Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing and elongation processivity. Spt5 was also recognized for its roles in the transcription of expanded-repeat genes that are related to neurodegenerative diseases. Recently, a set of Spt5-Pol II small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well as interaction sites of these SPIs with Pol II and Spt5 are not entirely known. In this study, we predicted the binding sites of three selected SPIs at the Pol II-Spt5 interface by docking and molecular dynamics simulations. Two molecules out of three demonstrated strong binding with Spt5 and Pol II, while the other molecule was more loosely bound and sampled multiple binding sites. Strongly bound SPIs indirectly affected RNA and DNA dynamics at the exit site as DNA became more flexible while RNA was stabilized by increased interactions with Spt5. Our results suggest that the transcription inhibition mechanism induced by SPIs can be related to Spt5-nucleic acid interactions, which were altered to some extent with strong binding of SPIs.

Spt5 是一种延伸因子，在转录过程中与 RNA 聚合酶 II (Pol II) 相关，在启动子近端暂停和延伸持续性中具有重要功能。Spt5 还因其在与神经退行性疾病相关的扩展重复基因转录中的作用而得到认可。最近，报道了一组Spt5-Pol II小分子抑制剂（SPI），可选择性抑制突变亨廷顿基因转录。这些 SPI 与 Pol II 和 Spt5 的抑制机制以及相互作用位点尚不完全清楚。在本研究中，我们通过对接和分子动力学模拟预测了 Pol II-Spt5 界面上三个选定 SPI 的结合位点。三分之二的分子表现出与 Spt5 和 Pol II 的强烈结合，而另一个分子的结合更为松散，并采样了多个结合位点。强结合的 SPI 间接影响退出位点的 RNA 和 DNA 动力学，因为 DNA 变得更加灵活，而 RNA 通过增加与 Spt5 的相互作用而稳定。我们的结果表明，SPIs 诱导的转录抑制机制可能与 Spt5 核酸相互作用有关，而 SPIs 的强结合会在一定程度上改变这种相互作用。