乙酰羟酸合成酶突变体对除草剂阔草清抗性的预测研究

doi:10.6023/A21110526

摘要/Abstract

本工作测定了商品化除草剂阔草清对大肠杆菌乙酰羟酸合成酶II及其突变体的抑制常数. 利用生物大分子的定量构效关系方法(MB-QSAR)建立了定量、可视的突变体性质与结构关系模型. 实验数据与计算数据之间显示了良好的相关性: MB-QSAR/CoMFA (comparative molecular field analysis)模型的交叉验证系数q²=0.691, 非交叉验证相关性系数r²=0.947, 外部预测能力r²_pred=0.759; MB-QSAR/CoMSIA (comparative molecular similarity indices analysis)模型的相应值分别为0.625, 0.960和0.619. 模型的三维结构-性质关系图为突变体抗性提供了直观阐释, 为抗性规避性农药的设计提供了有价值的信息. 同时, 该模型也在一定程度上显示了除草剂种属选择性的预测能力.

关键词: 乙酰羟酸合成酶, 阔草清, 除草剂抗性, 抗性预测, MB-QSAR (mutation-dependent biomacromolecular quantitative structure-activity relationship)

Flumetsulam is a widely used herbicide that targets the acetohydroxyacid synthase (AHAS). Mutations in AHAS have caused serious herbicide resistance which threatened the field application of this herbicide. We have recently established a mutation-dependent biomacromolecular quantitative structure-activity relationship method, called MB-QSAR, which could be used to quantitatively predict the mutational drug resistance in molecular level and elucidating the three dimensional structure-resistance relationships for the design of resistance evading inhibitors. In this work, we employ MB-QSAR method to predict the molecular drug resistance of AHAS mutants towards flumetsulam, and to depict the structure resistance relationships in AHAS mutants. A series of AHAS mutants concerned with the herbicide resistance were constructed, and the inhibitory properties of flumetsulam against these mutants were measured. Then the structures of these mutants were constructed, optimized and aligned for the subsequent MB-QSAR modelling. The CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) molecular field values (steric, electrostatic, hydrophobic, hydrogen-bond donor and hydrogen-bond acceptor descriptors) were calculated in the flumetsulam binding pocket for these mutants. The CoMFA and CoMSIA molecular field values were used as independent variables, while the pK_i values for each mutants were used as dependent variables in the partial least squares (PLS) regression analyses to derive the MB-QSAR models. The built MB-QSAR model showed excellent correlation between experimental and computational data (MB-QSAR/CoMFA model: q²=0.691, r²=0.947, r²_pred=0.759; MB-QSAR/CoMSIA model: q²=0.625, r²=0.960, r²_pred=0.619), indicating the good prediction for the inhibition properties of flumetsulam against AHAS mutants. The comparison of the molecular interaction diagrams from MB-QSAR models provides information about which positions in the polypeptide chain could have a higher propensity to acquire herbicide resistant mutations, which in turn provides guidelines for modifying the existing herbicide as well as for designing new resistance-evading herbicides. The obtained MB-QSAR model also showed reasonable predictive power toward AHAS from various species, indicating the potential application of our MB-QSAR method in the prediction of the selectivity of drugs towards targets from different species.

Key words: acetohydroxyacid synthase, flumetsulam, herbicide resistance, resistance prediction, MB-QSAR (mutation- dependent biomacromolecular quantitative structure-activity relationship)

引用此文

王白帆, 何寅武, 文欣, 牛聪伟, 席真. 乙酰羟酸合成酶突变体对除草剂阔草清抗性的预测研究[J]. 化学学报, 2022, 80(2): 141-149.

Baifan Wang, Yinwu He, Xin Wen, Congwei Niu, Zhen Xi. Prediction on the Resistance of Acetohydroxyacid Synthase Mutants to Herbicide Flumetsulam[J]. Acta Chimica Sinica, 2022, 80(2): 141-149.

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MB-QSAR/CoMFA
	A-I	A-II				A-III
	A-I	A-II-3	A-II-4	A-II-5	A-II-6	A-III
ONC^a	5	5	5	5	5	5
q²(LOO)^b	0.580	0.666	0.673	0.691	0.684	0.372
SEE^c	0.315	0.261	0.256	0.259	0.264	0.401
r²^d	0.922	0.947	0.948	0.947	0.945	0.874
F-value^e	125.318	187.64	195.036	190.608	182.745	73.208
F-value^e	(5, 53)	(5, 53)	(5, 53)	(5, 53)	(5, 53)	(5, 53)
r²_pred^f	0.725	0.746	0.747	0.759	0.754	0.621
Contributions^g
S	0.657	0.709	0.706	0.695	0.701	0.809
E	0.343	0.291	0.294	0.305	0.299	0.191

MB-QSAR/CoMFA
	A-I	A-II				A-III
	A-I	A-II-3	A-II-4	A-II-5	A-II-6	A-III
ONC^a	5	5	5	5	5	5
q²(LOO)^b	0.580	0.666	0.673	0.691	0.684	0.372
SEE^c	0.315	0.261	0.256	0.259	0.264	0.401
r²^d	0.922	0.947	0.948	0.947	0.945	0.874
F-value^e	125.318	187.64	195.036	190.608	182.745	73.208
F-value^e	(5, 53)	(5, 53)	(5, 53)	(5, 53)	(5, 53)	(5, 53)
r²_pred^f	0.725	0.746	0.747	0.759	0.754	0.621
Contributions^g
S	0.657	0.709	0.706	0.695	0.701	0.809
E	0.343	0.291	0.294	0.305	0.299	0.191

