Characterization of Zn(II)·Deglycobleomycin A₂ and Interaction with d(CGCTAGCG)₂:  Direct Evidence for Minor Groove Binding of the Bithiazole Moiety

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(II)·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.