article · Environmental Sciences Europe
This computational study examined how azoreductase enzymes from the bacterium Bacillus megaterium H2 interact with four commercial dyes: acid orange 7, cresol red, methylene blue, and malachite green. Using machine learning algorithms alongside molecular docking, specific binding sites across three enzyme variants were identified. Molecular dynamics simulations confirmed that the resulting enzyme-dye complexes remained stable over time, forming between zero and five hydrogen bonds with binding affinities ranging from minus 9.4 to minus 5.4 kilocalories per mole. Further energetic calculations showed that hydrophobic interactions driven by van der Waals forces largely stabilised these pairings, except in the case of malachite green. Overall, the findings demonstrate the capacity of these bacterial enzymes to bind various synthetic dyes, providing structural insights into how Bacillus megaterium H2 azoreductases could function in dye decolorisation.
Industrial dyes are frequent environmental pollutants that can contaminate water bodies and resist natural degradation. By clarifying how specific bacterial enzymes interact with and bind common commercial dyes, this research improves the understanding of biological dye decolorisation. These insights support the ongoing development of targeted enzymatic methods for wastewater bioremediation.
The findings are relevant to industrial wastewater management and environmental biotechnology, where enzyme-based solutions are sought to clean up dye-rich effluent. Intended users include industrial effluent treatment providers and biotechnology firms developing biological remediation products. As the work relies entirely on computational predictions and molecular dynamics simulations, it sits at an early stage of research and requires physical laboratory testing and scaling before commercial deployment.
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Abstract The present study aimed to investigate the decolorization of various commercial dyes by azoreductases (AzrBmH21, AzrBmH22/3, and AzrBmH24/5) through bioinformatics means, comprising molecular docking, molecular dynamics simulation, and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA). Therefore, four commercial dyes, namely acid orange 7, cresol red, methylene blue, and malachite green, were selected as potential targets for degradation by the above said azoreductases derived from Bacillus megaterium H2. The prediction of ligand binding or catalytic sites for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 were performed using a machine learning algorithm based on the Prank Web and DeepSite chemoinformatic tool. This analysis revealed that several amino acids of AzrBmH2 interacted with the tested dyes, indicating the presence of distinct ligand-binding sites for AzrBmH2-dye complexes. Likewise, the binding affinity for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 ranged from − 9.4 to − 5.5 kcal/mol, − 9.2 to − 5.4 kcal/mol, and − 9.0 to − 5.4 kcal/mol, respectively, with each complex stabilized at a minimum of 0–5 hydrogen bonds. MD simulations revealed stable AzrBmH2-dye complexes with RMSD and RMSF values ranging from 0.15 to 0.42 nm and 0.05 to 0.48 nm, respectively, with Rg values between 1.75 and 1.88 nm. MM-PBSA calculations indicated that the AzrBmH2–dye complexes, except for AzrBmH2–malachite green, exhibited the lowest binding energy (− 191.05 ± 7.08 to 314.19 ± 6.88 kcal/mol), with prevalent hydrophobic interactions (− 268.25 ± 12.25 to − 418.92 ± 29.45 kcal/mol) through van der Waals forces. Therefore, this study was able to highlight the potential role of enzymes, specifically azoreductases from Bacillus megaterium H2, in predicting the decolorization of commercial dyes. These findings could contribute to our understanding of the azoreductases’ mechanisms in bioremediation and for biotechnological applications.
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DOI: 10.1186/s12302-024-00853-5
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