Constructing catalytic antimicrobial nanoparticles by encapsulation of hydrogen peroxide producing enzyme inside the P22 VLP

Nanoreactor-based catalytic systems for therapeutic applications: Principles, strategies, and challenges

Inspired by natural catalytic compartments, various synthetic compartments that seclude catalytic reactions have been developed to understand complex multistep biosynthetic pathways, bestow therapeutic effects, or extend biosynthetic pathways in living cells. These emerging nanoreactors possessed many advantages over conventional biomedicine, such as good catalytic activity, specificity, and sustainability. In the past decade, a great number of efficient catalytic systems based on diverse nanoreactors (polymer vesicles, liposome, polymer micelles, inorganic-organic hybrid materials, MOFs, etc.) have been designed and employed to initiate in situ catalyzed chemical reactions for therapy. This review aims to present the recent progress in the development of catalytic systems based on nanoreactors for therapeutic applications, with a special emphasis on the principles and design strategies. Besides, the key components of nanoreactor-based catalytic systems, including nanocarriers, triggers or energy inputs, and products, are respectively introduced and discussed in detail. Challenges and prospects in the fabrication of therapeutic catalytic nanoreactors are also discussed as a conclusion to this review. We believe that catalytic nanoreactors will play an increasingly important role in modern biomedicine, with improved therapeutic performance and minimal side effects.

Virus-like nanoparticles as enzyme carriers for Enzyme Replacement Therapy (ERT)

Enzyme replacement therapy (ERT) has been used to treat a few of the many existing diseases which are originated from the lack of, or low enzymatic activity. Exogenous enzymes are administered to contend with the enzymatic activity deficiency. Enzymatic nanoreactors based on the enzyme encapsulation inside of virus-like particles (VLPs) appear as an interesting alternative for ERT. VLPs are excellent delivery vehicles for therapeutic enzymes as they are biodegradable, uniformly organized, and porous nanostructures that transport and could protect the biocatalyst from the external environment without much affecting the bioactivity. Consequently, significant efforts have been made in the production processes of virus-based enzymatic nanoreactors and their functionalization, which are critically reviewed. The use of virus-based enzymatic nanoreactors for the treatment of lysosomal storage diseases such as Gaucher, Fabry, and Pompe diseases, as well as potential therapies for galactosemia, and Hurler and Hunter syndromes are discussed.

Bacteriophage P22 Capsid as a Pluripotent Nanotechnology Tool

The Salmonella enterica bacteriophage P22 is one of the most promising models for the development of virus-like particle (VLP) nanocages. It possesses an icosahedral T = 7 capsid, assembled by the combination of two structural proteins: the coat protein (gp5) and the scaffold protein (gp8). The P22 capsid has the remarkable capability of undergoing structural transition into three morphologies with differing diameters and wall-pore sizes. These varied morphologies can be explored for the design of nanoplatforms, such as for the development of cargo internalization strategies. The capsid proteic nature allows for the extensive modification of its structure, enabling the addition of non-native structures to alter the VLP properties or confer them to diverse ends. Various molecules were added to the P22 VLP through genetic, chemical, and other means to both the capsid and the scaffold protein, permitting the encapsulation or the presentation of cargo. This allows the particle to be exploited for numerous purposes-for example, as a nanocarrier, nanoreactor, and vaccine model, among other applications. Therefore, the present review intends to give an overview of the literature on this amazing particle.

Delayed In Vivo Encapsulation of Enzymes Alters the Catalytic Activity of Virus-Like Particle Nanoreactors

Encapsulation of enzymes inside protein cage structures, mimicking protein-based organelle structures found in nature, has great potential for the development of new catalytic materials with enhanced properties. In vitro and in vivo methodologies have been developed for the encapsulation of enzymes within protein cage structures of several types, particularly virus-like particles (VLPs), with the ability to retain the activity of the encapsulated enzymes. Here, we examine the in vivo encapsulation of enzymes within the bacteriophage P22 derived VLP and show that some enzymes may require a delay in encapsulation to allow proper folding and maturation before they can be encapsulated inside P22 as fully active enzymes. Using a sequential expression strategy, where enzyme cargoes are first expressed, allowed to fold, and later encapsulated by the expression of the P22 coat protein, altered enzymatic activities are obtained in comparison to enzymes encapsulated in P22 VLPs using a simultaneous coexpression strategy. The strategy and results discussed here highlight important considerations for researchers investigating the encapsulation of enzymes inside confined reaction environments via in vivo routes and provide a potential solution for those that have been unable to produce active enzymes upon encapsulation.

