Molecular docking and molecular dynamics simulation approaches for evaluation of laccase-mediated biodegradation of various industrial dyes

References

• Adams, M. A., Luo, Y., Hove-Jensen, B., He, S. M., van Staalduinen, L. M., Zechel, D. L., & Jia, Z. (2008). Crystal structure of PhnH: An essential component of carbon-phosphorus lyase in Escherichia coli. Journal of Bacteriology, 190(3), 1072–1083. https://doi.org/10.1128/JB.01274-07
   PubMed Web of Science ®Google Scholar
• Ahlawat, S., Singh, D., Virdi, J. S., & Sharma, K. K. (2019). Molecular modeling and MD-simulation studies: Fast and reliable tool to study the role of low-redox bacterial laccases in the decolorization of various commercial dyes. Environmental Pollution (Barking, Essex: 1987), 253, 1056–1065. https://doi.org/10.1016/j.envpol.2019.07.083
   PubMed Web of Science ®Google Scholar
• Albahnasawi, A., Yüksel, E., Gürbulak, E., & Duyum, F. (2020). Fate of aromatic amines through decolorization of real textile wastewater under anoxic-aerobic membrane bioreactor. Journal of Environmental Chemical Engineering, 8(5), 104226. https://doi.org/10.1016/j.jece.2020.104226
   Web of Science ®Google Scholar
• Benkhaya, S., M' Rabet, S., & El Harfi, A. (2020a). A review on classifications, recent synthesis and applications of textile dyes. Inorganic Chemistry Communications, 115, 107891. https://doi.org/10.1016/j.inoche.2020.107891
   Web of Science ®Google Scholar
• Bhatia, S. C., & Devraj, S. (2017). Pollution control in textile industry. WPI Publishing.
   Google Scholar
• Bhatt, P., Joshi, T., Bhatt, K., Zhang, W., Huang, Y., & Chen, S. (2021). Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies. Journal of Hazardous Materials, 409, 124927. https://doi.org/10.1016/j.jhazmat.2020.124927
   PubMed Web of Science ®Google Scholar
• Bhatt, K., & Maheshwari, D. K. (2020). Insights into zinc-sensing metalloregulator ‘Zur’ deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking. Journal of Biomolecular Structure and Dynamics, 1–16.
   Web of Science ®Google Scholar
• Chandra Pandey, S., Dhami, D. S., Jha, A., Chandra Shah, G., Kumar, A., & Samant, M. (2019). Identification of trans-2-cis-8-Matricaria-ester from the essential oil of Erigeron multiradiatus and evaluation of its antileishmanial potential by in vitro and in silico approaches. ACS Omega, 4(11), 14640–14649. https://doi.org/10.1021/acsomega.9b02130
   PubMed Web of Science ®Google Scholar
• Chen, M., Zeng, G., Lai, C., Zhang, C., Xu, P., Yan, M., & Xiong, W. (2017). Interactions of carbon nanotubes and/or graphene with manganese peroxidase during biodegradation of endocrine disruptors and triclosan. Chemosphere, 184, 127–136. https://doi.org/10.1016/j.chemosphere.2017.05.162
   PubMed Web of Science ®Google Scholar
• Chivukula, M., & Renganathan, V. (1995). Phenolic azo dye oxidation by laccase from Pyricularia oryzae. Applied and Environmental Microbiology, 61(12), 4374–4377. https://doi.org/10.1128/aem.61.12.4374-4377.1995
   PubMed Web of Science ®Google Scholar
• Gupta, V. K. (2019). Fundamentals of natural dyes and its application on textile substrates. In Chemistry and technology of natural and synthetic dyes and pigments. IntechOpen.
   Google Scholar
• Gürses, A., Açıkyıldız, M., Güneş, K., & &Gürses, M. S. (2016). Classification of dye and pigments. In Dyes and pigments (pp. 31–45). Springer.
   Google Scholar
• IARC (1972). Monographs on the evaluation of the carcinogenic risk of chemicals to humans (pp. V4 62). Geneva: World Health Organization, International Agency for Research on Cancer, (http://monographs.iarc.fr/ENG/Classification/index.php),
   Google Scholar
• Jia, B., Jia, X., Kim, K. H., Pu, Z. J., Kang, M. S., & Jeon, C. O. (2017). Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway. Scientific Reports, 7(1), 1–13.
