Identification of novel antitubercular compounds through hybrid virtual screening approach

Growing resistance of prevalent antitubercular (antiTB) agents in clinical isolates of Mycobacterium tuberculosis (MTB) provoked an urgent need to discover novel antiTB agents. Enoyl acyl carrier protein (ACP) reductase (InhA) from Mtb is a well known and thoroughly studied as antitubucular therapy target. Here we have reported the discovery of potent antiTB agents through ligand and structure based approaches using computational tools. Initially compounds with more than 0.500 Tanimoto similarity coefficient index using functional class fingerprints (FCFP_4) to the reference chemotype were mined from the chemdiv database. Further, the molecular docking was performed to select the compounds on the basis of their binding energies, binding modes, and tendencies to form reasonable interactions with InhA (PDB ID = 2NSD) protein. Eighty compounds were evaluated for antitubercular activity against H37RV M. tuberculosis strain, out of which one compound showed MIC of 5.70 μM and another showed MIC of 13.85 μM. We believe that these two new scaffolds might be the good starting point from hit to lead optimization for new antitubercular agents.     

Novel GSK-3beta inhibitors from sequential virtual screening

Glycogen synthase kinase-3 (GSK-3beta) has been emerging as a key therapeutic target for type-2 diabetics, Alzheimer's disease, cancer, and chronic inflammation. For the purpose of finding biologically active and novel compounds and providing new idea for drug-design, we performed virtual screening using commercially available database. Three-dimensional common feature pharmacophore model was developed by using HipHop program provided in Catalyst software and it was used as a query for screening database. Recursive partitioning (RP) model was developed as a filtering system, which was able to classify active and inactive compounds. Eventually, a sequential virtual screening procedure (SQSP) was conducted by applying the common feature pharmacophore and RP model in succession to discover novel potent GSK-3beta inhibitors. The final 56 hit compounds were carefully selected considering predicted docking mode in crystal structures. Subsequent enzyme assay for human GSK-3beta protein confirmed that three compounds of these hit compounds exhibit micromolar inhibitory activity. Here, we report novel hit compounds and their binding mode in the active site of GSK-3beta crystal structure.     

3D QSAR studies on T-type calcium channel blockers using CoMFA and CoMSIA

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of isoxazolyl compounds as a potent T-type calcium channel blockers. A set of 24 structurally similar compounds served to establish the model. Four different conformations of the most active compound were used as template structures for the alignment, three of which were obtained from Catalyst pharmacophore modeling and one by using SYBYL random search option. All CoMFA and CoMSIA models gave cross-validated r(2) (q(2)) value of more than 0.5 and conventional r(2) value of more than 0.85. The predictive ability of the models was validated by an external test set of 10 compounds, which gave satisfactory pred r(2) values ranging from 0.577 to 0.866 for all models. Best predictions were obtained with CoMFA std model of Conformer no: 3 alignment (q(2)=0.756, r(2)=0.963), giving predictive r(2) value of 0.866 for the test set. CoMFA and CoMSIA contour maps were used to analyze the structural features of the ligands accounting for the activity in terms of positively contributing physicochemical properties: steric, electrostatic, hydrophobic and hydrogen bonding fields.     

Hologram quantitative structure activity relationship studies on 5-HT6 antagonists

Predictive hologram quantitative structure activity relationship (HQSAR) models were developed for a series of arylsulfonamide compounds acting as specific 5-HT6 antagonists. A training set containing 48 compounds served to establish the model. The best HQSAR model was generated using atoms, bond, and connectivity as fragment distinction and 4-7 as fragment size showing cross-validated r2(q2) value of 0.702 and conventional r2 value of 0.971. The predictive ability of the model was validated by an external test set of 20 compounds giving satisfactory predictive r2 value of 0.678. The efficiency of HQSAR approach was further evidenced by the generation of predictive models for a training set containing 30 highly diverse, both specific and nonspecific 5-HT6 antagonists. The best HQSAR model for this training set was generated using atoms, bond, and connectivity as fragment distinction and 4-7 as fragment size showing cross-validated r2(q2) value of 0.693 and conventional r2 value of 0.923. This model was also validated by using an external test set of 10 compounds giving satisfactory predictive r2 value of 0.692. The contribution maps obtained from these models were used to explain the individual atomic contributions to the overall activity.     

QSAR studies on piperazinylalkylisoxazole analogues selectively acting on dopamine D3 receptor by HQSAR and CoMFA

QSAR studies for piperazinylalkylisoxazole analogues were conducted by hologram QSAR (HQSAR) and comparative molecular field analysis (CoMFA) to explain the binding affinities of 264 ligands acting on dopamine D(3) receptor. The HQSAR was assessed by r(2) value of 0.917 and cross validated q(2) value of 0.841. In the CoMFA, r(2) is 0.919 and cross validated q(2) is 0.727. The results provide the tools for predicting the affinity of related compounds and guiding the design of new ligands.     

