Protein and DNA-sequence homologies between the V3-loop of human immunodeficiency virus type I envelope protein gp120 and immunoglobulin variable regions

Aerobic exercise training as a potential source of natural antibodies protective against human immunodeficiency virus-1

Despite the effectiveness of HAART in controlling HIV-1 replication, the emergence of drug-resistant viruses in infected patients and the severe side effects caused by the currently used drug regimens and the lack of an effective vaccine necessitate the continued search for new therapeutic strategies for prevention and therapy of HIV disease. Previously we reported that natural autoantibodies, recognizing peptide FTDNAKTI (peptide NTM1) derived from the C2 domain of HIV-1 gp120, contribute to the control of HIV disease. Here we demonstrated that sera from well-trained athletic (HIV-negative) subjects showed high reactivity with peptide NTM1. This result confirms that aerobic exercise training stimulates production of natural autoantibodies, which recognize peptide NTM1. Bioinformatics analysis indicates that these natural autoantibodies could slow down disease progression by blocking the superantigenic site on HIV-1 gp120. The results suggest that aerobic exercise training may be a promising non-toxic and inexpensive adjunctive anti-HIV therapy.

AIDS vaccine: efficacy, safety and ethics

Human immunodeficiency virus (HIV) has infected 50 million people worldwide and killed 16 million so far, and the epidemic is still spreading with 16,000 new cases of HIV infection daily and a projection of 100 million infected individuals by the end of the next decade. There is no question that a safe and effective acquired immunodeficiency syndrome (AIDS) vaccine is urgently needed to bring the current AIDS pandemic under control. But, is preventive AIDS vaccine an attainable goal? Unfortunately, the results of many laboratory and clinical studies over the past two decades are not encouraging. We comment on the efficacy, safety and ethics of AIDS vaccine, and the urgent need for a new strategy for AIDS vaccine development.

Molecular mimicry of HIV gp120: Possible implications on prevention and therapy of AIDS

A broad range of similarities between HIV-1 gp120 and human proteins-especially those participating in immune responses-highlight gp120 as a pleiotropic protein which can influence many important functions of the human immune system. The molecular mimicry that serves to the human immunodeficiency virus as potent destructive arms against immune system could be the weak point we are in search of over decades. Examples involving sequence and informational similarities of HIV-1 gp120 and immunerelated host cell proteins important for prevention and treatment of HIV infection are presented. .

Template-based recognition of protein fold within the midnight and twilight zones of protein sequence similarity

Most homologous pairs of proteins have no significant sequence similarity to each other and are not identified by direct sequence comparison or profile-based strategies. However, multiple sequence alignments of low similarity homologues typically reveal a limited number of positions that are well conserved despite diversity of function. It may be inferred that conservation at most of these positions is the result of the importance of the contribution of these amino acids to the folding and stability of the protein. As such, these amino acids and their relative positions may define a structural signature. We demonstrate that extraction of this fold template provides the basis for the sequence database to be searched for patterns consistent with the fold, enabling identification of homologs that are not recognized by global sequence analysis. The fold template method was developed to address the need for a tool that could comprehensively search the midnight and twilight zones of protein sequence similarity without reliance on global statistical significance. Manual implementations of the fold template method were performed on three folds--immunoglobulin, c-lectin and TIM barrel. Following proof of concept of the template method, an automated version of the approach was developed. This automated fold template method was used to develop fold templates for 10 of the more populated folds in the SCOP database. The fold template method developed three-dimensional structural motifs or signatures that were able to return a diverse collection of proteins, while maintaining a low false positive rate. Although the results of the manual fold template method were more comprehensive than the automated fold template method, the diversity of the results from the automated fold template method surpassed those of current methods that rely on statistical significance to infer evolutionary relationships among divergent proteins.

Molecular makeup of HIV-1 envelope protein

A broad range of structural, functional, and immunological similarities between HIV-1 gp120 and human proteins, especially those participating in immune responses, highlight gp120 as a pleiotropic protein that can in different ways affect many important functions of the human immune system. Here we described some of these properties of HIV-1 gp120 that represent the main obstacle in the development of effective and safe AIDS vaccine.

