酵母AHAS酶与磺酰脲类抑制剂作用模型的分子对接研究

基于酵母乙酰羟酸合成酶(AHAS)与磺酰脲类抑制剂复合物的晶体结构, 用分子对接方法对AHAS与5个磺酰脲类抑制剂相互作用的方式进行了系统的分子对接研究. 晶体复合物对接和假复合物对接两种模式对接的结果基本相同, 并与实验结果吻合. 在进一步的对接中逐级考虑了辅酶FAD和TPP的影响, 结果表明, 辅酶FAD和TPP的加入, 对AHAS酶与磺酰脲类抑制剂的结合顺序基本没有影响. 其中FAD的加入使AHAS与抑制剂的结合更加稳定, 这主要是由于抑制剂的R2取代基与FAD中的平面基团Flavin环间存在的范德华相互作用所致; 抑制剂与TPP间存在的静电相互作用可能是加速TPP降解的原因.     

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.     

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.     

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...     

Design,Syntheses and Biological Activities of Novel Sulfonylureas Containing an Oxime Ether Moiety

Since sulfonylurea is one of the most potent acetohydroxyacid synthase(AHAS) inhibitors, a series of novel sulfonylureas containing an oxime ether moiety was designed and synthesized and their chemical structures were determined by means of ¹H nuclear magnetic resonance(NMR), ¹³C NMR and high-resolution mass spectrometry(HRMS). In the herbicidal bioassay, several compounds showed moderate to good herbicidal activities against dicotyledons, but their activities against monocotyledons decreased. The in vitro antifungal activity was tested at a dosage of 50 mg/L. And the results show that compounds 7l, 7m and 7n exhibit promising antifungal activities against six common plant pathogenic fungi. Further investigations on molecular modification are in progress.     

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.     

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.     

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.     

一些吲哚二酮类衍生物的合成及对AHAS的抑制活性

基于一些新结构特征的AHAS抑制剂, 设计并合成了一系列吲哚二酮类化合物. 初步的生物活性测试结果表明, 所合成的化合物在体内和体外均具有一定的生物活性, 其中, 化合物13在100 μg/mL浓度下对AHAS的抑制达到85%, 化合物7(平皿法)在100 μg/mL浓度条件下对油菜胚根生长抑制率可达84.7%, 是一类未见文献报道的结构新型的AHAS抑制剂, 有望为进一步设计合成更高活性的化合物提供参考.     

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.     

Experimental and computational correlation and prediction on herbicide resistance for acetohydroxyacid synthase mutants to Bispyribac

Bispyribac is a widely used herbicide that targets the acetohydroxyacid synthase(AHAS) enzyme.Mutations in AHAS have caused serious herbicide resistance that threatened the continued use of the herbicide.So far,a unified model to decipher herbicide resistance in molecular level with good prediction is still lacking.In this paper,we have established a new QSAR method to construct a prediction model for AHAS mutation resistance to herbicide Bispyribac.A series of AHAS mutants concerned with the herbicide resistance were constructed,and the inhibitory properties of Bispyribac against these mutants were measured.The 3D-QSAR method has been transformed to process the AHAS mutants and proposed as mutation-dependent biomacromolecular QSAR(MB-QSAR).The excellent correlation between experimental and computational data gave the MB-QSAR/CoMFA model(q2=0.615,r2=0.921,r2 pred=0.598) and the MB-QSAR/CoMSIA model(q2=0.446,r2=0.929,r2 pred=0.612),which showed good prediction for the inhibition properties of Bispyribac against AHAS mutants.Such MB-QSAR models,containing the three-dimensional molecular interaction diagram,not only disclose to us for the first time the detailed three-dimensional information about the structure-resistance relationships,but may also provide further guidance to resistance mutation evolution.Also,the molecular interaction diagram derived from MB-QSAR models may aid the resistance-evading herbicide design.     

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.     

Homologous and heterologous interactions between catalytic and regulatory subunits of <Emphasis Type="Italic">Escherichia coli</Emphasis> acetohydroxyacid synthase I and III

Homologous and heterologous interactions between acetohydroxyacid synthase (AHAS) I and III from E. coli have been studied by surface plasmon resonance (SPR). The catalytic and regulatory subunits association for AHAS I (K _D = 1.13 × 10⁻⁷ M) was stronger than that for AHAS III (K _D = 5.29 × 10⁻⁷ M). A strong heterologous association between regulatory and catalytic subunits and heterologous activation of catalytic subunits were observed. SPR results combined with enzyme kinetics indicate that the reconstituted heterologous enzymes had similar kinetic properties as homologous enzymes, implying that the regulatory subunit of AHAS I could be replaced by the regulatory subunit of AHAS III and vice versa. This work may be useful to further understandings of the mechanism of regulation of AHAS.     

