Computer simulations to predict the availability of peptides with known HLA class I motifs possibly generated by proteolysis of HIV-1 proteins in infected cells

CpG ODNs treatments of HIV-1 infected patients may cause the decline of transmission in high risk populations - a review, hypothesis and implications

The Joint United Nations Program on HIV-1/AIDS (UNAIDS) announced its goal to stop HIV-1 transmission by antiviral (HAART) treatment of patients since at the end of 2003 the number of people living with HIV-1 was 38 million, 25 million in the sub-Saharan region of Africa. The present review deals with a new approach to simultaneously treat HIV-1/AIDS patients in HIV-1 endemic regions with CpG oligodeoxynucleotides (ODNs) and people at high risk of infection with a vaccine containing CpG ODNs combined with synthetic HIV-1 peptides by intranasal and intradermal applications. During HIV-1 infection a gradual increase in the levels of IL-4 and IgE in the patients' serum, was reported. It was suggested that such an increase of the cytokine IL-4 and the IgE immunoglobulin are interconnected and may serve as indicators for the coming stage of AIDS. It was also suggested that the IL-4 and IgE increase in the serum of HIV-1 infected people resemble the increase of IL-4 and IgE levels in allergic patients that were exposed to endogenous or environmental allergens [Becker, Virus Genes 28, 5--18, 2004]. Indeed, it was reported that the HIV-1 virions' shed gp120 molecules, which contain a superantigen (superallergen) domain that enables the viral glycoprotein to bind the V(H)3 domain of IgE molecules that are bound to FcepsilonRI+ hematopoietic cells [basophils, mast cells, dendritic cells (DCs) and plasmacytoid DCs (pDCs)]. Such interaction was reported to induce the hematopoietic cells to release large amounts of Th2 cytokines IL-4, IL-5, IL-10 and IL-13. These findings led to the hypothesis [Op. cit.] that the cure of HIV-1/AIDS patients requires the induction of endogenous synthesis of type I interferons (INF alpha and beta) with a bacterial CpG rich DNA that will induce the patients' pDCs to release large amounts of type I IFNs. Under these conditions HIV-1 replication in polarized to Th2 cells is inhibited. Type I IFNs reactivate the patients' inhibited Th1 cells to synthesize IL-2 and IL-12 cytokines that activate the maturation of CTL precursors. The unmethylated bacterial DNA activates B synthesis to switch to IgG and IgA synthesis. The novel drug CpG ODNs is being tested for the prevention and the treatment of allergic humans and in the experimental system of allergic mice. It was also reported that treatment of mice with CpG ODN prior to or after retrovirus infections protected and cured, respectively, the retrovirus infection. It was also reported that CpG ODNs treatments of mice exposed to allergen protected them against the development of the allergic response. Phase I treatment of healthy people with CpG ODNs provided information on the safety of these compounds. The CpG ODNs A and B bind to Toll like receptors that are present in pDCs and B cells, respectively, CpG ODN - A is the ligand for TLR9+ pDCs and induce the release of large amounts of IFN-alpha, beta. CpG ODN-B is the ligand for TLR9+ in B cells and induce the synthesis of IgG and IgA. CpG ODN-C contains motifs from CpG ODNs A and B and is more active. The present review is based on findings from studies that reported that CpG ODNs treatment of retrovirus infected mice, monkeys and allergic mice prevented the virus and allergens caused diseases, respectively. Based on these studies, a hypothesis is presented that treatment of HIV-1 infected and AIDS patients with CpG ODN-A and B or CpG ODN-C have the potential to inhibit IL-4 synthesis and release from FcrepsilonRI+ hematopoietic cells by inducing TLR9+ pDCs to release large amounts of type I IFNs. TLR9+ B cells are induced by CpG ODN-B to switch from IgE to IgG, IgA synthesis. In addition, type I IFNs (alpha, beta) have the capacity to inhibit HIV-1 replication in polarized Th2 cells. Type I IFNs reactivate the patients' Th1 cells to synthesize IL-2 and IL-12 cytokines, activators of the precursor cytotoxic T cells (CTLs), leading to the reactivation of the inhibited adaptive immune response. Antiviral CTLs have the ability to clear the virus infection. The present novel approach to the treatment and of HIV-1/AIDS patients with CpG ODNs may prevent HIV-1 transmission and the AIDS pandemic if controlled studies on the treatments with CpG ODNs of HIV-1 infected people will be done by international and private agencies and companies to define the effective treatment regime and the efficacy of the treatments to HIV-1 infected people at different times post-infection. It is also hypothesized that in order to stop HIV-1 transmission in HIV-1 endemic regions the people at high risk of HIV-1 infection should be treated at the same time as HIV-1 infected people with a vaccine containing synthetic CpG-ODNs combined with synthetic HIV-1 peptides, compatible with the major HLA haplotypes of the regional population. The vaccine may be self-applied by people at high risk of infection by the intra-nasal route and by intra-dermal application as a "peplotion vaccine". The stimulation of the antiviral CTL response by HIV-1 infected people and the active antiviral immune response in the vaccinated population may lead to a decline in HIV-1 transmission and may be a model for control of the HIV-1/AIDS pandemic.

