Structure-Based and Knowledge-Informed Design of B‑Raf Inhibitors Devoid of Deleterious PXR Binding

Dabrafenib is an anticancer drug currently used in the clinics, alone or in combination. However, dabrafenib was recently shown to potently activate the human nuclear receptor pregnane X receptor (PXR). PXR activation increases the clearance of various chemicals and drugs, including dabrafenib itself. It may also enhance cell proliferation and tumor aggressiveness. Therefore, there is a need for rational design of a potent protein kinase B-Raf inhibitor devoid of binding to the secondary target PXR and resisting rapid metabolism. By determining the crystal structure of dabrafenib bound to PXR and analyzing its mode of binding to both PXR and its primary target, B-Raf-V600E, we were able to derive new compounds with nanomolar activity against B-Raf and no detectable affinity for PXR. The crystal structure of B-Raf in complex with our lead compound revealed a subdomain swapping of the activation loop with potentially important functional implications for a prolonged inhibition of B-Raf-V600E.达拉非尼（dabrafenib）是一款目前临床单用或联合使用的抗癌药物。然而近期研究表明，达拉非尼可强效激活人源核受体孕烷X受体（pregnane X receptor，PXR）。PXR激活会提升包括其自身在内的多种化学物质与药物的体内清除率，还可能促进细胞增殖与肿瘤侵袭性。因此，亟需合理设计一类强效蛋白激酶B-Raf抑制剂，使其既不结合次要靶点PXR，又能抵御快速代谢。通过解析达拉非尼与PXR结合的晶体结构，并分析其与PXR以及主要靶点B-Raf-V600E的结合模式，我们成功获得了对B-Raf具有纳摩尔级活性、且未检测到与PXR结合亲和力的新型化合物。我们的先导化合物与B-Raf形成的复合物的晶体结构显示，其激活环发生了亚结构域交换，这一现象可能对B-Raf-V600E的长效抑制具有重要的功能意义。