Ligand-based computer-aided pesticide design. A review of applications of the CoMFA and CoMSIA methodologies

An overview is given of the CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) methodologies that are established ligand-based molecular design tools widely used by medicinal and pesticide chemists. In the absence of a three-dimensional structure of the target biopolymer, CoMFA and CoMSIA often provide a practical solution to an otherwise intractable problem of proper characterization of ligand-receptor interactions. These techniques are especially important in agrochemistry, where the number of known molecular structures of pesticide targets is limited. The use of CoMFA and CoMSIA in the agrochemical field for modelling the interactions of insecticides, fungicides, herbicides and herbicide safeners with their target binding sites is illustrated by using some selected published work. The CoMFA and CoMSIA models developed have been used successfully to map the properties of unknown receptors, construct hypotheses for ligand-receptor interactions, optimize lead structures, design novel active compounds, and predict biological activities. The application of CoMFA by the present authors for deriving a binding site hypothesis for dichloroacetamide-type herbicide safeners is described in somewhat more detail.     

QSAR and 3D-QSAR analysis of structurally diverse ALS inhibitors: sulfonylureas and triazolopyrimidine-2-sulfonamides

For the purpose of better understanding the molecular mechanism of action of sulfonylurea and sulfonamide herbicides, the quantitative relationship between their structure and herbicidal activity against rape, Brassica campestris L, was analysed using physicochemical parameters and regression analysis and comparative molecular field analysis (CoMFA). The results showed that the structure–activity relationships of the two sets of compounds were identical, which suggested that the two different sets of compounds affect a common region of the receptor site. The CoMFA results were consistent with those derived from traditional QSAR analysis. Combining the traditional QSAR analysis with the CoMFA results, we can conclude that the variations in the herbicidal activity of the two sets of ALS inhibitors were governed dominantly by the three-dimensional steric and electrostatic field parameters of molecules participating in the interaction with the receptor site and there is apparently an optimum electronic property (Σσ or pKa) for the molecules to fit the receptor. © 1999 Society of Chemical Industry     

Sites of Action of Noncompetitive GABA Antagonists in Houseflies and Rats: Three-Dimensional QSAR Analysis

Quantitative structure–activity relationships for insecticidal activity (against houseflies) and competitive activity against a specific [³⁵S]tert-butylbicyclophosphorothionate binding (to rat brain membranes) of some picrotoxinin-type 4-aminobutyric acid antagonists, including γ-BHC, endosulfan, bicyclophosphates, dioxatricyclododecenes and related compounds, were examined three-dimensionally using comparative molecular field analysis (CoMFA). The antagonists were classified into two series according to their molecular shapes: i.e. whether their structure was ‘linearly’ extended beyond the ‘mast-head’ position of the ‘boat-like’ skeletons (series 1) or not (series 2). The CoMFA showed that the slopes in steric and electrostatic fields around the molecule were significant for both series in governing the potency variations in insecticidal and binding activities. Hydrophobicity, a possible factor controlling transport behaviour of compounds, was significant in governing variations in insecticidal activity, but not for the case of the rat membrane binding. Assuming that there is a slight topological difference between series 1 and 2 compounds in terms of the mode of binding with the housefly receptor site, the insecticidal activity was analysable with a single equation for the combined set of compounds, but the rat membrane binding was not. The sterically and electrostatically favourable regions surrounding the molecular series indicated by CoMFA were roughly located at positions so as to interact with the binding subsites on the receptors proposed previously. © of SCI.     

Comparative analysis of neonicotinoid binding to insect membranes: I. A structure-activity study of the mode of [3H]imidacloprid displacement in Myzus persicae and Aphis craccivora

