**2. Results and Discussion**

*2.1. In Silico Studies*

2.1.1. Docking Study

Molecular docking has been applied as an essential tool in the process of drug design and discovery for various bioactive compounds [39,40], including antispasmodics [41], antimicrobials [42], and antimalarials [43]. Compound **7** was docked into the VEGFR-2 ATP binding site to better understand the pattern by which it bounds to the active site [38–40]. Following the preparation of the downloaded protein (PDB ID: 2OH4, resolution: 2.05 Å), the native co-crystallized inhibitor was re-docked against the catalytic VEGFR-2 site as a validation step for the docking protocol. The validation process successfully formed an RMSD value of 0.79 that indicated the validity of the docking operation (Figure 3).

**Figure 3.** Validation step inside VEGFR-2 catalytic site; native ligand (green) and the obtained pose (yellow).

The surveillance of interaction types between sorafenib and the VEGFR-2 active pocket showed that it could form two main types of interactions (Figure 4). The first type was represented by three H-bonding interactions with the critical amino acids in the VEGFR-2 catalytic site. This includes Cys917 in the hinge region, and Asp1044, and Glu883 in the DFG motif. The second type of interactions comprised a huge network of π interactions between sorafenib and the hydrophobic amino acids (Val846, Val914, Val897, Phe1045, and Cys1043 in the linker region, Leu1033, Leu838, Val846, Phe1045, and Ala864 in the hinge region, and Leu1017, His1024, Ile890, Ile886, and Leu887 in the hydrophobic pocket).

**Figure 4.** *Cont*.

**Figure 4.** Sorafenib binding pattern, (**A**) 3D and (**B**) 2D.

Docking results for compound **7** revealed strong binding interactions with the VEGFR-2 enzyme, similar to sorafenib. Simply, compound **7** formed a critical hydrogen bond with Cys917 via its indole nitrogen, similar to the pyridine nitrogen of sorafenib. The methoxy group formed a hydrogen bond with Arg1049. Moreover, the amide moiety (inserted between the two phenyl groups) formed two hydrogen-bonding interactions with Glu883 and Asp1044 amino acids, similar to those of sorafenib's urea group. As well, the central phenyl moiety occupied the linker region to form hydrophobic interactions between Val897, and Val914. Similar to the 3-trifluoromethyl-4-chlorophenyl moiety of sorafenib, the hydrophobic allosteric site of the enzyme was occupied with the terminal phenyl group via interactions with Leu887 and Val897. The binding mode of compound **7** is presented in Figure 5.

**Figure 5.** *Cont*.

**Figure 5.** (**A**) Mapping surface, (**B**) 3D, and (**C**) 2D binding pattern of compound **7**.
