Design Of Synthetic Peptide Vaccines Research Articles

Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein

The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data.

Prediction of MHC Class Binding Peptide and High Affinity TAP Binders to Design Synthetic Peptide Vaccine of Long Neurotoxin 3 from Naja Naja

Naja naja is a highly poisonous snake species of cobra in Elapidae family and is commonly found in middle Asia. Long neurotoxin 3 from Naja naja binds to the nicotinic acetylcholine receptors in the postsynaptic membrane, preventing the binding of acetylcholine and blocks excitation of muscles. Antigenic peptides are complex biomolecules that have unique chemical and physical properties resulting of their amino acid composition. In this study, we have predicted the binding affinity of Long neurotoxin 3 from Naja naja having 71 amino acids, which shows 63 nonamers. Peptide fragments of the neurotoxin can be used to select nonamers for use in synthetic peptide vaccine design and to increase the understanding of roles of the immune system in neurotoxin studies. Antigenic peptides of Long neurotoxin 3 from Naja naja are most suitable for synthetic peptide vaccine development because with Small segment' 15-PNGHVCYTKT-24, 26-CDAFCSIRG-34, 36- RVDLGCAATCPTVKTGVDIQCCSTD-60 called the antigenic epitopes is sufficient for eliciting the desired immune response. In this research, we predict of MHC class I and II binding peptide because MHC molecules are cell surface proteins which take active part in immune response, antigenicity, Solvent accessibility, polar and nonpolar residue that are likely exposed on the surface of proteins that are potentially antigenic that allows to design synthetic peptide vaccine.

Identification of MHC Class, Transports Antigenic Peptides from Naja melanoleuca Long Neurotoxin 1

Long neurotoxin 1 is a dangerous protein occurs in N. melanoleuca. It is highly dangerous snake due to the quantity of venom inject in a single bite. Peptide fragments of N. Melanoleuca Long neurotoxin 1 antigen protein having 71 amino acids, which shows 63 nanomers can be used to select nanomers for use in synthetic peptide vaccine design and to increase the understanding of roles of the immune system against snake bite. We use to apply computational intelligence algorithm PSSM (Position Specific Scoring Matrices) for the Prediction of MHC class-I binding peptides, we also predict antigenicity, Solvent accessibility, polar and nonpolar residue to analyses the membrane-spanning regions (hydrophobic) or regions that are likely exposed on the surface of proteins (hydrophilic domains) that are potentially antigenic that allows potential drug targets to identify active sites, for protection of host form Snake bites and to design synthetic peptide vaccine.

Quantitative Immunoproteomics Approach for the Development of MHC Class I Associated Peptide Antigens of Alpha-Cobra Toxin from Naja kaouthia

Alpha-Cobratoxin from N. kaouthia binds to acetylcholine receptors which are located in neuromuscular junctions, once activated; they cause contract muscles and block their actions thereby bringing on muscle paralysis. Peptide fragments of Alpha-Cobratoxin from N. kaouthia having 71 amino acids, which shows 63 nonamers and are used synthetic peptide vaccine design and to increase the understanding of roles of the immune system against snake bite. For the immune responses against a protein antigen, it is clear that the whole protein is not necessary for raising the immune response, but small segments (15-PNGHVCYTKT-24, 26-CDAFCSIRG-34 and 36-RVDLGCAATCPTVKTGVDIQCCSTD-60) of Alpha-Cobratoxin protein from N. kaouthia called the antigenic determinants or the epitopes are sufficient for eliciting the desired immune response. The identification of specific peptides that binds to MHC class I molecules is important to recognize T-cell epitopes. In this research work, we predict antigenicity, Solvent accessibility to identify the membrane-spanning regions (hydrophobic) or regions that are likely exposed on the surface of proteins (hydrophilic domains) which are potentially antigenic that are used to design synthetic peptide vaccine.

Prediction of Wuchereria Bancrofti Troponin Antigenic Peptides: Application in Synthetic Vaccine Design to Counter Lymphatic Filariasis

