Bioinspired assembly of small molecules in cell milieu

Fluorescent Nanocable as a Biomedical Tool: Intracellular Self-Assembly Formed by a Natural Product Interconnects and Synchronizes Mitochondria

Self-assembly processes commonly occur in various biological contexts to form functional biological structures. However, the self-assembly of nanofibers within cells by heterologous molecules showing a biological function is rare. In this work, we reported the intracellular formation of fluorescent nanofibers by a natural small molecule, lycobetaine (LBT), which facilitated the direct physical connection between mitochondria and synchronized their membrane potential oscillations. The luminescent properties of LBT enabled the real-time observation of nanofiber formation, while the semiconductive nature of the LBT nanofiber facilitated electrical signal transduction among the connected mitochondria. This study introduces an approach to modulate mitochondrial connectivity within cells using "nano-cables" which facilitate studies on synchronized mitochondrial operations and the underlying mechanisms of drug action.

Enzyme-Responsive Supramolecular Self-Assembly in Small Amphiphiles

Enzyme-responsive molecular assemblies have recently made remarkable progress, owing to their widespread applications. As a class of catalysts with high specificity and efficiency, enzymes play a critical role in producing new molecules and maintaining metabolic stability in living organisms. Therefore, the study of enzyme-responsive assembly aids in understanding the origin of life and the physiological processes occurring within living bodies, contributing to further advancements across various disciplines. In this Review, we summarize three kinds of enzyme-responsive assembly systems in amphiphiles: enzyme-triggered assembly, disassembly, and structural transformation. Furthermore, motivated by the fact that biological macromolecules and complex structures all originated with small molecules, our focus lies on the small amphiphiles (e.g., peptides, surfactants, fluorescent molecules, and drug molecules). We also provide an outlook on the potential of enzyme-responsive assembly systems for biomimetic development and hope this Review will attract more attention to this emerging research branch at the intersection of assembly chemistry and biological science.

Enzymatic Dissociation of DNA-Histone Condensates in an Electrophoretic Setting: Modulating DNA Patterning and Hydrogel Viscoelasticity

Development of an energy-driven self-assembly process is a matter of interest for understanding and mimicking diverse ranges of biological and environmental patterns in a synthetic system. In this article, first we demonstrate transient and temporally controlled self-assembly of a DNA-histone condensate where trypsin (already present in the system) hydrolyzes histone, resulting in disassembly. Upon performing this dynamic self-assembly process in a gel matrix under an electric field, we observe diverse kinds of DNA patterning across the gel matrix depending on the amount of trypsin, incubation time of the reaction mixture, and gel porosity. Notably, here, the micrometer-sized DNA-histone condensate does not move through the gel and only free DNA can pass; therefore, transport and accumulation of DNA at different zones depend on the release rate of DNA by trypsin. Furthermore, we show that the viscoelasticity of the native gel increases in the presence of DNA and a pattern over gel viscoelasticity at different zones can be achieved by tuning the amount of enzyme, i.e., the dissociation rate of the DNA-histone condensate. We believe enabling spatiotemporally controlled DNA patterning by applying an electric field will be potentially important in designing different kinds of spatiotemporally distinct dynamic materials.

Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation

Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.

Bioinspired Supramolecular Hydrogel from Design to Applications

Nature offers a wealth of opportunities to solve scientific and technological issues based on its unique structures and function. The dynamic non-covalent interaction is considered to be the main base of living functions of creatures including humans, animals, and plants. Supramolecular hydrogels formed by non-covalent bonding interactions has become a unique platform for constructing promising materials for medicine, energy, electronic, and biological substitute. In this review, the self-assemble principle of supramolecular hydrogels is summarized. Next, the stimulation of external environment that triggers the assembly or disassembly of supramolecular hydrogels are recapitulated, including temperature, mechanics, light, pH, ions, etc. The main applications of bioinspired supramolecular hydrogels in terms of bionic objects including humans, animals, and plants are also described. Although so many efforts are done for revealing the synergized mechanism of the function and non-covalent interactions on the supramolecular hydrogel, the complexity and variability between stimulus and non-covalent bonding in the supramolecular system still require impeccable theories. As an outlook, the bioinspired supramolecular hydrogel is just beginning to exhibit its great potential in human life, offering significant opportunities in drug delivery and screening, implantable devices and substitutions, tissue engineering, micro-fluidic devices, and biosensors.

Biosystem-Inspired Engineering of Nanozymes for Biomedical Applications

Nanozymes with intrinsic enzyme-mimicking activities have shown great potential to become surrogates of natural enzymes in many fields by virtue of their advantages of high catalytic stability, ease of functionalization, and low cost. However, due to the lack of predictable descriptors, most of the nanozymes reported in the past have been obtained mainly through trial-and-error strategies, and the catalytic efficacy, substrate specificity, as well as practical application effect under physiological conditions, are far inferior to that of natural enzymes. To optimize the catalytic efficacies and functions of nanozymes in biomedical settings, recent studies have introduced biosystem-inspired strategies into nanozyme design. In this review, recent advances in the engineering of biosystem-inspired nanozymes by leveraging the refined catalytic structure of natural enzymes, simulating the behavior changes of natural enzymes in the catalytic process, and mimicking the specific biological processes or living organisms, are introduced. Furthermore, the currently involved biomedical applications of biosystem-inspired nanozymes are summarized. More importantly, the current opportunities and challenges of the design and application of biosystem-inspired nanozymes are discussed. It is hoped that the studies of nanozymes based on bioinspired strategies will be beneficial for constructing the new generation of nanozymes and broadening their biomedical applications.

