Structure activity relationships for tricyclic‐carboxamide topoisomerase II poisons indicate that cytotoxicity is enhanced by the presence of methyl, and other, groups in the position peri to the carboxamide. Linked dimers of phenazine‐1‐carboxamides are potent cytotoxins and one phenazine dimer, MLN944 (alternatively XR5944), has been in clinical trial. MLN944 is a template inhibitor of transcription, whereas corresponding monomers are not. Nevertheless, its cytotoxic potency is also diminished by removal of its peri methyl groups. Here, we describe NMR and molecular dynamic studies of the interaction of desmethyl MLN944 with d(ATGCAT)₂, d(TATGCATA)₂, and d(TACGCGTA)₂ to investigate the influence of the nine‐methyl group on the structure of MLN944 complexes. As with MLN944, the carboxamide group hydrogen bonds to the phenazine ring nitrogen, the ligand sandwiches the central GC base pairs in the major groove, and the protonated linker amines hydrogen bond primarily to the O6 atom of the guanines. Molecular dynamics studies reveal that the linker exists in multiple conformations, none of which produce an ideal set of hydrogen bonds. In distinction, however, the carboxamide‐to‐phenazine ring nitrogen hydrogen bond is weaker, the overall helix winding is less and the NMR resonances are broader in the desmethyl complexes. Exchange between free and complexed DNA, quantified using two‐dimensional NOESY spectra, is faster for the desmethyl MLN944 complexes than for MLN944 complexes. Overall, the data suggest that desmethyl MLN944 DNA complexes are “looser” and more unwound at the binding site, leading to faster dissociation rates, which could account for the diminished efficacy of the desmethyl analog.

中文翻译：

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细胞毒素 MLN944 的去甲基类似物的 DNA 复合物的结构和动力学：深入了解甲基无效时的活性。

三环甲酰胺拓扑异构酶 II 毒物的结构活性关系表明，甲酰胺周围位置的甲基和其他基团的存在增强了细胞毒性。吩嗪-1-甲酰胺的连接二聚体是有效的细胞毒素，一种吩嗪二聚体 MLN944（或者 XR5944）已在临床试验中。MLN944 是转录的模板抑制剂，而相应的单体则不是。然而，其细胞毒性效力也因去除其周甲基而减弱。在这里，我们描述了去甲基 MLN944 与 d(ATGCAT) ₂、d(TATGCATA) ₂和 d(TACGCGTA) ₂相互作用的核磁共振和分子动力学研究研究九甲基基团对 MLN944 复合物结构的影响。与 MLN944 一样，羧酰胺基团与吩嗪环氮氢键结合，配体将中央 GC 碱基对夹在大沟中，质子化的连接胺主要与鸟嘌呤的 O6 原子氢键结合。分子动力学研究表明，接头存在多种构象，没有一种会产生一组理想的氢键。然而，不同的是，甲酰胺-吩嗪环氮氢键较弱，整体螺旋缠绕较少，去甲基配合物中的核磁共振共振较宽。使用二维 NOESY 光谱量化的游离 DNA 和复合 DNA 之间的交换，去甲基 MLN944 复合物比 MLN944 复合物更快。总体，