Structural studies of atom-specific anticancer drugs acting on DNA

Pharmacology and Therapeutics

Volumn 83, Issue 3, 1999, Pages 181-215

  Yang, Xiang Lei ^a   Wang, Andrew H J ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Adducts; Anticancer drugs; DNA cleavage; DNA structures; Intercalators; Minor groove binding

Indexed keywords

ACLACINOMYCIN; ACLARUBICIN; ALKYLATING AGENT; ANTHRACYCLINE; ANTINEOPLASTIC AGENT; ANTINEOPLASTIC ANTIBIOTIC; CALICHEAMICIN; CHLOROACETALDEHYDE; CISPLATIN; DACTINOMYCIN; DAUNORUBICIN; DAUNOSAMINE; DISTAMYCIN A; DOXORUBICIN; DUOCARMYCIN A; ECHINOMYCIN; ESPERAMICIN; HEDAMYCIN; LUZOPEPTIN; MITHRAMYCIN; MITOMYCIN; NOGALAMYCIN; PLATINUM DERIVATIVE; PLURAMYCIN; PYRAZOLE; QUINOXALINE; ZINOSTATIN;

ANTINEOPLASTIC ACTIVITY; COVALENT BOND; CROSS LINKING; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA ALKYLATION; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; DRUG CONFORMATION; HUMAN; HYDROGEN BOND; MOLECULE; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 0032824901     PISSN: 01637258     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0163-7258(99)00020-0     Document Type: Review

References (203)

1. 7]TANDEM complexes with DNA oligonucleotides Nucleic Acids Res. 22:1994;5484-5491.
2. Bailly C., Chaires J.B. Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjug Chem. 9:1998;513-538.
3. Bailly C., Hamy F., Waring M.J. Cooperativity in the binding of echinomycin to DNA fragments containing closely spaced CpG sites. Biochemistry. 35:1996;1150-1161.
4. Bailey S.A., Graves D.E., Rill R., Marsch G. Influence of DNA base sequence on the binding energetics of actinomycin D. Biochemistry. 32:1993;5881-5887.
5. nT motif of double-stranded DNA. determination of the guanine requirement in nonclassical, non-GpC binding sites Biochemistry. 33:1994;11493-11500.
6. Bauer C., Wang A.H.-J. Bridged cobalt amine complexes induce DNA conformational changes effectively. J Inorg Biochem. 68:1997;129-135.
7. Bauer C., Peleg-Shulman T., Gibson D., Wang A.H.-J. Monofunctional platinum amine complexes destabilize DNA significantly. Eur J Biochem. 256:1998;253-260.
8. Berman H. Crystal studies of B-DNA. the answers and the questions Biopolymers. 44:1997;23-44.
9. Bernal-Mendez E., Boudvillain M., Gonzalez F., Leng M. Chemical versatility of transplatin monofunctional adducts within multiple site-specifically platinated DNA. Biochemistry. 36:1997;7281-7287.
10. Boger D.L. The duocarmycins - synthetic and mechanistic studies. Acc Chem Res. 28:1995;20-29.
11. Boger D.L., Johnson D.S. CC-1065 and the duocarmycins. unraveling the keys to a new class of naturally derived DNA alkylating agents Proc Natl Acad Sci USA. 92:1995;3642-3649.
12. Borman S. Quadruplex DNA. anticancer knot? Chem Eng News October. 5:1998;42-46.
13. Brownlee, R. T. C., Cacioli, P., Chandler, C. J., Phillips, D. R., Scourides, P. A., & Reiss, J. A. (1986). The synthesis and characterization of a series of bis-intercalating bis-anthracyclines. J Chem Soc Chem Commun 659-661.
14. Burger R.M. Cleavage of nucleic acids by bleomycin. Chem Rev. 98:1998;1153-1189.
15. Caceres-Cortes J., Wang A.H.-J. Binding of antitumor drug nogalamycin to bulged DNA structures. Biochemistry. 35:1996;616-625.
16. Caceres-Cortes J., Sugiyama H., Ikudome K., Saito I., Wang A.H.-J. Structures of cobalt(III)-pepleomycin and cobalt(III)-deglycopepleomycin (green forms) and their interactions with DNA by NMR studies. Eur J Biochem. 244:1997;818-828. a.
17. Caceres-Cortes J., Sugiyama H., Ikudome K., Saito I., Wang A.H.-J. Interactions of deglycosylated cobalt(III)-pepleomycin (green form) with DNA based on NMR structural studies. Biochemistry. 36:1997;9995-10005. b.
18. Caceres-Cortes J., Sugiyama H., Ikudome K., Saito I., Wang A.H.-J. NMR studies of the anticancer drug pepleomycin and its complexes with DNA. Sarma R.H., Sarma M.H. Proceedings of the 10th Conversation in Biomolecular Stereodynamics (. 1998;207-225 Adenine Press, Schenectady.
19. Chaires J.B. Drug-DNA interactions. Curr Opin Struct Biol. 8:1998;314-320.
20. Chaires J.B., Leng F., Przewloka T., Fokt I., Ling Y.-H., Perez-Soler R., Priebe W. Structure-based design of a new bisintercalating anthracycline antibiotic. J Med Chem. 40:1997;261-266.