Nanofibers in Organelles: From Structure Design to Biomedical Applications

Nanofibers are one of the most important morphologies of molecular self-assemblies, the formation of which relies on the diverse intermolecular interactions of fibrous-forming units. In the past decade, rapid advances have been made in the biomedical application of nanofibers, such as bioimaging and tumor treatment. An important topic to be focused on is not only the nanofiber formation mechanism but also where it forms, because different destinations could have different influences on cells and its formation could be triggered by unique stimuli in organelles. It is therefore necessary and timely to summarize the nanofibers assembled in organelles. This minireview discusses the formation mechanism, triggering strategies, and biomedical applications of nanofibers, which may facilitate the rational design of nanofibers, improve our understanding of the relationship between nanofiber properties and organelle characteristics, allow a comprehensive recognition of organelles affected by materials, and enhance the therapeutic efficiency of nanofibers.

Bioinspired Amino Acid Based Materials in Bionanotechnology: From Minimalistic Building Blocks and Assembly Mechanism to Applications

Inspired by natural hierarchical self-assembly of proteins and peptides, amino acids, as the basic building units, have been shown to self-assemble to form highly ordered structures through supramolecular interactions. The fabrication of functional biomaterials comprised of extremely simple biomolecules has gained increasing interest due to the advantages of biocompatibility, easy functionalization, and structural modularity. In particular, amino acid based assemblies have shown attractive physical characteristics for various bionanotechnology applications. Herein, we propose a review paper to summarize the design strategies as well as research advances of amino acid based supramolecular assemblies as smart functional materials. We first briefly introduce bioinspired reductionist design strategies and assembly mechanism for amino acid based molecular assembly materials through noncovalent interactions in condensed states, including self-assembly, metal ion mediated coordination assembly, and coassembly. In the following part, we provide an overview of the properties and functions of amino acid based materials toward applications in nanotechnology and biomedicine. Finally, we give an overview of the remaining challenges and future perspectives on the fabrication of amino acid based supramolecular biomaterials with desired properties. We believe that this review will promote the prosperous development of innovative bioinspired functional materials formed by minimalistic building blocks.

Therapeutic Supramolecular Polymers: Designs and Applications

The self-assembly of low-molecular-weight building motifs into supramolecular polymers has unlocked a new realm of materials with distinct properties and tremendous potential for advancing medical practices. Leveraging the reversible and dynamic nature of non-covalent interactions, these supramolecular polymers exhibit inherent responsiveness to their microenvironment, physiological cues, and biomolecular signals, making them uniquely suited for diverse biomedical applications. In this review, we intend to explore the principles of design, synthesis methodologies, and strategic developments that underlie the creation of supramolecular polymers as carriers for therapeutics, contributing to the treatment and prevention of a spectrum of human diseases. We delve into the principles underlying monomer design, emphasizing the pivotal role of non-covalent interactions, directionality, and reversibility. Moreover, we explore the intricate balance between thermodynamics and kinetics in supramolecular polymerization, illuminating strategies for achieving controlled sizes and distributions. Categorically, we examine their exciting biomedical applications: individual polymers as discrete carriers for therapeutics, delving into their interactions with cells, and in vivo dynamics; and supramolecular polymeric hydrogels as injectable depots, with a focus on their roles in cancer immunotherapy, sustained drug release, and regenerative medicine. As the field continues to burgeon, harnessing the unique attributes of therapeutic supramolecular polymers holds the promise of transformative impacts across the biomedical landscape.

Controlling Supramolecular Fiber Formation of Nucleopeptide by Guanosine Triphosphate

Cells use dynamic self-assembly to construct functional structures for maintaining cellular homeostasis. However, using a natural biological small molecule to mimic this phenomenon remains challenging. This work reports the dynamic microfiber formation of nucleopeptide driven by guanosine triphosphate, the small molecule that controls microtubule polymerization in living cells. Deactivation of GTP by enzyme dissociates the fibers, which could be reactivated by adding GTP. Molecular dynamic simulation unveils the mystery of microfiber formation of GBM-1 and GTP. Moreover, the microfiber formation can also be controlled by diffusion-driven GTP gradients across a semipermeable membrane in bulk conditions and the microfluidic method in the defined droplets. This study provides a new platform to construct dynamic self-assembly materials of molecular building blocks driven by GTP.

Supramolecular nanofiber of indomethacin derivative confers highly cyclooxygenase-2 (COX-2) selectivity and boosts anti-inflammatory efficacy

Herein, we report a facile method for converting carboxylate-containing indomethacin (Idm) into a cyclooxygenase-2 (COX-2) selective inhibitor via the amidation of an unnatural peptide sequence (Nal-Nal-Asp). The resulting indomethacin amides (i.e., Idm-Nal-Nal-Asp) have high selectivity for COX-2, and can self-assemble into a one-component supramolecular hydrogel that acts as a 'self-delivery' system for boosting anti-inflammatory efficacy. Self-assembled Idm-Nal-Nal-Asp hydrogel robustly inhibits COX-2 expression in lipopolysaccharide (LPS)-activated Raw 264.7 macrophages while also exhibits superior anti-inflammatory and antioxidant activities via reactive oxygen species (ROS)-related NF-κB and Nrf2/HO-1 pathways. Moreover, a rabbit model of endotoxin-induced uveitis (EIU) reveals that the Idm-Nal-Nal-Asp hydrogel outperforms clinically used 0.1 wt% diclofenac sodium eye drops in terms of in vivo anti-inflammatory efficacy via topical instillation route. As a rational approach to designing and applying COX-2 selective inhibitors, this work presents a simple method for converting non-selective nonsteriodal anti-inflammatory drugs (NSAIDs) into highly selective COX-2 inhibitors that can self-assemble into supramolecular hydrogel for anti-inflammation applications.

Self-Assembled Homopolymeric Spherulites from Small Molecules in Solution

Polymeric spherulites are typically formed by melt crystallization: spherulitic growth in solution is rare and requires complex polymers and dilute solutions. Here, we report the mild and unique formation of luminescent spherulites at room temperature via the simple molecule benzene-1,4-dithiol (BDT). Specifically, BDT polymerized into oligomers (PBDT) via disulfide bonds and assembled into uniform supramolecular nanoparticles in aqueous buffer; these nanoparticles were then dissolved back into PBDT in a good solvent (i.e., dimethylformamide) and underwent chain elongation to form spherulites (rPBDT) in 10 min. The spherulite geometry was modulated by changing the PBDT concentration and reaction time. Due to the step-growth polymerization and reorganization of PBDT, these spherulites not only exhibited robust structure but also showed broad clusterization-triggered emission. The biocompatibility and efficient cellular uptake of the spherulites further underscore their value as traceable drug carriers. This system provides a new pathway for designing versatile superstructures with value for hierarchical assembly of small molecules into a complicated biological system.

