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

Abstract

Dyes are being increasingly utilized across the globe, but there is no appropriate method of bioremediation for their full mineralization from the environment. Laccases are key enzymes that help microbes to degrade dyes as well as their intermediate metabolites. Various dyes have been reported to be degraded by bacteria, but it is still unclear how these enzymes function during dye degradation. To effectively eradicate toxic dyes from the system, it is essential to understand the molecular function of enzymes. As a result, the interaction of laccase with different toxic dyes was investigated using molecular docking. Based on the highest binding energy we have screened ten dyes with positive interaction with laccase. Evaluating the MD simulation results, three out of ten dyes were more stable as potential targets for degradation by laccase of Bacillus subtilis. As a result, subsequent research focused solely on the results of three substrates: pigment red, fuchsin base, and Sudan IV. Analysis of MD simulation revealed that pigments red 23, fuchsin base, and Sudan IV form hydrogen and hydrophobic bond as well as Vander Waals interactions with the active site of laccase to keep it stable in aqueous solution. The conformation of laccase is greatly altered by the inclusion of all three substrates in the active site. The MD simulation findings show that laccase complexes remain stable throughout the catalytic reaction. Therefore, this research provides a molecular understanding of laccase expression and its role in the bioremediation of the pigments red 23, fuchsin base, and Sudan IV.

Communicated by Ramaswamy H. Sarma

Keywords:

• Laccase
• molecular docking
• molecular dynamic simulation
• pigment red23
• fuchsin base
• and Sudan IV

Author contributions

Veni Pande conceived, designed, performed the experiments, and prepared the original draft. Tushar Joshi and Satish Chandra Pandey performed the experiments, analyzed the data, and wrote the manuscript. Diksha Sati and Shalini Mathpal helped in writing, reviewing, and editing the manuscript. Mukesh Samant, Subhash Chandra and, Veena Pande supervised, helped in data analysis and writing, reviewing and editing the manuscript.

Disclosure statement

The authors have declared no conflict of interest.

Additional information

Funding

Authors are thankful to the Department of Zoology, Department of Botany, Kumaun University SSJ Campus, Almora (Uttarakhand) India and DST FIST grant SR/FST/LS-I/2018/131 for providing the facility for this work.