Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis

Background: An explosive global spreading of multidrug resistant Mycobacterium tuberculosis (Mtb) is a catastrophe, which demands an urgent need to design or develop novel/potent antitubercular agents. The Lysine/DAP biosynthetic pathway is a promising target due its specific role in cell wall and amino acid biosynthesis. Here, we report identification of potential antitubercular candidates targeting Mtb dihydrodipicolinate synthase (DHDPS) enzyme of the pathway using virtual screening protocols. Results: In the present study, we generated three sets of drug-like molecules in order to screen potential inhibitors against Mtb drug target DHDPS. The first set of compounds was a combinatorial library, which comprised analogues of pyruvate (substrate of DHDPS). The second set of compounds consisted of pyruvate-like molecules i.e. structurally similar to pyruvate, obtained using 3D flexible similarity search against NCI and PubChem database. The third set constituted 3847 anti-infective molecules obtained from PubChem. These compounds were subjected to Lipinski's rule of drug-like five filters. Finally, three sets of drug-like compounds i.e. 4088 pyruvate analogues, 2640 pyruvate-like molecules and 1750 anti-infective molecules were docked at the active site of Mtb DHDPS (PDB code: 1XXX used in the molecular docking calculations) to select inhibitors establishing favorable interactions. Conclusion: The above-mentioned virtual screening procedures helped in the identification of several potent candidates that possess inhibitory activity against Mtb DHDPS. Therefore, these novel scaffolds/candidates which could have the potential to inhibit Mtb DHDPS enzyme would represent promising starting points as lead compounds and certainly aid the experimental designing of antituberculars in lesser time

KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials

Background: Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general. Results: This paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value (Ki) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R/q2 of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R/q2 values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values (q2/r2) in the range of 0.78-0.83/0.93-0.95. Conclusions: Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq webcite, which allows the prediction of Ki value of a new ligand molecule against DHDPS

Chitinase from Enterobacter sp. NRG4: Its purification, characterization and reaction pattern

Enterobacter sp. NRG4 was shown to excrete chitinase into the culture supernatant when cultivated in medium containing chitin. A 60 kDa extracellular chitinase was purified to homogeneity and characterized. The enzyme hydrolyzed swollen chitin, colloidal chitin, regenerated chitin and glycol chitin but did not hydrolyze chitosan. The chitinase exhibited Km and Vmax values of 1.43 mg ml-1 and 83.33 \u3bcM \u3bcg-1 h-1 for swollen chitin, 1.41 mg ml-1 and 74.07 \u3bcM \u3bcg-1 h-1 for colloidal chitin, 1.8 mg ml-1 and 40 M \u3bcg-1 h-1 for regenerated chitin and 2.0 mg ml-1 and 33.33 \u3bcM \u3bcg-1 h-1 for glycol chitin, respectively. The optimal temperature and pH for activity were 45\ub0C and pH 5.5, respectively. Mg2+, K+ and Ca2+ stimulated chitinase activity by 13, 16 and 18%, respectively whereas Cu2+, Co2+, Ag+ and Hg2+ inhibited chitinase activity by 9.7, 15, 22 and 72.2%, respectively at 1 mM concentration. N-bromosuccinamide (NBS) at 1 mM and iodoacetamide at 10 mM concentration completely inhibited the enzyme activity. Dithiobisnitrobenzoic acid (DTNB) at 10 mM concentration inhibited chitinase activity by 97.2%. Chitin was hydrolyzed to chitobiose and N-acetyl D-glucosamine when incubated with the purified enzyme. The hydrolysis pattern of the purified enzyme indicated that the chitinase was an endochitinase

Paraoxonase 1 gene polymorphisms (Q192R and L55M) are associated with coronary artery disease susceptibility in Asian Indians

