Search Results (639)

Background/Objectives: Protein nanocages are versatile platforms with potential applications in drug delivery, enzyme encapsulation, and bioreactor systems, owing to their precise self-assembly and excellent biocompatibility. However, most protein cage systems have limited accessibility to their internal space, which hinders the efficient encapsulation of large molecules or complex proteins. Methods and results: In this study, we propose a programmable reassembly system by artificially splitting the monomer of lumazine synthase, a protein that naturally forms a nanocage through self-assembly. Using intein-mediated protein splicing, the self-assembly of the monomer was converted into a condition-dependent reaction, enabling the incorporation of large or functional biomolecules prior to the assembly stage. Furthermore, to achieve targeted delivery, an EGFR-binding affibody (EGFRAfb) was fused to the split monomer so that it is exposed on the cage surface after reassembly, thereby providing selective binding capability toward EGFR-expressing cells. Successfully reassembled nanocages were visualized, and the fluorescent proteins encapsulated within them were delivered to the target and activated in specific cells. Conclusions: Therefore, the programmable protein nanoplatform presented in this study can overcome the spatial limitations of conventional protein cages while allowing for precise control over both the timing of cage assembly and targeted molecular delivery. Full article

Adeno-associated viruses (AAVs) have emerged as promising vectors for gene therapy due to their non-pathogenic nature and ability to transduce various cell types efficiently. In recent years, there has been an increasing effort to optimize the production and purification of AAV to support clinical applications; however, challenges exist in affinity ligand design, synthesis, and characterization. Understanding the binding interactions of these viruses with functional molecules is pivotal for the development of affinity-based separation methods of AAVs. Classical methods to measure thermodynamic parameters such as Isothermal Titration Calorimetry (ITC) are challenging to employ in these scenarios, as the concentrations of the viral titers are significantly lower than those used in binding experiments with small biomolecules. Here, we present design principles that enable ITC-based determination of binding interactions between AAV2 and heparin. We observe increasing binding affinity with increasing molecular weight of heparin. We also elucidate the binding stoichiometry between AAV2 and heparins of varying molecular weights. Additionally, we report on the impact of buffer conditions and pH values on AAV2–heparin binding properties. Lastly, we also present the binding affinities and thermodynamic properties of interactions between the two species with heparin immobilized onto surfaces, namely, silica nanoparticles, as surface immobilization of the ligand is a common pathway for affinity-based separations. Overall, our results may provide key information for optimization of AAV-ligand binding protocols that are an essential step toward optimizing AAV capture and immobilization methods. Full article

Peptide therapeutics have emerged as a versatile class of biomolecules bridging the gap between small-molecule drugs and large biologics. Advantages of such molecules include high target specificity, potent bioactivity and reduced off-target toxicity. Despite these, broader clinical translation remains constrained by inherent limitations like poor metabolic stability, rapid renal clearance, limited membrane permeability and scalable synthesis. This review aims to systematically integrate advances in peptide science across natural discovery, synthetic methodologies, structural engineering, and translational delivery systems, while identifying critical research gaps hindering clinical adoption. We highlight diverse natural sources of bioactive peptides, including plant- (lunasin), animal- (Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP)), microbial- (nisin and cyclosporine), marine- (dolastatins) and venom-derived (chlorotoxin and ω-conotoxin MVIIA (ziconotide)) agents. Advances in solid-phase peptide synthesis (SPPS), green chemistry, and catalytic strategies are discussed alongside emerging in silico approaches, including artificial intelligence-driven sequence design and molecular modeling. Structural modifications such as cyclization, hydrocarbon stapling, PEGylation, and lipidation are critically evaluated for their role in enhancing pharmacokinetic and pharmacodynamic properties. Furthermore, nanoformulation strategies, including self-assembling peptides and cell-penetrating systems, are examined for their potential to overcome biological barriers. Importantly, this review identifies key unresolved challenges, including the lack of predictive models for peptide delivery systems, safety concerns associated with long-term modifications, and limited in vivo validation of naturally derived peptides. Addressing these gaps through integrated computational and experimental approaches will be essential for advancing next-generation peptide therapeutics. Collectively, this work provides a comprehensive framework for the rational design and translation of peptide-based precision medicines. Full article

