Characterization of Zn(II)·deglycobleomycin A2 and interaction with d(CGCTAGCG)2

Direct-evidence for minor groove binding of the bithiazole moiety

Steven J. Sucheck, Jeffrey F. Ellena, Sidney Hecht

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

Deglycobleomycin (dgBLM) binds to and degrades the self-complementary oligonucleotide d(CGCTAGCG)2 in a sequence-selective fashion. To characterize the binding interaction, a 1:1 complex of Zn(II)·dgBLM A2 with the DNA octanucleotide has been examined using two-dimensional NMR experiments and restrained molecular dynamics calculations. Critical elements of the mode of DNA interaction within two structural domains of Zn(n)·dgBLM A2 were fundamentally different than those observed previously for Zn(II) BLM A2 (Manderville, R. A.; Ellena, J. F.; Hecht, S. M. J. Am. Chem. Soc. 1995, 117, 7891). A minor groove mode of binding by the bithiazole moiety is supported by the present study. Only slight upfield shifting of the bithiazole (Bit) protons Bit H5 and Bit H5' is observed, and the sequential intrastrand NOE connectivities are retained upon Zn(II) dgBLM A2 binding. The orientation of the drug molecule in the complex is based on the finding of 16 intermolecular Zn(II) dgBLM A2-DNA NOEs. The cationic C-substituent of Zn(II) dgBLM A2 is positioned in the minor groove of the DNA based on the appearance of 10 NOEs between hydrogens located in the minor groove of DNA and the C-substituent of BLM. Additionally, the results are consistent with the interpretation that the DNA octanucleotide cleavage specificity observed from Fe(II) dgBLM A2 and possibly for Fe(II)·BLM A2 is due in part to recognition of the T4-A5 region of the octanucleotide by the bithiazole. Using the NMR-derived NOE distance and dihedral bond angle restraints to guide the molecular dynamics calculations, a binding model for the interaction of Zn(II)·dgBLM A2 with the octanucleotide has been derived.

Original languageEnglish (US)
Pages (from-to)7450-7460
Number of pages11
JournalJournal of the American Chemical Society
Volume120
Issue number30
DOIs
StatePublished - Aug 5 1998
Externally publishedYes

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DNA
Molecular dynamics
Molecular Dynamics Simulation
varespladib methyl
Nuclear magnetic resonance
Oligonucleotides
DNA Cleavage
deglycobleomycin
Protons
Hydrogen
Molecules
Experiments
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Characterization of Zn(II)·deglycobleomycin A2 and interaction with d(CGCTAGCG)2 : Direct-evidence for minor groove binding of the bithiazole moiety. / Sucheck, Steven J.; Ellena, Jeffrey F.; Hecht, Sidney.

In: Journal of the American Chemical Society, Vol. 120, No. 30, 05.08.1998, p. 7450-7460.

Research output: Contribution to journalArticle

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abstract = "Deglycobleomycin (dgBLM) binds to and degrades the self-complementary oligonucleotide d(CGCTAGCG)2 in a sequence-selective fashion. To characterize the binding interaction, a 1:1 complex of Zn(II)·dgBLM A2 with the DNA octanucleotide has been examined using two-dimensional NMR experiments and restrained molecular dynamics calculations. Critical elements of the mode of DNA interaction within two structural domains of Zn(n)·dgBLM A2 were fundamentally different than those observed previously for Zn(II) BLM A2 (Manderville, R. A.; Ellena, J. F.; Hecht, S. M. J. Am. Chem. Soc. 1995, 117, 7891). A minor groove mode of binding by the bithiazole moiety is supported by the present study. Only slight upfield shifting of the bithiazole (Bit) protons Bit H5 and Bit H5' is observed, and the sequential intrastrand NOE connectivities are retained upon Zn(II) dgBLM A2 binding. The orientation of the drug molecule in the complex is based on the finding of 16 intermolecular Zn(II) dgBLM A2-DNA NOEs. The cationic C-substituent of Zn(II) dgBLM A2 is positioned in the minor groove of the DNA based on the appearance of 10 NOEs between hydrogens located in the minor groove of DNA and the C-substituent of BLM. Additionally, the results are consistent with the interpretation that the DNA octanucleotide cleavage specificity observed from Fe(II) dgBLM A2 and possibly for Fe(II)·BLM A2 is due in part to recognition of the T4-A5 region of the octanucleotide by the bithiazole. Using the NMR-derived NOE distance and dihedral bond angle restraints to guide the molecular dynamics calculations, a binding model for the interaction of Zn(II)·dgBLM A2 with the octanucleotide has been derived.",
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