Sulfonylurea类ALS/AHAS抑制剂作用方式的分子对接研究和新抑制剂的虚拟筛选

采用Dock5和Autodock3的组合, 从乙酰乳酸合成酶(ALS)的晶体结构出发, 对五个磺酰脲分子和三个类磺酰脲分子与ALS的相互作用方式进行了详细的分子对接研究, 并结合对ALS与氯嘧磺隆(类磺酰脲)共结晶的复合物晶体结构的分析得出了一个简化的药效团模型, 与前人利用其它手段得到的药效团模型一致. 结合此药效团模型并根据sulfonylurea类分子与ALS的作用机理, 我们对425个具有不同除草和杀虫作用的已知农药和ALS进行了分子对接研究和筛选, 从中发现了一些可能对ALS有抑制作用的农药分子. 此结果可以很好地解释这类农药的结构和活性的关系, 对设计、开发新ALS抑制剂的先导化合物提供依据和指导.     

基于受体结构的AHAS抑制剂的设计、合成及生物活性

在AHAS与磺酰脲类除草剂复合物的晶体结构基础上, 利用分子对接程序DOCK 4.0, 通过MDL/ACD三维数据库虚拟筛选, 得到了296个与AHAS结合能较低的小分子化合物结构信息, 从中选取了部分小分子进行化学合成, 并且测试了其生物活性. 部分化合物的体内和体外活性表现出一定的一致性.     

N-[2-(4-甲基)嘧啶基]-N′-2-硝基苯磺酰脲的合成、晶体结构、生物活性及其与酵母AHAS的分子对接

合成了磺酰脲化合物N-[2-(4-甲基)嘧啶基]-N′-2-硝基苯磺酰脲,用元素分析、红外、核磁共振氢谱对产物进行了表征,培养并测定了其晶体结构.晶体属三斜晶系,P1空间群,晶胞参数a=0.54159(1)nm,b=1.1533(3)nm,c=1.1857(4)nm,α=83.907(6)°,β=81.048(5)°,γ=77.637(4)°,V=0.7126(4)nm3,Dc=1.572g/cm3,Z=2,F(000)=348,R=0.0659,wR=0.1217.在晶体结构中,杂环上的一个N原子与脲桥上邻近的N原子上的H构成分子内氢键.测定了对酵母AHAS的离体抑制活性,其抑制常数Ki为(2.48±0.35)×10-7mol/L.用分子对接方法,将目标化合物晶体结构对接到靶酶酵母AHAS的活性位点,发现对接完毕目标化合物的构象与复合物晶体中的磺酰脲分子构象接近,并得到了合理的生物活性预测值.该研究为进一步理解磺酰脲类的分子结构、药物活性并设计新的分子提供了帮助和指导.     

拟南芥乙酰羟基酸合成酶与磺酰脲的相互作用以及CoMFA研究

在分子水平上较为详尽地研究了85个磺酰脲类化合物与植物源野生型拟南芥AHAS酶的离体相互作用, 测定了这些化合物对AHAS酶的抑制常数Kiapp. 采用比较分子力场方法(CoMFA)对这些化合物与AHAS酶的相互作用进行了三维构效关系研究, 用此模型预测了检验组10个化合物的pKiapp值, 模型的预测结果与测试结果一致.     

4,5,6-三取代嘧啶苯磺酰脲类化合物的生物活性、分子对接与3D-QSAR关系研究

用柔性分子对接方法(FlexX)将15个4,5,6-三取代嘧啶苯磺酰脲化合物以及3个不含5-位取代嘧啶苯磺酰脲化合物(分别为4,6-双取代嘧啶和4-取代嘧啶)和乙酰羟酸合成酶(AHAS)活性口袋进行了对接, 对接程序预测的抑制剂和酶之间的相互作用能与抑制活性之间有一定的相关性, 相关系数为0.660. 然后采用比较分子相似性指数分析(CoMSIA)对27个新型4,5,6-三取代嘧啶苯磺酰脲类化合物的除草活性进行三维定量构效关系(3D-QSAR)研究. 建立了三维定量构效关系CoMSIA模型, 立体场、静电场和氢键的贡献分别为47.3%, 32.8%, 19.9%. 交叉验证系数q2值为0.520. 根据CoMSIA模型的立体场、静电场、氢键给体场三维等值线图不仅直观地解释了结构与活性的关系, 并且与用FlexX预测的结合模式相一致, 证明了我们预测的结合模式是可靠的, 为进一步设计高活性的标题化合物提供较好的理论指导.     

