Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
Nucleic Acids Res. 2019 Nov 4;47(19):10134-10150. doi: 10.1093/nar/gkz515.
Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.
酪氨酰 DNA-磷酸二酯酶 I（TDP1）修复拓扑异构酶 I 型抑制剂（TOP1 抑制剂）产生的 TOP1 切割复合物，TOP1 抑制剂常用于抗癌药物。TDP1 还可以去除由链终止核苷和烷化剂以及核和线粒体基因组中碱基氧化产生的 DNA 3'端阻断损伤。TDP1 抑制剂联合治疗被提议与拓扑异构酶靶向药物协同作用，以增强对平行 DNA 修复途径缺陷的癌细胞的选择性。针对 TDP1 催化结构域进行了晶体片段筛选活动，以鉴定新的先导化合物。晶体结构揭示了两个结合到 TDP1 活性位点并对 TDP1 表现出抑制活性的片段。这些片段在 TDP1 活性位点中占据与先前与结合的钒酸盐（过渡态模拟物）的 TDP1 晶体结构中相同的位置。利用对片段结合的结构见解，已经制备了几种片段衍生物并在生化测定中进行了评估。这些结果表明，基于片段的方法可能是发现针对 TDP1 的小分子化学支架的高度可行的方法，并且我们首次提供了与 TDP1 结合的小分子抑制剂的共晶结构，这可能有助于合理开发药用 TDP1 抑制剂。
