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

doi:10.12302/j.issn.1000-2006.202212012

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (5): 211-220.doi: 10.12302/j.issn.1000-2006.202212012

Previous Articles Next Articles

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

XIE Jiaming¹(), CAO Chuanwang¹^,^*(), SUN Lili¹, LI Mingjun², ZHANG Ruiqiong¹

1. Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, China
2. Ningcheng County Kuntouhe Forest Farm of Inner Mongolia, Ningcheng 024228, China

Received:2022-12-10 Revised:2024-03-22 Online:2024-09-30 Published:2024-10-03
Contact: CAO Chuanwang E-mail:1095334984@qq.com;chuanwangcao@nefu.edu.cn

Abstract

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.

Key words: Lymantria dispar, glutathione S-transferase(GST), poplar secondary metabolites, homology modeling, molecular docking, binding energy

CLC Number:

S763
Q89

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

Figures/Tables 10

Fig. 1

Fig. 2

Table 1

Table 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Fig. 7

Fig. 8

References 43

[1]	郭冰, 郝恩华, 王菁桢, 等. 入侵害虫松树蜂气味结合蛋白与其相关信息化学物质的分子对接[J]. 植物保护学报, 2019, 46(5):1004-1017.
	GUO B, HAO E H, WANG J Z, et al. Molecular docking of odorant binding proteins and its related semiochemicals of sirex woodwasp Sirex noctilio,an invasive insect pest[J]. J Plant Prot, 2019, 46(5):1004-1017.DOI: 10.13802/j.cnki.zwbhxb.2019.2019035.
[2]	李敏, 郭美琪, 相伟芳, 等. 分子对接技术在昆虫化学感受研究中的应用进展[J]. 植物保护, 2019, 45(5):121-127.
	LI M, GUO M Q, XIANG W F, et al. Research progress in molecular docking in insect chemosense[J]. Plant Prot, 2019, 45(5):121-127.DOI: 10.16688/j.zwbh.2018464.
[3]	李红亮, 张林雅, 庄树林, 等. 中华蜜蜂普通气味结合蛋白ASP2的气味结合功能模式分析[J]. 中国农业科学, 2013, 46(1):154-161.
	LI H L, ZHANG L Y, ZHUANG S L, et al. Interpretation of odorant binding function and mode of general odorant binding protein ASP2 in Chinese honeybee (Apis cerana cerana)[J]. Sci Agric Sin, 2013, 46(1):154-161.DOI: 10.3864/j.issn.0578-1752.2013.01.018.
[4]	LIU Q J, WANG H, LI H L, et al. Impedance sensing and molecular modeling of an olfactory biosensor based on chemosensory proteins of honeybee[J]. Biosens Bioelectron, 2013, 40(1):174-179.DOI: 10.1016/j.bios.2012.07.011.
[5]	LI H L, ZHANG L Y, NI C X, et al. Molecular recognition of floral volatile with two olfactory related proteins in the eastern honeybee (Apis cerana)[J]. Int J Biol Macromol, 2013, 56:114-121.DOI: 10.1016/j.ijbiomac.2013.01.032.
[6]	LI H L, NI C X, TAN J, et al. Chemosensory proteins of the eastern honeybee,Apis cerana:identification,tissue distribution and olfactory related functional characterization[J]. Comp Biochem Physiol B Biochem Mol Biol, 2016, 194/195:11-19.DOI: 10.1016/j.cbpb.2015.11.014.
[7]	LI H L, TAN J, SONG X M, et al. Sublethal doses of neonicotinoid imidacloprid can interact with honey bee chemosensory protein 1 (CSP1) and inhibit its function[J]. Biochem Biophys Res Commun, 2017, 486(2):391-397.DOI: 10.1016/j.bbrc.2017.03.051.
[8]	LIU N Y, ZHU J Y, JI M, et al. Chemosensory genes from Pachypeltis micranthus,a natural enemy of the climbing hemp vine[J]. J Asia Pac Entomol, 2017, 20(2):655-664.DOI: 10.1016/j.aspen.2017.01.016.
