Peptide Dendrimer-Based Antibacterial Agents: Synthesis and Applications

Pathogenic bacteria cause the deaths of millions of people every year. With the development of antibiotics, hundreds and thousands of people's lives have been saved. Nevertheless, bacteria can develop resistance to antibiotics, rendering them insensitive to antibiotics over time. Peptides containing specific amino acids can be used as antibacterial agents; however, they can be easily degraded by proteases in vivo. To address these issues, branched peptide dendrimers are now being considered as good antibacterial agents due to their high efficacy, resistance to protease degradation, and low cytotoxicity. The ease with which peptide dendrimers can be synthesized and modified makes them accessible for use in various biological and nonbiological fields. That is, peptide dendrimers hold a promising future as antibacterial agents with prolonged efficacy without bacterial resistance development. Their in vivo stability and multivalence allow them to effectively target multi-drug-resistant strains and prevent biofilm formation. Thus, it is interesting to have an overview of the development and applications of peptide dendrimers in antibacterial research, including the possibility of employing machine learning approaches for the design of AMPs and dendrimers. This review summarizes the synthesis and applications of peptide dendrimers as antibacterial agents. The challenges and perspectives of using peptide dendrimers as the antibacterial agents are also discussed.

Peptide-Carrier Conjugation

To produce antibodies against synthetic peptides, it is necessary to couple them to a protein carrier. This chapter provides a nonspecialist overview of peptide-carrier conjugation. Furthermore, a protocol for coupling cysteine-containing peptides to bovine serum albumin is outlined.

Peptide Multimerization as Leads for Therapeutic Development

Multimerization of peptide structures has been a logical evolution in their development as potential therapeutic molecules. The multivalent properties of these assemblies have attracted much attention from researchers in the past and the development of more complex branching dendrimeric structures, with a wide array of biocompatible building blocks is revealing previously unseen properties and activities. These branching multimer and dendrimer structures can induce greater effect on cellular targets than monomeric forms and act as potent antimicrobials, potential vaccine alternatives and promising candidates in biomedical imaging and drug delivery applications. This review aims to outline the chemical synthetic innovations for the development of these highly complex structures and highlight the extensive capabilities of these molecules to rival those of natural biomolecules.

Simple and Rapid Synthesis of Branched Peptides through Microwave-Assisted On-Bead Ligation

A rapid on-bead convergent method for preparing branched peptides was reported. Linear peptides were prepared on Dbz resin and ligated various branched cores, including lysine dendrons and other dendritic compounds. Alongside microwave irradiation, <1.5 equiv of peptides is sufficient to afford 50-65% yields of pure branched peptides without chromatographic purification. Remarkably, the desired compounds were prepared within hours.

Peptide-Based Vaccines: Foot-and-Mouth Disease Virus, a Paradigm in Animal Health

Vaccines are considered one of the greatest global health achievements, improving the welfare of society by saving lives and substantially reducing the burden of infectious diseases. However, few vaccines are fully effective, for reasons ranging from intrinsic limitations to more contingent shortcomings related, e.g., to cold chain transport, handling and storage. In this context, subunit vaccines where the essential antigenic traits (but not the entire pathogen) are presented in rationally designed fashion have emerged as an attractive alternative to conventional ones. In particular, this includes the option of fully synthetic peptide vaccines able to mimic well-defined B- and T-cell epitopes from the infectious agent and to induce protection against it. Although, in general, linear peptides have been associated to low immunogenicity and partial protection, there are several strategies to address such issues. In this review, we report the progress towards the development of peptide-based vaccines against foot-and-mouth disease (FMD) a highly transmissible, economically devastating animal disease. Starting from preliminary experiments using single linear B-cell epitopes, recent research has led to more complex and successful second-generation vaccines featuring peptide dendrimers containing multiple copies of B- and T-cell epitopes against FMD virus or classical swine fever virus (CSFV). The usefulness of this strategy to prevent other animal and human diseases is discussed.

