Phage display as a technology delivering on the promise of peptide drug discovery

Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria

Antibiotic-resistant bacteria are rapidly emerging, and the increasing prevalence of multidrug-resistant (MDR) Acinetobacter baumannii poses a severe threat to humans and healthcare organizations, due to the lack of innovative antibacterial drugs. Endolysins, which are peptidoglycan hydrolases encoded by a bacteriophage, are a promising new family of antimicrobials. Endolysins have been demonstrated as an effective therapeutic agent against bacterial infections of A. baumannii and many other Gram-positive and Gram-negative bacteria. Endolysin research has progressed from basic in vitro characterization to sophisticated protein engineering methodologies, including advanced preclinical and clinical testing. Endolysin are therapeutic agent that shows antimicrobial properties against bacterial infections caused by drug-resistant Gram-negative bacteria, there are still barriers to their implementation in clinical settings, such as safety concerns with outer membrane permeabilizers (OMP) use, low efficiency against stationary phase bacteria, and stability issues. The application of protein engineering and formulation techniques to improve enzyme stability, as well as combination therapy with other types of antibacterial drugs to optimize their medicinal value, have been reviewed as well. In this review, we summarize the clinical development of endolysin and its challenges and approaches for bringing endolysin therapies to the clinic. This review also discusses the different applications of endolysins.

Improving Pharmacokinetics of Peptides Using Phage Display

Phage display is a versatile method often used in the discovery of peptides that targets disease-related biomarkers. A major advantage of this technology is the ease and cost efficiency of affinity selection, also known as biopanning, to identify novel peptides. While it is relatively straightforward to identify peptides with optimal binding affinity, the pharmacokinetics of the selected peptides often prove to be suboptimal. Therefore, careful consideration of the experimental conditions, including the choice of using in vitro, in situ, or in vivo affinity selections, is essential in generating peptides with high affinity and specificity that also demonstrate desirable pharmacokinetics. Specifically, in vivo biopanning, or the combination of in vitro, in situ, and in vivo affinity selections, has been proven to influence the biodistribution and clearance of peptides and peptide-conjugated nanoparticles. Additionally, the marked difference in properties between peptides and nanoparticles must be considered. While peptide biodistribution depends primarily on physiochemical properties and can be modified by amino acid modifications, the size and shape of nanoparticles also affect both absorption and distribution. Thus, optimization of the desired pharmacokinetic properties should be an important consideration in biopanning strategies to enable the selection of peptides and peptide-conjugated nanoparticles that effectively target biomarkers in vivo.

Disulfide-constrained peptide scaffolds enable a robust peptide-therapeutic discovery platform

Peptides present an alternative modality to immunoglobulin domains or small molecules for developing therapeutics to either agonize or antagonize cellular pathways associated with diseases. However, peptides often suffer from poor chemical and physical stability, limiting their therapeutic potential. Disulfide-constrained peptides (DCP) are naturally occurring and possess numerous desirable properties, such as high stability, that qualify them as drug-like scaffolds for peptide therapeutics. DCPs contain loop regions protruding from the core of the molecule that are amenable to peptide engineering via direct evolution by use of phage display technology. In this study, we have established a robust platform for the discovery of peptide therapeutics using various DCPs as scaffolds. We created diverse libraries comprising seven different DCP scaffolds, resulting in an overall diversity of 2 x 1011. The effectiveness of this platform for functional hit discovery has been extensively evaluated, demonstrating a hit rate comparable to that of synthetic antibody libraries. By utilizing chemically synthesized and in vitro folded peptides derived from selections of phage displayed DCP libraries, we have successfully generated functional inhibitors targeting the HtrA1 protease. Through affinity maturation strategies, we have transformed initially weak binders against Notch2 with micromolar Kd values to high-affinity ligands in the nanomolar range. This process highlights a viable hit-to-lead progression. Overall, our platform holds significant potential to greatly enhance the discovery of peptide therapeutics.

Developing Lipase Inhibitor as a Novel Approach to Address the Rice Bran Rancidity Issue─A Critical Review

Rice bran is a valuable byproduct from the food processing industry, which contains abundant protein, essential unsaturated fatty acids, and numerous bioactive compounds. However, its susceptibility to rancidity greatly restricts its wide utilization. Many strategies have been proposed to delay the rancidity of rice bran, but most of them have their respective limitations. Here, we proposed that developing rice ban lipase peptide inhibitors represents an alternative and promising prescription for impeding the rancidity of rice bran, in contrast to the conventional stabilization approaches for rice bran. For this reason, the rancidity mechanisms of rice bran and the research progress of rice bran lipases were discussed. In addition, the feasibility of utilizing in silico screening and phage display, two state-of-the-art technologies, in the design of the related peptide inhibitors was also highlighted. This knowledge is expected to provide a theoretical basis for opening a new avenue for stabilizing rice bran.

Chemical Strategies towards the Development of Effective Anticancer Peptides

Cancer is increasingly recognized as one of the primary causes of death and has become a multifaceted global health issue. Modern medical science has made significant advancements in the diagnosis and therapy of cancer over the past decade. The detrimental side effects, lack of efficacy, and multidrug resistance of conventional cancer therapies have created an urgent need for novel anticancer therapeutics or treatments with low cytotoxicity and drug resistance. The pharmaceutical groups have recognized the crucial role that peptide therapeutic agents can play in addressing unsatisfied healthcare demands and how these become great supplements or even preferable alternatives to biological therapies and small molecules. Anticancer peptides, as a vibrant therapeutic strategy against various cancer cells, have demonstrated incredible anticancer potential due to high specificity and selectivity, low toxicity, and the ability to target the surface of traditional "undruggable" proteins. This review will provide the research progression of anticancer peptides, mainly focusing on the discovery and modifications along with the optimization and application of these peptides in clinical practice.

