Search Results (125)

γ-Glutamyl transpeptidase (GGT) is overexpressed in a variety of diseases, making it an important diagnostic criterion for diseases. Herein, a new fluorescence probe based on naphthalimide (Glu-MDA) was developed and employed for the rapid detection of GGT in tumor cells or samples. Alkynylated naphthalimide is the fluorescent core for excellent fluorescence response. The covalent bridging of self-immolative short linkers reduces the steric hindrance between probes and enzyme cleavage sites, which leads to improved enzymatic reaction kinetics. Glu-MDA shows a rapid response and excellent selectivity with a detection limit of 0.044 U/L. This allows the efficient detection of GGT levels in solution and cells. Simultaneously, the construction of Glu-MDA pre-stained test strips provided an innovative strategy for the qualitative detection of GGT activity, helping to detect GGT faster, more portably, and cost-effectively in various scenarios. Full article

This study addresses energy transition challenges through the development of NiCuCe catalysts for high-purity hydrogen production via methanol decomposition, with carbon deposition issues mitigated by CO₂-assisted regeneration. As fossil fuel depletion advances and the urgency of climate change increases, methanol-derived hydrogen (CH₃OH → CO + 2H₂) emerges as a carbon-neutral alternative to conventional fossil fuel-based energy systems. The catalyst’s dual Cu²⁺/Ni²⁺ active sites facilitate selective C–O bond cleavage, achieving more than 80% methanol conversion at temperatures exceeding 280 °C without the need for fossil methane inputs. Crucially, CO₂ gasification enables catalyst regeneration through the conversion of 90% carbon deposits into reusable media, circumventing energy-intensive combustion processes. This dual-function system couples carbon capture to hydrogen infrastructure, thereby stabilizing production while valorizing waste CO₂. This innovation minimizes reliance on rare metals through efficient regeneration cycles, mitigating resource constraints during energy crises. Full article

Catalytic hydrogenolysis of lignin to produce high-value monophenols has emerged as a pivotal strategy in modern biorefineries. In this study, we synthesized spherical nitrogen-doped porous carbon (SNCB) materials by using Al/Co-BTC as a precursor, introducing melamine as a supplementary carbon and nitrogen source, and activating the material with NaOH solution. The SNCB framework was decorated with Cu-Pd bimetallic nanoparticles, exhibiting outstanding catalytic activity in the hydrogenolytic depolymerization of organosolv lignin. The Cu-Pd@SNCB catalyst exhibited remarkable activity, attributed to the hierarchical porous structure of SNCB that facilitated metal nanoparticle dispersion and reactant accessibility. The synergistic effect between Cu as the reactive site for reactant adsorption and Pd as the reactive site for H₂ adsorption enhanced the catalytic activity of the catalyst. Systematically optimized conditions (2 MPa H₂, 270 °C, 3 h) yielded 43.02 wt% phenolic monomers, with 4-(3-hydroxypropyl)-2,6-dimethoxyphenol dominating the product profile at 46.3% selectivity. The catalyst and its reaction products were analyzed using advanced characterization techniques, including XPS, XRD, TEM, SEM, BET, GC-MS, GPC, 2D HSQC NMR, and FT-IR, to elucidate the reaction mechanism. The mechanism proceeds through: (1) nucleophilic substitution of the β-O-4 hydroxyl group by MeOH, followed by (2) simultaneous hydrogenolytic cleavage of C_β-O and C_α-O bonds mediated by Cu-Pd@SNCB under H₂ atmosphere, which selectively produces 4-(3-hydroxypropyl)-2,6-dimethoxyphenol and 4-propyl-2,6-dimethoxyphenol. This study proposes a bimetallic synergistic mechanism, offering a general blueprint for developing selective lignin valorization catalysts. Full article

