CoMFA Model of Anti-tumor Activity for Fluoroquinolon-3-yl s-Triazole Sulfide-ketone Derivatives and Implications for Molecular Design

Comparative molecular field analysis(CoMFA) techniques were used to perform three-dimensional quantitative structure-activity relationship(3D-QSAR) studies on the anti-tumor activity(p IH and p IC) of 28 fluoroquinolon-3-yl s-triazole sulfide-ketone derivatives(FQTSDs) against two cancer cell lines, including human hepatoma Hep-3B cells and human pancreatic cancer Capan-1 cells. 23 compounds were randomly selected as the training set to establish the prediction models, which were verified by the test set of 6 compounds containing template molecule. The obtained cross-validation(R_(cv)~2) and non-cross-validation correlation coefficients(R~2) of the CoMFA models were 0.477 and 0.850 for p IH, and 0.421 and 0.836 for p IC, respectively. The contributions of steric and electrostatic fields to p IH were determined to be 48.1% and 51.9%, and those to p IC were 49.4% and 50.6%, respectively. The CoMFA models were then used to predict the activities of the compounds in the training and testing sets, and the models had a strong stability and good predictability. Based on the 3D contour maps, four novel FQTSDs with a higher anti-tumor activity were designed. However, the effectiveness of these novel FQTSDs is still needed to be verified by experimental results.     

新型三唑并噻二唑衍生物对PTP1B的抑制活性的比较分子力场分析研究

基于比较分子力场分析(CoMFA)方法建立21种新型三唑并噻二唑衍生物对PTP1B的抑制活性(pMP)的三维定量构效关系(3D-QSAR)。训练集中17个化合物用于建立预测模型,测试集5个化合物作为模型验证。已建立的CoMFA模型的交叉验证系数(Rcv2)、非交叉验证系数(R2)分别为0.432、0.975,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59.2%、40.8%,表明影响抑制活性(pMP)的主要因素是取代基的空间位阻及疏水性,其次是取代基的氢键及配位作用。基于此研究结果,设计了3个具有较高抑制活性的新化合物,有待医学实验验证。     

CoMFA Study on Anti-proliferative Activity of Fluoroquinolone Amide Derivatives

The in vitro anti-proliferative activity （pICi,i=hp,ca,hl） of fluoroquinolone （rhodanineα,β-unsaturated ketone）amide compounds,referred to as“fluoroquinolone amide derivatives （FQADs）”towards Hep-3B,Capan-1 and HL60 cells,was studied by the 3D-QSAR method of comparative molecular field analysis （Co MFA）.Based on the training set of 14 compounds,the prediction model was established,which was further verified by the test set of 5 compounds with template molecule included.It is found that steric an...     

Studies on a Series of Coumarin Derivatives for Anticancer Activity against Breast Carcinoma Cell Line MCF-7 and Their Molecular Design

Breast cancer is one of the most common malignant tumors in women, and is also the focus of researchers. In this article, 3D-QSAR(three-dimensional quantitative structure-activity relationship) was performed on 24 molecules which are a series of coumarin derivatives for their anticancer activity. Our team divided these compounds randomly into the training and test sets to build the CoMFA(comparative molecular field analysis) and CoMSIA(comparative molecular similarity index analysis) models. The coefficients of cross-validation Q~2 and non cross-validation R~2 for CoMFA model were 0.684 and 0.949, and 0.579 and 0.930 for the CoMSIA model, respectively. The result demonstrates that the model has strong stability and satisfactory predictability. 3D contour maps suggest that the electrostatic factor has the greatest impact on activity followed by the H-bonding acceptor and hydrophilic factors. Taking the above results into account, we designed several molecules with high anticancer activity against breast carcinoma cell line MCF-7.     

Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation

Lysine-specific demethylase 1 (LSD1) is a histone-modifying enzyme, which is a significant target for anticancer drug research. In this work, 40 reported tetrahydroquinoline-derivative inhibitors targeting LSD1 were studied to establish the three-dimensional quantitative structure–activity relationship (3D-QSAR). The established models CoMFA (Comparative Molecular Field Analysis (q² = 0.778, Rpred2 = 0.709)) and CoMSIA (Comparative Molecular Similarity Index Analysis (q² = 0.764, Rpred2 = 0.713)) yielded good statistical and predictive properties. Based on the corresponding contour maps, seven novel tetrahydroquinoline derivatives were designed. For more information, three of the compounds (D1, D4, and Z17) and the template molecule 18x were explored with molecular dynamics simulations, binding free energy calculations by MM/PBSA method as well as the ADME (absorption, distribution, metabolism, and excretion) prediction. The results suggested that D1, D4, and Z17 performed better than template molecule 18x due to the introduction of the amino and hydrophobic groups, especially for the D1 and D4, which will provide guidance for the design of LSD1 inhibitors.     