Design, Synthesis and Biological Activity of Substituted-N-[4-（substituted-phenylsulfamoyl）phenyl]benzamide as Potential AHAS Inhibitors

Acetohydroxyacid synthase (AHAS) is an ideal target for the design of environmental benign herbicides, because it catalyzes the first step in the biosynthesis of branched chain amino acids, which does not exist in mammal bodies1-4. Typical AHAS inhibitors…     

新型取代苯甲酰胺类化合物的合成及对 AHAS酶的抑制和除草活性

在对乙酰乳酸合成酶(AHAS)抑制剂进行生物合理设计的基础上, 分别以4-氟-3硝基苯胺和2-胺基-5硝基苯腈为原料, 合成了8个苯磺酰胺基苯甲酰胺类化合物和7个双苯磺酰胺基苯甲酰胺类化合物, 其结构通过核磁共振谱、质谱、红外光谱及元素分析验证. 初步的生物活性测定结果表明, 部分化合物在体内和体外均具有一定的生物活性, 其中化合物4c, 4d和7c在100 μg/mL浓度下对拟南芥AHAS的抑制率分别为66%, 76% 和68%, 而化合物4a, 4c, 7a和7b在100 μg/mL浓度下对油菜根长的抑制率分别为76%, 70%, 89% 和82%. 研究结果为进一步设计合成潜在的AHAS抑制剂提供了有益参考.     

新型含噻二唑环磺酰脲的合成及其生物活性的研究

新型含噻二唑环磺酰脲的合成及其生物活性的研究杨新玲,陈馥衡（北京农业大学应用化学系,北京,１０００９４）关键词噻二唑,磺酰脲,合成,生物活性磺酰脲是７０年代末出现的一类新型超高效除草剂［１］,它以极低的用量和良好的环境安全性而引起世人注目。２－氨基－...     

Synthesis and Herbicidal Activity of Novel Sulfonylureas Containing 1,2,4-Triazolinone Moiety

A series of new sulfonylureas incorporating 1,2,4-triazolinone moiety was synthesized, which were further bio-assayed for the herbicidal activity against four herbs, representative of monocotyledons and dicotyledons. Some of them exhibited high potency to inhibit the growth of dicotyledons(Bassica napus and Amaranthus retroflexus) in the pot experiment. Compounds 9a and 9b also displayed an excellent herbicidal activity against Bassica napus at a concentration of 15 g/hectare, which were comparable with commercial triasulfuron.     

Computational determination of fundamental pathway and activation barriers for acetohydroxyacid synthase‐catalyzed condensation reactions of α‐keto acids

Acetohydroxyacid synthase (AHAS) is the first common enzyme in the biosynthetic pathway leading to the production of various branched‐chain amino acids. AHAS is recognized as a promising target for new antituberculosis drugs, antibacterial drugs, and herbicides. Extensive first‐principles quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have enabled us, in this study, to uncover the fundamental reaction pathway, determine the activation barriers, and obtain valuable insights concerning the specific roles of key amino acid residues for the common steps of AHAS‐catalyzed condensation reactions of α‐keto acids. The computational results reveal that the rate‐determining step of the AHAS‐catalyzed reactions is the second reaction step and that the most important amino acid residues involved in the catalysis include Glu144′, Gln207′, Gly121′, and Gly511 that form favorable hydrogen bonds with the reaction center (consisting of atoms from the substrate and cofactor) during the reaction process. In addition, Glu144′ also accepts a proton from cofactor thiamin diphosphate (ThDP) through hydrogen bonding during the catalytic reaction. The favorable interactions between the reaction center and protein environment remarkably stabilize the transition state and, thus, lower the activation barrier for the rate‐determining reaction step by ～20 kcal/mol. The activation barrier calculated for the rate‐determining step is in good agreement with the experimental activation barrier. The detailed structural and mechanistic insights should be valuable for rational design of novel, potent AHAS inhibitors that may be used as promising new anti‐tuberculosis drugs, antibacterial drugs, and/or herbicides to overcome drug resistance problem. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

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.