Pavlopoulos S, Bicknell W, Craik D J, Wickham G
Department of Medicinal Chemistry, Victorian College of Pharmacy, Monash University, Melbourne, Victoria, Australia.
Biochemistry. 1996 Jul 23;35(29):9314-24. doi: 10.1021/bi952542c.
2D NMR spectroscopic methods have been used to determine the structure of the adduct formed between the antitumor antibiotic hedamycin and the oligodeoxyribonucleotide duplex d(CACGTG)2. Evidence for both intercalation and alkylation in the adduct was observed, and a model for the binding interaction was constructed based on intermolecular NOEs and distance-restrained molecular dynamics. In our computationally refined model, the anthrapyrantrione chromophore of hedamycin is intercalated between the 5'-CG-3' bases with the two aminosugar groups placed in the minor groove and the six carbon bisepoxide side chain located in the major groove. The anglosamine sugar attached at C8 is oriented in the 3' direction relative to the intercalation site, while the N,N-dimethylvancosamine attached at C10 is oriented to the 5' side, with each aminosugar wedged between a guanine exocyclic amino group and one of the groove walls. The terminal epoxide carbon C18 is covalently bound to the N7 atom of the central guanine, as evidenced by lability of the C8 hydrogen of this purine upon reaction with hedamycin. Our binding model places the C10-attached N,N-dimethylvancosamine of hedamycin in van der Waals contact with the alkylated strand. A strong NOE contact verifies the close proximity of the terminal methyl group (C19) of the bisepoxide side chain to the methyl group of the thymine on the 3' side of the alkylated guanine. This, in conjunction with other data, suggests hydrophobic interactions between the bisepoxide chain and the floor of the major groove may contribute to sequence recognition. Furthermore, it is proposed that the 5'-CGT sequence selectivity of hedamycin arises, in part, from complementarity in shape between the chromophore substituents and the major and minor groove at the binding site.
二维核磁共振光谱方法已被用于确定抗肿瘤抗生素赫达霉素与寡脱氧核糖核苷酸双链体d(CACGTG)₂形成的加合物的结构。在加合物中观察到了嵌入和烷基化的证据，并基于分子间的核Overhauser效应（NOE）和距离约束分子动力学构建了结合相互作用模型。在我们通过计算优化的模型中，赫达霉素的蒽并吡喃三酮发色团嵌入在5'-CG-3'碱基之间，两个氨基糖基团位于小沟中，六个碳的双环氧化物侧链位于大沟中。连接在C8位的氨基葡萄糖糖相对于嵌入位点沿3'方向定向，而连接在C10位的N,N-二甲基万古霉素糖定向到5'侧，每个氨基糖楔入鸟嘌呤的环外氨基和其中一个沟壁之间。末端环氧化物碳C18与中心鸟嘌呤的N7原子共价结合，这一点通过该嘌呤的C8氢与赫达霉素反应时的不稳定性得到证明。我们的结合模型表明，赫达霉素连接在C10位的N,N-二甲基万古霉素糖与烷基化链存在范德华接触。一个强的NOE接触证实了双环氧化物侧链的末端甲基（C19）与烷基化鸟嘌呤3'侧胸腺嘧啶的甲基非常接近。这与其他数据一起表明，双环氧化物链与大沟底部之间的疏水相互作用可能有助于序列识别。此外，有人提出，赫达霉素对5'-CGT序列的选择性部分源于发色团取代基与结合位点的大沟和小沟之间形状的互补性。