Topomer CoMFA,HQSAR Studies and Molecular Docking of 2,5-Diketopiperazine Derivatives as Oxytocin Inhibitors

Topomer comparative molecular field analysis(Topomer Co MFA) and holographic quantitative structure-activity relationship(HQSAR) for 130 2,5-diketopiperazine derivatives were used to build a three-dimensional quantitative structure-activity relationship(3D-QSAR) model. The results show that the models have high predictive ability. For Topomer CoMFA, the cross-validated q~2 value is 0.710 and the non-cross-validated r~2 value is 0.834. The most effective HQSAR model shows that the cross-validation q~2 value is 0.700, the non-cross-validated r~2 value is 0.815, and the best hologram length value is 353 using connections and bonds as fragment distinctions. 50 highly active 2,5-diketopiperazine derivatives were designed based on the three-dimensional equipotential map and HQSAR color code map. Finally, the molecular docking method was also used to study the interactions of these new molecules by docking the ligands into the diketopiperazine active site, which revealed the likely bioactive conformations. This study showed that there are extensive interactions between the new molecule and Arg156, Arg122 residues in the active site of diketopiperazine. These results provide useful insights for the design of potent of the new 2,5-diketopiperazine derivatives.     

Structure–Activity Relationship Assessment of Sophorolipid Ester Derivatives against Model Bacteria Strains

Sophorolipids (SLs) are glycolipids that consist of a hydrophilic sophorose head group covalently linked to a hydrophobic fatty acid tail. They are produced by fermentation of non-pathogenic yeasts such as Candida Bombicola. The fermentation products predominantly consist of the diacetylated lactonic form that coexists with the open-chain acidic form. A systematic series of modified SLs were prepared by ring opening of natural lactonic SL with n-alkanols of varying chain length under alkaline conditions and lipase-selective acetylation of sophorose primary hydroxyl groups. The antimicrobial activity of modified SLs against Gram-positive human pathogens was a function of the n-alkanol length, as well as the degree of sophorose acetylation at the primary hydroxyl sites. Modified SLs were identified with promising antimicrobial activities against Gram-positive human pathogens with moderate selectivity (therapeutic index, TI = EC₅₀/MIC_{B. cereus} = 6–33). SL-butyl ester exhibited the best antimicrobial activity (MIC = 12 μM) and selectivity (TI = 33) among all SLs tested. Kinetic studies revealed that SL-ester derivatives kill B. cereus in a time-dependent manner resulting in greater than a 3-log reduction in cell number within 1 h at 2×MIC. In contrast, lactonic SL required 3 h to achieve the same efficiency.     

Synthesis and Antiproliferative Activity against Cancer Cells of Indole-Aryl-Amide Derivatives

Indoles constitute a large family of heterocyclic compounds widely occurring in nature which are present in a number of bioactive natural and synthetic compounds, including anticancer agents or atypical opioid agonists. As a result, exponential increases in the development of novel methods for the synthesis of indole-containing compounds have been reported in the literature. A series of indole-aryl amide derivatives 1–7 containing tryptamine or an indolylacetic acid nucleus were designed, synthesized, and evaluated as opioid ligands. These new indole derivatives showed negligible to very low affinity for μ- and δ-opioid receptor (OR). On the other hand, compounds 2, 5 and 7 showed Ki values in the low μM range for κ-OR. Since indoles are well known for their anticancer potential, their effect against a panel of tumor cell lines was tested. The target compounds were evaluated for their in vitro cytotoxicity in HT29, HeLa, IGROV-1, MCF7, PC-3, and Jurkat J6 cells. Some of the synthesized compounds showed good activity against the selected tumor cell lines, with the exception of IGROV1. In particular, compound 5 showed a noteworthy selectivity towards HT29 cells, a malignant colonic cell line, without affecting healthy human intestinal cells. Further studies revealed that 5 caused the cell cycle arrest in the G1 phase and promoted apoptosis in HT29 cells.     

Synthesis,Antimicrobial Activity and Molecular Docking Study of Thiazole Derivatives

The reaction of 4‐thiochromane thiocarbohydrazone with a series of hydrazonoyl halides in dioxane in the presence of triethylamine afforded novel thiochromane derivatives incorporating 1,3‐thiazole moiety. The structure of the latter compounds was established by elemental analysis and spectral technique and by their chemical transformation. Moreover, the antimicrobial activity of the newly synthesized compounds was screened and the results showed that some compounds have higher activity than the applied fungicide and bactericide. The antimicrobial activity of the most active compounds was interpreted by molecular docking study.     

