ChemBioChem最新文献

The CH-oxidative activity of Wolfiporia cocos cultures of different ages was studied utilizing diamondoid derivatives as conformationally rigid models. Adamantane-1-ol and 1-bromoadamantane, traditional precursors for the synthesis of polysubstituted adamantanes, gave qualitatively similar reaction mixtures in which adamantane diols dominated. While the reactions occurred with high preparative yields, the biotransformation does not display clear differences from classic electrophilic or radical adamantane functionalization reactions. In contrast, the fungal oxidation of diamantane-4-ol occurred with unexpected selectivity yielding diamantane-4,9-diol and diamantane-1,9-diol. The latter product is quite uncharacteristic for diamantane chemistry because the most deactivated CH-position is attacked. To elucidate the active fungal component, additional experiments were performed with supernatant and resting cells harvested at various culture ages. Oxidative activity was detected in resting cells from 4- and 6-day-old cultures in pure water medium, and from 6-day-old cultures in buffer at pH 2, but disappeared at higher pH values.

Genetically encoded photo-cross-linkable amino acids (PAAs) are powerful tools for analyzing direct protein-protein interactions (PPIs) in mammalian cells. Cleavable PAAs are particularly useful, enabling covalent capture and subsequent release of interacting partners, which facilitates the characterization of interaction interfaces using mass spectrometry. However, the limited options for cleavable linker structures have restricted the design of PAAs. In this study, we genetically encoded a novel trifunctional PAA, DiZAAsu, which contains three distinct chemical groups: diazirine, alkyne, and alkaline-cleavable alkyl ester moieties. An archaeal pyrrolysyl-tRNA synthetase was engineered to incorporate DiZAAsu efficiently into proteins in mammalian cells. We demonstrated the in-cell photoreactive function of diazirine by cross-linking the DiZAAsu-introduced GRB2 protein to its binding partner, SHC. Using the alkyne group for biotinylation, we established a tandem affinity purification strategy that enabled efficient enrichment of the cross-linked complex, thereby reducing nonspecific protein contamination. The alkaline-based cleavage of the ester group in DiZAAsu was also demonstrated, confirming its potential for the dissociation of covalently linked complexes. This system thus expands the design space of multifunctional PAAs and adds alkaline-based dissociation to the limited repertoire of available cleavage strategies.

Cu(II) complexes with monoalkylated oxacyclen ligands (C₁₂, C₁₆, and C₁₈) have been investigated regarding their interaction with DNA by different methods: circular dichroism, UV/VIS (ultraviolet-visible) and fluorescence spectroscopy as well as by gel electrophoresis. The results demonstrate that the complexes can cleave DNA through both hydrolytic and oxidative mechanisms, with hydroxyl radicals and hydrogen peroxide identified as the reactive oxygen species involved. The targeted incorporation of alkyl chains significantly enhances the DNA-binding affinity of the Cu(II) complexes, and the length of the alkyl substituents plays an important role, as they can interact with the major groove of the DNA. Alkylation is the determining structural factor responsible for the enhanced DNA interaction, since such an interaction is not observed with unsubstituted complexes. Moreover, the length of the alkyl chains significantly influences this behavior, as longer substituents induce a concentration-dependent DNA aggregation, a phenomenon absent in the nonalkylated analog. This aggregation and condensation behavior is examined using atomic force microscopy and dynamic light scattering. Moreover, DNA/small molecule interactions are also investigated using molecular dynamics simulations.

Cryopreservation effectively halts biological metabolism, placing living specimens in a state of ‘suspended animation’ for future revival. As a foundational technology for cell-based biomedicine, cryopreservation relies on cryoprotectants (CPAs) to mitigate freezing-induced damage, such as ice formation, protein denaturation, and oxidative stress. However, conventional CPAs like dimethyl sulfoxide and glycerol face practical limitations, including cytotoxicity and cumbersome removal processes, driving the need for novel alternatives. In nature, psychrophilic organisms produce stress-tolerant proteins, such as antifreeze proteins and late embryogenesis abundant proteins, thus enabling themselves to survive in subzero conditions by controlling ice growth, stabilizing membranes, and performing other protective functions. Inspired by these natural systems, this review aims to explore the potential of protein and peptide-based materials as next-generation CPAs. We systematically summarize the characteristics, mechanisms, and cryopreservation applications of natural stress-resistant proteins and their synthetic mimics. Moreover, we discuss key challenges including immunogenicity, scalability, and the rational design of these synthetic mimics, and outline future directions for the development of these biomimetic cryoprotective materials.

The amazing potential of tiny metabolites to self-assemble into amyloid-like structures, which are usually built from the self-assembly of contiguous polypeptide chains. These metabolite-nanostructures mimic characteristics of protein amyloids, and they possess striking potential for prion-like cross-seeding effect, triggering the amyloid aggregation of diverse proteins, generating protein amyloids, which becomes the foundational event for the onset of devastating amyloid-linked diseases. Deciphering the mechanism of prion-like activity of metabolite aggregates would certainly add new insights into the mechanistic understanding of both metabolic disorders and the complex cascade of the amyloid hypothesis. More details can be found in the Review Article by Bibin Gnanadhason Anand, Karunakar Kar, and co-workers (DOI: 10.1002/cbic.202500492).

