Enzyme-Mimicking Materials from Designed Self-Assembly of Lysine-Rich Peptides and G-Quadruplex DNA/Hemin DNAzyme: Charge Effect of the Key Residues on the Catalytic Functions

Impact of NH4+ on the catalytic activity of G-quadruplex/hemin DNAzyme for chemiluminescent sensing

G-quadruplex/hemin DNAzyme, a versatile tool for biosensing, is challenged by its low peroxidase-mimic activities. The addition of NH4+ may offer an efficient approach to improve its activity. However, the detailed impact of NH4+ on its catalytic activity remains unclear, confusing the selection of appropriate DNAzymes for biosensing applications. Here, we conducted a comprehensive examination of the influence of NH4+ on G-quadruplex/hemin DNAzyme. The results revealed that all DNAzymes with different G-quadruplex topologies exhibited increased catalytic activities in the presence of NH4+ relative to K+, followed by the subsequent activity order: parallel > hybrid > antiparallel. Further investigations indicated that the increased catalytic activity can be ascribed to the increased stability of the G-quadruplex/hemin complex, elevated reaction velocity, and improved substrate affinity. Leveraging the significant disparity in enzymatic activity between parallel and antiparallel G-quadruplexes, an allosteric sensor based on the Pb2+-induced topological conformation was developed for sensitive detection of Pb2+ in the NH4+-boosted G-quadruplex/hemin DNAzyme system (LOD, 1.56 nM), indicating potential for practical applications. Our discovery improves the understanding of NH4+-boosted G-quadruplex/hemin DNAzyme and may facilitate the development of biosensors.

Intramolecular distance-regulated G4 DNA enzymatic activity-based chromophotometric system for visual monitoring of diquat

BACKGROUND

As global food production continues to surge, the widespread use of herbicides has also increased concurrently, posing challenges like health risks and environmental pollution. Traditional detection methods for pesticide residues, such as diquat (DQ), were hampered by limitations like high expenses, lengthy detection times and complex operations, restricting their practical application in rapid clinical diagnosis.

RESULTS

In light of the pressing necessity for the identification of minute pesticide residues and the intrinsic constraints of small molecule analysis, a novel chromophotometric biosensor targeting small molecules was developed based on bi-epitopes on single antibody to immobilize two DQ-PAL, inhibiting the hybridization of DQ-PAL. Accordingly, the free DQ-PAL could hybridize with each other to form a G-quadruplex for a highly selective analysis of DQ with a detection limit of 26.3 pg/mL and 10 pg/mL by chromophotometric and image colorimetric method respectively. Furthermore, this designed biosensor has been successfully applied to evaluate the levels of DQ residues in real samples, providing an efficient solution for the biological analysis of small molecule targets and enhancing food safety concerning pesticide residues.

SIGNIFICANCE

In comparison to conventional techniques, this biosensor has the advantages of user-friendly operations, portability, high sensitivity, low detection limit and minimal background interference, making it well-suited for clinical diagnostics. At the same time, this technology provides a new idea for the rapid in vitro detection of biological small molecules, and shows great potential applications in agricultural residue-related food safety.

Designing Nano-Hemin for Ferroptosis-Mediated Cell Death via Enzymatic Hemin Digestion

Hemin is a protoporphyrin complex of ferric ion which catalyzes H2O2 degradation and produces reactive oxygen species (ROS). This ROS generation property induces oxidative stress to hemin-exposed cells that can lead to various situations such as intracellular Fenton reaction, ferroptosis, or autophagy. Therapeutic performance of hemin is hindered due to low bioavailability of the active monomeric form with an intact ROS generation property. Here, we demonstrate a colloidal nanoparticle form of hemin (nano-hemin) with a high ROS generation property and high cell uptake property. We have shown that nano-hemin produces ROS inside a cell that upregulate heme oxygenase-1 in order to metabolize hemin. This leads to the ferroptosis-mediated cell death. Furthermore, we show that the ROS generation property of nano-hemin can be modulated to control hemin cytotoxicity for either ferroptosis or autophagy. Our findings suggest that nano-hemin can be designed with modular cytotoxicity for different therapeutic applications.

