Targeting antibacterial agents by using drug-carrying filamentous bacteriophages

Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update

Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.

Current developments and prospects of the antibiotic delivery systems

Antibiotics have remained the cornerstone for the treatment of bacterial infections ever since their discovery in the twentieth century. The uproar over antibiotic resistance among bacteria arising from genome plasticity and biofilm development has rendered current antibiotic therapies ineffective, urging the development of innovative therapeutic approaches. The development of antibiotic resistance among bacteria has further heightened the clinical failure of antibiotic therapy, which is often linked to its low bioavailability, side effects, and poor penetration and accumulation at the site of infection. In this review, we highlight the potential use of siderophores, antibodies, cell-penetrating peptides, antimicrobial peptides, bacteriophages, and nanoparticles to smuggle antibiotics across impermeable biological membranes to achieve therapeutically relevant concentrations of antibiotics and combat antimicrobial resistance (AMR). We will discuss the general mechanisms via which each delivery system functions and how it can be tailored to deliver antibiotics against the paradigm of mechanisms underlying antibiotic resistance.

Living virus-based nanohybrids for biomedical applications

Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Rare antibody phage isolation and discrimination (RAPID) biopanning enables identification of high-affinity antibodies against challenging targets

In vitro biopanning platforms using synthetic phage display antibody libraries have enabled the identification of antibodies against antigens that were once thought to be beyond the scope of immunization. Applying these methods against challenging targets remains a critical challenge. Here, we present a new biopanning pipeline, RAPID (Rare Antibody Phage Isolation and Discrimination), for the identification of rare high-affinity antibodies against challenging targets. RAPID biopanning uses fluorescent labeled phage displayed fragment antigen-binding (Fab) antibody libraries for the isolation of high-affinity binders with fluorescent activated sorting. Subsequently, discriminatory hit screening is performed with a biolayer interferometry (BLI) method, BIAS (Biolayer Interferometry Antibody Screen), where candidate binders are ranked and prioritized according to their estimated kinetic off rates. Previously reported antibodies were used to develop the methodology, and the RAPID biopanning pipeline was applied to three challenging targets (CHIP, Gαq, and CS3D), enabling the identification of high-affinity antibodies.

Self-assembly of Au@AgNR along M13 framework: A SERS nanocarrier for bacterial detection and killing

Self-assembled functional nanomaterials with electromagnetic hot spots are crucial and highly desirable in surface-enhanced Raman scattering (SERS). Due to its versatile biological scaffold, the M13 phage has been employed to produce novel nano-building blocks and devices. In this study, we propose a novel M13 phage-based SERS nanocarrier, that utilizes the pVIII capsid in M13 to conjugate Au@Ag core-shell nanorod (Au@AgNR) with linker carboxy-PEG-thiol (M13-Au@AgNR) and the pIII capsid to specifically target Escherichia coli (E. coli). The M13-Au@AgNR@DTTC (3,3'- diethylthiocarbocyanine iodide) SERS probe was used to detect E. coli in a concentration range of 6 to 6 × 105 cfu/mL, achieving a limit of detection (LOD) of 0.5 cfu/mL. The proposed SERS platform was also tested in real samples, showing good recoveries (92%-114.3%) and a relative standard deviation (RSD) of 1.2%-4.7%. Furthermore, the system demonstrated high antibacterial efficiency against E. coli, approximately 90%, as measured by the standard plate-count method. The investigation provides an effective strategy for in vitro bacteria detection and inactivation.

Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides

Helicobacter pylori is the primary cause of 78% of gastric cancer cases, providing an opportunity to prevent cancer by controlling a single bacterial pathogen within the complex gastric microbiota. We developed highly selective antimicrobial agents against H. pylori by fusing an H. pylori-binding guide peptide (MM1) to broad-spectrum antimicrobial peptides. The common dairy probiotic Lactococcus lactis was then engineered to secrete these guided antimicrobial peptides (gAMPs). When co-cultured in vitro with H. pylori, the gAMP probiotics lost no toxicity compared to unguided AMP probiotics against the target, H. pylori, while losing >90% of their toxicity against two tested off-target bacteria. To test binding to H. pylori, the MM1 guide was fused to green fluorescent protein (GFP), resulting in enhanced binding compared to unguided GFP as measured by flow cytometry. In contrast, MM1-GFP showed no increased binding over GFP against five different off-target bacteria. These highly selective gAMP probiotics were then tested by oral gavage in mice infected with H. pylori. As a therapy, the probiotics outperformed antibiotic treatment, effectively eliminating H. pylori in just 5 days, and also protected mice from challenge infection as a prophylactic. As expected, the gAMP probiotics were as toxic against H. pylori as the unguided AMP probiotics. However, a strong rebound in gastric species diversity was found with both the selective gAMP probiotics and the non-selective AMP probiotics. Eliminating the extreme microbial dysbiosis caused by H. pylori appeared to be the major factor in diversity recovery. IMPORTANCE Alternatives to antibiotics in the control of Helicobacter pylori and the prevention of gastric cancer are needed. The high prevalence of H. pylori in the human population, the induction of microbial dysbiosis by antibiotics, and increasing antibiotic resistance call for a more sustainable approach. By selectively eliminating the pathogen and retaining the commensal community, H. pylori control may be achieved without adverse health outcomes. Antibiotics are typically used as a therapeutic post-infection, but a more targeted, less disruptive approach could be used as a long-term prophylactic against H. pylori or, by extension, against other gastrointestinal pathogens. Furthermore, the modular nature of the guided antimicrobial peptide (gAMP) technology allows for the substitution of different guides for different pathogens and the use of a cocktail of gAMPs to avoid the development of pathogen resistance.