Airway epithelial cells (AECs) serve as the first line of defense against environmental pollutants, with exposure to traffic-related particles known to exacerbate allergic asthma. In this study, a series of adamantane-containing N-acylthiourea compounds are designed, synthesized, and structurally characterized by ¹H NMR, ¹³C NMR, HR-ESI-MS, FT-IR, and UV–vis spectroscopy. Among them, compound AD3, is crystallized in the triclinic P-1 space group. Here, it is found that AD4 upregulated the expression of protein phosphatase 4 (PP4) in BEAS-2B airway epithelial cells in a concentration-dependent manner. AD4 treatment also significantly restored epithelial barrier integrity and suppressed the production of thymic stromal lymphopoietin (TSLP) production challenged by diesel exhaust particles (DEP). To the author's knowledge, this represents the first report identifying AD4 as a potential therapeutic agent for allergic asthma, highlighting a novel strategy for antiallergic drugs.

Speckle-type POZ protein (SPOP) functions as the substrate adaptor of the Cullin3-RING ligase complex and is recurrently mutated in multiple cancer types. Among these, F102C and F133L are frequent prostate cancer mutations within the substrate-binding domain, yet their biochemical consequences remain incompletely understood. Using quantitative proteomics, we show that SPOP-F133L, unlike SPOP-F102C, retains degradative activity toward the nuclear basket proteins NUP153 and TPR, indicating substrate-dependent loss-of-function. Moreover, SPOP-F133L induces partial down-regulation of p53 through a Cullin-RING ligase-dependent, post-translational mechanism, revealing a potential neo-substrate relationship. Finally, we demonstrate that both SPOP-F102C and SPOP-F133L support targeted protein degradation in an engineered cellular system. These findings define the degradative capacities of SPOP mutants and highlight opportunities to repurpose these variants as mutant-selective E3 ligases for therapeutic applications.

Spatial proteomics has emerged as a powerful approach to systematically map the subcellular localization of thousands of proteins in parallel, providing insights into organelle composition, protein trafficking, and context-dependent relocalization events. Building on advances in mass spectrometry sensitivity, and acquisition as well as quantification strategies, organelle-resolved protein maps can now be generated with unprecedented depth and resolution, and recent workflows have expanded the applicability of spatial proteomics to diverse experimental and challenging contexts. Complementary bioinformatic pipelines enable the assignment of proteins to compartments, the detection of distribution shifts, and the integration of spatial data with other omics layers. Beyond fundamental cell biology, the technology holds great potential for clinical research, where limited input material and the complexity of primary samples pose specific challenges. Emerging low-input preparation methods, antibody-based organelle enrichment, and microscopy-guided approaches offer promising solutions, while robust, marker-independent data analysis will be essential to handle the biological variability of patient-derived samples. As protocols become more automated, low-input compatible, and bioinformatically standardized, spatial proteomics is poised to become a valuable tool for mechanistic disease research, biomarker discovery, and therapeutic target identification.

This study aimed to investigate the role and clinical significance of RHNO1 in nonsmall cell lung cancer (NSCLC). By analyzing clinical samples and cell lines, we assessed RHNO1 expression and its correlation with clinicopathological features and patient prognosis, validating its potential as a diagnostic and prognostic biomarker. Furthermore, in vitro and in vivo experiments revealed the functional role of RHNO1 in NSCLC progression and its molecular interaction with the NF-κB signaling pathway, defining the regulatory mechanism of the “RHNO1–NF-κB axis.” In parallel, we developed a chitosan-based delivery system (CS-1@RHNO1), which markedly enhanced the loading efficiency and targeting specificity of RHNO1 regulatory agents, enabling precise modulation of the “RHNO1–NF-κB axis.” Our findings demonstrate that RHNO1 functions not only as a potential diagnostic and prognostic marker but also as a promising therapeutic target, while the CS-1@RHNO1 system provides a novel strategy for targeted delivery in NSCLC. Collectively, this study offers new theoretical insights and technological advances for understanding NSCLC pathogenesis and developing targeted therapies.

This study reports the design, synthesis, and structure–property analysis of an original family of three-dimensional cyanine dyes based on the [2.2]paracyclophane (pCp) scaffold. By converting planar polymethine chromophores into three-dimensional architectures, we developed fluorogenic dyes with enhanced selectivity for single-stranded RNA containing stem-loop motifs. Comparative studies with planar analogs show that benzothiazole- and benzoselenazole-containing pCp derivatives exhibit strong fluorescence turn-on upon nucleic-acid binding, with responses varying by nucleic acid type and structure. Circular dichroism analyses suggest that these three-dimensional dyes interact with RNA via a nonintercalative mode, distinct from classical planar intercalators. Expanding upon preliminary findings, this work explores an extended series of pCp-derived cyanines, revealing how three-dimensionality modulates both photophysical behavior and nucleic-acid recognition. These results provide new directions for the design of selective RNA-targeting ligands and for future exploration of their interactions with more complex RNA architectures.