, 22, No. 5, 849-859.
    • (2000) J. Pharm. Biomed. Anal. , vol.22 , Issue.5 , pp. 849-859
    • Geall, A.J.1    Blagbrough, I.S.2
  • 19
    • 0034685930 scopus 로고    scopus 로고
    • Cheno-, urso- And deoxycholic acid spermine conjugates: Relative binding affinities for Calf thymus DNA
    • Blagbrough, I. S.; Al-Hadithi, D.; Geall, A. J. Cheno-, urso- and deoxycholic acid spermine conjugates: relative binding affinities for Calf thymus DNA. Tetrahedron 2000, 56, No. 21, 3439-3447.
    • (2000) Tetrahedron , vol.56 , Issue.21 , pp. 3439-3447
    • Blagbrough, I.S.1    Al-Hadithi, D.2    Geall, A.J.3
  • 21
    • 0034833710 scopus 로고    scopus 로고
    • A simple high resolution method for establishing DNA binding affinity and sequence selectivity
    • Boger, D. L.; Brian, F. E.; Brunette, S. R.; Tse, W. C.; Hedrick, M. P. A simple high resolution method for establishing DNA binding affinity and sequence selectivity. J. Am. Chem. Soc. 2001, 123, No. 25, 5878-5891.
    • (2001) J. Am. Chem. Soc. , vol.123 , Issue.25 , pp. 5878-5891
    • Boger, D.L.1    Brian, F.E.2    Brunette, S.R.3    Tse, W.C.4    Hedrick, M.P.5
  • 22
    • 0021988089 scopus 로고
    • A quantitative structure-activity relationship and molecular graphics study of carbonic-anhydrase inhibitors
    • Hansch, C.; McClarin, J.; Klein, T.; Langridge, R. A Quantitative Structure-Activity Relationship and Molecular Graphics Study of Carbonic-Anhydrase Inhibitors. Mol. Pharmacol. 1985, 27, No. 5, 493-498.
    • (1985) Mol. Pharmacol. , vol.27 , Issue.5 , pp. 493-498
    • Hansch, C.1    McClarin, J.2    Klein, T.3    Langridge, R.4
  • 23
    • 0032112107 scopus 로고    scopus 로고
    • Prediction of human intestinal absorption of drug compounds from molecular structure
    • Wessel, M. D.; Jurs, P. C.; Tolan, J. W.; Muskal, S. M. Prediction of human intestinal absorption of drug compounds from molecular structure. J. Chem. Inf. Comput. Sci. 1998, 38, No. 4, 726-735.
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , Issue.4 , pp. 726-735
    • Wessel, M.D.1    Jurs, P.C.2    Tolan, J.W.3    Muskal, S.M.4
  • 24
    • 0036489450 scopus 로고    scopus 로고
    • E-state modeling of HIV-1 protease inhibitor binding independent of 3D information
    • Hall, L. H.; Maw, H. H. E-state modeling of HIV-1 protease inhibitor binding independent of 3D information. J. Chem. Inf. Comput. Sci. 2002, 42 (2), 290-298.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , Issue.2 , pp. 290-298
    • Hall, L.H.1    Maw, H.H.2
  • 25
    • 0037069852 scopus 로고    scopus 로고
    • New density functional and atoms in molecules method of computing relative pK(a) values in solution
    • Adam, K. R. New density functional and atoms in molecules method of computing relative pK(a) values in solution. J. Phys. Chem. A 2002, 106, No. 49, 11963-11972.
    • (2002) J. Phys. Chem. A , vol.106 , Issue.49 , pp. 11963-11972
    • Adam, K.R.1
  • 26
    • 1442324408 scopus 로고    scopus 로고
    • Successful in silico predicting of intestinal lymphatic transfer
    • Holm, R.; Hoest, J. Successful in silico predicting of intestinal lymphatic transfer. Int. J. Pharm. 2004, 272, No. 1-2, 189-193.