Calpains, calcium-dependent cytosolic cysteine proteases, perform controlled proteolysis of their substrates for various cellular and physiological activities. In different cancers, missense mutations accumulate in the genes coding for the calpain cleavage sites in various calpain substrates termed as the calpain cleavage-related mutations (CCRMs). However, the impact of such CCRMs on the calpain–substrate interaction is yet to be explored. This study focuses on the interaction of wild-type and mutant β-integrins with calpain-1 and 2 in uterine corpus endometrial carcinoma (UCEC). A total of 48 calpain substrates with 176 CCRMs were retrieved from different datasets and shortlisted on the basis of their involvement in cancer pathways. Finally, three calpain substrates, ITGB1, ITGB3, and ITGB7, were selected to assess the structural changes due to CCRMs. These CCRMs were observed towards the C-terminal of the cytoplasmic domain within the calpain cleavage site. The wild-type and mutant proteins were docked with calpain-1 and 2, followed by molecular simulation. The interaction between mutant substrates and calpains showcased variations compared to their respective wild-type counterparts. This may be attributed to mutations in the calpain cleavage sites, highlighting the importance of the cytoplasmic domain of β-integrins in the interactions with calpains and subsequent cellular signaling. Highlights: 1. Calpain cleavage-related mutations (CCRMs) can alter cellular signaling. 2. CCRMs impact the structure of C-domains of human integrin-β subunits. 3. Altered structure influences the cleavability of human integrin-β subunits by human calpains. 4. Altered cleavability impacts the cell signaling mediated through calpain–integrin-β axis. 5. Presence of CCRMS may influence the progression of uterine corpus endometrial carcinoma (UCEC). Full article

The electrochemical reduction of toxic nitrate wastewater to green fuel ammonia under mild conditions has become a goal that researchers have relentlessly pursued. Existing designed electrocatalysts can effectively promote the nitrate reduction reaction (NO₃RR), but the study of the catalytic mechanism is not extensive enough, resulting in no breakthroughs in performance. In this study, a novel mechanism of hydrogenation-facilitated spontaneous N-O cleavage was explored based on density functional theory calculations. Furthermore, the E_ad−*OH (adsorption energy of the adsorbed *OH) was used as a key descriptor for predicting the occurrence of spontaneous N-O bond cleavage. We found that E_ad−*OH < −0.20 eV results into spontaneous N-O bond cleavage. However, excessively strong adsorption of OH* hinders the formation of water. To address this challenge, we designed the eligible Fe₂B₂ MBene, which shows excellent catalytic activity with an ultra-low limiting potential for NO₃RR of −0.22  V under this novel reaction mechanism. Additionally, electron-deficient Fe active sites could inhibit competing hydrogen evolution reactions (HERs), which provides high selectivity. This work may offer valuable insights for the rational design of advanced electrocatalysts with enhanced performance. Full article

The Bunyavirales order includes a range of zoonotic viruses, which can cause severe disease in humans. The viral replication machinery is a logical target for the development of direct-acting antivirals. Inhibition of the cap-snatching endonuclease activity of related influenza viruses provides a proof of concept. Using the influenza B virus (IBV) RNA-dependent RNA polymerase complex as a benchmark, we conducted a comparative analysis of endonuclease activities of recombinant full-length bunyaviral L proteins using gel-based assays. The IBV complex demonstrates specific endonucleolytic cleavage and a clear preference for capped substrates. In contrast, severe fever with thrombocytopenia syndrome, Sin Nombre, and Hantaan virus L proteins readily cleave capped and uncapped RNAs to a broader spectrum of RNA fragments. Active site mutants further help to control for the potential of contaminating nucleases, exonuclease activity, and RNA hydrolysis. The influenza cap-snatching inhibitor baloxavir and derivatives have been used to validate this approach. In conclusion, the results of this study demonstrate the importance of assays with single nucleotide resolution and the use of full-length L proteins as a valuable experimental tool to identify selective endonuclease inhibitors. Full article

We describe a method tailored to the in-cell selection of protease inhibitors. In this method, a target protease is co-expressed with a selective substrate, the product of which kills host cells. Therefore, the method can be applied to identify potential inhibitors based on cell host survival when inhibition of the target protease occurs. The TEV protease was chosen for this proof-of-concept experiment. The genetically encoded selective substrate is a single polypeptide chain composed of three parts: (1) a ccdB protein, which can cause host cell death when it accumulates inside the cell; (2) a protease cleavage sequence that can be changed according to the target protease, in this case the TEV substrate ENLYFQ↓G (↓-predicted cleavage site); and (3) the ssrA sequence (AANDENYALAA), which drives the polypeptide to degradation by the ClpX/ClpP complex inside host E. coli cells. In our experiment, co-expression of the active TEV protease and this selective substrate (ccdB-ENLYFQG-ssrA) caused the death of a significant host cell population, while control assays with an inactive mutant TEV Asp81Asn did not. Details of the methodology used are given, providing the basis for the application of similar systems for other proteases of interest. Full article

