Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach

Abstract

Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of −4.1, −3.2, and −3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of −27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.

Communicated by Ramaswamy H. Sarma

Keywords:

• Biomineralization
• urease inhibition
• molecular docking studies
• coastal pollutants
• molecular dynamics simulation
• binding energy analysis

Acknowledgements

AGS is grateful to SASTRA Deemed to be University for the Ph.D. fellowship. NVK is grateful to UGC for start-up research grants (30–561/2021(BSR)).

Author contributions

All authors contributed to the manuscript writing. The manuscript draft was prepared by Aparna Ganapathy Vilasam Sreekala. Vinod Kumar Nathan and Krishna Kant Gupta contributed to the editing of the manuscript. All authors read and approved the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This was funded by UGC, India through start-up research grants [30–561/2021(BSR)].