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In Silico Design and Development of Herbicides

against Phalarsis minor to resign Sensitivity

Thesis July 2014

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3 authors, including:

Nandan Kumar Durg Vijay Singh

Indian Institute of Chemical Technology Central University of Bihar Patna-800014
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 Abstract:

Phalaris minor (P. minor) is a major weed of wheat crop which has evolved resistance against
herbicides. Isoproturon is the most accepted herbicide developed resistance in 1992. Later,
introduced herbicides also developed resistance and cross resistance to their respective
binding sites. Isoproturon binds at the QB binding site of the D1 protein of photosystem-II
(PS-II) which blocks the electron transport pathway to photosynthesis. In this work, a series
of computational approaches have been implemented to discover herbicides against the D1
protein of P. minor. The methods implemented are comparative modelling, virtual screening,
de-novo drug designing and molecular docking. Through docking study, twenty four lead
molecules are reported which have shown a higher binding affinity and inhibition constant
compare to reference ligand (ref_lig) triazine. The conformational stability of docked
complexes was evaluated by molecular dynamics (MD) simulation and MM/PBSA method.
Ala225, Ser226, Phe227 and Asn229 present in the binding site of protein play an important
role in the stability of the protein-lead complex via hydrogen bond interaction and pi-pi
interaction. Moreover, interactions and binding free energy between protein-lead complexes
have been calculated using g_energy and MM/PBSA method. It has revealed that binding
was energetically favourable and driven by the electrostatic interactions. Among 24 leads,
results have uncovered eight promising compounds as potential herbicides which have shown
comparable ADME, better docking scores, system stability, H-bond occupancy and binding
free energy than ref_lig (triazine; complex with PD:3PRQ).

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