Urease inhibitory activity of H. pylori using selected CDs was determined by measuring the urease catalyzed release of ammonia by Berthelot reaction. 20 In brief, the H. pylori cells were harvested from the BHI broth by centrifugation at 4 °C (4000 g, 5 min) and resuspended in ice-cold 0.1 M sodium phosphate buffer (pH 7.3) containing 10 mM EDTA. Cells were disrupted by sonication

(Sonics Vibra Cell model, USA), and the supernatant obtained after centrifugation at 4 °C (12,000 g, 5 min) was used as a source of enzyme for urease assay. The 96 well microtitre plate reaction mixture contained urea (2, 4, 6, 8, 10 mM), sodium phosphate buffer 30 μl and different concentration NVP-BKM120 mouse of selected CDs 10, 50, 100 μg/ml [3]. After incubation for 10 min at 37 °C 0.66 N hydrogen sulphate 30 μl, sodium

tungstate 30 μl and of 30 μl Nessler’s reagent was added. Absorbance of the reaction mixture was recorded at 625 nm. The amount of ammonia produced was equivalent to the hydrolysis of urea. A high absorption value indicated high urease activity in the reaction mixture. IC50 of the urease inhibition was calculated using GraphPad Prism version 6.00. Docking studies were carried out as per our earlier Baf-A1 concentration investigation.21 The selected CDs were docked onto the ligand binding sites of the H. pylori urease using ArgusLab 4.0.1 (Mark Thmopson and Planaria Software LLC). The X-ray crystallographic structures of the H. pylori urease (PDB ID-1E9Y) complexed with acetohydroxamic acid (ref), were downloaded online (www.rcsb.org) from the Research Collaboratory for Structural Bioinformatics (RCSB). The files were opened in ArgusLab window, the geometry, valency and hybridization of the structure were corrected. The structures of the selected CDs were drawn in working window of ArgusLab and were energy optimized using PM3 semi-empirical QM method. The optimizations were performed up to 500 iterations or an automatic

energy optimization gets converged. The active sites of the selected receptor were defined to include residues within a 3.5 Å radius of the complexed ligand. For docking we have used the ArgusLab scoring GBA3 function AScore, Argus Dock engine, grid resolution of 0.4 Å with a flexible mode of ligand docking. The docking score was calculated as best ligand pose energy (kcal/mol) and the docked complexes were geometry optimized and were further analyzed for the hydrogen bonding. The distance (Å) between hydrogen bond forming residues was measured. The experimental values summarized for (MIC) of CDs against H. pylori are expressed as the mean ± SD. For inhibition of H. pylori urease studies the significance of the difference from the respective controls for each experimental test condition was assayed by using Student’s t test for each paired experiment. A p* value <0.05 was considered as a significant difference when compared with control. Results of the anti-H. pylori activity and MICs of the selected CDs are summarized in Table 1.