21. Chen A., Yu C., Gatto B., Liu L.F. DNA minor groove-binding ligands. a different class of mammalian DNA topoisomerase I inhibitors Proc Natl Acad Sci USA. 90:1993;8131-8135.
22. Chen F.-M. Binding specificities of actinomycin D to self-complementary tetranucleotide sequences -XGCY-. Biochemistry. 27:1988;6393-6397.
23. Chen F.-M. Binding of actinomycin D to DNA oligomers of CXG trinucleotide repeats. Biochemistry. 37:1998;3955-3964.
24. Chen H., Patel D.J. Solution structure of a quinomycin bisintercalator-DNA complex. J Mol Biol. 246:1995;164-179. a.
25. Chen H., Patel D.J. Solution structure of the menogaril-DNA complex. J Am Chem Soc. 117:1995;5901-5913. b.
26. Chen H., Liu X., Patel D.J. DNA binding and unwinding associated with actinomycin D antibiotics bound to partially overlapping sites on DNA. J Mol Biol. 258:1996;457-479.
27. Chen X., Ramakrishnan B., Rao S.T., Sundaralingam M. Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. Nature Struct Biol. 1:1994;169-175.
28. Chen X., Ramakrishnan B., Sundaralingam M. Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC). J Mol Biol. 267:1997;1157-1170.
29. Chen Y.-H., Yang Y., Lown J.W. Optimization of cross-linked lexitropsins. J Biomol Struct Dyn. 14:1996;341-355.
30. Chu G. Cellular responses to cisplatin. The roles of DNA-binding proteins and DNA repair. J Biol Chem. 269:1994;787-790.
31. 2 Nucleic Acids Res. 24:1996;4882-4889.
32. Coll M., Frederick C.A., Wang A.H.-J., Rich A. A bifurcated hydrogen bonded conformation in the d(A·T) base pairs of the DNA dodecamer of d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci USA. 84:1987;8385-8389.
33. Cullinane C., Cutts S.M., van Rosmalen A., Phillips D.R. Formation of adriamycin-DNA adducts in vitro. Nucleic Acids Res. 22:1994;2296-2303.
34. Dickerson R.E. DNA bending. the prevalence of kinkiness and the virtues of normality Nucleic Acids Res. 26:1998;1906-1926.
35. 5C]CG complexes Nucleic Acids Res. 26:1998;2981-2988.
36. Egli M., Williams L.D., Frederick C.A., Rich A. DNA-nogalamycin interactions. Biochemistry. 30:1991;1364-1372.
37. Evans J.N.S. Biomolecular NMR Spectroscopy. 1995;Oxford University Press, New York.
38. Fan Y., Weistein J.N., Kohn K.W., Shi L.M., Pommier Y. Molecular modeling studies of the DNA-topoisomerase I ternary cleavable complex with camptothecin. J Med Chem. 41:1998;2216-2226.
39. Farrell N. DNA binding of dinuclear platinum complexes. Hurley L.H., Chaires J.B. Advances in DNA Sequence Specific Agents, Vol. 2 (. 1996;187-216 JAI Press, Inc, Greenwich.
40. Federoff O.Y., Salazar M., Han H., Chemeris V.V., Kerwin S.M., Hurley L.H. NMR-based model of a telomerase-inhibiting compound bound to G-quadruplex DNA. Biochemistry. 37:1998;12367-12374.
41. Fenick D.J., Taatjes D.J., Koch T.H. Doxoform and daunoform. anthracycline-formaldehyde conjugates toxic to resistant tumor cells J Med Chem. 40:1997;2452-2461.
42. Figueiredo-Pereira M.E., Chen W.E., Li J., Johdo O. The antitumor drug aclacinomycin A, which inhibits the degradation of ubiqutinated proteins, shows selectivity for the chymotrypsin-like activity of the bovine pituitary 20S proteosome. J Biol Chem. 271:1996;16455-16459.
43. Fletcher M.C., Fox K.R. Dissociation kinetics of echinomycin from CpG binding sites in different sequence environments. Biochemistry. 35:1996;1064-1075.
44. Fourmy D., Recht M.I., Puglisi J.D. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16S rRNA. J Mol Biol. 277:1998;347-362.
45. Friedberg E.C., Walker G.C., Siede W. DNA Repair and Mutagenesis. 1995;ASM Press, Washington, D.C.
46. Gacy A.M., McMurray C.T. Influence of hairpins on template reannealing at trinucleotide repeat duplexes. a model for slipped DNA Biochemistry. 37:1998;9426-9434.
47. Gao X., Patel D.J. NMR Studies of echinomycin bisintercalation complexes with d(A1-C2-G3-T4) and d(T1-C2-G3-A4) duplexes in aqueous solution. sequence-dependent formation of Hoogsteen A1-T4 and Watson-Crick T1-A4 flanking the bisintercalation within a DNA duplex Biochemistry. 27:1988;1744-1751.