Candida albicans and Antifungal Peptides

Candida albicans, a ubiquitous opportunistic fungal pathogen, plays a pivotal role in human health and disease. As a commensal organism, it normally resides harmlessly within the human microbiota. However, under certain conditions, C. albicans can transition into a pathogenic state, leading to various infections collectively known as candidiasis. With the increasing prevalence of immunocompromised individuals and the widespread use of invasive medical procedures, candidiasis has become a significant public health concern. The emergence of drug-resistant strains further complicates treatment options, highlighting the urgent need for alternative therapeutic strategies. Antifungal peptides (AFPs) have gained considerable attention as potential candidates for combating Candida spp. infections. These naturally occurring peptides possess broad-spectrum antimicrobial activity, including specific efficacy against C. albicans. AFPs exhibit several advantageous properties, such as rapid killing kinetics, low propensity for resistance development, and diverse mechanisms of action, making them promising alternatives to conventional antifungal agents. In recent years, extensive research has focused on discovering and developing novel AFPs with improved efficacy and selectivity against Candida species. Advances in biotechnology and synthetic peptide design have enabled the modification and optimization of natural peptides, enhancing their stability, bioavailability, and therapeutic potential. Nevertheless, several challenges must be addressed before AFPs can be widely implemented in clinical practice. These include optimizing peptide stability, enhancing delivery methods, overcoming potential toxicity concerns, and conducting comprehensive preclinical and clinical studies. This commentary presents a short overview of candidemia and AFP; articles and reviews published in the last 10 years were searched on The National Library of Medicine (National Center for Biotechnology Information-NIH-PubMed). The terms used were C. albicans infections, antimicrobial peptides, antifungal peptides, antifungal peptides mechanisms of action, candidemia treatments and guidelines, synthetic peptides and their challenges, and antimicrobial peptides in clinical trials as the main ones. Older publications were cited if they brought some relevant concept or helped to bring a perspective into our narrative. Articles older than 20 years and those that appeared in PubMed but did not match our goal to bring updated information about using antifungal peptides as an alternative to C. albicans infections were not considered.

The power of phages: revolutionizing cancer treatment

Cancer is a devastating disease with a high global mortality rate and is projected to increase further in the coming years. Current treatment options, such as chemotherapy and radiation therapy, have limitations including side effects, variable effectiveness, high costs, and limited availability. There is a growing need for alternative treatments that can target cancer cells specifically with fewer side effects. Phages, that infect bacteria but not eukaryotic cells, have emerged as promising cancer therapeutics due to their unique properties, including specificity and ease of genetic modification. Engineered phages can transform cancer treatment by targeting cancer cells while sparing healthy ones. Phages exhibit versatility as nanocarriers, capable of delivering therapeutic agents like gene therapy, immunotherapy, and vaccines. Phages are extensively used in vaccine development, with filamentous, tailed, and icosahedral phages explored for different antigen expression possibilities. Engineered filamentous phages bring benefits such as built in adjuvant properties, cost-effectiveness, versatility in multivalent formulations, feasibility of oral administration, and stability. Phage-based vaccines stimulate the innate immune system by engaging pattern recognition receptors on antigen-presenting cells, enhancing phage peptide antigen presentation to B-cells and T-cells. This review presents recent phage therapy advances and challenges in cancer therapy, exploring its versatile tools and vaccine potential.

Phage therapy: a revolutionary shift in the management of bacterial infections, pioneering new horizons in clinical practice, and reimagining the arsenal against microbial pathogens

The recent approval of experimental phage therapies by the FDA and other regulatory bodies with expanded access in cases in the United States and other nations caught the attention of the media and the general public, generating enthusiasm for phage therapy. It started to alter the situation so that more medical professionals are willing to use phage therapies with conventional antibiotics. However, more study is required to fully comprehend phage therapy's potential advantages and restrictions, which is still a relatively new field in medicine. It shows promise, nevertheless, as a secure and prosperous substitute for antibiotics when treating bacterial illnesses in animals and humans. Because of their uniqueness, phage disinfection is excellent for ready-to-eat (RTE) foods like milk, vegetables, and meat products. The traditional farm-to-fork method can be used throughout the food chain to employ bacteriophages to prevent food infections at all production stages. Phage therapy improves clinical outcomes in animal models and lowers bacterial burdens in numerous preclinical investigations. The potential of phage resistance and the need to make sure that enough phages are delivered to the infection site are obstacles to employing phages in vivo. However, according to preclinical studies, phages appear to be a promising alternative to antibiotics for treating bacterial infections in vivo. Phage therapy used with compassion (a profound understanding of and empathy for another's suffering) has recently grown with many case reports of supposedly treated patients and clinical trials. This review summarizes the knowledge on the uses of phages in various fields, such as the food industry, preclinical research, and clinical settings. It also includes a list of FDA-approved bacteriophage-based products, commercial phage products, and a global list of companies that use phages for therapeutic purposes.

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.

Exploring shark VNAR antibody against infectious diseases using phage display technology

Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.

Phage based vaccine: A novel strategy in prevention and treatment

The vaccine was first developed in 1796 by a British physician, Edward Jenner, against the smallpox virus. This invention revolutionized medical science and saved lives around the world. The production of effective vaccines requires dominant immune epitopes to elicit a robust immune response. Thus, applying bacteriophages has attracted the attention of many researchers because of their advantages in vaccine design and development. Bacteriophages are not infectious to humans and are unlikely to bind to cellular receptors and activate signaling pathways. Phages could activate both cellular and humoral immunity, which is another goal of an effective vaccine design. Also, phages act as an effective adjuvant, along with the antigens, and induce a robust immune response. Phage-based vaccines can also be administered orally because of their stability in the gastrointestinal tract, in contrast to common vaccination routes, which are intradermal, subcutaneous, or intramuscular. This review presents the current improvements in phage-based vaccines and their applications as preventive or therapeutic vaccines.

