Synthetic anticancer vaccine candidates: rational design of antigenic peptide mimetics that activate tumor-specific T-cells

A rational design approach was followed to develop peptidomimetic analogues of a cytotoxic T-cell epitope capable of stimulating T-cell responses as strong as or stronger (heteroclytic) than those of parental antigenic peptides. The work described herein focused on structural alterations of the central amino acids of the melanoma tumor-associated antigenic peptide Melan-A/MART-1(26-35) using nonpeptidic units. A screening was first realized in silico to select altered peptides potentially capable of fitting at the interface between the major histocompatibilty complex (MHC) class-I HLA-A2 molecule and T-cell receptors (TCRs). Two compounds appeared to be high-affinity ligands to the HLA-A2 molecule and stimulated several Melan-A/MART-1 specific T-cell clones. Most remarkably, one of them even managed to amplify the response of one clone. Together, these results indicate that central TCR-contact residues of antigenic peptides can be replaced by nonpeptidic motifs without loss of binding affinity to MHC class-I molecules and T-cell triggering capacity.     

A systems biology perspective on Nrf2-mediated antioxidant response

Cells in vivo are constantly exposed to reactive oxygen species (ROS) generated endogenously and exogenously. To defend against the deleterious consequences of ROS, cells contain multiple antioxidant enzymes expressed in various cellular compartments to scavenge these toxic species. Under oxidative stresses, these antioxidant enzymes are upregulated to restore redox homeostasis. Such an adaptive response results from the activation of a redox-sensitive gene regulatory network mediated by nuclear factor E2-related factor 2. To more completely understand how the redox control system is designed by nature to meet homeostatic goals, we have examined the network from a systems perspective using engineering approaches. As with man-made control devices, the redox control system can be decomposed into distinct functional modules, including transducer, controller, actuator, and plant. Cells achieve specific performance objectives by utilizing nested feedback loops, feedforward control, and ultrasensitive signaling motifs, etc. Given that endogenously generated ROS are also used as signaling molecules, our analysis suggests a novel mode of action to explain oxidative stress-induced pathological conditions and diseases. Specifically, by adaptively upregulating antioxidant enzymes, oxidative stress may inadvertently attenuate ROS signals that mediate physiological processes, resulting in aberrations of cellular functions and adverse consequences. Lastly, by simultaneously considering the two competing cellular tasks-adaptive antioxidant defense and ROS signaling-we re-examine the premise that dietary antioxidant supplements is generally beneficial to human health. Our analysis highlights some possible adverse effects of these widely consumed antioxidants.     

The rational design of vaccine adjuvants for mucosal and neonatal immunization

There is an urgent requirement for neonatal vaccines that induce effective and long-lasting immune responses at the mucosal surfaces of the gut and respiratory tract. The delay in their development has been due in part to a lack of understanding of the mucosal and neonatal immune systems. This work reviews recent advances in the understanding of the cells and molecules that mediate immunity, describing the importance of different T helper populations in determining the success of vaccination strategies. These advances have allowed the rational design of novel vaccine adjuvants and delivery systems that can selectively induce immunity at different anatomical sites mediated by distinct T cell populations. Five functional classes of adjuvant are described. These exploit mechanisms which a) create an antigen depot, b) preserve antigen conformation, c) direct antigen to specific immune cells, d) induce mucosal responses and e) induce cytotoxic T cell responses. Comparisons are made between the chemical structures of bacterial toxins and non-toxic derivatives that retain adjuvanticity. The concept of DNA immunization is introduced and the advantages and disadvantages of this novel approach are discussed. The specific problems relating to neonatal immunization are explored with particular reference to the functional immaturity of the neonatal immune system and interference by maternal antibody. Finally, recent work suggesting that there is no intrinsic barrier to designing effective neonatal vaccines deliverable by the mucosal route is discussed.     

Progress in structure-based drug design against influenza A virus

Introduction: The 2009-H1N1 influenza pandemic has prompted new global efforts to develop new drugs and drug design techniques to combat influenza viruses. While there have been a number of attempts to provide drugs to treat influenza, drug resistance has been a major problem with only four drugs currently approved by the FDA for its treatment.

Areas covered: In this review, the drug-resistant problem of influenza A viruses is discussed and summarized. The article also introduces the experimental and computational structures of drug targeting proteins, neuraminidases, and of the M2 proton channel. Furthermore, the article illustrates the latest drug candidates and techniques of computer-aided drug design with examples of their application, including virtual in silico screening and scoring, AutoDock and evolutionary technique AutoGrow.

