Search Results (1,996)

Biocatalysis is one of the oldest fields that has been used in industrial applications, with one of the earliest purposeful examples being the mass production of acetic acid from an immobilized Acinetobacter strain in the year 1815. Efficiency, specificity, reduced reaction times, lower overall costs, and environmental friendliness are some advantages biocatalysis has over conventional chemical synthesis, which has made biocatalysis increasingly used in industry. We highlight three necessary fields that are fundamental to advancing industrial biocatalysis, including biocatalyst engineering, solvent engineering, and mechanistic engineering. However, the fundamental mechanism of enzyme function is often overlooked or given less attention, which can limit the engineering process. In this review, we describe how mechanistic enzymology benefits industrial biocatalysis by elucidating key fundamental principles, including the k_cat and k_cat/K_m parameters. Mechanistic enzymology presents a unique field that provides in-depth insights into the molecular mechanisms of enzyme activity and includes areas such as reaction kinetics, catalytic mechanisms, structural analysis, substrate specificity, and protein dynamics. In line with the objective of protein engineering to optimize enzyme activity, we summarize a range of strategies reported in the literature aimed at improving the product release rate, the chemical step of catalysis, and the overall catalytic efficiency of enzymes. Further into this review, we delineate kinetic solvent viscosity effects (KSVEs) as a very efficient, cost-effective, and easy-to-perform method to probe different aspects of enzyme reaction mechanisms, including diffusion-dependent kinetic steps and rate-limiting steps. KSVEs are cost-effective because simple kinetic enzyme assays, such as the Michaelis–Menten kinetic approach, can be combined with them without the need for specialized and costly equipment. Other techniques in protein engineering and genetic engineering are also covered in this review. Additionally, we provide information on solvent systems in enzymatic reactions, details on immobilized biocatalysts, and common misconceptions that misguide enzyme design and optimization processes. Full article

Background: Previous research has demonstrated that 20 kHz probe or 37 kHz bath sonication of poloxamers comprising polypropylene glycol (PPG) and polyethylene glycol (PEG) blocks can generate degradation byproducts that are toxic to mammalian cells and organisms. Herein, an investigation of a PEGylated phospholipid micelle was undertaken to identify low-molecular-weight sonolytic degradation byproducts that could be cytotoxic. The concern here lies with the fact that sonication is a frequently employed step in drug delivery manufacturing processes, during which PEGylated phospholipids can be subjected to shear forces and other extreme oxidative and thermal conditions. Methods: Control and 20 kHz-sonicated micelles of DSPE-mPEG2000 were analyzed using dynamic light scattering (DLS) and zeta potential analyses to study colloidal properties, matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectroscopy (MS) and proton nuclear magnetic resonance (¹H-NMR) spectroscopy to study the structural integrity of DSPE-mPEG2000, and ¹H-NMR spectroscopy and high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection to quantitate the formation of low-molecular-weight degradation byproducts. Results: MALDI-TOF-MS analyses of 20 kHz-sonicated DSPE-mPEG2000 revealed the loss of ethylene glycol moieties in accordance with depolymerization of the PEG chain; ¹H-NMR spectroscopy showed the presence of formate, a known oxidative/thermal degradation product of PEG; and HPLC-UV showed that the generation of formate was dependent on 20 kHz probe sonication time between 5 and 60 min. Conclusions: It was found that 20 kHz sonication can degrade the PEG chain of DSPE-mPEG2000, altering the micelle’s PEG corona and generating formate, a known ocular toxicant. Full article

Icariin (ICA) is widely recognized for its health benefits. In this work, we examined the intermolecular interactions between ICA and proteinase K (PK) via multi-spectroscopic techniques and molecular simulations. The experimental findings revealed that ICA quenched the fluorescence emission of PK by forming a noncovalent complex. Both hydrogen bonding and van der Waals interactions are essential for the complex’s formation. Then Förster resonance energy transfer (FRET), competitive experiments, and synchronous fluorescence spectroscopy were adopted to verify the formation of the complex. Molecular docking studies demonstrated that ICA could spontaneously bind to PK by hydrogen bonding and hydrophobic interactions, which is consistent with the spectroscopic results. The PK-ICA complex’s dynamic stability was evaluated using a 50 ns molecular dynamics (MD) simulation. The simulation results revealed no significant structural deformation or positional changes throughout the entire simulation period. The complex appears to be rather stable, as seen by the average root-mean-square deviation (RMSD) fluctuations for the host protein in the PK-ICA complex of 1.08 Å and 3.09 Å. These outcomes of molecular simulations suggest that ICA interacts spontaneously and tightly with PK, consistent with the spectroscopic findings. The approach employed in this research presents a pragmatic and advantageous method for examining protein–ligand interactions, as evidenced by the concordance between empirical and theoretical findings. Full article