48. Gao X.L., Mirau P., Patel D.J. Structure refinement of the chromomycin dimer-DNA oligomer complex in solution. J Mol Biol. 223:1992;259-279.
49. Gao X., Stassinopoulos A., Gu J., Goldberg I.H. NMR studies of the post-activated neocarzinostatin chromophore-DNA complex. Conformational changes induced in drug and DNA. Bioorg Med Chem. 3:1995;795-809. a.
50. Gao X., Stassinopoulos A., Rice J., Goldberg I.H. Structural basis for the sequence-specific DNA strand cleavage by the enediyne neocarzinostatin chromophore. Structure of the post-activated chromophore-DNA complex. Biochemistry. 34:1995;40-49. b.
51. Gao Y.-G., Wang A.H.-J. Crystal structures of four morpholino-doxorubicin anticancer drugs complexed with d(CGTACG) and d(CGATCG). implications in drug-DNA crosslink J Biomol Struct Dyn. 13:1995;103-117.
52. Gao Y.G., Liaw Y.C., Robinson H., Wang A.H.-J. Binding of the antitumor drug nogalamycin and its derivatives to DNA. structural comparison Biochemistry. 29:1990;10307-10316.
53. Gao Y.-G., Liaw Y.-C., Li Y.-K., van der Marel G.A., van Boom J.H., Wang A.H.-J. Facile formation of a crosslinked adduct between DNA and the daunorubicin derivative MAR70 mediated by formaldehyde. molecular structure of the MAR70-d(CGTnACG) covalent adduct Proc Natl Acad Sci USA. 88:1991;4845-4849.
54. 7 of guanines in Z-DNA and drug-DNA complex Nucleic Acids Res. 21:1993;4093-4101.
55. 2+ to A-DNA. Biophys J. 69:1995;559-568.
56. Gao Y., Robinson H., van Boom J.H., Wang A.H.-J. Substitutions at C2′ of daunosamine in the anticancer drug daunorubicin alter its DNA-binding sequence-specificity. Eur J Biochem. 240:1996;331-335.
57. Gao Y., Robinson H., Wijsman E.R., van der Marel G., van Boom J.H., Wang A.H.-J. Binding of daunorubicin to β-D-glucosylated DNA found in protozoa Trypanosoma brucei studied by X-ray crystallography. J Am Chem Soc. 119:1997;1496-1497.
58. Gao Y.-G., Su S.-Y., Robinson H., Padmanabhan S., Lim L., McCrary B.S., Edmondson S.P., Shriver J.W., Wang A.H.-J. The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nature Struct Biol. 5:1998;782-786.
59. Geierstanger B.H., Dwyer T.J., Bathini Y., Lown J.W., Wemmer D.E. NMR characterization of a heterocomplex formed by distamycin and its analog 2-ImD with d(CGCAAGTTGGC):d(GCCAACTTGCG). preference for the 1:1:1 2-ImD:Dst:DNA complex over the 2:1 2-ImD:DNA and the 2:1 Dst:DNA complexes J Am Chem Soc. 115:1993;4474-4482.
60. Geierstanger B.H., Jacobsen J.-P., Mrksich M., Dervan P.B., Wemmer D.E. Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA. Biochemistry. 33:1994;3055-3062. a.
61. Geierstanger B.H., Mrksich M., Dervan P.B., Wemmer D.E. Design of a G·C-specific groove-binding peptide. Science. 266:1994;646-650. b.
62. Geierstanger B.H., Mrksich M., Dervan P.B., Wemmer D.E. Extending the recognition site of designed minor groove binding molecules. Nature Struct Biol. 3:1996;321-324.
63. Gelasco A., Lippard S.J. NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin. Biochemistry. 37:1998;9230-9239.
64. 2 Biochemistry. 30:1991;2483-2494.
65. Gmeiner W.H. NMR spectroscopy as a tool to investigate the structural basis of anticancer drugs. Curr Med Chem. 5:1998;115-135.
66. Guan Y., Gao Y.-G., Liaw Y.-C., Robinson H., Wang A.H.-J. Molecular structure of cyclic diguanylic acid at 1 Å resolution of two crystal forms. self-association, interactions with metal ion/planar dyes, modeling studies J Biomol Struct Dyn. 11:1993;253-276. a.
67. Guan Y., Sakai R., Rinehart K.L., Wang A.H.-J. Molecular and crystal structures of ecteinascidins. potent anticancer compounds from the Caribbean tunicate Ecteinascidia turbinata J Biomol Struct Dyn. 10:1993;793-818. b.
68. Hansen M., Yun S., Hurley L. Hedamycin intercalates the DNA helix and, through carbohydrate-mediated recognition in the minor groove, directs N7-alkylation of guanine in the major groove in a sequence-specific manner. Chem Biol. 2:1995;229-240.
69. Hecht S.M. Bleomycins. Bioconjug Chem. 5:1994;513-526.
70. Heinemann U., Alings C. Crystallographic study of one turn of G/C-rich B-DNA. J Mol Biol. 210:1989;369-381.
71. Holmes C.E., Duff R.J., van der Marel G.A., van Boom J.H., Hecht S.M. On the chemistry of RNA degradation by Fe·bleomycin. Bioorg Med Chem. 5:1997;1235-1248.
