SOLUTION STRUCTURE OF THE MENOGARIL-DNA COMPLEX

Menogaril (7-con-O-methylnogarol) is a derivative of the anthracycline antitumor drug nogalamycin lacking both the nogalose sugar and acetyl functionality that are positioned in the minor groove of the nogalamy cin-DNA complex. Two menogaril molecules bind to the self-complementar y d(G1-A2-C3-A4-T5-G6-T7-C8) duplex in a cooperative manner and form a symmetric two drugs per duplex complex. We have obtained the solution structure of the menogaril-d(G-A-C-A-T-G-T-C) complex by a combined N MR-molecular dynamics study including intensity-based refinement. The aglycon chromophore of menogaril intercalates between (C3-A4).(T5-G6) base pairs, with its long axis orthogonal to the long axis of the flan king Watson-Crick base pairs. The B, C, and D aromatic rings of the ag lycon chromophore stack primarily with the G6 base with the OH-4/OH-6 bearing edge directed toward the C3-A4 strand, while the nonplanar cyc lohexene ring A protrudes into the minor groove and adopts a half-chai r conformation. An intermolecular hydrogen bond is detected between th e OH-9 of the cyclohexene ring A and O2P of the G6-T7 step in the mino r groove. The positively charged bicyclic aminoglucose sugar which is fused to the aromatic ring D of the aglycon is positioned in the major groove and spans the three base pair d(A2-C3-A4). d(T5-G6-T7) segment . The aminoglucose sugar adopts a chair conformation with the bridgehe ad oxygen atom directed toward the A4 . T5 base pair and the charged N (CH3)(2)-3'' group directed toward the A2 . T7 base pair. A strong int ermolecular hydrogen bond is detected between the OH-2'' of the bicycl ic aminoglucose sugar and the N7 of 06 in the major groove, which acco unts for the sequence specificity of menogaril for its target sites on DNA. Intercalation of the aglycon of menogaril through the major groo ve contrasts with the majority of antitumor antibiotics which intercal ate into DNA through the minor groove.