Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment

Alam, Rafiqul; Mahmood, Raisul Awal; Islam, Syful; Ardiati, Fenny Clara; Solihat, Nissa Nurfajrin; Alam, Md. Shahin; Lee, Sang‐Han; Yanto, Dede Heri Yuli; Kim, Sungjune

doi:10.1016/j.chemosphere.2022.137505

Cited by 35 publications

(12 citation statements)

References 70 publications

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“…It is worth noting that hydrogen bond energy plays a crucial role in the degradation of acid orange 7, cresol red, and methylene blue, while van der Waals interactions are involved in the degradation of malachite green. These results are in alignment with the previous analyses, providing further support to the overall findings (Zhang et al, 2016;Srinivasan and Sadasivam, 2018;Hossain et al, 2022;Alam et al, 2023). This result indicates that optimizing hydrogen bond interactions between acid orange 7, cresol red, and methylene blue and AzrBmH2 proteins, as well as optimizing van der Waals interactions between malachite green and AzrBmH2 proteins, could potentially enhance the degradation or decolorization of the AzrBmH2-dyes interaction.…”

Section: Mm-pbsa Binding Free Energy Calculationsupporting

confidence: 90%

Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes

Oyewusi,

Wahab,

Akinyede

et al. 2023

Preprint

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The present study aimed to investigate the decolorization of various commercial dyes through bioinformatics analysis, utilizing techniques such as molecular docking, molecular dynamics simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). These analyses were conducted on different commercial dyes to evaluate their potential for biodegradation. In this study, four commercial dyes, namely acid orange 7, cresol red, methylene blue, and malachite green, were selected as potential targets for degradation by azoreductases (AzrBmH21, AzrBmH22/3, and AzrBmH24/5) derived from Bacillus megaterium H2. The prediction of ligand binding or catalytic sites for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 was performed using a machine learning algorithm based on the Prank Web and DeepSite chemoinformatic tool. The 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. 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. Each complex was stabilized by a minimum of 0–5 hydrogen bonds. MD simulations revealed stable AzrBmH2-dye complexes (with RMSD 0.15–0.42 nm, RMSF 0.05–0.48 nm, Rg 1.75–1.88 nm). MMPBSA 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). The AzrBmH2-malachite green complex showed a prevalence of hydrophobic interactions (-268.25 ± 12.25 to -418.92 ± 29.45 kcal/mol) through van der Waals forces. This study highlights the potential role of enzymes, specifically azoreductases from Bacillus megaterium H2, in predicting the decolorization of commercial dyes. These findings contribute to our understanding of enzyme mechanisms in bioremediation and for biotechnological applications.

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Section: Mm-pbsa Binding Free Energy Calculationsupporting

confidence: 90%

Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes

Oyewusi,

Wahab,

Akinyede

et al. 2023

Preprint

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“…There have been several suggested RB5 breakdown pathways using different fungi, predominantly using liquid culture to assess the potential of using fungi as bioremediation agents for dye-contaminated water. None of the breakdown products suggested for pathways in Aspergillus 28 or the basidiomycetous wood decay specialist Trametes 18 were identified in the samples in this study. Somewhat surprisingly, the RB5 breakdown metabolites identified by 24 using the ascomycete Trichoderma atroviride did provide a match (Table S1 ).…”

Section: Discussioncontrasting

confidence: 56%

“…Laccases and peroxidases have previously been suggested as important candidates for breakdown of the RB5 dye 17 , 18 . While all species had very similar numbers of laccases (all in the range 11–15), the peroxidase complement showed greater variance between species with A. bisporus having almost double the number of peroxidases of P. ostreatus .…”

Section: Resultsmentioning

confidence: 99%

Successful cultivation of edible fungi on textile waste offers a new avenue for bioremediation and potential food production

Hazelgrove,

Moody

2024

Sci Rep

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Textile waste contains both natural fibres such as cotton and bamboo viscose, and synthetic fibres such as elastane and polyester. As a complex mixture, textiles present a challenging pollution issue as breakdown in landfill results in microplastics entering water and soil environments, and incineration results in particulate air pollution. Here the use of edible fungi as bioremediation agents of waste textiles is described for the first time. Three species of filamentous fungi were shown to colonise and grow on mixed fibre textile waste (underpants made from 28% cotton: 68% bamboo viscose: 4% elastane). All three fungi were able to metabolise the common textile dye Reactive Black 5 to some extent. The metabolome was captured to elucidate the dye remediation pathway utilized and to characterise the volatiles released during bioremediation with a view to assessing the safety profile of this process for future industrial applications. The results suggest that edible fungi may be cultivated on textiles, and that some interesting and useful compounds may be produced in the process. This has great biotechnological potential. No mushrooms were produced in this study, suggesting that further work will be needed to optimise conditions for crop production from waste textiles.

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“…Several molecular docking simulations have been conducted to evaluate the activity of various enzymes that potentially degrade the various polymers, including polyethylene, aromatic hydrocarbons, polyesters, and dyes [ [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , 32 , 33 ]. In these works, laccase is the predominant enzyme used to degrade polymers and dyes due to its oxidoreductive mechanisms.…”

Section: Resultsmentioning

confidence: 99%

“…In particular, Trametes versicolor fungi produce an enzyme, called laccase, that predominantly degrades phenolic compounds like lignin [ 22 ]. This particular enzyme has been applied successfully for various materials including aromatic polymers and dyes [ [23] , [24] , [25] , [26] , [27] , [28] ] as the authors reported that the active laccase enzyme in the Trametes versicolor is capable of degrading these materials efficiently. This enzyme contains active sites, containing four copper ions where the substrate (e.g., polymers) binds and where the enzyme-catalyzed chemical reactions, especially oxidoreductive, occur during the degradation process.…”

Section: Introductionmentioning

confidence: 99%

Fungal enzyme degradation of lignin-PLA composites: Insights from experiments and molecular docking simulations

Esakkimuthu,

Ponnuchamy,

Mikuljan

et al. 2024

Heliyon

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Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment

Cited by 35 publications

References 70 publications

Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes

Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes

Successful cultivation of edible fungi on textile waste offers a new avenue for bioremediation and potential food production

Fungal enzyme degradation of lignin-PLA composites: Insights from experiments and molecular docking simulations

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