72. Hu G.G., Shui X., Leng F., Priebe W., Chaires J.B., Williams L.D. Structure of a DNA-bisdaunomycin complex. Biochemistry. 36:1997;5940-5946.
73. Huang H., Zhu L., Reid B.R., Drobny G.P., Hopkins P.B. Solution structure of a cisplatin-induced DNA interstrand cross-link. Science. 270:1995;1842-1845.
74. Hurley, L. H., & Chaires, J. B. (Eds.). (1996). Advances in DNA Sequence Specific Agents. Greenwich: JAI Press, Inc.
75. Jensen P.B., Sorensen B.S., Sehested M., Demant E.J.F., Kjeldsen E., Friche E., Hansen H.H. Different modes of anthracycline interaction with topoisomerase II. Biochem Pharmacol. 45:1993;2025-2035.
76. Kamitori S., Takusagawa F. Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D. J Mol Biol. 225:1992;445-456.
77. 2-actinomycin D complexes and its host DNA J Am Chem Soc. 116:1994;4154-4165.
78. Keniry M.A., Shafer R. NMR studies of drug-DNA complexes. Methods Enzymol. 261:1995;575-604.
79. 2. Evidence that the saccharide chains have a role in sequence specificity. J Mol Biol. 231:1993;753-767.
80. Kielkopf C.L., Baird E.E., Dervan P.B., Rees D.C. Structural basis for G·C recognition in the DNA minor groove. Nature Struct Biol. 5:1998;104-109. a.
81. Kielkopf C.L., White S., Szewczyk J.W., Turner J.M., Baird E.E., Dervan P.B., Rees D.C. A structural basis for recognition of A·T and T·A base pairs in the minor groove of B-DNA. Science. 282:1998;111-115. b.
82. Kim K.H., Kwon B.M., Myers A.G., Rees D.C. Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex. Science. 262:1993;1042-1046.
83. Kimura K.-I., Takahashi H., Takaoka H., Miyata N., Kawanishi I. Biological activities of anthracycline antibiotic SN-07 chromophore and SN-07 chromophore-DNA complexes. Agric Biol Chem. 54:1990;1645-1650.
84. Konishi M., Okuma H., Tsuno T., vanDuyne G.D., Clardy J. Crystal and molecular structure of dynemicin A. a novel 1,5-diyne-3-ene antitumor antibiotic J Am Chem Soc. 112:1990;3715-3716.
85. Kopka M.L., Larsen T.A. Netropsin and the lexitropsins. The search for sequence-specific minor-groove binding ligands. Propst C.L., Perun T.J. Nucleic Acid Targeted Drug Design (. 1992;303-374 Marcel Dekker, New York.
86. Kopka M.L., Goodsell D.S., Baikalov I., Grzeskowiak K., Cascio D., Dickerson R.E. Crystal structure of a covalent DNA-drug adduct. anthramycin bound to CCAACGTTGG and a molecular explanation of specificity Biochemistry. 33:1994;13593-13610.
87. Kopka M.L., Goodsell D.S., Han G.W., Chiu T.K., Lown J.W., Dickerson R.E. Defining GC-specificity in the minor groove. side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G Structure. 5:1997;1033-1046.
88. Krishna A.G., Kumar D.V., Khan B.M., Rawal S.K., Ganesh K.N. Taxol-DNA interactions. fluorescence and CD studies of DNA groove binding properties of taxol Biochim Biophys Acta. 1381:1998;104-112.
89. Krugh T. Drug-DNA interactions. Curr Opin Struct Biol. 4:1994;351-364.
90. 1-DNA complex. J Mol Biol. 265:1997;173-186. a.
91. Kumar R.A., Ikemoto N., Patel D.J. Solution structure of the calicheamicin gamma1I-DNA complex. J Mol Biol. 265:1997;187-201. b.
92. Leach D.R.F. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays. 16:1994;893-900.
93. Leng F., Savkur R., Fokt I., Przewloka T., Priebe W., Chaires J.B. Base specific and regioselective chemical cross-linking of daunorubicin to DNA. J Am Chem Soc. 118:1996;4731-4738.
94. n triplet sequence by NMR analysis. J Am Chem Soc. 118:1996;8791-8801.
95. Liaw Y.C., Gao Y.G., Robinson H., van der Marel G.A., van Boom J.H., Wang A.H.-J. Antitumor drug nogalamycin binds DNA in both grooves simultaneously. molecular structure of nogalamycin-DNA complex Biochemistry. 28:1989;9913-9918.
96. Lin C.H., Patel D. Solution structure of the covalent duocarmycin A-DNA duplex complex. J Mol Biol. 248:1995;162-179.
97. Lin C.H., Beale J.M., Hurley L. Structure of the (+)-CC-1065-DNA adduct. critical role of ordered water molecules and implications for involvement of phosphate catalysis in the covalent reaction Biochemistry. 30:1991;3597-3602.
