Design of peptide-based vaccines for cancer

The immune system responds efficiently to bacteria, viruses and other agents however, the immune response to cancers is not as effective. In most cases other than specific genetic rearrangements leading to non-self proteins such as in leukemia and idiotypes in lymphoma, tumor associated proteins are self proteins and are not recognized by the immune system to prevent malignancy. In most cancers, patients develop antibodies and/or CTL-precursors to tumor associated antigens but are not effective in generating a therapeutic immune response. Adjuvants have been used with either whole tumors, subunits or peptides with the aim of increasing their immunity. Whole tumor antigens have certain advantages associated with it, such as ready availability as recombinant proteins, potential epitopes that can be presented by a number of MHC class I/II alleles and antibody development. The methods of identification of CD8 and CD4 epitopes either by use of epitope prediction algorithms or use of transgenic mice has made the use of defined synthetic peptides more attractive. The possibility to synthesize long peptides and introduce multiple epitopes (CD4 or CD8) from single or multiple antigens makes peptide a viable alternative to whole proteins. As an alternative to totally synthetic peptide constructs or polymers, polytopes have been generated by genetic engineering methods. In addition, to deliver immunogens to and to activate DC, receptor-mediated delivery of peptides using antibodies, cytokines and carbohydrates have been used. This review will encompass the various strategies, preclinical and clinical applications in designing peptide-based vaccines for cancer.     

Peptide mimicking antigenic and immunogenic epitope of neuwiedase from Bothrops neuwiedi snake venom

Peptides derived from a phage display library may mimic essential features of epitopes (mimotopes), including their immunogenicity. A recombinant peptide library of 12 amino acids displayed on the phage capsid was used to obtain peptides that mimic epitopes of antigens that are reactive to specific polyclonal antibodies anti-neuwiedase (NEU), a toxin from Bothrops neuwiedi snake venom. These polyclonal antibodies are protective against NEU activity and were used as target for the peptide library biopannings, resulting in the selection of 80 peptides. Antibody-binding epitopes were obtained by sequence alignment with the primary and tertiary structures of the NEU protein. Antigenicity and specificity of the mimotopes mixture were confirmed by dot blot, immuno dot blot, plaque reduction and Western blot assays. Their immunogenicity was demonstrated by immunization of BALB/c mice and ELISA tests. The NEU toxin is an important antigen that has many common structural regions to several toxic venom metalloproteinases, in which two epitope regions have been detected. The two mapped epitopes were found in primary sequences of several snake venom toxins, thus demonstrating the potential application of these NEU mimotopes as possible antigen components that are toxicity free.     

DR (MHC class II) ligands: an approach to rheumatoid arthritis therapeutics

The presentation of peptide antigens to T-cells by MHC Class II proteins is a central process in cellular and humoral immune responses. Blockade of this presentation event via synthetic ligands that bind to disease-associated MHCs (such as DR1 and DR4) may be useful for the treatment of autoimmune diseases such as rheumatoid arthritis, Type 1 diabetes, multiple sclerosis, lupus erthymatosis and Graves disease. Recently reported synthetic ligands for DR1 and DR4 are short modified peptides (2-7 mers) capable of competing at nanomolar concentrations with antigenic peptides for the DR (MHC) binding groove.     

An alpha helix conformationally restricted peptide is recognized by cervical carcinoma patients' sera

Human papillomavirus type 16 (HPV-16) represents the major cervical carcinoma associated virus among women, especially in Colombia. It has thus become important to develop reliable inexpensive tests for detecting the presence of this virus. It has been shown that HPV16-E7 oncoprotein structural features have three alpha-helical structures and a loop-like structure. The hydrazone link approach was used to mimic helix secondary substructures. Sera from women with invasive cervical carcinoma were tested against conformationally restricted peptides and their respective linear peptides to identify conformational epitopes. One peptide that was conformationally restricted to an alpha-helix showed very strong positive reaction with sera from women having invasive cervical carcinoma; there was no reaction with sera from patients with other carcinomas, children, or healthy women. NMR studies confirmed this peptide's alpha-helical structure. The observation that constrained protein substructure peptidomimetics can identify new conformationally sensitive antibodies in cervical carcinoma patients' sera is very important, since these antibodies are almost all generated by native proteins, providing a new selection of antibodies for diagnostic and vaccine studies.     

