Monitoring of proteolytic enzyme activity using phase transition-based peptide arrays

Discovery of Phenolic Matrix Metalloproteinase Inhibitors by Peptide Microarray for Osteosarcoma Treatment

Because of the abnormal upregulation of matrix metalloproteinase (MMP) activities in tumors, MMP inhibitors (MMPIs) are validated anticancer drug candidates. We identified several MMPIs including mangiferin as an MMP-9 inhibitor with a half maximal inhibitory concentration (IC₅₀) value of 250 nM, isosilybin as an MMP-13 inhibitor with an IC₅₀ value of 250 nM, and isoliquiritigenin as a broad-spectrum MMPI (with IC₅₀ values of 16 nM for MMP-1, 10 nM for MMP-2, 81 nM for MMP-3, 8 nM for MMP-7, 10 nM for MMP-9, and 14 nM for MMP-13) through studying the interactions of 6 MMPs secreted by U-2OS cells with 51 phenolic natural products on the peptide microarray platform. In addition, the inhibitory mechanisms of as-discovered MMPIs were evaluated by a molecular docking simulation. The antitumor efficiencies of MMPIs were demonstrated by both a cell scratch test and growth suppression of mouse-born OS tumors. The results of the cell scratch test suggested that isoliquiritigenin significantly inhibited the migration of U-2OS cells. In addition, administration of isoliquiritigenin significantly reduced the tumor size (by about 80%) and prolonged the survival time (by more than 70 days). This study suggests that the discovery of MMPIs from phenolic natural products is a meaningful way to screen anticancer agents.

Biosensors and bioassays for determination of matrix metalloproteinases: state of the art and recent advances

Matrix metalloproteinases (MMPs) are closely associated with various physiological and pathological processes, and have been regarded as potential biomarkers for severe diseases including cancer. Accurate determination of MMPs would advance our understanding of their roles in disease progression, and is of great significance for disease diagnosis, treatment and prognosis. In this review, we present a comprehensive overview of the developed bioassays/biosensors for detection of MMPs, and highlight the recent advancement in nanomaterial-based immunoassays for MMP abundance measurements and nanomaterial-based biosensors for MMP activity determination. Enzyme-linked immunosorbent assay (ELISA)-based immunoassays provide information about total levels of MMPs with high specificity and sensitivity, while target-based biosensors measure the amounts of active MMPs, and allow imaging of MMP activities in vivo. For multiplex and high-throughput analysis of MMPs, microfluidics and microarray-based assays are described. Additionally, we put forward the existing challenges and future prospects from our perspective.

Polymorphisms in matrix metalloproteinases 2, 3, and 8 increase recurrence and mortality risk by regulating enzyme activity in gastric adenocarcinoma

The association of polymorphisms in matrix metalloproteinases (MMPs) with clinical outcomes of gastric adenocarcinoma has not been examined. Ten polymorphisms in MMP1, 2, 3, 7, 8, 9, 12, and 13 were genotyped and investigated, and patients were followed for an average of 58 months. The activities of MMP2, 3, and 8 were measured. Recurrence risk increased in patients with the MMP2 rs2285053 CC genotype (hazard ratio [HR], 1.85), MMP3 rs679620 AA genotype (HR, 2.15), and MMP8 rs1940475 TT genotype (HR, 2.22) on recurrence free survival (RFS). Co-presence of the unfavorable MMP2 rs2285053 CC and MMP8 rs1940475 TT genotypes resulted in an additional increased risk of recurrence (RFS: HR, 4.42; 95% confidence interval [CI], 2.15-9.09; p<0.0001) and risk of death (overall survival ( OS) : HR, 6.59; 95% CI, 3.15-13.19; p<0.0001). Theoretical survival tree analysis revealed that recurrence-free survival significantly varied from 15.5 to 87 months among patients with different polymorphisms in MMP2, 3, and 8. The enzymatic activities of MMP2 and MMP3 increased (MMP2 rs2285053 CC: 888.60 vs. CT: 392.00, p <0.0001; MMP3 rs679620 AA: 131.10 vs. GG: 107.74, p=0.015), whereas those of MMP8 decreased (MMP8 rs1940475 TT: 133.78 vs. CC: 147.54, p=0.011) in gastric cancer tissues. These results suggest that polymorphisms in MMP2, 3, and 8 may increase cancer recurrence and patient death by increasing or decreasing enzyme activity in patients with gastric adenocarcinoma.

