Molecular Docking
The FGFR1 protein complex (PDB ID: 4ZSA) contains the entire protein and its original ligand, which is immobilized at the active site of the FGFR1 protein, and key amino acid residues are determined by non-bonding action to define the active site. The ligand was extracted and then docked with the FGFR1 protein, with a high degree of molecular overlap and a RMSD value of 1.7. It can be concluded that the LibDock docking has a high reliability and can be used for the next virtual screening.
The well-known inhibitor of FGFR, E-3810, can effectively inhibit the activity of FGFR1, which is used as a reference compound. E-3810 inhibits the activity of FGFR1 by forming hydrogen bonds between methylamino group, phenoxy group and key residues such as Gly485, Asp641, Glu562, Glu531 on the phenyl ring(Figure 6). The docking score of E-3810 and FGFR1 is 145.145. A series of compounds with docking score greater than this value were screened using LibDock.
In LibDock, 659 compounds were successfully docked, and these compounds were docked on the receptor protein using the CDOCKER module. We selected the molecules with the highest LibDock score and -CDOCKER energy score for visual observation, and found 6 small molecules, and the docking results of 6 small molecules are shown in Table 3.
Table 3
The docking results of 7 potential FGFR1 inhibitors.
Name | 2D Structure | LibDock Score | -CDOCKER Energe | Estimated IC50 |
ZINC000038579824 | | 158.868 | 44.3841 | 0.110979 |
ZINC000230274254 | | 151.735 | 12.6032 | 0.143403 |
ZINC000011878462 | | 146.958 | 30.956 | 0.181035 |
ZINC000219521723 | | 148.581 | 31.1579 | 0.511363 |
ZINC000072436123 | | 148.899 | 18.813 | 0.877224 |
ZINC000097657383 | | 150.456 | 20.7042 | 0.88008 |
E-3810 | | 145.145 | 3.35382 | 1.63942 |
All the selected molecules can be linked to the key residues of the receptor protein, thus inhibiting the activity of the protein. The hydrogen bond interaction between the six molecules and the protein is shown in Table 4.
Table 4
Hydrogen bond interaction parameters of each compound
Name | Donor Atom | Receptor Atom | H-Bond Distance (Å) |
ZINC000038579824 | Asp641:HN Phf642:HN Asn568:HD21 | ZINC000038579824 O2 N25 | 3.04 2.39 2.20 |
ZINC000230274254 | Phe489:O Asp641:HN Ala564:HN Ala564:O | H43 O15 N11 H28 | 2.79 2.96 2.60 1.57 |
ZINC000011878462 | Ala564:HN Ala564:O Ala564:O | O6 H31 H33 | 2.70 2.45 2.86 |
ZINC000219521723 | Asp641:HN Ala564:O Tyr563:HA | O24 H28 O3 | 2.01 2.74 2.89 |
ZINC000072436123 | Phe642:HN Asp641:HA Ala:564:O | N23 N24 H41 | 2.09 2.15 2.76 |
ZINC000097657383 | Ala564:HN Gly643:HN Asp641:OD1 | O10 N27 H46 | 2.53 2.41 2.92 |
The docking score was 158.868 for ZINC000038579824 (2-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)-N-(2-((6-methoxy-3,4-dihydroisoquinolin-2(1H)-yl)sulfonyl)ethyl)acetamide) has − 44.3841 CDOCKER energy, and its predicted activity value is only 0.110979, which can be well mapped on the pharmacophore Fig. 7A). The oxygen atom at the end and the nitrogen atom on the imidazole group form hydrogen bonds with Phf64 2 and Asn5688, respectively (Fig. 8A). ZINC000230274254 ((R)-3-(2,5-dimethyl-7-oxo-4,7-dihydro-[1, 2, 4]triazolo[1,5-a]pyrimidin-6-yl)-N-(1-hydroxy-3-phenylpropan-2-yl)propanamide) can form four hydrogen bonds with Phe489, Ala564, Asp641 (Fig. 8B), and the pharmacophore predicted activity is 0.143403 (Fig. 7B). ZINC000011878462 ((R)-2-(3-oxo-1-phenethylpiperazin-2-yl)-N-(2-(2-oxooxazolidin-3-yl) ethyl) acetamide) had higher docking score and lower CDOCKER energy, formed three hydrogen bonds on Ala564 (Fig. 8C), and could bind stably on the pharmacophore (Fig. 7C). ZINC000219521723 ((R)-2-(5-phenyl-2H-tetrazol-2-yl)-N-(2-(5-(tetrahydrofuran-2-yl)-1,2,4-oxadiazol-3-yl)ethyl)acetamide) with docking score of 148.581 formed three hydrogen bonds with Asp641, Ala564, Tyr563, Oxadiazole and Phf489 formed a pi-pi conjugate system (Fig. 8D), and tetrazolium group mapped on HBA (Fig. 7D). ZINC000072436123 ((R)-2-(4-(2-(3-(1H-tetrazol-1-yl) phenoxy) acetyl) morpholin-3-yl)-N, N-dimethylacetamide) formed three hydrogen bond interactions with Ala564, Asp641, Phe642 (Fig. 8E), and the tetrazolium group was mapped on HBA (Fig. 7E). ZINC000097657383 ((R)-N-(3-(1H-imidazol-1-yl)propyl)-2,7-dioxo-N-(pyridin-3-ylmethyl)-1,3-diazepane-4-carboxamide) with docking score of 150.456 formed three hydrogen bonds with Ala564, Gly643, Asp641, and benzene ring formed a pi-pi conjugate system with Phf642 (Fig. 8F), which could be mapped on the pharmacophore (Fig. 7F).
