Vascular endothelial growth factor A (VEGFA) stimulates angiogenesis in human endothelial cells, and increasing its expression is a potential treatment for heart failure. Here, we report the design of a small molecule (TGP-377) that specifically and potently enhances VEGFA expression by the targeting of a non-coding microRNA that regulates its expression. A selection-based screen, named two-dimensional combinatorial screening, revealed preferences in small-molecule chemotypes that bind RNA and preferences in the RNA motifs that bind small molecules. The screening program increased the dataset of known RNA motif–small molecule binding partners by 20-fold. Analysis of this dataset against the RNA-mediated pathways that regulate VEGFA defined that the microRNA-377 precursor, which represses Vegfa messenger RNA translation, is druggable in a selective manner. We designed TGP-377 to potently and specifically upregulate VEGFA in human umbilical vein endothelial cells. These studies illustrate the power of two-dimensional combinatorial screening to define molecular recognition events between ‘undruggable’ biomolecules and small molecules, and the ability of sequence-based design to deliver efficacious structure-specific compounds.

血管内皮生长因子A（VEGFA）刺激人内皮细胞中的血管生成，增加其表达是治疗心力衰竭的潜在方法。在这里，我们报道了一种小分子（TGP-377）的设计，该小分子通过靶向调节其表达的非编码微RNA来特异性和有效地增强VEGFA的表达。基于选择的筛选称为二维组合筛选，揭示了结合RNA的小分子化学型的偏好和结合小分子的RNA图案的偏好。筛选程序将已知RNA基序-小分子结合伴侣的数据集增加了20倍。针对调节VEGFA的RNA介导的通路对该数据集进行分析后得出结论，即抑制vegfa的microRNA-377前体。信使RNA翻译可以选择性地进行药物处理。我们设计了TGP-377在人的脐静脉内皮细胞中有效和特异性上调VEGFA。这些研究说明了二维组合筛选定义“不可药物”生物分子与小分子之间的分子识别事件的能力，以及基于序列的设计可提供有效的结构特异性化合物的能力。