The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.
Vascular endothelial growth factor (VEGF) is an important signaling protein involved in both the growth of blood vessels from preexisting vasculature (angiogenesis) and the formation of the circulatory system (vasculogenesis). VEGF binding to tyrosine kinase receptors (VEGFR) can cause itself dimerization and become activated through transphosphorylation. There are three main subtypes of VEGFR: VEGFR1, VEGFR2, and VEGFR3. Among which VEGFR2 appears to mediate almost all of the known cellular responses to VEGF. Inhibiting the tyrosine kinase VEGFR2 signaling pathway may disrupt the angiogenesis process of solid tumor, thus blocking tumor growth and spread [
Recently, lots of VEGR2 inhibitors have been reported. Among them sorafenib (codeveloped and comarketed by Bayer and Onyx pharmaceuticals as Nexavar) is one of the potent inhibitors of VEGFR
Recently Garofalo and coworkers [
The structure of VEGFR2 receptor was taken from Protein Data Bank with the ID code 2RL5 [
Structure of VEGFR2 receptor. The protein is shown in cartoon scheme and ligand 2RL is shown in sphere scheme.
Both the unbound and bound VEGFR2 were used as the initial structures for MD simulation. The topology parameter of sorafenib was obtained through Dundee PRODRG server (
The structures of 11 aryloxy-quinazolines derivatives
Structure of sorafenib and compounds
Compounds
Figure
Docking pose of sorafenib with VEGFR2. The residues are colored in atom scheme while sorafenib is colored in green carbon scheme.
Figure
(a) RMSD of backbone of VEGFR2 unbound (pink) and VEGFR2-sorafenib complex (blue); (b) radius of gyration of VEGFR2 unbound (pink) and VEGFR2-sorafenib complex (blue).
Figure
Distance fluctuations of hydrogen bonds (distances between two heavy atoms) between sorafenib and VEGFR2.
OAT
NAJ
NAU
NAR
Through the bond distance and bond angle variation results, we can see that the hydrogen bond formed with Asp1046 is stable during the MD simulation, which with Cys919 is less stable, while the bifurcated hydrogen bond with Glu885 is the most unstable one.
Figure
Hydrogen bond existence map for VEGFR2-sorafenib. Bond 0: Asp1046 | Bonds 1, 2, 4: Cys919 | Bond 3: Gly841 | Bond 5: Thr916| Bonds 6, 7: Glu885.
From what was previously mentioned we can see that the urea linkage of sorafenib could form hydrogen bonds with ASP1046 and GLU885. Besides, the nitrogen atom of pyridine ring also could form hydrogen bond with CYS919. Holding this in mind we further studied the interaction mode between VEGFR2 and a serial of urea derivatives with such functional groups [
Supplementary Figure 3 lists the hydrogen bond existence of the 11 compounds with VEGFR2 protein, from which we can see that all the compounds forms hydrogen bond with Asp1046 and the occurrence is almost persistent, suggesting that this hydrogen bond is very stable. Among all the 11 complexes, only three form hydrogen bond with Lys868:
The hydrogen bonding modes of
All of the compounds form more than 2 hydrogen bonds with VEGFR2 except
VEGFR-2 inhibitory and their computed interaction energies.
Compound | R | IC50 ( |
|
||
---|---|---|---|---|---|
A | B | C | |||
Sorafenib | — | −101.62 | −144.25 | −103.37 | |
|
n-Pr | 0.40 | −123.77 | −161.43 | −47.82 |
|
Benzyl | 0.06 | −119.34 | −160.18 | −72.73 |
|
4-Methoxybenzyl | 0.07 | −114.74 | −127.62 | −95.51 |
|
4-Bromobenzyl | 0.05 | −201.94 | −127.53 | −90.16 |
|
2,4-Difluorobenzyl | 0.09 | −144.71 | −163.77 | −81.30 |
|
3-Chloro-4-fluorobenzyl | 0.04 | −111.40 | −97.60 | −86.86 |
|
4-Trifluoromethyl-benzyl | 0.06 | −153.32 | −124.31 | −84.85 |
|
4-Methyl-benzyl | 0.05 | −128.24 | −121.51 | −82.76 |
|
2-Naphthyl | 0.03 | −117.25 | −119.72 | −109.77 |
|
1-Naphthyl | 5.50 | −136.48 | −104.12 | −109.31 |
|
Cyclohexyl | 1.00 | −108.64 | −91.12 | −47.69 |
Table
Correlation between pIC50 and calculated interaction energy of part C.
Docking and molecular dynamics simulations of VEGFR2-sorafenib complex show that the possible mechanism that sorafenib inhibits VEGFR2 is by forming hydrogen bonds with residues Asp1046, Cys919, and Glu885 of the VEGFR2 binding pocket as well as by hydrophobic contacts with a set of hydrophobic residues. The aforementioned interaction affects the activity of such inhibitors to inhibit VEGFR2. The interaction energy between compounds
MD simulations were performed on TianHe-1A supercomputer of National Supercomputing Center in Tianjin. The project was supported by the National Natural Science Foundation of China (21103125) and National Key Project for Innovative Drug (2011ZX09401-009).