[9]	DU S Q, YANG Z K, QIN Y G, et al. Computational investigation of the molecular conformation-dependent binding mode of (E)-β-farnesene analogs with a heterocycle to aphid odorant-binding proteins[J]. J Mol Model, 2018, 24(3):70.DOI: 10.1007/s00894-018-3612-0.
[10]	LIU N Y, YANG K, LIU Y, et al. Two general-odorant binding proteins in Spodoptera litura are differentially tuned to sex pheromones and plant odorants[J]. Comp Biochem Physiol A Mol Integr Physiol, 2015, 180:23-31.DOI: 10.1016/j.cbpa.2014.11.005.
[11]	ZHANG Y L, FU X B, CUI H C, et al. Functional characteristics,electrophysiological and antennal immunolocalization of general odorant-binding protein 2 in tea geometrid,Ectropis obliqua[J]. Int J Mol Sci, 2018, 19(3):875.DOI: 10.3390/ijms19030875.
[12]	ZHU J, PAOLO P, LIU Y, et al. Ligand-binding properties of three odorant-binding proteins of the diamondback moth Plutella xylostella[J]. J Integr Agric, 2016, 15(3):580-590.DOI: 10.1016/S2095-3119(15)61067-X.
[13]	张龙. 飞蝗嗅觉的细胞与分子机制研究进展[J]. 生命科学, 2010, 22(12):1215-1228.
	ZHANG L. Cellular and molecular olfaction mechanisms of locust[J]. Chin Bull Life Sci, 2010, 22(12):1215-1228.DOI: 10.13376/j.cbls/2010.12.004.
[14]	WANG Y L, JIN Y C, CHEN Q, et al. Selectivity and ligand-based molecular modeling of an odorant-binding protein from the leaf beetle Ambrostoma quadriimpressum (Coleoptera:Chrysomelidae) in relation to habitat-related volatiles[J]. Sci Rep, 2017, 7(1):15374.DOI: 10.1038/s41598-017-15538-8.
[15]	杨雪清, 刘吉元, 张雅林. 分子模拟技术及其在苹果蠹蛾代谢杀虫剂分子机制研究中的应用进展[J]. 生物安全学报, 2015, 24(4):265-273.
	YANG X Q, LIU J Y, ZHANG Y L. Molecular simulation and its application progress on molecular metabolic mechanisms of insecticide in Cydia pomonella[J]. J Biosaf, 2015, 24(4):265-273.DOI: 10.3969/j.issn.2095-1787.2015.04.003.
[16]	张元. 氟虫腈与昆虫GABA受体相互作用的研究[D]. 上海: 上海师范大学, 2016.
	ZHANG Y. Study on the interaction between fipronil and insect GABA receptor[D]. Shanghai: Shanghai Normal University, 2016.
[17]	CAO C W, SUN L L, WEN R R, et al. Characterization of the transcriptome of the Asian Gypsy moth Lymantria dispar identifies numerous transcripts associated with insecticide resistance[J]. Pestic Biochem Physiol, 2015, 119:54-61.DOI: 10.1016/j.pestbp.2015.02.005.
[18]	OHNUMA T, ANAN E, HOASHI R, et al. Dietary diacetylene falcarindiol induces phase 2 drug-metabolizing enzymes and blocks carbon tetrachloride-induced hepatotoxicity in mice through suppression of lipid peroxidation[J]. Biol Pharm Bull, 2011, 34(3):371-378.DOI: 10.1248/bpb.34.371.
[19]	CHEN L Q, HALL P R, ZHOU X E, et al. Structure of an insect δ-class glutathione S-transferase from a DDT-resistant strain of the malaria vector Anopheles gambiae[J]. Acta Crystallogr D Biol Cryst, 2003, 59(12):2211-2217.DOI: 10.1107/s0907444903018493.
[20]	KAKUTA Y, USUDA K, NAKASHIMA T, et al. Crystallographic survey of active sites of an unclassified glutathione transferase from Bombyx mori[J]. Biochim Biophys Acta, 2011, 1810(12):1355-1360.DOI: 10.1016/j.bbagen.2011.06.022.
[21]	周郑, 程新胜, 王方晓, 等. 烟碱和芸香苷对斜纹夜蛾药剂敏感性及相关酶活性的影响[J]. 农药学学报, 2007, 9(3):305-308.