Background: Coronary artery disease (CAD) is a complex metabolic disorder in which lifestyle and genetic factors are known to play key roles in pathogenesis. The paraoxonase 1 (PON1) enzyme has a defensive effect against CAD progression, as it safeguards low-density lipoproteins (LDLs) from oxidative modifications. The most extensively studied genetic variants in the PON1 gene are Q192R and L55M, which have been related with LDL antioxidative activity and risk of CAD. Objective: The present case-control study intended to examine the Q192R and L55M polymorphisms and their association with the risk of CAD patients in north Indians. Methods: A total of 872 subjects (412 CAD patients and 460 controls) were recruited from north India. The PON1 gene was amplified and genotypes were studies using PCR-RFLP. χ2 analysis was performed to compare genotype/allele frequencies in patients and controls. Results: The present study indicated abdominal obesity, elevated body mass index, and dyslipidemia with increased levels of total cholesterol and triglycerides as well as reduced high-density lipoprotein cholesterol in CAD subjects compared to healthy controls (p < 0.05). Logistic regression analysis of the data revealed an association of the RR genotype of the Q192R polymorphism with an about 2-fold elevated risk of CAD (OR = 2.23, 95% CI = 1.47–3.37, p = 0.0001). Contrariwise, the L55M polymorphism did not show significant association with CAD (OR = 1.81, 95% CI = 0.66–4.95, p = 0.326). Conclusions: The Q192R polymorphism in the PON1 gene may be a susceptibility gene associated with increased risk of CAD in an Asian Indian population

Remediation of intramacrophageal Shigella dysenteriae type 1 by probiotic lactobacilli isolated from human infants' stool samples

Background & objectives: Shigella dysenteriae is one of the most virulent pathogens causing bacillary dysentery and is responsible for high mortality in infants. To reduce the load of antibiotic therapy for treating shigellosis, this study was carried out to assess the ex vivo effect of novel probiotic lactobacilli, isolated from infant's stool samples, on killing S. dysenteriae type 1 residing in the rat macrophages. Methods: Stool samples from infants were collected, processed for the isolation of lactobacilli and screened for the probiotic attributes (acid tolerance, bile tolerance, ability to adhere intestinal cells and anti-S. dysenteriae activity). The effect of cell-free supernatant of lactobacilli on Shigella- infected macrophages in terms of phagocytic ability, extent of lipid peroxidation, nitrite, superoxide dismutase and glutathione levels was evaluated. Results: Based on the probiotic attributes, three lactobacilli were isolated from the stool samples of infants. Using classical and molecular tools, these isolates were identified as Lactobacillus pentosus, L. Paraplantarum and L. rhamnosus. All the three lactobacilli had the ability to kill intramacrophage S. dysentriae type 1. The anti-Shigella activity of the probiotic lactobacilli was attributed to increased antioxidative ability and decreased free radical production by the infected macrophages. Interpretation & conclusions: Probiotic cocktail of L. pentosus, L. paraplantarum and L. rhamnosus showed ex vivo killing of S. dysenteriae residing inside the rat macrophages significantly. This cocktail has the potential to be used as a natural alternative for treating S. dysenteriae infection, especially in infants, however, further studies need to be done to confirm these finding in vivo

Optimization of Phospholipase A1 (PLA1) Production from a Soil Isolate Bacillus subtilis subsp. inaquosorum RG1 via Solid State Fermentation

Microbial sources for phospholipase A1 (PLA1) are economic and industry relevant for degumming of oils and also their product lyso-phospholipids have been widely used as emulsifying agent. Numerous PLAs1 have been reported, but still the few enzymes have got position in the commercial sector. Due to enormous demand of PLA1 in the industrial sector, the present study was carried out to optimize PLA1 production using cheaper agro-industrial waste like defatted rice bran. For this, defatted rice bran was used in solid state fermentation for the production of PLA1.One-factor at a time approach was used to obtain maximum production of 51.5 U/gm which is 2.15 folds more than un-optimized medium. The optimized medium components were (pH 7): defatted rice bran (5gm), glucose (1% w/v), peptone (1% w/v) and olive oil (0.5 % v/v) with moisture content of 1:1.5 and after 48h of incubation at 37°C. This approach will provide the cleaner solution for degumming of oil as compare to the acid degumming and also help to reduce the stress of the environment by utilizing waste. This is the first report where in Bacillus subtilis subsp. inaquosorum was employed for PLA1 production via solid state fermentation