Section Reviews: Biologicals & Immunologicals: Sjögren's syndrome: Pathogenesis and prospects for therapy

Primary Sjögren's syndrome (SS) is characterised by focal lymphocytic infiltrates in salivary and lacrimal glands, leading to dryness of eyes and mouth, induction of class II major histocompatibility antigens on the glandular epithelial cells, and high titre antinuclear antibodies directed against ribonuclear proteins including Sjögren's-associated antigens (termed SS-A and SS-B). It is proposed that T-cells directed against self epitopes escape ‘tolerance’ in the thymus due to the relatively weak binding of a self peptide to self major histocompatibility complex molecules. As a result, these nascent T-cells with potential autoimmune reactivity are released into the peripheral lymphoid system. Subsequent exposure of these T-cells to the self peptide or a foreign (microbial) mimic in the salivary/lacrimal glands of SS patients can lead to expansion of these autoreactive T-cell clones and diversification of the T-cell response to include additional antigenic epitopes. Recent studies have emphasised the role of co-stimulatory factors including cytokines, growth factors, neurotransmitters, and reproductive hormones. Each of these sites of immune-neuro-hormonal interaction represents an opportunity for novel therapeutic intervention.     

Linear epitopes of sperm whale myoglobin identified by polyclonal antibody screening of random peptide library

Distinct enhancement of antibody-specific clones was apparent during the screening against random peptide libraries with antigen-specific polyclonal antibodies. Several sequence motifs obtained from these screenings were homologous with the primary sequence of myoglobin. Two of these motifs have been confirmed as antigenic determinants by competitive inhibition tests using eight-branched synthetic peptides. One of the peptides has a sequence that corresponds to amino acid residues 42-50, KFDRFKHLK, of the myoglobin sequence. This is a new epitope of myoglobin that is reported for the first time. The epitope is located precisely in the ‘turn’ or ‘loop’ region between helices C and D of the crystal structure of myoglobin. The second antibody binding site has a sequence of DIAAKYKELGYQG, and this is located between residues 141-153, which is the C-terminus of myoglobin. This epitope encompassed two linear epitopes of myoglobin, amino acid residues 145-151 and 147-153, that have been reported earlier based on immunochemical characterisation of cleavage fragments of the protein. These results clearly indicate that epitope mapping using polyclonal antibodies against random peptide libraries can identify new epitopes precisely, as well as confirm epitopes of myoglobin obtained earlier using established methodologies. © Munksgaard 1996.     

Prediction of MHC binding peptides and epitopes from alfalfa mosaic virus

Peptide fragments from alfalfa mosaic virus involved multiple antigenic components directing and empowering the immune system to protect the host from infection. MHC molecules are cell surface proteins, which take active part in host immune reactions and involvement of MHC class-I & II in response to almost all antigens. Coat protein of alfalfa mosaic virus contains 221 aa residues. Analysis found five MHC ligands in coat protein as 64-LSSFNGLGV-72; 86- RILEEDLIY-94; 96-MVFSITPSY-104; 100- ITPSYAGTF-108; 110- LTDDVTTED-118; having rescaled binding affinity and c-terminal cleavage affinity more than 0.5. The predicted binding affinity is normalized by the 1% fractil. The MHC peptide binding is predicted using neural networks trained on c-terminals of known epitopes. In analysis predicted MHC/peptide binding is a log transformed value related to the IC50 values in nM units. Total numbers of peptides found are 213. Predicted MHC binding regions act like red flags for antigen specific and generate immune response against the parent antigen. So a small fragment of antigen can induce immune response against whole antigen. This theme is implemented in designing subunit and synthetic peptide vaccines. The sequence analysis method allows potential drug targets to identify active sites against plant diseases. The method integrates prediction of peptide MHC class I binding; proteosomal c-terminal cleavage and TAP transport efficiency.     