Expert opinion: Structure-based drug design is the inventive process for finding new drugs based on the structural knowledge of the biological target. Computer-aided drug design strategies and techniques will make drug discovery more effective and economical. It is anticipated that the recent advances in structure-based drug design techniques will greatly help scientists to develop more powerful and specific drugs to fight the next generation of influenza viruses.     

A perspective on rational drug design with cyclopentenone: targeting the proteome with the cyclopentenone chemical moiety

The biological activity of cyclopentenone prostaglandins, of members of clavulones, and of other natural and synthetic compounds is strongly related to the presence of a conjugate cylcopentenone (CP) chemical moiety in their structure. CP reactivity is specifically directed toward the proteome, to covalent binding of crucial sulphydril groups on targeted proteins. In the literature it has been shown that directing this special CP biochemical reactivity by means of additional orienting constituents is a feasible strategy for inactivating specific enzymes in a cell. The introduction of a CP moiety into anticancer molecules, such as jasmonates and chalcones, has been shown to greatly boost their activity, probably due to the stable covalent chemical interaction with their targets. In general, similar strategies could lead to the development of a novel repertoire of therapeutic molecules targeted against specific pathogenetic anomalies of the proteome of diseased cells.     

Progress in structure-based drug design against influenza A virus

Introduction: The 2009-H1N1 influenza pandemic has prompted new global efforts to develop new drugs and drug design techniques to combat influenza viruses. While there have been a number of attempts to provide drugs to treat influenza, drug resistance has been a major problem with only four drugs currently approved by the FDA for its treatment. Areas covered: In this review, the drug-resistant problem of influenza A viruses is discussed and summarized. The article also introduces the experimental and computational structures of drug targeting proteins, neuraminidases, and of the M2 proton channel. Furthermore, the article illustrates the latest drug candidates and techniques of computer-aided drug design with examples of their application, including virtual in silico screening and scoring, AutoDock and evolutionary technique AutoGrow. Expert opinion: Structure-based drug design is the inventive process for finding new drugs based on the structural knowledge of the biological target. Computer-aided drug design strategies and techniques will make drug discovery more effective and economical. It is anticipated that the recent advances in structure-based drug design techniques will greatly help scientists to develop more powerful and specific drugs to fight the next generation of influenza viruses.     

A conserved matrix epitope based DNA vaccine protects mice against influenza A virus challenge

DNA vaccination represents a unique strategy to overcome the limitations of immunization with conventional vaccines which is restricted by the high variability of influenza viruses. We evaluated the protective efficacy of a plasmid DNA (pDNA), encoding an evolutionarily conserved epitope of viral matrix protein, against the influenza A virus infection. It was found that the mice immunized via the intra-muscular route purely elicited cell mediated immune response to the pDNA, with enhanced level of Th1 cytokines viz. IL-12 and IFNγ production in the stimulated splenocyte supernatant. The cytotoxic T lymphocytes in the spleen of immunized mice significantly lysed the virus-infected MDCK cells. A significant decrease in virus replication was also observed in the lungs of immunized mice and 83% of the mice were protected against the lethal challenge of influenza A viruses. These findings suggest that the plasmid DNA expressing a single matrix epitope may serve as a promising vaccine candidate to provide effective immunity in the susceptible (mouse) population.     

The biology of oral tolerance and issues related to oral vaccine design

Intestinal tissues are continuously exposed to tremendous amount of foreign material, either beneficial or harmful. Although strong protective immune responses are required to clear harmful pathogen infections, similar responses against food antigen can lead to harmful inflammation. Therefore, oral tolerance or unresponsiveness against dietary and commensal bacteria is also important to maintain tissue integrity by preventing harmful inflammatory responses in the intestine. While oral tolerance is an important phenomenon to protect unnecessary inflammatory responses, it presents an obstacle in the development of oral vaccines. Therefore an understanding of the gut immune system and the induction of oral tolerance is important. This review will focus on important aspects of the intestinal immune system and how immune responses in the intestine maintain homeostasis via oral tolerance. Also it will provide new insights in the development of oral vaccines.     