A bio-safe multiple antigenic peptide (MAP) enzyme-linked immunoassay for the detection of antibodies to infectious bronchitis virus in chickens

The objective of the study was to develop a bio-safe synthetic peptide ELISA for the detection of antibodies against the infectious bronchitis virus (IBV) using a novel multiple antigenic peptide approach (MAP). After initial ELISA optimization, diagnostic sensitivity (DSn) and specificity (DSp) for the linear peptides were determined using receiver operator curve (ROC) analysis. The peptide IBVP1 showed 90.44% DSn and 88.64% DSp at ROC cut off 22.8% while IBVP2 showed 88.24% DSn and 85.23% DSp at ROC cut off 23.05%. The multimerization of linear peptides to MAP design resulted in the improvement of the diagnostic efficiency up to 94.85% DSn and 92.05% DSp for IBVM1 with 19.95% cut off. A similar improvement in the performance was also observed with 92.65% DSn and 90.91% DSp for IBVM2 at 20.72% cut off. All the peptides were tested for diagnostic specificity and did not show the cross-reactivity with Newcastle disease virus and infectious bursal disease virus positive serum samples. In addition, repeatability testing for all linear and multimeric peptide showed that the coefficient of variation for intra-assay was within the expected limits, ranging from 2.4 to 10.4% and inter-assay coefficient of variation was ranging from 5.56 to 14.3%. In a nutshell, the present study used predicted B cell epitope, the synthetic peptide in linear and multimeric design for IBV antibody detection. The study also highlights peptide antigen with modified scaffold design could be a safe alternative to whole virion-based ELISA for IBV antibody detection.

Peptide-Based Multiepitopic Vaccine Platforms via Click Reactions

Multimeric antigen display and high overall valency are increasingly regarded as strategic goals for potent and broadly efficacious synthetic vaccines with potential market prospects. Herein, a modular and versatile approach to multifunctional peptide-based vaccine platforms at multimilligram scale in reasonable yields is reported. Preparation of chemoselectively modified peptide building blocks of medium-to-large size, conjugation of these subunits, and final assembly were achieved by a combination of Michael-type thiol-ene addition and copper(I)-mediated alkyne-azide cycloaddition. The size and structural complexity of the building blocks required exploration of a further level of orthogonality, namely furan/maleimide Diels-Alder chemistry. After process optimization, a finely tuned, stepwise click approach has emerged as a workable, on-demand strategy to create macromolecular therapeutic vaccine assemblies.

Covalent Graft of Lipopeptides and Peptide Dendrimers to Cellulose Fibers

Introduction: Bacterial proliferation in health environments may lead to the development of specific pathologies, but can be highly dangerous under particular conditions, such as during chemotherapy. To limit the spread of infections, it is helpful to use gauzes and clothing containing antibacterial agents. As cotton tissues are widespread in health care environments, in this contribution we report the preparation of cellulose fibers characterized by the covalent attachment of lipopeptides as possible antimicrobial agents. Aim: To covalently link peptides to cotton samples and characterize them. Peptides are expected to preserve the features of the fabrics even after repeated washing and use. Peptides are well tolerated by the human body and do not induce resistance in bacteria. Materials and Methods: A commercially available cotton tissue (specific weight of 150 g/m2, 30 Tex yarn fineness, fabric density of 270/230 threads/10 cm in the warp and weft) was washed with alkali and bleached and died. A piece of this tissue was accurately weighed, washed with methanol (MeOH) and N,N-dimethylformamide (DMF), and air-dried. Upon incubation with epibromohydrin, followed by treatment with Fmoc-NH-CH2CH2-NH2 and Fmoc removal, the peptides were synthesized by incorporating one amino acid at a time, beginning with the formation of an amide bond with the free NH2 of 1,2–diaminoethane. We also linked to the fibers a few peptide dendrimers, because the mechanism of action of these peptides often requires the formation of clusters. We prepared and characterized seven peptide-cotton samples. Results: The new peptide-cotton conjugates were characterized by means of FT-IR spectroscopy and X-ray Photoelectron Spectroscopy (XPS). This latter technique allows for discriminating among different amino acids and thus different peptide-cotton samples. Some samples maintain a pretty good whiteness degree even after peptide functionalization. Interestingly, these samples also display encouraging activities against a Gram positive strain. Conclusions: Potentially antimicrobial lipopeptides can be covalently linked to cotton fabrics, step-by-step. It is also possible to build on the cotton Lys-based dendrimers. XPS is a useful technique to discriminate among different types of nitrogen. Two samples displaying some antibacterial potency did also preserve their whiteness index.

