Biology subjects

Nakaya, T.

Publications and source records attributed to Nakaya, T..

5 recordsLinked to original sources

bioRxiv2026

Elucidation of the anti-inflammatory mechanism of isoliquiritigenin from Glycyrrhiza uralensis using activity-based protein profiling

Glycyrrhiza uralensis is a widely used medicinal plant present in more than 70% of Kampo formulations in Japan owing to its diverse pharmacological activities, including immunomodulatory, antitumor, and antioxidant effects. Isoliquiritigenin (ILG), a major chalcone constituent of G. uralensis, exhibits anti-inflammatory activity; however, its molecular mechanism remains unclear. Here, we employed an activity-based protein profiling approach to identify the molecular targets of ILG. Given that the ,{beta}-unsaturated carbonyl moiety of ILG can covalently react with reactive cysteine residues via nucleophilic addition, we used an iodoacetamide-based probe to globally profile cysteine-reactive proteomes. The comparative analysis between ILG- and vehicle-treated RAW 264.7 macrophages identified cysteine 65 (Cys65) of lipocalin-type prostaglandin D2 synthase (L-PGDS) as a potential covalent target. ILG treatment did not alter L-PGDS expression levels, indicating that reduced probe labeling reflects direct covalent competition rather than changes in expression. Consistently, ILG significantly suppressed prostaglandin D2 (PGD2) production, comparable to the selective L-PGDS inhibitor AT-56. Although both ILG and AT-56 reduced interleukin-6 expression, ILG exerted a stronger inhibitory effect. Our results demonstrate that covalent inhibition of L-PGDS and subsequent suppression of PGD2 production represent a key mechanism underlying the anti-inflammatory activity of ILG.

biochemistry↗

bioRxiv2025

Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics

Glycyrrhiza uralensis, known for its diverse pharmacological effects, including immunoregulation, anti-tumor, and antioxidant properties, is a widely used medicinal plant found in more than 70% of traditional herbal medicines (Kampo) in Japan. Although over 300 compounds have been discovered in G. uralensis, the molecular mechanisms underlying its bioactivity remain largely unknown due to the chemical diversity of its compounds. Here, we performed a multiomics analysis incorporating untargeted hydrophilic metabolomics, lipidomics, and phosphoproteomics to elucidate the molecular mechanisms distinguishing the effects of a single bioactive compound, isoliquiritigenin (ILG), and the extract of G. uralensis (GU). Multiomics time-course data were obtained for lipopolysaccharide (LPS)-stimulated RAW264.7 cells under four experimental conditions: control, LPS(+), LPS(+)/ILG(+), and LPS(+)/GU(+), where 182 hydrophilic metabolites, 381 lipids, and 13,211 phosphopeptides were characterized. The metabolic signatures of inflammatory macrophages, including increased levels of glycolytic intermediates, succinate, citrulline, triacylglycerols, and cholesteryl esters, were attenuated in both the GU(+) and ILG(+) groups. Using a multivariate approach based on a partial least squares algorithm with an imposed inflammation level order information, we identified upregulated phosphorylation of sirtuin 1 and 2 (SIRT1/2) along with alterations in nicotinamide adenine dinucleotide metabolism in the ILG(+) group. The inhibition of SIRT2 suppressed the anti-inflammatory effect of ILG, as indicated by a reduction in interleukin-6 (IL-6) levels. Furthermore, we discovered a substantial increase in {gamma}-aminobutyric acid (GABA) and its downstream metabolite, 4-guanidinobutyric acid, in the GU(+) group. These increases were attributed to endogenous GABA production through glutamic acid decarboxylase rather than uptake via GABA transporters. Exogenous GABA administration significantly suppressed IL-6 and IL-1{beta} expression in LPS-stimulated cells, and the simultaneous administration of GABA and ILG enhanced the anti-inflammatory effects. Consequently, this study presents an approach to elucidating the importance of traditional herbal formulations and demonstrates the utility of multiomics in uncovering that endogenous GABA production would facilitate anti-inflammatory effects with ILG in GU administration.

systems biology↗

bioRxiv2024

Using variable data independent acquisition for capillary electrophoresis-based untargeted metabolomics

