Antimicrobial peptide capsids of de novo design

A self-assembled protein β-helix as a self-contained biofunctional motif

Nature constructs matter by employing protein folding motifs, many of which have been synthetically reconstituted to exploit function. A less understood motif whose structure-function relationships remain unexploited is formed by parallel β-strands arranged in a helical repetitive pattern, termed a β-helix. Herein we reconstitute a protein β-helix by design and endow it with biological function. Unlike β-helical proteins, which are contiguous covalent structures, this β-helix self-assembles from an elementary sequence of 18 amino acids. Using a combination of experimental and computational methods, we demonstrate that the resulting assemblies are discrete cylindrical structures exhibiting conserved dimensions at the nanoscale. We provide evidence for the structures to form a carpet-like three-dimensional scaffold promoting and inhibiting the growth of human and bacterial cells, respectively, while being able to mediate intracellular gene delivery. The study introduces a self-assembled β-helix as a self-contained bio- and multi-functional motif for exploring and exploiting mechanistic biology.

Selective recognition of bacterial phospholipids by antimicrobial peptides: Employing a host-guest-mediated competitive inhibition strategy

The distinct phospholipid compositions of bacterial and mammalian cell membranes offer a promising target for the development of antimicrobial peptides (AMPs). However, distinguishing between the similarly charged anionic phospholipids-bacterial phosphatidylglycerol (PG) and mammalian phosphatidylserine (PS)-poses a significant challenge. Here we introduce a competitive inhibition strategy that leverages host-guest interactions to enable AMPs to selectively recognize PG without engaging with PS. After analyzing the binding interactions of various radially amphiphilic AMPs (RAPs), host molecules, and phospholipids, we discovered that a RAP, named C6HO, exhibited a higher affinity for cucurbit[7]uril (CB[7]) compared to PS, yet a lower affinity than for PG. Consequently, CB[7] functions as a competitive inhibitor: by forming a complex with C6HO upon simple mixing, it prevents C6HO from interacting with PS. Notably, PG can outcompete CB[7] for binding to C6HO within the complex, leading to the aggregation of PG molecules and the subsequent disruption of membranes rich in PG. Furthermore, the competitive inhibitor CB[7] effectively neutralizes C6HO's cytotoxic effects on mammalian cells while preserving the antimicrobial potency of C6HO. In vivo experiments in a subcutaneous infection model demonstrated that CB[7] reduced both systemic and local toxicity of C6HO without compromising its antimicrobial efficacy. Our study presents a strategy for the specific recognition of bacterial phospholipids and the design of highly selective AMPs.

De novo-designed amphiphilic α-helical peptide Z2 exhibits broad-spectrum antimicrobial, anti-biofilm, and anti-inflammatory efficacy in acute Pseudomonas aeruginosa pneumonia

Antimicrobial peptides (AMPs) show considerable promise in combating bacterial infections due to their broad-spectrum efficacy, unique mechanisms of action, and resistance capabilities. In this study, we de novo designed a series of α-helical AMPs (Z1-Z6) with enhanced antimicrobial activity, anti-biofilm, and anti-inflammatory effects. The design incorporated isoleucine with long alkyl side chains and carefully balanced the positive charge and hydrophobicity. Among the designed peptides, Z2 demonstrated remarkable properties. In vitro assays revealed a high therapeutic index, with effective inhibition of 10 pathogenic and drug-resistant bacterial strains by disrupting cell membranes and interacting with bacterial genomes. Z2 also significantly suppressed biofilm formation and reduced reactive oxygen species production in RAW264.7 cells, leading to a decrease in inflammatory cytokine expression, thus showing anti-inflammatory activity. In a mouse model of acute Pseudomonas aeruginosa pneumonia, Z2 significantly improved survival rates, efficiently cleared bacteria from the lungs, and alleviated lung damage. Overall, Z2's unique design endows it with excellent antimicrobial, anti-biofilm, and anti-inflammatory activities, suggesting its great potential as a novel antimicrobial agent for further development. Future research will focus on the studying the drug formulations, elucidating the mechanisms underlying Z2's anti-inflammatory effects and exploring its therapeutic potential in other infection models.

Self-assembling of coiled-coil peptides into virus-like particles: Basic principles, properties, design, and applications with special focus on vaccine design and delivery

Self-assembling peptide nanoparticles (SAPN) based delivery systems, including virus-like particles (VLP), have shown great potential for becoming prominent in next-generation vaccine and drug development. The VLP can mimic properties of natural viral capsid in terms of size (20-200 nm), geometry (i.e., icosahedral structures), and the ability to generate a robust immune response (with multivalent epitopes) through activation of innate and/or adaptive immune signals. In this regard, coiled-coil (CC) domains are suitable building blocks for designing VLP because of their programmable interaction specificity, affinity, and well-established sequence-to-structure relationships. Generally, two CC domains with different oligomeric states (trimer and pentamer) are fused to form a monomeric protein through a short, flexible spacer sequence. By using combinations of symmetry axes (2-, 3- and 5- folds) that are unique to the geometry of the desired protein cage, it is possible, in principle, to assemble well-defined protein cages like VLP. In this review, we have discussed the crystallographic rules and the basic principles involved in the design of CC-based VLP. It also explored the functions of numerous noncovalent interactions in generating stable VLP structures, which play a crucial role in improving the properties of vaccine immunogenicity, drug delivery, and 3D cell culturing.