Synthesizing biomaterials in living organisms

Living organisms fabricate biomacromolecules such as DNA, RNA, and proteins by the self-assembly process. The research on the mechanism of biomacromolecule formation also inspires the exploration of in vivo synthesized biomaterials. By elaborate design, artificial building blocks or precursors can self-assemble or polymerize into functional biomaterials within living organisms. In recent decades, these so-called in vivo synthesized biomaterials have achieved extensive applications in cell-fate manipulation, disease theranostics, bioanalysis, cellular surface engineering, and tissue regeneration. In this review, we classify strategies for in vivo synthesis into non-covalent, covalent, and genetic types. The development of these approaches is based on the chemical principles of supramolecular chemistry and synthetic chemistry, biological cues such as enzymes and microenvironments, and the means of synthetic biology. By summarizing the design principles in detail, some insights into the challenges and opportunities in this field are provided to  enlighten further research.

Telomerase-Mediated Self-Assembly of DNA Network in Cancer Cells Enabling Mitochondrial Interference

The precise control of the artificially induced reactions inside living cells is emerging as an effective strategy for the regulation of cell functions. Nevertheless, the manipulation of the assembly of exogenous molecules into artificial architectures in response to intracellular-specific signals remains a grand challenge. Herein, we achieve the precise self-assembly of deoxyribonucleic acid (DNA) network inside cancer cells, specifically responding to telomerase, and realize effective mitochondrial interference and the consequent regulation of cellular behaviors. Two functional DNA modules were designed: a mitochondria-targeting branched DNA and a telomerase-responsive linear DNA. Upon uptake by cancer cells, the telomerase primer in linear DNA responded to telomerase, and a strand displacement reaction was triggered by the reverse transcription of telomerase, thus releasing a linker DNA from the linear DNA. The linker DNA afterward hybridized with the branched DNA to form a DNA network on mitochondria. The DNA network interfered with the function of mitochondria, realizing the apoptosis of cancer cells. This system was further administered in a nude mouse tumor model, showing remarkable suppression of tumor growth. We envision that the telomerase-mediated intracellular self-assembly of the DNA network provides a promising route for cancer therapy.

Insight on the Intracellular Supramolecular Assembly of DTTO: A Peculiar Example of Cell-Driven Polymorphism

The assembly of supramolecular structures within living systems is an innovative approach for introducing artificial constructs and developing biomaterials capable of influencing and/or regulating the biological responses of living organisms. By integrating chemical, photophysical, morphological, and structural characterizations, it is shown that the cell-driven assembly of 2,6-diphenyl-3,5-dimethyl-dithieno[3,2-b:2',3'-d]thiophene-4,4-dioxide (DTTO) molecules into fibers results in the formation of a "biologically assisted" polymorphic form, hence the term bio-polymorph. Indeed, X-ray diffraction reveals that cell-grown DTTO fibers present a unique molecular packing leading to specific morphological, optical, and electrical properties. Monitoring the process of fiber formation in cells with time-resolved photoluminescence, it is established that cellular machinery is necessary for fiber production and a non-classical nucleation mechanism for their growth is postulated. These biomaterials may have disruptive applications in the stimulation and sense of living cells, but more crucially, the study of their genesis and properties broadens the understanding of life beyond the native components of cells.

Formation of Highly Emissive Anthracene Excimers for Aggregation-Induced Emission/Self-Assembly Directed (Bio)imaging

AIEgens have emerged as a promising alternative to molecular rotors in bioimaging applications. However, transferring the concept of aggregation-induced emission (AIE) from solution to living systems remains a challenge. Given the highly heterogeneous nature and the compartmentalization of the cell, different approaches are needed to control the self-assembly within the crowded intricate cellular environment. Herein, we report for the first time the self-assembly mechanism of an anthracene-guanidine derivative (AG) forming the rare and highly emissive T-shaped dimer in breast cancer cell lines as a proof of concept. This process is highly sensitive to the local environment in terms of polarity, viscosity, and/or water quantity that should enable the use of the AG as a fluorescence lifetime imaging biosensor for intracellular imaging of cellular structures and the monitoring of intracellular state parameters. Different populations of the monomer and T-shaped and π-π dimers were observed in the cell membrane, cytoplasm, and nucleoplasm, related to the local viscosity and presence of water. The T-shaped dimer is formed preferentially in the nucleus because of the higher density and viscosity compared to the cytoplasm. The present results should serve as a precursor for the development of new design strategies for molecular systems for a wide range of applications such as cell viscosity, density, or temperature sensing and imaging.

Recent progress in the development of small-molecule double-locked logic gate fluorescence probes

Various bioactive substances are simultaneously involved in physiological processes, and research on the synergistic effect of them can promote the study of pathological mechanisms. To achieve this purpose, several small-molecule double-locked logic gate fluorescence probes have been developed recently. They overcome many shortcomings of the traditional "single-signal" fluorescent probes, with fluorescence that can be activated by two analytes of interest order-independently or order-dependently with one output. In this review, we summarize recently published small-molecule double-locked logic gate probes for the optical detection of two bioactive substances in living systems. We envision that this review will attract significant attention from researchers to exploit more powerful functional double-locked logic gate probes.

