3D－QSAR Study on Diindolylmethane and Its Analogues with Comparative Molecular Field Analysis(CoMFA)

Comparative molecular field analysis (CoMFA),a three dimensional quantitative structure-activity relationship (3D-QSAR) method was applied to a series of diindolylmethane(DIM) analogs to study the relationship between their structure and their induction of CYP 1A1-associated ethoxyresorufin-O-deethylase(EROD) activity.A DISCO model of pharmacophore was derved to guide the superposition of the compounds.The coefficient of cross-validation (q^2) and non cross-validation(r^2) for the model established by the study are 0.827 and 0.988 respectively,the value of variance ratio (F) is 103.53 and standard error estimate (SEE)is 0.044.These values indicate that the CoMFA model derived is significant and might have a good prediction for the catalytic activity of DIM compounds.As a consequence,the predicted activity values of new designed compounds were all higher than that of the reported value.     

Grid potential analysis,virtual screening studies and ADME/T profiling on N‐arylsulfonylindoles as anti‐HIV‐1 agents

A grid potential analysis employing a novel approach of 3D quantitative structure–activity relationships (QSAR) as AutoGPA module in MOE2009.10 was performed on a dataset of 42 compounds of N‐arylsulfonylindoles as anti‐HIV‐1 agents. The uniqueness of AutoGPA module is that it automatically builds the 3D‐QSAR model on the pharmacophore‐based molecular alignment. The AutoGPA‐based 3D‐QSAR model obtained in the present study gave the cross‐validated Q² value of 0.588, r²_pred value of 0.701, r²_m statistics of 0.732 and Fisher value of 94.264. The results of 3D‐QSAR analysis indicated that hydrophobic groups at R₁ and R₂ positions and electron releasing groups at R₃ position are favourable for good activity. To find similar analogues, virtual screening on ZINC database was carried out using generated AutoGPA‐based 3D‐QSAR model and showed good prediction. In addition to those mentioned earlier, in‐silico ADME absorption, distribution, metabolism and excretion profiling and toxicity risk assessment test was performed, and results showed that majority of compounds from current dataset and newly virtually screened hits generated were within their standard limit. Copyright © 2013 John Wiley & Sons, Ltd.     

CoMFA 3D-QSAR Analysis of Epothilones Based on Docking Conformation and Alignment

Epothilones belong to a class of novel microtubule stabilizing and anti-mitotic agents, which have a paclitaxel-like mechanism of action. A three-dimensional quantitative structure-activity relationship （3D-QSAR） model was built for epothilones by the method of comparative molecular field analysis （CoMFA） combined with the flexible docking technology. The docking CoMFA model gave a good cross-validated value of q2=0.784 with an optimized component of 6 and the conventional correlation coefficient of r^2=0.985. The statistical results show that the model has good ability to predict the activity of the studied compounds. At last, the docking CoMFA model was analyzed through contour maps complemented with MOLCAD-generated active site potential surface in the α,β-tubulin receptor, which can provide important information for the structure-based drug design.     

Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using three‐dimensional quantitative structure‐activity relationship,virtual screening,and docking simulations

In this paper, two 3‐dimensional quantitative structure‐activity relationship models for 60 human immunodeficiency virus (HIV)‐1 protease inhibitors were established using random sampling analysis on molecular surface and translocation comparative molecular field vector analysis (Topomer CoMFA). The non–cross‐validation (r²), cross‐validation (q²), correlation coefficient of external validation (Q²_ext), and F of 2 models were 0.94, 0.80, 0.79, and 198.84 and 0.94, 0.72, 0.75, and 208.53, respectively. The results indicated that 2 models were reasonable and had good prediction ability. Topomer Search was used to search R groups in the ZINC database, 20 new compounds were designed, and the Topomer CoMFA model was used to predicate the biological activity. The results showed that 18 new compounds were more active than the template molecule. So the Topomer Search is effective in screening and can guide the design of new HIV/AIDS drugs. The mechanism of action was studied by molecular docking, and it showed that the protease inhibitors and Ile50, Asp25, and Arg8 sites of HIV‐1 protease have interactions. These results have provided an insight for the design of new potent inhibitors of HIV‐1 protease.     

