Glioblastoma (GBM) is the primary brain tumor with the highest incidence in the skull, among which glioblastoma has a very high degree of malignancy. Even after radiotherapy and chemotherapy, the median survival of patients is very short(18). c-MET, encoded by proto-oncogene. Met, is a highly binding receptor tyrosine kinase belonging to the RON subfamily and is the only known receptor of scatter factor or hepatocyte growth factor (HGF). The interaction between c-MET and membrane receptors affects the role of signal molecules such as HGF/c-Met signal pathway and VEGFR, and further affects the process of tumor invasion, metastasis and neovascularization, which leads to the emergence of tumor drug resistance, and is an important reason for the failure of drug therapy(19). Therefore, the key to inhibit tumor growth is to find an inhibitor of c-MET to limit its activity, so as to resist tumor growth. At present, there are more than a dozen small molecule c-met kinase inhibitors in preclinical or clinical research stage used as single drug therapy or in combination with other targeted drugs or chemotherapy drugs to treat multiple malignant tumors. As a result, the results of this study can also be applied to other tumors(20).
Although great progress has been made in the design and development of small molecular drugs for c-MET, sorafenib is still the only systemic first-line treatment option(21, 22). Tivantinib (ARQ-197) (selected as a reference drug in this study) is an oral, highly selective, non-ATP competitive c-MET receptor tyrosine kinase inhibitor(23). It has been shown to be effective as a second-line treatment for a variety of solid tumors in early clinical trials. Therefore, there is an urgent need to screen more compounds targeting c-MET for clinical applications.
Although phase I and II trials of Tivantinib in second-line use showed encouraging results, the manufacturer's press release said that the phase III study of Tivantinib in the treatment of Hepatocellular carcinoma (HCC) did not achieve the ultimate goal of improving overall survival(24). The future of Tivantinib, like many other drugs, depends on choosing the right patient. Some researchers have shown that patients with high expression of tumor MET showed great survival benefits compared with placebo group(25); for patients with low expression of tumor MET, there was no difference between Tivantinib group and placebo group, which indicated that Tivantinib still had a number of defects. Therefore, there is an urgent need to screen more compounds targeting c-MET for clinical applications
In this study, LibDock, ADME/TOPKAT, CDOCKER and Molecular Dynamics Simulation, five sections of Discovery Studio were used for virtual screening and analysis. As a result, 17931 biogenic-for sale-named ligands were screened from the ZINC15 database for virtual screening. Compared with other compounds, compounds with high LibDock score showed better energy optimization and a stable conformation. After the calculation of module, 8827 compounds were found to be eligible to bind stably with c-MET than Tivantinib. The top 20 compounds were selected and pooled for further study on the basis of LibDock score.
ADME and toxicity predictions of the selected compounds were used to evaluate the pharmacologic properties of these compounds. Outcomes illustrated that ZINC000005879645 and ZINC000002528509 were regarded as safe drug and chosen for the following study. Since they could dissolve in water and also had a good absorption level. Additionally, they didn`t have hepatotoxicity and they were non-inhibitors of cytochrome P450 2D6 (CYP2D6). Besides, these two compounds were also found to have less mutagenicity, rodent carcinogenicity and developmental toxicity potential compared with other compounds. Therefore, ZINC000005879645 and ZINC000002528509 were regarded as safe drug candidates. For another, the remaining drugs still had possible function in drug development despite they possessed toxicities or negative effects. In view of all the results above, ZINC000005879645 and ZINC000002528509 were selected as ideal lead compounds and further analysis were performed.
The bonding mechanism and chemical bonds of the selected candidate compounds were also researched. CDOCKER module computation illustrated that CDOCKER interaction energy of ZINC000008220033 and ZINC000001529323 was obviously lower than the reference ligand Tivantinib (-35. kcal/mol), which could indicate that these two compounds had a higher binding affinity with c-MET than Tivantinib.
Finally, their stabilities in the natural environment were investigated by molecular dynamics simulation. Calculation of RMSD and potential energy of these ligand-MGMT complexes demonstrated the trajectories of complexes reached equilibrium after 18 ps. With time going by, RMSD and potential energy of these complexes got stabilized gradually, which showed ZINC000005879645 and ZINC000002528509 could interact with c-MET and the complexes were stable in the natural environment. On account of the results, these 2 compounds could be used for drug development and refinement.
This study elucidated that the most important step in current drug designation was to screen ideal lead compounds. In this study, a battery of computer-aided virtual techniques was used to identify possible inhibitors of c-MET. LibDock is applied for structure-based screening followed by ADME (absorption, distribution, metabolic, excretion) and toxicity prediction.
Molecular docking was conducted to confirm the binding affinity mechanism between the ligand and c-MET. Molecular dynamics simulations were used to assess the stability of ligand-c-MET complexes. The results showed these 2 compounds might have the most potential effect on glioblastoma. But it is all known that no single drug could be directly marketed without thousands of refinement and improvement. Therefore, the refinement and improvement of them are of great significance in the following research.
Although this study was well-designed and precise measurements have been conducted, it still has some shortcomings. Further experiments, for instance animal testing, need to be performed to confirm our results, and more indicators, such as half-maximal inhibitory concentration and half-maximal effective concentration, should be assessed in the future.