Molecular Docking Studies of Catechin and Its Derivatives as Anti-bacterial Inhibitor for Glucosamine-6-Phosphate Synthase

Workshop and International Seminar on Science of Complex Natural Systems

Fikrika, H.^1 ; Ambarsari, L.^1 ; Sumaryada, T.^2,3

Department of Biochemistry, Bogor Agricultural University, Jalan Agatis Kampus Dramaga IPB, 16880, Indonesia^1

Computational Biophysics and Molecular Modeling Research Group (CBMoRG), Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB, Dramaga Bogor

16680, Indonesia^2

Biopharmaca Research Center, Bogor Agricultural University, Jalan Taman Kencana No. 3, Bogor

16128, Indonesia^3

关键词: Anti-bacterial agents;    Bacterial cells;    Binding affinities;    Catechin derivatives;    Docking mechanisms;    Glucosamine-6-phosphate synthase;    Molecular docking;    Molecular docking simulations;   

Others  :  https://iopscience.iop.org/article/10.1088/1755-1315/31/1/012009/pdf
DOI  :  10.1088/1755-1315/31/1/012009

来源: IOP

【 摘 要 】

Molecular docking simulation of catechin and its derivatives on Glucosamine-6- Phosphate Synthase (GlmS) has been performed in this research. GlmS inhibition by a particular ligand will suppress the production of bacterial cell wall and significantly reduce the population of invading bacteria. In this study, catechin derivatives i.e epicatechin, galloatechin and epigalloatechin were found to have stronger binding affinities as compared to natural ligand of GlmS, Fructose-6-Phosphate (F6P). Those three ligands were docked on the same pocket in GlmS target as F6P, with 70% binding sites similarity. Based on the docking results, gallocatechin turns out to be the most potent ligand for anti-bacterial agent with ΔG= -8.00 kcal/mol. The docking between GlmS and catechin derivatives are characterized by a constant present of a strong hydrogen bond between functional group O3 and Ser-349. This hydrogen bond most likely plays a significant role in the docking mechanism and binding modes selection. The surprising result is catechin itself exhibited a quite strong binding with GlmS (ΔG= -7.80 kcal.mol), but docked on a completely different pocket compared to other ligands. This results suggest that catechin might still have a curing effect but with a completely different pathway and mechanism as compared to its derivatives.