Transient receptor potential ankyrin 1 (TRPA1) is a nonselective calcium-permeable ion channel highly expressed in the primary sensory neurons functioning as a polymodal sensor for exogenous and endogenous stimuli and has generated widespread interest as a target for inhibition due to its implication in neuropathic pain and respiratory disease. Herein, we describe the optimization of a series of potent, selective, and orally bioavailable TRPA1 small molecule antagonists, leading to the discovery of a novel tetrahydrofuran-based linker. Given the balance of physicochemical properties and strong in vivo target engagement in a rat AITC-induced pain assay, compound 20 was progressed into a guinea pig ovalbumin asthma model where it exhibited significant dose-dependent reduction of inflammatory response. Furthermore, the structure of the TRPA1 channel bound to compound 21 was determined via cryogenic electron microscopy to a resolution of 3 Å, revealing the binding site and mechanism of action for this class of antagonists.

Transient receptor potential ankyrin 1 (TRPA1) is a non-selective cation channel expressed in sensory neurons where it functions as an irritant sensor for a plethora of electrophilic compounds and is implicated in pain, itch, and respiratory disease. To study its function in various disease contexts, we sought to identify novel, potent, and selective small-molecule TRPA1 antagonists. Herein we describe the evolution of an N-isopropylglycine sulfonamide lead (1) to a novel and potent (4 R,5 S)-4-fluoro-5-methylproline sulfonamide series of inhibitors. Molecular modeling was utilized to derive low-energy three-dimensional conformations to guide ligand design. This effort led to compound 20, which possessed a balanced combination of potency and metabolic stability but poor solubility that ultimately limited in vivo exposure. To improve solubility and in vivo exposure, we developed methylene phosphate prodrug 22, which demonstrated superior oral exposure and robust in vivo target engagement in a rat model of AITC-induced pain.

The N-methyl-d-aspartate receptor (NMDAR) is an ionotropic glutamate receptor, gated by the endogenous coagonists glutamate and glycine, permeable to Ca2+ and Na+. NMDAR dysfunction is associated with numerous neurological and psychiatric disorders, including schizophrenia, depression, and Alzheimer's disease. Recently, we have disclosed GNE-0723 (1), a GluN2A subunit-selective and brain-penetrant positive allosteric modulator (PAM) of NMDARs. This work highlights the discovery of a related pyridopyrimidinone core with distinct structure-activity relationships, despite the structural similarity to GNE-0723. GNE-5729 (13), a pyridopyrimidinone-based NMDAR PAM, was identified with both an improved pharmacokinetic profile and increased selectivity against AMPARs. We also include X-ray structure analysis and modeling to propose hypotheses for the activity and selectivity differences.

The N-methyl-D-aspartate receptor (NMDAR) is a Na(+) and Ca(2+) permeable ionotropic glutamate receptor that is activated by the coagonists glycine and glutamate. NMDARs are critical to synaptic signaling and plasticity, and their dysfunction has been implicated in a number of neurological disorders, including schizophrenia, depression, and Alzheimer's disease. Herein we describe the discovery of potent GluN2A-selective NMDAR positive allosteric modulators (PAMs) starting from a high-throughput screening hit. Using structure-based design, we sought to increase potency at the GluN2A subtype, while improving selectivity against related α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). The structure-activity relationship of channel deactivation kinetics was studied using a combination of electrophysiology and protein crystallography. Effective incorporation of these strategies resulted in the discovery of GNE-0723 (46), a highly potent and brain penetrant GluN2A-selective NMDAR PAM suitable for in vivo characterization.

Our earlier research has shown that mono-substituted N-phenyl-2, 2-dichloroacetamide exhibited much higher anti-cancer activity than the lead compound sodium dichloroacetate (DCA). In this paper, a variety of multi-substituted N-phenyl-2, 2-dichloroacetamides were synthesized and biologically evaluated. The results showed that 3, 5-disubstituted N-phenyl-2, 2-dichloroacetamide analogues had satisfactory potency. Among them, N-(3, 5-diiodophenyl)-2, 2-dichloroacetamide had an IC50 of 2.84 micromol x L(-1) against non-small cell lung cancer cell line A549 and could induce cancer cell apoptosis.

A series of benzamide derivatives including two scaffolds were designed and synthesized as potential histone deacetylase inhibitors. Most of synthesized compounds showed moderate enzymatic potency at the same order of magnitude, and compound 12b possessed better potency to the positive control (3.8 mu M vs 13.0 mu M). It also showed a 50-fold increase in vitro anticancer activity against DU-145 cell-lines. Molecular docking studies were carried out and used to explain the structure-activity relationships observed in vitro. Then we found that the cavity surrounded by ASP104, HIS33, PRO34 and PHE155 may be crucial for the inhibitors' activity. The docking results provide some useful information for future design of more potent inhibitors. (C) 2011 Elsevier Ltd. All rights reserved.