Array-Based High-Throughput Analysis of Silk-Elastinlike Protein Polymer Degradation and C-Peptide Release by Proteases

The objective of this study was to utilize an on-chip degradation assay to evaluate polymer depots and the predicted drug release from the depots. We conjugated four silk-elastinlike protein (SELP) polymers including SELP-815K, SELP-815K-RS1, SELP-815K-RS2, and SELP-815K-RS5 with a Cy5-NHS ester and fabricated SELP arrays by immobilizing the conjugated polymers onto well-type amine arrays. SELP polymer degradation rates were investigated by calculating the half-maximal effective concentration (EC50). Eight cleavage enzymes were applied, all of which exhibited distinctive EC50 values for SELP-815K and its three analogues. We successfully utilized this assay to study the in vitro release of the Cy5-conjugated C-peptide from SELP-815K hydrogel arrays. Additionally, cumulative C-peptide release from the SELP-815K depots was also demonstrated using repetitive elastase treatments. Therefore, this array-based on-chip degradation assay could potentially be used for evaluating depot degradation and controlled drug release from polymer depots at the molecular level.

Real-time monitoring of glucose-6-phosphate dehydrogenase activity using liquid droplet arrays and its application to human plasma samples

Glucose-6-phosphate dehydrogenase (G6PD) regulates nicotinamide adenine dinucleotide phosphate (NADPH) levels and is related to the pathogenesis of various diseases, including G6PD deficiency, type 2 diabetes, aldosterone-induced endothelial dysfunction, and cancer. Therefore, a highly sensitive array-based assay for determining quantitative G6PD activity is required. Here, we developed an on-chip G6PD activity assay using liquid droplet fluorescence arrays. Quantitative G6PD activity was determined by calculating reduced resorufin concentrations in liquid droplets. The limit of detection (LOD) of this assay was 0.162 mU/ml (2.89 pM), which is much more sensitive than previous assays. We used our activity assay to determine kinetic parameters, including Michaelis-Menten constants (Km) and maximum rates of enzymatic reaction (Vmax) for NADP(+) and G6P, and half-maximal inhibitory concentrations (IC50). We successfully applied this new assay to determine G6PD activity in human plasma from normal healthy individuals (n=30) and patients with inflammation (n=30). The inflammatory group showed much higher G6PD activities than did the normal group (p<0.001), with a high area under the curve value of 0.939. Therefore, this new activity assay has the potential to be used for diagnosis of G6PD-associated diseases and utilizing kinetic studies.

Enzymatic reactions on immobilised substrates

This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.

Integrative proteomic profiling of protein activity and interactions using protein arrays

Proteomic studies based on abundance, activity, or interactions have been used to investigate protein functions in normal and pathological processes, but their combinatory approach has not been attempted. We present an integrative proteomic profiling method to measure protein activity and interaction using fluorescence-based protein arrays. We used an on-chip assay to simultaneously monitor the transamidating activity and binding affinity of transglutaminase 2 (TG2) for 16 TG2-related proteins. The results of this assay were compared with confidential scores provided by the STRING database to analyze the functional interactions of TG2 with these proteins. We further created a quantitative activity-interaction map of TG2 with these 16 proteins, categorizing them into seven groups based upon TG2 activity and interaction. This integrative proteomic profiling method can be applied to quantitative validation of previously known protein interactions, and in understanding the functions and regulation of target proteins in biological processes of interest.