The biomedical and bioengineering potential of protein nanocompartments

Protein nanocompartments (PNCs) are self-assembling biological nanocages that can be harnessed as platforms for a wide range of nanobiotechnology applications. The most widely studied examples of PNCs include virus-like particles, bacterial microcompartments, encapsulin nanocompartments, enzyme-derived nanocages (such as lumazine synthase and the E2 component of the pyruvate dehydrogenase complex), ferritins and ferritin homologues, small heat shock proteins, and vault ribonucleoproteins. Structural PNC shell proteins are stable, biocompatible, and tolerant of both interior and exterior chemical or genetic functionalization for use as vaccines, therapeutic delivery vehicles, medical imaging aids, bioreactors, biological control agents, emulsion stabilizers, or scaffolds for biomimetic materials synthesis. This review provides an overview of the recent biomedical and bioengineering advances achieved with PNCs with a particular focus on recombinant PNC derivatives.

Synthesis and Assembly of Hepatitis B Virus-Like Particles in a Pichia pastoris Cell-Free System

Virus-like particles (VLPs) are supramolecular protein assemblies with the potential for unique and exciting applications in synthetic biology and medicine. Despite the attention VLPs have gained thus far, considerable limitations still persist in their production. Poorly scalable manufacturing technologies and inconsistent product architectures continue to restrict the full potential of VLPs. Cell-free protein synthesis (CFPS) offers an alternative approach to VLP production and has already proven to be successful, albeit using extracts from a limited number of organisms. Using a recently developed Pichia pastoris-based CFPS system, we have demonstrated the production of the model Hepatitis B core antigen VLP as a proof-of-concept. The VLPs produced in the CFPS system were found to have comparable characteristics to those previously produced in vivo and in vitro. Additionally, we have developed a facile and rapid synthesis, assembly and purification methodology that could be applied as a rapid prototyping platform for vaccine development or synthetic biology applications. Overall the CFPS methodology allows far greater throughput, which will expedite the screening of optimal assembly conditions for more robust and stable VLPs. This approach could therefore support the characterization of larger sample sets to improve vaccine development efficiency.

Tuning the catalytic properties of P22 nanoreactors through compositional control

Enzymes are biomacromolecular protein catalysts that are widely used in a plethora of industrial-scale applications due to their high selectivity, efficiency and ability to work under mild conditions. Many industrial processes require the immobilization of enzymes to enhance their performance and stability. Encapsulation of enzymes in protein cages provides an excellent immobilization platform to create nanoreactors with enhanced enzymatic stability and desired catalytic activities. Here we show that the catalytic activity of nanoreactors, derived from the bacteriophage P22 viral capsids, can be finely-tuned by controlling the packaging stoichiometry and packing density of encapsulated enzymes. The packaging stoichiometry of the enzyme alcohol dehydrogenase (AdhD) was controlled by co-encapsulating it with wild-type scaffold protein (wtSP) at different stoichiometric ratios using an in vitro assembly approach and the packing density was controlled by selectively removing wtSP from the assembled nanoreactors. An inverse relationship was observed between the catalytic activity (k_cat) of AdhD enzyme and the concentration of co-encapsulated wtSP. Selective removal of the wtSP resulted in the similar activity of AdhD in all nanoreactors despite the difference in the volume occupied by enzymes inside nanoreactors, indicating that the AdhD enzymes do not experience self-crowding even under high molarity of confinement (M_conf) conditions. The approach demonstrated here not only allowed us to tailor the activity of encapsulated AdhD catalysts but also the overall functional output of nanoreactors (enzyme-VLP complex). The approach also allowed us to differentiate the effects of crowding and confinement on the functional properties of enzymes encapsulated in an enclosed system, which could pave the way for designing more efficient nanoreactors.

Virus-derived materials: bury the hatchet with old foes

Viruses, with special architecture and unique biological nature, can be utilized for various biomedical applications.