In the context of the circular economy, the valorization of natural biomolecules from by-products has recently represented a major goal in health promotion. From this perspective, this study examined the antioxidant potential of Sicilian white grape pomace from the Pinot Gris variety, using subcritical water extraction as an eco-friendly and innovative method to recover bioactive compounds. Different extraction parameters allowed for comparing the potential of various fractions. Among these, the Subcritical Water Extract obtained after 5 min at 160 °C (SWE^160.1) was rich in gallic acid and protocatechuic acid, as evidenced by characterization with UHPLC-Q Exactive Orbitrap-HRMS system. SWE^160.1 showed efficacious antioxidant activity, as confirmed by DPPH assay and total polyphenol and flavonoid content. Interestingly, SWE^160.1 displayed cytotoxic activity in tumor cell lines, while preserving the viability of non-tumor bronchial epithelial cells. Specifically, SWE^160.1 protected these cells from exogenous oxidative stress, reducing the ROS levels and activating Nrf2-mediated antioxidant response. Surprisingly, upregulation of antioxidant enzymes (HO-1 and SOD-2) induced by SWE^160.1 was maintained in the presence of lipopolysaccharide, indicating a specific involvement of SWE^160.1 in the anti-inflammatory response. Finally, SWE^160.1 was also able to limit the formation of stress granules following acute stress, thereby supporting its potential to maintain cellular homeostasis. Overall, this study highlights the potential of grape pomace as a source of active molecules to prevent oxidative stress and inflammation. Full article

Mycogenic nanomaterials, nanoparticles (NPs) biosynthesized through fungal enzymatic and metabolic activity, have emerged as a compelling alternative to chemically synthesized nanomaterials, offering fundamental biocompatibility, green production conditions, and biologically functional surface coatings. Fungi, acting as natural “nanofactories,” harness reductases, oxidoreductases, secreted proteins, and secondary metabolites to reduce metal ions into stable NPs under ambient conditions, simultaneously capping the particles with biomolecules that enhance colloidal stability, biocompatibility, and secondary biological activity. Unlike previous reviews that have addressed either biosynthesis mechanisms or applications in isolation, this review uniquely adopts a structured “Promise vs. Barrier” framework across six interconnected thematic pillars, offering the first comprehensive critical synthesis that simultaneously maps mechanistic frontiers, biodiversity gaps, and translational barriers within mycogenic nanotechnology. The present review critically examines both the extraordinary promise and the persistent barriers facing mycogenic nanotechnology across biosynthetic mechanisms, fungal biodiversity, nanomaterial portfolio expansion, biomedical applications, environmental and agricultural utility, and industrial scalability. We highlight how emerging multiomics approaches, integrating transcriptomics, proteomics, and metabolomics, are beginning to decode the molecular blueprints of fungal NP synthesis, while acknowledging that mechanistic knowledge gaps, limited genetic toolkits for non-model fungi, and the absence of standardized protocols continue to impede progress. The fungal kingdom represents a vast, underexplored reservoir of nanofactory potential, with fewer than 1% of known species evaluated to date; strategic bioprospecting using genome mining and machine learning is beginning to unlock this diversity. Mycogenic NPs demonstrate broad-spectrum antimicrobial activity against multidrug-resistant pathogens, selective anticancer activity, biosensing capacity, and applications in wound healing, sustainable agriculture, environmental remediation, and smart food packaging. However, critical deficits persist in clinical validation, long-term toxicity data, manufacturing reproducibility, and regulatory clarity. The review concludes with a tiered roadmap, spanning immediate mechanistic priorities through to long-term synthetic biology and AI-integrated commercialization, and calls for coordinated international action on standardization, reference material development, and harmonized regulatory frameworks to bridge the gap between laboratory promise and real-world application. Full article