Background. Medulloblastoma (MB) prognosis and response to therapy depend largely on genetic changes in tumor cells. Many genes and chromosomal abnormalities have been identified as prognostic factors, including amplification of MYC oncogenes, gains in 1q and 17q, deletions in 10q and 21p, or isochromosomes 17 (i(17)(q10)). The frequency of these abnormalities varies greatly between ethnic populations, but the frequency of specific abnormalities, such as MYCC and MYCN amplification, 17q gain, and deletions, in the Russian population is unknown. Objective: The aim is to study the frequency of MYCC and MYCN amplifications, 17q gain, and 17p deletion and determine their prognostic value in Russian patients with MB. Methods. This study was performed on MB cells obtained from 18 patients (12 boys and 6 girls, aged between 3 months and 17 years, with a median age of 6.5 years). Determination of cytogenetic aberrations was carried out using FISH assays with MYCC-SO, MYCN-SO, and MYCN-SG/cen2 probes, as well as cen7/p53 dual color probes and PML/RARα dual color probes (Abbott Molecular, USA). One-way ANOVA and Fisher’s F-test were used to compare the two groups. The differences were considered significant when p < 0.05. Results. In 77.7% of patients (14/18), the classical type of MB was present; in 16.7% (3/18), desmoplastic type; and in 5.6% (1/18), nodular desmoplasic types of neoplasms. Amplification of MYC genes was detected in 22.2% of Russian patients (n = 4 out of 18). Patients with MYC amplification had the worst overall survival (OS: 0% vs. 68%, p = 0.0004). Changes on the 17th chromosome were found in 58.3% of patients. Deletion of 17p occurred in 23.1%, and gain of 17q occurred in 46.2%. There were no significant differences in OS, clinical signs, or the presence of additional 17q material or 17p deletion among patients with MB. Conclusions: Amplification of the MYC gene is a predictor of poor overall survival to therapy and a high risk of metastatic relapse. This allows us to more accurately stratify patients into risk groups in order to determine the intensity and duration of therapy. Full article

Inelastic electron tunneling spectroscopy (IETS) has emerged as a powerful vibrational spectroscopy technique for molecular electronic junctions, providing unique insights into molecular vibrations and electron–phonon coupling at the nanoscale. In this review, we present a comprehensive overview of IETS in molecular junctions, tracing its development from foundational principles to the latest advances. We begin with the theoretical background, detailing the mechanisms by which inelastic tunneling processes generate vibrational fingerprints of molecules, and highlighting how IETS complements optical spectroscopies by accessing electrically driven vibrational excitations. We then discuss recent progress in experimental techniques and device architectures that have broadened the applicability of IETS. Central focus is given to emerging applications of IETS over the last decade: molecular sensing (identification of chemical bonds and conformational changes in junctions), thermoelectric energy conversion (probing vibrational contributions to molecular thermopower), molecular switches and functional devices (monitoring bias-driven molecular state changes via vibrational signatures), spintronic molecular junctions (detecting spin excitations and spin–vibration interplay), and advanced data analysis approaches such as machine learning for interpreting complex tunneling spectra. Finally, we discuss current challenges, including sensitivity at room temperature, spectral interpretation, and integration into practical devices. This review aims to serve as a thorough reference for researchers in physics, chemistry, and materials science, consolidating state-of-the-art understanding of IETS in molecular junctions and its growing role in molecular-scale device characterization. Full article

