Virtual Screening of Small Molecular Stabilizer for Y220C Mutant of p53†

doi:10.7503/cjcu20150790

Abstract

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:

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

Figures/Tables 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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