RESEARCH ARTICLE - Chitinase from Enterobacter sp. NRG4: Its purification, characterization and reaction pattern

Enterobacter sp. NRG4 was shown to excrete chitinase into the culture supernatant when cultivated in medium containing chitin. A 60 kDa extracellular chitinase was purified to homogeneity and characterized. The enzyme hydrolyzed swollen chitin, colloidal chitin, regenerated chitin and glycol chitin but did not hydrolyze chitosan. The chitinase exhibited Km and Vmax values of 1.43 mg ml-1 and 83.33 μM μg-1 h-1 for swollen chitin, 1.41 mg ml-1 and 74.07 μM μg-1 h-1 for colloidal chitin, 1.8 mg ml-1 and 40 M μg-1 h-1 for regenerated chitin and 2.0 mg ml-1 and 33.33 μM μg-1 h-1 for glycol chitin, respectively. The optimal temperature and pH for activity were 45°C and pH 5.5, respectively. Mg2+, K+ and Ca2+ stimulated chitinase activity by 13, 16 and 18%, respectively whereas Cu2+, Co2+, Ag+ and Hg2+ inhibited chitinase activity by 9.7, 15, 22 and 72.2%, respectively at 1 mM concentration. N-bromosuccinamide (NBS) at 1 mM and iodoacetamide at 10 mM concentration completely inhibited the enzyme activity. Dithiobisnitrobenzoic acid (DTNB) at 10 mM concentration inhibited chitinase activity by 97.2%. Chitin was hydrolyzed to chitobiose and N-acetyl D-glucosamine when incubated with the purified enzyme. The hydrolysis pattern of the purified enzyme indicated that the chitinase was an endochitinase

Review of Quantum Dot Technologies for Cancer Detection and Treatment

Semiconductor quantum dots (QDs) are nanoparticles that have attracted widespread interest in biology and medicine due to their unique optical and electronic properties. These properties, especially their reduced tendency to photobleach and the dependence of their fluorescence wavelength on their size, make them suitable for fluorescent probing applications to detect cancer biomarkers in vitro and in vivo in cells/tissues/whole body. There is considerable interest among researchers due to the recent developments in QD technology. QDs have been encapsulated in amphiphilic polymers and bound to tumor-targeting ligands and drug delivery vesicles for targeting, imaging and treating tumor cells. Present efforts are focussed on exploring the massive multiplexing capabilities of the QDs for the simultaneous detection of multiple cancer biomarkers in blood assays and cancer tissue biopsies. These advances in the QD technology have unravelled a great deal of information about the molecular events in tumor cells and early diagnosis of cancer

A NOVEL STRAIN OF Aspergillus niger PRODUCING A COCKTAIL OF HYDROLYTIC DEPOLYMERISING ENZYMES FOR THE PRODUCTION OF SECOND GENERATION BIOFUELS

The screening and isolation of fungi producing a cocktail of hydrolytic enzymes was studied. Among the various isolates obtained from different soil samples, a strain NS-2 was selected. The phylogenetic analysis of this strain showed highest homology (99%) with Aspergillus niger. It was capable of producing cellulolytic, hemicellulolytic, amylolytic, and pectinolytic enzymes in appreciable titers on wheat bran based liquid and solid state media. The mixture of enzymes produced by this organism could effectively hydrolyze various domestic waste residues, revealing conversion efficiencies of 89 to 92% and produced high reducing sugar yields of 0.48 to 0.66 g/g of dry residue. This enzyme cocktail could potentially find a significant application in the conversion of agricultural and other waste residues having cellulose, hemicellulose, starch, and pectin as carbohydrates to produce simpler sugars which can be fermented for the production of second generation biofuels