新型芳磺酰基色氨酸酯以及芳磺酰基谷氨酸二酯类化合物的合成与生物活性研究

在乙酰羟酸合成酶(AHAS)与磺酰脲类化合物复合物晶体结构的基础上, 利用分子对接法进行MDL/ACD三维数据库虚拟筛选, 得到了部分结合能较低的小分子化合物结构. 对其中的芳磺酰基色氨酸酯以及芳磺酰基谷氨酸二酯类化合物进行了合成, 共合成22个具有潜在活性的新衍生化合物, 其结构通过核磁、质谱、红外及元素分析验证, 并对所有新化合物进行了体内、体外活性测试. 初步的体外生物活性测试结果表明, 两类化合物对AHAS具有较低的抑制性; 体内生物活性测试结果表明, 化合物4d, 4g和4k具有一定的除草活性, 在100 μg/mL的浓度下, 它们对油菜根长的抑制率分别为70.8%, 52.4%和50.2%.     

拟南芥TIR1与生长素IAA相互作用的分子对接及分子动力学研究

基于最新得到的拟南芥运输抑制剂响应蛋白质1(TIR1)与吲哚乙酸(IAA)复合物的晶体结构, 使用分子对接方法和分子动力学方法对TIR1与生长素IAA相互作用的方式进行了研究. 分子对接结果表明, 通过逐级考察辅酶InsP₆和中心水分子的影响, 发现辅酶InsP₆和中心水分子对生长素IAA正确结合到活性位点有重要作用. 分子动力学结果表明, 复合物体系在整个模拟过程中较为稳定, 2个水分子相继作为中心水分子与生长素IAA形成了稳定的氢键作用, IAA与活性位点处残基的相互作用与晶体结构相比略有差异.     

N-[2-(4-甲基)嘧啶基]-N′-2-硝基苯磺酰脲的合成、晶体结构、生物活性及其与酵母AHAS的分子对接

合成了磺酰脲化合物N-[2-(4-甲基)嘧啶基]-N′-2-硝基苯磺酰脲, 用元素分析、红外、核磁共振氢谱对产物进行了表征, 培养并测定了其晶体结构. 晶体属三斜晶系, 空间群, 晶胞参数a＝0.54159(1) nm, b＝1.1533(3) nm, c＝1.1857(4) nm, α＝83.907(6)°, β＝81.048(5)°, γ＝77.637(4)°, V＝0.7126(4) nm³, D_c＝1.572 g/cm³, Z＝2, F(000)＝348, R＝0.0659, wR＝0.1217. 在晶体结构中, 杂环上的一个N原子与脲桥上邻近的N原子上的H构成分子内氢键. 测定了对酵母AHAS的离体抑制活性, 其抑制常数K_i为(2.48±0.35)×10^－7 mol/L. 用分子对接方法, 将目标化合物晶体结构对接到靶酶酵母AHAS的活性位点, 发现对接完毕目标化合物的构象与复合物晶体中的磺酰脲分子构象接近, 并得到了合理的生物活性预测值. 该研究为进一步理解磺酰脲类的分子结构、药物活性并设计新的分子提供了帮助和指导.     

N-(5'-溴-4'-取代嘧啶-2'-基)苯磺酰脲化合物的合成和生物活性

乙酰羟基酸合成酶(Acetohydroxyacid synthase,AHAS,EC 4.1.3.18)是植物和微生物中亮氨酸、异亮氨酸和缬氨酸合成途径的一个关键酶,以AHAS为靶标的磺酰脲类除草剂具有高效、高选择性和对环境友好的特点.通过2-氨基-4-甲基嘧啶溴代反应以及进一步的衍生、磺酰基异氰酸酯的胺解,合成了一系列含有5-溴嘧啶基的新磺酰脲.其结构经1H NMR、质谱和元素分析确定.生物活性测试表明目标化合物在离体水平对大肠杆菌乙酰羟基酸合成酶同工酶AHASⅡ表现出了与市售除草剂苯磺隆相当甚至更优的抑制活性,而盆栽除草活性低于苯磺隆.     

