Design,synthesis and computational approach to study novel pyrrole scaffolds as active inhibitors of enoyl ACP reductase (InhA) and Mycobacterium tuberculosis antagonists

Novel 54 pyrrolyl acetohydrazide analogues were designed, synthesized and screened for antitubercular activity against InhA. Enoyl-ACP reductase/InhA one of the significant enzymes implicated in type II FAS (fatty acid synthase) biosynthetic pathway of bacterial outer cell membrane, in addition Mycobacterium tuberculosis H37Rv inhibition potency has proven to be one of the most promising drug target used for designing and testing against TB. In silico molecular modeling was achieved using Surflex-docking method to recognize important binding sites of the enoyl-ACP reductase. 3D-QSAR studies like CoMFA and CoMSIA approaches were studied to create 3D-QSAR depictions for InhA inhibitors. Based on docking results the synthesized molecules are oriented towards the core of the active site. The pyrolyl acetohydrazides exhibited one or two H-bonding connections with InhA enzyme. Molecule 8l (MIC 0.4 μg/mL, InhA- 70% at 50 μM) showed H-bonding connections with Tyr158 and NAD⁺ in a similar mode to that of ligand pyrrolidine carboxamide. The tested molecules also showed good antibacterial (Escherichia coli, Staphylococcus aureus) activity (MIC 0.4–25 μg/mL), while the study against A549 lung adenocarcinoma cell line confirms nontoxic nature of the reported molecules. The QSAR model from CoMFA and CoMSIA through the database configuration showed the most excellent data. The prognostic ability of CoMFA and CoMSIA representations was developed by a test set of 15 molecules that produced cross validated correlation coefficients (q²) of 0.642 and 0.701, respectively. This study gives insight into structural requirement needed for the development of more active InhA inhibitors through in silico approach.     

Sample-distance partial least squares: PLS optimized for many variables,with application to CoMFA

Summary Three-dimensional molecular modeling can provide an unlimited number m of structural properties. Comparative Molecular Field Analysis (CoMFA), for example, may calculate thousands of field values for each model structure. When m is large, partial least squares (PLS) is the statistical method of choice for fitting and predicting biological responses. Yet PLS is usually implemented in a property-based fashion which is optimal only for small m. We describe here a sample-based formulation of PLS which can be used to fit any single response (bioactivity). SAMPLS reduces all explanatory data to the pairwise distances among n sample (molecules), or equivalently to an n-by-n covariance matrix C. This matrix, unmodified, can be used to fit all PLS components. Furthermore, SAMPLS will validate the model by modern resampling techniques, at a cost independent of m. We have implemented SAMPLS as a Fortran program and have reproduced conventional and cross-validated PLS analyses of data from two published studies. Full (leaveach-out) cross-validation of a typical CoMFA takes 0.2 CPU s. SAMPLS is thus ideally suited to structure-activity analysis based on CoMFA fields or bonded topology. The sample-distance formulation also relates PLS to methods like cluster analysis and nonlinear mapping, and shows how drastically PLS simplifies the information in CoMFA fields.Abbreviations PLS partial least squares - SAMPLS sample-distance partial least squares - CoMFA comparative molecular field analysis.     

苯环5位取代磺酰脲类化合物的水解动力学及三维定量构效关系初步研究

研究了除草活性较好的9个新型苯环5位取代的磺酰脲类化合物(A~I)分别在酸性、中性及碱性水溶液中的水解情况.采用HPLC-MS对水解产物进行分离鉴定,推测了水解产物的结构及水解路径.采用比较分子力场(Co MFA)方法,对化合物的结构与水解半衰期之间的关系进行了三维定量构效关系(3D-QSAR)研究.结果表明,苯环5位取代的苯磺酰脲类化合物的水解遵循一级动力学反应,容易发生酸性条件下的水解,水解反应第一步主要为酸催化下磺酰脲桥的断裂,形成5位取代的苯磺酰胺和氨基杂环.苯环5位取代的苯磺酰胺进一步发生5位酰胺基的水解,最后得到化合物c(6-氨基糖精)和d(糖精).苯环5位经修饰改造后,在相同条件下,其水解速度明显高于改造前的母体化合物单嘧磺酯和甲磺隆.苯环5位为酰胺基取代的化合物的水解速度随酰胺基上烷基碳原子数的增加及烷基体积的增大而降低.经计算所得的Co MFA模型能够对该系列化合物的水解半衰期进行较好的预测.     

三维定量结构-活性关系研究的近况*

本文介绍并综述了以CoMFA, APEX-3D, Ludi和Leapfrog为代表的三维定量结构一活性关系研究方法的近况。作为药物分子设计的新方法,它们在新药设计和先导化合物的产生中起着越来越重要的作版。     

光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

比较分子力场分析法(CoMFA)的研究新进展

CoMFA是目前3D-QSAR 中应用最广且最为成功的一种方法, 但其在设计思想和实施过程中还存在一定缺陷, 主要表现在匹配规则、新场引入、变量选择及数据处理等几个方面。本文对近年来关于CoMFA 方法的各种改进研究做了较为系统的综述, 并就CoMFA 在药物设计中的作用进行了展望。     

家蝇与大鼠GABA受体抑制剂的药效团模型及其3D-QSAR研究

采用DISCOtech方法,用7个大鼠γ-氨基丁酸(GABA)A受体抑制剂和11个家蝇GABAA受体抑制剂分别建立了其药效团模型;用CoMFA方法建立了22个大鼠GABAA受体抑制剂和29个家蝇GABAA受体抑制剂的3D-QSAR模型,模型的交叉验证相关系数分别为0.526和0.679,验证了药效团模型的合理性,为设计更高活性和更高选择性的化合物提供了参考     

三唑并嘧啶磺酰胺类除草剂的比较分子场法分析

用比较分子场分析方法,分析了三唑并嘧啶类化合物对乙酰乳酸合成酶(ALS)抑制活性的构效关系,推测其与ALs的空间结合模式.     

生物合理设计光系统Ⅱ抑制剂研究(Ⅲ)——3-(4-氯苄胺基)-2-氰基-3-烷基丙烯酸酯类光合作用抑制剂的CoMFA研究

在除草剂的分子设计中,抑制光合作用除草剂的研究一直受到极大的关注．其中,氰基丙烯酸酯类化合物对光合作用中电子传递（即希尔反应）抑制活性较高［１,２］．研究表明,这类化合物在结构上的细微变化对希尔反应抑制活性的影响均很显著．因此,对这类抑制剂进行系统的...     

亲电酮类HDAC抑制剂的3D-QSAR和分子对接研究

组蛋白去乙酰化酶抑制剂(histone deacetylase inhibitor,HDACi)是近年来治疗癌症的重要靶向药物,其中羟氨酸类,苯甲酰胺类多种药物已进入临床试验阶段,但对于亲电酮类HDACi还有待于进一步研究,本研究应用比较分子力场分析法(comparative molecular field analy...