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 duoc armycin SA is described and constitutes a detailed study of the role o f linked DNA binding subunit. In addition to enhancing the DNA binding affinity and selectivity through minor groove noncovalent contacts, t he studies in conjunction with those of the accompanying article illus trate that an extended rigid N-2 amide substituent is required for cat alysis of the DNA alkylation reaction. This activation for DNA alkylat ion is independent of pH, and we propose it results from a binding-ind uced conformational change in the agents which increases their inheren t reactivity. The ground state destabilization of the substrate result s from a twist in the linking amide that disrupts the vinylogous amide stabilization of the alkylation subunit and activates the agent for n ucleophilic addition. This leads to preferential activation of the age nts for DNA alkylation within the narrower, deeper AT-rich minor groov e sites where the inherent twist in the linking amide and helical rise of the bound conformation is greatest. Thus, shape-selective recognit ion (preferential AT-rich noncovalent binding) and shape-dependent cat alysis (induced twist in linking N-2 amide) combine to restrict S(N)2 alkylation to accessible adenine N3 nucleophilic sites within the pref erred binding sites. Additional ramifications of this DNA binding-indu ced conformational change on the reversibility of the DNA alkylation r eaction are discussed. The results of the study illustrate the importa nce of the C5' methoxy group and the C6 methyl ester of duocarmycin SA , and a previously unrecognized role for these substituents is propose d.