p53突变体Y220C小分子稳定剂的虚拟筛选

doi:10.7503/cjcu20150790

摘要/Abstract

摘要：

为了获得p53突变体的稳定剂, 依次利用利宾斯基五原则, 通过2次分子对接和全原子分子动力学(MD)模拟从DrugBank 4.0 数据库中筛选获得了潜在的稳定剂他克林. 利用MD模拟进一步验证他克林和目标蛋白质之间的亲和作用. 结果表明, 他克林能够紧密结合到Y220C突变所形成的疏水空腔之中; 他克林和目标蛋白质之间的主要作用力为疏水和静电相互作用, 其中疏水相互作用占主导地位. 此外, 他克林分别与目标蛋白质的残基Leu145, Val147和Asp228形成3个氢键. 基于MD模拟轨迹分析了他克林与p53C-Y220C的结合过程. 由硫黄素T荧光光谱进一步证明他克林能够提高p53C-Y220C突变体的稳定性.

关键词: 癌症, 蛋白质稳定剂, 分子对接, 分子动力学模拟, p53, 他克林

Abstract:

About half of cancers are caused by the mutation in the tumor suppressor p53. A hydrophobic cavity on the surface of p53 was caused by the Y220C mutation. The surface crevice is on the opposite side and distant from the DNA-binding domain, making it a particularly attractive target site for stabilizing small-molecule drugs. In order to obtain the effective stabilizers, Lipinski’s rule of five, twice docking methods and molecular dynamics(MD) simulations were successively used for virtual screening the DrugBank 4.0 library and tacrine was obtained as a candidate stabilizer. Then, all-atom MD simulations were used to verify the affinity between tacrine and the target protein. The MD simulation indicated that tacrine bound tightly to the pocket and the complex remained stable. The affinity between tacrine and the target protein was further analyzed. It was found that the hydrophobic and electrostatic interactions dominated the affinity between tacrine and the target protein. And, the hydrophobic interactions were dominant force. Moreover, there were 3 hydrogen bonds between tacrine and the residues Leu145, Val147 and Asp228 of p53C-Y220C. And then, the detailed binding process of tacrine and p53C-Y220C was probed based on MD simulations. Finally, the stabilizing capacity of tacrine on p53C-Y220C was further validated by thioflavine T fluorescent experiments.

Key words: Cancer, Protein stabilizer, Molecular dock, Molecular dynamics simulation, p53, Tacrine

TrendMD:

丁吉勇, 沈洪辰, 刘夫锋. p53突变体Y220C小分子稳定剂的虚拟筛选. 高等学校化学学报, 2016, 37(4): 706.

DING Jiyong, SHEN Hongchen, LIU Fufeng. Virtual Screening of Small Molecular Stabilizer for Y220C Mutant of p53^†. Chem. J. Chinese Universities, 2016, 37(4): 706.

图/表 10

Fig.1 Procedure of virtual screening

Fig.2 Binding affinity distribution of these small molecules and Y220C mutant of p53C analyzed by AutoDock Vina

Fig.3 Enrichment curve analysis of the five scoring functions in FlexXa. Random; b. F_Score; c. ChemScore; d. D_Score; e. G_Score; f. PMF_Score. A diagonal represents a random selection. Curves above the diagonal represent the corresponding scoring functions can select the known stabilizers from the library of small molecular compounds.

Fig.4 Comparison of binding sites of the 3 compounds on p53C mutant Y220C before and after MD simulations (A) Binding models obtained by docking(i.e., initial binding conformations in MD simulation); (B) binding models obtained after 100 ns MD simulations.

Fig.5 Time-dependent Coulomb(A) and LJ(B) potential energy of tacrine- p53C-Y200C

Fig.6 Snapshot of the hydrogen bonds between tacrine and the residues of p53C-Y220CHydrogen bonds between tacrine and the residues Leu145, Val147 and Asp228 of p53C-Y220C are shown in black dotted lines. The residue type and its sequence number which interacted with tacrine via hydrogen bonds are also shown.

Fig.7 Time-dependent contact number between the tacrine and Y220C mutant of p53C

Fig.8 Representative conformations of tacrine and p53C-Y220C complex during the 100 ns MD simulations

Fig.9 Representative binding modes of tacrine and the hydrophobic pocket created by Y220C mutation on p53C after 100 ns MD simulation (A) Secondary structure; (B) surface representation. The Y220C mutant and tacrine are shown in yellow and green dynamics bond models.

Fig.10 Effect of different concentrations of tarcrine on p53C-Y220C aggregation measured by ThT fluorescence The concentration of p53C-Y220C was 5 μmol/L.

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