BINDING INTERACTION OF INULOSUCRASE (2YFR) WITH β-D-FRUCTOFURANOSE THROUGH MOLECULAR DOCKING SIMULATION
DOI:
https://doi.org/10.20414/spin.v7i2.14117Keywords:
inulosucrase, β-D-fructofuranose ligand, Molecular docking, affinity, hydrogen bondingAbstract
Molecular docking is used to predict the binding of two or more molecular structures in 3D space and to analyze the distribution of compounds based on their chemical structures and their binding to specific target enzymes or proteins. This study aims to analyze the molecular interaction between the enzyme inulosucrase (PDB ID: 2YFR) and the ligand β-D-fructofuranose using molecular docking. The methods employed were ligand and receptor preparation in Chimera and docking and visualization analysis using AutoDock Tools 1.5.7, AutoDock Vina, and Discovery Studio Visualizer. The docking method was validated using grid box coordinates and the resulting affinity values. The docking results showed that the β-D-fructofuranose ligand has an affinity of –2.9 kcal/mol, indicating a stable interaction and the formation of two strong hydrogen bonds with the active residues ASP42 and GLU45. This indicates the stability of the ligand–receptor complex, suggesting that the β-D-fructofuranose ligand may influence the catalytic activity of the inulosucrase enzyme via a specific hydrogen-bonding mechanism.
ABSTRAK
Molecular docking digunakan untuk memprediksi dua atau lebih sruktur molekul yang dapat berikatan secara 3D untuk menganalisis pola distribusi senyawa berdasarkan struktur kimia dan keterikatan senyawa terhadap enzim atau protein target tertentu. Penelitian ini bertujuan untuk menganalisis interaksi molekuler antara inulosukrase (PDB ID: 2YFR) dengan ligan β-D-fructofuranose melalui pendekatan molecular docking. Metode yang digunakan yaitu preparasi ligan dan reseptor dilakukan menggunakan perangkat lunak Chimera dan proses docking dan visualisasi dianalisis menggunakan perangkat AutoDock Tools 1.5.7, AutoDock Vina, dan Discovery Studio Visualizer. Validasi metode docking dilakukan berdasarkan nilai koordinat grid box dan evaluasi nilai afinitas yang diperoleh. Hasil docking menunjukkan bahwa ligan β-D-fructofuranose memiliki afinitas sebesar –2,9 kkal/mol yang menunjukkan interaksi yang stabil serta dapat membentuk dua ikatan hidrogen kuat dengan residu aktif ASP42 dan GLU45. Hal ini menunjukkan kestabilan interaksi kompleks ligan–reseptor, sehingga ligan β-D-fructofuranose berpotensi mepengaruhi aktivitas katalitik enzim inulosukrase melalui mekanisme ikatan hidrogen spesifik.
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