Mapping enzyme activity in living systems by real-time mid-infrared photothermal imaging of nitrile chameleons

Simultaneous spatial mapping of the activity of multiple enzymes in a living system can elucidate their functions in health and disease. However, methods based on monitoring fluorescent substrates are limited. Here, we report the development of nitrile (C≡N)-tagged enzyme activity reporters, named nitrile chameleons, for the peak shift between substrate and product. To image these reporters in real time, we developed a laser-scanning mid-infrared photothermal imaging system capable of imaging the enzymatic substrates and products at a resolution of 300 nm. We show that when combined, these tools can map the activity distribution of different enzymes and measure their relative catalytic efficiency in living systems such as cancer cells, Caenorhabditis elegans, and brain tissues, and can be used to directly visualize caspase-phosphatase interactions during apoptosis. Our method is generally applicable to a broad category of enzymes and will enable new analyses of enzymes in their native context.

Mechanisms and influencing factors of peptide hydrogel formation and biomedicine applications of hydrogels

Self-assembled peptide-based hydrogels have shown great potential in bio-related applications due to their porous structure, strong mechanical stability, high biocompatibility, and easy functionalization. Herein, the structure and characteristics of hydrogels and the mechanism of action of several regular secondary structures during gelation are investigated. The factors influencing the formation of peptide hydrogels, especially the pH responsiveness and salt ion induction are analyzed and summarized. Finally, the biomedical applications of peptide hydrogels, such as bone tissue engineering, cell culture, antigen presentation, antibacterial materials, and drug delivery are reviewed.

Perspectives and trends in advanced optical and electrochemical biosensors based on engineered peptides

With the advancement of life medicine, in vitro diagnostics (IVD) technology has become an auxiliary tool for early diagnosis of diseases. However, biosensors for IVD now face some disadvantages such as poor targeting, significant antifouling properties, low density of recognized molecules, and poor stability. In recent years, peptides have been demonstrated to have various functions in unnatural biological systems, such as targeting properties, antifouling properties, and self-assembly properties, which indicates that peptides can be engineered. These properties of peptides, combined with their good biocompatibility, can be well applied to the design of biosensors to solve the problems mentioned above. This review provides an overview of the properties of engineered functional peptides and their applications in enhancing biosensor performance, mainly in the field of optics and electrochemistry.

Self-Assembly, Bioactivity, and Nanomaterials Applications of Peptide Conjugates with Bulky Aromatic Terminal Groups

The self-assembly and structural and functional properties of peptide conjugates containing bulky terminal aromatic substituents are reviewed with a particular focus on bioactivity. Terminal moieties include Fmoc [fluorenylmethyloxycarbonyl], naphthalene, pyrene, naproxen, diimides of naphthalene or pyrene, and others. These provide a driving force for self-assembly due to π-stacking and hydrophobic interactions, in addition to the hydrogen bonding, electrostatic, and other forces between short peptides. The balance of these interactions leads to a propensity to self-assembly, even for conjugates to single amino acids. The hybrid molecules often form hydrogels built from a network of β-sheet fibrils. The properties of these as biomaterials to support cell culture, or in the development of molecules that can assemble in cells (in response to cellular enzymes, or otherwise) with a range of fascinating bioactivities such as anticancer or antimicrobial activity, are highlighted. In addition, applications of hydrogels as slow-release drug delivery systems and in catalysis and other applications are discussed. The aromatic nature of the substituents also provides a diversity of interesting optoelectronic properties that have been demonstrated in the literature, and an overview of this is also provided. Also discussed are coassembly and enzyme-instructed self-assembly which enable precise tuning and (stimulus-responsive) functionalization of peptide nanostructures.