Site-specific release of reactive oxygen species from ordered arrays of microchambers based on polylactic acid and carbon nanodots

Illustration of the laser-assisted release of hydrophilic H₂O₂ cargo from free-standing ordered arrays of biopolymer-based microchambers in a highly controlled manner.

Nanomaterial-Supported Enzymes for Water Purification and Monitoring in Point-of-Use Water Supply Systems

Increasing pollution of global water sources and challenges in rapid detection and treatment of the wide range of contaminants pose considerable burdens on public health. The issue is particularly critical in rural areas, where building of centralized water treatment systems and pipe infrastructure to connect dispersed populations is not always practical. Point-of-use (POU) water supply systems provide cost-effective and energy-efficient approaches to store, treat, and monitor the quality of water. Currently available POU systems have limited success in dealing with the portfolio of emerging contaminants, particularly those present at trace concentrations. A site-to-site variation in contaminant species and concentrations also requires versatile POU systems to detect and treat contaminants and provide on-demand clean water. Among different technologies for developing rapid and sensitive water purification processes and sensors, enzymes offer one of the potential solutions because of their strong activity and selectivity toward chemical substrates. Many enzyme-nanomaterial composites have recently been developed that enhance enzymes' stability and activity and expand their functionality, thus facilitating the application of nanosupported enzymes in advanced POU systems. In this Account, we highlight the strengths and limitations of nanosupported enzymes for their potential applications in POU systems for water treatment as well as detection of contaminants, even at trace levels. We first summarize the mechanisms by which silica, carbon, and metallic nanosupports improve enzyme stability, selectivity, and catalysis. The unique immobilization properties and potential advantages of novel bioderived nanosupports over non-bioderived nanomaterials are emphasized. We illustrate prospective applications of nanosupported enzymes in POU systems with different roles: water purification, disinfection, and contaminant sensing. For each type of application, nanosupported enzymes offer higher performance than free enzymes. Nanosupports prolong enzymes' lifetimes and improve the rates of contaminant removal by concentrating contaminants near the enzymes. Nanosupports also stabilize antimicrobial enzymes while facilitating their attachment to bacterial surfaces, thereby increasing their potential uses for disinfection and prevention of biofouling in water purification and storage devices. As enzyme-based electrochemical sensors rely on electrochemical reactions of enzymatically generated species, the ability of conductive nanosupports to enhance enzyme activity and stability and to promote transfer of electrons onto the electrode greatly improves the sensitivity and durability of electroenzymatic contaminant sensors. Despite the promising results in laboratory settings, the application of nanosupported enzymes in real-world POU systems requires the implementation of multiple enzyme combinations and strategies for minimizing health risks associated with unintended releases of nanomaterials. Finally, we identify multidisciplinary research gaps in the development of nanosupported enzyme treatment systems and provide frameworks for the early adopters to make informed decisions on whether and how to use such POU systems.

Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis

The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.

Biotransporting Biocatalytic Reactors toward Therapeutic Nanofactories

Drug-delivery systems (DDSs), in which drug encapsulation in nanoparticles enables targeted delivery of therapeutic agents and their release at specific disease sites, are important because they improve drug efficacy and help to decrease side effects. Although significant progress has been made in the development of DDSs for the treatment of a wide range of diseases, new approaches that increase the scope and effectiveness of such systems are still needed. Concepts such as nanoreactors and nanofactories are therefore attracting much attention. Nanoreactors, which basically consist of vesicle-encapsulated enzymes, provide prodrug conversion to therapeutic agents rather than simple drug delivery. Nanofactories are an extension of this concept and combine the features of nanoreactors and delivery carriers. Here, the required features of nanofactories are discussed and an overview of current strategies for the design and fabrication of different types of nanoreactors, i.e., systems based on lipid or polymer vesicles, capsules, mesoporous silica, viral capsids, and hydrogels, and their respective advantages and shortcomings, is provided. In vivo applications of biocatalytic reactors in the treatment of cancer, glaucoma, neuropathic pain, and alcohol intoxication are also discussed. Finally, the prospects for further progress in this important and promising field are outlined.