取代苯丙酮肟衍生物的合成、QSAR研究以及优化

本文介绍了用结合化学、生物实验以及计算机辅助分子设计方法优化对瓜类白粉病毒有抑制作用的先导化合物的研究。用3－取代氨基－1－芳基丙酮－1－肟以及卤代烃合成了44个取代苯丙酮肟衍生物。生物测试的结果表示这些化合物大部分对瓜类白粉病毒有抑制作用。基于这些生物测试,对这44个化合物做了QSAR研究。根据所得CoMFA (rcv2, S 以及 r2 分别为0.577, 0.258, 0.962) 和 CoMSIA (rcv2, S 以及 r2 分别为0.583, 0.343, 0.932) 模型,设计了3个新化合物,而且预测结果显示,它们无致癌和致突变毒性。测试结果显示预测活性与实验活性相对应,说明这两个模型具有较高的预测准确率。     

Docking Study and Three‐Dimensional Quantitative Structure‐Activity Relationship (3D‐QSAR) Analyses and Novel Molecular Design of a Series of 4‐Aminoquinazolines as Inhibitors of Aurora B Kinase

The Aurora proteins are critical regulators of major mitotic events and attractive targets for anticancer therapy. 3D‐QSAR studies based on molecular docking were performed on a dataset of 40 4‐aminoquinazolines compounds. The CoMSIA model produced significantly better results than CoMFA model, with q²=0.652 and r²=0.991. The contours analysis provides useful information about the structural requirements for 4‐aminoquinazolines for inhibiting Aurora B. Scaffold hopping method was used to generate new structures based on the maximum common substructure of the training and test set compounds. The ADMET property, binding affinity and inhibitory activity of the new designed compounds were predicted, respectively. Finally 16 compounds were identified as the novel inhibitors for Aurora B kinase.     

Synthesis,Bioactivities and Structure Activity Relationship of N‐4‐Methyl‐1,2,3‐thiadiazole‐5‐carbonyl‐N′‐phenyl Ureas

Twenty nine novel N‐4‐methyl‐1,2,3‐thiadiazole‐5‐carbonyl‐N′‐phenyl ureas were designed and synthesized, and their structures were confirmed by proton nuclear magnetic resonance (¹H NMR), infra red spectroscopy (IR) and high‐resolution mass spectroscopy (HRMS). Compounds V‐9 , V‐11 , V‐12 , V‐15 , V‐19 , V‐21 , V‐22 and V‐24 exhibit excellent activity against Culex pipiens pallens. Compounds V‐12 and V‐22 present good insecticidal activity against Plutella xylostella L. Their median lethal concentrations (LC₅₀) are 164.15 and 89.69 mg·L^?1, respectively. Compound V‐11 also has potential wide spectrum of fungicide activity. Its median effective concentrations (EC₅₀) detected from 3.82 µg·mL^?1 against Physalospora piricola to 31.60 µg·mL^?1 against Cercospora arachidicola. Compounds V‐15 and V‐24 show outstanding induction activities as same as positive controls TDL and ningnanmycin, furthermore V‐24 has the highest induction activity of 41.85%±4.43%. To elucidate the structure activity relationship in these compounds, a 3D‐QSAR model has been built. The established model showed a reliable predicting ability with q² values of 0.643 and r² values of 0.982.     