Genetic Engineering and Biosynthesis Technology: Keys to Unlocking the Chains of Phage Therapy

Phages possess the ability to selectively eliminate pathogenic bacteria by recognizing bacterial surface receptors. Since their discovery, phages have been recognized for their potent bactericidal properties, making them a promising alternative to antibiotics in the context of rising antibiotic resistance. However, the rapid emergence of phage-resistant strains (generally involving temperature phage) and the limited host range of most phage strains have hindered their antibacterial efficacy, impeding their full potential. In recent years, advancements in genetic engineering and biosynthesis technology have facilitated the precise engineering of phages, thereby unleashing their potential as a novel source of antibacterial agents. In this review, we present a comprehensive overview of the diverse strategies employed for phage genetic engineering, as well as discuss their benefits and drawbacks in terms of bactericidal effect.

Genetically engineered filamentous phage for bacterial detection using magnetic resonance imaging

Detecting bacterial cells with high specificity in deep tissues is challenging. Optical probes provide specificity, but are limited by the scattering and absorption of light in biological tissues. Conversely, magnetic resonance imaging (MRI) allows unfettered access to deep tissues, but lacks contrast agents for detecting specific bacterial strains. Here, we introduce a biomolecular platform that combines both capabilities by exploiting the modularity of M13 phage to target bacteria with tunable specificity and allow deep-tissue imaging using T1-weighted MRI. We engineered two types of phage probes: one for detecting the phage's natural host, viz., F-pilus expressing E. coli; and the other for detecting a different (F-negative) bacterial target, V. cholerae. We show that these phage sensors generate 3-9-fold stronger T1 relaxation upon recognizing target cells relative to non-target bacteria. We further establish a preliminary proof-of-concept for in vivo applications, by demonstrating that phage-labeled bacteria can be detected in mice using MRI. The framework developed in this study may have potential utility in a broad range of applications, from basic biomedical research to in situ diagnostics, which require methods to detect and track specific bacteria in the context of intact living systems.

Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race

Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.

Yeast-Based Virus-like Particles as an Emerging Platform for Vaccine Development and Delivery

Virus-like particles (VLPs) are empty, nanoscale structures morphologically resembling viruses. Internal cavity, noninfectious, and particulate nature with a high density of repeating epitopes, make them an ideal platform for vaccine development and drug delivery. Commercial use of Gardasil-9 and Cervarix showed the usefulness of VLPs in vaccine formulation. Further, chimeric VLPs allow the raising of an immune response against different immunogens and thereby can help reduce the generation of medical or clinical waste. The economically viable production of VLPs significantly impacts their usage, application, and availability. To this end, several hosts have been used and tested. The present review will discuss VLPs produced using different yeasts as fermentation hosts. We also compile a list of studies highlighting the expression and purification of VLPs using a yeast-based platform. We also discuss the advantages of using yeast to generate VLPs over other available systems. Further, the issues or limitations of yeasts for producing VLPs are also summarized. The review also compiles a list of yeast-derived VLP-based vaccines that are presently in public use or in different phases of clinical trials.

Genetically Encoded Self-Assembling Protein Nanoparticles for the Targeted Delivery In Vitro and In Vivo

Targeted nanoparticles of different origins are considered as new-generation diagnostic and therapeutic tools. However, there are no targeted drug formulations within the composition of nanoparticles approved by the FDA for use in the clinic, which is associated with the insufficient effectiveness of the developed candidates, the difficulties of their biotechnological production, and inadequate batch-to-batch reproducibility. Targeted protein self-assembling nanoparticles circumvent this problem since proteins are encoded in DNA and the final protein product is produced in only one possible way. We believe that the combination of the endless biomedical potential of protein carriers as nanoparticles and the standardized protein purification protocols will make significant progress in "magic bullet" creation possible, bringing modern biomedicine to a new level. In this review, we are focused on the currently existing platforms for targeted self-assembling protein nanoparticles based on transferrin, lactoferrin, casein, lumazine synthase, albumin, ferritin, and encapsulin proteins, as well as on proteins from magnetosomes and virus-like particles. The applications of these self-assembling proteins for targeted delivery in vitro and in vivo are thoroughly discussed, including bioimaging applications and different therapeutic approaches, such as chemotherapy, gene delivery, and photodynamic and photothermal therapy. A critical assessment of these protein platforms' efficacy in biomedicine is provided and possible problems associated with their further development are described.