Neonicotinoids bind selectively to insect nicotinic acetylcholine receptors with nanomolar affinity to act as potent insecticides. While the members of the neonicotinoid class have many structural features in common, it is not known whether they also share the same mode of binding to the target receptor. Previous competition studies with [3H]imidacloprid, the first commercialised neonicotinoid, indicated that thiamethoxam, representing a novel structural sub-class, may bind in a different way from that of other neonicotinoids. In the present work we analysed the mode of [3H]imidacloprid displacement by established neonicotinoids and newly synthesized analogues in the aphids Myzus persicae Sulzer and Aphis craccivora Koch. We found two classes of neonicotinoids with distinct modes of interference with [3H]imidacloprid, described as direct competitive inhibition and non-competitive inhibition, respectively. Competitive neonicotinoids were acetamiprid, nitenpyram, thiacloprid, clothianidin and nithiazine, whereas thiamethoxam and the N-methyl analogues of imidacloprid and clothianidin showed non-competitive inhibition. The chloropyridine or chlorothiazole heterocycles, the polar pharmacophore parts, such as nitroimino, cyanoimino and nitromethylene, and the cyclic or acyclic structure of the pharmacophore were not relevant for the mode of inhibition. Consensus structural features of the neonicotinoids were defined for the two mechanisms of interaction with [3H]imidacloprid binding. Furthermore, two sub-classes of non-competitive inhibitors can be discriminated on the basis of their Hill coefficients for imidacloprid displacement. We conclude from the present data that the direct competitors share the binding site with imidacloprid, whereas non-competitive compounds, like thiamethoxam, bind to a different site or in a different mode.     

Three‐dimensional quantitative structure–activity relationship analysis of acyclic and cyclic chloronicotinyl insecticides

The binding activity of chloronicotinyl insecticides, including acetamiprid, nitenpyram and related compounds, to the nicotinic acetylcholine receptors (nAChR) of houseflies was measured. These compounds were defined as ‘acyclic’ compounds. Variations in the binding activity were analysed using comparative molecular field analysis (CoMFA) which is a technique for the analysis of three‐dimensional quantitative structure–activity relationships. The CoMFA results showed that steric interactions were more significant for the acyclic compounds than for imidacloprid and its derivatives (cyclic compounds). It was also shown that the acyclic compounds could bind to housefly‐nAChR in a similar manner to the cyclic compounds, and that the electrostatic natures of the acyclic amino‐ and cyclic imdazolidine‐moieties affected their binding activity. © 2000 Society of Chemical Industry     

Prediction of the binding mode of imidacloprid and related compounds to house-fly head acetylcholine receptors using three-dimensional QSAR analysis

The binding activity of imidacloprid and related compounds to nicotinic acetylcholine receptors (nAChR) of house flies was measured by use of radioactive α-bungarotoxin as a ligand. Variations in the activity were examined three-dimensionally using comparative molecular field analysis (CoMFA). The CoMFA results suggest that one conformer among the four stable ones is active and provide support for one of the proposed binding models for this class of compound, in which the nitrogen atom of the pyridine ring and the nitrogen atom at the 1-position of the imidazolidine ring interact with the hydrogen-donating and electron-rich sites of nAChR, respectively. The CoMFA field map showed that the nitroimino moiety and a portion of the imidazolidine ring were mainly surrounded by a sterically and electrostatically sensitive region of nAChR. © 1998 Society of Chemical Industry     

Rational herbicide design by synthesis of inhibitors for the peroxidase catalysed oxidation of indolyl-3-acetic acid

An attempt has been made to design a herbicide by synthesising active site directed irreversible inhibitors for the peroxidase-catalysed oxidation of indolyl-3-acetic acid (IAA). A variety of substituted indoles were prepared and found to bind reversibly to the enzyme, but none produced any progressive inhibition, nor showed any herbicidal activity. This may be related to the fact that the inhibitors can be degraded by peroxidase in vitro since, if this occurred in the plant, the compounds could not then interfere with IAA oxidation.     

