Investigating of the binding energy of DEP-A and DEP-B enzymes with DON mycotoxin chemotype by molecular docking

Document Type : Full Research Paper

Authors

1 Ferdowsi University of Mashhad

2 Animal science, agriculture, ferdowsi university of mashhad

3 Medicinal Plants and Drugs Research Institute, Shahid Beheshti University

Abstract

15acetyl-deoxynivalenol (15ADON) is the most common chemotype of dioxynivalenol (DON) mycotoxin, which cannot be controlled by common methods such as absorbents. Hence, enzyme-based methods are suggested for detoxification of these types of mycotoxins, which requires bioinformatics studies before laboratory investigations. Therefore, the aim of the present study was to investigate the binding energy of DEP-A and DEP-B enzymes with 15ADON through molecular docking. The three-dimensional structures of DEP-A and DEP-B proteins were predicted using the SWISS MODEL server. Then, the stability of these structures was evaluated in molecular dynamic conditions. For this purpose, the simulation was carried out with GROMACS software and then the RMSD curve of these two enzymes was drawn to check the stability of the predicted structure. H-DOCK online server was used to performed the interaction of DEP-A enzyme with 15ADON and DEP-B with Oxid15ADON intermediate. Checking the accuracy of the predicted structures by ERRAT Verify3D, Z-score and Ramachandran plots showed that the prediction of tertiary structures successfully performed. The RMSD curves showed that DEP-A and DEP-B were stabilized in 240 and 40 nanoseconds with 0.58 and 0.35 nm, respectively. The results of molecular docking also showed that both DEP-A and DEP-B enzymes could bind to their substrates with relatively strong binding energy -157.90 and -141.78, respectively. Overall, it can be concluded that both studied enzymes were able to bind to the 15ADON chemotype of DON in the appropriate position, which shows that these enzymes can be effective in deactivating this chemotype, although laboratory studies are needed to confirm the results

Keywords

Main Subjects

References

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Veterinary Research & Biological Products
Volume 37, Issue 1
March 2024
Pages 15-26

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History

  • Receive Date: 18 April 2023
  • Revise Date: 25 June 2023
  • Accept Date: 27 June 2023

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