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A Study on the Molecular Mechanisms of Herbicide Binding with Target Proteins in Weeds Using In Silico Methods

  • PLANT BREEDING, PLANT PROTECTION, AND BIOTECHNOLOGY
  • Published:
Russian Agricultural Sciences Aims and scope

Abstract

The research was carried out in order to study the molecular mechanisms of herbicide binding (pinoxaden, quizalofop-P-tefuril, prometrin, metribuzin, metsulfuron-methyl) with target proteins (acetyl-CoA-carboxylase, acetolactate synthase, cytochrome P450, 4-hydroxyphenylpyruvate dioxygenase) of weeds growing in Siberia: common wild oat (Avena fatua L.), couch grass (Elymus repens (L.) Gould), red-root amaranthus (Amaranthus retroflexus L.), white gauze (Chenopodium album L.), and green foxtail (Setaria viridis (L) P Beauv). The study was carried out in Novosibirsk oblast in 2022–2023. Using the bioinformatic methods, virtual three-dimensional complexes of pesticides and their targets have been created. A new approach to identifying the parameters of the cavity of binding sites is proposed, which consists in combining the alignment method and the machine-learning technology. Docking of pesticides with targets has been carried out. Calculation of the binding energy indicates a high degree of stability of the ligand-protein complexes. The proposed in silico approach may be useful for elucidating the behavior of herbicides when bound to weed enzymes. This approach allows a deeper understanding of the mechanism of action and ecotoxicological aspects of pesticide use. The complexes of herbicides and proteins involved have a potential high stability due to the low energy of binding to receptors, which varies from –5.60 to –13.24 kcal/mol. The value of the binding energy has not shown a direct dependence on the number of amino acid residues of the ligand-binding site. In general, the study has complemented some aspects of the molecular mechanisms of herbicide binding to weed target proteins; however, more in-depth study is required in order to localize critical amino acid points involved in the biological functions of target proteins.

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Funding

This study was carried out in accordance with grant no. 220-2961-3099 within the framework of Decree of the Government of Russia no. 220.

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Authors and Affiliations

  1. Siberian Federal Scientific Centre of Agro-BioTechnologies, 630501, Krasnoobsk, Novosibirsk oblast, Russia

    I. E. Pamirsky & K. S. Golokhvast

  2. All-Russia Research Institute of Soybean, 675027, Blagoveshchensk, Russia

    P. D. Timkin

  3. Amur State Medical Academy, 675009, Blagoveshchensk, Russia

    E. A. Timofeev, D. D. Kotelnikov & E. A. Borodin

  4. Gomel State Medical University, 246000, Gomel, Belarus

    L. N. Alekseiko & S. V. Klimovich

Authors
  1. I. E. Pamirsky
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  2. P. D. Timkin
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  3. E. A. Timofeev
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  4. D. D. Kotelnikov
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  5. L. N. Alekseiko
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  6. S. V. Klimovich
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  7. E. A. Borodin
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  8. K. S. Golokhvast
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Corresponding author

Correspondence to I. E. Pamirsky.

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In carrying out this work, all ethical standards were observed.

CONFLICT OF INTEREST

The authors declare that they have no conflicts of interest.

This article does not contain any studies involving humans and animals as objects.

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Translared by A. Ostyak

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Pamirsky, I.E., Timkin, P.D., Timofeev, E.A. et al. A Study on the Molecular Mechanisms of Herbicide Binding with Target Proteins in Weeds Using In Silico Methods. Russ. Agricult. Sci. 49, 374–384 (2023). https://doi.org/10.3103/S1068367423040110

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  • DOI: https://doi.org/10.3103/S1068367423040110

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