Design,Synthesis, Biological Activity and Molecular Docking Study of Coumarin Derivatives Bearing 2-Methylbiphenyl Moiety

A hybrid pharmacophore approach was used to design and synthesize a series of coumarin derivatives bearing 2-methylbiphenyl moiety, which were evaluated for their in vitro anticancer activities against four cancer cell lines(MCF-75 A549, H460 and HT29) and PD-1/PD-L1 inhibitory activities. Moreover, several compounds with excellent anticancer activities were selected to evaluate the cytotoxicities against one normal cell line(HEK-293). The most promising compound llo showed the best anticancer activities against the four tested cancer cell lines with the IC50 values of 6.45, 8.65, 6,57 and 8.13 gmol/L, respectively, and displayed weak cytotoxicity on the normal cell(HEK-293). Furthermore, screening of PD-1 /PD-L1 inhibitory activity revealed that compound llo could effectively inhibit the binding of PD-1/PD-L1, and the binding interactions of compound llo with PD-L1 protein were explored by molecular docking. All above evidences showed that compound llo might be worthy of further study as a valuable leading compound for the treatment of cancer.     

Design,Synthesis, Molecular Modeling and Antitumor Evaluation of Novel Indolyl-Pyrimidine Derivatives with EGFR Inhibitory Activity

Scaffolds hybridization is a well-known drug design strategy for antitumor agents. Herein, series of novel indolyl-pyrimidine hybrids were synthesized and evaluated in vitro and in vivo for their antitumor activity. The in vitro antiproliferative activity of all compounds was obtained against MCF-7, HepG2, and HCT-116 cancer cell lines, as well as against WI38 normal cells using the resazurin assay. Compounds 1–4 showed broad spectrum cytotoxic activity against all these cancer cell lines compared to normal cells. Compound 4g showed potent antiproliferative activity against these cell lines (IC₅₀ = 5.1, 5.02, and 6.6 μM, respectively) comparable to the standard treatment (5-FU and erlotinib). In addition, the most promising group of compounds was further evaluated for their in vivo antitumor efficacy against EAC tumor bearing mice. Notably, compound 4g showed the most potent in vivo antitumor activity. The most active compounds were evaluated for their EGFR inhibitory (range 53–79%) activity. Compound 4g was found to be the most active compound against EGFR (IC₅₀ = 0.25 µM) showing equipotency as the reference treatment (erlotinib). Molecular modeling study was performed on compound 4g revealed a proper binding of this compound inside the EGFR active site comparable to erlotinib. The data suggest that compound 4g could be used as a potential anticancer agent.     

Pharmacophore Screening on Piperidinecarboxamides Derivatives Based on GALAHAD and CoMFA Models

In order to discover the novel anticonvulsant drugs, pharmacophore screening of the anticonvulsant inhibitors was enforced. Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD) and Comparative Molecular Field Analysis (CoMFA) studies were combined to implement our research. Firstly, multiple models were generated using GALAHAG based on high active molecules. Secondly, several of them were validated using the CoMFA study. Finally, a good values of q² from training set and promising predictive power from test set were obtained based on one model simutaneously. One model had been selected as the most reasonable pharmacophore model. The results of the CoMFA study based on the model 1 suggested that both steric and electrostatic interactions played important roles.     

Synthesis and Antiviral Activity of Camphene Derivatives against Different Types of Viruses

To date, the ‘one bug-one drug’ approach to antiviral drug development cannot effectively respond to the constant threat posed by an increasing diversity of viruses causing outbreaks of viral infections that turn out to be pathogenic for humans. Evidently, there is an urgent need for new strategies to develop efficient antiviral agents with broad-spectrum activities. In this paper, we identified camphene derivatives that showed broad antiviral activities in vitro against a panel of enveloped pathogenic viruses, including influenza virus A/PR/8/34 (H1N1), Ebola virus (EBOV), and the Hantaan virus. The lead-compound 2a, with pyrrolidine cycle in its structure, displayed antiviral activity against influenza virus (IC₅₀ = 45.3 µM), Ebola pseudotype viruses (IC₅₀ = 0.12 µM), and authentic EBOV (IC₅₀ = 18.3 µM), as well as against pseudoviruses with Hantaan virus Gn-Gc glycoprotein (IC₅₀ = 9.1 µM). The results of antiviral activity studies using pseudotype viruses and molecular modeling suggest that surface proteins of the viruses required for the fusion process between viral and cellular membranes are the likely target of compound 2a. The key structural fragments responsible for efficient binding are the bicyclic natural framework and the nitrogen atom. These data encourage us to conduct further investigations using bicyclic monoterpenoids as a scaffold for the rational design of membrane-fusion targeting inhibitors.     