Phage display and human disease detection

Phage display is a significant and active molecular method and has continued crucial for investigative sector meanwhile its unearthing in 1985. This practice has numerous benefits: the association among physiology and genome, the massive variety of variant proteins showed in sole collection and the elasticity of collection that can be achieved. It suggests a diversity of stages for manipulating antigen attachment; yet, variety and steadiness of exhibited library are an alarm. Additional improvements, like accumulation of non-canonical amino acids, resulting in extension of ligands that can be recognized through collection, will support in expansion of the probable uses and possibilities of technology. Epidemic of COVID-19 had taken countless lives, and while indicative prescriptions were provided to diseased individuals, still no prevention was observed for the contamination. Phage demonstration has presented an in-depth understanding into protein connections included in pathogenesis. Phage display knowledge is developing as an influential, inexpensive, quick, and effectual method to grow novel mediators for the molecular imaging and analysis of cancer.

Characterization of a lytic Pseudomonas aeruginosa phage vB_PaeP_ASP23 and functional analysis of its lysin LysASP and holin HolASP

In this study, we isolated a lytic Pseudomonas aeruginosa phage (vB_PaeP_ASP23) from the sewage of a mink farm, characterized its complete genome and analyzed the function of its putative lysin and holin. Morphological characterization and genome annotation showed that phage ASP23 belonged to the Krylovirinae family genus Phikmvvirus, and it had a latent period of 10 min and a burst size of 140 pfu/infected cell. In minks challenged with P. aeruginosa, phage ASP23 significantly reduced bacterial counts in the liver, lung, and blood. The whole-genome sequencing showed that its genome was a 42,735-bp linear and double-stranded DNA (dsDNA), with a G + C content of 62.15%. Its genome contained 54 predicted open reading frames (ORFs), 25 of which had known functions. The lysin of phage ASP23 (LysASP), in combination with EDTA, showed high lytic activity against P. aeruginosa L64. The holin of phage ASP23 was synthesized by M13 phage display technology, to produce recombinant phages (HolASP). Though HolASP exhibited a narrow lytic spectrum, it was effective against Staphylococcus aureus and Bacillus subtilis. However, these two bacteria were insensitive to LysASP. The findings highlight the potential of phage ASP23 to be used in the development of new antibacterial agents.

Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions

Design of peptide binders is an attractive strategy for targeting "undruggable" protein-protein interfaces. Current design protocols rely on the extraction of an initial sequence from one known protein interactor of the target protein, followed by in-silico or in-vitro mutagenesis-based optimization of its binding affinity. Wet lab protocols can explore only a minor portion of the vast sequence space and cannot efficiently screen for other desirable properties such as high specificity and low toxicity, while in-silico design requires intensive computational resources and often relies on simplified binding models. Yet, for a multivalent protein target, dozens to hundreds of natural protein partners already exist in the cellular environment. Here, we describe a peptide design protocol that harnesses this diversity via a machine learning generative model. After identifying putative natural binding fragments by literature and homology search, a compositional Restricted Boltzmann Machine is trained and sampled to yield hundreds of diverse candidate peptides. The latter are further filtered via flexible molecular docking and an in-vitro microchip-based binding assay. We validate and test our protocol on calcineurin, a calcium-dependent protein phosphatase involved in various cellular pathways in health and disease. In a single screening round, we identified multiple 16-length peptides with up to six mutations from their closest natural sequence that successfully interfere with the binding of calcineurin to its substrates. In summary, integrating protein interaction and sequence databases, generative modeling, molecular docking and interaction assays enables the discovery of novel protein-protein interaction modulators.

Bacteriophages as Biotechnological Tools

Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.

pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides

The isoelectric point (pI) is a fundamental physicochemical property of peptides and proteins. It is widely used to steer design away from low solubility and aggregation and guide peptide separation and purification. Experimental measurements of pI can be replaced by calculations knowing the ionizable groups of peptides and their corresponding pK_a values. Different pK_a sets are published in the literature for natural amino acids, however, they are insufficient to describe synthetically modified peptides, complex peptides of natural origin, and peptides conjugated with structures of other modalities. Noncanonical modifications (nCAAs) are ignored in the conventional sequence-based pI calculations, therefore producing large errors in their pI predictions. In this work, we describe a pI calculation method that uses the chemical structure as an input, automatically identifies ionizable groups of nCAAs and other fragments, and performs pK_a predictions for them. The method is validated on a curated set of experimental measures on 29 modified and 119093 natural peptides, providing an improvement of R² from 0.74 to 0.95 and 0.96 against the conventional sequence-based approach for modified peptides for the two studied pK_a prediction tools, ACDlabs and pKaMatcher, correspondingly. The method is available in the form of an open source Python library at https://github.com/AstraZeneca/peptide-tools, which can be integrated into other proprietary and free software packages. We anticipate that the pI calculation tool may facilitate optimization and purification activities across various application domains of peptides, including the development of biopharmaceuticals.

Encoding Noncanonical Amino Acids into Phage Displayed Proteins

Phage display facilitates the evolution of peptides and proteins for affinity selection against targets, but it is mostly limited to the chemical diversity provided by the naturally encoded amino acids. The combination of phage display with genetic code expansion allows the incorporation of noncanonical amino acids (ncAAs) into proteins expressed on the phage. In this method, we describe incorporation of one or two ncAAs in a single-chain fragment variable (scFv) antibody in response to amber or quadruplet codon. We take advantage of the pyrrolysyl-tRNA synthetase/tRNA pair to incorporate a lysine derivative and an orthogonal tyrosyl-tRNA synthetase/tRNA pair to incorporate a phenylalanine derivative. The encoding of novel chemical functionalities and building blocks in proteins displayed on phage provides the foundation for further phage display applications in fields such as imaging, protein targeting, and the production of new materials.