Supramolecular Hydrogels: Design Strategies and Contemporary Biomedical Applications

Self-assembly of supramolecular hydrogels is driven by dynamic, non-covalent interactions between molecules. Considerable research effort has been exerted to fabricate and optimise supramolecular hydrogels that display shear-thinning, self-healing, and reversibility, in order to develop materials for biomedical applications. This review provides a detailed overview of the chemistry behind the dynamic physicochemical interactions that sustain hydrogel formation (hydrogen bonding, hydrophobic interactions, ionic interactions, metal-ligand coordination, and host-guest interactions). Novel design strategies and methodologies to create supramolecular hydrogels are highlighted, which offer promise for a wide range of applications, specifically drug delivery, wound healing, tissue engineering and 3D bioprinting. To conclude, future prospects are briefly discussed, and consideration given to the steps required to ultimately bring these biomaterials into clinical settings.

Enzyme-Instructed Self-Assembly of Peptides: From Concept to Representative Applications

Enzyme-instructed self-assembly, integrating enzymatic reaction and molecular self-assembly, has drawn noticeable attention over the last decade with the intension of being used in valuable applications. Recent advances in the field allow it possible to spatiotemporally control peptide self-assembly in cellular milieu, broadening the potential applications of peptide assemblies to cancer therapy and subcellular delivery. In this minireview, the concept of enzyme-instructed self-assembly of peptide, containing enzymatic trigger and spatiotemporal control, is described. Representative applications in cells are also discussed, followed by outlook on the field of enzyme-instructed self-assembly.

Enzymatic noncovalent synthesis of peptide assemblies generates multimolecular crowding in cells for biomedical applications

Enzymatic noncovalent synthesis enables the spatiotemporal control of multimolecular crowding in cells, thus offering a unique opportunity for modulating cellular functions. This article introduces some representative enzymes and molecular building blocks for generating peptide assemblies as multimolecular crowding in cells, highlights the relevant biomedical applications, such as anticancer therapy, molecular imaging, trafficking proteins, genetic engineering, artificial intracellular filaments, cell morphogenesis, and antibacterial, and briefly discusses the promises of ENS as a multistep molecular process in biology and medicine.

Simple and Rapid Synthesis of Branched Peptides through Microwave-Assisted On-Bead Ligation

A rapid on-bead convergent method for preparing branched peptides was reported. Linear peptides were prepared on Dbz resin and ligated various branched cores, including lysine dendrons and other dendritic compounds. Alongside microwave irradiation, <1.5 equiv of peptides is sufficient to afford 50-65% yields of pure branched peptides without chromatographic purification. Remarkably, the desired compounds were prepared within hours.

Enzyme-instructed supramolecular assemblies promote intracellular boron accumulation for boron neutron capture therapy

Selective accumulation of boron agents in cancer cells is of critical importance for BNCT. Here we involve enzyme-instructed supramolecular assembly (EISA) to facilitate the accumulation of a typical boron agent borylphenylalanine (BPA) in cancer cells. By covalently conjugating BPA to the phosphorylated assembly precursor, the boron-bearing precursors undergo phosphatase-catalyzed dephosphorylation to yield assembly molecules, which then self-assemble to form nanomaterials. Due to the up-regulated phosphatase activity of cancer cells, kinetic preference allows the EISA to accumulate boron in HeLa cells selectively. Interestingly, by attaching BPA on the backbone or side-chain of precursor, the boron-bearing isomers show different assembly propensity with time-dependent morphology change, which leads to the differentiated accumulation of boron inside cells. Overall, the optimized boron-bearing assembly precursor could significantly improve the boron accumulation compared with BPA in cancer cells. In this study, we have demonstrated a convenient method to introduce boron agents to cancer cells. We envision that the EISA-mediated accumulation of boron will be helpful in the design of boron agents to facilitate BNCT treatment.

