Department of Chemistry, University of Chicago, Chicago, IL, USA.
Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
Nat Biotechnol. 2023 Apr;41(4):541-551. doi: 10.1038/s41587-022-01504-x. Epub 2022 Oct 27.
Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.
尽管转录因子（TFs）在疾病中具有明确的作用，但由于靶向蛋白-蛋白和蛋白-DNA 相互作用的挑战，它们在很大程度上仍未被开发为药物靶点。在这里，我们报告了一种从 MAX 的 bHLH 结构域生成模块化合成转录抑制剂（STRs）的化学策略。我们的合成方法产生了化学稳定的三级结构模拟物，这些模拟物以纳摩尔亲和力协同结合 MYC/MAX 共有 E 盒基序，具有与全长 TF 相当或更高的特异性，并直接与 MYC/MAX 蛋白竞争 DNA 结合。一种先导 STR 可直接抑制细胞中 MYC 的结合，下调蛋白质组水平的 MYC 依赖性表达程序，并抑制 MYC 依赖性细胞增殖。STR：E 盒 DNA 复合物的共结晶和结构测定证实了 DNA 识别的保留方式与全长 bHLH TF 非常相似。我们还证明了源自其他 bHLH-TFs 的 STR 的无结构设计，证实了 STR 可用于开发针对其他基因调控元件的高特异性 TF 模拟物。