定量构效关系在农药设计合成中的应用进展

本文介绍了定量结构-活性关系（QSAR）的基本原理，重点评述了其中比较分子力场分析法（CoMFA）的主要理论及用该法建立QSAR模型的步骤，以及QSAR在农药合成设计中的应用进展。     

噁唑烷类安全剂的三维定量构效关系研究

针对25个噁唑烷类化合物,以玉米根部GST活性为衡量标准,运用三维定量构效关系中的比较分子力场分析(CoMFA)和比较分子相似性指数分析(CoMSIA)两种方法进行研究;应用20个化合物作为训练集,分别建立相应的模型,并对其进行结构和活性关系的分析。CoMFA模型的交叉验证系数q2为0.647,非交叉验证系数r2为0.999;CoMSIA模型交叉验证系数q2为0.527,非交叉验证系数r2为0.949。使用训练集以外的5个化合物进行了验证,两种模型预测值与实测值偏差较小,都显示出了较好的预测性和稳定性。研究结果可为设计新的噁唑烷类潜在的除草剂安全剂提供可靠信息。     

QSAR及其在农药设计中的应用和进展

在介绍定量结构 -活性关系 (QSAR)的基本原理后 ,重点评述了 QSAR各种方法的主要原理、优缺点及其在农药设计中的研究应用进展 ,包括取代基多参数法 (Hansch法 )、Free- Wilson法、分子轨道法 (MO)、距离比较法 (DISCO)、比较分子力场分析法 (Co MFA)、分子模拟法 (MS)、分子对接法 (MD)、人工神经网络法 (ANN)以及 Leapfrog法等。     

Design of Inhibitors of Photosystem II using a Model of the D1 Protein

Several inhibitors belonging to structurally different chemical classes were used to analyze the predictive power of an initial model of the herbicide binding niche of the D1 protein belonging to photosystem II (PS II) from plants. In the case of small PS II inhibitors, the estimation of relative activities was hampered by uncertainty about the binding modes. To overcome this problem, a bulky substituent was introduced into the inhibitors to act as a hook, resulting in an unambiguous orientation in the model. The comparison of the modelling results and the experimentally determined IC₅₀ values of different triazines suggested that the previously assumed volume of the binding niche had to be reduced by 20%. After refinement of the model, it was possible to estimate qualitatively, the relative in-vitro activity for inhibitors belonging to different families, as long as an unambiguous binding mode could be deduced either from steric demands or from IC₅₀ values of mutant D1 proteins. The usefulness of the refined model is demonstrated by the successful de-novo design of a potent class of herbicides, the triazolopyrimidines.     

Strobilurin类杀菌剂作用靶标的研究进展

Strobilurin类杀菌剂是在具有杀菌活性的天然β-甲氧基丙烯酸酯衍生物的基础上研发出来的,具有广谱、高效、安全的特点。主要以粘噻唑为例综述了该类杀菌剂作用靶标及作用位点的研究过程及最新进展。生化作用机理的研究明确了粘噻唑作用于线粒体呼吸链bc1复合物中的细胞色素b及铁硫蛋白,阻止了从细胞色素b到细胞色素c1的电子传递,从而抑制线粒体的呼吸作用;蛋白质晶体学研究明确了粘噻唑的作用位点(Qo位点)是通过氢键与铁硫蛋白及细胞色素b的残基结合的。其他strobilurin类杀菌剂和粘噻唑具有相同的靶标,但由于各化合物之间存在一定的结构差异,其具体作用位点亦有一定的差别。     

The inhibition of insect juvenile hormone esterase by trifluoromethylketones: Steric parameters at the active site

A rationally designed structure-activity relationship study has been accomplished using trifluoromethylketone inhibitors of insect juvenile hormone esterase from the cabbage looper, Trichoplusia ni (Hubner) (Lepidoptera: Noctuidae). Several α- and α′-substituted derivatives of 3-octylthio-1,1,1-trifluoropropan-2-one have been prepared and assayed for inhibitory potency against juvenile hormone esterase. The results indicate that the sulfur/protein interaction does not occur in a sterically constrained environment. Substitution adjacent to sulfur did not dramatically effect activity. However, substitution adjacent to the carbonyl of the trifluoromethylketone moiety reduced inhibitory potency substantially, indicating that the active site region of juvenile hormone esterase which interacts with the carbonyl is restricted to rather small substrates. A small hydrophobic pocket near the active site has been identified and can serve to increase inhibitory potency by secondary binding of appropriate substituents. The present study has resulted in the preparation of two more effective in vitro inhibitors of juvenile hormone esterase than those previously reported. Evidence that there are two naturally occurring forms of juvenile hormone esterase has also been provided.     

