Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides

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.

Functionalized hydrogen-bonded organic superstructures via molecular self-assembly for enhanced uranium extraction

Effective uranium extraction from water is essential for the development of nuclear power industry and the protection of human health and environment. Nevertheless, it still remains challenging to realize efficient and cost-effective uranium extraction. Herein, a fast and simple method for the direct fabrication of novel functionalized hydrogen-bonded organic superstructures via molecular self-assembly is reported. The as-constructed flower-like superstructures (MCP-5) can allow the exposure of adsorption sites and facilitate the transport of uranyl ions, while synergism between amino and phosphate groups can realize selective uranium extraction. Consequently, MCP-5 possesses excellent uranium adsorption ability with a high saturated adsorption capacity of 950.52 mg g-1, high utilization rate of adsorption sites and adsorption equilibrium time of simply 5 min in uranium-spiked aqueous solution. Furthermore, MCP-5 offers selective uranium adsorption over a broad range of metal ions. The facile synthesis and low-cost raw materials make it have promising potential for uranium capture. Simultaneously, this study opens a design avenue of functionalized hydrogen-bonded organic material for efficient uranium extraction.

Polyfluoroalkyl Chain-Based Assemblies for Biomimetic Catalysis

Amphiphobic fluoroalkyl chains are exploited for creating robust and diverse self-assembled biomimetic catalysts. Long terminal perfluoroalkyl chains (Cn F2n+1 with n=6, 8, and 10) linked with a short perhydroalkyl chains (Cm H2m with m=2 and 3) were used to synthesize several 1,4,7-triazacyclononane (TACN) derivatives, Cn F2n+1 -Cm H2m -TACN. In the presence of an equimolar amount of Zn2+ ions that coordinate the TACN moiety and drive the self-assembly into micelle-like aggregates, the critical aggregation concentration of polyfluorinated Cn F2n+1 -Cm H2m -TACN⋅Zn2+ was lowered by ∼1 order of magnitude compared to the traditional perhyroalkyl counterpart with identical carbon number of alkyl chain. When 2'-hydroxypropyl-4-nitrophenyl phosphate was used as the model phosphate substrate, polyfluorinated Cn F2n+1 -Cm H2m -TACN⋅Zn2+ assemblies showed higher affinity and catalytic activity, compared to its perhyroalkyl chain-based counterpart. Coarse-grained molecular dynamic simulations have been introduced to explore the supramolecular assembly of polyfluoroalkyl chains in the presence of Zn2+ ions and to better understand their enhanced catalytic activity.

Histidine-Based Supramolecular Nanoassembly Exhibiting Dual Enzyme-Mimetic Functions: Altering the Tautomeric Preference of Histidine to Tailor Oxidative/Hydrolytic Catalysis

Challenges persist in replicating enzyme-like active sites with functional group arrangements in supramolecular catalysis. In this study, we present a supramolecular material comprising Fmoc-modified histidine and copper. We also investigated the impact of noncanonical amino acids (δmH and εmH), isomers of histidine, on the catalytic process. The Fmoc-δmH-based nanoassembly exhibits an approximately 15-fold increase in oxidative activity and an ∼50-fold increase in hydrolytic activity compared to Fmoc-εmH (kcat/Km). This distinction arises from differences in basicity and ligation properties between the ε- and δ-nitrogen of histidine. The addition of guanosine monophosphate further enhances the oxidative activity of the histidine- and methylated histidine-based catalysts. The Fmoc-δmH/Cu2+-based nanoassembly catalyzes the oxidation/hydrolysis cascade of 2',7'-dichlorofluorescein diacetate, benefiting from the synergistic effect between the copper center and the nonligating ε-nitrogen of histidine. These findings advance the biomimetic catalyst design and provide insights into the mechanistic role of essential residues in natural systems.