Multimodal Membrane Poration by Thanatin

Antimicrobial resistance has motivated the search for antimicrobial agents with multimodal mechanisms of action. Host defense peptides and bacteriocins hold particular promise in this regard. Among many molecules discovered to date, thanatin appears to represent the properties of the two classes in that it, like bacteriocins, adopts a highly stable fold in solution and, like host defense peptides, exhibits broad-spectrum antibiotic activity. The peptide is believed to depolarize bacterial outer membranes and inhibit lipopolysaccharide transport while restoring bacterial susceptibility to β-lactam antibiotics. However, a direct observation of whether and how thanatin affects membranes is lacking. Here we reason that the peptide should promote bacteriocin-like multimodal poration in phospholipid bilayers. We demonstrate that thanatin induces poration with elements of membrane thinning, fractal ruptures, and transmembrane channels, a phenomenon common for bacteriocin folds but atypical of antimicrobial peptides. The results offer mechanistic insight into the action of antimicrobial agents emerging from different molecular classes but with similar properties.

Flexible Tail of Antimicrobial Peptide PGLa Facilitates Water Pore Formation in Membranes

PGLa, an antimicrobial peptide (AMP), primarily exerts its antibacterial effects by disrupting bacterial cell membrane integrity. Previous theoretical studies mainly focused on the binding mechanism of PGLa with membranes, while the mechanism of water pore formation induced by PGLa peptides, especially the role of structural flexibility in the process, remains unclear. In this study, using all-atom simulations, we investigated the entire process of membrane deformation caused by the interaction of PGLa with an anionic cell membrane composed of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG). Using a deep learning-based key intermediate identification algorithm, we found that the C-terminal tail plays a crucial role for PGLa insertion into the membrane, and that with its assistance, a variety of water pores formed inside the membrane. Mutation of the tail residues revealed that, in addition to electrostatic and hydrophobic interactions, the flexibility of the tail residues is crucial for peptide insertion and pore formation. The full extension of these flexible residues enhances peptide-peptide and peptide-membrane interactions, guiding the transmembrane movement of PGLa and the aggregation of PGLa monomers within the membrane, ultimately leading to the formation of water-filled pores in the membrane. Overall, this study provides a deep understanding of the transmembrane mechanism of PGLa and similar AMPs, particularly elucidating for the first time the importance of C-terminal flexibility in both insertion and oligomerization processes.

A Nonlinear Peptide Topology for Synthetic Virions

a nonlinear de novo peptide topology for the assembly of synthetic virions is reported. The topology is a backbone cyclized amino-acid sequence in which polar l- and hydrophobic d-amino acid residues of the same-type alternate. This arrangement introduces pseudo C4 symmetries of side chains within the same cyclopeptide ring, allowing for the lateral propagation of cyclopeptides into networks with a [3/6, 4]-fold rotational symmetry closing into virus-like shells. A combination of computational and experimental approaches was used to establish that the topology forms morphologically uniform, nonaggregating and nontoxic nanoscale shells. These effectively encapsulate genetic cargo and promote its intracellular delivery and a target genetic response. The design introduces a nanotechnology inspired solution for engineering virus-like systems thereby expanding traditional molecular biology approaches used to create artificial biology to chemical space.

Versatile Fabrication of Biocompatible Antimicrobial Materials Enabled by Cationic Peptide Bundles

Antimicrobial peptides (AMPs) are expected to be an alternative promising solution to the global public health problem of antibiotic resistance due to their unique antimicrobial mechanism. However, extensive efforts are still needed to improve the shortcomings of traditional AMPs, such as rapid proteolysis, hemolysis, slow response, toxicity, etc., by exploring AMP-based new antimicrobial strategies. Here, we develop cationic peptide bundles into novel antimicrobial architectures that can rapidly kill multiple types of bacteria including drug-resistant bacteria. Remarkably, cationic peptide bundles can be used as polymerization units to cross-link with other polymers through simple two-component polymerization to produce diverse antimicrobial materials. For the proof of concept, three materials were fabricated and investigated, including an antimicrobial hydrogel that can significantly accelerate the healing of infected wounds, a multifunctional antimicrobial bioadhesive that shows promise in antimicrobial coatings for medical devices, and a photo-cross-linked antimicrobial gelatin hydrogel with broad application potential. The integration of antimicrobial units into the materials' backbone endows their biocompatibility. Cationic peptide bundles not only represent a new antimicrobial strategy but also provide a versatile and promising processing method to create diversified, multifunctional, and biocompatible antimicrobial materials.

