Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and Center for Biotechnology, National Taiwan University, Taipei 106, Taiwan.
Nucleic Acids Res. 2013 Dec;41(22):10630-40. doi: 10.1093/nar/gkt828. Epub 2013 Sep 14.
Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme-DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m-AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3'-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs' structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.
II 型拓扑异构酶（Top2s）通过形成一种称为切割复合物的酶-DNA 加合物来改变 DNA 拓扑结构，该复合物在一条 DNA 上产生瞬时双链断裂，从而允许另一条 DNA 通过。靶向人类 Top2 的药物是临床上有效的抗癌药物，其捕获 Top2 介导的 DNA 断裂有效地诱导基因组碎片化和细胞死亡。为了了解这种药物作用的结构基础，我们之前确定了与人 Top2β 异构体形成切割复合物的结构，该复合物与药物依托泊苷和 DNA 结合，并描述了药物插入 DNA 切割位点和药物诱导的催化基团解耦。通过开发一种结晶后药物置换程序，简化了药物稳定切割复合物的结构特征分析，我们将分析扩展到其他结构不同的药物，米托蒽醌和米托蒽醌。除了预期的药物嵌入之外，在新结构中还观察到切割位点的 3'-核苷酸中核糖构象的明显变化，这代表了捕获 Top2 切割复合物的新机制。药物结合模式和药物结合口袋的构象景观的分析为药物的结构-活性关系提供了合理化，并解释了为什么 Top2 突变体对每种药物表现出不同的影响。提出了药物设计指南，以促进针对特定异构体的 Top2 靶向抗癌药物的开发。