Wuchereria bancrofti is a threadlike nematode one of the causative worm of lymphatic filariasis in which the lymphatic and genital organs get disabled either temporarily or permanently; till date no effective drug or vaccine has been discovered to treat lymphatic filariasis. In this analysis we have predicted antigenic peptides from Wuchereria bancrofti troponin protein for synthetic peptide vaccine design against lymphatic filariasis because with a single protein subunit immune response can be generated in large population. Analysis shows predicted epitopes of Wuchereria bancrofti troponin protein are important determinant for protection against lymphatic filariasis. In this assay we have analysed the binding affinity of Wuchereria bancrofti troponin protein having 136 amino acids, which shows 128 nonamers. In this research work, we predicted CTL-epitopes by two different methods namely SVM (Support Vector Machine) and ANN (Artificial Neural Network), SVM based prediction shown sixteen valid epitopes having optimal score of 1.129 at cut off 0.36 whereas ANN based prediction shown thirty-one valid epitopes having optimal score of 1.000 at cut off 0.51. We also predicted cascade SVM based TAP binders and four potential antigenic epitopes as, 31-LRKLIRK-37, 49-DEFCALVYTVANT-61, 87-SRPTLKALLKE-97, 108-EAAVDE-113 (optimal propensity 1.223) predicted on the basis of highest local hydrophilicity; in addition to this we also have experimentally predicted tertiary structure of the two longest potential epitopes those can aid our understanding in sequence-structure-function relationship of Wuchereria bancrofti troponin protein towards synthetic peptide vaccine design. Thus a small fragment of troponin protein can produce immune response against activity of Wuchereria bancrofti. This approach can be applied for designing subunit and synthetic peptide vaccines

Solution secondary structure of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK: A heteronuclear multidimensional NMR study.

The C-terminal receptor binding region of Pseudomonas aeruginosa pilin protein strain PAK (residues 128-144) has recently been the target for the design of a synthetic peptide vaccine effective against multiple strains of P. aeruginosa infection. We have successfully cloned and bacterially expressed a 15N-labeled PAK pilin peptide spanning residues 128-144 of the intact PAK pilin protein, PAK 128-144(Hs145), and have determined the solution secondary structure of this peptide using heteronuclear multidimensional NMR spectroscopy. The oxidized recombinant peptide exists as a major (trans) and minor (cis) species in solution, arising from isomerization around the Ile138-Pro139 peptide bond. The pattern of NOEs, temperature coefficients, and coupling constants observed for the trans isomer demonstrate the presence of a type I beta-turn and a type II beta-turn spanning Asp134-Glu-Gln-Phe137 and Pro139-Lys-Gly-Cys142, respectively. This is in agreement with the NMR solution structure of the trans isomer of a synthetic PAK 128-144 peptide which showed a type I and a type II beta-turn in these same regions of the sequence [McInnes, C., Sönnichsen, F. D., Kay, C. M., Hodges, R. S., and Sykes, B. D. (1993) Biochemistry 32, 13432-13440; Campbell, A. P., McInnes, C., Hodges, R. S., and Sykes, B. D. (1995) Biochemistry 34, 16255-16268]. The pattern of NOEs, temperature coefficients, and coupling constants observed for the cis isomer also demonstrate a type II beta-turn spanning Pro139-Lys-Gly-Cys142, but suggest a second beta-turn spanning Asp132-Gln-Asp-Glu135. Thus, the cis isomer may also possess a double-turn motif (like the trans isomer), but with different spacing between the turns and a different placement of the first turn in the sequence. The discovery of a double-turn motif in the trans (and cis) recombinant PAK pilin peptide is an extremely important result since the double turn has been implicated as a structural requirement for the recognition of both receptor and antibody. These results pave the way for future isotope-edited NMR studies of the labeled recombinant PAK pilin peptide bound to antibody and receptor, studies integral to the design of an effective synthetic peptide vaccine.

Enhanced immunogenicity of HIV-1 vaccine construct by modification of the native peptide sequence.

Viral proteins are not naturally selected for high affinity major histocompatibility complex (MHC) binding sequences; indeed, if there is any selection, it is likely to be negative in nature. Thus, one should be able to increase viral peptide binding to MHC in the rational design of synthetic peptide vaccines. The T1 helper peptide from the HIV-1 envelope protein was made more immunogenic for inducing T cell proliferation to the native sequence by replacing a residue that exerts an adverse influence on peptide binding to an MHC class II molecule. Mice immunized with vaccine constructs combining the more potent Th helper (Th) epitope with a cytotoxic T lymphocyte (CTL) determinant developed greatly enhanced CTL responses. Use of class II MHC-congenic mice confirmed that the enhancement of CTL response was due to class II-restricted help. Thus, enhanced T cell help is key for optimal induction of CTL, and, by modification of the native immunogen to increase binding to MHC, it is possible to develop second generation vaccine constructs that enhance both Th cell activation and CTL induction.