Trimeric heptad repeat synthetic peptides HR1 and HR2 efficiently inhibit HIV-1 entry

The trimeric heptad repeat domains HR1 and HR2 of the human immunodeficiency virus 1 (HIV-1) gp41 play a key role in HIV-1-entry by membrane fusion. To develop efficient inhibitors against this step, the corresponding trimeric-N36 and C34 peptides were designed and synthesized. Analysis by circular dichroism of monomeric and trimeric N36 and C34 peptides showed their capacities to adopt α-helical structures and to establish physical interactions. At the virological level, while trimeric-C34 conserves the same high anti-fusion activity as monomeric-C34, trimerization of N36-peptide induced a significant increase, reaching 500-times higher in anti-fusion activity, against R5-tropic virus-mediated fusion. This result was associated with increased stability of the N36 trimer peptide with respect to the monomeric form, as demonstrated by the comparative kinetics of their antiviral activities during 6-day incubation in a physiological medium. Collectively, our findings demonstrate that while the trimerization of C34 peptide had no beneficial effect on its stability and antiviral activity, the trimerization of N36 peptide strengthened both stability and antiviral activity. This approach, promotes trimers as new promising HIV-1 inhibitors and point to future development aimed toward innovative peptide fusion inhibitors, microbicides or as immunogens.

Branched BBB-shuttle peptides: chemoselective modification of proteins to enhance blood-brain barrier transport

The blood-brain barrier (BBB) hampers the delivery of therapeutic proteins into the brain. BBB-shuttle peptides have been conjugated to therapeutic payloads to increase the permeability of these molecules. However, most BBB-shuttles have several limitations, such as a lack of resistance to proteases and low effectiveness in transporting large biomolecules. We have previously reported on the THRre peptide as a protease-resistant BBB-shuttle that is able to increase the transport of fluorophores and quantum dots in vivo. In this work, we have evaluated the capacity of linear and branched THRre to increase the permeability of proteins in cellular models of the BBB. With this purpose, we have covalently attached peptides with one or two copies of the BBB-shuttle to proteins in order to develop chemically well-defined peptide-protein conjugates. While THRre does not enhance the uptake and transport of a model protein in BBB cellular models, branched THRre peptides displaying two copies of the BBB-shuttle result in a 2.6-fold increase.

Single-Molecule Peptide-Lipid Affinity Assay Reveals Interplay between Solution Structure and Partitioning

Interactions between short protein segments and phospholipid bilayers dictate fundamental aspects of cellular activity and have important applications in biotechnology. Yet, the lack of a suitable methodology for directly probing these interactions has hindered the mechanistic understanding. We developed a precision atomic force microscopy-based single-molecule force spectroscopy assay and probed partitioning into lipid bilayers by measuring the mechanical force experienced by a peptide. Protein segments were constructed from the peripheral membrane protein SecA, a key ATPase in bacterial secretion. We focused on the first 10 amino-terminal residues of SecA (SecA2-11) that are lipophilic. In addition to the core SecA2-11 sequence, constructs with nearly identical chemical composition but with differing geometry were used: two copies of SecA2-11 linked in series and two copies SecA2-11 linked in parallel. Lipid bilayer partitioning interactions of peptides with differing structures were distinguished. To model the energetic landscape, a theory of diffusive barrier crossing was extended to incorporate a superposition of potential barriers with variable weights. Analysis revealed two dissociation pathways for the core SecA2-11 sequence with well-separated intrinsic dissociation rates. Molecular dynamics simulations showed that the three peptides had significant conformational differences in solution that correlated well with the measured variations in the propensity to partition into the bilayer. The methodology is generalizable and can be applied to other peptide and lipid species.

Large-scale synthesis and structural analysis of a synthetic glycopeptide dendrimer as an anti-cancer vaccine candidate

A complex glycopeptide was obtained in multigram as a fully synthetic anti-cancer vaccine for human use.

Highly chemoselective ligation of thiol- and amino-peptides on a bromomaleimide core

Application of a bromomaleimide core allows for the incorporation of three different peptides. The key reactions of the process are the selective stapling of both thiol- and amino-peptides on two different sites of the core. The thiol-peptide attacks and replaces the bromide whereas the amino-peptide attaches to the ene-position of the core revealing differential and selective reactivity. This platform will have further application in protein chemistry, multidrug presentation and vaccine preparation.

