KRAS is one of the most highly mutated oncoproteins, which is overexpressed in various human cancers and implicated in poor survival. The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. However, no available KRAS-G4-ligand complex structure has yet been determined, which seriously hinders the structure-based rational design of KRAS-G4 targeting drugs. In this study, we report the NMR solution structures of a bulge-containing KRAS-G4 bound to berberine and coptisine, respectively. The determined complex structure shows a 2:1 binding stoichiometry with each compound recruiting the adjacent flacking adenine residue to form a “quasi-triad plane” that stacks over the two external G-tetrads. The binding involves both π-stacking and electrostatic interactions. Moreover, berberine and coptisine significantly lowered the KRAS mRNA levels in cancer cells. Our study thus provides molecular details of ligand interactions with KRAS-G4 and is beneficial for the design of specific KRAS-G4-interactive drugs.

KRAS 是突变率最高的癌蛋白之一，它在各种人类癌症中过度表达并与较差的生存率有关。在KRAS癌基因启动子 ( KRAS -G4) 中形成的 G-四链体是一种转录调节剂，适用于小分子靶向。然而，目前还没有确定可用的KRAS -G4-配体复合结构，这严重阻碍了基于结构的KRAS-G4靶向药物的合理设计。在这项研究中，我们报告了含有凸起的KRAS的 NMR 溶液结构-G4 分别与小檗碱和黄连碱结合。所确定的复杂结构显示出 2:1 的结合化学计量比，其中每种化合物募集相邻的腺嘌呤残基以形成堆叠在两个外部 G-四分体上的“准三联体平面”。结合涉及π堆积和静电相互作用。此外，小檗碱和黄连碱显着降低癌细胞中的KRAS mRNA 水平。因此，我们的研究提供了配体与KRAS -G4相互作用的分子细节，有利于设计特定的KRAS -G4 相互作用药物。