Molecular Docking of Laccase from Trametes Versicolor with Ligand Substrates from Textile Dyes and Antibiotics Impacting the Environment
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Abstract
Environmental pollution from textiles and pharmaceuticals is a primary source of concern for various environmental protection agencies. The nature of synthetic dyes and the increasing rate of antibiotic resistance by bacteria have made them a major health concern. Laccases are capable of degrading organic pollutants, including phenols, dyes, bisphenol, polyaromatic hydrocarbon (PAHs) and pharmaceuticals. This study focused on assessing the toxicity and binding interaction of eight ligands of environmental importance with laccase from a fungus, Trametes versicolor, via an in-silico approach. The canonical SMILES of the ligands were retrieved from the PubChem database and the 3D structures were obtained using UCSF Chimera 1.18. The 3D structure of laccase was retrieved from the Protein Data Bank (PDB) and blind docked with the ligands. Discovery Studio 4.5 software was used to observe the different bonding interactions between the enzyme and the docked ligands. The ADMET study of the ligands was done using their canonical SMILES on the admetlab3.0 servers. The binding energies of laccase with Indigo carmine (IC), Malachite green (MG), Remazol brilliant blue R (RBBR), Direct red 75 (DR75), Ciprofloxacin (CIP), Amoxicillin (AMO), 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid (ABTS), and Guaiacol were −6.6, −7.0, −7.0, −7.4, −6.8, −7.0, −6.4, and −5.2 kcal/mol, respectively. All the dyes showed high probability for toxicity with values close to 1 and also environmental toxicity, with Malachite green (MG) showing the highest probability with bioconcentration factors (BCF), 50 percent growth inhibition concentration of Tetrahymena pyriformis (IGC50), 96-hour fathead minnow 50 percent lethal concentration (LC50FM), and 48-hour Daphnia magna 50 percent lethal concentration (LC50DM) of 1.683, 3.858, 4.567, and 5.446. The active site of the enzyme that interacted with the eight ligands was found to contain one of these eleven (11) amino acid residues, namely, HIS, GLN, ASP, ALA, PHE, SER, LEU, ARG, VAL, PRO, and GLU in the docked complexes.
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