Botulinum toxin (BoNT), the most potent substance known to humans, likely evolved not to kill but to serve other biological purposes. While its use in cosmetic applications is well known, its medical utility has become increasingly significant due to the intricacies of its structure and function. The toxin’s structural complexity enables it to target specific cellular processes with remarkable precision, making it an invaluable tool in both basic and applied biomedical research. BoNT’s potency stems from its unique structural features, which include domains responsible for receptor recognition, membrane binding, internalization, and enzymatic cleavage. This division of labor within the toxin’s structure allows it to specifically recognize and interact with synaptic proteins, leading to precise cleavage at targeted sites within neurons. The toxin’s mechanism of action involves a multi-step process: recognition, binding, and catalysis, ultimately blocking neurotransmitter release by cleaving proteins like SNAP-25, VAMP, and syntaxin. This disruption in synaptic vesicle fusion causes paralysis, typically in peripheral neurons. However, emerging evidence suggests that BoNT also affects the central nervous system (CNS), influencing presynaptic functions and distant neuronal systems. The evolutionary history of BoNT reveals that its neurotoxic properties likely provided a selective advantage in certain ecological contexts. Interestingly, the very features that make BoNT a potent toxin also enable its therapeutic applications, offering precision in treating neurological disorders like dystonia, spasticity, and chronic pain. In this review, we highlight the toxin’s structural, functional, and evolutionary aspects, explore its clinical uses, and identify key research gaps, such as BoNT’s central effects and its long-term cellular impact. A clear understanding of these aspects could facilitate the representation of BoNT as a unique scientific paradigm for studying neuronal processes and developing targeted therapeutic strategies. Full article

The methylotrophic yeast Komagataella kurtzmanii belongs to the group of homothallic fungi that are able to spontaneously change their mating type by inversion of chromosomal DNA in the MAT locus region. As a result, natural and genetically engineered cultures of these yeasts typically contain a mixture of sexually dimorphic cells that are prone to self-diploidisation and spore formation accompanied by genetic rearrangements. These characteristics pose a significant challenge to the development of genetically stable producers for industrial use. In the present study, we constructed heterothallic strains of K. kurtzmanii, ensuring a constant mating type by unifying the genetic sequences in the active and silent MAT loci. To obtain such strains, we performed site-directed inactivation of one of the two yeast MAT loci, replacing its sequence with a selective HIS4 gene surrounded by I-SceI meganuclease recognition sites. We then used transient expression of the SCE1 gene, encoding a recombinant I-SceI meganuclease, to induce site-specific cleavage of HIS4, followed by damage repair by homologous recombination in mutant cells. As a result, heterothallic strains designated ‘Y-727-2(alpha)’ and ‘Y-727-9(a)’, which correspond to the α and a mating type, respectively, were obtained. The strains demonstrated a loss of the ability to self-diploidize. The results of PCR and whole genome analysis confirmed the identity of the contents of the MAT loci. Analysis of the genomes of the final strains, however, revealed a fusion of chromosome 3 and chromosome 4 in strain Y-727-2(alpha)-1. This finding was subsequently confirmed by pulsed-field gel electrophoresis of yeast chromosomes. However, the ability of the Y-727-2(alpha)-derived producers to efficiently secrete recombinant β-galactosidase was unaffected by this genomic rearrangement. Full article