The translational paradigm of nanobiomaterials: Biological chemistry to modern applications

Recently nanotechnology has evolved as one of the most revolutionary technologies in the world. It has now become a multi-trillion-dollar business that covers the production of physical, chemical, and biological systems at scales ranging from atomic and molecular levels to a wide range of industrial applications, such as electronics, medicine, and cosmetics. Nanobiomaterials synthesis are promising approaches produced from various biological elements be it plants, bacteria, peptides, nucleic acids, etc. Owing to the better biocompatibility and biological approach of synthesis, they have gained immense attention in the biomedical field. Moreover, due to their scaled-down sized property, nanobiomaterials exhibit remarkable features which make them the potential candidate for different domains of tissue engineering, materials science, pharmacology, biosensors, etc. Miscellaneous characterization techniques have been utilized for the characterization of nanobiomaterials. Currently, the commercial transition of nanotechnology from the research level to the industrial level in the form of nano-scaffolds, implants, and biosensors is stimulating the whole biomedical field starting from bio-mimetic nacres to 3D printing, multiple nanofibers like silk fibers functionalizing as drug delivery systems and in cancer therapy. The contribution of single quantum dot nanoparticles in biological tagging typically in the discipline of genomics and proteomics is noteworthy. This review focuses on the diverse emerging applications of Nanobiomaterials and their mechanistic advancements owing to their physiochemical properties leading to the growth of industries on different biomedical measures. Alongside the implementation of such nanobiomaterials in several drug and gene delivery approaches, optical coding, photodynamic cancer therapy, and vapor sensing have been elaborately discussed in this review. Different parameters based on current challenges and future perspectives are also discussed here.

A rapid colorimetric lateral flow test strip for detection of live Salmonella Enteritidis using whole phage as a specific binder

Specific antibodies are essential components of immunoassay, which can be applied for the detection of pathogens. However, producing an antibody specific to live bacterial pathogens by the classical method of immunizing animals with live pathogens can be impractical. Phage display technology is an effective alternative method to obtain antibodies with the desired specificity against selected antigenic molecules. In this study, we demonstrated the power of a microarray-based technique for obtaining specific phage-derived antibody fragments against Salmonella, an important foodborne pathogen. The selected phage-displayed antibody fragments were subsequently employed to develop a lateral flow test strip assay for the detection of live Salmonella. The test strips showed specificity to Salmonella Enteritidis without cross-reactivity to eight serovars of Salmonella or other bacteria strains. The test strip assay requires 15 min, whereas the conventional biochemical and serological confirmation test requires at least 24 h. The microarray screening technique for specific phage-based binders and the test strip method can be further applied to other foodborne pathogens.

A novel phage-displayed MilA ELISA for detection of antibodies against Myc. bovis in bovine milk

AIMS

The aim of this study was to assess a phage-displayed MilA protein of Myc. bovis in an indirect ELISA for the detection of Myc. bovis antibodies in milk samples.

METHODS AND RESULTS

The desired sequence of milA gene was synthesized and cloned into pCANTAB-F12 phagemid vector. The expression of the MilA on the phage surface was confirmed by Western blotting. The recombinant phage was used in the development of an indirect ELISA to detect Myc. bovis antibodies in milk samples. There was a significant agreement between the results of phage-based ELISA and recombinant GST-MilA ELISA for the detection of Myc. bovis antibodies in milk samples.

CONCLUSIONS

The inexpensive and convenient phage-based ELISA can be used instead of recombinant protein/peptide ELISA as an initial screening of Myc. bovis-associated mastitis.

SIGNIFICANCE AND IMPACT OF STUDY

Mastitis associated with Myc. bovis is a continuous and serious problem in the dairy industry. Sero-monitoring of Myc. bovis infection cases are one of the key factors for surveillance of the infections in dairy farms. Despite the existence of some commercially serological assays for Myc. bovis antibodies, they have some limitations regarding their sensitivity and availability. The development of accurate diagnosis tools could contribute to control programmes of Myc. bovis-associated mastitis in the dairy herds.

An overview on display systems (phage, bacterial, and yeast display) for production of anticancer antibodies; advantages and disadvantages

Antibodies as ideal therapeutic and diagnostic molecules are among the top-selling drugs providing considerable efficacy in disease treatment, especially in cancer therapy. Limitations of the hybridoma technology as routine antibody generation method in conjunction with numerous developments in molecular biology led to the development of alternative approaches for the streamlined identification of most effective antibodies. In this regard, display selection technologies such as phage display, bacterial display, and yeast display have been widely promoted over the past three decades as ideal alternatives to traditional methods. The display of antibodies on phages is probably the most widespread of these methods, although surface display on bacteria or yeast have been employed successfully, as well. These methods using various sizes of combinatorial antibody libraries and different selection strategies possessing benefits in screening potency, generating, and isolation of high affinity antibodies with low risk of immunogenicity. Knowing the basics of each method assists in the design and retrieval process of antibodies suitable for different diseases, including cancer. In this review, we aim to outline the basics of each library construction and its display method, screening and selection steps. The advantages and disadvantages in comparison to alternative methods, and their applications in antibody engineering will be explained. Finally, we will review approved or non-approved therapeutic antibodies developed by employing these methods, which may serve as therapeutic antibodies in cancer therapy.