The herbicide binding niche of photosystem II-a model

The Q_B binding niche of photosystem II is also the binding site for many different herbicides. In order to understand the mode of binding of the herbicides, a 3-dimensional model of the binding niche was constructed. The model was based upon a comparison of the known structure of the Q_B binding niche in purple bacteria with sequence and mutant data of the D-1 protein of photosystem II. Plastoquinone builds up hydrogen bonds to phenylalanine 265 backbone amide nitrogen, to serine 264 hydroxyl, and to histidine 215 delta-1 nitrogen. In addition to these hydrogen bond donors and acceptors, herbicides can build up hydrogen bonds to backbone carbonyl of alamine 263 and to serine 268 hydroxyl. This is supported by binding data of inhibitors in Chlamydomonas reinhardtii chloroplasts of wild type and of five D-1 protein mutants (Ser264 Ala, Ala251 Val, Phe255Tyr, Val2191le, Leu275Phe).     

靶向乙酰胆碱酯酶和几丁质合成酶杀虫剂衍生化合物三维定量构效关系模型构建

为获得活性更佳且同时具备苯甲酰基脲类和氨基甲酸酯类活性的新型双靶标杀虫剂——N-氯磺基-N-甲基氨基甲酸酯衍生物,构建此类化合物的三维定量构效关系（three-dimensional quantitative structure-activity relationship,3D-QSAR）模型,以18种具有双靶标活性的N-氯磺基-N-甲基氨基甲酸酯衍生物为训练集,分别采用比较分子力场分析（comparative molecular field analysis,CoMFA）法和比较分子相似性指数分析（comparative molecular similarity index analysis,CoMSIA）法进行3D-QSAR模型的构建,基于3D-QSAR模型分析同一骨架取代基的变化带给化合物的活性变化,预测不同力场对化合物活性的影响,并对设计的衍生化合物进行活性预测分析。结果表明,经CoMFA法和CoMSIA法构建的3D-QSAR模型可信度高（交叉验证系数q²分别为0.728和0.563）,且有良好的活性预测能力（非交叉验证系数r²分别为0.954和0.981）。基于该模型得到的化合物预测活性与实际活性残差较小且存在良好的线性关系,进一步证明所得3D-QSAR模型的可靠性。通过分析3D-QSAR模型的力场分布,推测在R¹基团处引入位阻较大的疏水性基团、在R²基团苯环的邻位引入同时具有负电性和疏水性但不含卤素原子的基团、用负电性的大位阻基团取代R基团等均可提高N-氯磺基-N-甲基氨基甲酸酯的活性。基于此设计的20种衍生化合物的活性变化从正反两方面印证了该推测的合理性。研究成果可用于指导兼具苯甲酰基脲类和氨基甲酸酯类杀虫剂作用机制的N-氯磺基-N-甲基氨基甲酸酯衍生物的设计。     

Piperonyl butoxide-mediated inhibition of cytochrome P450-catalysed insecticide metabolism: a rational approach

The inhibitory effect of piperonyl butoxide (PBO) on cytochrome P450 was studied by theoretical methods. Binding conformations of PBO were obtained by the recently developed low-mode conformational search within the active site of cytochrome P450_cam. Increased activity of PBO relative to other methylendioxyphenyl inhibitors was rationalized by its decreased conformational mobility and the steric block created by its long side-chain in the substrate access channel of the enzyme. © 1999 Society of Chemical Industry     

Conformational and intramolecular hydrogen bonding effects on post-emergence and pre-emergence selectivities of herbicidal pyrrole dicarboxylates

