Inhibition Docking Simulation of Zerumbone, Gingerglycolipid B, and Curzerenone Compound of Zingiber zerumbet from Timor Island Against MurA Enzyme

Origenes B. Kapitan*, Laksmi Ambarsari**, and Syamsul Falah*

*Departemen Biokimia, Fakultas Matematika dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor 16680, INDONESIA; **Pusat Penelitian Biofarmaka, Institut Pertanian Bogor, Jl. Taman Kencana No.3, Bogor 16128, INDONESIA

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pdf-vsmall PDF |Abstract

Zingiber zerumbet is a medicinal plant which is traditionally used to treat ulcerative lesions. In this research, it has been done an in vitro study of its antibacterial activity test from crude ethyl acetate, ethanol, and aqueous extracts. The result of LC-MS analysis showed that the most active antibacterial compounds in the ethyl acetate, ethanol, and aqueous extract were zerumbone, gingerglycolipid B, and curzerenone. Further molecular docking simulation was performed using Autodock Vina to filter based on the value of affinity zerumbone, gingerglycolipid B, and curzerenone in the active site of MurA enzymes (ΔGbinding). The result indicated that the affinity energy (ΔGbinding) molecular docking of the natural ligand (substrat), drug ligand (fosfomycin), zerumbone ligand, gingerglycolipid B ligand, and the curzerenone ligand against the MurA enzyme were respectively -10.1, -4.7, -8.3, -8,4 and -7.4  kcal mol-1. Further docking simulations indicated that there was a competitive reaction mechanism between zerumbone (test ligand) with an uridine-diphosphate-N-asetylglucosamine substrate in the enzyme as a test ligand to occupy the same spot as the substrate therefore inhibiting the formation of peptidoglycan, a major constituent of bacterial cell wall. Analysis of ΔGbinding value and the result of docking simulations interaction finally indicated that the zerumbone ligand had the highest potential to replace fosfomycin drug in inhibiting the synthesis of bacterial peptidoglycan.

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