Veenbaas Seth D, Koehn Jordan T, Irving Patrick S, Lama Nicole N, Weeks Kevin M
Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290.
bioRxiv. 2025 Mar 15:2025.03.13.643147. doi: 10.1101/2025.03.13.643147.
RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules - via well-defined ligand binding pockets - to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA-ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devise , a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experimentally confirmed the ligandability of novel pockets detected with using a fragment-based approach introduced here, Frag-MaP, that detects ligand-binding sites in cells. Analysis of pockets detected by and validated by Frag-MaP reveals dozens of newly identified sites able to bind drug-like ligands, supports a model for RNA secondary structural motifs able to bind quality ligands, and creates a broad framework for understanding the RNA ligand-ome.
RNA是基因表达的关键调节因子，其功能通常由复杂的二级和三级结构介导。RNA中的结构化区域可以通过明确的配体结合口袋与小分子选择性相互作用，从而调节RNA的调控功能。然而，由于在识别能够结合具有良好物理化学性质（通常称为类药物性质）的配体的紧密RNA基序方面存在挑战，通过RNA-配体相互作用有意调节生物学功能的广泛潜力尚未实现。在这里，我们设计了一种计算策略，能够准确检测RNA结构中能够结合类药物配体的口袋。迄今为止，能够可视化的此类口袋非常少，大约只有50个。我们使用在此引入的基于片段的方法Frag-MaP（该方法可检测细胞中的配体结合位点），通过实验证实了用该计算策略检测到的新口袋的配体结合能力。对该计算策略检测到并经Frag-MaP验证的口袋进行分析，揭示了数十个新发现的能够结合类药物配体的位点，支持了一种能够结合优质配体的RNA二级结构基序模型，并为理解RNA配体组创建了一个广泛的框架。
