J Am Chem Soc. 2021 Oct 13;143(40):16549-16555. doi: 10.1021/jacs.1c06200. Epub 2021 Sep 29.
The G-quadruplexes (G4s) formed in the gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.
基因启动子中形成的 G-四链体（G4s）是转录调节剂，可通过小分子靶向进行调控。小檗碱（BER）是一种临床重要的异喹啉生物碱，由于其作为抗癌药物的潜力而受到越来越多的关注。我们之前表明，基因启动子形成了一种独特的空位 G4（vG4），可以通过鸟嘌呤代谢物，如 dGMP 填充和稳定。在此，我们报告了小檗碱与 dGMP 填充的 PDGFR-β vG4 结合的三元复合物在钾溶液中的高分辨率 NMR 结构。这是第一个填充 vG4 的小分子复合物结构。该三元复合物具有 2:1:1 的结合比例，其中一个小檗碱分子结合在 5'-dGMP 填充的 PDGFR-β vG4 的 5'-和 3'-末端。每个小檗碱从 5'-或 3'-侧翼序列招募相邻的腺嘌呤残基，形成一个“准三联体平面”，分别覆盖填充 vG4 的外部 G-四联体。重要的是，小檗碱覆盖并稳定填充的 dGMP。小檗碱的结合涉及π堆积和静电相互作用，填充的 dGMP 被小檗碱覆盖并得到很好的保护。该 NMR 结构可以指导针对 PDGFR-β vG4 或 dGMP 填充 vG4 的小檗碱类似物的合理设计。此外，我们的结构为设计靶向 vG4 的小分子鸟嘌呤缀合物提供了分子基础。