Utility of azapeptides as major histocompatibility complex class II protein ligands for T-cell activation

Major histocompatibility complex class II (MHC II) protein binding and antigen specific activation of CD4+ "helper" T cells are demonstrated with peptides composed of the antigenic hen egg ovalbumin 325-339 peptide (OVA) substituted with azaamino acids. AzaAla and azaGly substitutions were made at 10 sequential peptide positions (326Ala-335Asn) that lie in the binding groove. The peptide positions substituted with azaamino acids encompass almost the entire binding groove, including positions where the identity of the amino acid side chain is known to have the most significant effect on MHC binding and the least effect on T-cell recognition. In addition, the T-cell contact 333Glu was substituted with azaGlu to generate a partial agonist ligand for the 3DO-54.8 T-cell hybridoma. Binding to MHC II protein was assayed by measuring the kinetic stability of complexes formed between detergent-solubilized MHC II I-A(d) protein and fluorescein-labeled OVA peptides using a fluorescence-HPLC assay. T-cell activation was also evaluated for aza-substituted peptides with azaamino acid substitutions at the peptide positions known to interact with the MHC II protein. All aza-substituted peptides showed detectable MHC binding, and some were found to show T-cell activation potency equal to the native peptide. Several of these were also found to be weak or partial agonists. Our results demonstrate that azaamino acids substituted into an antigenic peptide cause a subtle, global effect on peptide conformation that can be used to design altered peptide ligands (APL) as T-cell partial agonists. These may have potential as T-cell epitopes for synthetic vaccines and therapeutic agents for autoimmune diseases.     

Capsid-incorporation of antigens into adenovirus capsid proteins for a vaccine approach

Some viral vectors are potent inducers of cellular and humoral responses; therefore, viral vectors can be used to vaccinate against cancer or infectious diseases. This report will focus on adenovirus (Ad)-based vectors. Traditional viral-vector vaccination embodies the concept that the vector uses the host-cell machinery to express antigens that are encoded as transgenes within the viral vector. Several preclinical successes have used this approach in animal model systems. However, in some instances, these conventional Ad-based vaccines have yielded suboptimal clinical results. These suboptimal results are ascribed, in part, to preexisting Ad serotype 5 (Ad5) immunity. To address this issue, the "antigen capsid-incorporation" strategy has been developed to circumvent the drawbacks associated with conventional transgene expression of antigens by Ad vectors. This strategy embodies the incorporation of antigenic peptides within the capsid structure of viral vectors. Incorporating immunogenic peptides into the Ad capsid offers potential advantages. Importantly, vaccination by means of the antigen capsid-incorporated approach results in a strong humoral response, similar to the response generated by native Ad capsid proteins. This strategy also allows for the boosting of antigenic specific responses. This strategy may be the way forward for improved vaccine schemes, especially for those infections requiring a strong humoral antigenic response.     

Antibodies as predictors of complex autoimmune diseases

Emerging evidence has suggested environmental factors such as infections and xenobiotics and some dietary proteins and peptides in the pathogenesis of many autoimmune diseases. Considering the fact that autoantibodies can often be detected prior to the onset of a disease, in this study an enzyme immunoassay was used for measurement of antibodies against different highly purified antigens or synthetic peptides originating not only from human tissue, but also from cross-reactive epitopes of infectious agents, dietary proteins and xenobiotics. The measurement of antibodies against a panel of antigens allows for identification of patterns or antibody signatures, rather than just one or two markers of autoimmunity, thus establishing the premise for increased sensitivity and specificity of prediction, as well as positive predictive values. This panel of different autoantibodies was applied to 420 patients with different autoimmune diseases, including pernicious anemia, celiac disease, thyroiditis, lupus, rheumatoid arthritis, osteoarthritis, Addison's disease, type 1 diabetes, cardiovascular disease and autoimmunity, which are presented in this article. In all cases, the levels of these antibodies were significantly elevated in patients versus controls. Antibody patterns related to neuroautoimmune disorders, cancer, and patients with somatic hypermutation will be shown in a subsequent article. We believe that this novel 96 antigen-specific autoantibody or predictive antibody screen should be studied for its incorporation into routine medical examinations. Clinicians should be aware that the detection of antibodies should not automatically mean that a patient will definitely become ill, but would rather give a percentage of risk for autoimmune disease over subsequent months or years.     