Marine organisms have proven to be excellent sources of bioactive natural products with potential therapeutic applications. To date, seventeen marine-derived molecules are on the market for the treatment of human diseases, mainly cancer. While multiple bioactivities of marine compounds have been consecutively reported, peptides represent promising candidates for these applications. This review focuses on peptides from marine organisms living in extreme marine environments, such as the deep ocean, polar regions, and tropical ecosystems. These are particularly promising for further bioprospecting, since their distinctive conditions have driven the evolution of unique biomolecules, as well as unique stability profile that can improve efficacy, shelf life, and performance under a wide range of industrial conditions. Ziconotide (Prialt), a neurotoxic peptide derived from the venom of a marine snail (Conus sp.) found at depths greater than 1000 m, is already commercially available for the treatment of severe pain. Recent technologies and computational tools are speeding up the discovery of new peptides and enzymes (very few from extreme environments). Overall, the review reports about eight peptides with anticancer properties from deep environments, nine, two and seven from polar habitats with antioxidants, anti-inflammatory and anticancer properties, respectively, and approximately ninety peptides from tropical waters (five antioxidant, thirty-five anti-inflammatory and fifty-four anticancer peptides). However, future studies in extreme environments will need to develop and apply sampling technologies, cultivation systems, as well as methods to assess efficacy, side effects and mechanisms of action, in vitro and in vivo. Full article

Natural products display exceptional chemical diversity and a broad range of mechanisms of action that are not adequately captured by traditional classifications based on target class, pharmacological phenotype, or chemical scaffold. Such classification schemes often lead to fragmented understanding of mechanisms of action, obscuring the unified principles underlying different target systems while failing to recognize the stage-dependent mechanisms exhibited by the same molecule in varying contexts. Here, we propose a unified “space–interface–time” framework to classify the mechanisms of action by examining the physical principles through which natural products reshape the functions of different biomolecules. Within this framework for unifying the classification of natural product mechanisms of action, geometry-driven binding site occupancy and conformational constraints are assigned to the spatial dimension; induction or stabilization of multicomponent complexes and kinetic regulation of state lifetimes are assigned to the interfacial and temporal dimensions, respectively. Finally, we discuss the conceptual and technical challenges of bridging static structural snapshots with dynamic in vivo pharmacology, and highlight emerging opportunities offered by time-resolved structural methods and the integration of molecular dynamics, machine learning, and biophysical workflows for mechanism-guided drug discovery. Full article

Background: D-amino acids are increasingly recognized as bioactive molecules with diverse physiological and pathological roles in humans, particularly in the gut, kidneys, and nervous system. Advances in analytical techniques have revealed their widespread presence in biological fluids, including plasma, urine, cerebrospinal fluid, amniotic fluid, and saliva, challenging the long-standing assumption that D-amino acids are absent or biologically insignificant in mammals. Scope: This review systematically summarizes the current knowledge on D-amino acid sources, distribution, metabolic regulation, and biological functions, with emphasis on their roles in human physiology and disease. Key findings: Accumulating evidence indicates that major D-amino acids, including D-serine, D-aspartate, and D-alanine, are derived from multiple sources such as diet, intestinal microbiota, and endogenous racemization processes. Rather than being passive metabolic byproducts, D-amino acids are now understood to participate in host–microbe interactions, neurotransmission, and renal physiology. Importantly, a consistent trend across studies is their dual and concentration-dependent nature, exhibiting beneficial effects under physiological conditions but potential cytotoxic effects at elevated levels. Conclusions and perspectives: Overall, D-amino acids represent multifunctional biomolecules with tightly regulated physiological roles and context-dependent pathological implications. However, major gaps remain in understanding their quantitative dynamics, tissue-specific regulation, and microbiota-dependent metabolism. Future studies addressing these mechanisms will be essential for establishing their clinical utility as biomarkers and for developing D-amino acid-based therapeutic and nutritional strategies. Full article

Background: The increasing antimicrobial resistance has led to a greater demand for alternative treatment options, which in turn has increased interest in naturally occurring biomolecules such as pyocyanin. Methods: In this study, a three-factor Box–Behnken Design (BBD)-based response surface methodology (RSM) was employed to optimize the effects of glycerol, peptone, and pH on pyocyanin production by Pseudomonas aeruginosa OG1. The antimicrobial efficacy of the optimized pyocyanin was subsequently evaluated in vitro against three Candida species and four clinically important bacterial pathogens using the disk diffusion method, with gentamicin and fluconazole used as positive controls. Results: The second-order polynomial model demonstrated excellent fit (F = 176.3, p < 0.0001) with a non-significant lack of fit, indicating adequate representation of the experimental data. The optimal conditions were determined to be glycerol at 1.11% (w/v), peptone at 17.86 g/L, and a pH of 7.27, yielding a predicted pyocyanin concentration of 25.92 mg/L. Antimicrobial testing revealed broad-spectrum, dose-dependent activity against all tested microorganisms. The highest efficacy was observed against Bacillus cereus (26.4 ± 1.3 mm at 40 µg/mL), followed by Candida glabrata (21.5 ± 1.6 mm), Klebsiella pneumoniae (17.6 ± 1.4 mm), Candida albicans (15.4 ± 1.8 mm), Candida parapsilosis (13.2 ± 1.9 mm), Proteus mirabilis (12.5 ± 1.3 mm), and MRSA Staphylococcus aureus (9.2 ± 1.1 mm). Conclusions: These findings demonstrate that BBD-based RSM is a robust approach for optimizing pyocyanin production and that pyocyanin represents a promising dose-dependent antimicrobial agent against susceptible pathogens. Full article