Structurally Dynamic Hydrogels for Biomedical Applications: Pursuing a Fine Balance between Macroscopic Stability and Microscopic Dynamics

Owing to their unique chemical and physical properties, hydrogels are attracting increasing attention in both basic and translational biomedical studies. Although the classical hydrogels with static networks have been widely reported for decades, a growing number of recent studies have shown that structurally dynamic hydrogels can better mimic the dynamics and functions of natural extracellular matrix (ECM) in soft tissues. These synthetic materials with defined compositions can recapitulate key chemical and biophysical properties of living tissues, providing an important means to understanding the mechanisms by which cells sense and remodel their surrounding microenvironments. This review begins with the overall expectation and design principles of dynamic hydrogels. We then highlight recent progress in the fabrication strategies of dynamic hydrogels including both degradation-dependent and degradation-independent approaches, followed by their unique properties and use in biomedical applications such as regenerative medicine, drug delivery, and 3D culture. Finally, challenges and emerging trends in the development and application of dynamic hydrogels are discussed.

(Macro)molecular self-assembly for hydrogel drug delivery

Hydrogels prepared via self-assembly offer scalable and tunable platforms for drug delivery applications. Molecular-scale self-assembly leverages an interplay of attractive and repulsive forces; drugs and other active molecules can be incorporated into such materials by partitioning in hydrophobic domains, affinity-mediated binding, or covalent integration. Peptides have been widely used as building blocks for self-assembly due to facile synthesis, ease of modification with bioactive molecules, and precise molecular-scale control over material properties through tunable interactions. Additional opportunities are manifest in stimuli-responsive self-assembly for more precise drug action. Hydrogels can likewise be fabricated from macromolecular self-assembly, with both synthetic polymers and biopolymers used to prepare materials with controlled mechanical properties and tunable drug release. These include clinical approaches for solubilization and delivery of hydrophobic drugs. To further enhance mechanical properties of hydrogels prepared through self-assembly, recent work has integrated self-assembly motifs with polymeric networks. For example, double-network hydrogels capture the beneficial properties of both self-assembled and covalent networks. The expanding ability to fabricate complex and precise materials, coupled with an improved understanding of biology, will lead to new classes of hydrogels specifically tailored for drug delivery applications.

Pathological environment directed in situ peptidic supramolecular assemblies for nanomedicines

Peptidic self-assembly provides a powerful method to build biomedical materials with integrated functions. In particular, pathological environment instructed peptidic supramolecular have gained great progress in treating various diseases. Typically, certain pathology related factors convert hydrophilic precursors to corresponding more hydrophobic motifs to assemble into supramolecular structures. Herein, we would like to review the recent progress of nanomedicines based on the development of instructed self-assembly against several specific disease models. Firstly we introduce the cancer instructed self-assembly. These assemblies have exhibited great inhibition efficacy, as well as enhanced imaging contrast, against cancer models both in vitro and in vivo. Then we discuss the infection instructed peptidic self-assembly. A number of different molecular designs have demonstrated the potential antibacterial application with satisfied efficiency for peptidic supramolecular assemblies. Further, we discuss the application of instructed peptidic self-assembly for other diseases including neurodegenerative disease and vaccine. The assemblies have succeeded in down-regulating abnormal Aβ aggregates and immunotherapy. In summary, the self-assembly precursors are typical two-component molecules with (1) a self-assembling motif and (2) a cleavable trigger responsive to the pathological environment. Upon cleavage, the self-assembly occurs selectively in pathological loci whose targeting capability is independent from active targeting. Bearing the novel targeting regime, we envision that the pathological conditions instructed peptidic self-assembly will lead a paradigm shift on biomedical materials.

Enzymatic Noncovalent Synthesis for Mitochondrial Genetic Engineering of Cancer Cells

Since mitochondria contribute to tumorigenesis and drug resistance in cancer, mitochondrial genetic engineering promises a new direction for cancer therapy. Here, we report the use of the perimitochondrial enzymatic noncovalent synthesis (ENS) of peptides for delivering genes selectively into the mitochondria of cancer cells for mitochondrial genetic engineering. Specifically, the micelles of peptides bind to the voltage-dependent anion channel (VDAC) on mitochondria for the proteolysis by enterokinase (ENTK), generating perimitochondrial nanofibers in cancer cells. This process, facilitating selective delivery of nucleic acid or gene vectors into mitochondria of cancer cells, enables the mitochondrial transgene expression of CRISPR/Cas9, FUNDC1, p53, and fluorescent proteins. Mechanistic investigation indicates that the interaction of the peptide assemblies with the VDAC and mitochondrial membrane potential are necessary for mitochondria targeting. This local enzymatic control of intermolecular noncovalent interactions enables selective mitochondrial genetic engineering, thus providing a strategy for targeting cancer cells.

