Jiang Mao, Giannino Nicole, Goebel Georg L, Sievers Sonja, Wu Peng
Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany.
Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany.
ChemMedChem. 2025 Jan 2;20(1):e202400547. doi: 10.1002/cmdc.202400547. Epub 2024 Nov 12.
The probing of small molecules with heterocyclic scaffolds covering unexplored chemical space and the evaluation of their biological relevance are essential parts of forward chemical genetics approaches and for the development of potential small-molecule therapeutics. In this study, we profiled sets of chromenopyrazoles (CMPs) and tetrahydroquinolines (THQs), originally developed to target the protein-RNA interaction of LIN28-let-7, in a cell painting assay (CPA) measuring cellular morphological changes. Selected LIN28-inactive CMPs and THQs induced cellular morphological changes to different extents. The most CPA-active CMPs 2 and 3 exhibited high bio-similarity with the LCH and BET clusters, while the most CPA-active THQs 13 and 20 indicated a mechanism of action beyond the currently established biosimilarity clusters. Overall, this work demonstrated that CPA is useful in revealing "hidden" biological targets and mechanisms of action for biologically inactive small molecules, which are CMPs and THQs targeting the RNA-binding protein LIN28 in this case, evaluated in target-based strategies. When compared with annotated reference compounds, CMP 3 exhibited a high biosimilarity with the dual BRD7/9 degrading PROTAC VZ185, suggesting that CPA could potentially function as a new phenotypic approach to identify degrader molecules.
探索具有覆盖未开发化学空间的杂环支架的小分子，并评估其生物学相关性，是正向化学遗传学方法以及开发潜在小分子疗法的重要组成部分。在本研究中，我们对最初开发用于靶向LIN28-let-7的蛋白质-RNA相互作用的色烯并吡唑（CMPs）和四氢喹啉（THQs）进行了分析，采用细胞成像分析（CPA）来测量细胞形态变化。选定的对LIN28无活性的CMPs和THQs在不同程度上诱导了细胞形态变化。活性最高的CPA CMPs 2和3与LCH和BET簇表现出高度生物相似性，而活性最高的CPA THQs 13和20表明其作用机制超出了目前已建立的生物相似性簇。总体而言，这项工作表明CPA有助于揭示生物活性小分子的“隐藏”生物学靶点和作用机制，在基于靶点的策略中评估时，这些小分子在本案例中是靶向RNA结合蛋白LIN28的CMPs和THQs。与注释的参考化合物相比，CMP 3与双BRD7/9降解PROTAC VZ185表现出高度生物相似性，这表明CPA可能潜在地作为一种新的表型方法来鉴定降解分子。