Does freezing induce self-assembly of polymers? A molecular dynamics study

This work investigates the freezing-induced self-assembly (FISA) of polyvinyl alcohol (PVA) and PVA-like polymers using molecular dynamics simulations. In particular, the effect of the degree of supercooling, degree of polymerization, polymer type, and initial local concentration on the FISA was studied. It was found that the preeminent factor responsible for FISA is not the diffusion of the polymers away from the nucleating ice front, but the increase in the polymer's local concentration upon freezing of the solvent (water). At a higher degree of supercooling, the polymers are engulfed by the growing ice front, impeding their diffusion into the supercooled solution and finally inhibiting their self-assembly. Conversely, at a relatively lower degree of supercooling, the rate of diffusion of the polymers into the supercooled solution is higher, which increases their local concentration and results in FISA. FISA was also observed to depend on the polymer-solvent interactions. Strongly favorable solute-solvent interactions hinder the self-assembly, whereas unfavorable solute-solvent interactions promote the self-assembly. The polymer and aggregate morphology were investigated using the radius of gyration, end-to-end distance, and asphericity analysis. This study brings molecular insights into the quintessential factors governing self-assembly via freezing of the solvent, which is a novel self-assembly technique especially suitable for biomedical applications.

Lewis acid-driven self-assembly of diiridium macrocyclic catalysts imparts substrate selectivity and glutathione tolerance

Molecular inorganic catalysts (MICs) tend to have solvent-exposed metal centers that lack substrate specificity and are easily inhibited by biological nucleophiles. Unfortunately, these limitations exclude many MICs from being considered for in vivo applications. To overcome this challenge, a strategy to spatially confine MICs using Lewis acid-driven self-assembly is presented. It was shown that in the presence of external cations (e.g., Li+, Na+, K+, or Cs+) or phosphate buffered saline, diiridium macrocycles spontaneously formed supramolecular iridium-cation species, which were characterized by X-ray crystallography and dynamic light scattering. These nanoassemblies selectively reduced sterically unhindered C[double bond, length as m-dash]O groups via transfer hydrogenation and tolerated up to 1 mM of glutathione. In contrast, when non-coordinating tetraalkylammonium cations were used, the diiridium catalysts were unable to form higher-ordered structures and discriminate between different aldehyde substrates. This work suggests that in situ coordination self-assembly could be a versatile approach to enable or enhance the integration of MICs with biological hosts.

Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications

Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.

Supramolecular Nanozyme System Based on Polydopamine and Polyoxometalate for Photothermal-Enhanced Multienzyme Cascade Catalytic Tumor Therapy

The advent of enzyme-facilitated cascade events in which endogenous substrates within the human body are used to generate reactive oxygen species (ROS) has spawned novel cancer treatment possibilities. In this study, a supramolecular cascade catalytic nanozyme system was successfully developed, exhibiting photothermal-enhanced multienzyme cascade catalytic and glutathione (GSH) depletion activities and ultimately triggering the apoptosis-ferroptosis synergistic tumor therapy. The nanozyme system was fabricated using β-cyclodextrin-functionalized polydopamine (PDA) as the substrate, which was then entangled with polyoxometalate (POM) via electrostatic forces and assembled with adamantane-grafted hyaluronic acid and glucose oxidase (GOx) via host-guest supramolecular interaction for tumor targeting and GOx loading. The catalytic function of GOx facilitates the conversion of glucose to H2O2 and gluconic acid. In turn, this process affirms the propitious generation of hydroxyl radical (•OH) through the POM-mediated cascade catalysis. Additionally, the POM species actively deplete the intracellular GSH pool, initiating a cascade catalytic tumor therapy. In addition, the PDA-POM-mediated photothermal hyperthermia boosted the cascade catalytic effect and increased ROS production. This confers considerable promise for photothermal therapy (PTT)/nanocatalytic cancer therapy on supramolecular nanozyme systems. The in vitro and in vivo antitumor efficacy studies demonstrated that the supramolecular cascade catalytic nanozyme system was effective at reducing tumor development while maintaining an acceptable level of biocompatibility. Henceforth, this study is to widen the scope of cascade catalytic nanoenzyme production using supramolecular techniques, as well as endeavor to delineate a prospective pathway for the application of PTT-enhanced nanocatalytic tumor therapy.

