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.     

Syntheses of Lactam Derivatives of Chenodeoxycholic Acid and in vitro Antiproliferative Activity

With chenodeoxycholic acid as starting material,a series of lactam derivatives of chenodeoxycholic acid was synthesized and their antiproliferative activities against some cancer cells were determined.Among the synthesized derivatives,compounds 6 and 18 displayed distinct antiproliferative activity against PC-3,H-292,SKBR3 and Hey-1B cancer cells,and compounds 10,17 and 18 showed significant antiproliferative activity against SKBR3 cells.Our results reveal that the position of hydroximino on ring A or B of the parental scaffold dramatically affects the antiproliferative activity of these compounds.The conversion of 7-hydroximino to other substituent or 7-hydroximino to 3-hydroximino in the compounds resulted in a dramatic decrease of the antiproliferative activity,suggesting the importance of 7-hydroximino group for the biological activity of the compounds.The structure/activity correlation generated from the studies provides valuable information for the further design of novel chemotherapeutic drugs.     

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 Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors Combining Molecular Docking and 3D-QSAR Methods

The vascular endothelial growth factor (VEGF) and its receptor tyrosine kinases VEGFR-2 or kinase insertdomain receptor (KDR) have emerged as attractive targets for the design of novel anticancer agents. In the present work, molecular docking method combined with three dimensional quantitative structure-activity relationships (comparative molecular field analysis (CoMFA) and comparative molecular similarity indice analysis (CoMSIA)) to analyze the possible interactions between KDR and those derivatives which acted as selective inhibitors. The CoMFA and CoMSIA models gave a cross-validated coefficient Q2 of 0.713 and 0.549, non-cross-validated R2 values of 0.974 and 0.878, and predicted R2 values of 0.966 and 0.823, respectively. The 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. The information obtained from 3D-QSAR and docking studies were very helpful to design novel selective inhibitors of KDR with desired activity and good chemical property.     

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.     

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.     

Structure-Activity Relationship, Cytotoxicity and Mode of Action of 2-Ester-substituted 1,5-Benzothiazepines as Potent Antifungal Agents

Our studies examined the structural features responsible for the antifungal activity of 2-ethoxycarbonyl-1,5- benzothiazepine （7a）. Three series of 1,5-benzothiazepine derivatives were synthesized and screened for their antifungal activity. The results suggested that the ethoxycarbonyl group at the 2 position and the imine moiety on the seven-membered ring are essential for activity. The most potent of the synthesized analogues （7a, 7b） were further studied by evaluating their cytotoxicity and mode of action （for 7a）. The results showed that compounds 7a and 7b were relatively safe for BV2 cells, but compound 7a interfered with Cryptococcus neoformans cell wall integrity by increasing the chitinase activity. Therefore, compound 7a was considered safe as an antifungal agent for animal cells.     

Synthesis and Antitumor Activity of 4-tert-Butyl-5-benzyl-2-benzyliminothiazoles

A series of novel Schiff bases including 4-tert-butyl-5-benzyl-2-benzyliminothiazoles was synthesized by reacting the aromatic aldehydes with the corresponding 2-aminothiazoles.The antitumor bioassay revealed that compounds 2n and 2m exhibited potent cytotoxicity against human cervix cancer（HeLa） cell line with IC50 values of 0.001 and 0.007 mmol/L,respectively.The preliminary structure-activity relationship（SAR） investigations and the apoptosis evaluation suggest that 4-tert-butyl-5-benzyl-2-benzyliminothiazoles may be a satisfactory backbone for antitumor activity,and compound 2n can serve as an attractive candidate for the development of novel apoptosis in anticancer treatment.     

Design,Synthesis and Antitumor Activity of Pyrrolopyrazinone-chalcone Hybrids

A series of pyrrolopyrazinone-chalcone hybrids（12a-12q） was designed,synthesized and screened for their antitumor activity against SKOV-3,A549 and HeLa cell lines in vitro.Compared with the pyrrolopyrazinone（10a） and 5-fluorouracil（5-FU）,nearly all the tested compounds showed significantly-improved antitumor activities.The most promising compounds 12e and 12k（IC50=0.25 and 0.88 μmol/L） respectively show activities of 123and 35 times that of compound 10a（IC50=30.74 μmol/L） against HeLa cell line.The result reveals that the presence of chalcone moiety is beneficial to their activity and selectivity.     

