7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk.

Droplet-based microfluidic systems are a powerful tool for biological assays with high throughput. Water-in-oil droplets (WODLs) are typically used in droplet-based microfluidic systems to culture microorganisms and perform enzyme assays. However, because of the oil surrounding the nanoliter and picoliter volumes of WODLs, availability of suitable substrates is limited. For instance, although 7-amino-4-methylcoumarin (AMC) is commonly used as a fluorescent probe of the substrate to detect peptidase activity, AMC leaks from WODLs to the oil phase due to its high hydrophobicity. Thus, AMC substrates cannot be used in droplet-based microfluidic systems with WODLs. In this study, we developed a peptidase substrate consisting of a dipeptide and 7-aminocoumarin-4-acetic acid (ACA), an AMC-derived fluorogenic compound. ACA was retained in the WODL for more than 7 days, and the dipeptidyl ACA substrate detected dipeptidyl peptidase (DPP) activity in the WODL. Compared to AMC substrates, the substrate specificity constants of DPPs for ACA substrates increased up to 4.7-fold. Fluorescence-activated droplet sorting made high-throughput screening of microorganisms based on DPP activity using the dipeptidyl ACA substrate possible. Since ACA could be applied to various substrates as a fluorescent probe, detectable microbial enzyme activities for droplet-based microfluidic systems can be largely expanded.

Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.

Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.

Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.

Dipeptidyl peptidase IV (DPP IV, DPP4, or DAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position. The substrate recognition mechanism has been fully elucidated for mammalian DPP IV by crystal structure analyses but not for bacterial orthologues. Here, we report the crystal structures of a bacterial DPP IV (PmDAP IV) in its free form and in complexes with two kinds of dipeptides as well as with a non-peptidyl inhibitor at 1.90 to 2.47 Å resolution. Acyl-enzyme intermediates were observed for the dipeptide complexes of PmDAP IV, whereas tetrahedral intermediates were reported for the oligopeptide complexes of mammalian DPP IVs. This variation reflects the different structural environments of the active site Arg residues, which are involved in the recognition of a substrate carbonyl group, of mammalian and bacterial enzymes. A phylogenetic analysis revealed that PmDAP IV is a closer relative of dipeptidyl peptidases 8 and 9 (DPP8 and DPP9, DPP IV-family enzymes) than DPP IV. These results provide new insights into the substrate recognition mechanism of bacterial DAP IVs and may assist in the development of selective inhibitors for DAP IVs from pathogenic asaccharolytic bacteria, which utilise proteins or peptides as an energy source.

Periplasmic form of dipeptidyl aminopeptidase IV from Pseudoxanthomonas mexicana WO24: purification, kinetic characterization, crystallization and X-ray crystallographic analysis.

Dipeptidyl aminopeptidase IV (DAP IV or DPP IV) from Pseudoxanthomonas mexicana WO24 (PmDAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position [NH2-P2-P1(Pro/Ala)-P1'-P2'…]. For crystallographic studies, the periplasmic form of PmDAP IV was overproduced in Escherichia coli, purified and crystallized in complex with the tripeptide Lys-Pro-Tyr using the hanging-drop vapour-diffusion method. Kinetic parameters of the purified enzyme against a synthetic substrate were also determined. X-ray diffraction data to 1.90 Šresolution were collected from a triclinic crystal form belonging to space group P1, with unit-cell parameters a = 88.66, b = 104.49, c = 112.84 Å, α = 67.42, ß = 68.83, γ = 65.46°. Initial phases were determined by the molecular-replacement method using Stenotrophomonas maltophilia DPP IV (PDB entry 2ecf) as a template and refinement of the structure is in progress.

A simple method for screening emission sources of carbonyl compounds in indoor air.

Volatile organic compounds (VOCs) emitted from building and furnishing materials are frequently observed in high concentrations in indoor air. Nondestructive analytical methods that determine the main parameters influencing concentration of the chemical substances are necessary to screen for sources of VOC emissions. Toward this goal, we have developed a new flux sampler, referred to herein as an emission cell for simultaneous multi-sampling (ECSMS), that is used for screening indoor emission sources of VOCs and for determining the emission rates of these sources. Because the ECSMS is based on passive sampling, it can be easily used on-site at a low cost. Among VOCs, low-molecular-weight carbonyl compounds including formaldehyde are frequently detected at high concentrations in indoor environments. In this study, we determined the reliability of the ECSMS for the collection of formaldehyde and other carbonyl compounds emitted from wood-based composites of medium density fiberboards and particleboards. We then used emission rates determined by the ECSMS to predict airborne concentrations of formaldehyde emitted from a bookshelf in a large chamber, and these data were compared to formaldehyde concentrations that were acquired simultaneously by means of an active sampling method. The values obtained from the two methods were quite similar, suggesting that ECSMS measurement is an effective method for screening primary sources influencing indoor concentrations of formaldehyde.