The 3D-QSAR study of antitumor arylsulfonylimidazolidinone derivatives by CoMFA and CoMSIA

Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies for a series of arylsulfonylimidazolidinone derivatives having antitumor activity were conducted using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The in vitro cytotoxicity against human lung carcinoma (A549) exhibited a strong correlation with steric and electrostatic factors of the molecules. Four different types of models have been built using CoMFA and CoMSIA method with AM1 charge or Gasteiger-Huckel charge. By comparison of the statistical results of these models, model I obtained by CoMFA study with AM1 showed the best predictability of the antitumor activities based on the cross-validated value (0.642), conventional r2 (0.981), standard error of estimate (0.106) and PRESS value (0.170).     

Stereochemical control in diastereoselective reduction of α-substituted-β-ketoesters using a reductase purified from Kluyveromyces marxianus

An NADPH-dependent carbonyl reductase that shows (3R)-selective reducing activity for -substituted--ketoesters was purified from Kluyveromyces marxianus and racemic alkyl 2-substituted-3-oxobutanoates were reduced to the corresponding (2S,3R)- or (2R,3R)-2-substituted-3-hydroxybutanoates with enantiomeric purity (> 99%) and diastereoselectivity (24 98%).     

Fine needle aspiration cytology of pseudosarcomatous reactive proliferative lesions of soft tissue

OBJECTIVE: To summarize the diagnostic features of fine needle aspiration cytology (FNAC) of pseudosarcomatous reactive proliferative lesions of soft tissue and to establish the criteria for differentiating these lesions from true sarcoma, thus allowing conservative management. STUDY DESIGN: FNA of 17 cases (13 nodular fasciitis, 2 proliferative fasciitis, 2 proliferative myositis), from 1994 to 2001, were reviewed in correlation with the clinical course or results of biopsy. RESULTS: The FNAC features of pseudosarcomatous reactive proliferative soft tissue lesions were characterized by a pleomorphic pattern of proliferative cells and the presence of ganglion cell-like cells. The proliferative cells varied widely from spindle shaped, with long cytoplasmic processes, to more plump cells, with round to oval nuclei. In spite of the large nuclei and prominent nucleoli in ganglion cell-like cells, the nuclei were cytologically benign, with thin and smooth nuclear membranes and fine chromatin. Clinically, all lesions appeared as small, superficially located, rapidly growing nodules with a short duration of symptoms. Ten cases of nodular fasciitis, one case of proliferative fasciitis and two cases of proliferative myositis had a spontaneous resolution in 1-12 weeks (mean, 4.7) following diagnosis by FNAC. All patients were well and devoid of any symptoms or signs of recurrence or metastasis in a follow-up period of 1-64 months after FNAC or biopsies. CONCLUSION: It is possible to differentiate pseudosarcomatous reactive proliferative soft tissue lesions from true sarcoma based on cytologic criteria in FNAC together with clinical correlation. All such lesions diagnosed by FNAC should be managed nonsurgically first, with follow-up. If regression does not occur within four to eight weeks, surgery should be performed.     

Discovery of a broad spectrum antiproliferative agent with selectivity for DDR1 kinase: cell line-based assay,kinase panel,molecular docking,and toxicity studies

Herein, we report compound KST9046, a new agent possessing quinazoline-urea scaffold. Preliminary biological evaluation done by the National Cancer Institute (NCI), USA, showed a great inhibitory effect of KST9046 over the 60 cell-line tumor panel. Accordingly, it was selected for a dose-response assay; a broad spectrum antiproliferative activity with GI₅₀ ranging from 1.3 to 3.9?µM was exerted. To explore a potential kinase inhibitory effect, KST9046 was applied at a single dose of 10?µM against a kinase panel of 347 different enzymes representing >50% of the predicted human protein kinome. Interestingly, selective inhibition of 76% was observed on DDR1 kinase. Further, KST9046 showed an IC₅₀ value of 4.38?µM for DDR1. A molecular docking model presented KST9046 as a potential type III inhibitor for DDR1 kinase with an allosteric mode of interaction, which may offer an explanation for its selectivity. As further investigation, CYP450 assay was carried out for KST9046, it showed a promising toxicity profile against four different isoforms. Based on these findings, KST9046 can be further evaluated as a promising safe new hit for the development of broad spectrum anticancer agents with a selectivity for DDR1 kinase.