| Literature DB >> 26580609 |
Huiding Xie1,2, Yupeng Li3, Fang Yu4, Xiaoguang Xie5, Kaixiong Qiu6, Jijun Fu7.
Abstract
In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds) in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA), and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.Entities:
Keywords: B-Raf kinase; imidazopyridine; molecular docking; molecular dynamic simulation
Mesh:
Substances:
Year: 2015 PMID: 26580609 PMCID: PMC4661884 DOI: 10.3390/ijms161126026
Source DB: PubMed Journal: Int J Mol Sci ISSN: 1422-0067 Impact factor: 5.923
Figure 1Mol 1, Mol 2, and Mol 3 structures.
Figure 2Comparison between the docked and X-ray crystal structures of Mol 1 (red: docked structure; green: crystal structure).
Figure 3The correlation between C_score values and pIC50 values of 36 imidazopyridines.
Figure 4Docking modes between B-Raf kinase and Mol 1 (a), Mol 2 (b) and Mol 3 (c).
Figure 5RMSD versus time for the Mol 1 complex, Mol 2 complex, and Mol 3 complex.
Residues of the binding pocket and their RMSF values (Å).
| Residues | Mol 1 | Mol 2 | Mol 3 |
|---|---|---|---|
| ILE 463 | 0.075 | 0.109 | 0.127 |
| PHE 468 | 0.081 | 0.148 | 0.207 |
| VAL 471 | 0.275 | 0.194 | 0.265 |
| ALA 481 | 0.614 | 0.701 | 0.704 |
| LYS 483 | 0.452 | 0.512 | 0.563 |
| LEU 505 | 0.540 | 0.201 | 0.805 |
| LEU 514 | 0.621 | 0.573 | 0.597 |
| ILE 527 | 0.678 | 0.712 | 0.597 |
| THR 529 | 0.420 | 0.343 | 0.413 |
| GLN 530 | 0.166 | 0.148 | 0.452 |
| TRP 531 | 0.663 | 0.215 | 0.266 |
| CYS 532 | 0.245 | 0.328 | 0.442 |
| GLU 533 | 0.232 | 0.163 | 0.141 |
| GLY 534 | 0.712 | 0.330 | 0.203 |
| SER 535 | 0.158 | 0.244 | 0.217 |
| PHE 583 | 0.653 | 0.746 | 0.958 |
| GLY 593 | 0.177 | 0.248 | 0.512 |
| ASP 594 | 0.197 | 0.241 | 0.218 |
| PHE 595 | 0.086 | 0.098 | 0.064 |
| GLY 596 | 0.835 | 0.566 | 0.748 |
| LEU 597 | 0.405 | 0.610 | 0.604 |
H-bonds analysis for Mol 1, Mol 2, and Mol 3 in MD simulations.
| Complex | Acceptor | Donor | Occupancy (%) | Distance (Å) | Angle (°) |
|---|---|---|---|---|---|
| Mol 1 | CYS 532 C=O | Lig N1–H | 54.00 | 2.89 ± 0.07 | 18.51 ± 12.41 |
| THR 529 C=O | Lig N2–H | 41.00 | 2.90 ± 0.07 | 20.54 ± 10.55 | |
| ASP 594 C=O | Lig N3–H | 48.00 | 2.82 ± 0.07 | 19.96 ± 10.74 | |
| H2O | Lig N3–H | 36.00 | 2.86 ± 0.10 | 20.48 ± 9.44 | |
| Mol 2 | CYS 532 C=O | Lig N1–H | 66.00 | 2.84 ± 0.09 | 26.11 ± 13.57 |
| THR 529 C=O | Lig N2–H | 11.00 | 2.90 ± 0.05 | 23.84 ± 12.42 | |
| ASP 594 C=O | Lig N3–H | 69.00 | 2.81 ± 0.10 | 19.95 ± 10.67 | |
| Mol 3 | CYS 532 C=O | Lig N1–H | 10.00 | 2.91 ± 0.07 | 19.87 ± 11.91 |
| ASP 594 C=O | Lig N3–H | 97.00 | 2.77 ± 0.08 | 14.26 ± 8.55 | |
| Lig S=O | LYS 601 N–H1 | 42.50 | 2.82 ± 0.08 | 21.22 ± 11.35 | |
| Lig S=O | LYS 601 N–H2 | 26.00 | 2.82 ± 0.08 | 22.81 ± 11.08 |
Binding free energy (kcal·mol−1) for the three complexes.
| Energy/Activity | Mol 1 Complex | Mol 2 Complex | Mol 3 Complex |
|---|---|---|---|
| Δ | −52.94 | −59.02 | −56.25 |
| Δ | −45.71 | −46.95 | −48.48 |
| Δ | −98.65 | −105.97 | −104.73 |
| Δ | 53.66 | 56.45 | 61.94 |
| Δ | −6.61 | −6.97 | −7.11 |
| Δ | 47.05 | 49.48 | 54.83 |
| Δ | −51.60 | −56.49 | −49.90 |
| IC50 | 61 (nM) | 0.76 (nM) | 167 (nM) |
| pIC50 | 7.215 | 9.119 | 6.777 |
ΔEgas: molecular mechanics energy in gas phase; ΔEele: electrostatic energy; ΔEvdw: van der Waals potential energy; ΔGsol: solvation free energy; ΔGGB: polar salvation free energy; ΔGSA: non-polar solvation free energy; ΔGbind: binding free energy; IC50: half maximal inhibitory concentration; pIC50: −logIC50.