Anaplasma marginale: Diversity, Virulence, and Vaccine Landscape through a Genomics Approach

In order to understand the genetic diversity of A. marginale, several efforts have been made around the world. This rickettsia affects a significant number of ruminants, causing bovine anaplasmosis, so the interest in its virulence and how it is transmitted have drawn interest not only from a molecular point of view but also, recently, some genomics research have been performed to elucidate genes and proteins with potential as antigens. Unfortunately, so far, we still do not have a recombinant anaplasmosis vaccine. In this review, we present a landscape of the multiple approaches carried out from the genomic perspective to generate valuable information that could be used in a holistic way to finally develop an anaplasmosis vaccine. These approaches include the analysis of the genetic diversity of A. marginale and how this affects control measures for the disease. Anaplasmosis vaccine development is also reviewed from the conventional vaccinomics to genome-base vaccinology approach based on proteomics, metabolomics, and transcriptomics analyses reported. The use of these new omics approaches will undoubtedly reveal new targets of interest in the near future, comprising information of potential antigens and the immunogenic effect of A. marginale proteins.

Peptide-Carrier Conjugation

To produce antibodies against synthetic peptides it is necessary to couple them to a protein carrier. This chapter provides a nonspecialist overview of peptide-carrier conjugation. Furthermore, a protocol for coupling cysteine-containing peptides to bovine serum albumin is outlined.

Glycodendropeptides stimulate dendritic cell maturation and T cell proliferation: a potential influenza A virus immunotherapy

A GDP displaying the NP_366–374 influenza A virus epitope induces an immunostimulatory effect, emerging as a potential flu vaccine.

Branched polymer models and the mechanism of multilayer film buildup

The "in and out diffusion" hypothesis does not provide a conclusive explanation of the buildup displayed by some polyelectrolyte multilayer film systems. Here, we report initial tests of an alternative hypothesis, on which the completion of each adsorption cycle results in an increase in the number of polymer binding sites on the film surface. Polycationic dendrimeric peptides, which can potentially bind several oppositely-charged peptides each, have been designed, synthesized and utilized in comparative film buildup experiments. Material deposited, internal film structure and film surface morphology have been studied by ultraviolet spectroscopy (UVS), circular dichroism spectroscopy (CD), quartz crystal microbalance (QCM) and atomic force microscopy (AFM). Polycations tended to contribute more to film buildup than did polyanions on quartz but not on gold. Increasing the number of branches in the dendrimeric peptides from 4 to 8 reproducibly resulted in an increase in the film growth rate on quartz but not on gold. Peptide backbones tended to adopt a β-strand conformation on incorporation into a film. Thicker films had a greater surface roughness than thin films. The data are consistent with film buildup models in which the average number of polymer binding sites will increase with each successive adsorption cycle in the range where exponential growth is displayed.

Captides: rigid junctions between beta sheets and small molecules

An extensive series of covalently linked small molecule-peptide adducts based on a terminally capped-beta hairpin motif is reported. The constructs can be prepared by standard solid-phase Fmoc chemistry with one to four peptide chains linked to small molecule hubs bearing carboxylic acid moieties. The key feature of interest is the precise, buried environment of the small molecule, and its rigid orientation relative to one or more short but fully structured peptide chain(s). Most of this study employs a minimalist nine residue 'captide', a capped β-turn, but we illustrate general applicability to peptides which can terminate in a beta strand. The non-peptide portion of these adducts can include nearly any molecule bearing one or more carboxylic acid groups. Fold-dependent rigidity sets this strategy apart from the currently available bioconjugation methods, which typically engender significant flexibility between peptide and tag. Applications to catalyst enhancement, drug design, higher-order assembly, and FRET calibration rulers are discussed.