Despite extensive experience with influenza surveillance in humans in Senegal, there is limited knowledge about the actual situation and genetic diversity of avian influenza viruses (AIVs) circulating in the country, hindering control measures and pandemic risk assessment. Therefore, as part of the “One Health” approach to influenza surveillance, we conducted active AIV surveillance in two live bird markets (LBMs) in Dakar to better understand the dynamics and diversity of influenza viruses in Senegal, obtain genetic profiles of circulating AIVs, and assess the risk of emergence of novel strains and their transmission to humans. Cloacal swabs from poultry and environmental samples collected weekly from the two LBMs were screened by RT-qPCR for H5, H7, and H9 AIVs. Subsequently, a subset of H9-positive samples was selected for whole sequencing. From December 2023 to October 2024, 499 samples were tested, and AIV was detected in 58.3% of them. Among these, A/H9N2 was the only subtype detected in both markets, with a detection rate of 47.7% (82/172) in Thiaroye and 35.3% (42/119) in Tilene, resulting in an overall positivity rate of 42.6% (124/291). Genome sequencing of 22 A/H9N2 isolates, including 11 poultry drinking water samples, 7 carcass wash water samples, 3 fecal samples, and 1 cloacal swab, yielded 7 complete and 15 partial genomic sequences. Phylogenetic analyses of the resulting sequences showed that the A/H9N2 isolates obtained in this study formed a monophyletic cluster and were closely related to the Senegalese human strain (A/Senegal/0243/2019) identified through the national influenza sentinel surveillance program. These strains were also closely related to the A/H9N2 viruses of the G1 lineage circulating in neighboring countries, suggesting cross-border transmission. The A/H9N2 strains carried the low pathogenicity RSSR/GLF motif at the HA cleavage site and possessed several key amino acid mutations, including HA-I155T and HA-Q226L, which are associated with human host adaptation, PB2-T105V, PB2-A661T, and PB2-A588V, which are linked to the human-to-human transmission and increased polymerase activity, NS2-T14M, NS2-M100I, NS1-I106M, NS1-V222M, NS1-E223A, NS1-I226V, NS1-E227G, and NS1-P228S, which are known to alter virulence (increased or reduced) in humans or mice, and M2-S31N, which promotes drug resistance. Seven potential N-glycosylation sites were predicted in the HA protein and six in the NA protein. The selection pressure analysis revealed that the A/H9N2 isolates were primarily under neutral evolution or purifying selection pressure. Overall, our findings highlight the potential for cross-species transmission of Senegalese A/H9N2 viruses, emphasizing the need for sustained monitoring of these viruses in both animal and human populations. Full article

The solvent-free hydrogenolysis (HDL) of benzyl phenyl ether (BPE), a model for the C–O (α-O-4) linkage in lignin, was investigated using NiMo-pillared clay catalysts in their reduced (NiMoPR) and sulfided (NiMoPS) forms. NiMoPS show higher activity and selectivity to give an equimolar mixture of toluene and phenol, demonstrating selective cleavage of the C_aliphatic–O of BPE, while non-equimolar amounts were found for NiMoPR. Strong acid sites are dominant in NiMoPS, giving a higher total acidity compared to NiMoPR, which explains the higher selectivity of the sulfided catalyst towards the HDL products and monomeric aromatics. To understand the interaction of BPE on the catalyst surface, we carried out a comprehensive investigation of the 2D potential energy surface (PES) of BPE and the vibrational spectra using neutron scattering and computational studies. The results suggest that BPE is weakly adsorbed on NiMoPS and the pillared clay support (PILC) via a van der Waals or H-bonding interaction, but they are strongly chemisorbed on the NiMoPR due to covalent bonding. Weakly adsorbed BPE allows higher mobility during diffusion to the catalytic site, which promotes the higher activity of NiMoPS for the HDL. This work demonstrates the potential use of clay-supported NiMo catalysts for lignin valorization and the future circular economy. Full article

Homogeneous antibody–drug conjugates (ADCs) exhibit significantly improved pharmacological properties compared to their heterogeneous counterparts. Site-specific conjugation of the payload to the IgG required for homogeneity can be achieved using enzymes. One example is microbial transglutaminase (MTGase), which can selectively perform transamidation on the Q295 residue of human Fc when N297 glycans are removed. As a result, two modifications can be introduced per IgG molecule; however, achieving higher drug-to-antibody ratios (DARs) requires the use of branched linkers. While several such linkers have been reported, little information is available on the relationship between linker structure and ADC properties. To address this gap, we synthesized two branched amino triazide linkers, differing by a PEG₄ fragment inserted after the branching point, which were used to prepare two homogeneous trastuzumab-based DAR 6 ADCs (a “short” and a “long” one). This was achieved by a two-step process consisting of enzymatic linker conjugation followed by bioorthogonal coupling with a cleavable linker bearing monomethyl auristatin E (MMAE). Two other trastuzumab–MMAE conjugates were used as controls: a heterogeneous DAR 6 ADC, made using conventional thiol–maleimide chemistry, and a homogeneous DAR 2 ADC. We found that, while the four conjugates had identical affinity for HER2, their cytotoxicity differed significantly: the “long” homogeneous DAR 6 ADC was just as active as its heterogeneous counterpart, but the “short” DAR 6 ADC was an order of magnitude less potent, inferior even to the DAR 2 conjugate. Our findings indicate that the length of the branched linker critically affects the cytotoxic activity of ADCs, possibly due to steric hindrance influencing the rate of linker cleavage by lysosomal enzymes. Full article