The search for selective anticholinergic agents stems from varying cholinesterase levels as Alzheimer’s Disease progresses from the mid-to-late stage and from butyrylcholinesterase’s (BChE) role in β-amyloid plaque formation. While structure-based and pharmacophore-based virtual screening could search from large libraries in a short time, these methods do not consider dynamic features that result from a ligand’s inhibition of the enzyme and consequently may under- or overexaggerate enzyme selectivity of a given ligand. In this computational study, we probed the selectivity of representative secondary metabolite compounds against acetylcholinesterase and BChE through molecular dynamics simulations. The results were evaluated by analysis of the root mean squared deviation of ligand heavy atoms, the radius of gyration of each inhibited and uninhibited enzyme, root mean squared fluctuation of residues, intermolecular interaction energy, and linear interaction energy approximation of the Gibbs free energy of binding. These considerations further reveal the induced-fit characteristics contributing to ChE selectivity that are predominantly due to the greater flexibility of BChE’s active site gorge. Full article

The recent COVID-19 pandemic has made the public aware of the importance of combating pathogenic microorganisms before they enter the human body. This growing threat from microorganisms prompted us to conduct research into a new type of coating that would be an alternative to the continuous disinfection of touch surfaces. Our goal was to design, synthesise and thoroughly characterise such a coating. In this work, we present a nanocomposite material composed of a thin-layer mesoporous SBA-15 silica matrix containing copper phosphonate groups, which act as catalytic centres responsible for the generation of reactive oxygen species (ROS). In order to verify the structure of the material, including its molecular structure, microscopic observations and Raman spectroscopy were performed. The generation of ROS was confirmed by fluorescence microscopy analysis using a fluorogenic probe. The antimicrobial activity was tested against a wide spectrum of Gram-positive and Gram-negative bacteria, while cytotoxicity was tested on BALB/c3T3 mouse fibroblast cells and HeLa cells. The studies fully confirmed the expected structure of the obtained material, its antimicrobial activity, and the absence of cytotoxicity towards fibroblast cells. The results obtained confirmed the high application potential of the tested nanocomposite coating. Full article

The tumor microenvironment plays an important role in tumor incidence, metastasis, and chemotherapy resistance. Novel therapeutic strategies targeting the tumor microenvironment have become a research focus in the field of biomedicine. In this study, we developed a smart small-molecule probe, TZ2, featuring pH/GSH dual-responsive characteristics. TZ2 exhibits a unique pH-dependent reaction mechanism: GSH is preferentially covalently modified with maleimide groups in acidic microenvironments (pH < 7), while specifically activating nucleophilic substitutions under alkaline conditions (pH > 7). It is worth noting that TZ2 effectively eliminates intracellular glutathione (GSH) in a time and concentration-dependent manner, demonstrating significant GSH depletion ability in various tumor cell lines. Pharmacodynamic studies have shown that TZ2 not only inhibits the cell cycle by regulating the expression of cell cycle-related proteins, but also effectively suppresses the cloning ability of cancer cells. Furthermore, TZ2 significantly increases the sensitivity of drug-resistant cancer cells to cisplatin. By integrating microenvironment modulation, real-time monitoring, and synergistic therapy, TZ2 provides a novel molecular tool and theoretical basis for tumor theranostics integration. Full article

Deoxyribonucleic acid (DNA) is not only a fundamental biological molecule but also a versatile material for constructing sensitive and specific biosensing platforms. Its ability to undergo sequence-specific hybridization via Watson–Crick base pairing enables both precise target recognition and the programmable construction of nanoscale structures. The demand for ultrasensitive detection increases in fields such as disease diagnostics, therapeutics, and other areas, and the inherent characteristics of DNA have driven the development of a wide range of signal amplification strategies. Among these, polymerase chain reaction (PCR), rolling circle amplification (RCA), and loop-mediated isothermal amplification (LAMP) represent powerful target-based methods that enzymatically increase the concentration of nucleic acid targets, thereby boosting detection sensitivity. In parallel, structure-based strategies leverage the nanoscale spatial programmability of DNA to construct functional architectures with high precision. DNA can be used as a scaffold, such as DNA nanostructures, to organize sensing elements and facilitate signal transduction. It can also function as a probe, like aptamers, to recognize targets with high affinity. These versatilities enable the creation of highly sophisticated sensing platforms that integrate molecular recognition and signal amplification. Driven by DNA nano-assembly capability, both target-based and structure-based approaches are driving the advancement of highly sensitive, selective, and adaptable diagnostic technologies. This review highlights recent developments in DNA nano-assembly-driven amplification strategies. Full article