This study systematically investigated the characterization of 2Fe-CDs/12Mn-CeO₂ composites and the colorimetric sensing properties of H₂O₂, glucose (Glu), and glutathione (GSH). The morphology, structure, and optical properties of the 2Fe-CDs/12Mn-CeO₂ composite were analyzed in detail by XRD, FT-IR, SEM, TEM, XPS, and Raman spectroscopy, and its formation was supported by multiple complementary characterization techniques. The catalytic efficiency (kcat/Km) of the nanozyme is 152-fold higher than natural HRP under optimal conditions and remains 59-fold higher even after temperature normalization to 25 °C. In the colorimetric sensing experiments, the detection limits of Fe-CDs/Mn-CeO₂ were 0.21 μM, 2.7 μM, and 0.63 μM for H₂O₂, Glu, and GSH, respectively. Rapid and accurate determination of the concentrations of these biomolecules can be achieved by observing the color changes after Fe-CDs/Mn-CeO₂ reaction with the objects to be measured. The experimental results show that Fe-CDs/Mn-CeO₂ have high sensitivity and selectivity for H₂O₂, Glu, and GSH, which provides a solid theoretical and experimental basis for the application of Fe-CDs/Mn-CeO₂ in the field of biosensing and medical diagnosis. Full article

Green synthesis of nanoparticles has become one of the most popular research areas in recent decades due to its environmentally friendly nature and the minimization of harmful chemical by-products. This review focuses on the mechanism of palladium nanoparticle (PdNP) biosynthesis using bacteria, fungi, algae, and plants, and their potential biological activities, such as antibacterial, anticancer, antioxidant, and other properties, with the aim of their further biomedical applications. The role of various biomolecules in these processes is also discussed. Full article

Kombucha, a traditionally fermented tea, has gained increasing scientific and commercial interest due to its sensory quality and bioactive metabolites profile associated with different health-related activities. Recent research highlights the value of enriching traditional and honey kombucha with plant-based biomolecules to create new functional beverages with enhanced functional and nutraceutical properties, improved flavor, and chemical stability. Therefore, this study aimed to review and update the research on the enrichment of kombucha with these natural biomolecules that have been shown to expand the spectrum of health-promoting activities (e.g., antioxidant, antimicrobial, anticancer, and anti-aging), while also enhancing the physicochemical stability of raw kombucha. Yet this innovation must be navigated with a thoughtful understanding of safety, biochemical stability, and sensory evaluation. Thus, this review strongly advocates that the integrative enrichment approach presents a promising strategy for developing next-generation functional beverages with synergistic nutritional and therapeutic benefits. Further controlled studies are needed to elucidate the mechanistic interactions between the kombucha’s microbiome and these added bioactive substrates, as well as to optimize formulations for targeted health applications. Full article

