In-silico investigation of the efficiency of microbial dioxygenases in degradation of sulfonylurea group herbicides

Abstract

Sulfonylurea herbicides are widely used to control weeds due to their broad-spectrum activity and low animal toxicity. However, they have negative effects on environment. Microbial dioxygenases are known to degrade aromatic compounds. In this study, three types of dioxygenases (catechol-2,3-dioxygenases, iron dependent homoprotocatechuate 2,3-dioxygenase and manganese dependent homoprotocatechuate 2,3-dioxygenase) were chosen to study molecular interaction with chlorsulfuron and metsulfuron-methyl, respectively. Flexible protein-ligand molecular docking studies were conducted to investigate the efficiencies of these microbial enzymes in degrading the herbicidal residues. Our results indicate homoprotocatechuate 2,3-dioxygenases had more binding affinity than catechol-2,3-dioxygenases, and thus could be claimed to have good efficiency in bioremediation. Further analysis indicated that the higher binding affinity was contributed by the aliphatic residues present at the interacting sites within the glyoxalase domain and its close proximity. Our results provide an important framework for conducting further studies regarding the characterization and analysis of other enzymes involved in the degradation of herbicidal active ingredients. Our study can be considered as a reliable basis for identification and application of microbial enzymes for successful bioremediation of herbicide compounds. This will be very helpful as the number of such toxic compounds continue to increase in the environment.

Keywords:

• Catechol-2,3-dioxygenases
• herbicide
• homoprotocatechuate 2,3-dioxygenases
• microbial degradation
• molecular docking
• sulfonylurea

Acknowledgements

S.B. acknowledges Vidyasagar University, Midnapore, for its necessary supports. S.K.M. and R.D. acknowledges The University of Burdwan for necessary infrastructural support. M.K.S. acknowledges Czech University of Life Sciences Prague, for its necessary supports. The authors acknowledge Dr. Theresa Ann Reinhardt Piskáčková for English proofreading and revisions.

Disclosure statement

No fund has been received for this work by any of the author. The authors declare that they have no competing interests. Also, this study does not involve any data collected from live or dead humans or animals and does not involve any human participants and reports health related outcomes.