Peptide Self-Assembly Controlled Photoligation of Polymers

Highly efficient chemical ligations that operate in water under mild conditions are the foundation of bioorthogonal chemistry. However, the toolbox of suitable reactions is limited. Conventional approaches to expand this toolbox aim at altering the inherent reactivity of functional groups to design new reactions that meet the required benchmarks. Inspired by controlled reaction environments that enzymes provide, we report a fundamentally different approach that makes inefficient reactions highly efficient within defined local environments. Contrasting enzymatically catalyzed reactions, the reactivity controlling self-assembled environment is brought about by the ligation targets themselves─avoiding the use of a catalyst. Targeting [2 + 2] photocycloadditions, which are inefficient at low concentrations and readily quenched by oxygen, short β-sheet encoded peptide sequences are inserted between a hydrophobic photoreactive styrylpyrene unit and a hydrophilic polymer. In water, electrostatic repulsion of deprotonated amino acid residues governs the formation of small self-assembled structures, which enable a highly efficient photoligation of the polymer, reaching ∼90% ligation within 2 min (0.034 mM). Upon protonation at low pH, the self-assembly changes into 1D fibers, altering photophysical properties and shutting down the photocycloaddition reaction. Using the reversible morphology change, it is possible to switch the photoligation "ON" or "OFF" under constant irradiation simply by varying the pH. Importantly, in dimethylformamide, the photoligation reaction did not occur even at 10-fold higher concentrations (0.34 mM). The self-assembly into a specific architecture, encoded into the polymer ligation target, enables a highly efficient ligation that overcomes the concentration limitations and high oxygen sensitivity of [2 + 2] photocycloadditions.

A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function

Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.

A Paradigm Shift from 2D to 3D: Surface Supramolecular Assemblies and Their Electronic Properties Explored by Scanning Tunneling Microscopy and Spectroscopy

Exploring supramolecular architectures at surfaces plays an increasingly important role in contemporary science, especially for molecular electronics. A paradigm of research interest in this context is shifting from 2D to 3D that is expanding from monolayer, bilayers, to multilayers. Taking advantage of its high-resolution insight into monolayers and a few layers, scanning tunneling microscopy/spectroscopy (STM/STS) turns out a powerful tool for analyzing such thin films on a solid surface. This review summarizes the representative efforts of STM/STS studies of layered supramolecular assemblies and their unique electronic properties, especially at the liquid-solid interface. The superiority of the 3D molecular networks at surfaces is elucidated and an outlook on the challenges that still lie ahead is provided. This review not only highlights the profound progress in 3D supramolecular assemblies but also provides researchers with unusual concepts to design surface supramolecular structures with increasing complexity and desired functionality.

Switchable enzyme mimics based on self-assembled peptides for polyethylene terephthalate degradation

Polyethylene terephthalate (PET), the most abundant polyester plastic, has become a global concern due to its refractoriness and accumulation in the environment. In this study, inspired by the structure and catalytic mechanism of the native enzyme, peptides, based on supramolecular self-assembly, were developed to construct enzyme mimics for PET degradation, which were achieved by combining the enzymatic active sites of serine, histidine and aspartate with the self-assembling polypeptide MAX. The two designed peptides with differences in hydrophobic residues at two positions exhibited a conformational transition from random coil to β-sheet by changing the pH and temperature, and the catalytic activity followed the self-assembly "switch" with the fibrils formed β-sheet, which could catalyze PET efficiently. Although the two peptides possessed same catalytic site, they showed different catalytic activities. Analysis of the structure - activity relationship of the enzyme mimics suggested that the high catalytic activity of the enzyme mimics for PET could be attributed to the formation of stable fibers of peptides and ordered arrangement of molecular conformation; in addition, hydrogen bonding and hydrophobic interactions, as the major forces, promoted effects of enzyme mimics on PET degradation. Enzyme mimics with PET-hydrolytic activity are a promising material for degrading PET and reducing environmental pollution.

