Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy.
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
Cells. 2020 Oct 29;9(11):2370. doi: 10.3390/cells9112370.
NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo "metabolic rewiring" through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.
NF-Y 是一种转录因子 (TF)，由三个亚基 (NF-YA、NF-YB、NF-YC) 组成，它与 CCAAT 序列具有高度特异性结合，CCAAT 序列是生存、细胞周期促进和代谢基因启动子中广泛存在的调节元件。肿瘤细胞通过过度表达参与这些途径的基因进行“代谢重编程”，其中许多基因受 NF-Y 控制。此外，NF-YA 似乎在许多肿瘤类型中过度表达。因此，限制 NF-Y 活性可能代表一种理想的抗癌策略，这是一个正在进行的研究领域。通过对药理学活性化合物库进行虚拟筛选对接模拟，我们确定苏拉明是一种潜在的 NF-Y 抑制剂。我们专注于苏拉明，因为它的高水溶性是体外测试的一个重要因素，因为 NF-Y 对 DMSO 敏感。通过电泳迁移率变动分析 (EMSA)、等温热滴定 (ITC)、标准磁共振波谱 (STD NMR)、X 射线晶体学和分子动力学 (MD) 模拟，我们表明苏拉明结合到 NF-Y 的组蛋白折叠域 (HFD)，从而阻止 DNA 结合。我们的分析提供了苏拉明与 NF-Y 之间相互作用的原子水平细节，并揭示了蛋白质的一个区域，该区域靠近苏拉明结合位点，在其他含有 HFD 的 TF 中保守性较差，这可能代表一个有希望的起点，可用于合理设计更具特异性和更强效的抑制剂，具有潜在的治疗应用。
