Molecular Docking Insights into EDTA and Tween-20-Induced Inhibition of Lysozyme in Bacterial DNA Isolation Buffers

Ika Keumala Fitri; Meredith Jannaatu 'Adn; Tegar Cahya Widodo; Muktiningsih Nurjayadi; Futi Kusuma Hati

doi:10.21009/JRSKT.121.03

Authors

Ika Keumala Fitri Chemistry Study Program, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Rawamangun, Jakarta Timur, DKI Jakarta 13220, Indonesia
Meredith Jannaatu 'Adn Chemistry Study Program, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Rawamangun, Jakarta Timur, DKI Jakarta 13220, Indonesia
Tegar Cahya Widodo Chemistry Study Program, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Rawamangun, Jakarta Timur, DKI Jakarta 13220, Indonesia
Muktiningsih Nurjayadi Chemistry Study Program, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Rawamangun, Jakarta Timur, DKI Jakarta 13220, Indonesia
Futi Kusuma Hati Chemistry Study Program, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Rawamangun, Jakarta Timur, DKI Jakarta 13220, Indonesia

DOI:

https://doi.org/10.21009/JRSKT.121.03

Keywords:

Enzyme Inhibition, DNA Isolation, Lysozyme, Molecular Docking

Abstract

The efficiency of bacterial deoxyribonucleic acid (DNA) isolation is a critical bottleneck in Polymerase Chain Reaction (PCR) based pathogen detection. This study investigates the potential inhibitory effects of standard lysis buffer components, including ethylenediaminetetraacetic acid (EDTA), Tris base, and Tween-20, on Hen Egg White Lysozyme (HEWL) to address the low DNA yields observed in a locally developed isolation kit. Molecular docking simulations were performed using AutoDock 4.2.6. The protocol was validated by redocking the native ligand, which established the suitability of a 60x60x60 Å grid box. The results revealed that EDTA binds with high affinity, with an intermolecular energy of -6.44 kcal/mol, and interacts with crucial anchoring residues Trp62 and Asp101. Notably, the hydrophobic tail of Tween-20 exhibited the strongest binding (-7.12 kcal/mol), penetrating the active cleft and blocking the catalytic residue Glu35. Conversely, Tris base and the hydrophilic head of Tween-20 showed weaker, less stable interactions. These findings suggest a dual-inhibition mechanism in which EDTA blocks substrate access, while Tween-20 hinders the catalytic center. This study provides a molecular explanation for the kit's reduced performance and highlights the need for buffer optimization.

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