Resistance determination of the ACCase-inhibiting herbicide of clodinafop propargyl in Avena ludoviciana (Durieu), and study of their interaction using molecular docking and simulation

Abstract

Structural mutations providing herbicide resistance may cause a modification of the three dimensional structure of a protein which will lead to a decrease in the herbicide efficacy. Wild oat (Avena ludoviciana Durieu.) is an increasingly disruptive weed in areas of intensive cereal production, thus the aim of this research was to identify mutations conferring resistance to ACCase-inhibitor herbicides at greenhouse, laboratory and in silico scales. Among the selected biotypes, No. 3 in the position 1781 (Ile1781-Leu) and No. 14 in the position 2041 (Ile2041-Asn), showed resistance to ACCase-inhibitor. The above mutations were confirmed using the specific primers and PCR-based methods. Analysis of molecular docking indicated that residues of Trp1948 and Pro2001 are important in the binding site and showed remarkable variation in the mutation types. Using molecular dynamic simulation analysis, we demonstrated that mutation types changed the conformation of the enzyme. These changes resulted in compressed conformation in the active site, which limited the availability of binding herbicide-enzyme. In present, no crystallography molecular structure and modeling reported on the ACCase of plants and this study investigated interactions of clodinafop propargyl and ACCase CT domain in A. ludoviciana by modeling, docking and simulations for the first time. Totally, bioinformatics analysis as well as PCR-based method confirmed that herbicide resistance conferred by nucleotide mutations in the gene sequence.

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Correspondence to Ahmad Ismaili.

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Akbarabadi, A., Ismaili, A., Kahrizi, D. et al. Resistance determination of the ACCase-inhibiting herbicide of clodinafop propargyl in Avena ludoviciana (Durieu), and study of their interaction using molecular docking and simulation. Mol Biol Rep 46, 415–424 (2019). https://doi.org/10.1007/s11033-018-4489-9

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Keywords

  • Weed
  • Herbicide resistance
  • Point mutation
  • In silico
  • Binding energy
  • Modeling