Biofabrication of nanoparticles: sources, synthesis, and biomedical applications

Nanotechnology is an emerging applied science delivering crucial human interventions. Biogenic nanoparticles produced from natural sources have received attraction in recent times due to their positive attributes in both health and the environment. It is possible to produce nanoparticles using various microorganisms, plants, and marine sources. The bioreduction mechanism is generally employed for intra/extracellular synthesis of biogenic nanoparticles. Various biogenic sources have tremendous bioreduction potential, and capping agents impart stability. The obtained nanoparticles are typically characterized by conventional physical and chemical analysis techniques. Various process parameters, such as sources, ions, and temperature incubation periods, affect the production process. Unit operations such as filtration, purification, and drying play a role in the scale-up setup. Biogenic nanoparticles have extensive biomedical and healthcare applications. In this review, we summarized various sources, synthetic processes, and biomedical applications of metal nanoparticles produced by biogenic synthesis. We highlighted some of the patented inventions and their applications. The applications range from drug delivery to biosensing in various therapeutics and diagnostics. Although biogenic nanoparticles appear to be superior to their counterparts, the molecular mechanism degradation pathways, kinetics, and biodistribution are often missing in the published literature, and scientists should focus more on these aspects to move them from the bench side to clinics.

Phage display for the detection, analysis, disinfection, and prevention of Staphylococcus aureus

The World Health Organization has designated Staphylococcus aureus as a global health concern. This designation stems from the emergence of multiple drug-resistant strains that already account for hundreds of thousands of deaths globally. The development of novel treatment strategies to eradicate S. aureus or mitigate its pathogenic potential is desperately needed. In the effort to develop emerging strategies to combat S. aureus, phage display is uniquely positioned to assist in this endeavor. Leveraging bacteriophages, phage display enables researchers to better understand interactions between proteins and their antagonists. In doing so, researchers have the capacity to design novel inhibitors, biosensors, disinfectants, and immune modulators that can target specific S. aureus strains. In this review, we highlight how phage display can be leveraged to design novel solutions to combat S. aureus. We further discuss existing uses of phage display as a detection, intervention, and prevention platform against S. aureus and provide outlooks on how this technology can be optimized for future applications.

Strategies and progresses for enhancing targeted antibiotic delivery

Antibiotic resistance is a global health issue and a potential risk for society. Antibiotics administered through conventional formulations are devoid of targeting effect and often spread to various undesired body sites, leading to sub-lethal concentrations at the site of action and thus resulting in emergence of resistance, as well as side effects. Moreover, we have a very slim antibiotic pipeline. Drug-delivery systems have been designed to control the rate, time, and site of drug release, and innovative approaches for antibiotic delivery provide a glint of hope for addressing these issues. This review elaborates different delivery strategies and approaches employed to overcome the limitations of conventional antibiotic therapy. These include antibiotic conjugates, prodrugs, and nanocarriers for local and targeted antibiotic release. In addition, a wide range of stimuli-responsive nanocarriers and biological carriers for targeted antibiotic delivery are discussed. The potential advantages and limitations of targeted antibiotic delivery strategies are described along with possible solutions to avoid these limitations. A number of antibiotics successfully delivered through these approaches with attained outcomes and potentials are reviewed.

Treating bacterial infections with bacteriophages in the 21st century

Bacteriophages (phages) were discovered in the early part of the 20th century, and their ability to eliminate bacterial infections as bacterial viruses gathered interest almost immediately. Bacteriophage therapy was halted in the Western world due to inconclusive results in early experiments and the concurrent discovery of antibiotics. The spread of antibiotic-resistant bacteria has elicited renewed interest in bacteriophages as a natural alternative to conventional antibiotic therapy. Interest in the application of bacteriophages has also expanded to include the environment, such as wastewater treatment, agriculture and aquaculture. Although the complete phage is important in bacteriophage therapy, the focus is shifting to purified phage enzymes. These enzymes are an attractive option for pharmaceutical companies with their patent potential. They can be bio-engineered for enhanced adjuvant properties, such as a broadened spectrum of activity or binding capability. Enzymes also eliminate the concern that the prophage might integrate resistance genes into the bacterial genome. From a clinical perspective, the first randomised clinical controlled phage therapy trial was conducted with more pioneering phase I/II clinical studies on the horizon. In this opinion paper, the authors outline bacteriophages as naturally occurring bactericidal entities, their therapeutic potential against antibiotic-resistant bacteria and compare them to antibiotics. Their potential multipurpose application in the medical field is also addressed, including the use of bacteriophages for vaccination, and utilisation of the antimicrobial enzymes that they produce.

Bacteriophages and their potential for treatment of gastrointestinal diseases

Although bacteriophages have been overshadowed as therapeutic agents by antibiotics for decades, the emergence of multidrug-resistant bacteria and a better understanding of the role of the gut microbiota in human health and disease have brought them back into focus. In this Perspective, we briefly introduce basic phage biology and summarize recent discoveries about phages in relation to their role in the gut microbiota and gastrointestinal diseases, such as inflammatory bowel disease and chronic liver disease. In addition, we review preclinical studies and clinical trials of phage therapy for enteric disease and explore current challenges and potential future directions.