The invention provides a benzamide histone deacetylase inhibitor. The compound is a compound with a structure as shown in the formula (I) or its stereoisomer, enantiomer, diastereomer, hydrate or salt. The invention also relates to a preparation method of the compound, a pharmaceutical composition comprising the compound and an application thereof. The compound has differentiation and antiproliferative activity, and has a good curative effect for treating diseases caused by abnormal gene expression.

A series of novel dipeptidyl boronic acid proteasome inhibitors composed of beta-amino acids were synthesized, in vitro and in vivo biologically evaluated, and theoretically modeled for the first time. From the screened racemic compounds in enzyme, 4i was the most active. The IC(50) value of its pure enantiomer 4q was 9.6 nM, 36-fold more active than its isomer 4p and as active as the marketed bortezomib in inhibiting human 20S proteasome. This candidate also showed good activities with IC(50) values nearly less than 5 microM against several human solid and hematologic tumor cell lines. Safety evaluation in vivo with zebrafish and Sprague-Dawley (SD) rats showed that the candidate 4q was less toxic than bortezomib. Pharmacokinetic profiles suggested candidate 4q showed a more plasma exposure and longer half-life than bortezomib. Docking results indicated that 4q nearly interacted with 20S proteasome in a similar way as bortezomib.

A current study shows that sodium dichloroacetate (DCA) can induce cancer cell apoptosis and inhibit tumor growth, but its cytotoxic activity is low (IC50 > 1000 μM for A549). In this paper, a variety of DCA derivatives were synthesized, and their cytotoxic activities were evaluated. The result showed that the N-phenyl-2,2-dichloroacetamide analogues had satisfactory potencies. Among them, N-(3-iodophenyl)-2,2-dichloroacetamide (3e), an optimized lead compound, has an IC50 against A549 as low as 4.76 μM. Furthermore, it can induce cancer cell apoptosis and has a low toxicity in mice (LD50 = 1117 mg/kg).

A novel series of A-ring modified hexacyclic camptothecin derivatives containing a 1,3-oxazine ring were first designed and synthesized. All of the hexacyclic camptothecins were assayed for in vitro cytotoxicity against nine human cancer cell lines. Among these compounds, 9b and 9c showed most potent cytotoxicity against several cell lines. Particularly, 9c was about 13-fold more potent than camptothecin, and about sixfold more potent than topotecan toward HEPG-2. Furthermore, it was also found that the N-alkyl substituted derivatives were more potent than the N-aryl and N-benzyl substituted compounds against most cell lines.

Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed for a series of dipeptide boronate proteasome inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. A training set containing 46 molecules served to establish the models. The optimum CoMFA and CoMSIA models obtained for the training set were all statistically significant with cross-validated coefficients (q(2)) of 0.676 and 0.630 and conventional coefficients (r(2)) of 0.989 and 0.956, respectively. The predictive capacities of both models were successfully validated by calculating a test set of 13 molecules that were not included in the training set. The predicted correlation coefficients (r(2)(pred)) of CoMFA and CoMSIA are 0.963 and 0.919, respectively. The CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of beta5 subunit of 20S proteasome, which suggests that the 3D-QSAR models constructed in this paper can be used to guide the development of novel dipeptide boronate inhibitors of 20S proteasome.

AIM:To build up a quantitative structure-activity relationship (QSAR) model of 20 (S)-camptothecin (CPT) analogs for the prediction of the activity of new CPT analogs for drug design.METHODS:A training set of 43 structurally diverse CPT analogs which were inhibitors of topoisomerase I were used to construct a quantitative structure-activity relationship model with a comparative molecular field analysis (CoMFA). The QSAR model was optimized using partial least squares (PLS) analysis. A test set of 10 compounds was evaluated using the model.RESULTS:The CoMFA model was constructed successfully, and a good cross-validated correlation was obtained in which q(2) was 0.495. Then, the analysis of the non-cross-validated PLS model in which r(2) was 0.935 was built and permitted demonstrations of high predictability for the activities of the 10 CPT analogs in the test set selected in random.CONCLUSION:The CoMFA model indicated that bulky negative-charged group at position 9, 10 and 11 of CPT would increase activity, but excessively increasing bulky group at position 10 is adverse to inhibitory activity; substituents that occupy position 7 with the bulky positive group will enhance the inhibitive activity. The model can be used to design new CPT analogs and understand the mechanism of action.