Enveloped Viral Replica Equipped with Spike Protein Derived from SARS-CoV-2

Synthetic viral nanostructures are useful as materials for analyzing the biological behavior of natural viruses and as vaccine materials. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus embedding a spike (S) protein involved in host cell infection. Although nanomaterials modified with an S protein without an envelope membrane have been developed, they are considered unsuitable for stability and functionality. We previously constructed an enveloped viral replica complexed with a cationic lipid bilayer and an anionic artificial viral capsid self-assembled from β-annulus peptides. In this study, we report the first example of an enveloped viral replica equipped with an S protein derived from SARS-CoV-2. Interestingly, even the S protein equipped on the enveloped viral replica bound strongly to the free angiotensin-converting enzyme 2 (ACE2) receptor as well as ACE2 localized on the cell membrane.

Construction of Targeting-Peptide-Based Imaging Reagents and Their Application in Bioimaging

Molecular imaging was developed from basic molecular recognition. It can visualize not only the expression levels of specific molecules in a living system but also specific biological processes, thus providing guidance for early detection and treatment of diseases. As a noninvasive method, imaging agents are one of the foundations of high spatial resolution imaging, and their sensitivity and specificity can be improved by coupling targeting ligands to imaging probes. Among the various targeting ligands (antibodies, aptamers, etc.), targeting peptides are widely used in various modalities of molecular imaging due to their high affinities toward the molecular target and their excellent physicochemical properties. In this review, we summarize the design concepts and methods of targeting peptides in molecular imaging, introduce the combination of targeting peptides and imaging probes in different imaging modalities (e.g., fluorescence imaging, radionuclide imaging), and provide examples of their applications in bioimaging. Finally, the challenges and strategies for clinical translation and practical application of targeting peptide-based imaging reagents are briefly discussed.

Folding-Mediated DNA Delivery by α-Helical Amphipathic Peptides

The renaissance gene therapy experiences these days requires specialist biomaterials and a systemic understanding of major factors influencing their ability to deliver genetic material. Peptide transfection systems represent a major class of such biomaterials. Several peptidic reagents have been commercialized to date. However, a comparative assessment of peptide sequences alone without auxiliary support or excipients against a common determinant for their ability to complex and deliver DNA has been lacking. This study cross-compares commercial and experimental transfection reagents from the same family of helical amphiphiles. Factors defining the efficacy of DNA delivery including cell uptake and gene expression are assessed along with cytotoxicity and DNA complexation. The results show that despite differences in sequence composition, length, and origin, peptide reagents of the same structural family exhibit similar characteristics and limitations with common variability trends. The cross-comparison revealed that functional DNA delivery is independent of the peptide sequence used but is mediated by the ability of the reagents to co-fold with DNA. Peptide folding proved to be the common determinant for DNA complexation and delivery by peptidic transfection reagents.

Advancements, challenges and future perspectives on peptide-based drugs: Focus on antimicrobial peptides

Among other health related issues, the rising concerns on drug resistance led to look for alternative pharmaceutical drugs that are effective both against infectious and noninfectious diseases. Antimicrobial peptides (AMPs) emerged as potential therapeutic molecule with wide range of applications. With their limitations, AMPs have gained reputable attentions in research as well as in the pharmaceutical industry. This review highlighted the historical background, research trends, technological advancements, challenges, and future perspectives in the development and applications of peptide drugs. Some vital questions related with the need for pharmaceutical production, factors for the slow and steady journey, the importance of oral bioavailability, and the drug resistance possibilities of AMPs were raised and addressed accordingly. Therefore, the current study is believed to provide a profound understanding in the past and current scenarios and future directions on the therapeutic impacts of peptide drugs.

Host-Defense-Peptide-Mimicking β-Peptide Polymer Acting as a Dual-Modal Antibacterial Agent by Interfering Quorum Sensing and Killing Individual Bacteria Simultaneously

Host defense peptides (HDPs) are one of the potentially promising agents for infection diseases due to their broad spectrum and low resistance rate, but their clinical applications are limited by proteolytic instability, high-cost, and complicated synthesis process. Here, we report a host-defense-peptide-mimicking β-peptide polymer that resists proteolysis to have enhanced the activity under physiological conditions, excellent antimicrobial efficiency even at high density of bacteria, and low cost for preparation. The β-peptide polymer demonstrated quorum sensing (QS) interference and bactericidal effect against both bacterial communities and individual bacterium to simultaneously block bacterial communication and disrupt bacterial membranes. The hierarchical QS network was suppressed, and main QS signaling systems showed considerably down-regulated gene expression, resulting in excellent biofilm eradication and virulence reduction effects. The dual-modal antibacterial ability possessed excellent therapeutic effects in Pseudomonas aeruginosa pneumonia, which could inhibit biofilm formation and exhibit better antibacterial and anti-inflammatory efficiency than clinically used antibiotics, levofloxacin. Furthermore, the β-peptide polymer also showed excellent therapeutic effect Escherichia coli pyogenic liver abscess. Together, we believed that the β-peptide polymer had a feasible clinical potential to treat bacterial infection diseases.