98. Lipscomb L.A., Zhou F.X., Presnell S.R., Woo R.J., Peek M.E., Plaskon R.R., Williams L.D. Structure of a DNA-porphyrin complex. Biochemistry. 35:1996;2818-2823.
99. Liu X., Chen H., Patel D.J. Solution structure of actinomycin-DNA complexes. drug intercalation at isolated G-C sites J Biomol NMR. 1:1991;323-347.
100. Love J.J., Li X., Case D.A., Glese K., Grosschedl R., Wright P.E. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature. 376:1995;791-795.
101. Lown, J. W. (Ed.). (1988). Anthracycline and Anthracenedione-Based Anticancer Agents. Amsterdam: Elsevier.
102. Majee S., Chakrabarti A. A DNA-binding antitumor antibiotic binds to spectrin. Biochem Biophys Res Commun. 212:1995;428-432.
103. 3 and mithramycin with poly(dG-dC)·poly(dG-dC) and poly(dG)·poly(dC). Biochemistry. 36:1997;2291-2299.
104. 2 complex. Design of sequence-specific DNA-binding molecules. J Am Chem Soc. 116:1994;10851-10852.
105. 2. A binding model based on NMR experiments and restrained molecular dynamics calculations. J Am Chem Soc. 117:1995;7891-7903.
106. Moore B.M. II, Seaman F.C., Hurley L.H. NMR-based model of an ecteinascidin 743-DNA adduct. J Am Chem Soc. 119:1997;5475-5476.
107. Moore B.M. II, Seaman F.C., Wheelhouse R.T., Hurley L.H. Mechanism for the catalytic activation of ecteinascidin 743 and its subsequent alkylation of guanine N2. J Am Chem Soc. 120:1998;2490-2491.
108. Mrksich M., Wade W.S., Dwyer T.J., Geierstanger B.H., Wemmer D.E., Dervan P.E. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci USA. 89:1992;7586-7590.
109. Nitiss J.L., Pourquier P., Pommier Y. Aclacinomycin A stabilizes topoisomerase I covalent complexes. Cancer Res. 57:1997;4564-4569.
110. Norman D., Live D., Sastry M., Lipman R., Hingerty B.E., Tomasz M., Broyde S., Patel D.J. NMR and computational characterization of mitomycin cross-linked to adjacent deoxyguanosines in the minor groove of the d(T-A-C-G-T-A)·d(T-A-C-G-T-A) duplex. Biochemistry. 29:1990;2861-2875.
111. Ohndorf U.M., Rould M.A., He Q., Pabo C.O., Lippard S.J. Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature. 399:1999;708-712.
112. Peek M.E., Lipscomb L.A., Bertrand J.A., Gao Q., Roques B.P., Garbay-Jaureguiberry C., Williams L.D. DNA distortion in bis-intercalated complexes. Biochemistry. 33:1994;3794-3800.
113. 2 determined by two dimensional NMR. Proc Natl Acad Sci USA. 86:1989;5723-5727.
114. Petersen M., Jacobsen J.P. Solution structure of a DNA complex with the fluoresecent bis-intercalator TOTO modified on the benothiazole ring. Bioconjug Chem. 9:1998;331-340.
115. Pommier Y., Kohlhagen G., Bailly C., Waring M., Mazumder A., Kohn K.W. DNA sequence- and structure-selective alkylation of guanine N2 in the DNA minor groove by ecteinascidin 743, a potent antitumor compound from the Caribbean tunicate Ecteinascidia turbinata. Biochemistry. 35:1996;13303-13309.
116. Priebe, W. (Ed.). (1995a). Anthracyclines Antibiotics. New Analogs, Methods of Delivery, and Mechanisms of Action. Washington, D.C.: American Chemical Society.
117. Priebe W. Mechanism of action-governed design of anthracycline antibiotics. a "turn-off/turn-on" approach Curr Pharm Design. 1:1995;51-68. b.
118. Priebe W., Perez-Soler R. Design and tumor targeting of anthracyclines able to overcome multidrug resistance. a double-advantage approach Pharmacol Ther. 60:1993;215-234.
119. Propst, C. L., & Perun, T. J. (Eds.). (1992). Nucleic Acid Targeted Drug Design. New York: Marcel Dekker.
120. Quigley G.J., Ughetto G., van der Marel G.A., van Boom J.H., Wang A.H.-J., Rich A. Non-Watson-Crick GC and AT base pairs in a DNA-antibiotic complex. Science. 232:1986;1255-1258.
121. Redinbo M.R., Stewart L., Kuhn P., Champoux J.J., Hol W.G. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science. 279:1998;1504-1513.
122. Robinson H., Wang A.H.-J. A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy. Biochemistry. 31:1992;3524-3533.
123. Robinson H., Wang A.H.-J. Neomycin, spermine and hexaamminecobalt(III) share common structural motifs in converting B- to A-DNA. Nucleic Acids Res. 24:1996;676-682.
124. Robinson H., Yang D., Wang A.H.-J. Structure and dynamics of the antitumor drugs nogalamycin and disnogalamycin complexed to d(CGTACG). comparison of X-ray and NMR structures Gene. 149:1994;179-188.
