The FRET-based assay was performed in a final volume of 100 μl buffer F containing 10 μM SrtBΔN26 and 20 μM fluorogenic peptide in clear-bottomed, black polystyrene 384-well plates (Nunc). Plates were incubated for 48 hours at 37°C, during which fluorescence (excitation = 340 nm, emission = 490 nm) was measured
using a SpectraMax M3 plate reader (Molecular Devices). Five mM 2-(trimethylamonium)ethylmethanethiosulfonate (MTSET, Affymetrix) was added to the reaction as indicated. Each experiment was performed in triplicate with a minimum Lenvatinib ic50 of three biological replicates, and the results are presented as the means and the standard error of the data obtained. The two-tailed Student’s T-test was used to analyze the data. MALDI analysis of FRET reaction samples was performed by the Protein and Nucleic Acid Chemistry Facility (University of Cambridge) to determine exact cleavage site within each peptide. Kinetic measurements Kinetic data for SrtBΔN26 were obtained by incubating varying concentrations of peptide (8, buy Ruxolitinib 10, 20, 40, 80, 160, 200 and 240 μM) with 10 μM SrtBΔN26. All reactions were performed as described above, with fluorescence monitored every ten minutes over a 13 hour period. To correlate fluorescence signal,
expressed as arbitrary relative fluorescence units (RFU), with the concentration of product formed, standard curves of the fluorophore Edans were collected. The linear segment of the fluorophore standard curve generated a conversion ratio of 703.9 RFU/ μM Edans. Initial velocities (V) were determined from the progress curves and plotted against substrate concentration [S]. The data were fitted to a modified version of the Michaelis-Menten equation incorporating substrate inhibition using SciPy 0.11.0 in Python selleck kinase inhibitor 2.7.3, where V max is the maximal enzymatic velocity, K m is the Michaelis constant,
and K i is the inhibitor dissociation constant for unproductive substrate binding. All data points were collected in triplicate, and the overall assay was run in duplicate. Identification of SrtB MK-0518 order inhibitors The proprietary LeadBuilder virtual screening method (Domainex, Ltd) was used to interrogate a database (PROTOCATS) of 80,000 potential compounds which had been pre-selected as protease inhibitors. The virtual screening protocol used pharmacophoric and docking filters derived from analysis of the BaSrtB crystal structure (with which the C. difficile SrtB shows 70% identity and 90% similarity at the active site). Sixty-two compounds identified in this screen as potential SrtB inhibitors were obtained from Enamine, ChemBridge, and Key Organics, and solubilized in DMSO. Selected compounds and MTSET were incubated with 10 μM SrtBΔN26 at a range of concentrations in the FRET-based assay conditions described above, so that final DMSO concentrations were ≤ 3.75%, a concentration shown to have no significant effect on control fluorescence (data not shown).