## 4 Discussion
### Molecular Dynamics  
MMP-2: The a-tomatine compound started the molecular dynamics simulation by coordinating with the zinc atom in the binding pocket of the MMP-2 enzyme. This interaction was mediated by two hydroxyl moieties in the glycoside group of a-tomatine. a-Tomatine interacted with the zinc atom in two places at the same time. This interaction with the zinc atom continued throughout the molecular dynamics simulation and significantly inhibited enzyme functioning. While the steroid part of the a-tomatine compound oscillated in the solvent environment, the part containing the glycoside groups was extremely stable and rigid. The change in conformation was caused by the rotation of the glycoside groups around the single bond where the steroidal part was attached. Throughout the molecular dynamics simulation, the a-tomatine compound did not show any significant conformational change and remained in its initial binding position and conformation. The primary reason for the absence of a significant change was the strong coordination with the zinc atom and the rigidity of the structure of the compound. All these properties indicate that a-tomatine is a potential potent inhibitor of the MMP-2 enzyme. The chlorhexidine compound started the molecular dynamics simulation by forming a coordination with the zinc atom from the nitrogen atoms. Unlike a-tomatine, the chlorhexidine compound contained a part embedded in the protein structure of the MMP-2 enzyme. In this embedded part, Thr142 and Thr144 amino acid residues acted as a lid, and the conformational changes of these amino acids were very important for the chlorhexidine compound to provide continuity in the inhibition of the MMP-2 enzyme. At 21 nanoseconds of the molecular dynamics simulation, the part of the chlorhexidine compound embedded in the protein structure was directed further inwards, and three-quarters of the compound was embedded in the protein structure. Although the chlorhexidine compound was a compound with a large number of flexible and rotatable bonds, it completed the molecular dynamics simulation in the first binding pocket, thanks to the noncovalent interactions performed by the nitrogen atoms and coordination with the zinc atom, and it exhibited potential strong inhibitor properties. MMP-8: The a-tomatine compound started the molecular dynamics simulation by coordinating with the zinc atom and two hydroxyl moieties from the glycoside groups in interactions with the MMP-8 enzyme. Coordination with the zinc atom continued throughout the molecular dynamics simulation. The a-tomatine compound exhibited a flat structure and conformation, and this conformation continued throughout the molecular dynamics simulation. The compound remained in a rigid structure. The compound showed potential to be a good inhibitor when evaluated as a whole through the overall molecular dynamics simulation. The chlorhexidine compound, unlike the a-tomatine compound, started the molecular dynamics simulation slightly away from the zinc atom and without coordination with the zinc atom. The compound was in a \"U\" shaped conformation, and this conformation changed as the simulation time progressed. The simulation began with some of the part embedded in the protein structure. Although the embedded part remained inside the protein structure from the first moments of the simulation, the other end of the compound began to be released into the solvent environment. The molecular dynamics simulation ended with this repetitive motion. The chlorhexidine compound always remained in the binding pocket throughout the simulation. However, the lack of coordination with the zinc atom indicated a weak interaction. Therefore, it was observed that the chlorhexidine compound had less MMP-8 inhibition potential than a-tomatine. MMP-9: The interactions of the a-tomatine compound with the MMP-9 enzyme were much less than with the other enzymes.