Prediction and validation of potent peptides against herpes simplex virus type 1 via immunoinformatic and systems biology approach

The human herpes simplex virus type 1 (HSV‐1) is an extremely rampant human pathogen, and its infection could cause life‐long diseases, including the central nervous system disorders. The glycoproteins of HSV‐1 such as glycoprotein B, glycoprotein C, glycoprotein D, glycoprotein H, and glycoprotein L are highly involved in mediating the viral attachment and infection of the host cell. Therefore, immunoinformatic approaches followed by molecular dynamics simulation and systems biology has been used to analyze these glycoproteins in order to propose effective peptide‐based vaccine candidates against the HSV‐1 infection. The ElliPro and NetCTL.1.2 online tools were employed to forecast the B‐ and T‐lymphocyte (CTL) epitopes for gB, gC, gD, gH, and gL. The 3D coordinates of these epitopes were modeled and docked against the human major histocompatibility complex molecule‐1. The outcomes obtained from postdocking analysis along with TAP (Transporter associated with antigen processing), MHC binding, and C‐terminal cleavage score assisted in the selection of potential epitopes. These epitopes were further subjected to molecular dynamics simulation and systems biology approach which showed significant results. On the basis of these substantial outcomes, peptides are proposed that could be used to provoke immunity against the HSV‐1 infection.     

Immune modulators with defined molecular targets: cornerstone to optimize rational vaccine design

Vaccination remains the most valuable tool for preventing infectious diseases. However, the performance of many existing vaccines should be improved and there are diseases for which vaccines are still not available. The use of well-defined antigens for the generation of subunit vaccines has led to products with an improved safety profile. However, purified antigens are usually poorly immunogenic, making essential the use of adjuvants. Despite the fact that adjuvants have been used to increase the immunogenicity of vaccines for more than 70 years, only a handful has been licensed for human use (e.g., aluminium salts, the micro-fluidized squalene-in-water emulsion MF59 and monophosphoryl lipid A). Thus, the development of new adjuvants which are able to promote broad and sustained immune responses at systemic and mucosal levels still remains as a major challenge in vaccinology. Recent advances in our understanding of the immune system have facilitated the identification of new biological targets for screening programs aimed at the discovery of novel immune stimulators. This resulted in the identification of new candidate adjuvants, which made possible the modulation of the immune responses elicited according to specific needs. A number of promising adjuvants which are currently under preclinical or clinical development will be described in this review.     

Improved peptide vaccine strategies, creating synthetic artificial infections to maximize immune efficacy

Soon after it was realized that T-cells recognize their target antigens as small protein fragments or peptides presented by MHC molecules at the cell surface, these peptide epitopes have been tried as vaccines. Human testing of such vaccines, although protective in mouse models, has produced mixed results. Since these initial trials, there has been an tremendous increase in our understanding of how infectious organisms can induce potent immune responses. In this article we review the key changes in the design, formulation and delivery of synthetic peptide vaccines that are applied to improve peptide vaccine strategies.     

Design of three-component vaccines against group A streptococcal infections: importance of spatial arrangement of vaccine components

Immunological assessment of group A streptococcal (GAS) branched lipopeptides demonstrated the impact of spatial arrangement of vaccine components on both the quality and quantity of their immune responses. Each lipopeptide was composed of three components: a GAS B-cell epitope (J14), a universal CD4(+) T-cell helper epitope (P25), and an immunostimulant lipid moiety that differs only in its spatial arrangement. The best systemic immune responses were demonstrated by a lipopeptide featuring the lipid moiety at the lipopeptide C-terminus. However, this candidate did not achieve protection against bacterial challenge. The best protection (100%) was shown by a lipopeptide featuring a C-terminal J14, conjugated through a lysine residue to P25 at the N-terminus, and a lipid moiety on the lysine side chain. The former candidate features α-helical conformation required to produce protective J14-specific antibodies. Our results highlight the importance of epitope orientation and lipid position in the design of three-component synthetic vaccines.     

Toward a rational design of peptide inhibitors of ribonucleotide reductase: structure-function and modeling studies

Mammalian ribonucleotide reductase, a chemotherapeutic target, has two subunits, mR1 and mR2, and is inhibited by AcF(1)TLDADF(7), denoted P7. P7 corresponds to the C-terminus of mR2 and competes with mR2 for binding to mR1. We report results of a structure-function analysis of P7, obtained using a new assay measuring peptide ligand binding to mR1, that demonstrate stringent specificity for Phe at F(7), high specificity for Phe at F(1), and little specificity for the N-acyl group. They support a structural model in which the dominant interactions of P7 occur at two mR1 sites, the F(1) and F(7) subsites. The model is constructed from the structure of Escherichia coli R1 (eR1) complexed with the C-terminal peptide from eR2, aligned sequences of mR1 and eR1, and the trNOE-derived structure of mR1-bound P7. Comparison of this model with similar models constructed for mR1 complexed with other inhibitory ligands indicates that increased F(1) subsite interaction can offset lower F(7) subsite interaction and suggests strategies for the design of new, higher affinity inhibitors.     