    • (2004) Int. J. Pharm. , vol.272 , Issue.1-2 , pp. 189-193
    • Holm, R.1    Hoest, J.2
  • 29
    • 0037020489 scopus 로고    scopus 로고
    • Prediction of drug solubility in an acrylate adhesive based on the drug-polymer interaction parameter and drug solubility in acetonitrile
    • Guertin, J. A.; Li, J. W.; Masso, J. J. Prediction of drug solubility in an acrylate adhesive based on the drug-polymer interaction parameter and drug solubility in acetonitrile. J. Contr. Relat. 2002, 83 (2), 211-221.
    • (2002) J. Contr. Relat. , vol.83 , Issue.2 , pp. 211-221
    • Guertin, J.A.1    Li, J.W.2    Masso, J.J.3
  • 30
    • 0027892996 scopus 로고
    • Quantitative structure-retention relationships applied to reversed-phase high-performance liquid-chromatography
    • Kaliszan, R. Quantitative Structure-Retention Relationships Applied To Reversed-Phase High-Performance Liquid-Chromatography. J. Chromatogr. A 1993, 656 (1-2), 417-435.
    • (1993) J. Chromatogr. A , vol.656 , Issue.1-2 , pp. 417-435
    • Kaliszan, R.1
  • 31
    • 0035975898 scopus 로고    scopus 로고
    • Quantitative structure/retention relationships in affinity chromatography
    • Kaliszan, R.; Baczek, T. Quantitative structure/retention relationships in affinity chromatography. J. Biochem. Biophys. Methods 2001, 49 (1-3), 83-98.
    • (2001) J. Biochem. Biophys. Methods , vol.49 , Issue.1-3 , pp. 83-98
    • Kaliszan, R.1    Baczek, T.2
  • 32
    • 0035891173 scopus 로고    scopus 로고
    • Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure
    • Mazza, C. B.; Sukumar, N.; Breneman, C. M.; Cramer, S. M. Prediction of Protein Retention in Ion-Exchange Systems using Molecular Descriptors Obtained from Crystal Structure. Anal. Chem. 2001, 73, No. 22, 5457-5461.
    • (2001) Anal. Chem. , vol.73 , Issue.22 , pp. 5457-5461
    • Mazza, C.B.1    Sukumar, N.2    Breneman, C.M.3    Cramer, S.M.4
  • 33
    • 0036827078 scopus 로고    scopus 로고
    • Prediction of protein retention times in anion-exchange chromatography systems using support vector regression
    • Song, M.; Breneman, C. M.; Bi, J.; Sukumar, N.; Bennett, K. P.; Cramer, S. M.; Tugcu, N. Prediction of Protein Retention Times in Anion-Exchange Chromatography Systems Using Support Vector Regression. J. Chem. Inf. Comput. Sci. 2002, 42 (6), 1347-1357.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , Issue.6 , pp. 1347-1357
    • Song, M.1    Breneman, C.M.2    Bi, J.3    Sukumar, N.4    Bennett, K.P.5    Cramer, S.M.6    Tugcu, N.7
  • 34
    • 0141974140 scopus 로고    scopus 로고
    • Investigation of mobile phase salt type effects on protein retention and selectivity in cation exchange systems using quantitative structure-retention relationship models
    • Ladiwala, A.; Rege, K.; Breneman, C. M.; Cramer, S. M. Investigation of Mobile Phase Salt Type Effects on Protein Retention and Selectivity in Cation Exchange Systems using Quantitative Structure-Retention Relationship Models. Langmuir 2003, 19 (20), 8443-8454.
    • (2003) Langmuir , vol.19 , Issue.20 , pp. 8443-8454
    • Ladiwala, A.1    Rege, K.2    Breneman, C.M.3    Cramer, S.M.4
  • 35
    • 0037026928 scopus 로고    scopus 로고
    • High throughput screening and quantitative structure-efficacy relationship models of potential displacer molecules for ion-exchange systems
    • Mazza, C. B.; Rege, K.; Breneman, C. M.; Sukumar, N.; Dordick, J. S.; Cramer, S. M. High Throughput Screening and Quantitative Structure-Efficacy Relationship Models of Potential Displacer Molecules for Ion-Exchange Systems. Biotechnol. Bioeng. 2002, 80, No. 1, 60-73.