VLP-Based COVID-19 Vaccines: An Adaptable Technology against the Threat of New Variants

Virus-like particles (VLPs) are a versatile, safe, and highly immunogenic vaccine platform. Recently, there are developmental vaccines targeting SARS-CoV-2, the causative agent of COVID-19. The COVID-19 pandemic affected humanity worldwide, bringing out incomputable human and financial losses. The race for better, more efficacious vaccines is happening almost simultaneously as the virus increasingly produces variants of concern (VOCs). The VOCs Alpha, Beta, Gamma, and Delta share common mutations mainly in the spike receptor-binding domain (RBD), demonstrating convergent evolution, associated with increased transmissibility and immune evasion. Thus, the identification and understanding of these mutations is crucial for the production of new, optimized vaccines. The use of a very flexible vaccine platform in COVID-19 vaccine development is an important feature that cannot be ignored. Incorporating the spike protein and its variations into VLP vaccines is a desirable strategy as the morphology and size of VLPs allows for better presentation of several different antigens. Furthermore, VLPs elicit robust humoral and cellular immune responses, which are safe, and have been studied not only against SARS-CoV-2 but against other coronaviruses as well. Here, we describe the recent advances and improvements in vaccine development using VLP technology.

Modification of a Tumor-Targeting Bacteriophage for Potential Diagnostic Applications

BACKGROUND

Tumor-targeting bacteriophages can be used as a versatile new platform for the delivery of diagnostic imaging agents and therapeutic cargo. This became possible due to the development of viral capsid modification method. Earlier in our laboratory and using phage display technology, phages to malignant breast cancer cells MDA-MB 231 were obtained. The goal of this study was the optimization of phage modification and the assessment of the effect of the latter on the efficiency of phage particle penetration into MDA-MB 231 cells.

METHODS

In this work, we used several methods, such as chemical phage modification using FAM-NHS ester, spectrophotometry, phage amplification, sequencing, phage titration, flow cytometry, and confocal microscopy.

RESULTS

We performed chemical phage modification using different concentrations of FAM-NHS dye (0.5 mM, 1 mM, 2 mM, 4 mM, 8 mM). It was shown that with an increase of the modification degree, the phage titer decreases. The maximum modification coefficient of the phage envelope with the FAM-NHS dye was observed with 4 mM modifying agent and had approximately 804,2 FAM molecules per phage. Through the immunofluorescence staining and flow cytometry methods, it was shown that the modified bacteriophage retains the ability to internalize into MDA-MB-231 cells. The estimation of the number of phages that could have penetrated into one tumor cell was conducted.

CONCLUSIONS

Optimizing the conditions for phage modification can be an effective strategy for producing tumor-targeting diagnostic and therapeutic agents, i.e., theranostic drugs.

Development of a Novel Cytokine Vehicle Using Filamentous Phage Display for Colorectal Cancer Treatment

Due to its highly immunogenic nature and the great engineerability, filamentous phage has shown promising antitumor activities in preclinical studies. Previous designs of antitumor phage mainly focused on tumor targeting using a cancer-specific moiety displayed on the minor capsid protein, pIII. In this work, we developed a new therapeutic platform of filamentous phage, in which the major capsid protein pVIII was utilized for displaying an antitumor cytokine. We showcased that a 16.1-kD cytokine GM-CSF could be efficiently presented on the M13 phage particle using the 8 + 8 type display system through a highly tolerable pVIII variant P8(1a). We verified that the GM-CSF phage was a potent activator for STAT5 signaling in murine macrophage. The GM-CSF phage significantly reduced the tumor size by more than 50% as compared to the unmodified phage in a murine colorectal cancer model. Immunological profiling of the tumor-infiltrating leukocytes revealed that an increase of CD4+ lymphocytes in the GM-CSF phage treatment group. Furthermore, the combined therapy of the GM-CSF phage and radiation greatly improved the therapeutic potency with a 100% survival rate and a 25% complete remission rate. We observed that the IFN-γ expression was dramatically up-regulated by the combined therapy in multiple types of tumor-infiltrating immune cells. Overall, we created a novel vehicle for cytokine therapy using the pVIII filamentous phage display. This new platform can be multiplexed with other phage engineering approaches, such as displaying targeting ligands on pIII or encapsulating therapeutic genes inside phage capsids, to create multifunctional nanoparticles for cancer therapy.

The Many Applications of Engineered Bacteriophages-An Overview

Since their independent discovery by Frederick Twort in 1915 and Felix d’Herelle in 1917, bacteriophages have captured the attention of scientists for more than a century. They are the most abundant organisms on the planet, often outnumbering their bacterial hosts by tenfold in a given environment, and they constitute a vast reservoir of unexplored genetic information. The increased prevalence of antibiotic resistant pathogens has renewed interest in the use of naturally obtained phages to combat bacterial infections, aka phage therapy. The development of tools to modify phages, genetically or chemically, combined with their structural flexibility, cargo capacity, ease of propagation, and overall safety in humans has opened the door to a myriad of applications. This review article will introduce readers to many of the varied and ingenious ways in which researchers are modifying phages to move them well beyond their innate ability to target and kill bacteria.