The envelopes of Red Supergiants (RSGs) have a unique chemical environment not seen in other types of stars. They foster an oxygen-rich synthesis but are tempered by sporadic and chaotic mass loss, which distorts the envelope and creates complex outflow sub-structures consisting of knots, clumps, and arcs. Near the stellar photosphere, molecules and grains form under approximate LTE conditions, as predicted by chemical models. However, the complicated outflows appear to have distinct chemistries generated by shocks and dust destruction. Various RSG envelopes have been probed for their molecular content, mostly by radio and millimeter observations; however, VY Canis Majoris (VY CMa) and NML Cygni (NML Cyg) display the highest chemical complexity, and also the most complicated envelope structure. Thus far, over 29 different molecules have been identified in the envelopes of RSGs. Some molecules are common for circumstellar gas, including CO, SiO, HCN and H₂O, which have abundances of ∼10⁻⁶–10⁻⁴, relative to H₂. More exotic oxides have additionally been discovered, such as AlO, AlOH, PO, TiO₂, and VO, with abundances of ∼10⁻⁹–10⁻⁷. RSG shells support intricate maser emission in OH, H₂O and SiO, as well. Studies of isotope ratios in molecules suggest dredge-up at least into the H-burning shell, but further exploration is needed. Full article

Some pancreatic ductal-type (PDADK) and lung adenocarcinomas (LADK) lacking other molecular drivers are reported to harbor NRG1 fusions as potential novel therapeutic targets. We investigated the feasibility of a fluorescent in situ hybridization (FISH)-based diagnosis of NRG1 fusions in a case series of PDADK and LADK lacking other identified oncogenic drivers. First, among a case series of PDADK, KRAS analyses (PCR followed in PCR-negative cases by RNA sequencing—RNAseq) found 27/162 (16.7%) KRAS wild-type cases, among which 1/162 (0.6%) NRG1 fusion was diagnosed using FISH. Secondly, among a case series of LDAK, 191/446 (42.8%) cases had no molecular alterations in EGFR, KRAS, BRAF, HER2, MET, ALK, ROS1 and RET according to NGS and FISH analyses and, among them, 4/446 (0.9%) cases had NRG1 fusions using FISH. Finally, four additional cases out of the two previously mentioned cases series (1 PDADK and 3 LADK) with NRG1 fusions diagnosed by first-line RNAseq were also concluded as NRG1 FISH-positive. The NRG1 FISH tests for the nine NRG1 FISH-positive cases resulted in 50% to 80% of positive tumor nuclei, all with single 3′-NRG1 FISH signals. In our series, of the 22 cases analyzed with both NRG1 FISH (positivity criterion of at least 15% of tumor nuclei with a split between the 5′- and the 3′- parts of the probes and/or isolated single 3′-NRG1 signal) and RNAseq, 17 cases were FISH– RNAseq– and 5 cases were FISH+ RNAseq+ (no FISH+ RNAseq– or FISH– RNAseq+ cases in our study) resulting in 100% sensibility and specificity for the NRG1 FISH test. In the case of no access to RNAseq, NRG1 FISH consists of a valuable tool searching for NRG1 fusions in patients with advanced cancers. Full article

Background: Protein arginine methyltransferase 3 (PRMT3), a type I family PRMT, regulates the activity of downstream substrates by catalyzing the asymmetric dimethylation of arginine residues. While PRMT3 activity has been reported to be deregulated in many cancers, including glioblastoma (GBM), the underlying signalling mechanisms that contribute to disease progression are largely unknown. Methods: We tested the efficacy of a PRMT3 chemical probe, SGC707, in a cohort of GBM patient-derived primary and recurrent brain tumour stem cell (BTSC) lines. RNA-sequencing, CRISPR-cas9 knockout, and inducible overexpression methods were used to investigate the molecular mechanisms regulated by the aberrant activity of PRMT3 in different BTSC lines. Results: We show that expression of the tumour suppressor protein 4.1B, a negative regulator of PRMT3, predicts the response of GBM BTSCs to the PRMT3 chemical probe, SGC707. Furthermore, PRMT3 modulates the stability and subcellular localization of the downstream effector, UHRF1, a member of the DNA methylation complex. These findings suggest that UHRF1 and DNMT1 may suppress the expression of 4.1B through the increased promoter methylation of EPB4.1L3. Intriguingly, the inducible overexpression of EPB4.1L3 in the BT248^EPB4.1L3low BTSC line mimicked the effects of the pharmacologic and genetic inhibition of PRMT3. In contrast, knockout of EPB4.1L3 in BT143^EPB4.1L3high cells reduced the interactions between PRMT3 and 4.1B proteins, resulting in increased sensitivity of knockout cells to SGC707 treatment. Conclusions: These findings show that 4.1B, PRMT3, and UHRF1/DNMT1 function together to promote BTSC growth. Thus, targeting PRMT3 or UHRF1/DNMT1, especially in tumours with low endogenous 4.1B protein, may have high therapeutic relevance. Full article