	ZHOU Z, CHENG X S, WANG F X, et al. Effects of nicotine and rutin on the susceptibility of Spodoptera litura to insecticides and the activities of some enzymes[J]. Chin J Pestic Sci, 2007, 9(3):305-308.DOI: 10.3321/j.issn:1008-7303.2007.03.019.
[22]	高希武, 董向丽, 郑炳宗, 等. 棉铃虫的谷胱甘肽S-转移酶(GSTs):杀虫药剂和植物次生性物质的诱导与GSTs对杀虫药剂的代谢[J]. 昆虫学报, 1997, 40(2):122-127.
	GAO X W, DONG X L, ZHENG B Z, et al. Glutathione S-transferase (GSTs) of Helicoverpa armigera:induction of insecticides and plant allelochemicals and metabolism of insecticides[J]. Acta Entomol Sin, 1997, 40(2):122-127.DOI: 10.16380/j.kcxb.1997.02.002.
[23]	胡春祥. 舞毒蛾生物防治研究进展[J]. 东北林业大学学报, 2002, 30(4):40-43.
	HU C X. Research progress of the biological control for Lymantria dispar L[J]. J Northeast For Univ, 2002, 30(4):40-43.DOI: 10.3969/j.issn.1000-5382.2002.04.011.
[24]	王亚军, 邹传山, 王若茜, 等. 3种植物次生代谢物质对舞毒蛾的杀虫活性分析[J]. 北京林业大学学报, 2017, 39(11):75-81.
	WANG Y J, ZOU C S, WANG R X, et al. Insecticidal activity analysis of three plant secondary metabolites on Lymantria dispar[J]. J Beijing For Univ, 2017, 39(11):75-81.DOI: 10.13332/j.1000-1522.20170214.
[25]	鄢杰明, 廖月枝, 严善春, 等. 甲氧虫酰肼对舞毒蛾解毒酶和保护酶活性的影响[J]. 东北林业大学学报, 2010, 38(11):112-114.
	YAN J M, LIAO Y Z, YAN S C, et al. Effects of methoxyfenozide (RH-2485) on the activities of detoxifying enzymes and protective enzymes in Lymantria dispar (Lepidoptera:Lymantriidae)[J]. J Northeast For Univ, 2010, 38(11):112-114.DOI: 10.13759/j.cnki.dlxb.2010.11.036.
[26]	鄢杰明, 钟华, 严俊鑫, 等. 多杀菌素对舞毒蛾幼虫解毒酶活性的影响[J]. 林业科学, 2012, 48(9):82-87.
	YAN J M, ZHONG H, YAN J X, et al. Effect of spinosad to detoxifying enzymes activity in Lymantria dispar larva[J]. Sci Silvae Sin, 2012, 48(9):82-87.DOI: 10.11707/j.1001-7488.20120913.
[27]	冯春富, 严善春, 鲁艺芳, 等. 兴安落叶松诱导抗性对舞毒蛾幼虫解毒酶活性的影响[J]. 林业科学, 2011, 47(8):102-107.
	FENG C F, YAN S C, LU Y F, et al. Effects of induced resistance of Larix gmelinii on the activities of detoxifying enzymes in Lymantria dispar[J]. Sci Silvae Sin, 2011, 47(8):102-107.DOI: 10.11707/j.1001-7488.20110816.
[28]	MA J Y, SUN L L, ZHAO H Y, et al. Functional identification and characterization of GST genes in the Asian Gypsy moth in response to poplar secondary metabolites[J]. Pestic Biochem Physiol, 2021, 176:104860.DOI: 10.1016/j.pestbp.2021.104860.
[29]	吕春鹤, 张国财, 邹传山. 白屈菜总碱对舞毒蛾离体酶活性的影响[J]. 中国林副特产, 2017(4):33-36,38.
	LV C H, ZHANG G C, ZOU C S. Effects of total alkaloids from the Chelidonium majus on the enzymes activities in Lymantria dispar in vitro[J]. For Prod Speciality China, 2017(4):33-36, 38.DOI: 10.13268/j.cnki.fbsic.2017.04.009.
[30]	王振越. 杨树主要次生物质对舞毒蛾生长发育及主要解毒酶影响[D]. 哈尔滨: 东北林业大学, 2020.
	WANG Z Y. Effects of poplar secondary metabolites on performance and key detoxifying enzymatic activity of Lymantria dispar[D]. Harbin: Northeast Forestry University, 2020.
[31]	许力山. 三种次生物质与溴氰虫酰胺对舞毒蛾P450和GST影响研究[D]. 哈尔滨: 东北林业大学, 2021.
	XU L S. Study on effects of three secondary metabolites and cyanobromonamide on P450 and GST in Lymantria dispar[D]. Harbin: Northeast Forestry University, 2021.
[32]	杨欢, 郭冰, 郝恩华, 等. 禾谷缢管蚜气味降解酶鉴定及其与关键信息化学物质的分子对接[J]. 植物保护学报, 2022, 49(4):1119-1131.