Innovative Applications of Plant Viruses in Drug Targeting and Molecular Imaging- A Review

BACKGROUND

Nature had already engineered various types of nanoparticles (NPs), especially viruses, which can deliver their cargo to the host/targeted cells. The ability to selectively target specific cells offers a significant advantage over the conventional approach. Numerous organic NPs, including native protein cages, virus-like particles, polymeric saccharides, and liposomes, have been used for the preparation of nanoparticles. Such nanomaterials have demonstrated better performance as well as improved biocompatibility, devoid of side effects, and stable without any deterioration.

OBJECTIVE

This review discusses current clinical and scientific research on naturally occurring nanomaterials. It also illustrates and updates the tailor-made approaches for selective delivery and targeted medications that require a high-affinity interconnection to the targeted cells.

METHODS

A comprehensive search was performed using keywords for viral nanoparticles, viral particles for drug delivery, viral nanoparticles for molecular imaging, theranostics applications of viral nanoparticles and plant viruses in nanomedicine. We searched on Google Scholar, PubMed, Springer, Medline, and Elsevier from 2000 till date and by the bibliographic review of all identified articles.

RESULTS

The findings demonstrated that structures dependent on nanomaterials might have potential applications in diagnostics, cell marking, comparing agents (computed tomography and magnetic resonance imaging), and antimicrobial drugs, as well as drug delivery structures. However, measures should be taken in order to prevent or mitigate, in pharmaceutical or medical applications, the toxic impact or incompatibility of nanoparticle-based structures with biological systems.

CONCLUSION

The review provided an overview of the latest advances in nanotechnology, outlining the difficulties and the advantages of in vivo and in vitro structures that are focused on a specific subset of the natural nanomaterials.

Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future

The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.

Microbial Nano-Factories: Synthesis and Biomedical Applications

In the recent times, nanomaterials have emerged in the field of biology, medicine, electronics, and agriculture due to their immense applications. Owing to their nanoscale sizes, they present large surface/volume ratio, characteristic structures, and similar dimensions to biomolecules resulting in unique properties for biomedical applications. The chemical and physical methods to synthesize nanoparticles have their own limitations which can be overcome using biological methods for the synthesis. Moreover, through the biogenic synthesis route, the usage of microorganisms has offered a reliable, sustainable, safe, and environmental friendly technique for nanosynthesis. Bacterial, algal, fungal, and yeast cells are known to transport metals from their environment and convert them to elemental nanoparticle forms which are either accumulated or secreted. Additionally, robust nanocarriers have also been developed using viruses. In order to prevent aggregation and promote stabilization of the nanoparticles, capping agents are often secreted during biosynthesis. Microbial nanoparticles find biomedical applications in rapid diagnostics, imaging, biopharmaceuticals, drug delivery systems, antimicrobials, biomaterials for tissue regeneration as well as biosensors. The major challenges in therapeutic applications of microbial nanoparticles include biocompatibility, bioavailability, stability, degradation in the gastro-intestinal tract, and immune response. Thus, the current review article is focused on the microbe-mediated synthesis of various nanoparticles, the different microbial strains explored for such synthesis along with their current and future biomedical applications.

Bacteriophage Capsid Modification by Genetic and Chemical Methods

Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.

Filamentous Phages as Building Blocks for Bioactive Hydrogels

Filamentous bacteriophages (bacterial viruses) are semiflexible proteinous nanofilaments with high aspect ratios for which the surface chemistry can be controlled with atomic precision via genetic engineering. That, in addition to their ability to self-propagate and replicate a nearly monodisperse batch of biologically and chemically identical nanofilaments, makes these bionanofilaments superior to most synthetic nanoparticles and thus a powerful tool in the bioengineers' toolbox. Furthermore, filamentous phages form liquid crystalline structures at high concentrations; these ordered assemblies create hierarchically ordered macro-, micro-, and nanostructures that, once cross-linked, can form hierarchically ordered hydrogels, hydrated soft material with a variety of physical and chemical properties suitable for biomedical applications (e.g., wound dressings and tissue engineering scaffolds) as well as biosensing, diagnostic assays. We provide a critical review of these hydrogels of filamentous phage, and their physical, mechanical, chemical, and biological properties and current applications, as well as an overview of limitations and challenges and outlook for future applications. In addition, we present a list of design parameters for filamentous phage hydrogels to serve as a guide for the (bio)engineer and (bio)chemist interested in utilizing these powerful bionanofilaments for designing smart, bioactive materials and devices.

Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers

Virus-like particles (VLPs) are virus-derived structures made up of one or more different molecules with the ability to self-assemble, mimicking the form and size of a virus particle but lacking the genetic material so they are not capable of infecting the host cell. Expression and self-assembly of the viral structural proteins can take place in various living or cell-free expression systems after which the viral structures can be assembled and reconstructed. VLPs are gaining in popularity in the field of preventive medicine and to date, a wide range of VLP-based candidate vaccines have been developed for immunization against various infectious agents, the latest of which is the vaccine against SARS-CoV-2, the efficacy of which is being evaluated. VLPs are highly immunogenic and are able to elicit both the antibody- and cell-mediated immune responses by pathways different from those elicited by conventional inactivated viral vaccines. However, there are still many challenges to this surface display system that need to be addressed in the future. VLPs that are classified as subunit vaccines are subdivided into enveloped and non- enveloped subtypes both of which are discussed in this review article. VLPs have also recently received attention for their successful applications in targeted drug delivery and for use in gene therapy. The development of more effective and targeted forms of VLP by modification of the surface of the particles in such a way that they can be introduced into specific cells or tissues or increase their half-life in the host is likely to expand their use in the future. Recent advances in the production and fabrication of VLPs including the exploration of different types of expression systems for their development, as well as their applications as vaccines in the prevention of infectious diseases and cancers resulting from their interaction with, and mechanism of activation of, the humoral and cellular immune systems are discussed in this review.

Virus as nanocarrier for drug delivery redefining medical therapeutics - A status report

Over the last two decades, drug delivery systems have evolved at a tremendous rate. Synthetic nanoparticles have played an important role in the design of vaccine and their delivery as many of them have shown improved safety and efficacy over conventional formulations. Nanocarriers formulated by natural, biological building blocks have become an important tool in the field biomedicine. A successful nanocarrier must have certain properties like evading the host immune system, target specificity, cellular entry, escape from endosomes, and ability to release material into the cytoplasm. Some or all of these functions can be performed by viruses making them a suitable candidate for naturally occurring nanocarriers. Moreover, viruses can be made non-infectious and non-replicative without compromising their ability to penetrate cells thus making them useful for a vast spectrum of applications. Currently, various carrier molecules are under different stages of development to become bio-nano capsules. This review covers the advances made in the field of viruses as potential nanocarriers and discusses the related technologies and strategies to target specific cells by using virus inspired nanocarriers. In future, these virus-based nano-formulations will be able to provide solutions towards pressing and emerging infectious diseases.

Expanding the Chemical Diversity of Genetically Encoded Libraries

The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.

Investigation of intestinal transportation of peptide-displaying bacteriophage particles using phage display method

To investigate whether peptide sequences with specific translocation across the gastrointestinal barrier can be identified as drug delivery vehicles, in vivo phage display was conducted. For this purpose, a random library of 12-mer peptides displayed on M13 bacteriophage was orally administered to mice followed by recovery of the phage particles from the blood samples after three consecutive biopanning rounds. The obtained peptide sequences were analyzed using bioinformatics tools and software. The results demonstrated that M13 bacteriophage bearing peptides translocate nonspecifically across the mice intestinal mucosal barrier deduced from random distribution of amino acids in different positions of the identified peptide sequences. The most probable reason for entering the phage particles into systemic circulation after oral administration of the peptide library can be related to the nanoscale nature of their structures which provides a satisfying platform for the purpose of designing nanocarriers in pharmaceutical applications.

Viral Related Tools against SARS-CoV-2

At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.

Plant Viruses and Bacteriophage-Based Reagents for Diagnosis and Therapy

Viral nanotechnology exploits the prefabricated nanostructures of viruses, which are already abundant in nature. With well-defined molecular architectures, viral nanocarriers offer unprecedented opportunities for precise structural and functional manipulation using genetic engineering and/or bio-orthogonal chemistries. In this manner, they can be loaded with diverse molecular payloads for targeted delivery. Mammalian viruses are already established in the clinic for gene therapy and immunotherapy, and inactivated viruses or virus-like particles have long been used as vaccines. More recently, plant viruses and bacteriophages have been developed as nanocarriers for diagnostic imaging, vaccine and drug delivery, and combined diagnosis/therapy (theranostics). The first wave of these novel virus-based tools has completed clinical development and is poised to make an impact on clinical practice.

Viral nanoparticles for drug delivery, imaging, immunotherapy, and theranostic applications

Viral nanoparticles (VNPs) encompass a diverse array of naturally occurring nanomaterials derived from plant viruses, bacteriophages, and mammalian viruses. The application and development of VNPs and their genome-free versions, the virus-like particles (VLPs), for nanomedicine is a rapidly growing. VLPs can encapsulate a wide range of active ingredients as well as be genetically or chemically conjugated to targeting ligands to achieve tissue specificity. VLPs are manufactured through scalable fermentation or molecular farming, and the materials are biocompatible and biodegradable. These properties have led to a wide range of applications, including cancer therapies, immunotherapies, vaccines, antimicrobial therapies, cardiovascular therapies, gene therapies, as well as imaging and theranostics. The use of VLPs as drug delivery agents is evolving, and sufficient research must continuously be undertaken to translate these therapies to the clinic. This review highlights some of the novel research efforts currently underway in the VNP drug delivery field in achieving this greater goal.

