The chromatin reader protein Spindlin1 plays an important role in epigenetic regulation, through which it has been linked to several types of malignant tumors. In the current work, we report on the development of novel analogs of the previously published lead inhibitor A366. In an effort to improve the activity and explore the structure–activity relationship (SAR), a series of 21 derivatives was synthesized, tested in vitro, and investigated by means of molecular modeling tools. Docking studies and molecular dynamics (MD) simulations were performed to analyze and rationalize the structural differences responsible for the Spindlin1 activity. The analysis of MD simulations shed light on the important interactions. Our study highlighted the main structural features that are required for Spindlin1 inhibitory activity, which include a positively charged pyrrolidine moiety embedded into the aromatic cage connected via a propyloxy linker to the 2-aminoindole core. Of the latter, the amidine group anchor the compounds into the pocket through salt bridge interactions with Asp184. Different protocols were tested to identify a fast in silico method that could help to discriminate between active and inactive compounds within the A366 series. Rescoring the docking poses with MM-GBSA calculations was successful in this regard. Because A366 is known to be a G9a inhibitor, the most active developed Spindlin1 inhibitors were also tested over G9a and GLP to verify the selectivity profile of the A366 analogs. This resulted in the discovery of diverse selective compounds, among which 1s and 1t showed Spindlin1 activity in the nanomolar range and selectivity over G9a and GLP. Finally, future design hypotheses were suggested based on our findings.
染色质阅读蛋白Spindlin1在表观遗传调控中扮演重要角色,已与多种恶性肿瘤相关。在当前工作中,我们报道了先前发表的主要抑制剂A366的新类似物的开发。为了提高活性并探索结构-活性关系(SAR),合成了一系列21个衍生物,在体内进行了测试,并通过分子建模工具进行了研究。进行了对接研究和分子动力学(MD)模拟,以分析和理解负责Spindlin1活性的结构差异。MD模拟的分析揭示了重要的相互作用。我们的研究突出显示了用于Spindlin1抑制活性所需的主要结构特征,其中包括嵌入芳香笼中的带正电的吡咯烷基,通过丙氧基连接到2-氨基吲哚核心。在后者中,酰胺基固定化合物到通过与Asp184的盐桥相互作用的口袋中。测试了不同的协议以识别一种快速的计算机辅助方法,可以帮助区分A366系列中的活性和非活性化合物。使用MM-GBSA计算重新评分对接姿势在这方面取得了成功。由于A366被认为是G9a的抑制剂,因此还测试了最活跃的开发的Spindlin1抑制剂对G9a和GLP的选择性配置文件进行验证A366类似物。这导致了多种选择性化合物的发现,其中1s和1t显示出纳摩尔级别的Spindlin1活性,并且对G9a和GLP具有选择性。最后,基于我们的发现提出了未来的设计假设。