Search Results (139)

Background/Objectives: NANOBODY^® molecules (VHHs) are attractive vectors for radiopharmaceuticals due to their small size and high target affinity, but rapid clearance and pronounced kidney retention limit their therapeutic applicability. Binding to serum albumin is a widely used strategy to prolong circulation, yet the respective contributions of albumin-binding affinity and molecular format remain insufficiently defined. This study aimed to systematically evaluate how affinity and valency modulate VHH pharmacokinetics. Methods: Four monovalent albumin-binding VHHs spanning nanomolar to micromolar affinities and two bivalent constructs were engineered, generated by fusing an albumin-binding VHH to an irrelevant non-binding VHH. All constructs incorporated a site-specific cysteine for DFO* conjugation, enabling uniform zirconium-89 labeling with high radiochemical purity. Pharmacokinetics were assessed in healthy mice using serial blood sampling and positron emission tomography. Blood and kidney exposure were quantified by non-compartmental analysis. Results: All albumin-binding constructs showed increased systemic exposure and reduced kidney uptake relative to a non-binding control. Nanomolar-affinity binders reached maximal exposure, and further affinity increases (K_D < ~100 nM) did not improve pharmacokinetics, suggesting a threshold. The micromolar binder showed intermediate exposure but still reduced renal retention compared with control. Valency effects were affinity-dependent. They were negligible at high affinity but pronounced at low affinity, where bivalency reduced systemic exposure and increased kidney uptake toward control levels. Conclusions: Albumin binding enables tuning of VHH pharmacokinetics in an affinity-dependent manner. Above an apparent affinity threshold, pharmacokinetics become format independent, whereas below this threshold, molecular format substantially influences systemic and renal disposition. Full article

Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomics approach for profiling active amino acid residues, mapping functional proteins, and guiding covalent drug development in complex biological systems. Recent methodological advances have produced several novel formats, including tandem orthogonal proteolysis-ABPP (TOP-ABPP), isotopic tandem orthogonal proteolysis-ABPP (IsoTOP-ABPP), and competitive IsoTOP-ABPP, enabling broader target identification and quantitative analysis for varied experimental purposes. In parallel, chemical probe design has evolved to selectively target specific amino acid residues, such as cysteine (Cys), lysine (Lys), and histidine (His), and to incorporate photoaffinity labeling (PAL) functionalities for capturing transient or weak protein-ligand interactions. Additionally, the integration of cleavable linkers with diverse cleavage mechanisms, including acid/base-mediated, redox-mediated, and photo irradiation mechanisms, has enhanced probe versatility and downstream analytical workflows. This review summarizes recent advances in ABPP methodologies and the design of activity-based probes and PAL probes, emphasizing their implications for future work in chemical biology. Full article

The increasing frequency, duration, and intensity of wildfires over the past decade have raised significant concerns about widespread exposure to wildfire smoke. Inhalation of wildfire smoke poses a substantial risk to human health, with epidemiological studies linking exposure to cardiovascular, respiratory, and neurological dysfunction. Wildfire smoke contains hundreds of chemical compounds across diverse classes, with concentrations varying by fuel type and combustion conditions. Phenolic compounds are prominent constituents of wood smoke, and catechol is especially abundant under smoldering conditions that produce dense smoke. In this study, ¹⁴C-labeled catechol was spiked into smoldering eucalyptus wood smoke extract (WSE) and administered to rats via intranasal instillation. Plasma was collected at 5 min and 2 h post-exposure. Samples were analyzed using parallel accelerator and molecular mass spectrometry (PAMMS). Major catechol-derived metabolites identified included benzene oxide, catechol-cysteine conjugate, and catechol-glutamine conjugate; the parent compound was not detected. These results indicate that inhaled catechol in wood smoke is quickly metabolized upon entry into circulation. PAMMS enabled both identification and relative quantification of circulating catechol metabolites, demonstrating feasibility for biomarker discovery and exposure assessment. Full article