   PubMedGoogle Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Joshi, T., Joshi, T., Sharma, P., Chandra, S., & Pande, V. (2020). Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonasoryzaepv. Oryzae by targeting peptide deformylase. Journal of Biomolecular Structure and Dynamics, 39(3), 1–18.
   Web of Science ®Google Scholar
• Karigar, C. S., & Rao, S. S. (2011). Role of microbial enzymes in the bioremediation of pollutants: A review. Enzyme Research, 2011, 805187. https://doi.org/10.4061/2011/805187
   PubMedGoogle Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. https://doi.org/10.1038/nsb0902-646
   PubMedGoogle Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations . Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Ledakowicz, S., & Paździor, K. (2021). Recent Achievements in Dyes Removal Focused on Advanced Oxidation Processes Integrated with Biological Methods. Molecules (Basel, Switzerland), 26(4), 870. https://doi.org/10.3390/molecules26040870
   PubMed Web of Science ®Google Scholar
• Lellis, B., Fávaro-Polonio, C. Z., Pamphile, J. A., & Polonio, J. C. (2019). Effects of textile dyes on health and the environment and bioremediation potential of living organisms. Biotechnology Research and Innovation, 3(2), 275–290. https://doi.org/10.1016/j.biori.2019.09.001
   Google Scholar
• Li, X., & Zheng, Y. (2017). Lignin-enzyme interaction: Mechanism, mitigation approach, modeling, and research prospects. Biotechnology Advances, 35(4), 466–489. https://doi.org/10.1016/j.biotechadv.2017.03.010
   PubMed Web of Science ®Google Scholar
• Liu, Y., Liu, Z., Zeng, G., Chen, M., Jiang, Y., Shao, B., Li, Z., & Liu, Y. (2018). Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies. Journal of Hazardous Materials, 357, 10–18. https://doi.org/10.1016/j.jhazmat.2018.05.042
   PubMed Web of Science ®Google Scholar
• Maguire, J. B., Boyken, S. E., Baker, D., & Kuhlman, B. (2018). Rapid sampling of hydrogen bond networks for computational protein design. Journal of Chemical Theory and Computation, 14(5), 2751–2760. https://doi.org/10.1021/acs.jctc.8b00033
   PubMed Web of Science ®Google Scholar
• Mathews, S. L., Smithson, C. E., & Grunden, A. M. (2016). Purification and characterization of a recombinant laccase‐like multi‐copper oxidase from Paenibacillus glucanolyticus SLM 1. Journal of Applied Microbiology, 121(5), 1335–1345. https://doi.org/10.1111/jam.13241
   PubMed Web of Science ®Google Scholar
• Møller, P., & Wallin, H. (2000). Genotoxic hazards of azo pigments and other colorants related to 1-phenylazo-2-hydroxynaphthalene. Mutation Research/Reviews in Mutation Research, 462(1), 13–30. https://doi.org/10.1016/S1383-5742(99)00090-3
   PubMed Web of Science ®Google Scholar
• Muslem, W. H., Edbeib, M. F., Aksoy, H. M., Kaya, Y., Hamid, A. A. A., Hood, M. H. M., Wahab, R. A., & Huyop, F. (2020). Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis. Journal of Biomolecular Structure & Dynamics, 38(11), 3432–3441. https://doi.org/10.1080/07391102.2019.1655482
   PubMed Web of Science ®Google Scholar
• National Toxicology Program (1992). Toxicology and carcinogenesis studies of CI pigment Red 23 (CAS No. 6471-49-4) in F344 rats and B6C3F1 mice (feed studies). National Toxicology Program Technical Report Series, 411, 1–283.
   PubMedGoogle Scholar
• Ogola, H. J. O., Ashida, H., Ishikawa, T., & Sawa, Y. (2015). Explorations and applications of enzyme-linked bioremediation of synthetic dyes. Advances in Bioremediation of Wastewater and Polluted Soil, 111–144.
   Google Scholar
• Pande, V., Pandey, S. C., Joshi, T., Sati, D., Gangola, S., Kumar, S., & Samant, M. (2019). Biodegradation of toxic dyes: A comparative study of enzyme action in a microbial system. In Smart Bioremediation Technologies (pp. 255–287). Academic Press.