力场组合	SHA	SA	SH	SEA	SEHA	SEHDA	SDA	EHA	S
ONC	6	6	5	6	6	6	5	6	4
q²(LOO)^a	0.625	0.611	0.565	0.594	0.590	0.552	0.532	0.547	0.536
SEE	0.228	0.249	0.329	0.241	0.237	0.232	0.317	0.288	0.431
r²	0.960	0.952	0.915	0.955	0.957	0.959	0.921	0.936	0.851
F-value	208.110	172.876	113.771	184.961	192.019	200.976	123.593	127.218	77.340
r²_pred	0.619	0.536	0.468	0.608	0.581	0.417	0.361	0.556	0.708
Contributions^b
S	0.270	0.340	0.571	0.204	0.176	0.118	0.177		1.000
E				0.364	0.319	0.217		0.397
H	0.178		0.429		0.119	0.084		0.159
D						0.321	0.444
A	0.552	0.660		0.432	0.386	0.259	0.379	0.444

力场组合	SHA	SA	SH	SEA	SEHA	SEHDA	SDA	EHA	S
ONC	6	6	5	6	6	6	5	6	4
q²(LOO)^a	0.625	0.611	0.565	0.594	0.590	0.552	0.532	0.547	0.536
SEE	0.228	0.249	0.329	0.241	0.237	0.232	0.317	0.288	0.431
r²	0.960	0.952	0.915	0.955	0.957	0.959	0.921	0.936	0.851
F-value	208.110	172.876	113.771	184.961	192.019	200.976	123.593	127.218	77.340
r²_pred	0.619	0.536	0.468	0.608	0.581	0.417	0.361	0.556	0.708
Contributions^b
S	0.270	0.340	0.571	0.204	0.176	0.118	0.177		1.000
E				0.364	0.319	0.217		0.397
H	0.178		0.429		0.119	0.084		0.159
D						0.321	0.444
A	0.552	0.660		0.432	0.386	0.259	0.379	0.444

序列编号	种属	Pred. pK_i(氯磺隆)	Pred. pK_i(氯嘧磺隆)	Pred. pK_i(双草醚)	Pred. pK_i(阔草清)
AAO53551.1	小麦	3.18	4.28	4.71	1.12
ACD74789.1	籼稻	3.96	4.60	3.57	1.22
NP_001151761.1	玉米	2.95	3.84	4.44	0.75
CAA87083.1	棉花	3.51	6.03	4.86	0.25
ADI56521.1	马铃薯	4.25	5.04	3.65	0.60
P09342	烟草	3.70	4.43	4.64	1.14
P09114	烟草	3.56	4.79	4.42	1.34
ACU30048.1	大豆	3.38	4.50	4.90	0.63
ACV84152.1	菜豆	2.48	4.18	3.77	1.40
P27818	油菜	3.69	4.25	4.82	1.43
P14874	油菜	3.35	4.11	4.43	1.61
P27819	油菜	3.61	4.26	4.82	1.36
XP_002511176.1	蓖麻	3.58	5.84	5.15	0.35
EEF51778.1	蓖麻	3.58	5.84	5.15	0.35
ACR55067.1	燕麦	3.74	5.39	4.89	1.52
AAT07322.1	向日葵	3.51	5.17	4.75	1.24
AAT07327.1	向日葵	3.89	5.10	4.74	0.67
AAT07329.1	向日葵	3.72	3.91	4.27	2.30
AEL89170.1	臭甘菊	4.75	5.11	4.82	1.28
AEL89171.1	臭甘菊	4.48	4.89	5.15	1.06
ABY57315.1	苜蓿	3.58	5.07	3.62	0.58
ABY57318.1	苜蓿	3.70	5.02	3.34	0.51
AAK50821.1	藜	4.14	4.63	5.27	0.97
AAK50820.1	藜	4.12	4.76	5.31	1.04
ABM92357.2	莎草	3.42	4.90	4.01	0.80
ADQ54157.1	猪毛菜	4.15	5.24	4.84	0.90
ACF47582.1	苣荬菜	3.58	4.65	4.83	1.33
P17597	拟南芥	3.91 (7.04)	4.66 (7.50)	3.96 (6.09)	0.37 (6.30)
P36620	粟酒裂殖酵母	4.22 (6.11)	4.34 (8.15)	5.51 (5.12)	2.02 (3.95)
P00893	大肠杆菌I	3.45 (3.32)	2.90 (3.30)	3.05	0.86
P00892	大肠杆菌II	6.29 (6.49)	7.15 (7.66)	4.98 (4.62)	5.68 (5.73)
P08142	大肠杆菌III	4.38 (3.81)	4.02 (3.73)	3.45	2.23 (3.22)
P37251	枯草芽孢杆菌	4.81 (4.78)	4.25 (2.94)	4.06 (2.87)	2.33 (3.94)
P42463	谷氨酸棒杆菌	5.23	4.09	3.16	4.35
P0A622	结核分支杆菌	3.53	3.80	3.74	3.99
P0A623	牛分支杆菌	3.53	3.80	3.74	3.99
P45261	流感嗜血杆菌	5.33	5.77	3.71	2.52
O33112	麻风病分支杆菌	3.67	4.31	3.41	3.09
Q59498	副结核杆菌亚种	4.54	4.16	3.86	3.50
P57321	宿主豆长管蚜内共生菌	4.34	4.77	4.69	2.37
O85293	宿主麦二叉蚜内共生菌	4.06	4.67	4.93	1.85
Q89AP7	宿主木瘿蚜属内共生菌	4.01	4.12	4.39	2.50
Q02137	乳酸乳球菌	5.27	4.49	2.79	3.55
P40811	鼠伤寒沙门菌	4.38	4.23	3.75	2.47
Q9RQ65	宿主角倍蚜内共生菌	3.64	4.08	4.66	2.59