Structural requirements for synthetic immunogens to induce measles virus specific CTL responses

We have studied the immunogenicity of a synthetic peptide representing a cytotoxic T cell epitope (CTL) from the nucleoprotein of measles virus (MV). For the induction of peptide and MV-specific CTL responses after subcutaneous immunization, covalent linkage of the CTL epitope to a T-helper epitope was required. The presence of two copies of the T-helper epitope at the amino terminus of the CTL epitope (TT-CTL) resulted in the induction of strong CTL responses after administration in saline. In contrast, a chimeric peptide with one copy of the T-helper epitope at the amino terminus of the CTL epitope (T-CTL) was weakly immunogenic when given in saline. Analysis of the structure of the TT-CTL chimeric peptide by CD spectroscopy revealed an α-helical conformation, as compared to the random coil conformation favored by the T-CTL chimeric peptide. In addition, the CD spectra of the TT-CTL peptide in the presence of small unilamellar vesicules (SUV) revealed an increased helicity, as compared to the spectra of the T-CTL chimera in the presence of SUV. This suggests that the amphipathic character of the TT-CTL chimeric construct favors its interaction with the cell membrane of antigen presenting cells, therefore, facilitating its cytosolic delivery for class I presentation. These findings highlight the importance of antigen structure for the in vivo induction of CTL responses and may have implications for the design of synthetic peptide vaccines.

Solution conformation of an immunogenic peptide derived from the principal neutralizing determinant of the HIV-2 envelope glycoprotein gp125

The conformational preferences of a number of peptides with sequences related to the envelope glycoproteins of HIV-1 have been investigated in the past few years. Similar studies have not been made for HIV-2, which is a distinct virus with similar physiological effects to those of HIV-1. The discovery of common structural features would be a promising route to the design of immunogens for generally effective HIV vaccines. We present the results of an NMR conformational study of a sequence deriving from the V3 loop of HIV-2. Three synthetic immunogenic peptides were studied, of 12, 22 and 39 amino acids in length, all containing a central Met-Ser-Gly-Arg sequence conserved among a number of HIV-2 isolates. In addition, the 39-mer contained a disulfide bond between cysteine residues close to the ends of the molecule, forming a loop that is thought to comprise an important structural and immunological component of the intact glycoprotein. All three peptides display well defined beta-turns in the Met-Ser-Gly-Arg sequence, independent of the integrity of the disulfide bond. No other conformational preferences for folded conformations were found for the peptides. The presence of a beta-turn in the Met-Ser-Gly-Arg sequence is strikingly similar to the behavior seen for the corresponding principal neutralizing determinant sequence from gp120 of HIV-1 and argues, in the absence of information of the three-dimensional structure of the intact proteins, for a similarity in the structure of this region that could be exploited in the design of synthetic peptide vaccines generally effective against HIV infections.

T and B epitope determination and analysis of multiple antigenic peptides for the Schistosoma mansoni experimental vaccine triose-phosphate isomerase.

Abstract Schistosoma mansoni triose-phosphate isomerase (TPI), a glycolytic enzyme, was originally identified as the target of the mAb M.1 that conferred protection when the antibody was administered in vivo. In this study we increase the evidence that schistosome TPI is a potential vaccine Ag by showing that it also a potent inducer of IL-2 and IFN-gamma production (Th1 responses), driving production of these cytokines in the same cell populations of infected animals that have high Th2 responses directed at other parasite egg Ag. With the goal of synthetic peptide vaccine design, rTPI was used to determine specific T and B cell epitopes recognized by two strains of mice representing high and moderate responders (C57Bl/6J and CBA/J). All selected epitopes were from nonconserved regions of TPI and thus parasite-specific. We then defined minimal size immunoreactive epitopes and synthesized four-armed multiple antigenic peptides (MAP) consisting of T and B cell epitopes that could be recognized by both strains of mice in the same molecule. Characterization of the immunoreactivity of the MAP showed that higher antibody recognition of the MAP was attained when the B cell epitope was placed on the amino termini relative to the T cell epitope, whereas equivalent immunoreactivity occurred for the T cell epitopes when located at either position. Most interesting was the finding that one of the minimal T cell epitopes, when incorporated into the MAP, required enlarging to retain immunoreactivity. Finally we showed that both the full-length TPI molecule and the final version of the MAP were immunogenic to T cells in naive animals and induced cross-recognition in the form of IL-2 and IFN-gamma production.

Construction of an HIV-1 peptide vaccine containing a multideterminant helper peptide linked to a V3 loop peptide 18 inducing strong neutralizing antibody responses in mice of multiple MHC haplotypes after two immunizations.