Exploring the Enzymatic and Antibacterial Activities of Novel Mycobacteriophage Lysin B Enzymes

Mycobacteriophages possess different sets of lytic enzymes for disruption of the complex cell envelope of the mycobacteria host cells and release of the viral progeny. Lysin B (LysB) enzymes are mycolylarabinogalactan esterases that cleave the ester bond between the arabinogalactan and mycolic acids in the mycolylarabinogalactan-peptidoglycan (mAGP) complex in the cell envelope of mycobacteria. In the present study, four LysB enzymes were produced recombinantly and characterized with respect to their enzymatic and antibacterial activities. Examination of the kinetic parameters for the hydrolysis of para-nitrophenyl ester substrates, shows LysB-His₆ enzymes to be active against a range of substrates (C4–C16), with a catalytic preference towards p-nitrophenyl laurate (C12). With p-nitrophenyl butyrate as substrate, LysB-His₆ enzymes showed highest activity at 37 °C. LysB-His₆ enzymes also hydrolyzed different Tween substrates with highest activity against Tween 20 and 80. Metal ions like Ca²⁺ and Mn²⁺ enhanced the enzymatic activity of LysB-His₆ enzymes, while transition metal ions like Zn²⁺ and Cu²⁺ inhibited the enzymatic activity. The mycolylarabinogalactan esterase activity of LysB-His₆ enzymes against mAGP complex was confirmed by LC-MS. LysB-His₆ enzymes showed marginal antibacterial activity when tested alone against Mycobacterium smegmatis, however a synergetic activity was noticed when combined with outer membrane permealizers. These results confirm that LysB enzymes are lipolytic enzymes with potential application as antimycobacterials.

Selective Entropy Gain-Driven Adsorption of Nanospheres onto Spherical Bacteria Endows Photodynamic Treatment with Narrow-Spectrum Activity

Narrow-spectrum antimicrobials specifically eradicate the target pathogens but suffer from significantly lagging development. Photodynamic therapy eliminates cells with reactive oxygen species (ROS) generated upon light irradiation but is intrinsically a wide-spectrum modality. We herein converted photodynamic therapy into a narrow-spectrum modality by taking advantage of a previously unnoticed physics recognition pathway. We found that negatively charged nanospheres undergo selective entropy gain-driven adsorption onto spherical bacteria, but not onto rod-like bacteria. This bacterial morphology-targeting selectivity, combined with the extremely limited effective radii of action of ROS, enabled photodynamic nanospheres to kill >99% of inoculated spherical bacteria upon light irradiation and <1% of rod-like bacteria under comparable conditions, indicative of narrow-spectrum activity against spherical bacteria. This work unveils the bacterial morphology selectivity in the adsorption of negatively charged nanospheres and suggests a new approach for treating infections characterized by overthriving spherical bacteria in niches naturally dominated by rod-like bacteria.

Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections

The emerging occurrence of antibiotic-resistant bacterial pathogens leads to a recollection of bacteriophage as antimicrobial therapeutics. This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential "ideal" therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engineered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therapeutic candidates. Finally, we briefly summarize the use of phage for the detection and treatment of "Category A priority pathogens".

Nanocarriers for the Delivery of Medical, Veterinary, and Agricultural Active Ingredients

Nanocarrier-based delivery systems can be used to increase the safety and efficacy of active ingredients in medical, veterinary, or agricultural applications, particularly when such ingredients are unstable, sparingly soluble, or cause off-target effects. In this review, we highlight the diversity of nanocarrier materials and their key advantages compared to free active ingredients. We discuss current trends based on peer-reviewed research articles, patent applications, clinical trials, and the nanocarrier formulations already approved by regulatory bodies. Although most nanocarriers have been engineered to combat cancer, the number of formulations developed for other purposes is growing rapidly, especially those for the treatment of infectious diseases and parasites affecting humans, livestock, and companion animals. The regulation and prohibition of many pesticides have also fueled research to develop targeted pesticide delivery systems based on nanocarriers, which maximize efficacy while minimizing the environmental impact of agrochemicals.

Future impacts and trends in treatment of hospital wastewater

The world’s population growth and economic development result in the increased requirement of land, water, and energy. This increased demand leads to the deforestation, loss in biodiversity, imbalance in agriculture and food supply, climate change, and increase in food and travel trade, which result in emergence and reemergence of infectious diseases. This chapter discussed various emerging infectious diseases and their causative agents (Buruli ulcer and Bunyvirus). Furthermore, this chapter further illustrates the emergence of superbugs and the associated threat due to the presence of pharmaceutical compounds in the environment. The prevalence of pharmaceuticals in the environment exerts ecotoxic effects on living organisms and causes thousands of death every year. The threats associated with the pharmaceutical presence in the environment were briefly discussed in this chapter. Finally, this chapter provides the alternative methods to avoid the use of antibiotics and to develop novel treatment technologies (such as Phage therapy) to degrade and remove the pharmaceutical compounds.

Pharmacomicrobiomics informs clinical pharmacogenomics

Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.

Targeting virulence factors as an antimicrobial approach: Pigment inhibitors

The fascinating and dangerous colored pathogens contain unique chemically pigmented molecules, which give varied and efficient assistance as virulence factors to the crucial reproduction and growth of microbes. Therefore, multiple novel strategies and inhibitors have been developed in recent years that target virulence factor pigments. However, despite the importance and significance of this topic, it has not yet been comprehensively reviewed. Moreover, research groups around the world have made successful progress against antibacterial infections by targeting pigment production, including our serial works on the discovery of CrtN inhibitors against staphyloxanthin production in Staphylococcus aureus. On the basis of the previous achievements and recent progress of our group in this field, this article will be the first comprehensive review of pigment inhibitors against colored pathogens, especially S. aureus infections, and this article includes design strategies, representative case studies, advantages, limitations, and perspectives to guide future research.