125. Robinson H., Priebe W., Chaires J.B., Wang A.H.-J. Binding of two novel bis-daunorubicins to DNA studied by NMR spectroscopy. Biochemistry. 36:1997;8663-8670.
126. Robinson H., Gao Y.-G., Bauer C., Roberts C., Switzer C.Y., Wang A.H.-J. 2′-Deoxy-isoguanosine adopts more than one tautomers to base pair with thymidine observed by high resolution crystal structure. Biochemistry. 37:1998;10897-10905. a.
127. Robinson H., Gao Y.-G., McCrary B.S., Edmondson S.P., Shriver J.W., Wang A.H.-J. The hyperthermophile chromosomal protein Sac7d kinks DNA sharply. Nature. 392:1998;202-205. b.
128. Rubin E.H., Li T.K., Duann P., Liu L.F. Cellular resistance to topoisomerase poisons. Cancer Treat Res. 87:1996;243-260.
129. Sakai R., Rinehart K.L., Guan Y., Wang A.H.-J. Additional antitumor ecteinascidins from a Caribbean tunicate. in vivo activities and crystal structures Proc Natl Acad Sci USA. 89:1992;11456-11460.
130. Sastry M., Patel D.J. Solution structure of the mithramycin dimer-DNA complex. Biochemistry. 32:1993;6588-6604.
131. Sastry M., Fiala R., Lipman R., Tomasz M., Patel D.J. Solution structure of the monoalkylated mitomycin C-DNA complex. J Mol Biol. 247:1995;338-359. a.
132. Sastry M., Fiala R., Patel D.J. Solution structure of mithramycin dimers bound to partially overlapping sites on DNA. J Mol Biol. 251:1995;674-689. b.
133. 2. Biochemistry. 32:1993;12577-12585.
134. Seaman F.C., Hurley L. Molecular basis for the DNA sequence selectivity of ecteinascidin 736 and 743. evidence for the dominant role of direct readout via hydrogen bonding J Am Chem Soc. 120:1998;13028-13041.
135. 2 Biochem J. 304:1994;967-979.
136. 2 - an NMR and molecular modelling study. Eur J Biochem. 205:1992;45-58.
137. 2. Biochemistry. 27:1988;4340-4349.
138. Seshadri R., Israel M., Pegg W. Adriamycin analogues. Preparation and biological evaluation of some novel 14-thioadriamycins. J Med Chem. 26:1983;11-15.
139. Shui X., McFail-Isom L., Hu G.G., Williams L.D. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37:1998;8341-8355.
140. Sinden R.R. DNA Structure and Function. 1994;Academic Press, San Diego, CA.
141. Skorobogaty A., Brownlee R.T.C., Chandler C.J., Kyratzis I., Phillips D.R., Reiss J.A., Trist H. The DNA-association and biological activity of a new bis(14-thiadaunomycin). Anticancer Drug Des. 3:1988;41-56.
142. Smith A.L., Nicolaou K.C. The enediyne antibiotics. J Med Chem. 39:1996;2103-2117.
143. 2 J Mol Biol. 263:1996;237-258.
144. Snyder J.G., Hartman N.G., Langlois D'Estantoti B., Kennard O., Remeta D.P., Breslauer K.J. Binding of actinomycin D to DNA. evidence for a nonclassical high-affinity binding mode that does not require GpC sites Proc Natl Acad Sci USA. 86:1989;3968-3972.
145. Spielmann H.P., Wemmer D.E., Jacobsen J.P. Solution structure of a DNA complex with the fluoresecent bis-intercalator TOTO determined by NMR. Biochemistry. 34:1995;8542-8553.
146. Stassinopoulos A., Ji J., Gao X., Goldberg I.H. Solution structure of a two-base DNA bulge complexed with an enedyne cleaving analog. Science. 272:1996;1943-1946.
147. Stewart L., Redinbo M.R., Qiu X., Hol W.G., Champoux J.J. A model for the mechanism of human topoisomerase I. Science. 279:1998;1534-1541.
148. Stubbe J., Kozarich J.W., Wu W., Vanderwall D.E. Bleomycins. a structural model for specificity, binding and double stranded DNA cleavage Acc Chem Res. 29:1996;322-330.
149. Sugiyama H., Lian C., Isomura M., Saito I., Wang A.H.-J. Distamycin A modulates the sequence specificity of DNA alkylation by duocarmycin A. Proc Natl Acad Sci USA. 93:1996;14405-14410.
150. Sun D., Hansen M., Clement J.J., Hurley L.H. Structure of the altromycin B (N7-guanine)-DNA adduct. A proposed prototypic DNA adduct structure for the pluramycin antitumor antibiotics. Biochemistry. 32:1993;8068-8074.
151. Taatjes D.J., Gaudiano G., Resing K., Koch T.H. Redox pathway leading to the alkylation of DNA by the anthracycline, antitumor drugs adriamycin and daunomycin. J Med Chem. 40:1997;1276-1286.
152. Takahara P.M., Rosenzweig A.C., Frederick C.A., Lippard S.J. Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin. Nature. 377:1995;649-652.