Orderly Self-Assembly of Organic Fluorophores for Sensing and Imaging

Fluorescence imaging utilizing traditional organic fluorophores is extensively applied in both cellular and in vivo studies. However, it faces significant obstacles, such as low signal-to-background ratio (SBR) and spurious positive/negative signals, primarily due to the facile diffusion of these fluorophores. To cope with this challenge, orderly self-assembled functionalized organic fluorophores have gained significant attention in the past decades. These fluorophores can create nanoaggregates via a well-ordered self-assembly process, thus prolonging their residency time within cells and in vivo settings. The development of self-assembled-based fluorophores is an emerging field, and as such, in this review, we present a summary of the progress and challenges of self-assembly fluorophores, focusing on their development history, self-assembly mechanisms, and biomedical applications. We hope that the insights provided herein will assist scientists in further developing functionalized organic fluorophores for in situ imaging, sensing, and therapy.

Cyclic Macroscopic Assembly and Disassembly Driven by Ionic Strength Fuel: A Waste-Free Approach

Nonequilibrium assembling systems developed so far have relied on chemical fuels to drive the programmable pH cycles, redox reactions, and metastable bond formations. However, these methods often result in the unwanted accumulation of chemical waste. Herein, we present a novel strategy for achieving cyclic and waste-free nonequilibrium assembly and disassembly of macroscopic hydrogels, utilizing an ionic strength-mediated approach. Our strategy involves using ammonium carbonate as a chemical fuel to temporally regulate the attractions between oppositely charged hydrogels via ionic strength-controlled charge screening and hydrogel elasticity changes. This chemical fuel effectively mediates the assembly/disassembly processes and prevents waste accumulation, as ammonium carbonate can completely decompose into volatile chemical waste. The cyclic and reversible assembly process can be achieved without significant damping due to the self-clearance mechanism, as long as the chemical fuel is repeatedly supplied. This concept holds promise for creating macroscopic and microscopic nonequilibrium systems and self-adaptive materials.

Manipulating the Piezoelectric Response of Amino Acid-Based Assemblies by Supramolecular Engineering

Variation in the molecular architecture significantly affects the electronic and supramolecular structure of biomolecular assemblies, leading to dramatically altered piezoelectric response. However, relationship between molecular building block chemistry, crystal packing and quantitative electromechanical response is still not fully understood. Herein, we systematically explored the possibility to amplify the piezoelectricity of amino acid-based assemblies by supramolecular engineering. We show that a simple change of side-chain in acetylated amino acids leads to increased polarization of the supramolecular arrangements, resulting in significant enhancement of their piezoelectric response. Moreover, compared to most of the natural amino acid assemblies, chemical modification of acetylation increased the maximum piezoelectric tensors. The predicted maximal piezoelectric strain tensor and voltage constant of acetylated tryptophan (L-AcW) assemblies reach 47 pm V^-1 and 1719 mV m/N, respectively, comparable to commonly used inorganic materials such as bismuth triborate crystals. We further fabricated an L-AcW crystal-based piezoelectric power nanogenerator that produces a high and stable open-circuit voltage of over 1.4 V under mechanical pressure. For the first time, the illumination of a light-emitting diode (LED) is demonstrated by the power output of an amino acid-based piezoelectric nanogenerator. This work presents the supramolecular engineering toward the systematic modulation of piezoelectric response in amino acid-based assemblies, facilitating the development of high-performance functional biomaterials from simple, readily available, and easily tailored building blocks.

Enzyme-Activatable Polypeptide for Plasma Membrane Disruption and Antitumor Immunity Elicitation

Enzyme-instructed self-assembly of bioactive molecules into nanobundles inside cells is conceived to potentially disrupt plasma membrane and subcellular structure. Herein, an alkaline phosphatase (ALP)-activatable hybrid of ICG-CF₄ KY^p is facilely synthesized by conjugating photosensitizer indocyanine green (ICG) with CF₄ KY^p peptide via classical Michael addition reaction. ALP-induced dephosphorylation of ICG-CF₄ KY^p enables its transformation from small-molecule precursor into rigid nanofibrils, and such fibrillation in situ causes severe mechanical disruption of cytomembrane. Besides, ICG-mediated photosensitization causes additional oxidative damage of plasma membrane by lipid peroxidation. Hollow MnO₂ nanospheres devote to deliver ICG-CF₄ KY^p into tumorous tissue through tumor-specific acidity/glutathione-triggered degradation of MnO₂ , which is monitored by fluorescent probing and magnetic resonance imaging. The burst release of damage-associated molecular patterns and other tumor antigens during therapy effectively triggers immunogenetic cell death and improves immune stimulatory, as demonstrated by the promotion of dendritic cell maturation and CD8⁺ lymphocyte infiltration, as well as constraint of regulatory T cell population. Taken together, such cytomembrane injury strategy based on peptide fibrillation in situ holds high clinical promise for lesion-specific elimination of primary, abscopal, and metastatic tumors, which may enlighten more bioinspired nanoplatforms for anticancer theranostics.

Targeted Enzyme Activity Imaging with Quantitative Phase Microscopy

Quantitative phase imaging (QPI) is a powerful optical imaging modality for label-free, rapid, and three-dimensional (3D) monitoring of cells and tissues. However, molecular imaging of important intracellular biomolecules such as enzymes remains a largely unexplored area for QPI. Herein, we introduce a fundamentally new approach by designing QPI contrast agents that allow sensitive detection of intracellular biomolecules. We report a new class of bio-orthogonal QPI-nanoprobes for in situ high-contrast refractive index (RI) imaging of enzyme activity. The nanoprobes feature silica nanoparticles (SiO2 NPs) having higher RI than endogenous cellular components and surface-anchored cyanobenzothiazole-cysteine (CBT-Cys) conjugated enzyme-responsive peptide sequences. The nanoprobes specifically aggregated in cells with target enzyme activity, increasing intracellular RI and enabling precise visualization of intracellular enzyme activity. We envision that this general design of QPI-nanoprobes could open doors for spatial-temporal mapping of enzyme activity with direct implications for disease diagnosis and evaluating the therapeutic efficacy.