The future of recombinant host defense peptides

The antimicrobial resistance crisis calls for the discovery and production of new antimicrobials. Host defense peptides (HDPs) are small proteins with potent antibacterial and immunomodulatory activities that are attractive for translational applications, with several already under clinical trials. Traditionally, antimicrobial peptides have been produced by chemical synthesis, which is expensive and requires the use of toxic reagents, hindering the large-scale development of HDPs. Alternatively, HDPs can be produced recombinantly to overcome these limitations. Their antimicrobial nature, however, can make them toxic to the hosts of recombinant production. In this review we explore the different strategies that are used to fine-tune their activities, bioengineer them, and optimize the recombinant production of HDPs in various cell factories.

Quality assessment of virus-like particle: A new transmission electron microscopy approach

Transmission electron microscopy (TEM) is a gold standard analytical method for nanoparticle characterization and is playing a valuable role in virus-like particle (VLP) characterization extending to other biological entities such as viral vectors. A dedicated TEM facility is a challenge to both small and medium-sized enterprises (SMEs) and companies operating in low-and-middle income countries (LMICs) due to high start-up and running costs. A low-voltage TEM solution with assisted image acquisition and analysis such as the MiniTEM system, coupled with Vironova Imaging and Analysis Software (VIAS) could provide an affordable and practical alternative. The MiniTEM system has a small footprint and software that enables semi-automated data collection and image analysis workflows using built-in deep learning methods (convolutional neural networks) for automation in analysis, increasing speed of information processing and enabling scaling to larger datasets. In this perspective we outline the potential and challenges in the use of TEM as mainstream analytical tool in manufacturing settings. We highlight the rationale and preliminary findings from our proof-of-concept study aiming to develop a method to assess critical quality attributes (CQAs) of VLPs and facilitate adoption of TEM in manufacturing settings. In our study we explored all the steps, from sample preparation to data collection and analysis using synthetic VLPs as model systems. The applicability of the method in product development was verified at pilot-scale during the technology transfer of dengue VLPs development from a university setting to an LMIC- based vaccine manufacturing company, demonstrating the applicability of this analytical technique to VLP vaccine characterization.

Synthesis of Polylactic Acid Oligomers for Broad-Spectrum Antimicrobials

Infectious microbial diseases are a major public health hazard, calling for more innovative antimicrobials. Herein, polylactic acid (PLA) oligomers have been explored and reported as a bio-safe and eco-friendly functional antimicrobial agent against pathogens, such as viruses (H1N1, H3N2, and SARS-CoV-2), bacteria (E. coli, S. aureus, K. pneumoniae, MRSA), and fungi (C. albicans). The PLA oligomers were prepared by direct catalyst-free condensation polymerization of l-lactic acid monomers and characterized by FT-IR and 1H-NMR. The antiviral results demonstrate that PLA oligomers possess robust (inhibiting rate > 99%) and rapid (<20 min) antiviral activity against two pandemic ssRNA viruses, including influenza A virus (IAV) and coronavirus (CoV). Furthermore, the PLA oligomers exhibit high antibacterial activities against both Gram negative (G−) and Gram positive (G+) bacteria. The PLA oligomers also perform efficiently in killing a large amount of C. albicans as high as 105 cfu/mL down to zero at the concentration of 10 mg/mL. Thus, the broad-spectrum antimicrobial activity endowed the PLA oligomers with a promising biocidal option, except antibiotics in a wide range of applications, such as medical textiles, food preservation, water disinfection, and personal hygiene, in light of their unique biodegradability and biocompatibility.

Anticancer Activity of Reconstituted Ribonuclease S-Decorated Artificial Viral Capsid

Ribonuclease S (RNase S) is an enzyme that exhibits anticancer activity by degrading RNAs within cancer cells; however, the cellular uptake efficiency is low due to its small molecular size. Here we generated RNase S-decorated artificial viral capsids with a size of 70-170 nm by self-assembly of the β-annulus-S-peptide followed by reconstitution with S-protein at neutral pH. The RNase S-decorated artificial viral capsids are efficiently taken up by HepG2 cells and exhibit higher RNA degradation activity in cells compared with RNase S alone. Cell viability assays revealed that RNase S-decorated capsids have high anticancer activity comparable to that of standard anticancer drugs.

In situ nanoscale imaging reveals self-concentrating nanomolar antimicrobial pores

Host defence peptides are critical factors of immune systems in all life forms. Considered for therapeutic development in the post-antibiotic era, these molecules rupture microbial membranes at micromolar concentrations. Here we report a self-concentrating mechanism of membrane disruption, which occurs at therapeutically more relevant nanomolar concentrations. Induced by a four-helix bacteriocin the mechanism manifests in a multi-modal disruption pattern. Using in situ atomic force microscopy we show that the pattern and its kinetic profiles remain the same in a range of nano-to-micromolar concentrations. We reveal that the bacteriocin creates its own boundaries in phospholipid bilayers in which it self-concentrates to promote transmembrane poration. The findings offer an exploitable insight into nanomolar antimicrobial mechanisms.