N-取代邻苯二甲酰亚胺类衍生物的设计、合成及活性评价

结合中药脱皮马勃中分离得到的3,5-二羟基邻苯二甲酰亚胺和邻苯二甲酰亚胺类化合物的结构设计合成了一系列N-取代-3,5-二甲氧基邻苯二甲酰亚胺及N-取代-3,5-二羟基邻苯二甲酰亚胺类衍生物,其结构经¹H NMR,¹³C NMR和MS分析确证. 选取人肺腺癌细胞A549及人脐静脉血管内皮细胞HUEVC为测试细胞株,评价了所合成化合物的体外抗肿瘤及抗血管生成活性,结果表明,部分化合物表现出一定的活性.     

新型香豆素衍生物的设计、合成及除草活性研究

以(未)取代的间苯二酚与β-酮酸酯类化合物为起始原料,在酸的催化下发生Pechmann 反应,合成了4个关键中间体--7-羟基香豆素衍生物(1a~1d),其与芳氧乙(丙)酰氯作用,合成了8个结构新颖的7-芳氧乙酰氧基香豆素衍生物(2a~2h),其结构经¹H NMR、¹³C NMR和元素分析表征。油菜平皿法和稗草小杯法的测试结果表明,目标化合物对双子叶植物油菜根长的抑制效果好,与阳性对照药2,4-D相当,并表现出一定的构效关系。进一步的温室盆栽实验(50 g/亩)表明,茎叶处理时,部分目标化合物(如2a~2e)对双子叶植物的抑制率为100%,与2,4-D的防效相当,具有作为先导化合物进一步优化的价值。      

Design,Synthesis and Antifungal Activity of Novel Triazole Derivatives

Twenty-one 1-(1H-1,2,4-triazolyl)-2-(2,4-diflurophenyl)-3-(4-substituted-1-piperazinyl)-2-propanol derivatives were designed and synthesized,on the basis of the active site of lanosterol 14α-demethylase.In vitro antifungal activities showed that some of the target compounds had higher antifungal activity and broader antifungal spectrum than fluconazole.     

咪唑啉衍生物缓蚀剂的定量构效关系及分子设计

采用量子化学密度泛函理论(DFT)及线性回归分析方法, 对十一烷基咪唑啉衍生物缓蚀剂抗H2S、CO2腐蚀性能进行了定量构效关系(QSAR)研究. 通过回归分析, 筛选出了影响缓蚀剂缓蚀性能的主要因素, 建立了QSAR模型, 并使用留一法交叉验证对模型的稳定性及预测能力进行了分析. 结果表明, 电子转移参数△N、咪唑环上非氢原子静电荷之和∑Qring及分子极化率α对咪唑啉类缓蚀剂的缓蚀性能有很大的贡献, 所得模型的拟合相关系数(R2)和交叉验证相关系数(q2)分别为0.924 和0.917, 模型对此类缓蚀剂抗H2S、CO2腐蚀性能具有较好的预测效果. 应用QSAR研究结果进行了分子设计, 在理论上提出了一些具有较高抗H2S、CO2腐蚀性能的新型咪唑啉衍生物, 为实验工作者合成新型缓蚀剂提供理论参考.     

取代喹啉类化合物抗菌活性的定量构效关系及分子设计

采用密度泛函理论(DFT)和逐步回归分析法对15种新合成的取代喹啉类化合物进行了定量构效关系(QSAR)研究. 在B3LYP/6-31G(d,p)水平上计算了取代喹啉的量子化学参数, 通过逐步多元回归分析筛选出影响抗菌活性的主要因素, 建立了定量构效关系方程, 并用留一法交叉分析了模型的稳定性及预测能力. 结果表明, C5的亲核电子密度fNC5及C9-N1的键级BC9-N1是影响喹啉类化合物抗金黄色葡萄球菌活性的主要因素, 所得模型对该类化合物抗菌活性有较好的预测效果. 同时基于QSAR研究结果设计了4个活性较高的新喹啉衍生物.     

Molecular Modeling and Design of Arylthioindole Derivatives as Tubulin Inhibitors

Three-dimensional quantitative structure activity relationship （3D-QSAR） and docking studies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the comparative molecular field analysis （CoMFA） for training set with significant statistical quality （R2=0.898） and predictive ability （q2=0.654） was established. The same model was further applied to predict pIC50 values of the compounds in test set, and the resulting predictive correlation coefficient R2（pred） reaches 0.816, further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very interesting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some important factors improving the activities of these compounds were discussed in detail and were summarized as follows： the substituents R3-R5 （on the phenyl ring） with higher electronegativity, the substituent R6 with higher eleetropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.