DNA-guided self-assembly in living cells

Self-assembly processes exist widely in life systems and play essential roles in maintaining life activities. It is promising to explore the molecular fundamentals and mechanisms of life systems through artificially constructing self-assembly systems in living cells. As an excellent self-assembly construction material, deoxyribonucleic acid (DNA) has been widely used to achieve the precise construction of self-assembly systems in living cells. This review focuses on the recent progress of DNA-guided intracellular self-assembly. First, the methods of intracellular DNA self-assembly based on the conformational transition of DNA are summarized, including complementary base pairing, the formation of G-quadruplex/i-motif, and the specific recognition of DNA aptamer. Next, The applications of DNA-guided intracellular self-assembly on the detection of intracellular biomolecules and the regulation of cell behaviors are introduced, and the molecular design of DNA in the self-assembly systems is discussed in detail. Ultimately, the challenges and opportunities of DNA-guided intracellular self-assembly are commented.

Rethreading Design of Ratiometric roGFP2 Mimetic Peptide for Hydrogen Peroxide Sensing

Reconstruction of the miniaturized peptide to mimic the tailored functions of protein has been attractive but challenging. Herein, initialized from the crystal structure of redox-sensitive green fluorescent protein-2 (roGFP2), we propose a practical approach to construct the roGFP2 mimetic peptide by rethreading the aromatic residues adjacent to the chromophore fragment. By fine-tuning the residues of peptides, a mini tetrapeptide (Cys-Phe-Phe-His) was designed, which can act as a hydrogen peroxide sensor using its ratiometric fluorescence. The roGFP2 mimetic tetrapeptide is biocompatible and photostable and has competitive fluorescent properties with roGFP2 by the virtue of its assembly induced emissions. We expand the ratiometric tetrapeptide for sensing hydrogen peroxide in acidic chambers. The results provide a promising approach for the artificial design of miniaturized peptides with the desired function.

Quantitative Ratiometric Biosensors Based on Fluorescent Ferrocene-Modified Histidine Dipeptide Nanoassemblies

Fluorescent proteins (FPs) provide a ratiometric readout for quantitative assessment of the destination of internalized biomolecules. FP-inspired peptide nanostructures that can compete with FPs in their capacity are the most preferred building blocks for the synthesis of fluorescent soft matter. However, realizing a ratiometric emission from a single peptide fluorophore remains exclusive since multicolor emission is a rare property in peptide nanostructures. Here, we describe a bioinspired peptidyl platform for ratiometric intracellular quantitation by employing a single ferrocene-modified histidine dipeptide. The intensiometric ratio of green to blue fluorescence correlates linearly with the concentration of the peptide by three orders of magnitude. The ratiometric fluorescence of the peptide is an assembly-induced emission originating from hydrogen bonds and aromatic interactions. Additionally, modular design enables ferrocene-modified histidine dipeptides to use as a general platform for the construction of intricate peptides that retain the ratiometric fluorescent properties. The ratiometric peptide technique promises flexibility in the design of a wide spectrum of stoichiometric biosensors for quantitatively understanding the trafficking and subcellular fate of biomolecules.

A bispecific glycopeptide spatiotemporally regulates tumor microenvironment for inhibiting bladder cancer recurrence

Up to 75% of bladder cancer patients suffer from recurrence due to postoperative tumor implantation. However, clinically used Bacillus Calmette-Guerin (BCG) treatment failed to inhibit the recurrence. Here, we report a bispecific glycopeptide (bsGP) that simultaneously targets CD206 on tumor-associated macrophages (TAMs) and CXCR4 on tumor cells. bsGP repolarizes protumoral M2-like TAMs to antitumor M1-like that mediated cytotoxicity and T cell recruitment. Meanwhile, bsGP is cleaved by the MMP-2 enzyme to form nanostructure for the long-term inhibition of CXCR4 downstream signaling, resulting in reduced tumor metastasis and promoted T cell infiltration. In orthotopic bladder tumor models, bsGP reduced the postoperative recurrence rate to 22%. In parallel, the recurrence rates of 89 and 78% were treated by doxycycline and BCG used in clinic, respectively. Mechanistic studies reveal that bsGP reduces the matrix microenvironment barrier, increasing the spatially redirected CD8⁺ T cells to tumor cells. We envision that bis-targeting CD206 and CXCR4 may pave the way to inhibit tumor metastasis and recurrence.

Designed peptide amphiphiles as scaffolds for tissue engineering

Peptide amphiphiles (PAs) are peptide-based molecules that contain a peptide sequence as a head group covalently conjugated to a hydrophobic segment, such as lipid tails. They can self-assemble into well-ordered supramolecular nanostructures such as micelles, vesicles, twisted ribbons and nanofibers. In addition, the diversity of natural amino acids gives the possibility to produce PAs with different sequences. These properties along with their biocompatibility, biodegradability and a high resemblance to native extracellular matrix (ECM) have resulted in PAs being considered as ideal scaffold materials for tissue engineering (TE) applications. This review introduces the 20 natural canonical amino acids as building blocks followed by highlighting the three categories of PAs: amphiphilic peptides, lipidated peptide amphiphiles and supramolecular peptide amphiphile conjugates, as well as their design rules that dictate the peptide self-assembly process. Furthermore, 3D bio-fabrication strategies of PAs hydrogels are discussed and the recent advances of PA-based scaffolds in TE with the emphasis on bone, cartilage and neural tissue regeneration both in vitro and in vivo are considered. Finally, future prospects and challenges are discussed.

Caught in Action: Visualizing Dynamic Nanostructures Within Supramolecular Systems Chemistry

Supramolecular systems chemistry has been an area of active research to develop nanomaterials with life-like functions. Progress in systems chemistry relies on our ability to probe the nanostructure formation in solution. Often visualizing the dynamics of nanostructures which transform over time is a formidable challenge. This necessitates a paradigm shift from dry sample imaging towards solution-based techniques. We review the application of state-of-the-art techniques for real-time, in situ visualization of dynamic self-assembly processes. We present how solution-based techniques namely optical super-resolution microscopy, solution-state atomic force microscopy, liquid-phase transmission electron microscopy, molecular dynamics simulations and other emerging techniques are revolutionizing our understanding of active and adaptive nanomaterials with life-like functions. This Review provides the visualization toolbox and futuristic vision to tap the potential of dynamic nanomaterials.

