A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists.

In the quantitative structure-activity relationship (QSAR) study, local lazy regression (LLR) can predict the activity of a query molecule by using the information of its local neighborhood without need to produce QSAR models a priori. When a prediction is required for a query compound, a set of local models including different number of nearest neighbors are identified. The leave-one-out cross-validation (LOO-CV) procedure is usually used to assess the prediction ability of each model, and the model giving the lowest LOO-CV error or highest LOO-CV correlation coefficient is chosen as the best model.

A combined molecular modeling study on gelatinases and their potent inhibitors.

Zinc-dependent matrix metalloproteinase (MMP) family is considered to be an attractive target because of its important role in many physiological and pathological processes. In the present work, a molecular modeling study combining protein-, ligand- and complex-based computational methods was performed to analyze a new series of beta-N-biaryl ether sulfonamide hydroxamates as potent inhibitors of gelatinase A (MMP-2) and gelatinase B (MMP-9). Firstly, the similarities and differences between the binding sites of MMP-2 and MMP-9 were analyzed through sequence alignment and structural superimposition.

Novel approaches for retention time prediction of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography.

The base sequence autocorrelation (BSA) descriptors were used to describe structures of oligonucleotides and to develop accurate quantitative structure-retention relationship (QSRR) models of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography. Through the combination use of multiple linear regression (MLR) and genetic algorithm (GA), QSRR models were developed at temperatures of 30 degrees C, 40 degrees C, 50 degrees C, 60 degrees C and 80 degrees C, respectively. Satisfactory results were obtained for the single-temperature models (STM).

8-Chloro-adenosine-induced E2F1 promotes p14ARF gene activation in H1299 cells through displacing Sp1 from multiple overlapping E2F1/Sp1 sites.

The regulation of p14ARF gene by E2F transcription factor, which differs from that of classical E2F targets, has recently been attributed to a variant E2F-response element. However, promoter assays suggest multiple elements present in the p14ARF promoter and argue against the idea that the ARF promoter has a unique ability to distinguish between aberrant and physiological levels of E2F1. Therefore, the functional characterization of the promoter still needs to be done.

Inhibition of CHK1 kinase by Gö6976 converts 8-chloro-adenosine-induced G2/M arrest into S arrest in human myelocytic leukemia K562 cells.

8-Chloro-cAMP (8-Cl-cAMP) and its metabolite 8-chloro-adenosine (8-Cl-Ado) inhibit cell growth by 8-Cl-Ado-converted 8-Cl-ATP that targets cell-cycle control and RNA metabolism. However, the cell-cycle checkpoint pathways remain to be identified. Recent studies have shown that 8-Cl-cAMP administration and 8-Cl-Ado exposure may damage chromosomal DNA in vivo and in vitro.

Inhibition of topoisomerase II by 8-chloro-adenosine triphosphate induces DNA double-stranded breaks in 8-chloro-adenosine-exposed human myelocytic leukemia K562 cells.

8-Chloro-cAMP and 8-chloro-adenosine (8-Cl-Ado) are known to inhibit proliferation of cancer cells by converting 8-Cl-Ado into an ATP analog, 8-chloro-ATP (8-Cl-ATP). Because type II topoisomerases (Topo II) are ATP-dependent, we infer that 8-Cl-Ado exposure might interfere with Topo II activities and DNA metabolism in cells. We found that 8-Cl-Ado exposure inhibited Topo II-catalytic activities in K562 cells, as revealed by decreased relaxation of the supercoiled pUC19 DNA and inhibited decatenation of the kinetoplast DNA (kDNA).

Synergistic up-regulation of muscle LIM protein expression in C2C12 and NIH3T3 cells by myogenin and MEF2C.

Although the role of muscle LIM protein (MLP, also known as CRP3), a LIM-only protein of LIM domain-containing protein family, is well-characterized, the mechanism by which the MLP gene expresses remains unclear. Herein, we demonstrate that myogenin and myocyte enhancer factor 2C (MEF2C) cooperate in activating the MLP gene in myogenesis. RT-PCR, real-time PCR and Western blotting showed that overexpression of myogenin or myogenin plus MEF2C led to induction of the MLP gene in differentiating C2C12 and NIH3T3 fibroblasts.

A novel method for protein-ligand binding affinity prediction and the related descriptors exploration.

In this study, a novel method was developed to predict the binding affinity of protein-ligand based on a comprehensive set of structurally diverse protein-ligand complexes (PLCs). The 1300 PLCs with binding affinity (493 complexes with K(d) and 807 complexes with K(i)) from the refined dataset of PDBbind Database (release 2007) were studied in the predictive model development. In this method, each complex was described using calculated descriptors from three blocks: protein sequence, ligand structure, and binding pocket.

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors.

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a series of thiazolone derivatives as novel inhibitors bound to the allosteric site of hepatitis C virus (HCV) NS5B polymerase were developed based on CoMFA and CoMSIA analyses. Two different conformations of the template molecule and the combinations of different CoMSIA field/fields were considered to build predictive CoMFA and CoMSIA models. The CoMFA and CoMSIA models with best predictive ability were obtained by the use of the template conformation from X-ray crystal structures.

QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling.

Quantitative structure-activity relationship (QSAR) of a series of structural diverse malonyl-CoA decarboxylase (MCD) inhibitors have been investigated by using the predictive single model as well as the consensus analysis based on a new strategy proposed by us. Self-organizing map (SOM) neural network was employed to divide the whole data set into representative training set and test set. Then a multiple linear regressions (MLR) model population was built based on the theoretical molecular descriptors selected by Genetic Algorithm using the training set.

4-Bromo-1-[2,6-dichloro-4-(trifluoro-meth-yl)phen-yl]-5-(4-methoxy-benzyl-ideneamino)-1H-pyrazole-3-carbonitrile.

