磺酰脲类乙酰羟基酸合成酶抑制剂的拓扑物比较分子力场分析

磺酰脲类除草剂是一类高选择性、广谱、低毒的化合物,在世界范围内得到了广泛的应用。本文采用拓扑物比较分子力场分析(Topomer-CoMFA)对75个磺酰脲类化合物与植物源野生型拟南芥AHAS酶的离体相互作用进行了三维定量构效关系研究,构建了Topomer CoMFA模型,该模型具有较强的预测能力(交叉验证相关系数q2为0.890,非交叉验证相关系数r2为0.967)。此模型对测试集的10个化合物的pKi值进行预测,其预测值与实际值基本一致。     

磺酰脲类乙酰羟基酸合成酶抑制剂Topomer CoMFA研究

磺酰脲类除草剂是一类高选择性、广谱、低毒的化合物,在世界范围内得到了广泛的应用。本文采用易位体-比较分子力场法（Topomer CoMFA）对75个磺酰脲类化合物与植物源野生型拟南芥AHAS酶的离体相互作用进行了三维定量构效关系研究,快速准确地构建了Topomer CoMFA模型,该模型具有较强的预测能力（交叉验证相关系数q2为0.890,非交叉验证相关系数r2为0.967）。此模型对测试集的10个化合物的pKi值进行预测,其预测值与实际值一致。     

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.     

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.     

酪氨酸激酶抑制剂的柔性原子受体模型方法研究

用柔性原子受体模型方法对一系列嘧啶类衍生物酪氨酸激酶抑制剂进行了3D－ QSAR研究，建立了相关性很好的模型，这些模型对测试集中化合物活性的预测结果 表明其具有较强的预测能力。柔性原子受体模型方法还给出了虚拟的受体模型，表 明了受体和配体之间可能的相互作用，包括两个氢键相互作用、一个疏水作用和一 个硫－芳香相互作用，这与Novartis的药效团模型非常一致。     

基于药效团模型的DHODH抑制剂构效关系研究

利用药效团模型研究二氢乳清酸脱氢酶(Dihydroorotate dehydrogenase,DHODH)抑制剂的构效关系,为DHODH抑制剂的虚拟筛选提供新的方法.以31个具有DHODH抑制活性的化合物为训练集化合物,半数抑制浓度(IC50)范围为7~63000 nmol/L,利用Catalyst/HypoGen算法构建DHODH抑制剂药效团模型,通过对训练集化合物多个构象进行叠合,提取药效团特征及三维空间限制构建药效团模型.利用基于CatScramble的交叉验证方法及评价模型对已知活性化合物的活性预测能力,确定较优药效团模型.模型包含1个氢键受体、3个疏水中心,表征了受体配体相互作用时可能发生的氢键相互作用、疏水相互作用和π-π相互作用,4个药效特征在三维空间的排列概括了DHODH抑制剂产生活性的结构特点.所得较优模型对训练集化合物及测试集化合物的计算活性值与实验活性值的相关系数分别为0.8405和0.8788.利用药效团模型对来源于微生物的系列化合物进行虚拟筛选,筛选出59个预测活性较好的化合物,可作为进一步药物研发的候选化合物.     

3位苯甲酰腙和亚氨基取代硫脲取代的吲哚满二酮衍生物的合成及对AHAS的抑制活性

基于前期生物设计AHAS抑制剂的研究,设计合成了15个吲哚满二酮类衍生物,其中9个为新化合物,其结构均经过1H NMR,MS和元素分析确证,并对所有化合物进行了离体和活体活性测试.实验结果表明,这类化合物在体内和体外均具有一定的生物活性,在离体活性测试中,所有化合物在100μg/mL浓度下对拟南芥AHAS均表现出明确的抑制活性,其中化合物4d,4e,5a和5f在10μg/mL浓度下仍然对AHAS表现出45%以上的抑制率,但此类化合物除草活性普遍较差.     

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.     

利用网络药理学方法研究热毒宁注射液抗流感病毒的分子作用机制

采用分子对接、网络分析预测热毒宁注射液抗流感病毒的分子作用机制, 并通过已建立的体外流感病毒神经氨酸酶筛选模型对网络预测结果验证. 结果表明, 热毒宁注射液所含化合物在化学空间上具有类药性质; 网络分析揭示出热毒宁注射液是通过与流感病毒吸附、脱壳、复制以及释放等环节的多个蛋白相互作用发挥抗流感病毒作用的; 对于预测的15 个活性分子而言, 实验结果初步证实, 对A型流感病毒, 木犀草素呈现较强的抑制作用, 槲皮素则呈现较弱的抑制作用, 这也初步证实了预测结果.     

基于计算机模拟技术对JAK2抑制剂的定量构效关系、分子设计和分子动力学研究

本文选取了52个对Janus激酶2(JAK2)有抑制作用的小分子化合物,分别使用3D-QSAR中的CoMFA和CoMSIA方法构建了两个可靠的、具有预测能力的模型,并利用分子对接分析数据集化合物与JAK2蛋白的相互作用,表明化合物主要通过氢键和范德华作用与JAK2靶蛋白结合。根据3D-QSAR模型的分析结果,设计了40个化合物,利用构建的模型预测其抑制活性;使用软件预测了化合物的药代动力学(ADME)参数,开展分子对接模拟,最终选择化合物D01和D22与JAK2靶蛋白进行了分子动力学模拟研究,结果显示两个复合物结合构象稳定,与分子对接结果趋势一致。本研究的结果可以为JAK2抑制剂的研发提供一些新的思路,为临床开发此类药物提供理论支撑。     

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.     

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.     

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.     

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...     

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     

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.     

Synthesis and Characterization of Novel Acetohydroxyacid Synthase Inhibitors

IntroductionAcetohydroxyacid synthase(AHAS)serves as thefirst common enzyme in the pathway for the biosynthesisof the branch-chained amino acids,isoleucine,valine,and leucine[1].This pathway is found in bacteria,fun-gi,algae,and higher plants,butnotin ani…     

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.     

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.