Bacteriophages, Part B: 83 (Advances in Virus Research)
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Bacteriophages: Their Structural Organisation and Function
Johnson, Staquicini, F. Sulakvelidze, A. Morris, Tanji, Y. Some of these molecules have been developed as therapeutics and are currently in clinical or preclinical trials; on the other hand, others have been crucial to describe protein-protein interactions and revealed important therapeutic targets [ 19 , 20 ]. Briefly, this method focuses on the construction of a library of peptides or antibody variants, which are then selected for their affinity to the target of interest since they are fused to a phage-coat protein.
On the other hand, pIII can be used for larger peptides, resulting only in a slight loss of infectivity in a few cases [ 21 ]. Each library is composed by phagemid vectors containing only the sequence of a phage-coat protein fused to the peptide of interest; therefore, a helper phage with a reduced packaging efficiency is needed in order to obtain a population of phages both infectious and composed by modified coating proteins.
The biopanning procedure is then performed and phages are selected for their ability to bind the antigen of interest.
Bacteriophages and Their Immunological Applications against Infectious Threats
Many factors must be taken into account: library variability, target conformation, affinity, and avidity of the molecules exposed on phages. As mentioned, phage display has been widely used to find novel therapeutics against pathogens, particularly mAbs. This has been possible through two different biopanning strategies: using specific molecular targets, such as enzymes or membrane receptors, or using whole viruses or bacterial cells.
The main difference between these two approaches is that the second one allows the identification of pathogen structures not already identified as drug targets. Moreover, surface antigens often present motifs able to elicit non-neutralizing mAbs and elude host immune response, so the screening procedure of the biopanning outcome must be done properly in order to identify only the few effective molecules.
Several human infectious diseases have been successfully addressed for drug discovery using phage display. As stated above, many of the molecules developed using phage display technique are currently in clinical trials or under evaluation at a preclinical stage. MedImmune developed motavizumab, a version of their lead compound against RSV infection palivizumab which was optimized by enhancing its affinity to the target [ 35 ].
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Its target is phosphatidylserine, a molecule that is located in the inner part of the cell membrane of healthy cells, but becomes exposed on the surface of infected cells or solid cancer cells, allowing their immune evasion. Moreover, Human Genome Sciences developed raxibacumab for anthrax using a part of the toxin itself, the B.
Neutralizing mAbs are very useful as therapeutics but can also be of great importance for the identification of protective epitopes on pathogen structures. In fact, the characterization of these regions on viruses and bacteria could suggest which elements should be included into a vaccine formulation in order to be effective.
To date, there are several human infectious diseases that cannot be treated with vaccination, since all the approaches tested so far proved to be unsuccessful. One of the causes of failure is the nature of the antigens included into the vaccine. In fact, the use of recombinant proteins may limit, though not eliminate, the mechanisms of immunodominance that pathogens use to evade host immune response.
Immunodominant epitopes are those regions that can be mutated without affecting the pathogen protein functions, both rerouting the adaptive immune response against non-neutralizing epitopes and masking epitopes that can impair infection mechanisms. Thus, bacterial and viral proteins often elicit a varying humoral response, with a minimal neutralizing fraction, unable to defeat the infection [ 39 — 41 ]. Moreover, also antibody-mediated interference has been widely described [ 22 , 42 ]. Dulbecco et al. Later observations in both chronic and acute infections confirmed this assumption.
Two mechanisms have been proposed for this evasion strategy: non-nAbs interference by steric hindrance due to proximity of neutralizing and non-neutralizing epitopes; inhibition of binding of nAbs due to epitope conformational changes caused by non-nAbs binding to the pathogen protein. Furthermore, it has been speculated that non-nAbs may enhance infections through interaction with Fc receptors or complement receptors [ 44 ].
On the other hand, neutralizing mAbs as molecular probes could be extremely useful for a rational design of vaccine formulations: the administration of their mimotopes should elicit only an effective humoral response against pathogens [ 45 , 46 ].
Canadian Journal of Microbiology
For this purpose, phage display technique has been widely employed: HCV, HIV, and Plasmodium falciparum proteins are just examples of molecular targets used in the biopanning procedure for epitope mapping [ 26 , 47 , 48 ]. In addition, phage particles themselves can induce both cellular and humoral immune response when recognised by the immune system [ 49 ]. Moreover, they proved to be unaffected by harsh physical and chemical conditions, resulting suitable for vaccine delivery [ 50 ].
In fact, these peculiar characteristics, as well as cost-effective production and ease of modification, made bacteriophages attractive for industrial development of phage-based vaccines. Two different approaches have been developed: the first one is based on phage particles with antigens transcriptionally fused to their coat proteins, resembling the phage display technique described above. This strategy proved to be effective against Yersinia pestis [ 51 ], where T4 phages displayed an engineered structural subunit of the pathogen on its capsid, and against HIV and influenza, using phage T4 and T7, respectively [ 52 , 53 ].
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The second approach consists of phage DNA vaccines: the antigen gene is delivered by phages into antigen-presenting cells to be expressed and processed by them, leading to enhanced immune response compared to naked DNA delivery. Due to their high level of organization, their unique morphology, and biological properties, bacteriophages appear as sophisticated nanomachines and, as described above, have been immediately employed for therapeutic purposes. Typically, only lytic phages are exploited for phage therapy: firstly, because they kill the host bacteria in a more efficient manner; subsequently because, after lysogenic induction, temperate phages can transfer bacteria DNA fragments to other species, and if these fragments contain gene-encoding toxins or antibiotic resistance elements, they could generate new dangerous bacteria.
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On the contrary, lytic phages are unable to perform transduction, thus ensuring a safer profile. Nowadays, many bacteria have collected multiple resistance mechanisms, thus rendering some antibiotic classes useless. Beyond the quite high level of natural resistance, patients are concomitantly treated with broad-spectrum antibiotic molecules, increasing the rate of blind selection of multidrug resistance isolates MDR. In hospital settings, Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , and Enterobacter cloacae ESKAPE are examples of multidrug-resistant strains that solicit novel therapeutic measures [ 56 ].
This challenge forced modern medicine to review methods against bacterial infections, reconsidering the beneficial potential of phages. In , the Food and Drug Administration FDA approved the first Phase I clinical trial evaluating the safety of an eight-phage cocktail able to kill Staphylococcus aureus , Pseudomonas aeruginosa , and Escherichia coli ; 42 patients with venous leg ulcers were treated and a high-safety profile was demonstrated ClinicalTrials.
This study aimed at demonstrating the potential of a novel therapy for childhood diarrhea, a major cause of morbidity and deaths in Bangladesh and other developing countries, and thus a priority for improving child health: as shown in Table 1 , oral phages showed a safe gut transit, even if it failed to achieve intestinal amplification and did not improve diarrhea outcome. This was possibly related to insufficient phage coverage and too low E.
The treatment uses GMP-produced cocktails of anti- E.