Definition of the effect and role of the bleomycin A2 valerate substituents:: Preorganization of a rigid, compact conformation implicated in sequence-selective DNA cleavage

The synthesis and a comparative study of deglycobleomycin A(2) analogues containing key modifications in the valerate subunit are described in efforts that define the role of the linker length and its substituents. In addition to demonstrating that the C3-hydroxy group exhibits only a modest effect (1-2x) that may be attributed to an intermolecular H-bond with DNA and that the length of the linker is important (C4 > C5 > C3 > C2), the studies illustrate that the substantial impact of the C4-methyl group is linked to the presence of the C2-methyl group, while the modest impact of the C2-methyl group itself (ca. 2x) is not coupled to the presence of the C4-methyl group. These effects may be explained by the conformational properties of the agents resulting from the substitutions and beautifully fit the models of DNA-bound Co(III)OOH bleomycin A(2) and deglycobleomycin A(2). The magnitude of the effects suggests that an important functional role of the linker region is to facilitate adoption of a rigid, compact conformation productive for DNA cleavage. The studies also identify a second potential site that may adopt two nearly equivalent conformations which may constitute a swivel point that permits access to a class of related bound structures adaptable to the conformational characteristics of the multiple cleavage sites or access to both strands of DNA from a common intercalation site important for both primary (single strand) and secondary (double strand) cleavage.