Phage-based technologies for highly sensitive luminescent detection of foodborne pathogens and microbial toxins: A review

Foodborne pathogens and microbial toxins are the main causes of foodborne illness. However, trace pathogens and toxins in foods are difficult to detect. Thus, techniques for their rapid and sensitive identification and quantification are urgently needed. Phages can specifically recognize and adhere to certain species of microbes or toxins due to molecular complementation between capsid proteins of phages and receptors on the host cell wall or toxins, and thus they have been successfully developed into a detection platform for pathogens and toxins. This review presents an update on phage-based luminescent detection technologies as well as their working principles and characteristics. Based on phage display techniques of temperate phages, reporter gene detection assays have been designed to sensitively detect trace pathogens by luminous intensity. By the host-specific lytic effects of virulent phages, enzyme-catalyzed chemiluminescent detection technologies for pathogens have been exploited. Notably, these phage-based luminescent detection technologies can discriminate viable versus dead microbes. Further, highly selective and sensitive immune-based assays have been developed to detect trace toxins qualitatively and quantitatively via antibody analogs displayed by phages, such as phage-ELISA (enzyme-linked immunosorbent assay) and phage-IPCR (immuno-polymerase chain reaction). This literature research may lead to novel and innocuous phage-based rapid detection technologies to ensure food safety.

Identification and validation of LGR5-binding peptide for molecular imaging of gastric cancer

Leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5) is a stem cell marker in gastric cancer. In this study, we aimed to produce the LGR5-targeting peptide probe for the use of molecular imaging for gastric cancer. We used phage display libraries to produce a LGR5-specific peptide probe. This peptide was validated for targeting gastric cancer with in vitro and in vivo studies. This peptide was tagged with fluorescein isothiocyanate (FITC) and cyanine 5.5 (Cy5.5). We used two normal and three gastric cancer cell lines. Immunocytochemistry (ICC) and fluorescence-activated cell sorting (FACS) analysis were used to validate the target specificity of the peptide. After three rounds of bio-panning, we found a novel 7-mer peptides, IPQILSI (IPQ∗). FITC-conjugated IPQ∗ showed 2 to 10 times higher fluorescence in gastric cancer cells vs. control cells in ICC. This discrimination was consistently observed using Cy5.5-conjugated IPQ∗ in ICC. FACS analysis showed right shift of peak point in gastric cancers compared to the control cells. In the peritoneal metastasis animal model, we could find Cy5.5-conjugated IPQ∗ accumulated specifically to gastric tumors. In conclusion, IPQ∗ peptide showed a specific probe for gastric cancer diagnosis. This probe can be applied to theragnosis for gastric cancer diagnosis including peritoneal metastasis.

Application of phage display for T-cell receptor discovery

The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.

Design and Preparation of "corn-like" SPIONs@DFK-SBP-M13 Assembly for Improvement of Effective Internalization

Purpose

Superparamagnetic iron oxide nanoparticles (SPIONs) have exhibited preeminent diagnosis and treatment performances, but their low internalization severely limits predesigned functions. The low cell internalization is now an urgent bottleneck problem for almost all nanomaterials. To achieve more internalization of SPIONS, recombinant M13 phage was designed for targeted delivery and smart release.

Methods

M13 phages were designed to co-express exogenous SPARC binding peptide (SBP) and cathepsin B cleavage peptide (DFK), formed recombinant DFK-SBP-M13. 3.37± 0.06 nm of SPIONs were modified by 3, 4-dihydroxyhydrocinnamic acid (DHCA) to gain 10.80 ± 0.21 nm of DHCA-coated SPIONs, i.e., DHCA@SPIONs. Upon adjusting the proportions of DHCA@SPIONs and DFK-SBP-M13, the multi-carboxyl SPIONs assembled onto recombinant M13 phages via covalent bonding. The assemblies were co-cultured with MDA-MB-231 cells to interpret their internalization and smart release.

Results

The “corn-like” SPIONs@DFK-SBP-M13 (261.47±3.30 nm) assemblies have not been reported previously. The assembly was stable, dispersible, superparamagnetic and biocompatible. After co-cultivation with MDA-MB-231 cells, the SPIONs@DFK-SBP-M13 assemblies quickly bond to the cell surface and are internalized. The enrichment rate of SPIONs@DFK-SBP-M13 assembly was 13.9 times higher than free SPIONs at 0.5 h, and intracellular Fe content was 3.6 times higher at 1 h. Furthermore, the DFK peptides favored cathepsin B to cleave SPIONs from the M13 templates resulting in release of SPIONs inside cells.

Conclusion

The novel SPIONs@DFK-SBP-M13 assembly can rapidly deliver SPIONs to the targeted sites and enabled smart release. The combination of genetic recombination and nanotechnology is beneficial for designing and optimizing some new nanomaterials with special functions to achieve wider applications.

Phage display and other peptide display technologies

Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.

A mechanistic perspective, clinical applications, and phage-display-assisted discovery of TNFα inhibitors

TNFα participates in a variety of physiological processes, but at supra-physiological concentrations it has been implicated in the pathology of inflammatory and autoimmune diseases. Therefore, much attention has been devoted to the development of strategies that overcome the effects of aberrant TNFα concentration. Promising strategies include drugs that destabilize the active (trimeric) form of TNFα and antagonists of TNFα receptor type I. Underpinning these strategies is the successful application of phage-display technology to identify anti-TNFα peptides and antibodies. Here, we review the development of inhibitors of the TNFα-TNF receptor system, with particular focus on the phage-display-assisted identification of molecules that interfere with this system by acting as inhibitors of TNFα or by sequestering TNFα away from its receptor.