	YANG H, GUO B, HAO E H, et al. Identification of odor degrading enzymes and molecular docking with crucial semiochemicals in bird cherry-oat aphid Rhopalosiphum padi[J]. J Plant Prot, 2022, 49(4):1119-1131.DOI: 10.13802/j.cnki.zwbhxb.2022.2020292.
[33]	LU X P, XU L, MENG L W, et al. Divergent molecular evolution in glutathione S-transferase conferring malathion resistance in the oriental fruit fly,Bactrocera dorsalis (Hendel)[J]. Chemosphere, 2020, 242:125203.DOI: 10.1016/j.chemosphere.2019.125203.
[34]	崔琳琳, 宋亚刚, 苗明三. 基于网络药理学和分子对接的陈皮干预COVID-19的可能机制[J]. 中药药理与临床, 2020, 36(5):28-33.
	CUI L L, S Y, MIAO M S. Possible mechanism of citri reticulatae pericarpium intervening on COVID-19 based on network pharmacology and molecular docking[J]. Pharmacology Clin Chin Materia Med, 2020, 36(5):28-33.DOI: 10.13412/j.cnki.zyyl.20200630.003.
[35]	马天翔, 顾志荣, 孙岚萍, 等. 荆芥-防风药对治疗荨麻疹作用机制的网络药理学研究[J]. 中药新药与临床药理, 2020, 31(4):435-440.
	MA T X, GU Z R, SUN L P, et al. Mechanism of herb pair Schizonepetae herba-Saposhnikoviae radix on treatment of urticaria based on network pharmacology[J]. Tradit Chin Drug Res Clin Pharmacol, 2020, 31(4):435-440.DOI: 10.19378/j.issn.1003-9783.2020.04.011.
[36]	VOGT R G. Molecular basis of pheromone detection in insects[M]. Amsterdam: Elsevier, 2005:753-803.DOI: 10.1016/b0-44-451924-6/00047-8.
[37]	GAWANDE N D, SUBASHINI S, MURUGAN M, et al. Molecular screening of insecticides with sigma glutathione S-transferases (GST) in cotton aphid Aphis gossypii using docking[J]. Bioinformation, 2014, 10(11):679-683.DOI: 10.6026/97320630010679.
[38]	虞唯道, 刘淼, 宋萍, 等. 鞣花酸的生物活性与分析研究进展[J]. 生物加工过程, 2023, 21(1):83-90.
	YU W D, LIU M, SONG P, et al. The biological activity and detection methods of ellagic acid[J]. Chi J Bio Eng, 2023, 21(1):83-90.DOI:10.3969/j.issn.1672-3678.2023.01.010.
[39]	史宗畔, 冉永红, 张晶晶, 等. 中华按蚊气味结合蛋白AsinOBP1与避蚊胺(DEET)的结合特性分析[J]. 昆虫学报, 2018, 61(1):139-148.
	SHI Z P, RAN Y H, ZHANG J J, et al. Binding characteristics of the odorant binding protein AsinOBP₁ of Anopheles sinensis (Diptera:Culicidae) with the mosiquito repellent DEET[J]. Acta Entomol Sin, 2018, 61(1):139-148.DOI: 10.16380/j.kcxb.2018.01.015.
[40]	LIU G X, MA H M, XIE H Y, et al. Biotype characterization,developmental profiling,insecticide response and binding property of Bemisia tabaci chemosensory proteins:role of CSP in insect defense[J]. Plos One, 2016, 11(5):e0154706.DOI: 10.1371/journal.pone.0154706.
[41]	YI X, ZHANG Y B, WANG P D, et al. Ligands binding and molecular simulation:the potential investigation of a biosensor based on an insect odorant binding protein[J]. Int J Biol Sci, 2015, 11(1):75-87.DOI: 10.7150/ijbs.9872.
[42]	AHMED T, ZHANG T T, WANG Z Y, et al. Three amino acid residues bind corn odorants to McinOBP1 in the polyembryonic endoparasitoid of Macrocentrus cingulum Brischke[J]. Plos One, 2014, 9(4):e93501.DOI: 10.1371/journal.pone.0093501.
[43]	詹丽, 李敬丹, 付璇, 等. 紫茉莉种子中对草地贪夜蛾的杀虫活性成分及杀虫机制[J]. 江苏农业学报, 2024, 40(1):47-54.
	ZHAN L, LI J D, FU X, et al. Insecticidal active ingredients and mechanism against Spodoptera frugiperda in Mirabilis jalapa seeds[J]. Jiangsu J Agr Sci, 2024, 40(1):47-54.DOI:10.3969/j.issn.1000-4440.2024.01.005.