A three-dimensional pharmacophore model was developed based on 25 currently available inhibitors, which were carefully selected with great diversity in both molecular structure and bioactivity as required by HypoGen program in the Catalyst software, for discovering new farnesyltransferase (FTase) inhibitors. The best hypothesis (Hypo1), consisting of four features, namely, two hydrogen-bond acceptors, one hydrophobic point, and one ring aromatic feature, has a correlation coefficient of 0.949, a root-mean-square deviation of 1.321, and a cost difference of 163.15, suggesting that a highly predictive pharmacophore model was successfully obtained. The application of the model shows great success in predicting the activities of 227 known FTase inhibitors in our test set with a correlation coefficient of 0.776 with a cross-validation of 98% confidence level. Accordingly, our model should be reliable in identifying structurally diverse compounds with desired biological activity.

Data mining is a new technology in information processing, and we apply association rule to processing traditional Chinese medicine (TCM) chemical data. A series of strong rules have been found by mining inter-dimensional association rules in database including fields of TCM effects, family of plant, activity of chemical component and modern pharmacody of TCM extracts. After analysis of these rules, the interesting rules are gained. The result of association rules also demonstrates the difference between TCM and western medicine description. This paper provides a new idea for related research filed such as modernization of TCM and plant chemistry.

Histone deacetylase (HDAC) greatly affects the chromatin topology and gene expression, and HDAC can be a new strategy in human cancer or tumour therapy. Hydroxamic acid compounds are component of most of the HDAC inhibitors. Studies on quantitative structure-activity relationship (QSAR) with CoMFA for the bioactivities of a series of sulfonamide hydroxamic acid HDAC inhibitors were carried out successfully, and a good cross-validated correlation (q(2) = 0.704) was obtained. The non-cross-validated partial least squares (PLS) model was also well built and analyzed by the prediction of the active data CoMFA steric, and electrostatic contours. The results show that steric field (0.697) plays a more important role in increasing bioactivity than that of electrostatic field (0.303), and the R5 position prefers a larger group, but the R1 position prefers a smaller group.

The quantitative structure activity relationship (QSAR) of the insecticidal activities of 28 (m-phenoxybenzyl) oxime-ethers and 30 biphenylbenzyl oxime-ethers against Nephotettix cincticeps (using) comparative molecular field analysis (CoMFA) method was investigated. Separate studies of QSAR models on each set of compounds and whole set of compounds were carried out. Three models show that p-substituent on phenyl ring of oxime moiety is the main factor affecting the activity. The larger volume and stronger electricity p-substituent has, the higher activity the compound has. By comparing these 3 models, it is found that the integrated model shows a higher ability to predict the activities of these oxime-ethers than other models, crossvalidated R~2_(cv)=0.628, non-crossvalidated (R~(2)=0.971,) standard error(SE)=(0.109,) F=133.84. The integrated model also shows a high (ability) to predict the biological activity(-lgLC_(50)) for 10 testing set compounds. QSAR models will give some guidance on synthesizing compounds with enhanced activities.

The quantitative relationship between the structure of oxime-ether compounds containing sulfur (oxygen) and their insecticidal activity against leafhopper was studied by comparative molecular field analysis(CoMFA). The results showed that the contributions of. steric and electrostatic fields to the activity were 47.5% and 52.5%, respectively. The coefficient q(2) of cross validation and the relation coefficient r(2) of non cross validation for the model established by the study were 0.628 and 0.971, respectively, its F value was 133.840 and the standard deviation was 0.109. These values indicated that the model might have a good predictability. The contour maps of the model will give the basis on the structure modification.

The compound that distributes in the herbs with one common effect was named as "co-effect compound" (CEC). The CECs of three traditional Chinese medicine(TCM) effects, purgative, relieving pain and clearing heat, had been found and studied. A strong corresponding relationship was found between the pharmacological activities of CECs and the TCM effect they belong to. The study shows that it may be a feasible method to connect traditional effect of TCM with modem pharmacological activity.

GABA(A) receptor is the major neurotransmitter system in the central nervous system(CNS) and elicits a wide range of neuronal physiological activities. Since anxiolytic/anticonvulsant agents have been employed widely in clinic, the receptor sites for the benzodiazepine are of prime importance. Studies on quantitative structure-activity relationship with CoMFA for the binding affinities of a series of imidazobenzodiazepines at five recombinant receptor subtypes were carried out successfully, and a good crossvalidated correlation was obtained for each receptor subtype. Then a set of non-cross-validated PLS models was built and permitted demonstration of high predictability for the affinities of the six ligands in the test set selected in random at all five receptorsubtypes. The modals can help design high affinitiy ligands on the GABA(A)/BZ receptor and understand the GABAA receptor modal.