*3.4. Buried Surface Area (BSA)*

Molecular interactions are the critical factors in determining the stability of protein– ligand complexes. Molecular interactions existing between protein–ligand complexes can be modelled by taking into account the physicochemical properties and complementarity of the shape of the binding interface. A useful method for determining the complementarity of the shape and extent of molecular interactions is the estimation of the buried surface area (BSA) of a protein–ligand complex. In the current study, the BSA of best complexes was calculated using a new Shrake–Ruply algorithm-based tool (*dr\_sasa*) [57] used for calculating the solvent accessible surface area (SASA), buried surface area (BSA), and contact surface area (CSA). All four top compounds (**208**, **248**, **255**, and **762**) were subjected to the calculation of BSA. It was observed that the targeted NEK7 protein was buried up to 80% and 70% by compounds **208** and **248,** respectively. In particular, amino acid residues ILE40 and PHE168 were strongly buried by compound **208** (49 Å<sup>2</sup> ). Compound **248**, on the other hand, was strongly engaging the ARG121 and PHE168 with BSA of 39 Å<sup>2</sup> and 41.3 Å<sup>2</sup> respectively. The detailed buried surface area of both compounds is shown in Figure 9.

**Figure 9.** Buried surface area (BSA) of compound **208** and **248**.

In terms of compounds **255** and **762**, it was observed that both compounds significantly engaged the amino acid residues of the target protein. Compound **255**, in particular, was burying the surface area of the NEK7 protein by up to 360 Å<sup>2</sup> . The BSA of compound **255** with VAL48, LYS63, ALA114, and PHE168 was 168, 212, 187, and 351 Å<sup>2</sup> , respectively, which was the best among all top hits. These values demonstrate the strong nature of molecular interactions existing between the target protein and compound **255**. In the case of compound **762**, important amino acid residues were buried by compound **762**. In particular, TYR201, TYR237, and MET241 were significantly buried by compound **762** with BSA of 64, 72, and 25.6 Å<sup>2</sup> . Moreover, it was worth noticing that the major contributing atoms were oxygen, nitrogen, fluorine, sulphur, and chlorine, which were involved in increasing the contact surface area of compounds with a targeted protein. The BSA of compounds **255** and **762** is shown in Figure 10.

**Figure 10.** Buried surface area (BSA) of compound **255** and **762**.