153. Takahara P.M., Frederick C.A., Lippard S.J. Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J Am Chem Soc. 118:1996;12309-12321.
154. Tao Z.-F., Fujiwara T., Saito I., Sugiyama H. Sequence-specific DNA alkylation by hybrid molecules between segment A of duocarmycin A and pyrrole/imidazole diamide. Angew Chem Int Ed Engl. 38:1999;650-653.
155. Teng M.-K., Frederick C.A., Usmann N., Wang A.H.-J. The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res. 16:1988;2671-2690.
156. Tereshko V., Minasov G., Egli M. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J Am Chem Soc. 121:1999;470-471.
157. Treiber D.K., Zhai X., Jantzen H.-M., Essigmann J. Cisplatin-DNA adducts are molecular decoys for the ribosomal RNA transcription factor hUBF (human upstream binding factor). Proc Natl Acad Sci USA. 91:1994;5672-5676.
158. Ughetto G., Wang A.H.-J., Quigley G.J., van der Marel G.A., van Boom J.H., Rich A. A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. Nucleic Acids Res. 13:1985;2305-2323.
159. van Boom S.S.G.E., Yang D., Reedijk J., van der Marel G.A., Wang A.H.-J. Structure and isomerization of an intra-strand cisplatin-cross-linked octamer DNA duplex by NMR analysis. J Biomol Struct Dyn. 13:1996;989-998.
160. Vanderwall D.E., Lui S.M., Wu W., Turner C.J., Kozarich J.W., Stubbe J. A model of the structure of HOO-Co.bleomycin bound to d(CCAGTACTGG). recognition at the d(GpT) site and implications for double stranded DNA cleavage Chem Biol. 4:1997;373-387.
161. van Houte L.P.A., van Garderen C.J., Patel D.J. The antitumor drug nogalamycin forms two different intercalation complexes with d(GCGT)·d(ACGC). Biochemistry. 32:1993;1667-1674.
162. Vichi P., Song J., Hess J., Tritton T.R. Signal transduction systems in doxorubicin hydrochloride mechanism of action. Priebe W. Anthracycline Antibiotics (. 1995;241-247 American Chemical Society, Washington, D.C.
163. Wadkins R.M., Vladu B., Tung C.-S. Actinomycin D binds to metastable hairpins in single stranded DNA. Biochemistry. 37:1998;11915-11923.
164. Wahl M.C., Sundaralingam M. Crystal structures of A-DNA duplexes. Biopolymers. 44:1997;45-63.
165. Wakelin L.P.J. Polyfunctional DNA intercalating agents. Med Res Rev. 6:1986;275-340.
166. Wang A.H.-J. Intercalative drug binding to DNA. Curr Opin Struct Biol. 2:1992;361-368.
167. Wang A.H.-J. X-ray crystallographic and NMR structural studies of anthracycline anticancer drugs. implication in drug design Hurley L., Chaires B. Advance in DNA Sequence Specific Agents, Vol. 2 (. 1996;59-100 JAI Press, Greenwich.
168. Wang A.H.-J., Teng M.-K. Molecular recognition of DNA minor groove binding drugs. Bugg C.E., Ealick S.E. Crystallographic and Modeling Methods in Molecular Design (. 1990;123-150 Springer-Verlag, New York.
169. Wang A.H.-J., Quigley G.J., Kolpak F.J., Crawford J.L., van Boom J.H., van der Marel G.A., Rich A. Molecular structure of a left-handed double helix DNA fragment at atomic resolution. Nature. 282:1979;680-686.
170. Wang A.H.-J., Ughetto G., Quigley G.J., Hakoshima T., van der Marel G.A., van Boom J.H., Rich A. The molecular structure of a DNA-triostine A complex. Science. 225:1984;1115-1121.
171. Wang A.H.-J., Ughetto G., Quigley G.J., Rich A. Interactions between an anthracycline antibiotic and DNA. molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2 Å resolution Biochemistry. 26:1987;1152-1163.
172. Wang A.H.-J., Gao Y.-G., Liaw Y.-C., Li Y.-K. Formaldehyde cross-links daunorubicin and DNA efficiently. HPLC and X-ray diffraction studies Biochemistry. 30:1991;3812-3815.
173. Wang J.C. DNA topoisomerases as targets of therapeutics. an overview Adv Pharmacol. 29A:1994;1-19.
174. Wang J.C. DNA topoisomerases. Annu Rev Biochem. 65:1996;635-692.
175. Wang J.Y.-T., Chao M., Wang A.H.-J. Adducts of DNA and anthracycline antibiotics. Structures, interactions, and activities. Priebe W. Anthracycline Antibiotics (. 1995;168-182 American Chemical Society, Washington, D.C.
176. Wemmer D., Dervan P.B. Targeting the minor groove of DNA. Curr Opin Struct Biol. 7:1997;355-361.
177. Wemmer D.E., Geierstanger B.H., Fagan P.A., Dwyer T.J., Jacobsen J.P., Pelton J.G., Ball G.E., Leheny A.R., Chang W.-H., Bathini Y., Lown J.W., Rentzeperis D., Marky L.A., Singh S., Kollman P. Minor groove recognition of DNA by distamycin and its analogs. Sarma R.H., Sarma M.H. Structural Biology: The State of Art (. 1994;301-323 Adenine Press, Schenectady.