A Self-Catalytic NO/O2 Gas-Releasing Nanozyme for Radiotherapy Sensitization through Vascular Normalization and Hypoxia Relief

Radiotherapy (RT), essential for treating various cancers, faces challenges from tumor hypoxia, which induces radioresistance. A tumor-targeted "prosthetic-Arginine" coassembled nanozyme system, engineered to catalytically generate nitric oxide (NO) and oxygen (O2) in the tumor microenvironment (TME), overcoming hypoxia and enhancing radiosensitivity is presented. This system integrates the prosthetic heme of nitric oxide synthase (NOS) and catalase (CAT) with NO-donating Fmoc-protected Arginine and Ru3+ ions, creating HRRu nanozymes that merge NOS and CAT functionalities. Surface modification with human heavy chain ferritin (HFn) improves the targeting ability of nanozymes (HRRu-HFn) to tumor tissues. In the TME, strategic arginine incorporation within the nanozyme allows autonomous O2 and NO release, triggered by endogenous hydrogen peroxide, elevating NO and O2 levels to normalize vasculature and improve blood perfusion, thus mitigating hypoxia. Employing the intrinsic O2-transporting ability of heme, HRRu-HFn nanozymes also deliver O2 directly to the tumor site. Utilizing esophageal squamous cell carcinoma as a tumor model, the studies reveal that the synergistic functions of NO and O2 production, alongside targeted delivery, enable the HRRu-HFn nanozymes to combat tumor hypoxia and potentiate radiotherapy. This HRRu-HFn nanozyme based approach holds the potential to reduce the radiation dose required and minimize side effects associated with conventional radiotherapy.

Effects of a semi-interpenetrating network hydrogel loaded with oridonin and DNase-I on the healing of chemoradiotherapy-induced oral mucositis

The aim of this study was to develop a semi-interpenetrating network (IPN) hydrogel system suitable for the oral environment, capable of controlled release of DNase-I and oridonin (ORI), to exert antimicrobial, anti-inflammatory, and reparative effects on chemoradiotherapy-induced oral mucositis (OM). This IPN was based on the combination of ε-polylysine (PLL) and hetastarch (HES), loaded with DNase-I and ORI (ORI/DNase-I/IPN) for OM treatment. In vitro studies were conducted to evaluate degradation, adhesion, release analysis, and bioactivity including cell proliferation and wound healing assays using epidermal keratinocyte and fibroblast cell lines. Furthermore, the therapeutic effects of ORI/DNase-I/IPN were investigated in vivo using Sprague-Dawley (SD) rats with chemoradiotherapy-induced OM. The results demonstrated that the IPN exhibited excellent adhesion to wet mucous membranes, and the two drugs co-encapsulated in the hydrogel were released in a controlled manner, exerting inhibitory effects on bacteria and degrading NETs in wound tissues. The in vivo wound repair effect, microbiological assays, H&E and Masson staining supported the non-toxicity of ORI/DNase-I/IPN, as well as its ability to accelerate the healing of oral ulcers and reduce inflammation. Overall, ORI/DNase-I/IPN demonstrated a therapeutic effect on OM in rats by significantly accelerating the healing process. These findings provide new insights into possible therapies for OM.

A Self‐Catalytic NO/O2 Gas‐Releasing Nanozyme for Radiotherapy Sensitization through Vascular Normalization and Hypoxia Relief

Radiotherapy (RT), essential for treating various cancers, faces challenges from tumor hypoxia, which induces radioresistance. A tumor‐targeted “prosthetic‐Arginine” coassembled nanozyme system, engineered to catalytically generate nitric oxide (NO) and oxygen (O2) in the tumor microenvironment (TME), overcoming hypoxia and enhancing radiosensitivity is presented. This system integrates the prosthetic heme of nitric oxide synthase (NOS) and catalase (CAT) with NO‐donating Fmoc‐protected Arginine and Ru3+ ions, creating HRRu nanozymes that merge NOS and CAT functionalities. Surface modification with human heavy chain ferritin (HFn) improves the targeting ability of nanozymes (HRRu‐HFn) to tumor tissues. In the TME, strategic arginine incorporation within the nanozyme allows autonomous O2 and NO release, triggered by endogenous hydrogen peroxide, elevating NO and O2 levels to normalize vasculature and improve blood perfusion, thus mitigating hypoxia. Employing the intrinsic O2‐transporting ability of heme, HRRu‐HFn nanozymes also deliver O2 directly to the tumor site. Utilizing esophageal squamous cell carcinoma as a tumor model, the studies reveal that the synergistic functions of NO and O2 production, alongside targeted delivery, enable the HRRu‐HFn nanozymes to combat tumor hypoxia and potentiate radiotherapy. This HRRu‐HFn nanozyme based approach holds the potential to reduce the radiation dose required and minimize side effects associated with conventional radiotherapy.