Phage Display Technology and its Applications in Cancer Immunotherapy

Background:

Phage display is an effective technology for generation and selection targeting protein for a variety of purpose, which is based on a direct linkage between the displayed protein and the DNA sequence encoding it and utilized in selecting peptides, improving peptides affinity and indicating protein-protein interactions. Phage particles displaying peptide have the potential to apply in the identification of cell-specific targeting molecules, identification of cancer cell surface biomarkers, identification anti-cancer peptide, and the design of peptide-based anticancer therapy.

Method/Results:

Literature searches, reviews and assessments about Phage were performed in this review from PubMed and Medline databases.

Conclusion:

The phage display technology is an inexpensive method for expressing exogenous peptides, generating unique peptides that bind any given target and investigating protein-protein interactions. Due to the powerful ability to insert exogenous gene and display exogenous peptides on the surface, phages may represent a powerful peptide delivery system that can be utilized to develop rapid, efficient, safe and inexpensive cancer therapy methods.

Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics

Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.

Nonconventional Therapeutics against Staphylococcus aureus

Staphylococcus aureus is one of the most important human pathogens that is responsible for a variety of diseases ranging from skin and soft tissue infections to endocarditis and sepsis. In recent decades, the treatment of staphylococcal infections has become increasingly difficult as the prevalence of multi-drug resistant strains continues to rise. With increasing mortality rates and medical costs associated with drug resistant strains, there is an urgent need for alternative therapeutic options. Many innovative strategies for alternative drug development are being pursued, including disruption of biofilms, inhibition of virulence factor production, bacteriophage-derived antimicrobials, anti-staphylococcal vaccines, and light-based therapies. While many compounds and methods still need further study to determine their feasibility, some are quickly approaching clinical application and may be available in the near future.

Dye Aggregate-Mediated Self-Assembly of Bacteriophage Bioconjugates

One of the central themes of biomolecular engineering is the challenge of exploiting the properties of biological materials. Part of this challenge has been uncovering and harnessing properties of biological components that only emerge following their ordered self-assembly. One biomolecular building block that has received significant interest in the past decade is the M13 bacteriophage. There have been a number of recent attempts to trigger the ordered assembly of M13 bacteriophage into multivirion structures, relying on the innate tendency of M13 to form liquid crystals at high concentrations. These, in general, yield planar two-dimensional materials. Presented here is the production of multivirion assemblies of M13 bacteriophage via the chemical modification of its surface by the covalent attachment of the xanthene-based dye tetramethylrhodamine (TMR) isothiocyanate (TRITC). We show that TMR induces the formation of three-dimensional aster-like assemblies of M13 by providing "adhesive" action between bacteriophage particles through the formation of H-aggregates (face-to-face stacking of dye molecules). We also show that the H-aggregation of TMR is greatly enhanced by covalent attachment to M13 and is enhanced further still upon the ordered self-assembly of M13, leading to the suggestion that M13 could be used to promote the self-assembly of dyes that form J-aggregates, a desirable arrangement of fluorescent dye, which has interesting optical properties and potential applications in the fields of medicine and light harvesting technology.

Detection of Acidic Pharmaceutical Compounds Using Virus-Based Molecularly Imprinted Polymers

Molecularly imprinted polymers (MIPs) have proven to be particularly effective chemical probes for the molecular recognition of proteins, DNA, and viruses. Here, we started from a filamentous bacteriophage to synthesize a multi-functionalized MIP for detecting the acidic pharmaceutic clofibric acid (CA) as a chemical pollutant. Adsorption and quartz crystal microbalance with dissipation monitoring experiments showed that the phage-functionalized MIP had a good binding affinity for CA, compared with the non-imprinted polymer and MIP. In addition, the reusability of the phage-functionalized MIP was demonstrated for at least five repeated cycles, without significant loss in the binding activity. The results indicate that the exposed amino acids of the phage, together with the polymer matrix, create functional binding cavities that provide higher affinity to acidic pharmaceutical compounds.

Mutation of M13 Bacteriophage Major Coat Protein for Increased Conjugation to Exogenous Compounds

Over the past ten years there has been increasing interest in the conjugation of exogenous compounds to the surface of the M13 bacteriophage. M13 offers a convenient scaffold for the development of nanoassemblies with useful functions, such as highly specific drug delivery and pathogen detection. However, the progress of these technologies has been hindered by the limited efficiency of conjugation to the bacteriophage. Here we generate a mutant version of M13 with an additional lysine residue expressed on the outer surface of the M13 major coat protein, pVIII. We show that this mutation is accommodated by the bacteriophage and that up to an additional 520 exogenous groups can be attached to the bacteriophage surface via amine-directed conjugation. These results could aid the development of high payload drug delivery nanoassemblies and pathogen detection systems with increased sensitivity.