Cargo Retention inside P22 Virus-Like Particles

Viral protein cages, with their regular and programmable architectures, are excellent platforms for the development of functional nanomaterials. The ability to transform a virus into a material with intended structure and function relies on the existence of a well-understood model system, a noninfectious virus-like particle (VLP) counterpart. Here, we study the factors important to the ability of P22 VLP to retain or release various protein cargo molecules depending on the nature of the cargo, the capsid morphology, and the environmental conditions. Because the interaction between the internalized scaffold protein (SP) and the capsid coat protein (CP) is noncovalent, we have studied the efficiency with which a range of SP variants can dissociate from the interior of different P22 VLP morphologies and exit by traversing the porous capsid. Understanding the types of cargos that are either retained or released from the P22 VLP will aid in the rational design of functional nanomaterials.

Preparation of gold nanoparticles supported on graphene oxide with flagella as the template for nonenzymatic hydrogen peroxide sensing

Gold nanoparticles supported on graphene oxide with flagella as the template were developed as an electrochemical sensor for the detection of hydrogen peroxide (H₂O₂) in serum. The flagella-Au nanoparticles composite and graphene oxide were dropped onto a glassy carbon electrode (GCE) to form a new H₂O₂ electrochemical sensor. The structure morphology of the prepared sensor was characterized by transmission electron microscopy (TEM), and the electrocatalytic performance towards H₂O₂ reduction was evaluated by cyclic voltammetry (CV) and amperometric methods. The response current of the sensor showed a good linear relationship with the concentration of H₂O₂ in the range of 10-1000 μM (R² = 0.9916). The minimum detection limit of 1 μM was obtained (S/N = 3). Finally, the sensor was applied to the detection of H₂O₂ in serum, and the recoveries were satisfactory. As the sensor is sensitive, fast, and easy to make, it is expected to be used for rapid detection of H₂O₂. Graphical abstract ᅟ.

Protein cage assembly across multiple length scales

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

Templated Assembly of a Functional Ordered Protein Macromolecular Framework from P22 Virus-like Particles

Bottom-up construction of mesoscale materials using biologically derived nanoscale building blocks enables engineering of desired physical properties using green production methods. Virus-like particles (VLPs) are exceptional building blocks due to their monodispersed sizes, geometric shapes, production ease, proteinaceous composition, and our ability to independently functionalize the interior and exterior interfaces. Here a VLP, derived from bacteriophage P22, is used as a building block for the fabrication of a protein macromolecular framework (PMF), a tightly linked 3D network of functional protein cages that exhibit long-range order and catalytic activity. Assembly of PMFs was electrostatically templated, using amine-terminated dendrimers, then locked into place with a ditopic cementing protein that binds to P22. Long-range order is preserved on removal of the dendrimer, leaving a framework material composed completely of protein. Encapsulation of β-glucosidase enzymes inside of P22 VLPs results in formation of stable, condensed-phase materials with high local concentration of enzymes generating catalytically active PMFs.

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.

Encapsulation of Active Enzymes within Bacteriophage P22 Virus-Like Particles

Virus-like particles (VLPs) are nonpathogenic protein cage structures derived from viral coat proteins that have found utility in the area of biomaterials and nanotechnology. VLPs have been exploited as containers for the sequestration and encapsulation of a wide range of guest molecules in their hollow interiors. The robust nature of VLPs lend them as versatile scaffolds that can be exploited to provide protection to encapsulated guest molecules, such as enzymes which are often susceptible to inactivation and degradation, and for organization and construction of new nanomaterials incorporating the chemical properties of the guest molecules. In this chapter a background and methodology for the encapsulation of enzymes on the interior of the bacteriophage P22 derived VLP is described.

In Vivo Packaging of Protein Cargo Inside of Virus-Like Particle P22

Protein cages are ubiquitous in nature and have been manipulated to encapsulate a range of nonnative cargos including organic, inorganic, and small molecules. Many protein cages are derived from virus capsids that have been rendered noninfectious through the preferential production and use of proteins that are solely involved in capsid assembly, but which do not encapsulate genetic material and therefore do not contribute to infectivity. Here, we describe the production of protein cargo(s) encapsulated inside of P22 virus-like particles (VLPs), derived from bacteriophage P22. This is achieved via genetic fusion of the cargo to a scaffolding protein, which becomes encapsulated in the P22 VLP during templated assembly of the protein cage.