Development of WT1 peptide cancer vaccine against hematopoietic malignancies and solid cancers

Wild-type Wilms' tumor gene WT1 is highly expressed not only in hematopoietic malignancies, including leukemia and myelodysplastic syndromes (MDS), but also in various kinds of solid tumors. Human cytotoxic T lymphocytes (CTLs) which could specifically lyse WT1-expressing tumor cells with HLA class I restriction were generated in vitro. We have also demonstrated that mice immunized with the WT1 peptide or WT1 cDNA rejected challenges by WT1-expressing tumor cells and survived with no signs of auto-aggression to normal organs which physiologically expressed WT1 in prophylactic and therapeutic models. Furthermore, we and others detected IgM and IgG WT1 antibodies in the patients with hematopoietic malignancies, indicating that WT1 protein was highly immunogenic, and that immunoglobulin class-switch-inducing WT1-specific cellular immune responses were elicited in the patients. CD8+ WT1-specific CTLs were also detected in peripheral blood or tumor-draining lymph nodes of cancer patients. These results provided us with the rationale for elicitation of CTL responses targeting the WT1 product for cancer immunotherapy. On the basis of the findings mentioned above, we performed a phase I clinical trial of WT1 peptide cancer vaccine for the patients with malignant neoplasms. These results strongly suggested that WT1 peptide cancer vaccine had efficacy in the clinical setting, because clinical responses, including reduction of leukemic blast cells or regression of tumor masses, were observed after the WT1 vaccination in patients with hematopoietic malignancies or solid cancers. The power of TAA-derived cancer vaccine may be enhanced by combination with stronger adjuvants, helper peptide, or conventional treatments such as molecular-target-based drugs.     

The rational design of vaccines

This review provides an insight into the various opportunities for vaccine intervention, analysis of strategies for vaccine development, vaccine ability to modulate immune responses and resultant rational vaccine design. In addition, wider aspects are considered, such as biotechnological advances, advances in immunological understanding and host-pathogen interactions. The key question addressed here is, with all our research and understanding, have we reached a new echelon in vaccine development, that of rational design?     

Development of peptide 3D structure mimetics: rational design of novel peptoid cholecystokinin receptor antagonists

The two hormones cholecystokinin and gastrin share the same C-terminal sequence of amino acids, namely Gly(29)-Trp(30)-Met(31)-Asp(32)-Phe(33)-NH(2). Nevertheless, this congruence has not precluded using this structure to develop selective ligands for either CCK(1) or CCK(2) receptors. Manipulation of the hydrophobic residues at positions 31 and 33 gave a series of CCK(1) tripeptide antagonists, typified by N-t-BOC-Trp-2-Nal-Asp-2-(phenyl)ethylamide (pK(B) 6.8 +/- 0.3). Molecular modeling was used to identify the bioactive conformation of these CCK(1)-selective compounds and prompted the design of new peptoid structures. We aimed to maintain the conformation of the parent series by exploiting patterns of hydrogen-bonding and pi-stacking interactions present in the original molecule, rather than introducing additional covalent bonds. The prototype, N-(succinyl-D-Asp-2-phenylethylamido)-L-Trp-2-(2-naphthyl)ethylami de, was a potent and selective CCK(1) antagonist (pK(B) 7.2 +/- 0.3). Furthermore, the new series showed patterns of biological activity that mirrored those of the parent tripeptides. These compounds contain elements of both peptide primary and secondary structure and represent a novel approach to designing peptidomimetics. Interesting results were obtained from comparing models of a representative tripeptide CCK(1) antagonist with a conformation of CCK(30)(-)(33) that others have proposed to be responsible for its activity at the CCK(2) receptor. The results suggest that CCK(1) and CCK(2) receptors recognize enatiomeric dispositions of the Trp(30) indole, Asp(32) carboxylic acid, and C-terminal phenyl groups arrayed about a common backbone configuration. This "functional chirality" may underpin the mechanism by which these closely related receptor systems bind CCK(30)(-)(33) and explain patterns of selectivity observed with optical isomers of a number of peptoid and nonpeptide ligands.