Metrics

Comments

www.nldxb.njfu.edu.cn

Edited ＆ Published by Editorial Department of Nanjing Forestry University(Natural Sciences Edition)
Address： No.159 Longpan Road,Nanjing 210037 Jiangsu,P.R.China
E-mail ：xuebao@njfu.edu.cn , xuebao@njfu.com.cn
Telephone +86-25-85428247,85427076
Distributed by China International Book Trading Corporation P.O. Box 399, Beijing ,P.R. China

谷胱甘肽 S-转移酶 glutathione S-transferase	最佳影响区域中占比 percentage in best affected area	额外允许区域中占比 percentage in additional allowed area	宽松允许区域中占比 percentage in loose allowable area
LdGSTe1	91.6	6.5	0.8
LdGSTe2	91.1	7.3	1.0
LdGSTe3	92.4	6.0	0.8
LdGSTo1	92.6	6.4	1.0
LdGSTo2	93.8	5.8	0
LdGSTs1	91.1	6.9	1.7
LdGSTs2	91.9	6.7	1.4
LdGSTt1	90.2	8.0	0
LdGSTz1	94.8	4.7	0.5
LdGSTz2	92.5	7.0	0.5

谷胱甘肽 S-转移酶 glutathione S-transferase	水杨苷 salicin	咖啡酸 caffeic acid	邻苯二酚 catechol	黄酮 flavone	芦丁 rutin	槲皮素 quercetin
LdGSTe1	-39.53	-36.13	-18.17	-24.19	-47.60	-53.74
LdGSTe2	-37.78	-23.14	-20.15	-32.49	-56.45	-54.02
LdGSTe3	-32.07	-37.71	-15.95	-23.26	-41.28	-48.60
LdGSTo1	-42.00	-39.03	-21.61	-26.48	-76.46	-58.19
LdGSTo2	-24.55	-26.55	-12.67	-17.89	-43.55	-62.09
LdGSTs1	-41.14	-28.34	-19.39	-26.02	-68.58	-47.96
LdGSTs2	-45.70	-40.30	-21.08	-29.44	-73.24	-60.05
LdGSTt1	-32.25	-30.39	-20.50	-25.02	-61.55	-43.28
LdGSTz1	-43.50	-39.21	-25.85	-27.22	-95.46	-49.54
LdGSTz2	-43.48	-43.96	-18.48	-30.92	-82.14	-37.88

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

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 10

References 43

Related Articles 1

Recommended Articles

Metrics

Comments

Author

Reader

Reviewer