Sortase-Mediated Ligation as a Modular Approach for the Covalent Attachment of Proteins to the Exterior of the Bacteriophage P22 Virus-like Particle

Virus-like particles are unique platforms well suited for the construction of nanomaterials with broad-range applications. The research presented here describes the development of a modular approach for the covalent attachment of protein domains to the exterior of the versatile bacteriophage P22 virus-like particle (VLP) via a sortase-mediated ligation strategy. The bacteriophage P22 coat protein was genetically engineered to incorporate an LPETG amino acid sequence on the C-terminus, providing the peptide recognition sequence utilized by the sortase enzyme to catalyze peptide bond formation between the LPETG-tagged protein and a protein containing a polyglycine sequence on the N-terminus. Here we evaluate attachment of green fluorescent protein (GFP) and the head domain of the influenza hemagglutinin (HA) protein by genetically producing polyglycine tagged proteins. Attachment of both proteins to the exterior of the P22 VLP was found to be highly efficient as judged by SDS-PAGE densitometry. These results enlarge the tool kit for modifying the P22 VLP system and provide new insights for other VLPs that have an externally displayed C-terminus that can use the described strategy for the modular modification of their external surface for various applications.

Phage-Enabled Nanomedicine: From Probes to Therapeutics in Precision Medicine

Both lytic and temperate bacteriophages (phages) can be applied in nanomedicine, in particular, as nanoprobes for precise disease diagnosis and nanotherapeutics for targeted disease treatment. Since phages are bacteria-specific viruses, they do not naturally infect eukaryotic cells and are not toxic to them. They can be genetically engineered to target nanoparticles, cells, tissues, and organs, and can also be modified with functional abiotic nanomaterials for disease diagnosis and treatment. This Review will summarize the current use of phage structures in many aspects of precision nanomedicine, including ultrasensitive biomarker detection, enhanced bioimaging for disease diagnosis, targeted drug and gene delivery, directed stem cell differentiation, accelerated tissue formation, effective vaccination, and nanotherapeutics for targeted disease treatment. We will also propose future directions in the area of phage-based nanomedicines, and discuss the state of phage-based clinical trials.

Assembling Enzymatic Cascade Pathways inside Virus-Based Nanocages Using Dual-Tasking Nucleic Acid Tags

The packaging of proteins into discrete compartments is an essential feature for cellular efficiency. Inspired by Nature, we harness virus-like assemblies as artificial nanocompartments for enzyme-catalyzed cascade reactions. Using the negative charges of nucleic acid tags, we develop a versatile strategy to promote an efficient noncovalent co-encapsulation of enzymes within a single protein cage of cowpea chlorotic mottle virus (CCMV) at neutral pH. The encapsulation results in stable 21-22 nm sized CCMV-like particles, which is characteristic of an icosahedral T = 1 symmetry. Cryo-EM reconstruction was used to demonstrate the structure of T = 1 assemblies templated by biological soft materials as well as the extra-swelling capacity of these T = 1 capsids. Furthermore, the specific sequence of the DNA tag is capable of operating as a secondary biocatalyst as well as bridging two enzymes for co-encapsulation in a single capsid while maintaining their enzymatic activity. Using CCMV-like particles to mimic nanocompartments can provide valuable insight on the role of biological compartments in enhancing metabolic efficiency.

Design of virus-based nanomaterials for medicine, biotechnology, and energy

This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.

Programmed Self-Assembly of an Active P22-Cas9 Nanocarrier System

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) RNA-guided endonucleases are powerful new tools for targeted genome engineering. These nucleases provide an efficient and precise method for manipulating eukaryotic genomes; however, delivery of these reagents to specific cell-types remains challenging. Virus-like particles (VLPs) derived from bacteriophage P22, are robust supramolecular protein cage structures with demonstrated utility for cell type-specific delivery of encapsulated cargos. Here, we genetically fuse Cas9 to a truncated form of the P22 scaffold protein, which acts as a template for capsid assembly as well as a specific encapsulation signal for Cas9. Our results indicate that Cas9 and a single-guide RNA are packaged inside the P22 VLP, and activity assays indicate that this RNA-guided endonuclease is functional for sequence-specific cleavage of dsDNA targets. This work demonstrates the potential for developing P22 as a delivery vehicle for cell specific targeting of Cas9.