Three-dimensional Quantitative Structure-activity Relationship Models of HIV-1 Integrase Inhibitors of DKAs

As one of the three viral encoded enzymes of HIV-1 infection, HIV-1 integrase has become an attractive drug target for the treatment. Diketoacid compounds (DKAs) are one kind of potent and selective inhibitors of HIV-1 IN. In the present work, two three-dimensional QSAR techniques (CoMFA and CoMSIA) were employed to correlate the molecular structure with the activity of inhibiting the strand transfer for 147 DKAs. The all-oritation search (AOS) and all-placement search (APS) were used to optimize the CoMFA model. The diketo and keto-enol tautomers of DKAs were also used to establish the CoMFA models. The results indicated that the enol was the dominant conformation in the HIV-1 IN and DKAs complexes. It can provide a new method and reference to identify the bioactive conformation of drugs by using QSAR analysis. The best CoMSIA model, with five fields combined, implied that the hydrophobic field is very important as well as the steric and electrostatic fields. All models indicated favorable internal validation. A comparative analysis with the three models demonstrated that the CoMFA model seems to be more predictive. The contour maps could afford steric, electrostatic, hydrophobic and H-bond information about the interaction of ligand-receptor complex visually. The models would give some useful guidelines for designing novel and potent HIV-1 integrase inhibitors.     

Structural Insight into the Design on Oleanolic Acid Derivatives as Potent Protein Tyrosine Phosphatase 1B Inhibitors

Oleanolic acid derivatives act as newer protein tyrosine phosphatase 1B(PTP-1B) inhibitors for type 2 diabetes mellitus(T2DM). In order to understand the structural requirement of PTP-1B inhibitors, 52 oleanolic acid derivatives were divided into a training set(34 compounds) and a test set(18 compounds). The highly reliable and predictive 3D-QSAR models were constructed by CoM FA, CoM SIA and topomer Co MFA methods, respectively. The results showed that the cross validated coefficient(q2) and non-cross-validated coefficient(R~2) were 0.554 and 0.999 in the CoM FA model, 0.675 and 0.971 in the CoM SIA model, and 0.628 and 0.939 in the topomer Co MFA model, which suggests that three models are robust and have good exterior predictive capabilities. Furthermore, ten novel inhibitors with much higher inhibitory potency were designed. Our design strategy was that(i) the electronegative substituents(Cl,-CH_2OH, OH and-CH_2Cl) were introduced into the double bond of ring C,(ii) the hydrogen bond acceptor groups(C≡N and N atom), electronegative groups(C≡N, N atom,-COOH and-COOCH_3) and bulky substituents(C_6H_5N) were connected to the C-3 position, which would result in generating potent and selective PTP-1B inhibitors. We expect that the results in this paper have the potential to facilitate the process of design and to develop new potent PTP-1B inhibitors.     

QSAR and Pharmacophore Studies of Thiazolidine-4-carboxylic Acid Derivatives as Novel Influenza Neuraminidase Inhibitors Using HQSAR, Topomer CoMFA and CoMSIA

In order to understand the chemical-biological interactions governing their activities toward neuraminidase (NA), QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. The obtained HQSAR (hologram quantitative structure activity relationship), Topomer CoMFA and CoMSIA (comparative molecular similarity indices analysis) models were robust and had good exterior predictive capabilities. Moreover, QSAR modeling results elucidated that hydrogen bonds highly contributed to the inhibitory activity, then electrostatic and hydrophobic factors. Squared multiple correlation coefficients (R2) of HQSAR, Topomer CoMFA and CoMSIA models were 0.994, 0.978 and 0.996, respectively. Squared cross-validated correlation coefficients (Q2) of HQSAR, Topomer CoMFA and CoMSIA models were in turn 0.951, 919 and 0.820. Furthermore, squared multiple correlation coefficients for the test set (R2test) of HQSAR, CoMFA and CoMSIA models were 0.879, 0.912 and 0.953, respectively. Squared cross-validated correlation coefficients for the test set (Q2ext) of HQSAR, Topomer CoMFA and CoMSIA models were 0.867, 0.884 and 0.899, correspondingly.     