Molecular Docking and 3D-QSAR Studies on a Series of Fused Heterocyclic Amides as B-Raf Inhibitors

B-Raf has been identified as promising targets for novel anticancer agents. To further explore the interactions between small molecules and B-Raf, and to elucidate structural characteristics that influence the B-Raf kinase activity, molecular docking and three-dimensional quantitative structure-activity relationship(3D-QSAR) studies were performed on a dataset of 75 Type Ⅱ inhibitors. Molecular docking was applied to explore the detailed binding process between the inhibitors and B-Raf kinase in its DFG-out inactive conformation. Based on the conformations obtained by molecular docking strategy, 3D-QSAR models, including comparative molecular field analysis(CoMFA) and comparative molecular similarity indexes analysis(CoMSIA), were constructed. The established 3D-QSAR models show significant statistical quality and satisfactory predictive ability, with high q~2 and r~2 values: CoMFA model(q~2= 0.759, r~2 = 0.922), and CoMSIA model(q~2 = 0.685, r~2 = 0.945). The systemic external validation indicated that both CoMFA and CoMSIA models were quite robust and possess high predictive abilities with r~2 pred values of 0.633 and 0.708, respectively. Several key structural features accounting for the inhibitory activities of these compounds were discussed based on the 3D contour maps generated by the CoMFA and CoMSIA models, which were in good accordance with the docking results. These theoretical results rendered by 3D-QSAR models along with the docking may provide a useful reference for understanding the action mechanism and designing novel potential B-Raf inhibitors.     

Synthesis and Antitumor Activities of 1,3,4-Thiadiazole Derivatives Possessing Benzisoselenazolone Scaffold

A series of novel 1,3,4-thiadiazole derivatives possessing benzisoselenazolone scaffold were designed and synthesized, and their antitumor activities against human cervix adenocarcinoma（HeLa）, human liver cancer cell（SMMC-7721）, human breast cancer cell（MCF-7） and human lung cancer cell（A549） lines were evaluated by CCK-8 assay, The bioassay results demonstrate that most of the tested compounds showed potent antiproliferative effects against various cell lines. Furthermore, compounds 7c, 7e, 7h, 7i and 7k showed significant antiproliferative activities against SMMC-7721 cells, with IC5o values of 2.38, 2.67, 1.35, 2.75 and 2.48 μmol/L, respectively. Com- pounds 7a, 7e, 7j and 71 exhibited highly effective antitumor activities against MCF-7 cells, with IC50 values of 2.89, 2.95, 1.12 and 2.75 μmol/L, respectively. Compound 7j was found to be the most potent compound against A549 cells, with an IC50 value of 1.25 μmol/L. The pharmacological results suggest that the substituents of benzylthio-moiety at position 2 on 1,3,4-thiadiazole are vital for modulating antitumor activities against various cancer cell lines.     

Study on the Three-dimensional Quantitative Structure-activity Relationship of Pyridazinonyl-substituted 1,3,4-Thiadiazoles

The three-dimensional quantitative structure-activity relationships of a series of 5-[ 1-aryl-1,4-dihydro-6-methylpyridazin-4-one-3-yl]-2-arylamino-1,3,4-thiadiazoles, related to the fungicidal activity, were studied using the comparative molecular field analysis （CoMFA）. The results show that the contributions of steric and electrostatic fields to the activity are 0.505 and 0.495, respectively. The cross-validated q^2 and the correlation coefficient r^2 for the model established by the study are 0.769 and 0.938, respectively, with the F value of 60.996, and the standard deviation s of 0.074. These values indicate that the model is significant and has good predictability. The analysis results are in good agreement well with the study of 2D-QSAR, and offered important structural insights into designing highly active compounds prior to synthesis.     

Silica-supported Thionyl Chloride-assisted Synthesis and Bioassay of Novel Tetrazinan-3-thione and 3-Oxo-pyrazolidine-4-carbonitrile Derivatives of Steroids

A series of tetrazinan-3-thione and 3-oxo-pyrazolidine-4-carbonitrile derivatives of steroids（1-3） were synthesized with silica-chloride as a heterogeneous catalyst.The synthesized compounds 4-9 were obtained in substantial yields.In vitro evaluation of anticancer and antioxidant activity of the synthesized compounds was carried out via 3-（4,5-dimethylthiazol-2-yl）-2,5-diphenyltetrazolium bromide（MTT） and 1,1-diphenyl-2-picrylhydrazyl（DPPH）assays,respectively.Compound 6 exhibited promising anti-proliferative activity towards a panel of cancer cell lines.The significant activity of compound 6 was further ascertained on structural,molecular modelling and docking studies.This study may provide a valuable insight into the further design and development of more potent biologically active compounds.     

3D-QSAR Study on the Inhibitory Activity of Flavonoids on PIM-1 Kinase

20 Typical flavonoids were selected for study on the interaction between them and PIM-1 kinase with the comparative molecular field analysis method(CoMFA) as well as the comparative molecular similarity index analysis method(CoMSIA) based on molecule docking.3D-QSAR models between these flavonoids and receptor PIM-1 kinase were established.The obtained optimal cross-validation correlation coefficient Q2 for CoMFA model was 0.582,and the non-cross-validation correlation coefficient R2 was 0.955;the corresponding values for CoMSIA model were 0.790 and 0.974,respectively.These two models showed fairly fine stability and predictive ability.In addition,molecule docking results revealed the key residues in the receptor cavity and their specific action ways with flavonoids.     