Developing Isomeric Peptides for Mimicking the Sequence-Activity Landscapes of Enzyme Evolution

Enzymes catalyze almost all material conversion processes within living organisms, yet their natural evolution remains unobserved. Short peptides, derived from proteins and featuring active sites, have emerged as promising building blocks for constructing bioactive supramolecular materials that mimic native proteins through self-assembly. Herein, we employ histidine-containing isomeric tetrapeptides KHFF, HKFF, KFHF, HFKF, FKHF, and FHKF to craft supramolecular self-assemblies, aiming to explore the sequence-activity landscapes of enzyme evolution. Our investigations reveal the profound impact of peptide sequence variations on both assembly behavior and catalytic activity as hydrolytic simulation enzymes. During self-assembly, a delicate balance of multiple intermolecular interactions, particularly hydrogen bonding and aromatic-aromatic interactions, influences nanostructure formation, yielding various morphologies (e.g., nanofibers, nanospheres, and nanodiscs). Furthermore, the analysis of the structure-activity relationship demonstrates a strong correlation between the distribution of the His active site on the nanostructures and the formation of the catalytic microenvironment. This investigation of the sequence-structure-activity paradigm reflects how natural enzymes enhance catalytic activity by adjusting the primary structure during evolution, promoting fundamental research related to enzyme evolutionary processes.

Robust Oxidase-Mimetic Supramolecular Nanocatalyst for Lignin Biodegradation

Enzymatic catalysis presents an eco-friendly, energy-efficient method for lignin degradation. However, challenges arise due to the inherent incompatibility between enzymes and native lignin. In this work, we introduce a supramolecular catalyst composed of fluorenyl-modified amino acids and Cu2+, designed based on the aromatic stacking of the fluorenyl group, which can operate in ionic liquid environments suitable for the dissolution of native lignin. Amino acids and halide anions of ionic liquids shape the copper site's coordination sphere, showcasing remarkable catechol oxidase-mimetic activity. The catalyst exhibits thermophilic property, and maintains oxidative activity up to 75 °C, which allows the catalyzed degradation of the as-dissolved native lignin with high efficiency even without assistance of the electron mediator. In contrast, at this condition, the native copper-dependent oxidase completely lost its activity. This catalyst with superior stability and activity offer promise for sustainable lignin valorization through biocatalytic routes compatible with ionic liquid pretreatment, addressing limitations in native enzymes for industrially relevant conditions.

Self-Assembly of Designed Peptides with DNA to Accelerate the DNA Strand Displacement Process for Dynamic Regulation of DNAzymes

Toehold-mediated DNA strand displacement (TMSD) is a powerful tool for controlling DNA-based molecular reactions and devices. However, the slow kinetics of TMSD reactions often limit their efficiency and practical applications. Inspired by the chemical structures of natural DNA-operating enzymes (e.g., helicase), we designed lysine-rich peptides to self-assemble with DNA-based systems. Our approach allows for accelerating the TMSD reactions, even during multiple displacement events, enhancing their overall efficiency and utility. We found that the acceleration is dependent on the peptide's sequence, length, and concentration as well as the length of the DNA toehold domain. Molecular dynamics simulations revealed that the peptides promote toehold binding between the double-stranded target and the single-stranded invader, thereby facilitating strand displacement. Furthermore, we integrated our approach into a horseradish peroxidase-mimicking DNAzyme, enabling the dynamic modulation of enzymatic functions on and off. We anticipate that the established acceleration of strand displacement reactions and the modulation of enzymatic activities offer enhanced functionality and control in the design of programmable DNA-based nanodevices.

Heme-Dependent Supramolecular Nanocatalysts: A Review

Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..

A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing

Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.

Supramolecular enzyme-mimicking catalysts self-assembled from peptides

Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.

Introducing Nanozymes: New Horizons in Periodontal and Dental Implant Care

The prevalence of periodontal and peri-implant diseases has been increasing worldwide and has gained a lot of attention. As multifunctional nanomaterials with enzyme-like activity, nanozymes have earned a place in the biomedical field. In periodontics and implantology, nanozymes have contributed greatly to research on maintaining periodontal health and improving implant success rates. To highlight this progress, we review nanozymes for antimicrobial therapy, anti-inflammatory therapy, tissue regeneration promotion, and synergistic effects in periodontal and peri-implant diseases. The future prospects of nanozymes in periodontology and implantology are also discussed along with challenges.