Investigation of the inhibitory effects of different antimicrobial agents on enterococcus faecalis using in silico modelling methods

Pulpal infections in the deciduous teeth of paediatric patients lead to the loss of deciduous teeth at an early age. In the treatment of pulpal infections in deciduous teeth, it is necessary to eliminate pathogenic bacteria, especially Enterococcus Faecalis. In order to prevent the premature loss of deciduous teeth, lesion sterilization and tissue repair treatment have been applied with antibiotic paste combinations. The antibiotic paste combinations used consist of antibiotics such as metronidazole, ciprofloxacin, minocycline and amoxicillin trihydrate. The antibiotic pastes have disadvantages such as causing discoloration of the teeth, resistance and the development of allergic reactions. Because of these disadvantages, there is a need for the design of reliable, highly effective, and side-effect reduced antimicrobial drugs derived from natural sources. Therefore, in this study, molecular modelling methods were utilized to determine the inhibition mechanisms and structural properties of flavonoid and chalcone derived compounds with inhibitory effects against Enterococcus Faecalis enzymes (dihydrofolate reductase, ß-ketoacyl-acyl carrier protein synthase III, agmatine deiminase, alanine racemase, and enterococcal surface protein) at the molecular level. In this way, this study is intended to guide future experimental studies. In the first phase of the study, the three dimensional structures of the target enzymes and the binding sites of the inhibitor compounds were determined; three dimensional structures of flavonoid and chalcone derived ligand compounds were prepared. In the second phase, free binding energies of control group compounds (metronidazole, amoxicillin trihydrate, doxycycline, chlorhexidine and ciprofloxacin) along with flavonoid and chalcone derived compounds were calculated using molecular docking method with target enzymes. In the third phase, the pharmacokinetic properties of the control group compounds were evaluated. In the final stage, the amino acids involved in the binding of enzyme-ligand structures were analysed at the molecular level. As a result of the study, compound number 9 (C15H11NO4) has been identified as the compound showing the highest binding affinity with the dihydrofolate reductase enzyme, with a binding energy of -8.45 kcal/mol. Additionally, compound number 9 has been formed a hydrogen bond with Val102 amino acid, which is located in the binding region of the dihydrofolate reductase enzyme and plays a significant role in the inhibition mechanism. The molecular docking of ß-ketoacyl-acyl carrier protein synthase III enzyme with ligand compound number 2 (C15H11BrO2) has been resulted in a binding energy of -8.41 kcal/mol, exhibiting the best binding affinity. Compound number 2 has been formed a hydrogen bond with Asn280 amino acid, a residue located in the binding site of β-ketoacyl-acyl carrier protein synthase III enzyme, playing a crucial role in its inhibition mechanism. As a result of docking studies with flavonoid and chalcone derived compounds, compound number 20 (C16H13BrO3) has been determined as the compound with the best binding affinity against the target enzyme agmatine deaminase with a binding energy of -8.82 kcal/mol. For alanine racemase enzyme all selected ligand compounds have been found to be more effective than both control group compounds and the reference compound, among these ligand compound number 9, with a binding energy of -8.94 kcal/mol, has been identified as the compound exhibiting the best binding affinity against the target enzyme alanine racemase. Ligand compound number 9 has been bound to the amino acids Arg139, His169, and Ser207 located in the binding site, playing a significant role in the inhibition mechanism. Based on the results of molecular docking analysis, the ligand compound number 20 has been identified as having the highest binding affinity with a binding energy of -9.81 kcal/mol among the flavonoid and chalcone-derived compounds, when interacting with the enterococcal surface protein enzyme. As a result of this study, we have contributed to the development of inhibitors of natural chemical compounds that act on Enterococcus Faecalis enzymes and show specific binding by testing them in silico method in a short time for the prevention of primary tooth pulpal infections.