Self-Assembling Peptide-Based Functional Biomaterials

Peptides can self-assemble into various hierarchical nanostructures through noncovalent interactions and form functional materials exhibiting excellent chemical and physical properties, which have broad applications in bio-/nanotechnology. The self-assembly mechanism, self-assembly morphology of peptide supramolecular architecture and their various applications, have been widely explored which have the merit of biocompatibility, easy preparation, and controllable functionality. Herein, we introduce the latest research progress of self-assembling peptide-based nanomaterials and review their applications in biomedicine and optoelectronics, including tissue engineering, anticancer therapy, biomimetic catalysis, energy harvesting. We believe that this review will inspire the rational design and development of novel peptide-based functional bio-inspired materials in the future.

Rip it, stitch it, click it: A Chemist's guide to VLP manipulation

Viruses are some of nature's most ubiquitous self-assembled molecular containers. Evolutionary pressures have created some incredibly robust, thermally, and enzymatically resistant carriers to transport delicate genetic information safely. Virus-like particles (VLPs) are human-engineered non-infectious systems that inherit the parent virus' ability to self-assemble under controlled conditions while being non-infectious. VLPs and plant-based viral nanoparticles are becoming increasingly popular in medicine as their self-assembly properties are exploitable for applications ranging from diagnostic tools to targeted drug delivery. Understanding the basic structure and principles underlying the assembly of higher-order structures has allowed researchers to disassemble (rip it), reassemble (stitch it), and functionalize (click it) these systems on demand. This review focuses on the current toolbox of strategies developed to manipulate these systems by ripping, stitching, and clicking to create new technologies in the biomedical space.

Enzyme-instructed morphology transformation of mitochondria-targeting peptide for the selective eradication of osteosarcoma

The treatment of osteosarcoma involves an adjuvant therapy that combines surgery and chemotherapy. However, considering that children are the main victims of osteosarcoma, replacing such a harsh treatment with a soft but powerful method that ensures a complete cure while having no adverse effects is highly desirable. To achieve this aim, we have developed a supramolecular therapeutic strategy based on morphology-transformable mitochondria-targeting peptides for the eradication of osteosarcoma with enhanced selectivity and reduced side effects. A newly designed micelle-forming amphiphilic peptide, l-Mito-FFYp, consisting of a phosphate substrate for the biomarker enzyme of osteosarcoma alkaline phosphatase (ALP), disassembles in response to the ALP enzyme in the cell membrane to generate positively charged l-Mito-FFY molecules, which diffuse inside the targeted cell and self-assemble to form nanostructures specifically inside the mitochondria to induce cell apoptosis.

Accurate Quantum-Mechanically Derived Force-Fields through a Fragment-Based Approach: Balancing Specificity and Transferability in the Prediction of Self-Assembly in Soft Matter

The wide range of time/length scales covered by self-assembly in soft matter makes molecular dynamics (MD) the ideal candidate for simulating such a supramolecular phenomenon at an atomistic level. However, the reliability of MD outcomes heavily relies on the accuracy of the adopted force-field (FF). The spontaneous re-ordering in liquid crystalline materials stands as a clear example of such collective self-assembling processes, driven by a subtle and delicate balance between supramolecular interactions and single-molecule flexibility. General-purpose transferable FFs often dramatically fail to reproduce such complex phenomena, for example, the error on the transition temperatures being larger than 100 K. Conversely, quantum-mechanically derived force-fields (QMD-FFs), specifically tailored for the target system, were recently shown (J. Phys. Chem. Lett.2022,13, 243) to allow for the required accuracy as they not only well reproduced transition temperatures but also yielded a quantitative agreement with the experiment on a wealth of structural, dynamic, and thermodynamic properties. The main drawback of this strategy stands in the computational burden connected to the numerous quantum mechanical (QM) calculations usually required for a target-specific parameterization, which has undoubtedly hampered the routine application of QMD-FFs. In this work, we propose a fragment-based strategy to extend the applicability of QMD-FFs, in which the amount of QM calculations is significantly reduced, being a single-molecule-optimized geometry and its Hessian matrix the only QM information required. To validate this route, a new FF is assembled for a large mesogen, exploiting the parameters obtained for two smaller liquid crystalline molecules, in this and previous work. Lengthy MD simulations are carried out with the new transferred QMD-FF, observing again a spontaneous re-orientation in the correct range of temperatures, with good agreement with the available experimental measures. The present results strongly suggest that a partial transfer of QMD-FF parameters can be invoked without a significant loss of accuracy, thus paving the way to exploit the method's intrinsic predictive capabilities in the simulation of novel soft materials.

Modulating the Electromechanical Response of Bio-Inspired Amino Acid-Based Architectures through Supramolecular Co-Assembly

Supramolecular packing dictates the physical properties of bio-inspired molecular assemblies in the solid state. Yet, modulating the stacking modes of bio-inspired supramolecular assemblies remains a challenge and the structure-property relationship is still not fully understood, which hampers the rational design of molecular structures to fabricate materials with desired properties. Herein, we present a co-assembly strategy to modulate the supramolecular packing of N-terminally capped alanine-based assemblies (Ac-Ala) by changing the amino acid chirality and mixing with a nonchiral bipyridine derivative (BPA). The co-assembly induced distinct solid-state stacking modes determined by X-ray crystallography, resulting in significantly enhanced electromechanical properties of the assembly architectures. The highest rigidity was observed after the co-assembly of racemic Ac-Ala with a bipyridine coformer (BPA/Ac-DL-Ala), which exhibited a measured Young's modulus of 38.8 GPa. Notably, BPA crystallizes in a centrosymmetric space group, a condition that is broken when co-crystallized with Ac-L-Ala and Ac-D-Ala to induce a piezoelectric response. Enantiopure co-assemblies of BPA/Ac-D-Ala and BPA/Ac-L-Ala showed density functional theory-predicted piezoelectric responses that are remarkably higher than the other assemblies due to the increased polarization of their supramolecular packing. This is the first report of a centrosymmetric-crystallizing coformer which increases the single-crystal piezoelectric response of an electrically active bio-inspired molecular assembly. The design rules that emerge from this investigation of chemically complex co-assemblies can facilitate the molecular design of high-performance functional materials comprised of bio-inspired building blocks.