The title compound, C(19)H(10)BrCl(2)F(3)N(4)O, is an imine with an overall Y shape. The dihedral angles between the pyrazole ring and the methoxy- and trifluoromethyl-substituted benzene ring planes are 88.4 (2) and 65.

4-Bromo-1-[2,6-dichloro-4-(trifluoro-meth-yl)phen-yl]-5-(4-nitro-benzyl-idene-amino)-1H-pyrazole-3-carbonitrile.

The title compound, C(18)H(7)BrCl(2)F(3)N(5)O(2), is an L-shaped tricyclic imine. The pyrazole ring is essentially coplanar with the nitro-substituted benzene ring [dihedral angle = 3.6 (2)°] and approximately perpendicular to the trifluoro-methyl-substituted ring [dihedral angle = 88.

Synthesis, characterization of Ag(I), Pd(II) and Pt(II) complexes of a triazine-3-thione and their interactions with bovine serum albumin.

Ag(I), Pd(II) and Pt(II) complexes of 5-methoxy-5,6-diphenyl-4,5-dihydro-2H-[1,2,4]triazine-3-thione (LH(2)OCH(3)) have been synthesized and characterized by elemental analysis, molar conductance, (1)H NMR, IR spectra, UV spectra and thermal analysis (TG-DTA). The components of the three complexes are [Ag(C(15)H(10)N(3)S)](6), Pd(C(15)H(10)N(3)S)(2) and Pt(C(15)H(10)N(3)S)(2).C(3)H(6)O.

Prediction of T-cell epitopes based on least squares support vector machines and amino acid properties.

T-lymphocyte (T-cell) is a very important component in human immune system. It possesses a receptor (TCR) that is specific for the foreign epitopes which are in a form of short peptides bound to the major histocompatibility complex (MHC). When T-cell receives the message about the peptides bound to MHC, it makes the immune system active and results in the disposal of the immunogen.

Prediction of binding affinities to beta1 isoform of human thyroid hormone receptor by genetic algorithm and projection pursuit regression.

Quantitative structure-activity relationship (QSAR) has been applied to a set of thyroid hormone receptor beta(1) (TRbeta(1)) antagonists, which are of special interest because of their potential role in safe therapies for nonthyroid disorders while avoiding the cardiac side effects. Using the calculated structural descriptors by CODESSA program, principal component analysis (PCA) was performed on the whole compounds to assist the separation of the data into the training set and the test set in QSAR analysis. Six molecular descriptors selected by genetic algorithm (GA) were used as inputs for a projection pursuit regression (PPR) study to develop a more accurate QSAR model.

8-Chloro-adenosine inhibits growth at least partly by interfering with actin polymerization in cultured human lung cancer cells.

A key feature of actin is its ability to bind and hydrolyze ATP. 8-Chloro-adenosine (8-Cl-Ado), which can be phosphorylated to the moiety of 8-Cl-ATP in living cells, inhibits tumor cell proliferation. Therefore we tested the hypothesis that 8-Cl-Ado can interfere with the dynamic state of actin polymerization.

Kainate exposure suppresses activation of GluR2 subunit promoter in primary cultured cerebral cortical neurons through induction of RE1-silencing transcription factor.

The AMPA receptor subunit GluR2 is downregulated in neurons following a wide range of neurological insults. Here we report that suppression of GluR2 gene promoter activity is associated with kainate (KA)-induced downregulation of GluR2 subunit levels in primary cultured cortical neurons. RT-PCR and Northern blotting showed a significant decrease in GluR2 mRNA in cultured neurons after KA exposure.

Exposure of human lung cancer cells to 8-chloro-adenosine induces G2/M arrest and mitotic catastrophe.

8-Chloro-adenosine (8-Cl-Ado) is a potent chemotherapeutic agent whose cytotoxicity in a variety of tumor cell lines has been widely investigated. However, the molecular mechanisms are uncertain. In this study, we found that exposure of human lung cancer cell lines A549 (p53-wt) and H1299 (p53-depleted) to 8-Cl-Ado induced cell arrest in the G2/M phase, which was accompanied by accumulation of binucleated and polymorphonucleated cells resulting from aberrant mitosis and failed cytokinesis.

AGS-induced expression of Narp is concomitant with expression of AMPA receptor subunits GluR1 and GluR2 in hippocampus but not inferior colliculus of P77PMC rats.

To explore mechanisms of epileptogenesis in audiogenic seizures (AGS), we examined the expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazoleopropionic acid (AMPA) receptor subunits GluR1 and GluR2 and of the GluR-associated protein Narp in the hippocampus and the inferior colliculus (IC) from AGS-susceptible P77PMC rats after a single AGS and audiogenic kindling. Western blotting and immunohistochemistry showed that Narp was rapidly induced in both the hippocampus and the IC by AGS. In the hippocampus, up-regulation of Narp was concomitant with GluR1 and GluR2 under both conditions of a single AGS and AGS kindling.

Down-regulation of GluR2 is associated with Ca2+-dependent protease activities in kainate-induced apoptotic cell death in cultured [correction of culturd] rat hippocampal neurons.

In the present study, the molecular mechanisms underlying kainate-induced neurotoxicity were characterized in cultured rat hippocampal neurons. Long-term exposure to kainate caused typically apoptotic cell death, which was accompanied by the accumulation of calcium, marked down-regulation of GluR2 subunit, and the activation of calpain and caspase-3. All these alterations were prevented by alpha-amino-3-hydroxy-5-methylisoxazole-4-proprionic acid (AMPA) receptor antagonist CNQX, but not by NMDA receptor antagonist MK801 and membrane L-type calcium channel antagonist nifedipine.