Legumain (LGMN), a lysosomal cysteine protease, is crucial for tumor progression, invasion, and metastasis, making it a promising target for cancer imaging and therapy. This study developed novel ⁶⁷Ga-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA)-conjugated LGMN-cleavable peptide probes ([⁶⁷Ga]Ga-NOTA-LCPs) composed of polyarginine and polyglutamic acid sequences linked by LGMN-cleavable sites for nuclear medicine imaging of LGMN activity. The probes were synthesized via fluorenylmethoxycarbonyl solid-phase peptide synthesis and radiolabeled in high radiochemical yields. In vitro assays with HCT116 cells showed significantly higher uptake of [⁶⁷Ga]Ga-NOTA-LCPs compared to non-cleavable controls, confirming efficient cleavage and cellular uptake. In vivo studies in tumor-bearing mice revealed rapid renal clearance, low non-specific binding, and favorable tumor-to-blood ratios, particularly for [⁶⁷Ga]Ga-NOTA-LCP-1. These results demonstrate the potential of [⁶⁷Ga]Ga-NOTA-LCPs as effective LGMN-responsive imaging agents, with further optimization needed to improve tumor specificity and reduce off-target accumulation. Full article

Phenol red is a widely used, low-cost, label-free colorimetric pH indicator that bridges traditional colorimetric assays with modern quantitative imaging and cell-based screening platforms. Its protonation-dependent absorbance shift (430–560 nm) allows for the real-time monitoring of extracellular acidification, which indirectly reflects cellular metabolism, growth, and respiration. Although phenol red lacks the molecular specificity of genetically encoded or fluorogenic biosensors, it remains useful in systems where pH changes are effective proxies for physiological processes. Existing tissue digestion protocols often overlook key parameters, especially pH control and enzyme cofactor use. This study presents a straightforward, spectrophotometric method to monitor and adjust the pH of low-volume (1 mL) buffered enzymatic dissociation media using phenol red and a plate reader. We titrated dissociation solutions to physiological pH (~7.4) using spectrophotometric pH measurements validated against conventional glass pH probe readings, confirming method reliability. Accurate pH assessment is critical for isolating viable primary cells for downstream applications such as tissue engineering, single-cell omics, and neurophysiological assays. We highlight that papain-based dissociation media supplemented with L-cysteine can be acidic (pH 6.6) if unadjusted, compromising cell viability. This accessible approach enhances reproducibility by promoting pH documentation concerning dissociation conditions that contribute to advancing consistency in biomedical, cellular, neuronal, and tissue engineering research. Full article

Leaf senescence is a developmental process that allows nutrients to be remobilized and transported to sink organs. Previously, papain-like cysteine proteases (PLCPs) have been found to be highly expressed during leaf senescence in different plant species. In this study, we analyzed active PLCPs in barley (Hordeum vulgare L.) leaves during the terminal stage of natural senescence. Anion exchange chromatography of protein extracts from barley leaves, harvested six weeks after anthesis, followed by activity assays using the substrates Z-FR-AMC and Z-RR-AMC, revealed a single prominent peak corresponding to active PLCPs. This hydrolytic activity was completely inhibited by E-64, a potent and irreversible inhibitor of cysteine proteases. Fractions enriched for PLCP activity were affinity-labeled with DCG-04 and subjected to SDS-PAGE fractionation, separating two major bands at 43 and 38 kDa. These bands were analyzed using tandem mass spectrometry, allowing the identification of eleven PLCPs. Identified enzymes belong to eight PLCP subfamilies, including CTB/cathepsin B-like (HvPap-19 and -20), RD19/cathepsin F-like (HvPap-1), ALP/cathepsin H-like (HvPap-12 or aleurain), SAG12/cathepsin L-like A (HvPap-17), CEP/cathepsin L-like B (HvPap-14), RD21/cathepsin L-like D (HvPap-6 and -7), cathepsin L-like E (HvPap-13 and -16), and XBCP3 (HvPap-8). Among the identified PLCPs, HvPap-6 was the most abundant. Peptides corresponding to HvPap-6 were identified in both the 43 kDa and 38 kDa bands in approximately the same quantity based on total spectral count. Thus, our results indicate that two active HvPap-6 isoforms can be isolated from barley leaves at late senescence. Full article

