Targeting RNA including viral RNAs with small molecules is an emerging field. The hepatitis C virus internal ribosome entry site (HCV IRES) is a potential target for translation inhibitor development to raise drug resistance mutation preparedness. Using RNA-focused and unbiased molecule libraries, a structure-based virtual screening (VS) by molecular docking and pharmacophore analysis was performed against the HCV IRES subdomain IIa. VS hits were validated by a microscale thermophoresis (MST) binding assay and a Förster resonance energy transfer (FRET) assay elucidating ligand-induced conformational changes. Ten hit molecules were identified with potencies in the high to medium micromolar range proving the suitability of structure-based virtual screenings against RNA-targets. Hit compounds from a 2-guanidino-quinazoline series, like the strongest binder, compound 8b with an EC₅₀ of 61 μM, show low molecular weight, moderate lipophilicity and reduced basicity compared to previously reported IRES ligands. Therefore, it can be considered as a potential starting point for further optimization by chemical derivatization.

中文翻译：

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基于结构的无偏性和以 RNA 为中心的文库的虚拟筛选，以确定 HCV IRES 模型系统的新配体

用小分子靶向 RNA（包括病毒 RNA）是一个新兴领域。丙型肝炎病毒内部核糖体进入位点（HCV IRES）是翻译抑制剂开发的潜在目标，以提高耐药突变准备。使用以 RNA 为中心的无偏分子库，通过分子对接和药效团分析针对 HCV IRES 子域 IIa 进行基于结构的虚拟筛选 (VS)。 VS 命中通过微尺度热泳 (MST) 结合测定和福斯特共振能量转移 (FRET) 测定进行验证，阐明配体诱导的构象变化。鉴定出 10 种具有高至中微摩尔范围效力的命中分子，证明了针对 RNA 靶标的基于结构的虚拟筛选的适用性。 2-胍基-喹唑啉系列的热门化合物，如最强的结合剂化合物8b （ EC ₅₀为 61 μM），与之前报道的 IRES 配体相比，表现出低分子量、中等亲脂性和降低的碱性。因此，它可以被认为是化学衍生化进一步优化的潜在起点。