Characterization of novel antimicrobial peptides designed on the basis of amino acid sequence of peptides from egg white hydrolysate

Salmonella enterica subsp. enterica serotype Typhimurium (S. Typhimurium) is one of the most prevalent foodborne pathogens responsible for food poisoning and is spread through the consumption of contaminated poultry products. In this study, four antimicrobial peptides (AMPs) with varying hydrophobicity and helical structure-forming tendencies were designed and synthesized based on the amino acid sequences of peptides from egg white hydrolysate. Two of these AMPs, P1R3 (KSWKKHVVSGFFLR) and P1C (KSWKKHVVSGFFLRLWVHKK), exhibited inhibitory activity against S. Typhimurium and compromised its biofilm-forming ability. Investigation of their modes of action revealed that P1R3 and P1C interact with and permeabilize the cytoplasmic membrane of bacteria, leading to membrane potential dissipation, damage to membrane integrity, and consequent bacterial death. P1R3 also bound to S. Typhimurium DNA, resulting in DNA aggregation or precipitation. Moreover, both peptides showed negligible cytotoxicity to Vero cells, and P1C displayed significant antimicrobial activity in chicken meat. Peptides P1R3 and P1C, therefore, have the potential to be developed as promising food preservatives, especially against pathogenic S. Typhimurium.

An SI-traceable reference material for virus-like particles

A reference material for virus-like particles traceable to the International System of Units (Système International d'Unités – the SI) is reported. The material addresses the need for developing reference standards to benchmark virus-like gene delivery systems and help harmonize measurement approaches for characterization and testing. The material is a major component of synthetic polypeptide virus-like particles produced by the state-of-the-art synthetic and analytical chemistry methods used to generate gene delivery systems. The purity profile of the material is evaluated to the highest metrological order demonstrating traceability to the SI. The material adds to the emerging toolkit of reference standards for quantitative biology.

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A reference material for virus-like particles with traceability to the SI

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The material is a major component of virus-like particles capable of gene delivery

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Purity profile of the material is evaluated to the highest metrological order

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The material allows comparability of physicochemical properties of virus-like systems

Protein Nanoparticles: Uniting the Power of Proteins with Engineering Design Approaches

Protein nanoparticles, PNPs, have played a long-standing role in food and industrial applications. More recently, their potential in nanomedicine has been more widely pursued. This review summarizes recent trends related to the preparation, application, and chemical construction of nanoparticles that use proteins as major building blocks. A particular focus has been given to emerging trends related to applications in nanomedicine, an area of research where PNPs are poised for major breakthroughs as drug delivery carriers, particle-based therapeutics or for non-viral gene therapy.

Peptide Self-assembly into stable Capsid-Like nanospheres and Co-assembly with DNA to produce smart artificial viruses

Smart artificial viruses have been successfully developed by co-assembly of de novo designed peptides with DNA, which achieved stimuli-responsibility and efficient gene transfection in cancer cells. The peptides were designed to incorporate several functional segments, including a hydrophobic aromatic segment to drive self-assembly, two or more cysteines to regulate the assemblage shape and stabilize the assembled nanostructures via forming disulfide bonds, several lysines to facilitate co-assembly with DNA and binding to cell membranes, and an enzyme-cleavable segment to introduce cancer sensitivity. The rationally designed peptides self-assembled into stable nanospheres with a uniform diameter of < 10 nm, which worked as capsid-like subunits to further interact with DNA to produce hierarchical virus-mimicking structures by encapsulating DNA in the interior. Such artificial viruses can effectively protect DNA from nuclease digestion and achieve efficient genome release by enzyme-triggered structure disassembly, which ensured a high level of gene transfection in tumor cells. The system emulates very well the structural and functional properties of natural viruses from the aspects of capsid formation, genome package and gene transfection, which is highly promising for application as efficient gene vectors.

Helical structure motifs made searchable for functional peptide design

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .

Embedding a membrane protein into an enveloped artificial viral replica

Natural enveloped viruses, in which nucleocapsids are covered with lipid bilayers, contain membrane proteins on the outer surface that are involved in diverse functions, such as adhesion and infection of host cells. Previously, we constructed an enveloped artificial viral capsid through the complexation of cationic lipid bilayers onto an anionic artificial viral capsid self-assembled from β-annulus peptides. Here we demonstrate the embedding of the membrane protein Connexin-43 (Cx43), on the enveloped artificial viral capsid using a cell-free expression system. The expression of Cx43 in the presence of the enveloped artificial viral capsid was confirmed by western blot analysis. The embedding of Cx43 on the envelope was evaluated by detection via the anti-Cx43 antibody, using fluorescence correlation spectroscopy (FCS) and transmission electron microscopy (TEM). Interestingly, many spherical structures connected to each other were observed in TEM images of the Cx43-embedded enveloped viral replica. In addition, it was shown that fluorescent dyes could be selectively transported from Cx43-embedded enveloped viral replicas into Cx43-expressing HepG2 cells. This study provides a proof of concept for the creation of multimolecular crowding complexes, that is, an enveloped artificial viral replica embedded with membrane proteins.

