A Colorimetric Assay to Identify and Characterize Bacterial Primase Inhibitors

Bacterial DNA primase DnaG is an attractive target for antibiotic discovery since it plays an essential role in DNA replication. Over the last 10 years, we have developed and optimized a robust colorimetric assay that enabled us to identify and validate inhibitors of bacterial primases. Here, we provide a detailed protocol for this colorimetric assay for DnaG from three different pathogenic bacteria (Mycobacterium tuberculosis, Bacillus anthracis, and Staphylococcus aureus), which can be performed in high throughput. We also describe secondary assays to characterize hits from this high-throughput screening assay. These assays are designed to identify inhibitors of the coupled enzyme inorganic pyrophosphatase, DNA binding agents, and elucidate the mode of inhibition of primase inhibitors.

Generation and characterization of dipeptidyl peptidase-IV inhibitory peptides from trypsin-hydrolyzed α-lactalbumin-rich whey proteins

Dipeptidyl peptidase-IV (DPP-IV) is an enzyme that break down the antidiabetic hormone glucagon-like peptide-1. Therefore, inhibition of DPP-IV could be an effective strategy to treat Type 2 diabetes (T2D). The α-lactalbumin-rich whey protein concentrate was hydrolyzed by trypsin, and the hydrolysates were then fractionated at a semi-preparative scale using a Superdex Gel filtration Chromatography. The peptides were analyzed by using HPLC coupled with tandem mass spectrometry (RP-HPLC-MS/MS), and their Dipeptidyl peptidase-IV inhibitory activity was determined by the enzymatic assay. Among tested fragments, a potent fragment (LDQWLCEKL), with the half-maximal inhibitory concentration (IC₅₀) of 131 μM was obtained. Further analysis shows that the LDQWLCEKL peptide corresponds to the amino acid sequence of f(115-123) in α-lactalbumin. Furthermore, LDQWLCEKL exhibited a typical non-competitive mode of inhibition. The results indicate that α-lactalbumin contains active peptides with DPP-IV inhibitory activity that may be used to prevent and treat T2D.

Mechanism & inhibition kinetics of bioassay-guided fractions of Indian medicinal plants and foods as ACE inhibitors

Hypertension is a becoming a major threat to the world. Angiotensin converting enzyme (ACE) is a key part in the renin angiotensin aldosterone system (RAAS) which control blood pressure. Over expression of RAAS is related with vascular hypertension, ACE inhibition has turned into a noteworthy target for controlling hypertension. In the search of lead molecules from plant origin as a substitute for toxic synthetic drugs, 25 Indian medicinal plants and foods were screened for their ACE inhibitory activity. IC₅₀ (50% inhibition of ACE) values of hydroalcoholic crude extracts and fraction were determined by a colorimetric method. Active fractions were further screened to determine the enzyme kinetics, mode, specificity and mechanism of inhibition. Standardization was done by determining total phenolics and flavonoids as gallic acid and quercetin equivalents/mg of extract respectively. Among 25 crude extracts, Cynara scolymus extract showed the best activity, IC₅₀ value 356.62 μg/mL. ACE inhibition resulting from protein precipitation was highest in Coscinium fenestratum. Lineweaver-Burk plots revealed a competitive mode of inhibition for Punica granatum ethyl acetate fraction. Fractions of Cassia occidentalis, Cynara scolymus and Embelia ribes were found to be non-specific inhibitors of ACE. Embelia ribes, Cassia occidentalis and Coscinium fenestratum fractions inhibited the ACE by Zn²⁺ ion chelation. Research revealed the potential of tested plants fractions as ACE inhibitors along with their inhibition kinetics and mechanism of inhibition. These active plant fractions might find importance in the development of potential antihypertensive agents after further investigations using preclinical and clinical trials.

Fluorescence-Based Real-Time Activity Assays to Identify RNase P Inhibitors

Transfer RNA is transcribed as precursor molecules that are processed before participating in translation catalyzed by the ribosome. Ribonuclease P is the endonuclease that catalyzes the 5' end maturation of precursor tRNA and it is essential for cell survival. Bacterial RNase P has a distinct subunit composition compared to the eukaryal counterparts; therefore, it is an attractive antibacterial target. Here, we describe a real-time fluorescence-based RNase P activity assay using fluorescence polarization/anisotropy with a 5' end fluorescein-labeled pre-tRNA^Asp substrate. This FP/FA assay is sensitive, robust, and easy to transition to a high-throughput mode and it also detects ligands that interact with pre-tRNA. We apply this FP/FA assay to measure Bacillus subtilis RNase P activity under single and multiple turnover conditions in a continuous format and a high-throughput screen of inhibitors, as well as determining the dissociation constant of pre-tRNA for small molecules.

Isolation and characterization of peptides with dipeptidyl peptidase-IV inhibitory activity from pepsin-treated bovine whey proteins

Inhibition of the enzyme dipeptidyl peptidase (DPP)-IV is one of the strategies used for the treatment of type 2 diabetes. In the present study, pepsin-treated whey protein isolate (WPI) and α-lactalbumin displaying DPP-IV inhibitory activity were fractionated by successive chromatographic steps and the resulting active fractions analyzed for their constituent peptides by liquid chromatography-electrospray ionization-tandem mass spectrometry. Among the identified sequences, 24 peptides derived from α-lactalbumin and 11 from β-lactoglobulin were synthesized and their effects on DPP-IV activity assessed. The most potent fragments, LKPTPEGDL and LKPTPEGDLEIL (IC50=45 and 57 μM, respectively), were found to inhibit DPP-IV in an un-competitive manner. Although several of the peptides tested showed some inhibitory activity, only two were as effective as the un-fractionated WPI hydrolysate and none were as potent as the un-fractionated α-lactalbumin hydrolysate. The peptides' structural features, including length and amino acid composition, were found to impact their inhibitory activity. This study provides new insights on the active components responsible for the DPP-IV inhibitory activity of pepsin-treated whey proteins.