small molecule targeting α-synuclein mRNA

The protein α-synuclein is an important drug target for the treatment of Parkinson’s disease, but it is an intrinsically disordered protein lacking typical small molecule binding pockets. The mRNA encoding α-synuclein (SNCA), on the other hand, has regions of ordered structure in the 5’ untranslated region (UTR) near the start codon. Here, we present an integrated approach to identify small molecules that bind this structure and inhibit α-synuclein translation. A drug-like, RNA-focused compound collection was studied for binding to the 5’UTR of SNCA mRNA, affording Synucleozid-2.0, a drug-like small molecule that mechanistically inhibits ribosomes from assembling onto SNCA mRNA. We further converted it into a ribonuclease recruiting chimera (RIBOTAC) to degrade the SNCA mRNA in cells with improved potency. RNA-seq and proteomics studies demonstrated that Synucleozid-RIBOTAC (Syn-RIBOTAC) is selective in cells. Syn-RIBOTAC also improved ~50% of genes abnormally expressed in patient-derived iPSC-induced dopamine neurons. The RIBOTAC optimization strategy improved the bioactivity of lead compound by at least 5-fold. Broadly, one strategy to expand druggability of the proteome is to target the mRNAs that encode for “undruggable” proteins. This is the supplemental dataset for our manuscript currently published at PNAS (doi: 10.1073/pnas.2306682120)α-突触核蛋白（α-synuclein）是治疗帕金森病的重要药物靶点，但其为内在无序蛋白，缺乏典型的小分子结合口袋。编码α-突触核蛋白的mRNA（SNCA）在起始密码子附近的5'非翻译区（UTR）存在有序结构区域。本研究提出一套整合性策略，用于筛选可结合该有序结构并抑制α-突触核蛋白翻译的小分子。我们使用了一类兼具类药性、聚焦于RNA的化合物库，针对SNCA mRNA的5'UTR开展结合活性筛选，最终得到Synucleozid-2.0——一种类药小分子，可通过机制性抑制核糖体结合至SNCA mRNA。我们进一步将其改造为核糖核酸酶招募嵌合体（RIBOTAC），以在细胞中降解SNCA mRNA，且效力得到提升。RNA测序（RNA-seq）与蛋白质组学研究表明，Synucleozid-RIBOTAC（Syn-RIBOTAC）在细胞中具有良好的选择性。该化合物还可改善患者来源的诱导多能干细胞（iPSC）诱导的多巴胺能神经元中约50%的异常表达基因。本RIBOTAC优化策略使先导化合物的生物活性提升至少5倍。广义而言，拓展蛋白质组可成药性的策略之一，是靶向编码“不可成药”蛋白的mRNA。本数据集为我们发表于《美国国家科学院院刊（PNAS，doi: 10.1073/pnas.2306682120）》的研究论文的补充数据集。