We demonstrate the embedding membrane protein, Cx43, on the enveloped artificial viral capsid using a cell-free expression system. The embedding of Cx43 on the envelope was evaluated by detection with anti-Cx43 antibody using FCS and TEM.

Chemical syntheses of bioinspired and biomimetic polymers toward biobased materials

The rich structures and hierarchical organizations in nature provide many sources of inspiration for advanced material designs. We wish to recapitulate properties such as high mechanical strength, colour-changing ability, autonomous healing and antimicrobial efficacy in next-generation synthetic materials. Common in nature are non-covalent interactions such as hydrogen bonding, ionic interactions and hydrophobic effects, which are all useful motifs in tailor-made materials. Among these are biobased components, which are ubiquitously conceptualized in the space of recently developed bioinspired and biomimetic materials. In this regard, sustainable organic polymer chemistry enables us to tune the properties and functions of such materials that are essential for daily life. In this Review, we discuss recent progress in bioinspired and biomimetic polymers and provide insights into biobased materials through the evolution of chemical approaches, including networking/crosslinking, dynamic interactions and self-assembly. We focus on advances in biobased materials; namely polymeric mimics of resilin and spider silk, mechanically and optically adaptive materials, self-healing elastomers and hydrogels, and antimicrobial polymers.

Self-Assembling Peptide Dendron Nanoparticles with High Stability and a Multimodal Antimicrobial Mechanism of Action

Self-assembling nanometer-scale structured peptide polymers and peptide dendrimers have shown promise in biomedical applications due to their versatile properties and easy availability. Herein, self-assembling peptide dendron nanoparticles (SPDNs) with potent antimicrobial activity against a range of bacteria were developed based on the nanoscale self-assembly of an arginine-proline repeat branched peptide dendron bearing a hexadecanoic acid chain. The SPDNs are biocompatible, and our most active peptide dendron nanoparticle, C₁₆-3RP, was found to have negligible toxicity after both in vitro and in vivo studies. Furthermore, the C₁₆-3RP nanoparticles showed excellent stability under physiological concentrations of salt ions and against serum and protease degradation, resulting in highly effective treatment in a mouse acute peritonitis model. Comprehensive analyses using a series of biofluorescence, microscopy, and transcriptome sequencing techniques revealed that C₁₆-3RP nanoparticles kill Gram-negative bacteria by increasing bacterial membrane permeability, inducing cytoplasmic membrane depolarization and drastic membrane disruption, inhibiting ribosome biogenesis, and influencing energy generation and other processes. Collectively, C₁₆-3RP nanoparticles show promising biocompatibility and in vivo therapeutic efficacy without apparent resistance development. These advancements may facilitate the development of peptide-based antibiotics in clinical settings.

Designer protein pseudo-capsids targeting intracellular bacteria

The emergence of multidrug-resistant bacteria stimulates the search for antimicrobial materials capable of addressing challenges conventional antibiotics fail to address. The ability to target intracellular bacteria remains one of the most fundamental tasks for contemporary antimicrobial treatments. Here we report engineered protein pseudo-capsids targeting bacteria internalised in macrophages. Using a combination of live-cell imaging and single-cell electron microscopy analysis we show that these materials effectively disrupt the bacteria without affecting the host cells. The study offers a disruptive antimicrobial strategy demonstrating potential for developing principally more challenging mechanisms for bacteria to overcome.

Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics

Viruses are natural supramolecular nanostructures that form spontaneously by molecular self-assembly of complex biomolecules. Peptide self-assembly is a versatile tool that allows mimicking viruses by creating their simplified versions through the design of functional, supramolecular materials with modularity, tunability, and responsiveness to chemical and physical stimuli. The main challenge in the design and fabrication of peptide materials is related to the precise control between the peptide sequence and its resulting supramolecular morphology. We provide an overview of existing sequence patterns employed for the development of spherical and fibrillar peptide assemblies that can act as viral mimetics, offering the opportunity to tackle the challenges of viral infections.

Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid

Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (K_d) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.

Self-assembly of trigonal building blocks into nanostructures: molecular design and biomedical applications

Trigonal molecules have a special triskelion structure similar to clathrin protein, providing great inspiration for constructing artificial nanoassemblies. To date, various synthetic trigonal conjugates have been designed for supramolecular self-assembly, which have demonstrated versatile and controllable self-assembly ability in materials science. Here we will review the design of trigonal (sometimes called three-legged, tripodal, C3-symmetric, or triskelion) building blocks that can self-assemble into various nanostructures and discuss the biomedical applications of the self-assembled nanomaterials.

Functional Peptide Nanocapsules Self-Assembled from β-Annulus Peptides

Spherical viruses are unique nanocapsules formed by self-assembly of coat proteins (capsids). By mimicking natural spherical capsids, various artificial viral capsids are developed by using self-assembled proteins and peptides as building blocks. We developed an artificial viral capsid consisting of a β-annulus peptide designed from natural viruses. The "β-annulus capsid" can be functionalized by encapsulating guest molecules to the inside and decoration of exogenous molecules on the outside. Here, we describe the encapsulation and decoration on the β-annulus capsids by connecting additional sequences to the β-annulus peptide, conjugation with objective molecules, and subsequent self-assembly in aqueous solutions.

