苯并吡喃酮类化合物与Skp2蛋白的分子识别及其抑制机理

S期激酶相关蛋白2(S-phase kinase-associated protein 2,Skp2)与Skp1形成的蛋白质聚合物在调控癌细胞生长周期中发挥着重要作用,而苯并吡喃酮类抑制剂(简称BPC)可有效抑制Skp1-Skp2的形成,但其分子识别机制尚不明确.通过生物信息学统计分析已报道的Skp1-Skp2晶体结构,确定模拟体系后,首先用同源模建对其模拟体系缺失的结构进行补全;然后用分子对接方法获得Skp1-Skp2-BPC复合物模型并用于后续分子动力学模拟.计算结果表明:疏水相互作用是促使BPC特异性结合在由Skp2 W109、D110、L117、I120、R138和W139所构成口袋中的主要驱动力,自由能计算值与实验数据吻合较好.Skp2结合BPC后,结合口袋周围的氢键网络有所加强,口袋附近的溶剂化水分子数量明显减少,导致Skp1-Skp2的体系稳定性下降.体系构象成簇与运动性分析显示,Skp1-Skp2在结合BPC抑制剂后,Skp1的运动更加剧烈,这可能是BPC主要的抑制机理.

Molecular Recognition and Inhibition Mechanism of Benzopyrone Compounds With Skp2 Proteins

The protein aggregate of S-phase kinase-associated protein 2 (Skp2) complex with Skp1 plays an important role in regulating the growth cycle of cancer cells. The benzopyrone inhibitor BPC can effectively hinder the formation of Skp1-Skp2 complex. The simulation system was determined through bioinformatics statistical analyses of the available Skp1-Skp2 crystal complex, and the missing structural unit was mended via homology modeling. Then, the Skp1-Skp2-BPC complex model was obtained by using molecular docking and adopted for subsequent molecular dynamics (MD) simulations. Computational results show that hydrophobic interaction is the major driving force impelling BPC to specially bind to the pocket composed of W109, D110, L117, I120, R138 and W139 of Skp2. The calculated free energy values agree well with the experimental data. After the association of Skp2 with BPC,the hydrogen bond network of active pocket moderately strengthens and the number of solvated water molecule around the pocket decrease significantly, which leads to the reduction of Skp1-Skp2 systemic stability. According to the analyses of conformational clustering and motion characteristics, the motion of Skp1 becomes more vigorous after Skp1-Skp2 binding with BPC,which may be one of the main inhibitory mechanisms of BPC. This work provides a theoretical basis for deeply understanding the structure-function relationships of Skp1-Skp2 and rationally designing novel anticancer inhibitors based on receptor structure.