Peptide constructs comprised of multideterminant Th peptides from the envelope glycoprotein of HIV previously identified to induce proliferative responses in four different haplotypes of mice and IL-2 responses in 52 to 73% of HIV positive, Ag-responsive patients, were colinearly synthesized with the peptide 18 of the V3 loop of HIV-1 gp 160, corresponding to the principal neutralizing determinant of HIV-IIIB. The segments containing clusters of overlapping Th epitopes were called cluster peptides. Cognate help for peptide 18 antibody was elicited after a single immunization in all strains of mice that had previously responded to a T cell epitope encompassed by the cluster peptides. Animals boosted with cluster peptide-peptide 18 constructs 36 to 52 wk later displayed secondary antibody responses. Cluster peptide 3-peptide 18 induced antibody that neutralized homologous virus in one strain of mice although strong peptide 18 antibody responses were detected in all four strains of mice. The most promising construct, cluster peptide 6-peptide 18, induced neutralizing antibody in all strains of mice tested, and in two strains the level of neutralizing antibody achieved was comparable to levels adequate for protection from homologous viral challenge in chimpanzees. After a single boost, antibody titers for 90% neutralization in the range of 1/1000 to 1/16,000 were achieved. These neutralizing titers against the homologous viral strain, after just two immunizations, are at least four- to eightfold higher than the highest titered other polyclonal V3-specific immune sera we have ever observed in our laboratories. We also asked why some sera neutralized and others with similar ELISA titers did not. No correlation was found between neutralization and isotype or affinity for peptide or gp 120. We could not account for neutralization by antibodies to the helper sites. Substitutions made in the central loop region of peptide 18, amino acid residues PGRAF, dramatically reduced binding of both neutralizing and non-neutralizing sera although some fine specificity differences between neutralizing and nonneutralizing sera were noted. These results have implications for the design of synthetic peptide vaccines for HIV.

A rational design of synthetic peptide vaccine with a built-in adjuvant. A modular approach for unambiguity.

We describe a peptide vaccine model containing a built-in adjuvant. This model used a multiple antigen peptide system (MAPS) to amplify peptide antigens and a lipoamino acid, tripalmitoyl glyceryl cysteine (P3C), as a built-in adjuvant. An 18-residue peptide antigen (B2) derived from the third variable domain (amino acid 312-329) of the glycoprotein gp120 of type I human immunodeficiency virus (HIV-1) was used in this model. This peptide antigen is a suitable target since it consists of neutralizing, T-helper, and T-cytotoxic epitopes. The peptide antigen in a tetravalent MAPS format (B2M-P3C) with a lipophilic attachment was synthesized by two routes for comparison: a direct stepwise approach and an indirect modular approach. In the stepwise approach, each residue was sequentially added to the peptide resin to give B2M-P3C and the P3C was incorporated to the side chain of a carboxyl terminal lysine as Fmoc-Lys(P3C). In the modular approach, a module containing a chloroacetylated core matrix of MAPS (M-P3C) with a carboxyl tetrapeptide bearing Lys(P3C) and a second module containing the peptide antigen B2 with a cysteine at its terminus were synthesized and purified separately, and then coupled to each other to form B2M-P3C. In the modular approach, the molecular ion of B2M-P3C was unambiguously identified by ion-spray mass spectrometry. B2M-P3C, administered in liposomes without any adjuvant such as Freund's complete adjuvant, was used to immunize mice and found to induce gp120-specific antibodies in vitro, and prime cytotoxic T lymphocytes in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthetic peptide vaccine design: synthesis and properties of a high-density multiple antigenic peptide system.

A convenient and versatile approach to the direct synthesis of a peptide-antigen matrix by the solid-phase method is described. The approach is called the multiple antigen peptide system (MAP) and it utilizes a simple scaffolding of a low number of sequential levels (n) of a trifunctional amino acid as the core matrix and 2n peptide antigens to form a macromolecule with a high density of peptide antigens of final Mr 10,000. The MAP model chosen for study was an octa-branching MAP consisting of a core matrix made up of three levels of lysine and eight amino terminals for anchoring peptide antigens. The MAP, containing both the core matrix and peptides of 9-16 amino acids, was prepared in a single synthesis by the solid-phase method. Six different MAPs elicited specific antibodies in rabbits and mice, of which five produced antibodies that reacted with their corresponding native proteins. In rabbits, the sera had a considerably higher titer of antibodies than sera prepared from the same peptides anchored covalently to keyhole limpet hemocyanin as carrier. Thus, the MAP provided a general, but chemically unambiguous, approach for the preparation of carrier-bound antigens of predetermined and reproducible structure and might be suitable for generating vaccines.