   Google Scholar
• Pande, V., Pandey, S. C., Sati, D., Pande, V., & Samant, M. (2020). Bioremediation: An emerging effective approach towards environment restoration. Environmental Sustainability, 3(1), 91–103. https://doi.org/10.1007/s42398-020-00099-w
   Google Scholar
• Pandey, S. C., Jha, A., Kumar, A., & Samant, M. (2019). Evaluation of antileishmanial potential of computationally screened compounds targeting DEAD-box RNA helicase of Leishmaniadonovani. International Journal of Biological Macromolecules, 121, 480–487. https://doi.org/10.1016/j.ijbiomac.2018.10.053
   PubMed Web of Science ®Google Scholar
• Paramo, T., East, A., Garzón, D., Ulmschneider, M. B., & Bond, P. J. (2014). Efficient characterization of protein cavities within molecular simulation trajectories: Trj_cavity. Journal of Chemical Theory and Computation, 10(5), 2151–2164. https://doi.org/10.1021/ct401098b
   PubMed Web of Science ®Google Scholar
• Pramanik, S., & Chaudhuri, S. (2018). Laccase activity and azo dye decolorization potential of Podoscypha elegans. Mycobiology, 46(1), 79–83. https://doi.org/10.1080/12298093.2018.1454006
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Sargsyan, K., Grauffel, C., & Lim, C. (2017). How molecular size impacts RMSD applications in molecular dynamics simulations. Journal of Chemical Theory and Computation, 13(4), 1518–1524. https://doi.org/10.1021/acs.jctc.7b00028
   PubMed Web of Science ®Google Scholar
• Sarkar, S., Banerjee, A., Halder, U., Biswas, R., & Bandopadhyay, R. (2017). Degradation of synthetic azo dyes of textile industry: A sustainable approach using microbial enzymes. Water Conservation Science and Engineering, 2(4), 121–131. https://doi.org/10.1007/s41101-017-0031-5
   Google Scholar
• Singh, D., Sharma, K. K., Jacob, S., & Gakhar, S. K. (2014). Molecular docking of laccase protein from Bacillus safensis DSKK5 isolated from earthworm gut: A novel method to study dye decolorization potential. Water, Air, & Soil Pollution, 225(11), 1–12.
   Web of Science ®Google Scholar
• Sridhar, S., Chinnathambi, V., Arumugam, P., & Suresh, P. K. (2013). In Silico and in Vitro Physicochemical Screening of Rigidoporus sp. Crude Laccase-assisted Decolorization of Synthetic dyes-approaches for a cost-effective enzyme-based remediation methodology . Applied Biochemistry and Biotechnology, 169(3), 911–922. https://doi.org/10.1007/s12010-012-0041-x
   PubMed Web of Science ®Google Scholar
• Srinivasan, S., Sadasivam, S. K., Gunalan, S., Shanmugam, G., & Kothandan, G. (2019). Application of docking and active site analysis for enzyme linked biodegradation of textile dyes. Environmental Pollution (Barking, Essex : 1987), 248, 599–608. https://doi.org/10.1016/j.envpol.2019.02.080
   PubMed Web of Science ®Google Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDockVina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461.
   PubMed Web of Science ®Google Scholar
• Vikrant, K., Giri, B. S., Raza, N., Roy, K., Kim, K. H., Rai, B. N., & Singh, R. S. (2018). Recent advancements in bioremediation of dye: Current status and challenges. Bioresource Technology, 253, 355–367. https://doi.org/10.1016/j.biortech.2018.01.029
   PubMed Web of Science ®Google Scholar
• Zhao, J., Wu, Q. X., Cheng, X. D., Su, T., Wang, X. H., Zhang, W. N., Lu, Y. M., & Chen, Y. (2021). Biodegradation and detoxification of the triphenylmethane dye coomassie brilliant blue by the extracellular enzymes from mycelia of Lactarius deliciosus. Frontiers of Chemical Science and Engineering, 15(2), 421–436. https://doi.org/10.1007/s11705-020-1952-7
   Web of Science ®Google Scholar