Dimethyl 2-methyl-5-(chloropyridin-2-yl)pyrrole-3,4-dicarboxylates in which the chlorine atom is substituted at different positions of the pyridine ring have widely varying biological properties. The 3-chloro analog (I) is a post-emergence and pre-emergence herbicide, the 4- and 5-chloro analogs (II, III) are post-emergence herbicides but not pre-emergence, and the 6-chloro analog (IV) is inactive. Computer graphic and molecular mechanics analyses of their molecular conformations showed that the 4- and 5-chloro analogs adopt a coplanar, intramolecularly hydrogen bonded conformation whereas the 3-chloro analog does not. High-level quantum mechanical calculations of the conformational preferences of related model systems were in agreement with these results. Based on this, II and III were predicted to have higher octanol/water partition coefficients relative to I, leading to higher soil binding and weaker xylem transport, hence their observed weaker pre-emergence activities. Experimental measurements of octanol/water partition coefficients, soil binding, and infrared hydrogen bonding studies verified these predictions. Molecular modeling techniques are usually used for designing compounds to fit enzyme active sites and designing putative receptor models. This study demonstrates the usefulness of these techniques for dealing with transport problems.     

Design, synthesis and insecticidal activities of novel pyrazole amides containing hydrazone substructures

BACKGROUND: Pyrazole and hydrazone derivatives possess good insecticidal activities; their substructural units are widely used in pesticide design. In an effort to discover new molecules with good insecticidal activities, a series of pyrazole amide derivatives containing hydrazone substructures were synthesised and bioassayed. RESULTS: Bioassays demonstrated that some of the title compounds exhibited notable control of Plutella xylostella (Linnaeus), Helicoverpa armigera (Hübner), Culex pipiens pallens, Laphygma exigua (Hübner), Spodoptera litura (Fabricius), Nilaparvata lugens (Stål) and Rhopalosiphum maidis (Fitch) at 5, 10, 0.25, 200, 20, 100 and 500 mg L^?1 respectively. Comparative molecular field analysis (CoMFA) based on the bioactivities for P. xylostella was studied; the values of q² and r² for the CoMFA model were 0.701 and 0.964 respectively. CONCLUSION: Some of the title compounds displayed good and broad‐spectrum insecticidal activities against different insect species; the CoMFA model revealed that a bulky and negatively charged group at the 4‐position of benzene could enhance insecticidal activity. These results could provide useful information for the design of novel insecticide containing substructural units of pyrazole amide and hydrazone. Copyright © 2011 Society of Chemical Industry     

3-芳胺甲烯基-6-烷(芳)基-5,6-2H-吡喃-2,4-二酮化合物的3D-QSAR研究

由蕃茄早疫病、马铃薯早疫病中的茄交链孢(Alternaricsolani)代谢物分离出的交链孢酸(Alternaricacid)是一种致病毒素,但对某些真菌却有拮抗作用[1～2]。李树正[3]等对交链孢酸的杀菌活性进行了研究。在此基础上,我们对交链孢酸的结构进行简化,设计合成了3-芳胺甲烯基-6-烷基(芳基)-5,6-2H-吡喃-2,4-二酮类化合物,并进行了生物测定。结果表明此类化合物具有不同程度的杀菌活性。为了进一步对分子进行结构修饰、改造,以得到活性更高的化合物,我们结合计算机辅助分子设计技术,采用比较力场分析(CoMFA)方法对3-芳胺甲烯基-6-烷基(芳基)-5,6-…     

反枝苋乙酰乳酸合成酶与烟嘧磺隆分子结合模式分析及抗性位点预测

为研究反枝苋对乙酰乳酸合成酶 (ALS) 抑制剂的抗性机制,本研究根据反枝苋的ALS氨基酸序列,利用同源模建的方法构建了其三维结构,并采用分子对接和分子动力学模拟的方法预测了反枝苋ALS与烟嘧磺隆分子的结合模式。根据结合模式对已报道的Pro 197和Trp 574等位点突变产生抗性的原因进行了分析。结果发现:Pro 197和Trp 574等位点的残基与烟嘧磺隆分子之间存在重要的疏水作用和π-π作用等其他相互作用,或该位点的残基具有特殊结构影响着通道形状。分析表明,ALS与烟嘧磺隆之间的氢键、疏水作用等非共价相互作用以及通道形状的改变都有可能影响二者结合稳定性,从而使杂草产生抗性。基于此结论,本研究预测Val 196、Met 200、Phe 206和Lys 256突变同样可能使杂草对ALS抑制剂敏感度发生变化。本研究利用计算机模拟技术分析了ALS抗性机制,为反抗性除草剂的分子设计提供了指导。