Institute of Functional Nano & Soft Materials and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China.
J Chem Inf Model. 2013 Apr 22;53(4):997-1006. doi: 10.1021/ci400066x. Epub 2013 Apr 3.
Originally isolated from natural products, camptothecin (CPT) has provided extensive playing fields for the development of antitumor drugs. Two of the most successful analogs of CPT, topotecan and irinotecan, have been approved by the FDA for the treatment of colon cancer and ovarian cancer, as well as other cancers. However, the emergence of drug resistance mutations in topoisomerase I is a big challenge for the effective therapy of these drugs. Therefore, in this study, a series of computational approaches from molecular dynamics (MD) simulations to steered molecular dynamics (SMD) simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were employed to uncover the molecular principle of the topotecan resistance induced by three mutations in DNA topoisomerase I, including E418K, G503S, and D533G. Our results demonstrate a remarkable correlation between the binding free energies predicted by MM/GBSA and the rupture forces computed by SMD, and moreover, the theoretical results given by MM/GBSA and SMD are in excellent agreement with the experimental data for ranking the inhibitory activities: WT > E418K > G503S > D533G. In order to explore the drug resistance mechanism that underlies the loss of the binding affinity of topotecan, the binding modes of topotecan bound to the WT and mutated receptors were presented, and comparisons of the binding geometries and energy contributions on a per residue basis of topotecan between the WT complex and each mutant were also discussed. The results illustrate that the mutations of E418K, G503S, and D533G have great influence on the binding of topotecan to topoisomerase I bound with DNA, and the variations of the polar interactions play critical roles in the development of drug resistance. The information obtained from this study provides useful clues for designing improved topoisomerase I inhibitors for combating drug resistance.
喜树碱（CPT）最初从天然产物中分离出来，为抗肿瘤药物的开发提供了广阔的领域。CPT 的两种最成功的类似物拓扑替康和伊立替康已被 FDA 批准用于治疗结肠癌和卵巢癌以及其他癌症。然而，拓扑异构酶 I 耐药突变的出现是这些药物有效治疗的一大挑战。因此，在这项研究中，我们采用了一系列计算方法，包括分子动力学（MD）模拟、导向分子动力学（SMD）模拟和分子力学/广义 Born 表面面积（MM/GBSA）结合自由能计算，以揭示三种 DNA 拓扑异构酶 I 突变（E418K、G503S 和 D533G）诱导的拓扑替康耐药的分子机制。我们的结果表明，MM/GBSA 预测的结合自由能与 SMD 计算的断裂力之间存在显著相关性，而且 MM/GBSA 和 SMD 的理论结果与实验数据在抑制活性的排序上非常吻合：WT > E418K > G503S > D533G。为了探讨拓扑替康结合亲和力丧失的耐药机制，我们展示了拓扑替康与 WT 和突变受体结合的结合模式，并讨论了 WT 复合物与每个突变体之间拓扑替康结合构象和基于残基的能量贡献的比较。结果表明，E418K、G503S 和 D533G 的突变对拓扑替康与 DNA 结合的拓扑异构酶 I 的结合有很大影响，极性相互作用的变化在耐药性的发展中起着关键作用。本研究获得的信息为设计用于克服耐药性的改良拓扑异构酶 I 抑制剂提供了有用的线索。