离子相互作用模型在HCl-LiCl-MgCl2-H2O体系20˚C时溶解度预测中的应用

Component solubility in HCl-LiCl-MgCl2-H2O system of high ionic strength at 20℃ was predicted by using the Pitzer＇s ion-interaction model. The results indicated that the model supplied a very good prediction of the component solubility of the system mentioned above. The values of parameters of β^0, β^1 and C^＊ of HCl, LiCl and MgCl2 were obtained from optimization of literature data, while those of θMN and ψMNX were calculated from a least-squares optimization procedure to couple activity coefficient with solubility data. According to the ion-interaction model, no additional parameters need to be determined for more complex systems. The study provided theoretical basis for the manufacture process, which was proposed by Gao and employed to extract LiCl and MgCl2·6H2O from salt lake brine.     

Insight into the structural requirements of benzimidazole derivatives as interleukin‐2 inducible t‐cell kinase inhibitors by computational explorations

In the present work, a set of ligand‐ and receptor‐based 3D‐QSAR models were developed to explore the structure–activity relationship of 109 benzimidazole‐based interleukin‐2‐inducible T‐cell kinase (ITK) inhibitors. In order to reveal the requisite 3D structural features impacting the biological activities, a variety of in silico modeling approaches including the comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), docking, and molecular dynamics were applied. The results showed that the ligand‐based CoMFA model (Q² = 0.552, R²_ncv = 0.908, R²_pred = 0.787, SEE = 0.252, SEP = 0.558) and CoMSIA model (Q² = 0.579, R²_ncv = 0.914, R²_pred = 0.893, SEE = 0.240, SEP = 0.538) were superior to other models with greater predictive power. In addition, a combined analysis between the 3D contour maps and docking results showed that: (1) Compounds with bulky or hydrophobic substituents near ring D and electropositive or hydrogen acceptor groups around rings C and D could increase the activity. (2) The key amino acids impacting the receptor–ligand interactions in the binding pocket are Met438, Asp500, Lys391, and Glu439. The results obtained from this work may provide helpful guidelines in design of novel benzimidazole analogs as inhibitors of ITK. © 2013 Wiley Periodicals, Inc.     

Design and Synthesis of α,β‐Epoxyketones as New Anticancer Agents

As epoxy functional group has high anticancer activity, α,β‐epoxyketones were designed and synthesized as new anticancer agents, and their structures were confirmed by UV, ¹H NMR, IR, MS technigeces and elemental analysis. Their in vitro anticancer activities were evaluated by MTT method and the results showed that the compound 4c exhibited good activity with IC₅₀ of 17.8, 22.0 and 24.1 µg/mL against A‐549, Hela and HepG2 cells, respectively. The dose of LD50 of the mice by intragastric administration was 1864.4 mg/kg. Therefore, the α,β‐epoxyketones could potentially provide as new anticancer agents.     

两种希夫碱对大肠杆菌抗菌活性的微量热法研究

The microcalorimetric method was used to study the antibacterial activity of two newly synthesized Schiff base compounds （H2L3＇ and H2L3） on Escherichia coli, trying to obtain the action on both of multiplying bacteria and non-multiplying bacteria at one experiment. The metabolic power-time curves of the bacteria treated with the compounds were obtained, and the thermokinetic parameters were analyzed, from which the antibacterial activities of these compounds were evaluated. The results showed that both of the two compounds have good activity on aerobic multiplying metabolism of E. coli, with the value of ICso 75.8 and 168.8 mg/L respectively, but have not effective action on fermentation metabolism of E. coli. The action of the compounds on the non-multiplying metabolism was investigated by taking the heat output of E. coli in the stationary phase as the guideline of the activity. The value of MSCso （minimum stationary-cidal concentration 50） of them is 118 and 187.5 mg/L, respectively. So, H2L^3 has stronger antibacterial action on E. coli than H2L^3 either for multiplying bacteria or non-multiplying bacteria, and their activity on the aerobic multiplying bacteria of E. coil is mainly shown. It does strongly suggest that the calorimetric method should play an important role in the fight against the drug-resistant bacteria.     