The design, structures and therapeutic potential of protein epitope mimetics

Using a biologically relevant peptide or protein structure as a starting point for lead identification represents one of the most powerful approaches in modern drug discovery. Here, we focus on the protein epitope mimetic (PEM) approach, where folded 3D structures of peptides and proteins are taken as starting points for the design of synthetic molecules that mimic key epitopes involved in protein-protein and protein-nucleic acid interactions. By transferring the epitope from a recombinant to a synthetic scaffold that can be produced by parallel combinatorial methods, it is possible to optimize target affinity and specificity as well as other drug-like ADMET properties. The PEM technology is a powerful tool for target validation, and for the development of novel PEM-based drugs.     

The use of chimeric vimentin citrullinated peptides for the diagnosis of rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes inflammation and, in many cases, destruction of the joints. To prevent progressive and irreversible structural damage, early diagnosis of RA is of paramount importance. The present study addresses the search of new RA citrullinated antigens that could supplement or complement diagnostic/prognostic existing tests. With this aim, the epitope anticitrullinated vimentin antibody response was mapped using synthetic peptides. To improve the sensitivity/specificity balance, a vimentin peptide that was selected, and its cyclic analogue, were combined with fibrin- and filaggrin-related peptides to render chimeric peptides. Our findings highlight the putative application of these chimeric peptides for the design of RA diagnosis systems and imply that more than one serological test is required to classify RA patients based on the presence or absence of ACPAs. Each of the target molecules reported here (fibrin, vimentin, filaggrin) has a specific utility in the identification of a particular subset of RA patients.     

Lipoamino acid-based adjuvant carrier system: enhanced immunogenicity of group a streptococcal peptide epitopes

Lipoamino acid-based synthetic peptides (lipid core peptides, LCP) derived from the type-specific and conserved region determinants of group A streptococci (GAS) were evaluated as potential candidate sequences in a vaccine to prevent GAS-associated diseases, including rheumatic heart disease and poststreptococcal acute glomerulonephritis. The LCP peptides had significantly enhanced immunogenicity as compared with the monomeric peptide epitopes. Furthermore, the peptides incorporated into the LCP system generated epitope-specific antibodies without the use of any conventional adjuvant.     

Synthesis and immunological characterization of a 134-mer synthetic peptide corresponding to the N-terminal half of the HIV-1 nucleoprotein,p24

A 134-mer peptide corresponding to the N-terminal sequence of p24 (residues 146–279 of the gag gene product of the LAV strain) was chemically synthesized using highly optimised protocols on an ABI 430A synthesizer. The crude peptide was obtained by treating the peptide-resin with HF, then purified by a combination of size exclusion and RP-HPLC. One hundred milligram of 90% pure 134-mer can be obtained within a month. Both mice and rabbit polyclonal antisera raised against a commercial preparation of recombinant p24, and a pooled sera from HIV-1 infected individuals reacted strongly with the 134-mer peptide in ELISA. Both mice and rabbits immunized with the free peptide emulsified in Freund's complete adjuvant generated strong anti-peptide and anti-p24 antibody responses as judged by immunoblots and ELISAs. Immunodominant epitopes were mapped to residues 201–227 (LKETINEEAAEWDRVHPVHAGPIAPG). These B-cell epitopes had previously been identified by mouse monoclonal antibodies raised against HIV-1 virus or gag gene products. Furthermore, murine T-cell lines generated against the 134-mer peptide were found to respond to two short peptides, P24B (residues 195–215) and P24D1 (residues 268–279). These two T-cell epitopes were previously reported as human helper T-cell and CTL epitopes, respectively. These results clearly indicate that the synthetic 134-mer peptide could elicit both T- and B-cell responses to HIV-1 similar to those obtained with the natural viral gag protein, and could be useful for the development of a synthetic HIV vaccine     