Fmoc-diphenylalanine gelating nanoarchitectonics: A simplistic peptide self-assembly to meet complex applications

9-fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF), has been has been extensively explored due to its ultrafast self-assembly kinetics, inherent biocompatibility, tunable physicochemical properties, and especially, the capability of forming self-sustained gels under physiological conditions. Consequently, various methodologies to develop Fmoc-FF gels and their corresponding applications in biomedical and industrial fields have been extensively studied. Herein, we systemically summarize the mechanisms underlying Fmoc-FF self-assembly, discuss the preparation methodologies of Fmoc-FF hydrogels, and then deliberate the properties as well as the diverse applications of Fmoc-FF self-assemblies. Finally, the contemporary shortcomings which limit the development of Fmoc-FF self-assembly are raised and the alternative solutions are proposed, along with future research perspectives.

Design of supramolecular hybrid nanomaterials comprising peptide-based supramolecular nanofibers and in situ generated DNA nanoflowers through rolling circle amplification

The artificial construction of multicomponent supramolecular materials comprising plural supramolecular architectures that are assembled orthogonally from their constituent molecules has attracted growing attention. Here, we describe the design and development of multicomponent supramolecular materials by combining peptide-based self-assembled fibrous nanostructures with globular DNA nanoflowers constructed by the rolling circle amplification reaction. The orthogonally constructed architectures were dissected by fluorescence imaging using the selective fluorescence staining procedures adapted to this study. The present, unique hybrid materials developed by taking advantage of each supramolecular architecture based on their peptide and DNA functions may offer distinct opportunities to explore their bioapplications as a soft matrix.

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.

Small Peptides in the Detection of Mycotoxins and Their Potential Applications in Mycotoxin Removal

Mycotoxins pose significant risks to humans and livestock. In addition, contaminated food- and feedstuffs can only be discarded, leading to increased economic losses and potential ecological pollution. Mycotoxin removal and real-time toxin level monitoring are effective approaches to solve this problem. As a hot research hotspot, small peptides derived from phage display peptide libraries, combinatorial peptide libraries, and rational design approaches can act as coating antigens, competitive antigens, and anti-immune complexes in immunoassays for the detection of mycotoxins. Furthermore, as a potential approach to mycotoxin degradation, small peptides can mimic the natural enzyme catalytic site to construct artificial enzymes containing oxidoreductases, hydrolase, and lyase activities. In summary, with the advantages of mature synthesis protocols, diverse structures, and excellent biocompatibility, also sharing their chemical structure with natural proteins, small peptides are widely used for mycotoxin detection and artificial enzyme construction, which have promising applications in mycotoxin degradation. This paper mainly reviews the advances of small peptides in the detection of mycotoxins, the construction of peptide-based artificial enzymes, and their potential applications in mycotoxin control.

Switchable aqueous catalytic systems for organic transformations

In living organisms, enzyme catalysis takes place in aqueous media with extraordinary spatiotemporal control and precision. The mechanistic knowledge of enzyme catalysis and related approaches of creating a suitable microenvironment for efficient chemical transformations have been an important source of inspiration for the design of biomimetic artificial catalysts. However, in "nature-like" environments, it has proven difficult for artificial catalysts to promote effective chemical transformations. Besides, control over reaction rate and selectivity are important for smart application purposes. These can be achieved via incorporation of stimuli-responsive features into the structure of smart catalytic systems. Here, we summarize such catalytic systems whose activity can be switched 'on' or 'off' by the application of stimuli in aqueous environments. We describe the switchable catalytic systems capable of performing organic transformations with classification in accordance to the stimulating agent. Switchable catalytic activity in aqueous environments provides new possibilities for the development of smart materials for biomedicine and chemical biology. Moreover, engineering of aqueous catalytic systems can be expected to grow in the coming years with a further broadening of its application to diverse fields.

An artificial self-assembling peptide with carboxylesterase activity and substrate specificity restricted to short-chain acid p-nitrophenyl esters

Natural enzymes possess remarkable catalytic activity and high substrate specificity. Many efforts have been dedicated to construct artificial enzymes with high catalytic activity. However, how to mimic the exquisite substrate specificity of a natural enzyme remains challenging because of the complexity of the enzyme structure. Here, we report artificial carboxylesterases that are specific for short chain fatty acids and were constructed via peptide self-assembly. These artificial systems have esterase-like activity rather than lipase-like activity towards p-nitrophenyl esters. The designer peptides self-assembled into nanofibers with strong β-sheet character. The extending histidine units and the hydrophobic edge of the fibrillar structure collectively form the active center of the artificial esterase. These artificial esterases show substrate specificity for short-chain acids esters. Moreover, 1-isopropoxy-4-nitrobenzene could function as a competitive inhibitor of hydrolysis of p-nitrophenyl acetate for an artificial esterase.

