Structural prediction of glutathione S-transferase (GST) in Lymantria dispar and its molecular docking analysis with poplar secondary metabolites

XIE Jiaming, CAO Chuanwang, SUN Lili, LI Mingjun, ZHANG Ruiqiong

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (5) : 211-220.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (5) : 211-220. DOI: 10.12302/j.issn.1000-2006.202212012

Structural prediction of glutathione S-transferase (GST) in Lymantria dispar and its molecular docking analysis with poplar secondary metabolites

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Abstract

【Objective】This study aims to determine the binding ability and mode of glutathione S-transferase (GST) in Lymantria dispar to key poplar secondary metabolites, provide a foundational theory for the adaptation mechanism of LdGST to these metabolites. Additionally, The GST molecular simulation was used to identify the best binding secondary metabolites, offering a novel strategy for controlling Lymantria dispar.【Method】Homology modeling, multiple sequence alignment, and three-dimensional structure determination of 10 GSTs were performed using templates with over 30% similarity via the Swiss-model website. The 10 GST models were evaluated using SAVES software. The 3D structures of six poplar secondary metabolites were obtained from the PubChem website. Molecular docking of the 10 GST models with the six poplar secondary metabolites was conducted using Discovery Studio 2019 Client software, and docking results analyzed through combined energy and visualization.【Result】 The models obtained through homology modeling of the 10 GSTs met the criteria, with more than 90% of amino acids in the Ramachandran Plot’s most favored and additional allowed regions. The percentage of amino acids with a compatibility score above 0.2 between the three-dimensional and primary structures was over 80%, and the ERRAT value ranged from 91.73% to 97.82%, indicating the models were qualified. Molecular docking revealed that the binding of GST to poplar secondary metabolites involved hydrogen and covalent bonds. The optimal protein bindings were as follows: Salicin, LdGSTs2 with a binding energy of -45.70 kJ/mol. Caffeic acid, LdGSTz2 with a binding energy of -43.96 kJ/mol. Catechol and rutin, LdGSTz1 with binding energies of -25.86 and -95.46 kJ/mol, respectively. Flavonoids, LdGSTe2 with a binding energy of -32.49 kJ/mol. Quercetin, LdGSTo2 with a binding energy of -62.09 kJ/mol.【Conclusion】The binding energy of LdGSTs to poplar secondary metabolites are all below -5 kJ/mol, involving hydrogen and covalent bonds. The similar binding energy of the same poplar secondary metabolites to different GSTs suggests good affinity and stable intermolecular binding, with low specificity of GST for secondary metabolites. However, the affinity of the same GST to different poplar secondary metabolites varied. These results provide a theoretical basis for reducing insecticide resistance by incorporating secondary metabolites.

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Lymantria dispar / glutathione S-transferase(GST) / poplar secondary metabolites / homology modeling / molecular docking / binding energy

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XIE Jiaming , CAO Chuanwang , SUN Lili , et al . Structural prediction of glutathione S-transferase (GST) in Lymantria dispar and its molecular docking analysis with poplar secondary metabolites[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2024, 48(5): 211-220 https://doi.org/10.12302/j.issn.1000-2006.202212012

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