新磺酰脲类除草活性构效关系的研究

磺酰脲类除草剂具有对环境友好和超高效的特点。本文采用X-衍射谱对其绝对构型进行分析,首次发现分子内氢键的存在。采用各种理论和软件计算,活性结构应符合三点要求：(a)分子内氢键使杂环和脲之间形成一个共轭体系;(b)羰基氧、磺酰氧和杂环氮形成分子中三个负电中心;(c)在磺酰胺与苯邻位取代基之间形成一个空穴。根据以上结论,构建了一个卡口模型,较合理地解释了磺酰脲类草活性的构效关系。建立了一个虚拟靶酶ALS的模拟作用模型,供进一步分子设计ALS抑制剂,包括一些非磺酰脲类先导化合物时参考。     

Study on the bioactivity changes of hydroxylated sulfonylureas derivatives: A possible metabolism

Some new sulfonylureas and their hydroxylation products had been synthesized from 2-amino-4-methylpyrimidine. Their bioactivities against E. coli AHAS II in vitro were tested and the results indicated that the hydroxylation decreased the inhibition activities of sulfonylureas significantly. Subsequently herbicidal tests against stem-growth of barnyard grass and root-growth of rape confirmed the above conclusion. The preliminary molecular docking studies were also carried out to investigate the binding modes of non-hydroxylated and hydroxylated sulfonylureas with AHAS.     

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase:molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase(AHAS) is the target enzyme of several classes of herbicides,such as sulfonylureas and imidazolinones.Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides,therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS.With the aid of available crystal structures of the Arabidopsis thaliana(At) AHAS-inhibitor complex,molecular dyn...     

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase: molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase (AHAS) is the target enzyme of several classes of herbicides, such as sulfonylureas and imidazolinones. Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides, therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS. With the aid of available crystal structures of the Arabidopsis thaliana (At) AHAS-inhibitor complex, molecular dynamics (MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level. Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors, separately, and binding free energy was calculated for each system using the MM-GBSA method. Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574, and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors, which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant. To our knowledge, it is the first report about MD simulations study on the AHAS-related system, which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically, and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.     

Commercial Herbicides Can Trigger the Oxidative Inactivation of Acetohydroxyacid Synthase

Acetohydroxyacid synthase (AHAS) inhibitors are highly successful commercial herbicides. New kinetic data show that the binding of these compounds leads to reversible accumulative inhibition of AHAS. Crystallographic data (to a resolution of 2.17 Å) for an AHAS–herbicide complex shows that closure of the active site occurs when the herbicidal inhibitor binds, thus preventing exchange with solvent. This feature combined with new kinetic data shows that molecular oxygen promotes an accumulative inhibition leading to the conclusion that the exceptional potency of these herbicides is augmented by subversion of an inherent oxygenase side reaction. The reactive oxygen species produced by this reaction are trapped in the active site, triggering oxidation reactions that ultimately lead to the alteration of the redox state of the cofactor flavin adenine dinucleotide (FAD), a feature that accounts for the observed reversible accumulative inhibition.     

N-(5 -溴-4 -取代嘧啶-2 -基)苯磺酰脲化合物的合成和生物活性

乙酰羟基酸合成酶(Acetohydroxyacid synthase, AHAS, EC 4.1.3.18)是植物和微生物中亮氨酸、异亮氨酸和缬氨酸合成途径的一个关键酶, 以AHAS为靶标的磺酰脲类除草剂具有高效、高选择性和对环境友好的特点. 通过2-氨基-4-甲基嘧啶溴代反应以及进一步的衍生、磺酰基异氰酸酯的胺解, 合成了一系列含有5-溴嘧啶基的新磺酰脲. 其结构经¹H NMR、质谱和元素分析确定. 生物活性测试表明目标化合物在离体水平对大肠杆菌乙酰羟基酸合成酶同工酶AHASII表现出了与市售除草剂苯磺隆相当甚至更优的抑制活性, 而盆栽除草活性低于苯磺隆.     

Structure-activity relationships for a new family of sulfonylurea herbicides

Summary Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) catalyzes the first common step in branched-chain amino acid biosynthesis. The enzyme is inhibited by several chemical classes of compounds and this inhibition is the basis of action of the sulfonylurea and imidazolinone herbicides. The commercial sulfonylureas contain a pyrimidine or a triazine ring that is substituted at both meta positions, thus obeying the initial rules proposed by Levitt. Here we assess the activity of 69 monosubstituted sulfonylurea analogs and related compounds as inhibitors of pure recombinant Arabidopsis thaliana AHAS and show that disubstitution is not absolutely essential as exemplified by our novel herbicide, monosulfuron (2-nitro-N-(4′-methyl-pyrimidin−2′-yl) phenyl-sulfonylurea), which has a pyrimidine ring with a single meta substituent. A subset of these compounds was tested for herbicidal activity and it was shown that their effect in vivo correlates well with their potency in vitro as AHAS inhibitors. Three-dimensional quantitative structure–activity relationships were developed using comparative molecular field analysis and comparative molecular similarity indices analysis. For the latter, the best result was obtained when steric, electrostatic, hydrophobic and H-bond acceptor factors were taken into consideration. The resulting fields were mapped on to the published crystal structure of the yeast enzyme and it was shown that the steric and hydrophobic fields are in good agreement with sulfonylurea-AHAS interaction geometry.     