Sustainable agricultural techniques can ensure food security around the world. Hydrogel based soilless culture is an ecological and efficient alternative compared to conventional agriculture. Here, a multi-component hydrogel (pectin, Kelcogel, and chitosan/Se hydrogel, PKCH) was prepared by synthesizing natural biomolecules to cultivate dandelion for stimulate dandelion growth and improve nutritional value. The germination percentage of dandelion on PKCH (88.89%), was significantly higher than that in traditional hydroponics and pure Kelcogel (p < 0.05). Compared with hydroponics, the long-term dandelion cultivation experiments demonstrated that the PKCH cultivation mode enhanced root vitality, further increasing the growth and yield of dandelions (shoot length: 18.36 ± 0.30 cm, root length: 9.28 ± 0.21 cm, main root diameter: 0.94 ± 0.02 cm). The hydrogel substrate was associated with improved nutrient solubilization and sustained release, which may be linked to the accumulation of low-molecular-weight organic acids in the rhizosphere. Exogenous Se was effectively assimilated and transported to the above-ground parts of dandelion, which stimulated the photosynthetic efficiency and nutritional accumulation of dandelion. The polysaccharide content of dandelion reached 69.40 ± 0.13% (expressed as glucose-equivalent total sugars), which demonstrated the potential antioxidant properties and medicinal value. Technical economic analysis revealed the cost-effectiveness of PKCH synthesis and application. This study enriches the application of hydrogels in dandelion cultivation and provides an alternative approach for cultivating dandelion in soilless environments and medicinal crop production techniques. Full article

As primary producers in aquatic ecosystems, microalgae function not only as a natural source of nourishment for several economically important aquatic species but also as reservoirs of bioactive molecules. Microalgae can secrete exosome-like nanoparticles that transport functional biomolecules, such as proteins and nucleic acids, into the extracellular milieu, thereby mediating intercellular signaling and eliciting ecological or biomedical responses. Although plant-derived exosome-like nanoparticles have attracted attention for their utility in drug delivery and dermatology, the functional properties of microalgae-derived nanoparticles—particularly from species extensively applied in aquaculture—remain inadequately characterized. In this study, exosome-like nanovesicles were isolated from Nannochloropsis oculata (N-ELNs), a microalgal species widely used in aquaculture, and their skin-whitening potential was evaluated using the B16-F10 mouse melanoma cell model. The highest N-ELN yield was observed during the adaptation, exponential, and stationary growth phases. Uptake analyses confirmed the efficient internalization of N-ELNs by B16-F10 cells. Cell counting kit-8 assays indicated that N-ELNs exhibited no cytotoxic effects on melanoma cells or normal human dermal fibroblasts (HFF-1). Scratch wound healing assays revealed that N-ELNs exerted no significant effect on cellular migration. In B16-F10 cells, N-ELNs suppressed tyrosinase activity by downregulating Mitf and its downstream genes Tyr and Tyrp1, resulting in a substantial reduction in melanin synthesis (p < 0.05). The inhibitory effects of N-ELNs on melanin production, tyrosinase activity, and gene expression of Tyr, Tyrp1, and Mitf were comparable to those of the positive control, arbutin. Collectively, these findings suggest that N. oculata exhibits promising skin-whitening properties, providing a novel perspective for clinical applications and supporting the high-value utilization of the microalgae aquaculture industry. Full article

The study of volatile organic compounds (VOCs)-mediated plant growth promotion has long focused on various beneficial microbial species. As an important natural source of functional biomolecules, the biological function and potential value of VOCs released by plant pathogenic fungi in regulating plant growth still lack sufficient research, and further exploration is needed. In this study, a phytopathogenic fungus Alternaria alstroemeriae (strain Z84) was isolated from Vaccinium dunalianum for the first time, and the effects of its VOCs on the growth of Arabidopsis thaliana and Nicotiana benthamiana were systematically investigated. The results showed that after Z84 VOCs treatment, multiple phenotypic traits of the two plants were significantly improved, and the chlorophyll content was also markedly increased. Transcriptome analysis showed that a total of 1401 differentially expressed genes (DEGs) were identified in the treated A. thaliana, of which 629 were up-regulated and 772 were down-regulated. KEGG enrichment analysis showed that these DEGs were mainly enriched in photosynthesis-antenna proteins, plant–pathogen interaction, glutathione metabolism, plant hormone signal transduction, flavonoid biosynthesis and photosynthesis-related pathways. Metabolomics analysis revealed that Z84 VOCs treatment significantly changed the metabolic profile of A. thaliana, with the most significant changes in amino acid metabolism-related pathways. It is noteworthy that the plant hormone spectrum of A. thaliana was significantly changed after treatment, and the contents of salicylic acid (SA), abscisic acid (ABA) and gibberellins (GAs) were significantly up-regulated. These results not only demonstrate the potential of Z84-derived VOCs to facilitate plant growth but also provide an important basis for further dissecting the molecular mechanisms of plant–pathogenic fungi interactions. Full article