Optimized Solid Phase-Assisted Synthesis of Dendrons Applicable as Scaffolds for Radiolabeled Bioactive Multivalent Compounds Intended for Molecular Imaging

Dendritic structures, being highly homogeneous and symmetric, represent ideal scaffolds for the multimerization of bioactive molecules and thus enable the synthesis of compounds of high valency which are e.g., applicable in radiolabeled form as multivalent radiotracers for in vivo imaging. As the commonly applied solution phase synthesis of dendritic scaffolds is cumbersome and time-consuming, a synthesis strategy was developed that allows for the efficient assembly of acid amide bond-based highly modular dendrons on solid support via standard Fmoc solid phase peptide synthesis protocols. The obtained dendritic structures comprised up to 16 maleimide functionalities and were derivatized on solid support with the chelating agent DOTA. The functionalized dendrons furthermore could be efficiently reacted with structurally variable model thiol-bearing bioactive molecules via click chemistry and finally radiolabeled with ⁶⁸Ga. Thus, this solid phase-assisted dendron synthesis approach enables the fast and straightforward assembly of bioactive multivalent constructs for example applicable as radiotracers for in vivo imaging with Positron Emission Tomography (PET).

Influence of conjugation chemistry and B epitope orientation on the immune response of branched peptide antigens

Multimeric presentation, a well-proven way of enhancing peptide immunogenicity, has found substantial application in synthetic vaccine design. We have reported that a combination of four copies of a B-cell epitope with one of a T-cell epitope in a single branched construct results in a peptide vaccine conferring total protection against foot-and-mouth disease virus in swine, a natural host (Cubillos et al. (2008) J. Virol. 82, 7223-7230). More recently, a downsized version of this prototype with only two copies of the B epitope has proven as effective as the tetravalent one in mice. Here we evaluate three approaches to bivalent platforms of this latter type, involving different chemistries for the conjugation of two B epitope peptides to a branching T epitope. Comparison of classical thioether, "reverse" thioether (Monsó et al. (2012) Org. Biomol. Chem. 10, 3116-3121) and thiol-ene conjugation chemistries in terms of synthetic efficiency clearly singles out the latter, maleimide-based strategy as most advantageous. We also examine how minor structural differences among the conjugates--including the N- or C-terminal attachment of the B epitope to the branching T epitope--bear on the immunogenicity of these vaccine candidates, with the maleimide-based conjugate again emerging as the most successful.

Chimeric infectious bursal disease virus-like particles as potent vaccines for eradication of established HPV-16 E7-dependent tumors

Cervical cancer is caused by persistent high-risk human papillomavirus (HR-HPV) infection and represents the second most frequent gynecological malignancy in the world. The HPV-16 type accounts for up to 55% of all cervical cancers. The HPV-16 oncoproteins E6 and E7 are necessary for induction and maintenance of malignant transformation and represent tumor-specific antigens for targeted cytotoxic T lymphocyte–mediated immunotherapy. Therapeutic cancer vaccines have become a challenging area of oncology research in recent decades. Among current cancer immunotherapy strategies, virus-like particle (VLP)–based vaccines have emerged as a potent and safe approach. We generated a vaccine (VLP-E7) incorporating a long C-terminal fragment of HPV-16 E7 protein into the infectious bursal disease virus VLP and tested its therapeutic potential in HLA-A2 humanized transgenic mice grafted with TC1/A2 tumor cells. We performed a series of tumor challenge experiments demonstrating a strong immune response against already-formed tumors (complete eradication). Remarkably, therapeutic efficacy was obtained with a single dose without adjuvant and against two injections of tumor cells, indicating a potent and long-lasting immune response.

A T-cell epitope on NS3 non-structural protein enhances the B and T cell responses elicited by dendrimeric constructions against CSFV in domestic pigs

It has been recently reported by our group that dendrimeric constructs combining B- and T-cell epitopes from classical swine fever virus (CSFV) provided partial protection against experimental infection. This research evaluated four newly designed constructions while taking into account our previous work, including the direct implication that a T-cell epitope from the NS3 protein contributes to the generation of the immune response against CSFV. To this end, the dendrimeric constructions, including either this NS3 T-cell epitope alone or two different B-cell epitopes without this T-cell epitope, were used to immunise pigs. Thus, construct 1, containing the NS3 T-cell epitope and four copies of a previously described B-cell epitope, significantly reduced the clinical scores and RNA viral loads after challenge relative to the control group. In three out of six animals in this group, vaccination achieved partial protection and was associated with IFN-gamma producing-cells and neutralising antibodies. In contrast, the pigs immunised with construct 2, again with four copies of the B epitope of construct 1 but lacking the T-cell motif, developed more severe clinical signs. Finally, the additional constructs 3 and 4 included four copies of a B epitope that was different from the epitope used in constructs 1 and 2 with or without the abovementioned NS3 T-cell epitope, respectively. Pigs immunised with these latter constructs developed low levels of peptide-specific antibodies that correlated with equally low levels of cellular responses, an absence of neutralising antibodies and a lack of protection. Even so, the clinical scores in the first week after the challenge were less severe for animals vaccinated with construct 3 than for those given construct 4. Our results confirm the relevant role of the B-cell epitope in residues 694-712 of the glycoprotein E2 (which is used in both constructs 1 and 2) for protection against CSFV, as well as the appropriateness of the newly used NS3 peptide as a specific T-cell epitope in domestic pigs.