Theoretical Study on Gas—phase Pyrolytic Reactions of N—Ethyl,Isopropyl and N—t—Butyl Substituted 2—Aminopyrazine

Density functional theory (DFT) and ab initio methods were used to study gas‐phase pyrolytic reaction mechanisms of iV‐ethyl, N‐isopropyl and N‐t‐butyl substituted 2‐aminopyrazine at B3LYP/6–31G* and MP2/6–31G*, respectively. Single‐point energies of all optimized molecular geometries were calculated at B3LYP/6–311 + G(2d,p) level. Results show that the pyrolytic reactions were carried out through a unimolecular first‐order mechanism which were caused by the migration of atom H(17) via a six‐member ring transition state. The activation energies which were verified by vibrational analysis and correlated with zero‐point energies along the reaction channel at B3LYP/6–311 + G(2d,p) level were 252.02 kJ. mo^?1 (N‐ethyl substituted), 235.92 kJ‐mol^?1 (N‐t‐isopropyl substituted) and 234.27 kJ‐mol^?1 (N‐t‐butyl substituted), respectively. The results were in good agreement with available experimental data.     

Design,Synthesis and Biological Evaluation of Isothiazole Based 1,2,4‐Trizaole Derivatives

A series of novel 3,4‐dichloroisothiazole based 1,2,4‐triazole derivatives were rationally designed and synthesized. Their structures were confirmed by ¹H NMR, ¹³C NMR, HRMS or elemental analysis; the typical crystal structure was determined by X‐ray diffraction for validation. All target compounds were evaluated for their in vitro fungicidal and in vivo anti‐TMV activities. The bioassay results indicated that compound 6b , namely 1‐(3,4‐dichloroisothiazol‐5‐yl)‐1‐(4‐fluorophenyl)‐2‐(1H‐1,2,4‐triazol‐1‐yl)ethanol, exhibited excellent growth inhibition against B. cinerea, C. arachidicola and P. piricola with median effective concentrations (EC₅₀) of 6.98, 2.73 and 3.07 μg/mL, respectively, and good in vivo anti‐TMV activity of over 60% of inactivation and induction activity at 100 μg/mL. These data demonstrate that compound 6b is both a fungicide and an anti‐TMV lead, deserving further studies.     

Synthesis,Molecular Docking and Potential Antioxidant Activity of Di/Trisubstituted Pyridazinone Derivatives

A number of pyridazinone derivatives bearing substituted benzylidene and heterocyclic/aromatic rings at 4^th and 6^th positions, respectively were synthesized in good to moderate yields and screened for antioxidant activity. Antioxidant activity of pyridazinone derivatives was evaluated by using several in vitro radical scavenging methods such as 1,1‐diphenylpicrylhydrazyl (DPPH), hydrogen peroxide (H₂O₂), nitric oxide (NO), reducing power, and metal chelating assay etc. Molegro virtual docker software was used to study the binding affinity of the title compounds with the xanthine oxidoreductase enzyme. Amongst the tested compounds, 5a, 5d, 5g & 5j were found to exhibit excellent antioxidant activity at par with the positive control, ascorbic acid. The molecular docking studies of these compounds demonstrated a good selectivity profile with xanthine oxidoreductase receptors. A preliminary study of the structural‐activity relationship showed that the presence of electron withdrawing group and heterocyclic ring on pyridazinone nucleus are associated with the best potency and selectivity profile. It could be proposed that xanthine oxidoreductase receptor may be involved in observed antioxidant activity of pyridazinone derivatives bearing aromatic ring and benzylidene substituents and thus the synthesized compounds are worthy of further exploration.     