Background/Objectives: Carbohydrate antigen 19-9 (CA19-9) is a clinically established biomarker primarily used for monitoring disease progression and recurrence in pancreatic and gastrointestinal cancers. Accurate and continuous quantification of CA19-9 in patient samples is critical for effective clinical management. This study aimed to develop dual-emitting molecularly imprinted nanopolymers (dual@nanoMIPs) for ratiometric and reliable detection of CA19-9 in serum. Methods: Dual-emitting nanoMIPs were synthesized via a one-step molecular imprinting process, incorporating both blue-emitting carbon dots (b-CDs) as internal reference fluorophores and yellow-emitting quantum dots (y-QDs) as responsive probes. The CA19-9 template was embedded into the polymer matrix to create specific recognition sites. Fluorescence measurements were carried out under 365 nm excitation in 1% human serum diluted in phosphate-buffered saline (PBS). Results: The dual@nanoMIPs exhibited a ratiometric fluorescence response upon CA19-9 binding, characterized by the emission quenching of the y-QDs at 575 nm, while the b-CDs emission remained stable at 467 nm. The fluorescence shift observed in the RGB coordinates from yellow to green in the concentration range of CA19-9 tested, improved quantification accuracy by compensating for matrix effects in serum. A linear detection range was achieved from 4.98 × 10⁻³ to 8.39 × 10² U mL⁻¹ in serum samples, with high specificity and reproducibility. Conclusions: The dual@nanoMIPs developed in this work enable a stable, sensitive, and specific detection of CA19-9 in minimally processed serum, offering a promising tool for longitudinal monitoring of cancer patients. Its ratiometric fluorescence design enhances reliability, supporting clinical decision-making in the follow-up of pancreatic cancer. Full article

Positron emission tomography (PET) imaging targeting glypican-3 (GPC3) holds promise for improving the detection and characterization of hepatocellular carcinoma (HCC). Preclinical and early clinical studies have largely utilized high-molecular-weight antibodies radiolabeled with isotopes such as ⁸⁹Zr and ¹²⁴I, demonstrating high affinity and tumor uptake but suffering from prolonged circulation times and suboptimal signal-to-background ratios. To address these limitations, interest has shifted toward low-molecular-weight vectors—synthetic peptides and small antibody fragments—labeled with shorter-lived radionuclides (e.g., ⁶⁸Ga and ¹⁸F) to enable rapid pharmacokinetics and same-day imaging protocols. Emerging platforms such as affibodies and aptamers offer further advantages in target affinity and reduced immunogenicity. However, clinical translation requires rigorous validation: larger, histologically confirmed cohorts, head-to-head comparison with CT/MRI, and correlation with hard clinical endpoints. Moreover, leveraging GPC3 expression as a biomarker could guarantee a deeper knowledge of tumor biology—differentiation grade and vascular invasion risk—and guide theranostic strategies. While β-emitters (⁹⁰Y, ¹⁷⁷Lu) have been explored for GPC3-directed therapy, their efficacy is influenced by oxygenation and cell-cycle status, whereas α-emitters (²²⁵Ac) may overcome these constraints, albeit with challenges in radionuclide selection and daughter nuclide management. Finally, dual-targeting probes combining GPC3 and prostate-specific membrane antigen (PSMA) have demonstrated superior uptake and retention in murine models, suggesting a versatile approach for future clinical diagnostics and therapy planning. Full article

In this narrative review, we aim to summarize recent advancements in nuclear molecular imaging techniques and their applications in BCa management. The main focus of this review is on the most relevant clinical investigations from the past 2–3 years that highlight the enhanced diagnostic and therapeutic value of these imaging modalities. A variety of radiolabeled probes introduced in molecular imaging is explored, detailing their roles in the accurate diagnosis and characterization of BCa, as well as their integration into radioligand therapy and theragnostic strategies. Full article