MEK/ERK signaling is a critical mediator for integrin-induced cell scattering in highly metastatic hepatocellular carcinoma cells.

The human hepatocellular carcinoma (HCC)-derived cell line KYN-2 is thought to provide a good model for studying the molecular basis of invasion and metastasis of human HCC, because it often shows cell scattering in vitro and intrahepatic metastasis in vivo. We previously found that integrin-mediated extracellular signals inactivated E-cadherin in KYN-2, and caused loss of cell-cell contact with gain of cell motility, which is considered to be a critical step in the process of cancer cell invasion and metastasis. To further understand molecular mechanisms involved in biological aggressiveness of HCC, we investigated intracellular signaling involved in integrin-mediated scattering of KYN-2 cells. Cultured KYN-2 cells formed trabecular aggregates in suspension, but when adhering to integrin-stimulating substrata, they scattered according to phosphorylation of extracellular signal-regulated kinase (ERK). Upon treatment with ERK kinase (MEK) inhibitor PD98059, adhered KYN-2 cell scattering was inhibited, tight cell-to-cell contact was recovered, and both E-cadherin and actin filaments accumulated in the area of intercellular contact zone. In contrast, constitutively active MEK1-transfected KYN-2 cells showed reduced E-cadherin and actin filaments in the intercellular contact zone, showing a flattened phenotype with broad lamellipodia. Enforced signaling of MEK-ERK pathway in KYN-2 cells suppressed cadherin-mediated homotypic adhesion and increased the potential of cell motility. An antibody-based protein microarray analysis revealed that the cytoplasmic protein c-Cbl was significantly downregulated in MEK1-transfected KYN-2 cells, suggesting that c-Cbl might be a candidate downstream mediator of integrin/MEK/ERK-mediated cell scattering. In conclusion, cell scattering of the highly metastatic cell line KYN-2 is regulated through the integrin-MEK-ERK signaling cascade, suggesting that this molecular pathway may be critical in intrahepatic metastasis of human HCC.

Liver metastasis 30 years after enucleation of the left eyeball for choroidal melanoma.

Here, we report a case of 70-year-old female with metastatic choroidal melanoma in the liver, which was detected 30 years after enucleation of the left eyeball. At first, two hypovascular tumors (4cm and 1cm in diameter) were detected in the liver as high-density areas on plain computed tomography (CT). They were demonstrated as hyper- and hypo-intensity lesions on T1- and T2-weighted image of magnetic resonance imaging (MRI), respectively, with superparamagnetic iron oxide uptake. During about 2-years follow-up, the larger tumor did not change significantly in size and in the character. However, the smaller one grew up in size and changed its nature to hypervascular and hyper-intensity on T2-weighted image of MRI. These hypervascular tumors increased in number and in size rapidly. The specimens obtained with tumor biopsy revealed epithelioid tumor cells positive for HMB45 immunohistochemical stain with and without brown pigment, and the tumors were diagnosed as melanoma. The patient underwent transcatheter arterial chemoembolization with cisplatin and epirubicin hydrochloride, and subsequent transcatheter arterial infusion chemotherapy with cisplatin, nimustine and dacarbazine. Unfortunately, however, the tumor rapidly progressed and she died. We discuss the imaging of the melanoma metastasized to the liver with the estimation of doubling time (DT) of the tumors.

Gross appearance of hepatocellular carcinoma reflects E-cadherin expression and risk of early recurrence after surgical treatment.

BACKGROUND AND AIMS: Correlation between the gross classification of hepatocellular carcinoma (HCC) and its vascular invasion or intrahepatic metastasis has been reported previously. Because E-cadherin-mediated epithelial cell-to-cell adhesion is thought to suppress cancer cell invasion, the present study was performed to analyze the correlation between E-cadherin expression and the gross classification of HCC. METHODS: Thirty-six resected solitary HCC <6 cm in diameter were each classified as single nodular type (type 1), single nodular with extranodular growth type (type 2) or contiguous multinodular type (type 3), and the clinicopathological and prognostic differences between type 1 HCC and the other types were analyzed. The expression of E-cadherin in each tumor was examined by immunoblotting and immunohistochemical analysis. RESULTS: Vascular invasion and microscopic intrahepatic metastasis were observed more frequently in types 2 and 3 (61%) than in type 1 (13%) HCC. Immunoblot analysis indicated that the relative level of E-cadherin expression in cancerous tissue was significantly lower in type 2 and 3 (0.75 +/- 0.49) than in type 1 (1.46 +/- 0.79) HCC. Immunohistochemical examination revealed decreased and partially absent E-cadherin expression in the tumorous area of type 2 and 3 HCC. The recurrence-free survival rate was higher for patients with type 1 HCC than for those with the other types. CONCLUSIONS: Types 2 and 3 HCC have marked metastatic and invasive potential and reduced expression of E-cadherin, predicting a high risk of recurrence after surgical treatment.