The ratio of hydrogelator to precursor controls the enzymatic hydrogelation of a branched peptide

Here, we report an apparently counterintuitive observation, in which a lower volume fraction of a branched peptide forms a stronger hydrogel after an enterokinase (ENTK) cleaves off the branch from the peptide. By varying the ratios of the branched peptide and ENTK and analysing the ratio of hydrogelator to precursor (H/P) in the enzymatic proteolysis reaction, our study shows that the H/P ratio controls the critical strain of the hydrogel formed, through enzymatic cleavage of the branch from the peptide. This work demonstrates that emergent properties (e.g., hydrogelation) of peptide assemblies, resulting from enzymatic noncovalent synthesis (ENS), are context-dependent, while also providing insights for developing dynamic soft materials via ENS.

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

Here, we report the use of an enzymatic reaction to cleave the branch off branched peptides for inducing the morphological transition of the assemblies of the peptides. The attachment of DEDDDLLI sequences to the ε-amine of the lysine residue of a tetrapeptide produces branched peptides that form micelles. Upon the proteolytic cleavage of the branch, catalyzed by proteinase K, the micelles turn into nanofibers. We also found that the acetylation of the N-terminal of the branch increased the stability of the branched peptides. Moreover, these branched peptides facilitate the delivery of the proteins into cells. This work contributes insights for the development of peptide supramolecular assemblies via enzymatic noncovalent synthesis in cellular environment.

Biomaterials based on noncovalent interactions of small molecules

Unlike conventional materials that covalent bonds connecting atoms as the major force to hold the materials together, supramolecular biomaterials rely on noncovalent intermolecular interactions to assemble. The reversibility and biocompatibility of supramolecular biomaterials render them with diverse range of functions and lead to rapid development in the past two decades. This review focuses on the noncovalent and enzymatic control of supramolecular biomaterials, with the introduction to various triggering mechanism to initiate self-assembly. Representative applications of supramolecular biomaterials are highlighted in four categories: tissue engineering, cancer therapy, drug delivery, and molecular imaging. By introducing various applications, we intend to show enzymatic control and noncovalent interactions as a powerful tool for achieving spatiotemporal control of biomaterials both invitro and in vivo for biomedicine.

Enzymatic Noncovalent Synthesis

Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.

Enzyme-Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells

Presently, little is known of how the inter-organelle crosstalk impacts cancer cells owing to the lack of approaches that can manipulate inter-organelle communication in cancer cells. We found that a negatively charged, enzyme cleavable peptide (MitoFlag) enables the trafficking of histone protein H2B, a nuclear protein, to the mitochondria in cancer cells. MitoFlag interacts with the nuclear location sequence of H2B to block it from entering the nucleus. A protease on the mitochondria cleaves the Flag from the MitoFlag/H2B complex to form assemblies that retain H2B on the mitochondria and facilitate H2B entering the mitochondria. Adding NLS, replacing aspartic acid by glutamic acid residues, or changing the l- to d-aspartic acid residue on MitoFlag abolishes the trafficking of H2B into mitochondria of HeLa cells. As the first example of the enzyme-instructed self-assembly of a synthetic peptide for trafficking endogenous proteins, this work provides insights for understanding and manipulating inter-organelle communication in cells.

