Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos

Abstract

The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (−3.3 − 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 − 0.25 nm) and DehH2-haloacetates (RMSF 0.05 − 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 − 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (−24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (−22.78 kcal/mol), DehH2-D-2CP (−21.82 kcal/mol), DehH2-3CP (−21.11 kcal/mol), DehH2-2,2-DCP (−18.34 kcal/mol), DehH2-2,3-DCP (−8.34 kcal/mol), DehH2-TCA (−7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.

Communicated by Ramaswamy H. Sarma

Keywords:

• Bacillus thuringiensis
• chlorpyrifos
• dehalogenase
• haloacids
• haloacetates
• molecular docking
• MD simulations
• MM-PBSA

Acknowledgements

The authors would like to express their gratitude to the Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia for their facilities. In addition, the HAO would like to thank the Ministry of Education through Tertiary Education Trust Fund (TETFund) Nigeria for studentship.

Disclosure statement

There are no conflicts to declare.

Additional information

Funding

This work was funded by the Fundamental Research Grant Scheme (FRGS)-Ministry of Higher Education Malaysia R.J130000.7854.5F189 and RUG-UTMHR Q.J130000.2414.08G59 for financial assistance.