178. Werner M.H., Huth J.R., Groenenborn A.M., Clore G.M. Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell. 81:1995;705-714.
179. Werner M.H., Gronenborn A.M., Clore G.M. Intercalation, DNA kinking, and the control of transcription. Science. 271:1996;778-783.
180. White S., Baird E.E., Dervan P.B. On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides. Chem Biol. 4:1997;569-578.
181. White S., Szewczyk J.W., Turner J.M., Baird E.E., Dervan P.B. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature. 391:1998;468-471.
182. Williams L.D., Gao Q. DNA-ditercalinium interactions. implications for recognition of damaged DNA Biochemistry. 31:1992;4315-4324.
183. Williams L.D., Egli M., Gao Q., Bash P., van der Marel G.A., van Boom J.H., Rich A., Frederick C.A. Structure of nogalamycin bound to a DNA hexamer. Proc Natl Acad Sci USA. 87:1990;2225-2229.
184. Wing R.M., Drew H.R., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R.E. Crystal structure analysis of a complete turn of B-DNA. Nature. 287:1980;755-758.
185. 2 green. its detailed structural characterization by NMR and molecular modeling and its sequence-specific interaction with DNA oligonucleotides J Am Chem Soc. 118:1996;1268-1280. a.
186. 2 green complexed with d(CCAGGCCTGG). J Am Chem Soc. 118:1996;1281-1294. b.
187. Xie Y., Miller G.G., Cubitt S.A., Soderlind K.J., Allalunis-Turner M.J., Lown J.W. Enediyne-lexitropsin DNA-targeted anticancer agents. Physicochemical and cytotoxic properties in human neoplastic cells in vitro, and intracellular distribution. Anticancer Drug Des. 12:1997;169-179.
188. Xu R.X., Nettesheim D., Otvos J.D., Petering D.H. NMR determination of the structures of peroxycobalt(III) bleomycin and cobalt(III) bleomycin, products of the aerobic oxidation of cobalt(II) bleomycin by dioxygen. Biochemistry. 33:1994;907-916.
189. Yamamoto K., Sugiyama H., Kawanishi S. Concerted DNA recognition and novel site-specific alkylation by duocarmycin A with distamycin A. Biochemistry. 32:1993;1059-1064.
190. Yang D., Wang A.H.-J. Structure by NMR of antitumor drugs aclacinomycin A and B complexed to d(CGTACG). Biochemistry. 33:1994;6595-6604.
191. Yang D., Wang A.H.-J. Structural studies of interactions between anticancer platinum compounds and DNA. Prog Biophys Mol Biol. 66:1996;81-111.
192. Yang D., van Boom S.S.G.E., Reedijk J., van Boom J.H., Farrell N., Wang A.H.-J. A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA. Nature Struct Biol. 2:1995;577-585. a.
193. Yang D., van Boom S.S.G.E., Reedijk J., van Boom J.H., Wang A.H.-J. Structure and isomerization of an intra-strand cisplatin-cross-linked octamer DNA duplex by NMR analysis. Biochemistry. 34:1995;12912-12920. b.
194. Yang D., Strode J.T., Spielmann H.P., Wang A.H.-J., Burke T.G. DNA interactions of two clinical camptothecin drugs stabilize their active lactone forms. J Am Chem Soc. 120:1998;2979-2980.
195. Yang X.-L., Sugiyama H., Ikeda S., Saito I., Wang A.H.-J. Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine base pairs by NMR. Biophys J. 75:1998;1163-1171.
196. Yang X.-L., Kaenzig C., Lee M., Wang A.H.-J. Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy. Eur J Biochem. in press:1999.
197. Ye X., Kimura K.-I., Patel D.J. Site-specific intercalation of an anthracycline antitumor antibiotic into a Y·RY DNA triplex through covalent adduct formation. J Am Chem Soc. 115:1993;9325-9326.
198. Ye X., Gorin A., Ellington A.D., Patel D.J. Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex. Nature Struct Biol. 3:1996;1026-1033.
199. Zamble D.B., Lippard S.J. Cisplatin and DNA repair in cancer chemotherapy. Trends Biochem Sci. 20:1995;435-439.
200. Zeman S.M., Phillips D.R., Crothers D.M. Characterization of covalent adriamycin-DNA adducts. Proc Natl Acad Sci USA. 95:1998;11561-11565.
201. Zhang X.L., Patel D.J. Solution structure of the nogalamycin-DNA complex. Biochemistry. 29:1990;9451-9466.
202. Zhang X.L., Patel D.J. Solution structure of the luzopeptin-DNA complex. Biochemistry. 30:1991;4026-4041.
203. Zou Y., van Houten B., Farrell N. Sequence specificity of DNA-DNA interstrand cross-link formation by cisplatin and dinuclear platinum complexes. Biochemistry. 33:1994;5404-5410.