Abstract

MOLECULAR DOCKING METHOD: ANTIBACTERIAL ACTIVITY OF EUGENOL FROM CLOVE PLANT

Danni Ramdhani* and Sri Agung Fitri Kusuma

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Abstract

Objective: Molecular docking is an approach method in finding the activity of a compound against a specific receptor. This is very useful in the rational design of drugs. This method allows providing information on the affinity and activity of the drug candidate molecule with the protein on which it will act. This study was to determine the mechanism of interaction between eugenol compounds from Eugenia caryophyllus against receptors associated with antibacterial activity. This study used 3 target receptors associated with antibacterial activity: Penicillin Binding protein 3 (PBP3), N-myristoyltransferase (NMT), and Cytochrome P450 14 alpha-sterol Demethylase (CYP51). The molecular interactions of eugenol were compared with the native ligands at the active site of the receptor. Materials and Methods: Ligand files and target receptors are obtained by downloading at https://pubchem.ncbi.nlm.nih.gov/ and https://www.rcsb.org/. The docking process begins with ligand and receptor preparations using Pyrx software, MgTool, then molecular docking processes and visualization of interactions with AutoDock Vina and Discovery Studio Visualizer. Results: The eugenol ligand binding activity score with PBP3 is -5. 4 kcal/mol; - 4.3 kcal/mol with CYP51, and -4.2 kcal/mol with NMT. Conclusions: The binding activity data from molecular docking concluded that the eugenol compound had less dominant antibacterial activity at the three receptors compared to each native ligand.

Keywords: Molecular docking, Antibacterial, Eugenol, PBP3, NMT, CYP51.