Enzyme-Instructed Self-Assembly for Cancer Therapy and Imaging

Enzymatic reactions and self-assembly are two fundamental attributes of cells. It is not surprising that one can use enzyme-instructed self-assembly (EISA)-the integration of enzymatic transformation and molecular self-assembly-to modulate the emergent properties of supramolecular assemblies for controlling cell behaviors. The exploration of EISA for developing cancer therapy and imaging has made considerable progress over the last five years. In this Topical Review, we discuss these exciting results and the future promise of EISA. After describing several key studies to illustrate the progress of EISA in developing cancer therapy, we discuss the use of EISA for molecular imaging. Then, we give the outlook of EISA for developing supramolecular anticancer medicine that inhibits multiple hallmark capabilities of cancer.

Enzymatic Noncovalent Synthesis of Supramolecular Soft Matter for Biomedical Applications

Enzymatic noncovalent synthesis (ENS), a process that integrates enzymatic reactions and supramolecular (i.e., noncovalent) interactions for spatial organization of higher-order molecular assemblies, represents an emerging research area at the interface of physical and biological sciences. This review provides a few representative examples of ENS in the context of supramolecular soft matter. After a brief comparison of enzymatic covalent and noncovalent synthesis, we discuss ENS of man-made molecules for generating supramolecular nanostructures (e.g., supramolecular hydrogels) in cell-free conditions. Then, we introduce ENS in a cellular environment. To illustrate the unique merits for applications, we discuss intercellular, peri- or intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and targeted delivery. Finally, we provide an outlook on the potential of ENS. We hope that this review offers a new perspective for scientists who develop supramolecular soft matter to address societal needs at various frontiers.

Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π⁻π stacking, DNA base pairing, and ligand⁻receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

Enzymatic hydrolysis-induced degradation of a lactose-coupled supramolecular hydrogel

Amphiphilic urea 1 with a hydrophilic lactose group was prepared as a low-molecular-weight hydrogelator, which formed a transparent supramolecular hydrogel. Enzymatic hydrolysis of the lactose moiety using β-galactosidase allowed a gel-to-sol phase transition of the supramolecular hydrogel. A β-galactosidase inhibitor enables us to control the time course of this phase transition.

Instructed-Assembly (iA): A Molecular Process for Controlling Cell Fate

Instructed-assembly (iAssembly or iA) refers to the formation of ordered superstructures of molecules as the consequence of at least one trigger event (e.g., a reaction or a ligand-receptor interaction). As a biomimetic process that transforms from an equilibrium to another equilibrium, iA has emerging as a powerful approach to provide spatiotemporal control for a range of potential biomedical applications, including molecular imaging, cancer therapy, and tissue engineering. This account introduces the general concept of iA in the context of cells and illustrates how to achieve iA for applications. By mainly describing the representative examples of iA and its applications in complex environment, such as cells or animals, and providing the perspectives of the future development of iA, we intend to show that, as a process that bridges self-assembly and self-organization, iA offers chemists a facile mean to explore the emergent properties of molecular assemblies and the dynamics of molecular processes to control cell fate. Particularly, iA promises many wonderful surprises and useful applications in physical and/or life sciences when multiple processes (e.g., self-assembly, instructed-assembly, and self-organization) are taking place simultaneously.

Enzymatic Cleavage of Branched Peptides for Targeting Mitochondria

Most of the reported mitochondria-targeting molecules are lipophilic and cationic, and thus they may become cytotoxic with accumulation. Here we show enzymatic cleavage of branched peptides that carry negative charges for targeting mitochondria. Conjugating a well-established protein tag (i.e., FLAG-tag) to self-assembling motifs affords the precursors that form micelles. Enzymatic cleavage of the hydrophilic FLAG motif (DDDDK) by enterokinase (ENTK) turns the micelles to nanofibers. After being taken up by cells, the micelles, upon the action of intracellular ENTK, turn into nanofibers to locate mainly at mitochondria. The micelles of the precursors are able to deliver cargos (either small molecules or proteins) into cells, largely to mitochondria and within 2 h. Preventing ENTK proteolysis diminishes mitochondria targeting. As the first report of using enzymatic self-assembly for targeting mitochondria and delivery cargos to mitochondria, this work illustrates a fundamentally new way to target subcellular organelles for biomedicine.