Bleomycins constitute a class of DNA-targeted anti-tumor antibiotics used clinically against several forms of cancer. The clinical efficacy of bleomycin is thought to derive from its ability to bind Fe(II) and O2 leading to site-selective, single- and double-strand DNA scission. In spite of the fact that the bleomycins have been studied extensively since their discovery more than 40 years ago, fundamental aspects of their DNA-bound state(s) that promote single- and double-strand DNA cleavage remain to be fully defined. Recently, two of us (ECL and MMG) reported the first crystal structures of DNA-bound Co(III)�bleomycin B2, a structural analogue of Fe(III)�bleomycin. The structure of bleomycin B2 and, more recently, the structure of bleomycin A2 revealed that bleomycins bind to DNA in two distinct modes: (1) a �tight� binding mode in which the DNA intercalating bithiazole of the drug is deeply inserted into the DNA base stack; and (2) a �loose� binding mode in which the bithiazole is only partially intercalated. Importantly, these two modes may contribute to binding site selection, drug activation, and binding reorganization leading to double-strand DNA cleavage. Using crystal structures as a starting point, MD simulations were carried out on Co(III)�bleomycin A2 bound to 5�-d(CTTAGTT AGC)�d(GCTAACTAAG) to examine the drug motions and points of flexibility that contribute to the attainment of these two binding modes. Our simulations revealed strong inter- and intra-molecular H-bonds that serve to pre-organize the disaccharide moiety, Co(III)-binding domain, and the peptide linker; these interactions support binding with the minor groove. Concurrently, the bithiazole and C-terminal �tail� is intercalated into the TpT portion of the binding site where it alternates between the �loose� and �tight� binding modes due to dynamic motions facilitated by the peptide linker.This work was supported by NIH/RCMI Grant # G12 MD007597.

Molecular dynamics simulations of DNA-bound Co(III)�bleomycin

246th National Meeting (2013)

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