Biothiols, including cysteine (Cys), homocysteine (Hcy), and glutathione (GSH), are crucial for physiological regulation and their imbalance poses severe health risks. Herein, we developed a pH-responsive liquid crystal (LC)-based sensing platform for detection of biothiols by doping 4-n-pentylbiphenyl-4-carboxylic acid (PBA) into 4-n-pentyl-4-cyanobiphenyl (5CB). Urease catalyzed urea hydrolysis to produce OH⁻, triggering the deprotonation of PBA, thereby inducing a vertical alignment of LC molecules at the interface corresponding to dark optical appearances. Heavy metal ions (e.g., Hg²⁺) could inhibit urease activity, under which condition LC presents bright optical images and LC molecules maintain a state of tilted arrangement. However, biothiols competitively bind to Hg²⁺, the activity of urease is maintained which enables the occurrence of urea hydrolysis. This case triggers LC molecules to align in a vertical orientation, resulting in bright optical images. This pH-driven reorientation of LCs provides a visual readout (bright-to-dark transition) correlated with biothiol concentration. The detection limits of Cys/Hcy and GSH for the PBA-doped LC platform are 0.1 μM and 0.5 μM, respectively. Overall, this study provides a simple, label-free and low-cost strategy that has a broad application prospect for the detection of biothiols. Full article

Calpain-5/CAPN5 is a calcium-activated, non-lysosomal cysteine (thiol) protease. The substrate repertoire of CAPN5 is not known. Calpains catalyze limited proteolysis of their substrates, generating neo-N-termini that correspond to internal residues of their nascent substrate proteins. To identify such neo-N-termini generated by CAPN5, we employed an N-terminomics approach called TAILS (Terminal amine isotopic labeling of substrates) to quantitatively compare the N-terminal peptides detected in parental and CAPN5-deficient SH-SY5Y neuroblastoma cells. Thirty neo-N-termini corresponding to 29 protein groups and 24 unique proteins were detected to be depleted in the CAPN5^−/− cells. A subset of the identified putative substrates was further studied with CAPN5 co-immunoprecipitation, in vitro calcium-induced CAPN5 proteolysis assay, and their cellular fragmentation patterns were compared in parental and CAPN5-deficient SH-SY5Y cells. Here, we provide evidence for CAPN5-mediated proteolysis of the synaptic proteins DLGAP4, IQSEC1 and MPDZ, the neurodegeneration-related EWS, hnRNPU, TFG and UGP2, the DNA replication regulator MCM3, and the neuronal differentiation regulator LMTK1. Our data provide new relevance for neovascular inflammatory vitreoretinopathy (NIV), a progressive eye disease caused by pathogenic mutations in CAPN5. Data are available via ProteomeXchange with identifier PXD064313. Full article

Schizothorax prenanti is an economically important cold-water fish in China. Lipopolysaccharide (LPS) can induce an immune response in S. prenanti; however, little is known about the effects of LPS on oxidative stress (OS) and apoptosis in S. prenanti. In this study, S. prenanti fish were stimulated with LPS at a dose of 10 mg/kg of body weight. After 0 h, 12 h and 24 h, the tissue samples were collected. The OS- and apoptosis-related genes and enzymatic activities in the liver, head kidney (HK), and spleen of S. prenanti were analyzed by a two-way repeated-measures analysis of variance (ANOVA). Hematoxylin and eosin and terminal transferase uridyl nick end labeling staining were also performed. In S. prenanti, LPS administration downregulated the catalase (CAT) and B-cell lymphoma/Leukemia-2 (Bcl-2) expression levels, and upregulated BCL2-associated X (Bax) and cysteine-aspartic-specific protease-3 (caspase-3) expression levels. Meanwhile, superoxide dismutase and CAT enzymatic activities were inhibited and malondialdehyde (MDA) content was increased by LPS treatment. Additionally, LPS treatment induced OS damage and apoptosis in tissue sections. These results indicated that apoptosis in the liver, HK, and spleen of LPS-administered S. prenanti may be mediated by OS via the mitochondrial apoptotic signaling pathway. Our findings are expected to contribute to a better understanding of the responses of different tissues to bacterial challenges. In addition, we can increase the tolerance of fish to the OS through dietary manipulation in the future. Full article