Cell-mediated immune response to epitopic MAP (multiple antigen peptide) construct of LcrV antigen of Yersinia pestis in murine model

Yersinia pestis is the causative agent of plague. Cellular immunity seems to play an important role in defense against this disease. The subunit vaccine based on V (Lcr V) antigen has been proved to be immunogenic in animals and in humans. The multiple antigen peptide (MAP), incorporating all the relevant B and T cell epitopes is highly immunogenic in mice through intranasal route of immunization in PLGA particles containing CpG-ODN as an immunoadjuvant inducing humoral and mucosal immune response. In the present study, cell-mediated immune response using same MAP was studied in murine model. Primary and memory T cell responses were studied in outbred and inbred mice immunized intranasally with MAP in the presence of two immunoadjuvants (Murabutide and CpG-ODN). All the three compartments (Spleen, Lamina propria and Peyer's patches) of the lymphoid system showed increased lymphoproliferative response. Highest lymphoproliferative response was observed especially with CpG-ODN. Cytokine profile in the culture supernatant showed highest Th(1) and Th(17) levels. FACS analysis showed expansion of both CD4(+) and CD8(+) T cells producing gamma-interferon, perforin and granzyme-B with major contribution from CD4(+) T cells.

Reverse thioether ligation route to multimeric peptide antigens

Multimeric presentation, a rather effective way of enhancing peptide immunogenicity, is best exemplified by MAP (multiple antigenic peptide) dendrimers consisting of a branched Lys core on which several copies of the peptide epitope are displayed. While accessible by solid-phase synthesis, MAPs can also be conveniently made in solution, e.g., by linking the epitope (N-acetylated and with a C-terminal Cys) through a thioether bond onto the α and ε (haloacetyl-activated) positions of the Lys core. We now report the reverse version of this approach, whereby a chloroacetyl-derivatised epitope is tethered to a thiol-functionalised form of a Lys dendron core. This convergent approach can be carried out either in solution or in the solid phase and is advantageous because (i) in situ tris(2-carboxyethyl)phosphine (TCEP)-mediated reduction of disulfide bonds maintains the thiol platform reactive throughout the ligation process; (ii) the low amounts of TCEP used pose minimal risk to chloroacetyl groups in the peptide, resulting in (iii) significantly reduced byproduct formation, hence cleaner products. For the solid phase version of the method, an optimised procedure has been devised to convert the Lys core into a tetrathiol dendron.

Production and characterization of peptide antibodies

Proteins are effective immunogens for generation of antibodies. However, occasionally the native protein is known but not available for antibody production. In such cases synthetic peptides derived from the native protein are good alternatives for antibody production. These peptide antibodies are powerful tools in experimental biology and are easily produced to any peptide of choice. A widely used approach for production of peptide antibodies is to immunize animals with a synthetic peptide coupled to a carrier protein. Very important is the selection of the synthetic peptide, where factors such as structure, accessibility and amino acid composition are crucial. Since small peptides tend not to be immunogenic, it may be necessary to conjugate them to carrier proteins in order to enhance immune presentation. Several strategies for conjugation of peptide-carriers applied for immunization exist, including solid-phase peptide-carrier conjugation and peptide-carrier conjugation in solution. Upon immunization, adjuvants such as Al(OH)(3) are added together with the immunogenic peptide-carrier conjugate, which usually leads to high-titred antisera. Following immunization and peptide antibody purification, the antibodies are characterized based on their affinity or specificity. An efficient approach for characterization of peptide antibodies is epitope mapping using peptide based assays. This review describes standard solid-phase approaches for generation of peptide antibodies with special emphasis on peptide selection, generation of peptide conjugates for immunization and characterization of the resulting peptide antibodies.