Biological Characterization and Evolution of Bacteriophage T7-△holin During the Serial Passage Process

Bacteriophage T7 gene 17.5 coding for the only known holin is one of the components of its lysis system, but the holin activity in T7 is more complex than a single gene, and evidence points to the existence of additional T7 genes with holin activity. In this study, a T7 phage with a gene 17.5 deletion (T7-△holin) was rescued and its biological characteristics and effect on cell lysis were determined. Furthermore, the genomic evolution of mutant phage T7-△holin during serial passage was assessed by whole-genome sequencing analysis. It was observed that deletion of gene 17.5 from phage T7 delays lysis time and enlarges the phage burst size; however, this biological characteristic recovered to normal lysis levels during serial passage. Scanning electron microscopy showed that the two opposite ends of E. coli BL21 cells swell post-T7-△holin infection rather than drilling holes on cell membrane when compared with T7 wild-type infection. No visible progeny phage particle accumulation was observed inside the E. coli BL21 cells by transmission electron microscopy. Following serial passage of T7-△holin from the 1st to 20th generations, the mRNA levels of gene 3.5 and gene 19.5 were upregulated and several mutation sites were discovered, especially two missense mutations in gene 19.5, which indicate a potential contribution to the evolution of the T7-△holin. Although the burst size of T7-△holin increased, high titer cultivation of T7-△holin was not achieved by optimizing the culture process. Accordingly, these results suggest that gene 19.5 is a potential lysis-related component that needs to be studied further and that the T7-△holin strain with its gene 17.5 deletion is not adequate to establish the high-titer phage cultivation process.

A novel approach to nonsurgical sterilization; application of menadione-modified gonocyte-targeting M13 bacteriophage for germ cell ablation in utero

There remains a compelling need for the development of nonsurgical sterilizing agents to expand the fertility management options for both domestic and feral animal species. We hypothesize that an efficacious sterilization approach would be to selectively ablate nonrenewable cell types that are essential for reproduction, such as the undifferentiated gonocytes within the embryonic gonad. Here, we report a novel strategy to achieve this goal centered on the use of a chemically modified M13 bacteriophage to effect the targeted delivery of menadione, a redox‐cycling naphthoquinone, to mouse gonocytes. Panning of the M13 random peptide ‘phage display library proved effective in the isolation of gonocyte‐specific targeting clones. One such clone was modified via N‐succinimidyl‐S‐acetylthioacetate (SATA) linkage to the N‐terminus of the major PVIII capsid protein. Subsequent deacetylation of the SATA was undertaken to expose a thiol group capable of reacting with menadione through Michael addition. This chemical modification was confirmed using UV spectrophotometry. In proof‐of‐concept experiments we applied the modified ‘phage to primary cultures of fetal germ cells and induced, an approximately, 60% reduction in the viability of the target cell population. These studies pave the way for in vivo application of chemically modified M13 bacteriophage in order to achieve the selective ablation of nonrenewable cell types in the reproductive system, thereby providing a novel nonsurgical approach the regulation of fertility in target species.

Discovery of Antivirals Using Phage Display

The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.

A screened PirB antagonist peptide antagonizes Aβ42-mediated inhibition of neurite outgrowth in vitro

Alzheimer's disease (AD) is a type of progressive neurodegenerative disease, and amyloid β-protein 42 (Aβ₄₂) serves an important role in the pathological process of development of AD. Paired immunoglobulin-like receptor B (PirB) is a functional receptor for myelin inhibitors of neuron regeneration in the CNS, and it has also been identified to function as a high-affinity receptor for Aβ. Here, we used a phage display to identify a specific PirB antagonist peptide 11(PAP11, PFRLQLS), which could reverse Aβ₄₂-induced neurotoxicity and promote neurite outgrowth in vitro. Immunofluorescence analysis showed that PAP11 colocalized with PirB on the membrane of cortical neurons. Horseradish peroxidase-streptavidin-biotin assay further proved that PAP11 directly binds to PirB and the dissociation constant (K_d) was 0.128μM. PAP11 functionally antagonized the neurite outgrowth inhibitory effect induced by Aβ₄₂ in cortical neurons, and the underlying mechanism was associated with a PirB-ROCK2/CRMP2 signaling pathway. The novel PirB antagonist peptide PAP11 may be a promising candidate therapeutic agent for the treatment of AD and other neurodegenerative diseases. KEY POINTS: • PAP11 was the first PirB antagonist peptide screened by phage display technology. • PAP11 could protect neurons by blocking the binding of Aβ₄₂ and PirB. • PAP11 reverse inhibitory effect of neurite outgrowth through ROCK2/CRMP2 pathway.

Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent "discriminating features" characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined "Deep-Panning", in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.

Phage-Displayed Peptides for Targeting Tyrosine Kinase Membrane Receptors in Cancer Therapy

Receptor tyrosine kinases (RTKs) regulate critical physiological processes, such as cell growth, survival, motility, and metabolism. Abnormal activation of RTKs and relative downstream signaling is implicated in cancer pathogenesis. Phage display allows the rapid selection of peptide ligands of membrane receptors. These peptides can target in vitro and in vivo tumor cells and represent a novel therapeutic approach for cancer therapy. Further, they are more convenient compared to antibodies, being less expensive and non-immunogenic. In this review, we describe the state-of-the-art of phage display for development of peptide ligands of tyrosine kinase membrane receptors and discuss their potential applications for tumor-targeted therapy.

Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5

WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein-protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.

iDRP-PseAAC: Identification of DNA Replication Proteins Using General PseAAC and Position Dependent Features

DNA replication is one of the specific processes to be considered in all the living organisms, specifically eukaryotes. The prevalence of DNA replication is significant for an evolutionary transition at the beginning of life. DNA replication proteins are those proteins which support the process of replication and are also reported to be important in drug design and discovery. This information depicts that DNA replication proteins have a very important role in human bodies, however, to study their mechanism, their identification is necessary. Thus, it is a very important task but, in any case, an experimental identification is time-consuming, highly-costly and laborious. To cope with this issue, a computational methodology is required for prediction of these proteins, however, no prior method exists. This study comprehends the construction of novel prediction model to serve the proposed purpose. The prediction model is developed based on the artificial neural network by integrating the position relative features and sequence statistical moments in PseAAC for training neural networks. Highest overall accuracy has been achieved through tenfold cross-validation and Jackknife testing that was computed to be 96.22% and 98.56%, respectively. Our astonishing experimental results demonstrated that the proposed predictor surpass the existing models that can be served as a time and cost-effective stratagem for designing novel drugs to strike the contemporary bacterial infection.

Cell primitive-based biomimetic functional materials for enhanced cancer therapy

Cell primitive-based functional materials that combine the advantages of natural substances and nanotechnology have emerged as attractive therapeutic agents for cancer therapy. Cell primitives are characterized by distinctive biological functions, such as long-term circulation, tumor specific targeting, immune modulation etc. Moreover, synthetic nanomaterials featuring unique physical/chemical properties have been widely used as effective drug delivery vehicles or anticancer agents to treat cancer. The combination of these two kinds of materials will catalyze the generation of innovative biomaterials with multiple functions, high biocompatibility and negligible immunogenicity for precise cancer therapy. In this review, we summarize the most recent advances in the development of cell primitive-based functional materials for cancer therapy. Different cell primitives, including bacteria, phages, cells, cell membranes, and other bioactive substances are introduced with their unique bioactive functions, and strategies in combining with synthetic materials, especially nanoparticulate systems, for the construction of function-enhanced biomaterials are also summarized. Furthermore, foreseeable challenges and future perspectives are also included for the future research direction in this field.

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.

Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.

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.

Peptide Probes of Colistin Resistance Discovered via Chemically Enhanced Phage Display

Colistin is an antibiotic of last resort used to treat infections caused by multidrug-resistant Gram-negative bacterial pathogens. The recent surge in reported cases of colistin-resistant infections urgently calls for fast and reliable diagnostic methods, which can be used for the facile detection and proper treatment of these challenging infections. A major mechanism of colistin resistance involves phosphoethanolamine (PE) modification of lipopolysaccharide (LPS), the molecular target of colistin. This LPS modification mechanism has been recently reported to be transferrable via a plasmid-carried mcr-1 gene, which is particularly concerning as it may readily confer colistin resistance to a wide array of bacterial pathogens. To develop molecular tools to allow facile detection of colistin resistance, we have herein enlisted a novel phage library that incorporates dynamic covalent warheads to recognize PE modifications on bacterial cells. Screening of this chemically modified phage library against colistin-resistant pathogens revealed a number of peptide probes that readily differentiate colistin-resistant bacterial strains from their colistin-susceptible counterparts. With a fluorophore label, these peptide probes selectively stain colistin-resistant bacteria at sub-to-low micromolar concentrations. The bacterial staining is minimally inhibited by the presence of serum proteins or even blood serum. Mechanistic studies indicate that our peptide probes bind colistin-resistant bacteria primarily by targeting PE-modified lipids. However, some species-specific features of the cell surface can also contribute to the peptides' association to bacterial cells. Further elucidation of such cell surface features may give molecular probes with improved species and strain specificity, which will enable bacterial infection diagnosis with high precision.

Bacteriophage-Based Vaccines: A Potent Approach for Antigen Delivery

Vaccines are considered one of the most important bioproducts in medicine. Since the development of the smallpox vaccine in 1796, several types of vaccines for many diseases have been created. However, some vaccines have shown limitations as high cost and low immune responses. In that regard, bacteriophages have been proposed as an attractive alternative for the development of more cost-effective vaccines. Phage-displayed vaccines consists in the expression of antigens on the phage surface. This approach takes advantage of inherent properties of these particles such as their adjuvant capacity, economic production and high stability, among others. To date, three types of phage-based vaccines have been developed: phage-displayed, phage DNA and hybrid phage-DNA vaccines. Typically, phage display technology has been used for the identification of new and protective epitopes, mimotopes and antigens. In this context, phage particles represent a versatile, effective and promising alternative for the development of more effective vaccine delivery systems which should be highly exploited in the future. This review describes current advances in the development of bacteriophage-based vaccines, with special attention to vaccine delivery strategies. Moreover, the immunological aspects of phage-based vaccines, as well as the applications of phage display for vaccine development, are explored. Finally, important challenges and the future of phage-bases vaccines are discussed.

A mimetic peptide of α2,6-sialyllactose promotes neuritogenesis

Oxidative stress contributes to the pathogenesis of neurodegenerative diseases. With the aim to find reagents that reduce oxidative stress, a phage display library was screened for peptides mimicking α2,6-sialyllactose (6'-SL), which is known to beneficially influence neural functions. Using Sambucus nigra lectin, which specifically binds to 6'-SL, we screened a phage display library and found a peptide comprising identical sequences of 12 amino acids. Mimetic peptide, reverse peptide and scrambled peptide were tested for inhibition of 6'-SL binding to the lectin. Indeed, lectin binding to 6'-SL was inhibited by the most frequently identified mimetic peptide, but not by the reverse or scrambled peptides, showing that this peptide mimics 6'-SL. Functionally, mimetic peptide, but not the reverse or scrambled peptides, increased viability and expression of neural cell adhesion molecule L1 in SK-N-SH human neuroblastoma cells, and promoted survival and neurite outgrowth of cultured mouse cerebellar granule neurons challenged by H₂O₂-induced oxidative stress. The combined results indicate that the 6'-SL mimetic peptide promotes neuronal survival and neuritogenesis, thus raising hopes for the treatment of neurodegenerative diseases. This study was approved by the Medical Ethics Committee of Shantou University Medical College, China (approval No. SUMC 2014-004) on February 20, 2014.