Computer simulations to identify in polyproteins of FMDV OK1 and A12 strains putative nonapeptides with amino acid motifs for binding to BoLA class I A11 and A20 haplotype molecules

The computer program "Findpatterns" was used to search FMDV- (OK1 and A12 strains) coded structural and nonstructural proteins for the availability of putative proteasome-generated nonapeptides with motifs reported for BoLA class I A11 and A20 haplotypes. These BoLA class I A11 and A20 nonapeptide motifs are identical to motifs of nonapeptides that interact with the peptide binding grooves of HLA class I B35 and B27 haplotypes, respectively. The computer findpattern program was used to analyze the FMDV-coded polyproteins for proteolytically cleavable nonapeptides with motifs for binding to the peptide binding grooves of BoLA class I A11 or 20 haplotypes. The computer simulations revealed that FMDV-infected cells (keratinocytes and antigen presenting cells. e.g., dendritic Langerhans cells in bovines) may be able to present viral nonapeptides to CD8+ cytolytic T cells (CTLs) in a BoLA-restricted manner. The role of the cellular arm of the immune response in the protection of bovines against FMDV is not known. Thus, the present computer analysis may encourage further experiments to develop a new generation of FMDV nonapeptide vaccines to stimulate the anti-FMDV cytolytic T cell response in bovine so this would complement the humoral immune response achieved by immunization with the inactivated virus vaccine.

The use of bovine MHC class I allele-specific peptide motifs and proteolytic cleavage specificities for the prediction of potential cytotoxic T lymphocyte epitopes of bovine viral diarrhea virus

Cell mediated immunity (CMI) is crucial for the defense against viruses. Cytotoxic T lymphocytes (CTLs) play a major role in CMI. They recognize endogenous antigenic peptides presented by antigen presenting cells in association with the major histocompatibility complex (MHC) class I molecules. The elucidation of the sequence of CTL epitopes of viruses should help in designing better vaccines. In this study, we have identified candidate epitopes restricted by five bovine MHC class I molecules that are potentially available for presentation to CTLs. The candidate peptide epitopes were identified by using the computer programs available as a part of the Genetics Computer Group package and applying the information on allele-specific peptide motifs and intracellular enzymatic cleavage patterns to the bovine viral diarrhea virus polyprotein. Several candidate peptides were found for each of the bovine lymphocyte antigens (BoLA)-A11, -A20, -HD1, and -HD6 whereas no peptide was found for BoLA-HD7. Based on this finding, the probable contribution of genomic segments of BVDV to the CTL response and strategies for recombinant vaccines are discussed.

Computer simulations of proteolysis of Marburg and Ebola-Zaire filovirus coded proteins to generate nonapeptides with motifs of known HLA class I haplotypes and detection of antigenic domains in the viral glycoproteins

The primary amino acid sequences of the proteins coded by Marburg and Ebola-Zaire filoviruses were studied by computer programs to search for putative proteolytic cleavages which yield nonapeptides with motifs of binding to known HLA class I haplotypes. The computer analyses predicted that numerous nonapeptides with motifs to bind HLA class I A68 and A2 haplotypes were detected. A few nonapeptides with motifs HLA class I A24, B8, B27 and B35 were predicted in Marburg virus proteins. A similar finding is reported for Ebola-Zaire viral proteins (the viral polymerase was not studied). The search for antigenic domains that may induce the humoral immune response in the viral glycoproteins was based on computer analyses of the physical properties and antigenicity predictions of amino acids in certain domains of the primary amino acid sequences. Twelve putative antigenic domains were detected in Marburg virus glycoprotein and 11 putative antigenic domains in Ebola-Zaire virus glycoprotein. Despite the marked differences in the primary amino acid sequences in the putative antigenic domains of the two viral glycoproteins, 8 antigenic domains were found to have similar locations in the viral glycoproteins of the two viruses. Each pair of antigenic domains resemble each other in the physical properties of the amino acids that are different. These computer analyses may provide an approach to developing synthetic peptides capable of induction of both the cellular and humoral responses to protect against infection with Marburg or Ebola viruses.

Prediction of potential cytotoxic T lymphocyte epitopes of bovine herpesvirus 1 based on allele-specific peptide motifs and proteolytic cleavage specificities

Major histocompatibility complex (MHC) class I molecules present endogenous peptides to cytotoxic T lymphocytes (CTLs). Elucidation of CTL epitopes of intracellular pathogens helps in designing better vaccines to control economically important human and animal diseases. In this study, candidate epitopes that are potentially available for presentation to the CTLs via five bovine MHC class I molecules have been identified. This was accomplished by using the computer programs "Find-patterns" and "Peptidestructure" of GCG package and applying the information on cleavage patterns of cytosolic and endoplasmic reticulum proteases and peptidases as well as MHC class I allele-specific peptide motifs on 23 bovine herpesvirus-1 (BHV-1) proteins available on protein sequence database. Several candidate peptides were found for each of the bovine lymphocyte antigens (BoLA)-A11, -A20, -HD1, and -HD6 whereas no peptide was found for BoLA-HD7. Majority of the candidate peptides were from the viral glycoproteins. The contribution of such studies towards the identification of CTL epitopes of BHV-1 and other intracellular pathogens is discussed.