Three-dimensional Quantitative Structure-Activity Relationship Analyses of a Series of Butenolide ETA Antagonists

Two kinds of Three-dimensional Quantitative Structure-activity Relationship(3D-QSAR) methods,comparative molecular filed analysis(CoMFA) and comparative molecular similarity indices analysis (CoMSIA) ,were applied to analyze the structure-activity relationship of a series of 63 butenolide ETA selective antagonists with respect to their inhibition against human ETA receptor,The CoMFA and CoMSIA models were developed for the conceivable alignment of the molecules based on a template structure from the crystallized data.The statistical results from the initial orientation of the aligned molecules show that the 3D-QSAR model from CoMFA(q^2=0.543) is obviously superior to that from the conventional CoMSIA(q^2=0.407).In order to refine the model,all-space search (ASS) was applied to minimize the field sampling process.By rotating and translating the molecular aggregate within the grid systematically,all the possible samplings of the molecular fields were tested and subsequently the one with the highest q^2 was picked out .The comparison of the sensitivity of CoMFA and CoMSIA to different space orientation shows that the CoMFA q^2 values are more sensitive to the translations and rotations of the aligned molecules with respect to the lattice than those of CoMSIA.The best CoMFA model from ASS was further refined by the region focused technique.The high quality of the best model is indicated by the high corss-validated correlation and the prediction on the external test set.The CoMFA coefficient contour plots identify several key features that explain the wide range of activities,which may help us to design new effective ETA selective antagonists.     

A High Pressure Study on NH4Pb2Br5 Type Compounds Part II: Electronic Structure and Changes under High Pressure

In this work, we present a theoretical study (based on DFT‐calculations) of the electronic properties of compounds crystallising in a NH₄Pb₂Br₅ type structure in a wide pressure range. The main focus of this study is to elucidate the nature of bonding of the ns²‐cations at ambient and elevated pressure. For a better understanding of the structure and bonding, the DOS of these compounds are evaluated and discussed on the basis of a simple model assuming mainly ionic interactions. The calculations are complemented by an orbital analysis using the crystal orbital Hamilton population (COHP) and an analysis of the electronic density topology with the electron localisation function (ELF). Structural and theoretical investigations give results that are in excellent agreement: The DFT‐calculations confirm the existence of bonding interactions between the ns²‐cations at elevated pressure. Our study indicates that the “character” of the additional electron pair changes with increasing pressure from nonbonding to bonding in agreement with a simple model system of two interacting ns²‐cations.     

Synthesis and Herbicidal Activity of α-Hydroxy Phosphonate Derivatives Containing Pyrimidine Moiety

A series of α‐hydroxy phosphonate derivatives containing pyrimidine moiety were designed and synthesized. Their structures were characterized by IR, ¹H NMR, MS and elemental analysis. The results of preliminary herbicidal activities (in vitro) showed that some of the title compounds 2 exhibited moderate herbicidal activities against dicotyledonous weeds (Brassica campestris L), and most of compounds 2 showed better activity against dicotyledonous weeds than monocotyledonous weeds (Echinochloa crus‐galli). Further bioassays (in vivo) indicated that some of the title compounds 2 possessed good and selective herbicidal activity against amaranth pigweed (A. retroflexus) in both pre‐ and post‐emergence treatments at the dose of 1.5 kg/ha. For exmple, compounds 2a , 2b and 2e exhibited 100% inhibition against A. retroflexus in pre‐emergence treatment, and 91.7%, 98.8% and 99.5% inhibition in post‐emergence treatment at the dose of 1.5 kg/ha, respectively.     

培氟沙星均三唑硫醚衍生物抗肝癌活性的CoMFA模型与分子设计

基于比较分子力场分析(CoMFA)方法建立24种培氟沙星均三唑硫醚衍生物抗肝癌活性(pM)的三维定量构效关系(3D-QSAR)。训练集中20个化合物用于建立预测模型,测试集10个化合物(含模板分子及新设计的5个分子)作为模型验证。已建立的3D-QSAR模型的交叉验证系数(R_cv²)、非交叉验证系数(R^₂)分别为0.705、0.940,说明所建模型具有较强的稳定性和良好的预测能力。该模型中立体场、静电场贡献率依次为74.8%、25.2%,表明影响抗肝癌活性(pM)的主要因素是取代基的疏水性和空间契合,其次是库仑力、氢键及配位。基于三维等势图,设计了5个具有较高抗肝癌活性的分子,有待医学实验验证。