Peptide-based assembled nanostructures that can direct cellular responses

Natural originated materials have been well-studied over the past several decades owing to their higher biocompatibility compared to the traditional polymers. Peptides, consisting of amino acids, are among the most popular programable building blocks, which is becoming a growing interest in nanobiotechnology. Structures assembled using those biomimetic peptides allow the exploration of chemical sequences beyond those been routinely used in biology. In this Review, we discussed the most recent experimental discoveries on the peptide-based assembled nanostructures and their potential application at the cellular level such as drug delivery. In particular, we explored the fundamental principles of peptide self-assembly and the most recent development in improving their interactions with biological systems. We believe that as the fundamental knowledge of the peptide assemblies evolves, the more sophisticated and versatile nanostructures can be built, with promising biomedical applications.

Construction of Zn-heptapeptide bionanozymes with intrinsic hydrolase-like activity for degradation of di(2-ethylhexyl) phthalate

Nanozyme with intrinsic enzyme-like activity has emerged as favorite artificial catalyst during recent years. However, current nanozymes are mainly limited to inorganic-derived nanomaterials, while biomolecule-sourced nanozyme (bionanozyme) are rarely reported. Herein, inspired by the basic structure of natural hydrolase family, we constructed 3 oligopeptide-based bionanozymes with intrinsic hydrolase-like activity by implementing zinc induced self-assembly of histidine-rich heptapeptides. Under mild condition, divalent zinc (Zn²⁺) impelled the spontaneous assembly of short peptides (i.e. Ac-IHIHIQI-CONH₂, Ac-IHIHIYI-CONH₂, and Ac-IHVHLQI-CONH₂), forming hydrolase-mimicking bionanozymes with β-sheet secondary conformation and nanofibrous architecture. As expected, the resultant bionanozymes were able to hydrolyze a serious of p-nitrophenyl esters, including not only the simple substrate with short side-chain (p-NPA), but also more complicated ones (p-NPB, p-NPH, p-NPO, and p-NPS). Moreover, the self-assembled Zn-heptapeptide bionanozymes were also proven to be capable of degrading di(2-ethylhexyl) phthalate (DEHP), a typical plasticizer, showing great potential for environmental remediation. Based on this study, we aim to provide theoretical references and exemplify a specific case for directing the construction and application of bionanozyme.

Switchable Enzyme-mimicking catalysts Self-Assembled from de novo designed peptides and DNA G-quadruplex/hemin complex

Reconstruction of enzymatic active site in an artificial system is key to achieving high catalytic efficiency. Herein, we report the self-assembly of the lysine-containing peptides with guanine-rich DNA and hemin to form peroxidase-mimicking active sites and catalytic nanoparticles. The DNA strand self-folds into a G-quadruplex structure that provides a supramolecular scaffold and a potential axial ligand for hemin. The β-sheet forming capability of the lysine-containing peptides is found to affect the catalytic synergy between the G-quadruplex DNA and the peptide. It is hypothesized that the β-sheet formation of the peptides results in the enrichment of the lysine residues, which distribute on the distal side of hemin to promote the formation of Compound I, like distal arginine residue in natural heme pocket. Incorporation of the histidine residues into the lysine-containing peptides further enhanced the hemin activities, indicating the cooperation between the lysine and histidine. Furthermore, the peptide/DNA/hemin complexes can be switched between active and inactive state by reversible formation and deformation of the DNA G-quadruplex, which was attributed to the peptides-promoted conformational changes of the DNA components. This work opens an avenue to mimic the catalytic residues and their spatial distribution in the natural enzymes, and shed light on the design of the smart biocatalysts that can respond to the environmental stimuli.

