Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
CAS, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.
Int J Mol Sci. 2019 Jun 30;20(13):3230. doi: 10.3390/ijms20133230.
The TDP-43 is originally a nuclear protein but translocates to the cytoplasm in the pathological condition. TDP-43, as an RNA-binding protein, consists of two RNA Recognition Motifs (RRM1 and RRM2). RRMs are known to involve both protein-nucleotide and protein-protein interactions and mediate the formation of stress granules. Thus, they assist the entire TDP-43 protein with participating in neurodegenerative and cancer diseases. Consequently, they are potential therapeutic targets. Protein-observed and ligand-observed nuclear magnetic resonance (NMR) spectroscopy were used to uncover the small molecule inhibitors against the tandem RRM of TDP-43. We identified three hits weakly binding the tandem RRMs using the ligand-observed NMR fragment-based screening. The binding topology of these hits is then depicted by chemical shift perturbations (CSP) of the N-labeled tandem RRM and RRM2, respectively, and modeled by the CSP-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK). These hits mainly bind to the RRM2 domain, which suggests the druggability of the RRM2 domain of TDP-43. These hits also facilitate further studies regarding the hit-to-lead evolution against the TDP-43 RRM domain.
TDP-43 最初是一种核蛋白，但在病理条件下会转移到细胞质中。TDP-43 作为一种 RNA 结合蛋白，由两个 RNA 识别基序（RRM1 和 RRM2）组成。RRMs 已知涉及蛋白-核苷酸和蛋白-蛋白相互作用，并介导应激颗粒的形成。因此，它们协助整个 TDP-43 蛋白参与神经退行性和癌症疾病。因此，它们是潜在的治疗靶点。使用观察蛋白和配体观察的核磁共振（NMR）光谱学来揭示针对 TDP-43 串联 RRM 的小分子抑制剂。我们使用配体观察 NMR 基于片段的筛选发现了三个弱结合串联 RRMs 的命中物。然后，通过对 N 标记的串联 RRM 和 RRM2 的化学位移扰动（CSP）分别描绘这些命中物的结合拓扑结构，并通过 CSP 引导的高歧义驱动生物分子对接（HADDOCK）进行建模。这些命中物主要结合到 RRM2 结构域，这表明 TDP-43 的 RRM2 结构域具有成药性。这些命中物还促进了针对 TDP-43 RRM 结构域的命中物到先导物进化的进一步研究。