Intercalation,Cytotoxicity,and Molecular Modeling of Acenaphtho[1,2-b]pyrrole Chromophores as a New Family of Antitumor Agents

To explore new platform for DNA intercalation and potent antitumor agent, a series of 8-oxo-8H- acenaphtho[1,2-b]pyrrole-9-carboxylic acid esters chromophores has been studied. Their intercalation geometries with DNA were rex;ealed through absorption titration, SYBR Green-DNA melt curve, circular dichroism（CD）, and docking studies. It was identified that some of the compounds could intercalate into DNA along their long axis parallel to the base-pair long axis, making right-handed B form DNA transform to A-like conformation. Their binding potency varied with the different steric hindrance. Their cytotoxicity（IC50） against MCF-7 cells was found to range between 1.3 to 40.9 umol/L by MTT assay. Interestingly, the IC50 values did not show any obvious correlation to their binding constants with DNA. The chromophore with a carboxyl group exhibited the most potency of intercalating DNA and could be the promising precursor for the future intercalator for DNA, while the bromide demonstrated the highest cytotoxic activity in this series of compounds.     

Synthesis,Docking and Biological Evaluation of Isoquinolonic Acid Derivatives

A series of isoquinolonic acid derivatives（4a-4o） was synthesized via one-pot synthesis for their anti-tumor activity. The structures of all the targeted compounds were confirmed by IH nuclear magnetic resonance （IH NMR） spectrometry and mass spectrometry（MS）. The anti-tumor activities of compounds 4a-4o against MG63（human osteosarcoma cells） and B16-F10（mouse melanoma cells） were examined. To evaluate the antitumor effect of the as-synthesized compounds, we compared the half maximal inhibitory concentration（1C50） of compounds 4a--4o to that of camptothecin（CPT） which appeared to be active against a broad range of human cancers. Among all the compounds, compound 41 shows the most potent biological activity against MG63 cells[IC50=（2.16i0.26） μmol/L] and B16-F10 cells[IC50=（6.95±0.24）μmol/L], thus providing useful information for the antitumor activity and potential practical use of isoquinolonic acid compounds. In addition, we screened out an efficient compound（41） that shows potential inhibit activity against Topoisomerase 1（Topo 1） by docking simulation.     

Design,synthesis and antiproliferative activities of diaryl urea derivatives bearing N-acylhydrazone moiety

A new series of diaryl urea derivatives bearing N-acylhydrazone moiety were designed and synthesized.All the target compounds were evaluated for their antiproliferative activities against human leukemia cell line(HL-60),human lung adenocarcinoma epithelial cell line(A549) and human breast cancer cell line(MDA-MB-231) in vitro by standard MTT assay.The pharmacological results indicated that some compounds exhibited promising antitumor activities.Compound 1j showed the most potent antiproliferative activity against the tested three cell lines with IC values of 0.13 mmol/L,0.7 mmol/L and 0.5 mmol/L,respectively.     

Microcalorimetric Evaluation of the Effect of Kanamycin： An Analysis Based on the Median-Effect Principle

A study of the effect of drug, kanamycin, on the growth metabolism of recombinant Escherichia coli B 1 was carded out by microcalorimeter monitoring of the metabolic activity of treated cells. Power-time curves of growing recombinant Escherichia coli cell suspensions, treated with different kanamycin doses, were recorded. The extent of the effect was evaluated by changes in the slopes of the microcalorimetric curves and the kinetics of the drug action was interpreted from the time at which these changes reached their maximum values and maintained their maximum values. Experimental dose-effect relationships conform to the median-effect principle of the mass-action law： fa/（1-fa）=（D/D50）^m. A plot of y=lg[（fa）^1-1]^-1 versus x=lg D gives the slope m, D50 and R∞. The experimental results revealed that high concentration of kanamycin had an inhibitory effect on the growth of recombinant Escherichia coli B 1 in the lg phase, and had a promoting effect in the stationary period. Moreover, it was demonstrated that microcalorimetry was a reliable method for the detection of modulatory effects in biology.     

A QSAR study and molecular design of benzothiazole derivatives as potent anticancer agents

A quantitative structure-activity relationship (QSAR) of a series of benzothiazole derivatives showing a potent and selective cytotoxicity against a tumorigenic cell line has been studied by using the density functional theory (DFT), molecular mechanics (MM ) and statistical methods, and the QSAR equation was established via a correlation analysis and a stepwise regression analysis. A new scheme determining outliers by "leave-one-out" (LOO) cross-validation coefficient (q2n-i) was suggested and successfully used. In the established optimal equation (excluding two outliers), the steric parameter (MRR) and the net charge (QFR) of the first atom of the substituent (R), as well as the square of hydrophobic parameter (lgP)2 of the whole molecule, are the main independent factors contributing to the anticancer activities of the compounds. The fitting correlation coefficient (R2) and the cross-validation coefficient (q2) values are 0.883 and 0.797, respectively. It indicates that this model has a significantly statistical quality and an excellent prediction ability. Based on the QSAR studies, 4 new compounds with high predicted anticancer activities have been theoretically designed and they are expected to be confirmed experimentally.