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Molecular modeling and computational simulation of the photosystem-II reaction center to address isoproturon resistance in Phalaris minor


Isoproturon is the only herbicide that can control Phalaris minor, a competitive weed of wheat that developed resistance in 1992. Resistance against isoproturon was reported to be due to a mutation in the psbA gene that encodes the isoproturon-binding D1 protein. Previously in our laboratory, a triazole derivative of isoproturon (TDI) was synthesized and found to be active against both susceptible and resistant biotypes at 0.5 kg/ha but has shown poor specificity. In the present study, both susceptible D1(S), resistant D1(R) and D2 proteins of the PS-II reaction center of P. minor have been modeled and simulated, selecting the crystal structure of PS-II from Thermosynechococcus elongatus (2AXT.pdb) as template. Loop regions were refined, and the complete reaction center D1/D2 was simulated with GROMACS in lipid (1-palmitoyl-2-oleoylglycero-3-phosphoglycerol, POPG) environment along with ligands and cofactor. Both S and R models were energy minimized using steepest decent equilibrated with isotropic pressure coupling and temperature coupling using a Berendsen protocol, and subjected to 1,000 ps of MD simulation. As a result of MD simulation, the best model obtained in lipid environment had five chlorophylls, two plastoquinones, two phenophytins and a bicarbonate ion along with cofactor Fe and oxygen evolving center (OEC). The triazole derivative of isoproturon was used as lead molecule for docking. The best worked out conformation of TDI was chosen for receptor-based de novo ligand design. In silico designed molecules were screened and, as a result, only those molecules that show higher docking and binding energies in comparison to isoproturon and its triazole derivative were proposed for synthesis in order to get more potent, non-resistant and more selective TDI analogs.

Pharmacophore of modeled and MD simulated (D1/D2) PS-II reaction center of Phalaris minor has been simulated for de novo synthesis of a TDI (triazole derivative of isoproturon)-based molecule. De novo synthesized molecules were redocked and reranked as more potent and selective herbicides for P. minor. The figure shows the modeled and MD simulated structure of the PS-II reaction center (D1(R)/D2) of P. minor (left), and the docked conformation of TDI in the binding cavity of D1(R) protein (right)

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Molecular dynamics simulation




Photosystem second reaction center


Trizole derivative of isoproturon


Resistant D1 protein


Susceptible D1 protein




Isotropic pressure coupling


Oxygen evolving center


Plastoquinone B


Coding sequence


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Correspondence to Krishna Misra.

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Singh, D.V., Agarwal, S., Kesharwani, R.K. et al. Molecular modeling and computational simulation of the photosystem-II reaction center to address isoproturon resistance in Phalaris minor . J Mol Model 18, 3903–3913 (2012).

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  • Phalaris minor
  • Isoproturon
  • D1/D2 PS-II reaction center
  • MD simulation
  • Pharmacophore
  • Docking
  • De novo ligand designing