Autolysis in sea cucumber has long been a threat to raw material storage and product processing. The involvement of endogenous cysteine protease in sea cucumber autolysis has been proved extendedly. However, as an essential part of the mechanism of autolysis, the role of its endogenous inhibitor has seldom been reported. To investigate the role of cysteine protease inhibitors in the early stage of hypoxic exposure-induced autolysis, a novel cystatin gene (SjCyt) belonging to the subfamily of cystatin C was cloned from Apostichopus japonicus by homology cloning and rapid amplification of cDNA ends. The affinity of SjCyt to cysteine protease (cathepsin L and cathepsin B) was investigated by molecular dynamics simulations. Pertinent metrics, including the root mean square deviation, radius of gyration, Gibbs free energy, binding free energy, and bond-forming frequency, showed that the conformation of SjCyt–SjCL was more stable and confirmed a stronger interaction of SjCyt with cathepsin L than with cathepsin B. Thus, cathepsin L (SjCL) was selected to further study its co-expression with SjCyt over a period of 9 h at an early stage of hypoxic exposure. Quantitative RT-qPCR revealed a ubiquitous transcriptional profile of SjCyt and SjCL in all the tested tissues, with the highest abundance in the dorsal epidermis, tube feet, and coelomocytes. Temporal transcription of them showed an overall up-regulated co-expression in the dorsal epidermis and tube feet. However, up-regulated SjCyt and down-regulated SjCL were observed at the protein level. Further immunofluorescence double labeling also found increased staining of SjCyt and SjCyt–SjCL complexes and decreased SjCL. Additionally, recombinant SjCyt was prepared and demonstrated an evident autolysis-inhibiting effect. The results of this study indicated that the anti-autolytic regulation of SjCyt functions at the very early stage of hypoxic exposure, exerting effects at both the transcriptional and translational levels. The above finding offers new insights into the mechanisms of sea cucumber autolysis. Full article

Mushrooms are a valuable source of bioactive compounds to develop efficient, secure medicines and environmentally friendly agrochemicals. Cylindracin is a small cysteine-rich protein that is specifically expressed in the immature fruiting body of the edible mushroom Cyclocybe cylindracea. Recombinant protein (rCYL), comprising the C-terminal cysteine-rich domain of cylindracin, inhibits the hyphal growth and conidiogenesis of filamentous fungi. Here, we show that rCYL represses the egg-laying and development of Caenorhabditis elegans and Drosophila melanogaster. The feeding of rCYL at 16 µM reduced the body volume of C. elegans larvae to approximately 60% when compared to the control. At the same concentration, rCYL repressed the frequencies of pupation and emergence of D. melanogaster to 74% and 40%, respectively, when compared to the control. In virgin adult flies, feeding of rCYL at 47 µM substantially repressed the frequency of egg-laying, and the pupation and emergence of the next generation, especially for females. These inhibitory effects of rCYL gradually disappeared after ceasing the ingestion of rCYL. The use of fluorescence-labeled rCYL revealed that the protein accumulates specifically at the pharynx cuticles of C. elegans. In D. melanogaster, fluorescence-labeled rCYL was detected primarily in the midguts and to a lesser degree in the hindguts, ovaries, testes, and malpighian tubules. rCYL was stable against trypsin, chymotrypsin, and pepsin, whereas it did not inhibit proteolytic and glycolytic enzymes in vitro. rCYL oligomerized and formed amyloid-like aggregates through the binding to heparin and heparan sulfate in vitro. These results suggest that rCYL has potential as a new biocontrol agent against pests. Full article

Fluorescent labeling of membrane proteins is essential for exploring their functions, signaling pathways, interaction partners, and structural dynamics. Organic fluorophores are commonly used for this purpose due to their favorable photophysical properties and photostability. However, a persistent challenge is the inaccessibility of the surface-exposed cysteine residues required for site-specific labeling, as these residues often become sequestered within detergent micelles during protein extraction. To address this limitation, we developed an approach based on polymer-encapsulated nanodiscs that preserves the protein’s native-like lipid-bilayer environment while ensuring the accessibility of surface-exposed cysteine residues. In this method, His-tagged proteins embedded in native nanodiscs are retained on a nickel affinity column, allowing for simultaneous purification and labeling by adding fluorescent dyes. This versatile technique was demonstrated with two challenging-to-label membrane proteins, the potassium channel KvAP and the urea channel HpUreI, for which detergent-based labeling had failed. This opens new possibilities for studying a wide range of fluorescently labeled membrane proteins in near-native states, advancing applications in biophysics, structural biology, and drug discovery. Full article