Covalent modification of proteins at specific, predetermined sites is essential for advancing biological and biopharmaceutical applications. Site-selective labeling techniques for protein modification allow us to effectively track biological function, intracellular dynamics, and localization. Despite numerous reports on modifying target proteins with functional chemical probes, unique organic reactions that achieve site-selective integration without compromising native functional properties remain a significant challenge. In this review, we delve into site-selective protein modification using synthetic probes, highlighting both chemical and computational methodologies for chemo- and regioselective modifications of naturally occurring amino acids, as well as proximity-driven protein-selective chemical modifications. We also underline recent traceless affinity labeling strategies that involve exchange/cleavage reactions and catalyst tethering modifications. The rapid development of computational infrastructure and methods has made the bioconjugation of proteins more accessible, enabling precise predictions of structural changes due to protein modifications. Hence, we discuss bioconjugational computational approaches, including molecular dynamics and artificial intelligence, underscoring their potential applications in enhancing our understanding of cellular biology and addressing current challenges in the field. Full article

Peroxynitrite (ONOO⁻) is a reactive oxygen species (ROS) that takes part in the oxidation-reduction homeostasis while at the same time being responsible for activating numerous pathological pathways. Accordingly, monitoring the dynamic changes in ONOO⁻ concentration has attracted a great deal of attention, undoubtedly prompting the development of appropriate fluorescent chemosensors. Herein, we developed a novel N,O-chelated diphenylboron-based fluorescent probe (DPB) for ONOO⁻ featuring high selectivity, a quick response time (2.0 min), and a low detection limit (55 nM). DPB incorporates tetra-coordinated boron in the center of the fluorogenic core and a three-coordinated boron from the pinacolphenylboronate fragment, which acts as the recognition site for ONOO⁻. As confirmed by HR-MS and ¹H NMR, the interaction of DPB with ONOO⁻ led to an oxidative cleavage of pinacolphenylboronate moiety to produce strongly emissive derivative DPB-OH. The fluorescence enhancement is likely a result of a substantial deactivation of non-radiative decay due to the replacement of the bulky pinacolphenylboronate moiety with a compact hydroxyl group. Importantly, DPB probe exhibits negligible cytotoxicity and favorable biocompatibility allowing for an efficient tracking of ONOO⁻ in living cells and zebrafish. Overall, the current study does not only represents the first N,O-chelated diphenylboron-based fluorescent probe for a specific analyte, but also serves as a guideline for designing more potent fluorescent probes based on the chemistry of boron chelates. Full article

The design and development of fluorescent materials for detecting cancer-related enzymes are crucial for cancer diagnosis and treatment. Herein, we present a substituted rhodamine derivative for the chromogenic and fluorogenic detection of the cancer-relevant enzyme γ-glutamyltranspeptidase (GGT). Initially, the probe is non-chromic and non-emissive due to its spirolactam form, which hinders extensive electronic delocalization over broader pathway. However, selective enzymatic cleavage of the side-coupled group triggers spirolactam ring opening, resulting in electronic flow across the rhodamine skeleton, and reduces the band gap for low-energy electronic transitions. This transformation turns the reaction mixture from colorless to intense pink, with prominent UV and fluorescence bands. The sensor’s selectivity was tested against various human enzymes, including urease, alkaline phosphatase, acetylcholinesterase, tyrosinase, and cyclooxygenase, and showed no response. Absorption and fluorescence titration analyses of the probe upon incremental addition of GGT into the probe solution revealed a consistent increase in both absorption and emission spectra, along with intensified pink coloration. The cellular toxicity of the receptor was evaluated using the MTT assay, and bioimaging analysis was performed on BHK-21 cells, which produced bright red fluorescence, demonstrating the probe’s excellent cell penetration and digestion capabilities for intracellular analytical detection. Molecular docking results supported the fact that probe-4 made stable interactions with the GGT active site residues. Full article