Binding of an Indenoisoquinoline to the Topoisomerase-DNA Complex Induces Reduction of Linker Mobility and Strengthening of Protein-DNA Interaction

Long-duration comparative molecular dynamics simulations of the DNA-topoisomerase binary and DNA-topoisomerase-indenoisoquinoline ternary complexes have been carried out. The analyses demonstrated the role of the drug in conformationally stabilizing the protein-DNA interaction. In detail, the protein lips, clamping the DNA substrate, interact more tightly in the ternary complex than in the binary one. The drug also reduces the conformational space sampled by the protein linker domain through an increased interaction with the helix bundle proximal to the active site. A similar alteration of linker domain dynamics has been observed in a precedent work for topotecan but the molecular mechanisms were different if compared to those described in this work. Finally, the indenoisoquinoline keeps Lys532 far from the DNA, making it unable to participate in the religation reaction, indicating that both short- and long-range interactions contribute to the drug poisoning effect.

本研究针对DNA-拓扑异构酶（DNA-topoisomerase）二元复合物与DNA-拓扑异构酶-茚并异喹啉（indenoisoquinoline）三元复合物开展了长时程比较分子动力学模拟。分析结果表明，该药物可在构象层面稳定蛋白质与DNA的相互作用。具体而言，夹持DNA底物的蛋白质钳口在三元复合物中的结合紧密程度显著高于二元复合物。该药物还通过增强与活性位点附近螺旋束的相互作用，压缩了蛋白质连接结构域的构象采样空间。此前一项针对拓扑替康（topotecan）的研究中已观察到类似的连接结构域动态变化，但二者的分子作用机制与本研究报道的存在差异。最终，茚并异喹啉可使Lys532远离DNA，使其无法参与DNA再连接反应，这表明短程与长程相互作用共同参与了该药物的毒杀效应。