Self-assembly hydrogels of therapeutic agents for local drug delivery

Advanced drug delivery systems are of vital importance to enhance therapeutic efficacy. Among various recently developed formulations, self-assembling hydrogels composed of therapeutic agents have shown promising potential for local drug delivery owing to their excellent biocompatibility, high drug-loading efficiency, low systemic toxicity, and sustained drug release behavior. In particular, therapeutic agents self-assembling hydrogels with well-defined nanostructures are beneficial for direct delivery to the target site via injection, not only improving drug availability, but also extending their retention time and promoting cellular uptake. In brief, the self-assembly approach offers better opportunities to improve the precision of pharmaceutical treatment and achieve superior treatment efficacies. In this review, we intend to cover the recent developments in therapeutic agent self-assembling hydrogels. First, the molecular structures, self-assembly mechanisms, and application of self-assembling hydrogels are systematically outlined. Then, we summarize the various self-assembly strategies, including the single therapeutic agent, metal-coordination, enzyme-instruction, and co-assembly of multiple therapeutic agents. Finally, the potential challenges and future perspectives are discussed. We hope that this review will provide useful insights into the design and preparation of therapeutic agent self-assembling hydrogels.

A pH-Driven Small-Molecule Nanotransformer Hijacks Lysosomes and Overcomes Autophagy-Induced Resistance in Cancer

Smart conversion of supramolecular structures in vivo is an attractive strategy in cancer nanomedicine, which is usually achieved via specific peptide sequences. Here we developed a lysosomal targeting small-molecule conjugate, PBC, which self-assembles into nanoparticles at physiological pH and smartly converts to nanofibrils in lysosomes of tumor cells. Such a transformation mechanically leads to lysosomal dysfunction, autophagy inhibition, and unusual cytoplasmic vacuolation, thus granting PBC a unique anticancer activity as a monotherapy. Importantly, the photo-activated PBC elicits significant phototoxicity to lysosomes and shows enormous advantages in overcoming autophagy-caused treatment resistance frequently occurring in conventional phototherapy. This improved phototherapy achieves a complete cure of oral cancer xenografts upon limited administration. Our work provides a new paradigm for the construction of nonpeptide nanotransformers with biomedical activities.

Constructing ECM-like Structure on the Plasma Membrane via Peptide Assembly to Regulate the Cellular Response

This feature article introduces the design of self-assembling peptides that serve as the basic building blocks for the construction of extracellular matrix (ECM)-like structure in the vicinity of the plasma membrane. By covalently conjugating a bioactive motif, such as membrane protein binding ligand or enzymatic responsive building block, with a self-assembling motif, especially the aromatic peptide, a self-assembling peptide that retains bioactivity is obtained. Instructed by the target membrane protein or enzyme, the bioactive peptides self-assemble into ECM-like structure exerting various stimuli to regulate the cellular response via intracellular signaling, especially mechanotransduction. By briefly summarizing the properties and applications (e.g., wound healing, controlling cell motility and cell fate) of these peptides, we intend to illustrate the basic requirements and promises of the peptide assembly as a true bottom-up approach in the construction of artificial ECM.

Stearoylamido-D-Glucamine Hydrogelators for Thixotropic Molecular Gels with Tunable Softness by Chemical Modification

Low-molecular-weight hydrogelators containing stearoyl, glycine, and D-glucamine moieties with or without methyl groups were synthesized to prepare chemically tuned molecular hydrogels. To evaluate the role of hydrogen bonding of hydrogelators in molecular hydrogel formation, the author has newly synthesized hydrogelators with or without methyl groups at their N-H in amide groups, contributing to the hydrogen bond formation in fiber in molecular hydrogels. The obtained hydrogels exhibited improved thixotropic performance with tunable softness, exhibiting pseudo-reversible thixotropic cycles that depended on the methyl substitution positions in the hydrogelators. To change the hydrogen bonds' positions by chemical modification has made it possible to tune the mechanical properties of molecular gels.

Enzyme-instructed self-assembly (EISA) assists the self-assembly and hydrogelation of hydrophobic peptides

Enzyme-instructed self-assembly (EISA) has several advantages in the preparation of supramolecular self-assembly materials for biomedical applications. In this study, we demonstrated that the enzyme-instructed self-assembly (EISA) strategy could assist the self-assembly and hydrogelation of two hydrophobic and bioactive peptides, tyroservatide (YSV) and laminin pentapeptide (YIGSR). We first synthesized the peptide derivatives of Nap-GFFYSV (peptide 1) and Nap-GFFYIGSR (peptide 2) and found that both peptides could not self-assemble into hydrogels due to their poor solubility. We therefore designed the phosphorylated precursors of the two hydrophobic peptides, Nap-GFFpYSV (precursor 1) and Nap-GFFpYIGSR (precursor 2), respectively, which had good solubility and can be dephosphorylated by alkaline phosphatase (ALP) to form supramolecular hydrogels. In addition, we found that the EISA could also occur on the surface of cells that overexpress ALP. The EISA strategy was a powerful method to generate hydrogels of hydrophobic compounds. We envision the big promise of the strategy in the preparation of biomaterials and nanomaterials of hydrophobic bioactive molecules.

