Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos
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-Poiss...
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my.utm.1029102023-09-26T06:23:09Z http://eprints.utm.my/id/eprint/102910/ Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos Oyewusi, Habeebat Adekilekun Huyop, Fahrul Abdul Wahab, Roswanira Q Science (General) 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. Taylor and Francis Ltd. 2022 Article PeerReviewed Oyewusi, Habeebat Adekilekun and Huyop, Fahrul and Abdul Wahab, Roswanira (2022) Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. Journal of Biomolecular Structure and Dynamics, 40 (5). pp. 1979-1994. ISSN 0739-1102 http://dx.doi.org/10.1080/07391102.2020.1835727 DOI: 10.1080/07391102.2020.1835727 |
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Q Science (General) Oyewusi, Habeebat Adekilekun Huyop, Fahrul Abdul Wahab, Roswanira Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
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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. |
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Oyewusi, Habeebat Adekilekun Huyop, Fahrul Abdul Wahab, Roswanira |
author_facet |
Oyewusi, Habeebat Adekilekun Huyop, Fahrul Abdul Wahab, Roswanira |
author_sort |
Oyewusi, Habeebat Adekilekun |
title |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
title_short |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
title_full |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
title_fullStr |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
title_full_unstemmed |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
title_sort |
molecular docking and molecular dynamics simulation of bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos |
publisher |
Taylor and Francis Ltd. |
publishDate |
2022 |
url |
http://eprints.utm.my/id/eprint/102910/ http://dx.doi.org/10.1080/07391102.2020.1835727 |
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