Fomite Transmission, Physicochemical Origin of Virus-Surface Interactions, and Disinfection Strategies for Enveloped Viruses with Applications to SARS-CoV-2

Inanimate objects or surfaces contaminated with infectious agents, referred to as fomites, play an important role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The long persistence of viruses (hours to days) on surfaces calls for an urgent need for effective surface disinfection strategies to intercept virus transmission and the spread of diseases. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, is important for understanding how diseases are transmitted and for developing effective intervention strategies. This review summarizes the current knowledge and underlying physicochemical processes of virus transmission, in particular via fomites, and common disinfection approaches. Gaps in knowledge and the areas in need of further research are also identified. The review focuses on SARS-CoV-2, but discussion of related viruses is included to provide a more comprehensive review given that much remains unknown about SARS-CoV-2. Our aim is that this review will provide a broad survey of the issues involved in fomite transmission and intervention to a wide range of readers to better enable them to take on the open research challenges.

Imaging and 3D Reconstruction of De Novo Peptide Capsids

Nanoscale systems encapsulating biomacromolecules hold promise for cell and gene therapies. Common issues hampering progress include polydispersity, heterogeneity in size and shape, agglomeration, and poor stability. Much attention is given to the search of novel designs. However, reliable protocols for the validation of encapsulating systems in the continuum of their physicochemical properties, from design to ultrastructure, are lacking. Herein, we report electron microscopy protocols for biologically functional shell-like peptide capsids, which exhibit the physical characteristics of viruses including folding-mediated self-assembly, hollow shell morphology, and uniformity in size.

Ultramicrotomy Analysis of Peptide-Treated Cells

Electron microscopy offers necessary precision for the characterization of peptide materials at the nanoscale. Analysis is typically performed for acellular material specimens, whereas measurements in more complex, cellular environments prompt additional considerations for sample processing. Herein, we describe a protocol for the ultramicrotomy analysis of peptide-treated bacterial and mammalian cells. An emphasis is made on cell analysis following peptide treatment, as opposed to peptide analysis in cells, and focuses on sample processing, including fixation and staining procedures, resin embedding, sectioning, and imaging. The application of the protocol is demonstrated for intracellular measurements using antimicrobial peptide materials.

Imaging the Effects of Peptide Materials on Phospholipid Membranes by Atomic Force Microscopy

Recent advances in biomolecular design require accurate measurements performed in native or near-native environments in real time. Atomic force microscopy (AFM) is a powerful tool to observe the dynamics of biologically relevant processes at aqueous interfaces with high spatial resolution. Here, we describe imaging protocols to characterize the effects of peptide materials on phospholipid membranes in solution by AFM. These protocols can be used to determine the mechanism and kinetics of membrane-associated activities at the nanoscale.

Horseradish Peroxidase-Decorated Artificial Viral Capsid Constructed from β-Annulus Peptide via Interaction between His-Tag and Ni-NTA

Artificial construction of spherical protein assemblies has attracted considerable attention due to its potential use in nanocontainers, nanocarriers, and nanoreactors. In this work, we demonstrate a novel strategy to construct peptide nanocapsules (artificial viral capsids) decorated with enzymes via interactions between His-tag and Ni-NTA. A β-annulus peptide derived from the tomato bushy stunt virus was modified with Ni-NTA at the C-terminus, which is directed toward the exterior surface of the artificial viral capsid. The β-annulus peptide bearing Ni-NTA at the C-terminus self-assembled into capsids of about 50 nm in diameter. The Ni-NTA-displayed capsids were complexed with recombinant horseradish peroxidase (HRP) with a C-terminal His-tag which was expressed in Escherichia coli. The β-annulus peptide-HRP complex formed spherical assemblies whose sizes were 30–90 nm, with the ζ-potential revealing that the HRP was decorated on the outer surface of the capsid.

Silver assisted stereo-directed assembly of branched peptide nucleic acids into four-point nanostars

Branched chiral peptide nucleic acids br(4S/R)-PNA with three arms of PNA-C4 strands were constructed on a central chiral core of 4(R/S)-aminoproline as the branching center. The addition of Ag+ triggered the self-assembly of branched PNAs through the formation of C-Ag+-C metallo base pairing of the three PNA C4 arms leading to non-covalent dendrimers, whose architecture is directed by the C4(R/S)-stereocenter of core 4-aminoproline. The 4S-aminoprolyl core enabled the precise formation of four-pointed nanostars that was not realised with 4R-aminoprolyl or acyclic, achiral aminoethyl glycyl PNA cores. The dendritic assembly of 4 pointed nanostars exhibited net chirality of base stacks in CD spectra, while the base stack assembly from br(4R)-PNA 2 was overall achiral. The results demonstrate that the silver assisted, 4S-aminoproline core stereo selective chiral assembly of branched PNAs manifests into nanostar morphology. The chiral branched PNAs open new vistas in the supramolecular organization of nucleic acids.