Synthesis and CDK2 kinase inhibitory activity of 7/7′-azaindirubin derivatives

<正>A series of novel 7'-azaindirubin(1a-g) and 7-azaindirubin(2a,2c,2e and 2f) derivatives were designed and synthesized.Their structures were characterized by ~1H NMR and MS spectroscopy as well as by elemental analysis.Their inhibitory properties against CDK2/cylinA were evaluated in vitro.In contrast to indirubin,some of the described azaindirubins emerged as potent inhibitors of CDK2/cylinA and compound 2b had more potent activity.Biological tests also showed that nitrogen atom at 7-position of azaindirubin was more beneficial to enhance the kinase inhibitory activity.     

Design and synthesis of new 7, 8-dimethoxy-α-naphthoflavones as CYP1A1 inhibitors

The flavonoids as inhibitors of CYP1Al exhibit chemopreventive effects against certain procarcinogens and have been considered as the promising cancer preventive agents.A series of novel 7,8-dimethoxy-αnaphthoflavones as the substrate analogs were designed and prepared.The enzyme assay suggested that all of these new flavones were stronger inhibitors of CYP1 Al than the lead compoundα-naphthoflavone. Among the tested ones,3h showed the most potent inhibitory effects.     

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.     

Acrosin structure-based design,synthesis and biological activities of 7-azaindol derivatives as new acrosin inhibitors

A series of 7-azaindol derivatives were designed based on the homologous 3D model of human acrosin.These compounds were synthesized and evaluated for their human acrosin inhibitory activities in vitro.Compounds 7a,7i,7j,7k and 7n showed highly inhibitory activity against human acrosin.The three-dimensional structure-activity relationship was investigated through a CoMFA model,which provided valuable information to further study of potential human acrosin inhibitors.     

Docking and 3D-QSAR Studies on the Imidazo[1,5-c]pyrimidine Derivative as EED Inhibitors

Embryonic ectoderm development(EED) has become a novel target for cancer treatment. In this study, a series of EED inhibitors was subjected to a three-dimensional quantitative structure-activity relationship(3D-QSAR) and molecular docking. Accordingly, this is the first of such 3D-QSAR studies in a series of EED inhibitors displaying anti-cancer pharmacological profiles. The CoMFA(q~2 = 0.792, r~2 = 0.994, r~2_(pred) = 0.74) and CoMSIA(q~2 = 0.873, r~2 = 0.994, r~2_(pred) = 0.81) models demonstrated good robustness and predictive ability. Moreover, molecular docking suggested that cation-π,π-π stacking and hydrogen bonding interactions were the main factors affecting the activity of these inhibitors. Five new small molecules were designed based on the CoMFA and CoMSIA contour maps. These molecules were then submitted to further ADME studies, in which the ADME properties of the five designed molecules were found to be within a reasonable range. In view of the corresponding findings, this study may provide theoretical guidance for the rational design of novel EED inhibitors.     

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.     

Design,synthesis and antifungal activities in vitro of novel tetralin compounds

Novel chiral tetralin compounds were designed and synthesized, and their antifungal activities in vitro were tested. The results showed that all of target compounds had potent antifungal activities, and were stronger than that of control compounds tetrahydroisoquinolines. The binding model of lead molecules in the active site of CYP51 of Candida albicans showed that lead compound specifically interacted with the amino acids residues in the active site, without binding with the heme of CYP51, which was different from azole antifungal drugs. The present study might afford a novel lead molecule to develop non-azole CYP51 inhihitars of fungi.     

Synthesis and anti-HIV-1 activity of the conjugates of gossypol with oligopeptides and D-glucosamine

A series of novel gossypol derivatives were synthesized and screened for their in vitro anti-HIV- 1I activity. The results showed that replacing the aldehyde groups of gossypol with certain oligopeptides and Dglucosamine not only reduced the cytotoxicity of gossypol derivatives but also enhanced their antiviral activity against HIV-1. Interestingly, D-glucosamine derivative of gossypol that lacked the COONa group also exhibited the same potent anti-HIV-1 activity as oligopeptide derivatives with the COONa group. These compounds blocked the entry of HIV-1ⅢB into target cell. which was similar to T20. Furthermore, the molecular docking analysis rationalized their anti-HIV-1 activity. The results also implied that certain oligopeptides and D-glucosamine were important moities to prepare gossypol derivatives as HIV- 1 entry inhibitors besides certain amino acids.     