Strategies for Biomaterial-Based Spinal Cord Injury Repair via the TLR4-NF-κB Signaling Pathway

The repair and motor functional recovery after spinal cord injury (SCI) has remained a clinical challenge. Injury-induced gliosis and inflammation lead to a physical barrier and an extremely inhibitory microenvironment, which in turn hinders the recovery of SCI. TLR4-NF-κB is a classic implant-related innate immunomodulation signaling pathway and part of numerous biomaterial-based treatment strategies for SCI. Numerous experimental studies have demonstrated that the regulation of TLR4-NF-κB signaling pathway plays an important role in the alleviation of inflammatory responses, the modulation of autophagy, apoptosis and ferroptosis, and the enhancement of anti-oxidative effect post-SCI. An increasing number of novel biomaterials have been fabricated as scaffolds and carriers, loaded with phytochemicals and drugs, to inhibit the progression of SCI through regulation of TLR4-NF-κB. This review summarizes the empirical strategies for the recovery after SCI through individual or composite biomaterials that mediate the TLR4-NF-κB signaling pathway.

Co-Assembly Induced Solid-State Stacking Transformation in Amino Acid-Based Crystals with Enhanced Physical Properties

The physical characteristics of supramolecular assemblies composed of small building blocks are dictated by molecular packing patterns in the solid-state. Yet, the structure-property correlation is still not fully understood. Herein, we report the unexpected cofacial to herringbone stacking transformation of a small aromatic bipyridine through co-assembly with acetylated glutamic acid. The unique solid-state structural transformation results in enhanced physical properties of the supramolecular organizations. The co-assembly methodology was further expanded to obtain diverse molecular packings by different bipyridine and acetylated amino acid derivatives. This study presents a feasible co-assembly approach to achieve the solid-state stacking transformation of supramolecular organization and opens up new opportunities to further explore the relationship between molecular arrangement and properties of supramolecular assemblies by crystal engineering.

Enhancing the Cellular Uptake of Macromolecules via Enzyme-Instructed Self-Assembly

Poor solubility, low cellular uptake, and poor cell selectivity are the main obstacles hampering the therapeutic potential and clinic application of macromolecules. To overcome these limitations, here we propose a chemical modification strategy of macromolecules based on enzyme-instructed self-assembly (EISA). By using protoporphyrin IX (PpIX) and its metal complex Zn-PpIX as the modification objects, we demonstrated that the integration of enzymatic transformation and molecular self-assembly of macromolecules successfully improved the solubility of macromolecules, enhancing their intracellular uptake selectively against cancer cells. The proposed strategy is potentially applicable as a general tool for the development of macromolecule-based nanomedicine.

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.

Predicting Spontaneous Orientational Self-Assembly: In Silico Design of Materials with Quantum Mechanically Derived Force Fields

De novo design of self-assembled materials hinges upon our ability to relate macroscopic properties to individual building blocks, thus characterizing in such supramolecular architectures a wide range of observables at varied time/length scales. This work demonstrates that quantum mechanical derived force fields (QMD-FFs) do satisfy this requisite and, most importantly, do so in a predictive manner. To this end, a specific FF, built solely based on the knowledge of the target molecular structure, is employed to reproduce the spontaneous transition to an ordered liquid crystal phase. The simulations deliver a multiscale portrait of such self-assembly processes, where conformational changes within the individual building blocks are intertwined with a 200 ns ensemble reorganization. The extensive characterization provided not only is in quantitative agreement with the experiment but also connects the time/length scales at which it was performed. Realizing QMD-FF predictive power and unmatched accuracy stands as an important leap forward for the bottom-up design of advanced supramolecular materials.

Injectable and pH-responsive self-assembled peptide hydrogel for promoted tumor cell uptake and enhanced cancer chemotherapy

Chemotherapy is the main treatment for cancer therapy. However, its anti-tumor efficiency is always impaired by the poor bioavailability and low tumor accumulation of chemotherapeutic drugs. The variation between the tumor microenvironment and normal tissue has been recognized as an effective tool to improve drug anti-tumor efficiency. Herein, we developed an injectable, pH-responsive, in situ self-assembled drug-peptide hydrogel (MTX-KKFKFEFEF(DA)) for highly efficient local tumor chemotherapy with few side effects. The small molecule drug, methotrexate (MTX), and pH-responsive linker, 2,3-dimethylmaleic anhydride (DA), were facilely conjugated onto the chain of the KKFKFEFEF peptide via an amidation reaction. The negatively charged drug-peptide (pH 7.4) can be activated to be positive and achieve a sol-gel phase transition under an acidic microenvironment (pH 6.5) both in vitro and in vivo, resulting in highly efficient cellular uptake and endocytosis capacities. Moreover, the in vivo anti-tumor therapeutic effect revealed that the MTX-KKFKFEFEF(DA) hydrogel exhibits long-term tumor retention time, much better tumor inhibition rate and negligible side effects after intratumoral injection into breast tumor-bearing mice. Therefore, this study reveals a versatile strategy for fabricating a pH-responsive drug-peptide hydrogel to improve the chemotherapeutic efficacy of drugs in cancer treatment.

Computational and Experimental Protocols to Study Cyclo-dihistidine Self- and Co-assembly: Minimalistic Bio-assemblies with Enhanced Fluorescence and Drug Encapsulation Properties

Our published studies on the self- and co-assembly of cyclo-HH peptides demonstrated their capacity to coordinate with Zn(II), their enhanced photoluminescence and their ability to self-encapsulate epirubicin, a chemotherapy drug. Here, we provide a detailed description of computational and experimental methodology for the study of cyclo-HH self- and co-assembling mechanisms, photoluminescence, and drug encapsulation properties. We outline the experimental protocols, which involve fluorescence spectroscopy, transmission electron microscopy, and atomic force microscopy protocols, as well as the computational protocols, which involve structural and energetic analysis of the assembled nanostructures. We suggest that the computational and experimental methods presented here can be generalizable, and thus can be applied in the investigation of self- and co-assembly systems involving other short peptides, encapsulating compounds and binding to ions, beyond the particular ones presented here.