Studi Molecular Docking Senyawa Aktif Dari Jahe Merah (Zingiber Officinale Var. Rubrum) Sebagai Antibakteri

Fadhilah, Dhia (2024) Studi Molecular Docking Senyawa Aktif Dari Jahe Merah (Zingiber Officinale Var. Rubrum) Sebagai Antibakteri. S1 thesis, Universitas Andalas.

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Abstract

The increasing level of antibiotic resistance challenged researchers to find new antibiotic drug candidates. Compounds from natural materials such as red ginger (Zingiber officinale var. rubrum) were used as a source in the discovery of new antibacterial candidates. Red ginger compounds have been reported to have antibacterial activity. The purpose of this study was to assess the binding affinity (kcal/mol), interaction, and the ADMET profile of red ginger compounds against antibacterial target proteins through molecular docking simulation. This study used four antibacterial target proteins were PDB codes 2W9G, 5L3J, 5OJ0, and 1FJG. This docking protocol uses Schrödinger software and the ADMET prediction using SwissADME, pkCSM, and Protox. The docking simulation results for the target protein DNA Gyrase subunit B showed that (-)-epicatechin, (+)-catechin, and rutin had the best docking scores compared to the native ligand benzothiazole. Hexahydrocurcumin had the best docking score for the target protein dihydrofolate reductase with the native ligand trimethoprim. The results of docking simulation with PBP 2X target protein with native ligand cefepime showed the best docking score which were rutin, morin, and (-)-epicatechin. The results of docking simulations with the target protein 30s ribosome with native ligand streptomycin showed the best docking score were anthocyanin, apigenin, and quercetin. The ADMET prediction results showed that that all compounds had good GI absorption except rutin. Anthocyanin compound could be distributed to the BBB. Some compounds acted as CYP inhibitors and P-gp substrates. Total clearance of compounds ranged from -0.369 to 0.716 and none acted as Renal OCT2 substrate. Predicted mutagenic toxicity were anthocyanin and quercetin, and toxicity classes of hit compounds were in the range of class 3 to 6. From the above results, the active compounds of red ginger showed potential in 4 antibacterial mechanisms of action.

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