More than one reason to rethink the use of peptides in vaccine design

The use of peptides as therapeutics is experiencing renewed enthusiasm owing to advances in delivery, stability and design. Moreover, there is a growing emphasis on the use of peptides in vaccine design as insights into tissue-specific processing of the immunogenic epitopes of proteins and the discovery of unusually long cytotoxic T-lymphocyte epitopes broaden the range of targets and give clues to enhancing peptide immunogenicity. Peptides can also be synthesized with known post-translational modifications and/or deliberately introduced protease-resistant peptide bonds to regulate their processing independent of tissue-specific proteolysis and to stabilize these compounds in vivo. We discuss the potential of peptide-based vaccines for the treatment of chronic viral diseases and cancer, and review recent developments in the field of peptide-based vaccines.     

Diagnostic potential for urinary proteomics

Urine represents a modified ultrafiltrate of plasma, with protein concentrations typically approximately 1000-fold lower than plasma. Urine's low protein concentration might suggest it to be a less promising diagnostic specimen than plasma. However, urine can be obtained noninvasively and tests of many urinary proteins are well-established in clinical practice. Proteomic technologies expand opportunities to analyze urinary proteins, identifying more than 1000 proteins and peptides in urine. Urine offers a sampling of most plasma proteins, with increased proportions of low-molecular-weight protein and peptide components. Urine also offers enriched sampling of proteins released along the urinary tract. Although urine presents some challenges as a diagnostic specimen, its diverse range of potential markers offers great potential for diagnosis of both systemic and kidney diseases. Examples of clinical situations where this may be of value are for more sensitive detection of kidney transplant rejection or of renal toxicity of medications.     

Soluble T cell receptors: novel immunotherapies

T cell receptors are antigen-specific proteins that have evolved to recognize peptide antigens presented by human leukocyte antigen molecules on most cell types. Like antibodies, T cell receptors are produced with huge diversity but, unlike antibodies, T cell receptors are not secreted and do not undergo somatic mutations that increase their affinities for antigen. Recently, however, methods have been developed that enable T cell receptors to be engineered as soluble proteins with extremely high affinities, and fused to various immune-modulator molecules. T cell receptors are now set to unlock a whole new range of targets with key roles in cancer, viral infections, autoimmune diseases and allergies.     

Nonapeptide analogues containing (R)-3-hydroxybutanoate and beta-homoalanine oligomers: synthesis and binding affinity to a class I major histocompatibility complex protein.

Crystal structures of antigenic peptides bound to class I MHC proteins suggest that chemical modifications of the central part of the bound peptide should not alter binding affinity to the MHC restriction protein but could perturb the T-cell response to the parent epitope. In our effort in designing nonpeptidic high-affinity ligands for class I MHC proteins, oligomers of (R)-3-hydroxybutanoate and(or) beta-homoalanine have been substituted for the central part of a HLA-B27-restricted T-cell epitope of viral origin. The affinity of six modified peptides to the B2705 allele was determined by an in vitro stabilization assay. Four out of the six designed analogues presented an affinity similar to that of the parent peptide. Two compounds, sharing the same stereochemistry (R,R,S,S) at the four stereogenic centers of the nonpeptidic spacer, bound to B2705 with a 5-6-fold decreased affinity. Although the chiral spacers do not strongly interact with the protein active site, there are configurations which are not accepted by the MHC binding groove, probably because of improper orientation of some lateral substituents in the bound state and different conformational behavior in the free state. However we demonstrate that beta-amino acids can be incorporated in the sequence of viral T-cell epitopes without impairing MHC binding. The presented structure-activity relationships open the door to the rational design of peptide-based vaccines and of nonnatural T-cell receptor antagonists aimed at blocking peptide-specific T-cell responses in MHC-associated autoimmune diseases.