高等学校化学学报 ›› 2016, Vol. 37 ›› Issue (4): 706-714.doi: 10.7503/cjcu20150790

• 物理化学 • 上一篇    下一篇

p53突变体Y220C小分子稳定剂的虚拟筛选

丁吉勇, 沈洪辰, 刘夫锋()   

  1. 天津大学化工学院生物工程系, 系统生物工程教育部重点实验室, 天津 300072
  • 收稿日期:2015-10-13 出版日期:2016-04-10 发布日期:2016-03-18
  • 基金资助:
    国家自然科学基金(批准号: 21576199)和中国博士后科学基金(批准号: 2013M530115, 2012T50241)资助

Virtual Screening of Small Molecular Stabilizer for Y220C Mutant of p53

DING Jiyong, SHEN Hongchen, LIU Fufeng*()   

  1. Key Laboratory of Systems Bioengineering of the Ministry of Education, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
  • Received:2015-10-13 Online:2016-04-10 Published:2016-03-18
  • Contact: LIU Fufeng E-mail:fufengliu@tju.edu.cn
  • Supported by:
    † Supported by the National Natural Science Foundation of China(No.21576199) and the China Postdoctoral Science Foundation(Nos.2012T50241, 2013M530115)

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