Discovery of Fuchsone Derivatives as Novel Nonpeptide Inhibitor of Caspase-3

Many degenerative diseases caused by uncontrolled cell death can be intervened pharmaceutically through inhibiting caspase-3 activity that leads to cell apoptosis. Here is presented the discovery of rosolic acid and phe- nolphthalein methyl ester, which both belong to fuchsone derivatives, as novel and potent nonpeptide inhibitors of caspase-3. They show high inhibitory potency against caspase-3 in vitro(IC50=0.28 and 0.13 μmol/L). Molecular modeling study provided further an insight into the interaction of phenolphthalein methyl ester with activated caspase-3. The structures of the present small-molecule caspase-3 inhibitors are different from the structures of known caspase-3 inhibitors, so the inhibitors were likely to provide some information for the discovery of anti-caspase-3 inhibitors.     

Synthesis and biological evaluation of a new series of histone deacetylases inhibitors

Histone deacetylases （HDACs） play an important role in tumorigenesis. Inhibition of HDACs is considered as a potent strategy for cancer therapy. Two lead compounds （ja and jb） were found to have activities against HDACs with IC50 at about 15 μmol/L. Then a new series of hydroximic acid derivatives were designed and synthesized based on them. The HDACs activity assay in vitro found that compounds J04 and ,109 are nearly as potent as the positive control drug Zolinza.     

3D-QSAR Analysis of Naphthyltriazole(Lesinurad) Analogs as Potent Inhibitors of Urate Transporter 1

To obtain useful information for identifying inhibitors of urate transporter 1(URAT1), three-dimensional quantitative structure-activity relationship(3 D-QSAR) analysis was conducted for a series of lesinurad analogs via Topomer comparative molecular field analysis(CoMFA). A 3 D-QSAR model was established using a training set of 51 compounds and externally validated with a test set of 17 compounds. The Topomer CoMFA model obtained(q^2 = 0.976, r2 = 0.990) was robust and satisfactory. Subsequently, seven compounds with significant URAT1 inhibitory activity were designed according to the contour maps produced by the Topomer CoMFA model.     

Synthesis and antibacterial activity of pleuromutilin derivatives with novel C(14) side chain

In order to find novel antibacterial agents with superior antibacterial activity and overcoming multidrug resistance,a series of pleuromutilin derivatives with novel C(14) side chain were synthesized and evaluated for their in vitro antibacterial activities.The results of antibacterial acticities indicated that most of the derivatives showed potent activities against Gram-positive organisms.In particular,compound lOd exhibited the most potent inhibitory activity compared with pleuromutilin and linezoid,emerged as potential molecule for further investigation.     

Synthesis and biological evaluation of novel N-(alkyoxyphenyl)- aminocarbonylbenzoic acid derivatives as PTP1B inhibitors

Based on the fact that petroselinic acid showed good inhibitory activity (IC50=6.99 µmol/L) against protein tyrosine phophatase 1B(PTP1B) in vitro，a series of novel N-(alkoxyphenyl)-aminocarbonyl benzoic acid derivatives were designed and synthesised. The results indicated that most of the derivatives showed more potent activities against PTP1B. Especially, compound 13 had obvious activity with an IC50 of 106 nmol/L in vitro.     

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.     

Discovery of a series of pyridopyrimidine derivatives as potential topoisomerase I inhibitors

A series of new 3-benzoheterocyclic substituted pyridopyrimidines were designed and synthesized. Structures of the compounds were determined by IR, 1H NMR, and elemental analyses. The anti- proliferation activity of 13 novel compounds was evaluated in A549, HL-60, BGC-823 and SMMC-7721 cell lines. Compounds 3, 5, 7, 8, 9,10 showed potent inhibitory activity against the four tested cancer cell lines. These six compounds were examined for Top I inhibition at 100 μmol/L by measuring the relaxation of supercoiled DNA in plasmid pBR322. Most of the tested compounds inhibited the enzyme at this concentration. The most potent compound 9 was as potent as camptothecin.