Design,synthesis and SAR study of novel sulfonylurea derivatives containing arylpyrimidine moieties as potential anti-phytopathogenic fungal agents

Three series of novel sulfonylureas (SUs) 9-11 containing aromatic-substituted pyrimidines were designed and synthesized. The 3D-QASR and molecular docking studies showed that SUs should be considered as potential antiphytopathogenic fungal agents.     

Design,synthesis and SAR study of novel sulfonylurea derivatives containing arylpyrimidine moieties as potential anti-phytopathogenic fungal agents

Acetohydroxyacid synthase(AHAS) was considered as a promising target for antifungal agents.Herein,three series of novel sulfonylureas(SUs) 9-11 containing aromatic-substituted pyrimidines were designed and synthesized according to pharmacophore-combination and bioisosterism strategy.The in vitro fungicidal activities against ten phytopathogenic fungi indicated that most of the title compounds exhibited broad-spectrum and excellent fungicidal activities.Based on the preliminary fungicidal activities,a CoMFA model was constructed and the 3 D-QSAR analysis indicated that either a bulky group around the 5-position of the pyrimidine ring or electropositive group around the 2-position of the benzene ring would be favour to fungicidal activities.In order to study interaction mechanism,10 k was automatically docked into yeast AHAS and it further indicated that bearing bulky groups-aryl at the pyrimidine ring was critical to enhance antifungal activities.It revealed that the antifungal activity of derivatives 9-11 probably results from the inhibition of fungal AHAS.Thus,the present results strongly showed that SUs should be considered as lead compounds or model molecules to develop novel antiphyt o pathogenic fungal agents.     

Rational design based on bioactive conformation analysis of pyrimidinylbenzoates as acetohydroxyacid synthase inhibitors by integrating molecular docking, CoMFA, CoMSIA, and DFT calculations

Pyrimidinylthiobenzoates constitute an important kind of herbicides targeting acetohydroxyacid synthase (AHAS, EC 2.2.1.6), which catalyze the first common step in branched-chain amino acid biosynthesis. Due to the symmetry of 4,6-dimethoxypyrimidyl, there are two kinds of conformation of pyrimidinylthiobenzoates: one's phenyl is left-extending (named conformation-L); the other's phenyl is right-extending (named conformation-R). On the basis of the assumption that 3D quantitative structure-activity relationship (QSAR) models derived from the bioactive conformation should give the best result, a strategy of density-functional-theory-based 3D-QSAR was proposed to identify the bioactive conformation of pyrimidinylthiobenzoates by integrating the techniques of molecular docking, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and density functional theory calculation. The combination of three criteria of q2, r2, and r2pred obtained from CoMFA and CoMSIA analyses clearly indicated that conformation-R rather than conformation-L might be the bioactive conformation for pyrimidinylthiobenzoates. A further comparison between the two binding modes indicated that pyrimidinylthiobenzoates and sulfonylureas have very similar binding sites, such as Trp586, Arg380, and Pro192. However, Lys251 formed H bonds with sulfonylureas rather than pyrimidinylthiobenzoates. In addition, the orientation of phenyl groups of the two classes of compounds in the binding pocket were revealed to be opposite, which explained why the mutation of Pro192 displayed different sensitivity to sulfonylureas and pyrimidinylthiobenzoates. On the basis of the understanding of interactions between pyrimidinyl-thiobenzoates and AHAS, we designed and synthesized six 8-(4,6-dimethoxypyrimidin-2-yloxy)-4-methylphthalazin-1-one derivatives according to the 3D-QSAR models. The excellent correlation between the tested Ki values against wild-type A. thaliana acetohydroxyacid synthase and the predicted IC50 values demonstrated the high reliability of the established 3D-QSAR models. To our knowledge, this is the first report highlighting the binding mode of herbicidal pyrimidinylthiobenzoates, which consisted of the reported results of herbicide resistance.