## 4 Discussion
### Molecular Docking  
a-Tomatine enveloped all three enzymes, MMP-2, MMP-8, and MMP-9, with its bulky structure. In addition, the hydroxyl moieties in the glucoside group in this compound coordinated with the zinc atom in the enzymes. This is one of the main reasons for the affinity of a-tomatine for enzymes.  
MMP-2: a-Tomatine and chlorheximide molecules are docked to the recesses and protrusions in the protein structure of the MMP-2 enzyme. The rotation of the rotatable bonds in the a-tomatine compound allows the molecule to reach the optimal conformation of the protein structure through electronegative and electropositive effects. The interaction of chlorhexiidine and a-tomatine with the protein structure of the MMP-2 enzyme is shown in Figure 3. The a-tomatine compound was well adhered to the surface of the protein structure, thanks to its hydroxyl groups, whereas the chlorhexiidine compound acted mostly by embedding itself in the protein structure. The spreading of the MMP-2 positive charge density on the surface enabled the a-tomatine compound to make non-covalent interactions.  
MMP-8: The a-tomatine compound interacts strongly with the MMP-8 enzyme through hydroxyl groups from glycoside groups. These interactions are not involved in the other end of the compound, and this part is released into the solvent medium without any interaction with the protein structure. This means that a-tomatine interacts only at the site of the glycoside groups. One end of the chlorhexiidine compound is embedded in the MMP-8 protein structure and interacts with the protein surface from the other end. Figure 4 shows the interactions of a-tomatine and chlorhexiidine with the MMP-8 protein. These interactions are noncovalent interactions. Nitrogen atoms in the chlorhexiidine compound strongly interact with electronegative sites on the protein structure.  
MMP-9: The enzyme for which the a-tomatine and chlorhexiidine compounds potentially show the least affinity is the MMP-9 protein structure. All groups of the a-tomatine compound formed strong interactions with the surface amino acids of the MMP-9 protein structure. The glycoside groups tended to penetrate deeper into the protein structure, while the other parts interacted less. One end of the chlorhexiidine compound is buried in the protein structure while the other part interacts with the surface of the protein structure. Figure 5 shows that the surface interactions are electropositive. These interactions are the driving force of the part of the chlorhexiidine compound embedded in the protein structure. This is mainly due to the fact that the nitrogen atoms in the chlorhexiidine compound on the outside are electropositive. The repulsion of two positive effects is one of the effects that reduce the docking score.  
Figure 3: Interactions of a-tomatine and chlorhexiidine with the protein structure of MMP-2 enzyme. a-tomatine on top and chlorhexiidine on the bottom.  
The movement of the enzymes in the solvent media was decisive for the enzyme activity. The movement of each enzyme was different when the ligand was bound and when the ligand was not bound. Simulations were successfully performed to investigate and compare the effect of a-tomatine and chlorhexidine molecules on the MMP-2, MMP-8, and MMP-9 enzymes. After calculating the affinity of a-tomatine and chlorhexidine molecules to the MMP-2, MMP-8, and MMP-9 enzymes via a molecular docking study, molecular dynamics simulations were performed to model the states of the formed ligand-protein complexes in a physiological environment. For this purpose, the complexes were modeled in a solvent medium.  
Figure 4: Interactions of a-tomatine and chlorhexidine with the protein structure of MMP\(-\)8 enzyme. a-tomatine on top and chlorhexidine on the bottom.  
Figure 5: Interactions of a-tomatine and chlorhexidine with the protein structure of MMP-9 enzyme. a-tomatine on top and chlorhexidine on the bottom.