Gintonin, a non-saponin glycolipoprotein from Panax ginseng, acts as a lysophosphatidic acid ligand. However, its anticancer effects, especially in melanoma, remain unclear. This study investigated the anti-proliferative effects and intracellular signaling mechanisms of a gintonin-enriched fraction (GEF) from Panax ginseng in human melanoma cell lines. In vitro, GEF treatment significantly inhibited cell proliferation, reduced clonogenic potential, and delayed wound healing in melanoma cells. Flow cytometry and terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining showed that GEF induced apoptosis, as evidenced by increased apoptotic cell populations and nuclear changes. GEF also caused cell cycle arrest in the G₁ phase for A375 cells and the G₂/M phase for A2058 cells. It triggered apoptotic signaling via activation of caspase-3, -9, poly (ADP-ribose) polymerase cleavage, and downregulation of B cell lymphoma-2 (Bcl-2). GEF treatment also raised intracellular reactive oxygen species (ROS) levels and mitochondrial stress, which were mitigated by N-acetyl cysteine (NAC), an ROS inhibitor. In vivo, GEF suppressed tumor growth in A375- and A2058-xenografted mice without toxicity. These findings suggest that GEF from Panax ginseng has potential antitumor effects in melanoma by inducing apoptosis and cell cycle arrest, presenting a promising therapeutic avenue. Full article

Protein S-palmitoylation is the process by which a palmitoyl fatty acid is attached to a cysteine residue of a protein via a thioester bond. A range of methodologies are available for the detection of protein S-palmitoylation. In this study, two methods for the S-palmitoylation of different proteins were compared after metabolic labeling of cells with 15-hexadecynoic acid (15-YNE) to ascertain their relative usefulness. It was hypothesized that labeling cells with a traceable lipid would affect lipid metabolism and the cellular lipidome. In this study, we developed a method to track 15-YNE incorporation into lipids using liquid chromatography high-resolution mass spectrometry (LC-HRMS) as well as protein palmitoylation in the same sample. We observed a time- and concentration-dependent S-palmitoylation of calnexin and succinate dehydrogenase complex flavoprotein subunit A (SDHA) depending on the cell type. The detection of S-palmitoylation with a clickable fluorophore or biotin azide followed by immunoprecipitation is shown to be equally useful. 15-YNE was observed to be incorporated into a wide array of lipid classes during the process, yet it did not appear to modify the overall lipid composition of the cells. In conclusion, we show that 15-YNE is a useful tracer to detect both protein S-palmitoylation and lipid metabolism in the same sample. Full article

Background: Acute liver injury (ALI) is a prevalent and potentially lethal condition globally, where pharmacotherapy plays a vital role. However, challenges such as rapid drug excretion and insufficient concentration at hepatic lesions often impede the treatment’s effectiveness. Methods: We successfully prepared glycyrrhizinate monoammonium cysteine (GMC)-loaded lipid nanoparticles (LNPs) using high-pressure homogenization. The characterization and safety of the LNPs were measured using electrophoretic light scattering (ELS), transmission electron microscopy (TEM), dynamic light scattering (DLS), cytotoxicity assays, and hemolysis tests. The distribution of LNPs in mice was explored using fluorescence labeling methods. The encapsulation efficiency of LNP-GMC was detected using High-Performance Liquid Chromatography (HPLC), and its slow-release effect on GMC was assessed through dialysis. The therapeutic effects of LNP-GMC and pure GMC on the ALI model were evaluated using fibroblast activation protein inhibitor (FAPI) PET imaging, blood biochemical indicators, and liver pathology slices. Results: The encapsulation of GMC in LNPs enhances drug stability and prolongs its hepatic retention, significantly improving its bioavailability and sustained release within the liver. This study also explores the expression of fibroblast activation protein (FAP) in ALI, employing ⁶⁸Ga-FAPI PET/CT imaging for effective differentiation and assessment of liver injury. Conclusions: Our results suggest that LNPs offer an enhanced therapeutic approach for ALI treatment, reducing the required drug dosage, and ⁶⁸Ga-FAPI PET/CT imaging provides a novel method for diagnosis and treatment assessment. This study contributes valuable insights into the utilization of LNPs in liver disease treatment, presenting a promising direction for future clinical applications. Full article