ADMET and Toxicity Prediction
The ADMET module of DS2016 was used to predict the absorption, distribution, metabolism, excretion level of all selected small molecules and E-3810. The results are shown in Table 5. The solubility level (in water at 25 ℃) indicates that all compounds are soluble in water. For human intestinal absorption, except ZINC00000385579824, it has good absorption level. CYP2 D6 is one of the important enzymes involved in drug metabolism. All compounds are non-inhibitors of cytochrome P4502D6 (CYP2D6). For hepatotoxicity, compared with E-3810 (toxic), ZINC0002219521723 was predicted to be toxic, and the other compounds were not hepatotoxic (Fig. 9).
Table 5
Name | Solubility Level1 | BBB Level2 | Absorption Level3 | CYP2D64 | Hepatotoxity5 | PPB Level6 |
ZINC000038579824 | 3 | 4 | 1 | 0 | 0 | 0 |
ZINC000230274254 | 3 | 3 | 0 | 0 | 0 | 0 |
ZINC000011878462 | 4 | 4 | 0 | 0 | 0 | 0 |
ZINC000219521723 | 3 | 4 | 0 | 0 | 0 | 1 |
ZINC000072436123 | 4 | 3 | 0 | 0 | 0 | 0 |
ZINC000097657383 | 4 | 4 | 0 | 0 | 1 | 0 |
E-3810 | 2 | 3 | 0 | 0 | 1 | 1 |
1 footer. a. Solubility level: 0 (extremely low); 1 (very low, but possible); 2 (low); 3 (good). 2 BBB(Blood Brain Barrier level)Level: 0(Very High Penetrant); 1(High); 2(Middle); 3(Low); 4(undefined). 3 Absorption (Human Intestinal Absorption) Level: 0(good); 1(moderate); 2(Poor); 3(Very Poor).4 CYP2D6(Cytochrome P4502D6) level: 0(non-inhibitor); 1(inhibitor).5 Hepatotoxicity: 0 (Nontoxic); 1 (Toxic). 6 PPB (Plasma Protein Binding): 0 (Binding is < 90%); 1 (Binding is > 90%); 2 (Binding is > 95%). |
To check the safety of the compound, the toxicity of all selected small molecules and E-3810 was predicted using the TOPKAT module, as shown in Table 6. The results showed that all compounds except ZINC0000038579824 were predicted to be non-mutagens. All of the three compounds have good aerobic biodegradation performance, four compounds have no potential developmental toxicity, and one is a non-carcinogen.
Table 6
Name | Ames1 | Mouse NTP2 | DTP3 | Aerobic Biodegradability4 |
Male | Female |
ZINC000038579824 | 1 | 1 | 1 | 1 | 0 |
ZINC000230274254 | 0 | 0 | 0 | 0 | 1 |
ZINC000011878462 | 0 | 1 | 0 | 0 | 1 |
ZINC000219521723 | 0 | 1 | 0 | 0 | 0 |
ZINC000072436123 | 0 | 0 | 1 | 1 | 0 |
ZINC000097657383 | 0 | 1 | 1 | 0 | 1 |
E-3810 | 0 | 1 | 1 | 1 | 1 |
1 Mutagenicity (Ames text): 0 (non-toxic), 1 (toxic); 2 Rodent Carcinogenicity: 0 (non-carcinogenicity), 1 (carcinogenicity); 3 Developmental Toxicity Potential: 0 (non-toxic), 1 (toxic); 4 Aerobic Biodegradability: 0 (non-aerobic biodegradability), 1 (aerobic biodegradability). |
Therefore, ZINC000230274254 can not inhibit CYP2D6, has no hepatotoxicity, mutagenicity and potential developmental toxicity, and has good aerobic biodegradation performance and absorption level. It is predicted to be a safe candidate drug and selected for further research.