Binding-Induced Activation of DNA Alkylation by Duocarmycin SA: Insights from the Structure of an Indole Derivative−DNA Adduct

The mechanism for catalysis of DNA alkylation by the potent antitumor antibiotic duocarmycin SA (DSA) has been probed by determining the structure of a DNA adduct of the indole analogue (DSA-indole, DSI) lacking three methoxy functional groups. The three-dimensional structure of DSI covalently bound to A19 in d-(G1ACTAATTGAC11)·d-(G12TCAATTAGTC22) was determined by 1H NMR spectroscopy using a total of 935 experimental distance and dihedral angle constraints. The representative ensemble of 20 conformers has no distance restraint violations greater than 0.03 A, no torsional restraint violations greater than 0.7°, and a pairwise rmsd over all atoms in the binding site of 0.48 A. Comparison of the structures of the DSA and DSI adducts reveals a structural basis for the critical role of one of the trimethoxy-indole functional groups in alkylation reactivity. A deeper penetration into the DNA minor groove in the vicinty of the indole subunit is observed for the DSI versus the DSA adduct, along with some variati...