    • (2002) Biotechnol. Bioeng. , vol.80 , Issue.1 , pp. 60-73
    • Mazza, C.B.1    Rege, K.2    Breneman, C.M.3    Sukumar, N.4    Dordick, J.S.5    Cramer, S.M.6
  • 36
    • 1542298909 scopus 로고    scopus 로고
    • Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems
    • Rege, K.; Ladiwala, A.; Tugcu, N.; Breneman, C. M.; Cramer, S. M. Parallel Screening of Selective and High-Affinity Displacers for Proteins in Ion-Exchange Systems. J. Chromatogr. A 2004, 1033, 19-28.
    • (2004) J. Chromatogr. A , vol.1033 , pp. 19-28
    • Rege, K.1    Ladiwala, A.2    Tugcu, N.3    Breneman, C.M.4    Cramer, S.M.5
  • 38
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik, V. N. An overview of statistical learning theory. IEEE Trans. Neural Networks 1999, 10, No. 5, 988-999.
    • (1999) IEEE Trans. Neural Networks , vol.10 , Issue.5 , pp. 988-999
    • Vapnik, V.N.1
  • 39
    • 0002935122 scopus 로고    scopus 로고
    • On mathematical programming methods and support vector machines
    • Schölkopf, A., Burges, C., Smola, A., Eds., MIT Press: Cambridge, MA
    • Bennett, K. P. On Mathematical Programming Methods and Support Vector Machines. In Advances in Kernel Methods - Support Vector Machines; Schölkopf, A., Burges, C., Smola, A., Eds., MIT Press: Cambridge, MA, 1998; pp 307-326.
    • (1998) Advances in Kernel Methods - Support Vector Machines , pp. 307-326
    • Bennett, K.P.1
  • 41
    • 4744357239 scopus 로고    scopus 로고
    • Chemoenzymatic synthesis and parallel screening of an aminoglycoside-polyamine library: Identification of high affinity displacers and DNA-binding ligands
    • accepted for publication
    • Rege, K.; Hu, S.; Moore, J. A.; Dordick, J. S.; Cramer, S. M. Chemoenzymatic Synthesis and Parallel Screening of an Aminoglycoside-Polyamine Library: Identification of High Affinity Displacers and DNA-Binding Ligands. J. Am. Chem. Soc. 2004, accepted for publication.
    • (2004) J. Am. Chem. Soc.
    • Rege, K.1    Hu, S.2    Moore, J.A.3    Dordick, J.S.4    Cramer, S.M.5
  • 42
    • 0037079669 scopus 로고    scopus 로고
    • Polyamine-nucleic acid interactions and the effects of structure in oriented DNA-fibers
    • van Dam, L.; Korolev, N.; Nordenskiold, L. Polyamine-Nucleic Acid Interactions and the Effects of Structure in Oriented DNA-fibers. Nucleic Acids Res. 2002, 30 (2), 419-428.
    • (2002) Nucleic Acids Res. , vol.30 , Issue.2 , pp. 419-428
    • Van Dam, L.1    Korolev, N.2    Nordenskiold, L.3
  • 43
    • 0000697995 scopus 로고
    • Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds
    • Petitjean, M. Applications of the Radius-Diameter Diagram to the Classification of Topological and Geometrical Shapes of Chemical Compounds. J. Chem. Inf. Comput. Sci. 1992, 32, 331-337.
    • (1992) J. Chem. Inf. Comput. Sci. , vol.32 , pp. 331-337
    • Petitjean, M.1
  • 44
    • 0001509942 scopus 로고    scopus 로고
    • Prediction of physiochemical parameters by atomic contributions
    • Wildman, S. A.; Grippen, G. M. Prediction of Physiochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, No. 5, 868-873.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , Issue.5 , pp. 868-873
    • Wildman, S.A.1    Grippen, G.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.