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Binding mode of aryloxyphenoxypropionate (FOP) and cyclohexanedione (DIM) groups of herbicides at the carboxyl transferase (CT) domain of Acetyl-CoA carboxylase of Phalaris minor

  • Priyanka Rani
  • Juli Kumari
  • Shikha Agarwal
  • Durg Vijay SinghEmail author
Original Article
  • 60 Downloads

Abstract

Phalaris minor (P. minor) is a major weed of wheat crop. It has developed resistance as well as cross-resistance against aryloxyphenoxypropionates (FOP) and cyclohexanediones (DIM) group of herbicides, probably due to mutations in the binding site of acetyl-CoA carboxylase (ACCase) at its carboxyl transferase domain (CT-domain). Binding of FOP and DIM group of herbicides inhibits de novo synthesis of fatty acids, which is essential for survival of P. minor. This work highlights atomistic details of binding mode of diclofop (FOP) and tepraloxydim (DIM) groups of herbicides in the CT-domain of modelled P. minor ACCase protein. Molecules have been extracted from ZINC database based upon their 2D structural similarities with existing FOP and DIM groups of herbicides, which has been further screened at FOP- and DIM-binding sites of the modelled protein. Rigid and flexible docking has been performed to prioritise hits considering the diclofop and tepraloxydim as a reference. Finally, two molecules of the FOP group and three molecules of DIM group have been obtained that have shown better predicted binding affinity, ligand efficiency, and inhibition constant as compared to the reference molecules. Molecular dynamics simulation of about 10 ns was performed for both the reference molecules as well as for all the five prioritised molecules to determine their conformational stability and prominent H-bond network. Amino acid residues A56 and I160 of D1 protein are equivalent to A1705 and I1181 amino acids of black grass, as well as A1627 and I1735 amino acids of yeast (PDB ID: 1UYR) forms invariant hydrogen bond with reference and screened molecules. It was concluded that common binding features of FOP and DIM may be utilised for development of bitopic herbicide.

Keywords

P. minor Herbicide resistance ACCase CT-domain Modelling Docking MD simulation 

Notes

Acknowledgements

The author Durg Vijay Singh is thankful to the Department of Science and Technology, India (File No.NASI/SoRF-I/2014-15/19) and Science and Engineering Research Board, India (File No. YSS/2015/001662), for financial assistance.

Compliance with ethical standards

Conflict of interest

The computational work has been carried out by Miss. Juli Kumari and Dr. Durg Vijay Singh. Manuscript was structured and prepared by the Juli Kumari, Priyanka Rani, Dr. Shikha Agarwal, and Dr. Durg Vijay Singh. The hypothesis was conceived and supervised by Dr. Durg Vijay Singh. The authors Priyanka Rani and Juli Kumari have equally contributed and should be considered individually as well as jointly as the first author.

Supplementary material

13721_2019_190_MOESM1_ESM.docx (495 kb)
Supplementary material 1 (DOCX 495 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Molecular Modelling and Computer Aided Drug Discovery Laboratory, Department of Bioinformatics, School of Earth, Biological and Environmental SciencesCentral University of South BiharGayaIndia
  2. 2.Department of Computer ScienceCentral University of South BiharGayaIndia

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