Capillary electrophoresis coupled with tandem mass spectrometry (CE-MS/MS) offers advantages in peak capacity and sensitivity for metabolic profiling, owing to the electroosmotic flow-based separation. However, the utilization of data-independent MS/MS acquisition (DIA) is restricted due to the absence of an optimal procedure for analytical chemistry and its related informatics framework. We assessed the mass spectral quality using two DIA techniques, namely, all-ion fragmentation (AIF) and variable DIA (vDIA), to isolate 60[~]800 Da precursor ions with respect to annotation rates. Our findings indicate that vDIA, coupled with the updated MS-DIAL chromatogram deconvolution algorithm, yields higher spectral matching scores and annotation rates compared to AIF. Additionally, we evaluated a linear migration time (MT) correction method using internal standards to accurately align chromatographic peaks in a dataset. After the correction, the peaks exhibited less than 0.1 min MT drifts, a difference mostly equivalent to that of conventional reverse-phase liquid chromatography techniques. Moreover, we conducted MT prediction for metabolites recorded in mass spectral libraries and metabolite structure databases containing a total of 469,870 compounds, achieving an accuracy of less than 1.5 min root mean squares. Thus, our platform provides a peak annotation platform utilizing MT information, accurate precursor m/z, and the MS/MS spectrum recommended by the metabolomics standards initiative. Applying this procedure, we investigated metabolic alterations in lipopolysaccharide (LPS)-induced macrophages, characterizing 170 metabolites. Furthermore, we assigned metabolite information to unannotated peaks using an in-silico structure elucidation tool, MS-FINDER. The results were integrated into the nodes in the molecular spectrum network based on the MS/MS similarity score. Consequently, we identified a significantly increased amount of metabolites in the LPS-administration group, glycinamide ribonucleotide, not present in any spectral libraries. Additionally, we retrieved metabolites of false-negative hits in the initial spectral annotation procedure. Overall, our study underscores the potential of CE-MS/MS with DIA and computational mass spectrometry techniques for metabolic profiling.

biochemistry↗

bioRxiv2022

Differences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability

SARS-CoV-2 variants of concern (VOCs) could cause significant human and economic damage owing to increased infectivity and transmissibility, and understanding their characteristics is crucial for infection control. Here, we analyzed differences in viral stability and disinfection efficacy between the Wuhan strain and all VOCs. On plastic and skin surfaces, Alpha, Beta, Delta, and Omicron variants exhibited more than two-fold longer survival than the Wuhan strain, and the Omicron variant had the longest survival time. Specifically, survival times of the Wuhan strain, Alpha variant, Beta variant, Gamma variant, Delta variant, and Omicron variant on skin surfaces were 8.6 h (95% CI, 6.5-10.9 h), 19.6 h (95% CI, 14.8-25.3 h), 19.1 h (95% CI, 13.9- 25.3 h), 11.0 h (95% CI, 8.1-14.7 h), 16.8 h (95% CI, 13.1-21.1 h), and 21.1 h (95% CI, 15.8- 27.6 h), respectively. In vitro, disinfectant effectiveness evaluations showed that Alpha, Beta, Delta, and Omicron were slightly more resistant to ethanol than the Wuhan strain. However, ex vivo evaluation showed that on human skin, all viruses were completely inactivated by exposure to 35 w/w % ethanol for 15 s. The high environmental stability of these VOCs could increase transmission risk and contribute to spread. Additionally, the Omicron variant might have been replaced by the Delta variant due to its increased environmental stability and rapid spread. To prevent VOC spread, it is highly recommended that current infection control practices use disinfectants with appropriate ethanol concentrations.

microbiology↗

bioRxiv2018

A transgenic mutant mouse line accompanied by the complete deletion of interleukin-33 showed insulin and leptin resistances

Interleukin (IL) -33 has been identified as a member of the IL-1 family. Members of the IL-1 family have been reported to be involved in the regulation of energy homeostasis and glucose metabolism. Homozygous transgenic mutant mice of FLP14 line, that we previously generated, unexpectedly developed mature-onset obesity and diabetes. Through genetic investigations, we found that insertion of the transgenes had resulted in complete deletion of the Il33 gene. These obese male homozygous mutant mice exhibited hyperphagia with hyperleptinemia and insulin resistance caused by increased hepatic gluconeogenesis and decreased glucose uptake in skeletal muscle. As a result of examining preobese male homozygous mutant mice to investigate with the exclusion of the effect of obesity, hyperphagia with hyperleptinemina and insulin resistance caused by decreased glucose uptake in skeletal muscle were already observed, but the increased hepatic glucose production was not. To investigate whether the insulin resistance was caused by deletion of the Il33 gene, we treated these preobese homozygous mutant mice with recombinant IL-33 protein and noted a significant improvement in insulin resistance. Thus, insulin resistance in these homozygous mutant mice was caused, at least in part, by IL-33 deficiency, suggesting a favorable role of IL-33 for glucose metabolism in the skeletal muscle.

molecular biology↗