Duocarmycin SA Shortened, Simplified, and Extended Agents: A Systematic Examination of the Role of the DNA Binding Subunit

The examination of shortened, simplified, and extended analogs of duocarmycin SA is described and constitutes a detailed study of the role of linked DNA binding subunit. In addition to enhancing the DNA binding affinity and selectivity through minor groove noncovalent contacts, the studies in conjunction with those of the accompanying article illustrate that an extended rigid N2 amide substituent is required for catalysis of the DNA alkylation reaction. This activation for DNA alkylation is independent of pH, and we propose it results from a binding-induced conformational change in the agents which increases their inherent reactivity. The ground state destabilization of the substrate results from a twist in the linking amide that disrupts the vinylogous amide stabilization of the alkylation subunit and activates the agent for nucleophilic addition. This leads to preferential activation of the agents for DNA alkylation within the narrower, deeper AT-rich minor groove sites where the inherent twist in the l...