Green fluorescent protein inspired fluorophores

Green fluorescence proteins (GFP) are appealing to a variety of biomedical and biotechnology applications, such as protein fusion, subcellular localizations, cell visualization, protein-protein interaction, and genetically encoded sensors. To mimic the fluorescence of GFP, various compounds, such as GFP chromophores analogs, hydrogen bond-rich proteins, and aromatic peptidyl nanostructures that preclude free rotation of the aryl-alkene bond, have been developed to adapt them for a fantastic range of applications. Herein, we firstly summarize the structure and luminescent mechanism of GFP. Based on this, the design strategy, fluorescent properties, and the advanced applications of GFP-inspired fluorophores are then carefully discussed. The diverse advantages of bioinspired fluorophores, such as biocompatibility, structural simplicity, and capacity to form a variety of functional nanostructures, endow them potential candidates as the next-generation bio-organic optical materials.

Atomic force microscopy to elucidate how peptides disrupt membranes

Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.

Molecular assemblies built with the artificial protein Pizza

Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric β -propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains.

Conjugated Protein Domains as Engineered Scaffold Proteins

Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of libraries of engineered multidomain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multidomain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation, and hydrogel formation.

Enveloped artificial viral capsids self-assembled from anionic β-annulus peptide and cationic lipid bilayer

Anionic artificial viral capsids were self-assembled from β-annulus-EE peptide, then complexed with lipid-bilayer-containing cationic lipids via electrostatic interaction to form enveloped artificial viral capsids. The critical aggregation concentration of the enveloped artificial viral capsid was significantly lower than that of the uncomplexed artificial viral capsid, indicating that the lipid bilayer stabilised the capsid structure.

Self-assembly of chimeric peptides toward molecularly defined hexamers with controlled multivalent ligand presentation

This work demonstrates a self-assembling peptide strategy to form finite, molecularly defined trigonal bipyramidal-like hexamers which offer control over multivalent ligand display for enhanced tumor targeting.

Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy

Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.

Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters

Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.

Cellular Metrology: Scoping for a Value Proposition in Extra- and Intracellular Measurements

The symptomatic irreproducibility of data in biomedicine and biotechnology prompts the need for higher order measurements of cells in their native and near-native environments. Such measurements may support the adoption of new technologies as well as the development of research programs across different sectors including healthcare and clinic, environmental control and national security. With an increasing demand for reliable cell-based products and services, cellular metrology is poised to help address current and emerging measurement challenges faced by end-users. However, metrological foundations in cell analysis remain sparse and significant advances are necessary to keep pace with the needs of modern medicine and industry. Herein we discuss a role of metrology in cell and cell-related R&D activities to underpin growing international measurement capabilities. Relevant measurands are outlined and the lack of reference methods and materials, particularly those based on functional cell responses in native environments, is highlighted. The status quo and current challenges in cellular measurements are discussed in the light of metrological traceability in cell analysis and applications (e.g., a functional cell count). An emphasis is made on the consistency of measurement results independent of the analytical platform used, high confidence in data quality vs. quantity, scale of measurements and issues of building infrastructure for end-users.

Aggregation determines the selectivity of membrane-active anticancer and antimicrobial peptides: The case of killerFLIP

Host defense peptides selectively kill bacterial and cancer cells (including those that are drug-resistant) by perturbing the permeability of their membranes, without being significantly toxic to the host. Coulombic interactions between these cationic and amphipathic peptides and the negatively charged membranes of pathogenic cells contribute to the selective toxicity. However, a positive charge is not sufficient for selectivity, which can be achieved only by a finely tuned balance of electrostatic and hydrophobic driving forces. A common property of amphipathic peptides is the formation of aggregated structures in solution, but the role of this phenomenon in peptide activity and selectivity has received limited attention. Our data on the anticancer peptide killerFLIP demonstrate that aggregation strongly increases peptide selectivity, by reducing the effective peptide hydrophobicity and thus the affinity towards membranes composed of neutral lipids (like the outer layer of healthy eukaryotic cell membranes). Aggregation is therefore a useful tool to modulate the selectivity of membrane active peptides and peptidomimetics.

Peptide-induced super-assembly of biocatalytic metal-organic frameworks for programmed enzyme cascades

Despite the promise of metal-organic frameworks (MOFs) as functional matrices for enzyme stabilization, the development of a stimulus-responsive approach to induce a multi-enzyme cascade reaction in MOFs remains a critical challenge. Here, a novel method using peptide-induced super-assembly of MOFs is developed for programmed enzyme cascade reactions on demand. The super-assembled MOF particles containing different enzymes show remarkable 7.3-fold and 4.4-fold catalytic activity enhancements for the two-enzyme and three-enzyme cascade reactions, respectively, as compared with the unassembled MOF nanoparticles. Further digestion of the coiled-coil forming peptides on the MOF surfaces leads to the MOF superstructure disassembly and the programmed enzyme cascade reaction being "switched-off". Research on these stimuli-responsive materials with controllable and predictable biocatalytic functions/properties provide a concept to facilitate the fabrication of next-generation smart materials based on precision chemistry.