A Self-Assembled Fmoc-Diphenylalanine Hydrogel-Encapsulated Pt Nanozyme as Oxidase- and Peroxidase-Like Breaking pH Limitation for Potential Antimicrobial Application

Nanomaterials with oxidase- and peroxidase-like activities have potential in antibacterial therapy. The optimal activity of most nanozymes occurred in acidic pH (3.0-5.0), while the pH in biological systems is mostly near neutral. Herein, a general system using 9-fluorenylmethoxycarbonyl-modified diphenylalanine (Fmoc-FF) hydrogel for enhancing oxidase- and peroxidase-like activities of Pt NPs and other typical enzyme-like nanomaterials at neutral or even alkaline pH is proposed. In this system, Fmoc-FF hydrogel provides an acidic microenvironment for Pt NPs due to hydrogen protons (H⁺ ) produced by the dissociation of F at neutral pH. As a result, Pt NPs exhibits 6-fold enhanced oxidase-like and 26-fold peroxidase-like activity after being encapsulated into Fmoc-FF hydrogel at pH 7.0. Based on outstanding enzymatic activities and the antibacterial activity of Fmoc-FF hydrogel itself, Pt-Fmoc-FF hydrogel realizes excellent antibacterial effect. This design provides a universal strategy to break pH limitation of nanozymes and promotes the biological applications of nanozymes.

Supramolecular assemblies of histidine-containing peptides with switchable hydrolase and peroxidase activities through Cu(II) binding and co-assembling

Modulating enzyme activities or functionalities is one of the primary features of biological systems, which is, however, a great challenge for artificial enzyme systems. In this work, we designed and synthesized a series of self-assembling peptides from histidine and other amino acids (Asp, Ser, Lys or Arg), which exist in the active site of natural enzymes. These peptides could undergo a conformational transition from random coils to β-sheet structures under physiological conditions and formed self-assembled nanotubes with obvious hydrolase activities. After incorporation of transition metal ions such as Cu²⁺, these peptides could coordinate with Cu²⁺ ions, switch molecular conformations, and self-assemble into hybrid nanomaterials with altered morphologies and peroxidase-like activities. This work illustrates a facile approach for constructing artificial enzymes from self-assembling peptides with histidine residues whose catalytic functions could be modulated by incorporation of Cu²⁺ ions.

DNA-based enzymatic systems and their applications

DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

Supramolecular assembly-enabled homochiral polymerization of short (dA)n oligonucleotides

A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation. We illustrate the power of this approach with short oligomers of deoxyadenosine monophosphate ((dA)_n3'p), n ≥ 3, which form supramolecular assemblies with cyanuric acid. The addition of a condensing agent to these assemblies results in their selective, non-enzymatic polymerization to form long polymers (e.g., (dA)₁₀₀3'p). Significantly, mixtures of D- and L-(dA)₅3'p form homochiral covalent polymers, which demonstrates self-sorting of racemic monomers and covalent bond formation exclusively in homochiral assemblies.

Catalytic amyloids: Is misfolding folding?

Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being 'misfolding' should rather be viewed as 'alternative folding.' Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.

Cross β amyloid assemblies as complex catalytic machinery

How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.

Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications

Bolaamphiphile, which is a class of amphiphilic molecules, has a unique structure of two hydrophilic head groups at the ends of the hydrophobic center. Peptidic bolaamphiphiles that employ peptides or amino acids as their hydrophilic groups exhibit unique biochemical activities when they self-organize into supramolecular structures, which are not observed in a single molecule. The self-assembled peptidic bolaamphiphiles hold considerable promise for imitating proteins with biochemical activities, such as specific affinity toward heterogeneous substances, a catalytic activity similar to a metalloenzyme, physicochemical activity from harmonized amino acid segments, and the capability to encapsulate genes like a viral vector. These diverse activities give rise to large research interest in biomaterials engineering, along with the synthesis and characterization of the assembled structures. This review aims to address the recent progress in the applications of peptidic bolaamphiphile assemblies whose densely packed peptide motifs on their surface and their stacked hydrophobic centers exhibit unique protein-like activity and designer functionality, respectively.