A Dodecapeptide Selected by Phage Display as a Potential Theranostic Probe for Colon Cancers

Aim

Colon cancer is one of the leading causes of cancer-related mortality. However, specific biomarkers for its diagnosis or treatment are not established well.

Methods

We developed a colon-cancer specific peptide probe using phage display libraries. We validated the specificity of this probe to colon cancer cells with immunohistochemical staining and FACS analysis using one normal cell and five colon cancer cell lines.

Results

This peptide probe maintained binding affinity even after serum incubation. For therapeutic applications, this peptide probe was conjugated to hematoporphyrin, a photosensitizer, which showed a significantly enhanced cellular uptake and high photodynamic effect to kill tumor cells. As another application, we made a nanoparticle modified from the peptide probe. It efficiently delivered SN-38, an anticancer drug, into tumor cells, and its tumor-targeting ability was observed in vivo after intravenous injection to the same xenograft model.

Conclusion

The noble dodecapeptide probe can be a promising candidate for both colon tumor diagnosis and targeted drug delivery.

The role of E3 ubiquitin ligase HECTD3 in cancer and beyond

Ubiquitin modification plays significant roles in protein fate determination, signaling transduction, and cellular processes. Over the past 2 decades, the number of studies on ubiquitination has demonstrated explosive growth. E3 ubiquitin ligases are the key enzymes that determine the substrate specificity and are involved in cancer. Several recent studies shed light on the functions and mechanisms of HECTD3 E3 ubiquitin ligase. This review describes the progress in the recent studies of HECTD3 in cancer and other diseases. We propose that HECTD3 is a potential biomarker and a therapeutic target, and discuss the future directions for HECTD3 investigations.

A Specific Nonenal-Binding Peptide, P4 Screened by Phage Display can Remove Trans-2-Nonenal

Trans-2-nonenal is a fatty aldehyde with a long-chain, containing nine carbons. It was known that trans-2-nonenal is a cause of the odor associated with aging, and mainly found from the ages of 40 years. Phage display was a famous laboratory technique for proteins, peptides, and DNA interaction using bacteriophages to connect proteins with the genetic information. In this study, we have carried out random phage display screening to identify specific binding peptides for trans-2-nonenal. Trans-2-nonenal was directly coated on the plate. To select the phages against trans-2-nonenal, the random phages were attached to trans-2-nonenal and selected by 1-5 panning steps. Individual DNA of phage after 5 panning was analyzed to find the specific peptide sequence against trans-2-nonenal. The affinity of positive and negative binding phages was verified by ELISA assay using M13 phage-specific antibody. Among the phages, the phage with sequence of AHKSKLHQHVMFGGG (called as P4) in the end of tail, has shown the highest response. To explore a role of the peptide selected in sequence analysis and ELISA assay, the peptide was connected to magnetic beads. The peptide-coated beads were treated within trans-2-nonenal: treatment of P4 peptide shows significant decrease of trans-2-nonenal compared to negative peptide. Based on our results, it is suggested that the peptide, which is selected by phage display, could be used for the removal of trans-2-nonenal and odor associated with aging.

Selection and characterization of a Vibrio parahaemolyticus OmpU antibody by phage display

Vibrio parahaemolyticus (V. parahaemolyticus) is a well-known food-borne human pathogen that can cause a variety of clinical manifestations after the consumption of raw or undercooked seafoods. The crucial roles of Vibrio OmpU in bacterial pathogenesis have been found in recent studies. In the present study, we screened for single domain antibody fragment (sdAb) candidates that bind to V. parahaemolyticus OmpU by using a sdAb phage display library and isolated several positive phage clones. The UAb28, which was one of the positive clones, was shown high enrichment and affinity. The CDRs of UAb28 are speculated to perform the OmpU binding function by molecular docking. The capable of recognizing OmpU was verified by binding and inhibition assays. The UAb28 might be useful in future studies to develop the potential sdAb-based immunotherapeutics against V. parahaemolyticus infection.

Screening of Duck Tembusu Virus NS3 Interacting Host Proteins and Identification of Its Specific Interplay Domains

NS3 protein is a member of the non-structural protein of duck Tembusu virus (DTMUV), which contains three domains, each of which has serine protease, nucleotide triphosphatase, and RNA helicase activities, respectively. It performs a variety of biological functions that are involved in the regulation of the viral life cycle and host immune response. Based on the yeast two-hybrid system, we successfully transformed pGBKT7-NS3 bait plasmid into Y2H Gold, tested it to prove that it has no self-activation and toxicity, and then hybridized it with the prey yeast strain of the duck embryo fibroblast cDNA library for screening. After high-stringency selection, positive alignment with the National Center for Biotechnology Information database revealed nine potential interactive proteins: MGST1, ERCC4, WIF1, WDR75, ACBD3, PRDX1, RPS7, ND5, and LDHA. The most interesting one (PRDX1) was selected to be verified with full-length NS3 protein and its three domains S7/DEXDc/HELICc using yeast regressive verification and GST Pull-Down assay. It denoted that PRDX1 does indeed interact with HELICc domains of NS3. NS3 is involved in the RNA uncoiling process of viral replication, which may cause mitochondrial overload to create oxidative stress (OS) during DTMUV attack. We deduced that the HELICc domain binding partner PRDX1, which regulates the p38/mitogen-activated protein kinase pathway (p38/MAPK) to avert OS, causing apoptosis, making it possible for viruses to escape host immune responses.