AIDS epidemic at the beginning of the third millennium: time for a new AIDS vaccine strategy

Current expansion of AIDS pandemic significantly accelerates AIDS vaccine research resulting in development and clinical testing of several AIDS vaccine candidates. At the same time, available experimental and clinical data demonstrate that current AIDS vaccine strategy is unsuccessful resulting in development of inefficient and harmful vaccines. This overview briefly summarizes reported results which point out the requirement for moratorium on the current clinical trials of HIV-1 gp120/160 vaccines and urgent need for development of a new, efficient and safe AIDS vaccine strategy.

Anti-V3 and anti-IgG antibodies of healthy individuals share complementarity structures

It was recently shown that antibodies reactive with a peptide from the tip of the HIV-1NY5 gp120 V3 loop (V3 peptide) are present not only in sera of HIV-positive patients but also in sera of healthy HIV-negative individuals. In the present study, we show that V3 peptide reactive antibodies are predominantly IgM in sera of HIV negative individuals and that a fraction of the IgG anti-V3 antibodies exhibit features of autoantibodies. These antibodies were purified by chromatography on IgG-sepharose columns from sera as well as from purified IgG anti-V3 antibodies. A higher IgG anti-V3 reactivity was detected in autoantibody preparations from HIV-positive sera as compared with the reactivity of sera and purified antibodies from HIV-negative individuals. This was confirmed by solid phase binding of IgG anti-V3 antibodies both to V3 and to human IgG F(ab')2 antigens. The autoantibodies did not bind to peptides that share sequence similarity with V3 peptide indicating a high epitope specificity. The detection of antibodies against HIV epitopes in HIV-negative individuals may suggest that anti-V3 antibodies after HIV infection represent at least in part a secondary immune response.

Human immunodeficiency virus V3 peptide-reactive antibodies are present in normal HIV-negative sera

A structural relation between consensus sequences of the portion of HIV-1 gp120 involving the V3 loop (V3 peptide) and the variable domains of human immunoglobulin members of the VH-III gene family was proposed to trigger an imbalance of the idiotypic network during the course of HIV infection. Thus, the repertoires of immunoglobulins in healthy individuals should contain antigenic determinant(s) complementary to particular V3 loop epitope(s). In this study we investigated the specific binding to the V3 peptide of antibodies present in sera of HIV-positive and of clinically normal HIV-negative subjects. Two groups of HIV-positive sera differing in antibody titers to V3 peptide, arbitrarily referred here as high- and low-reactive HIV-positive sera, were distinguished on the basis of an ELISA. Antibodies were affinity purified on V3 peptide and their titers in both HIV-negative and low-reactive HIV-positive sera were nearly superimposable and much lower than the titers of those from high-reactive HIV-positive sera. Also, the quality of the two groups of antibodies differed: much higher amounts of soluble V3 peptide were needed to partly compete the binding of antibodies from HIV-negative sera to insoluble V3 peptide as compared with those from HIV-positive sera, suggesting that the latter had higher affinity for V3 peptide. All of the affinity-purified antibodies bound poorly to unrelated peptides, even to those sharing sequence similarity with the V3 peptide. The present observations suggest that in HIV infection antigen-driven affinity maturation of preimmune immunoglobulins with idiotypes complementary to V3 epitope(s) participating in physiological autoreactivity might be at work.

The presence of antibodies against HIV peptides in the sera of alloimmune mice and thalassemic patients is due to a polyclonal activation mechanism

This paper analyses the HIV-1 gp120 epitope specificity and activation mechanisms (i.e., polyclonal versus oligoclonal) of antibodies present in the sera of alloimmune mice and humans. Sera from CBA mice engrafted with C57BL/6 lymphoid cells significantly reacted against the gp120-derived peptide as 261-270, which shares high homology with the membrane-proximal domain of HLA class II beta-chains (HLA/ gp120) and against the HIV gp120 V3 loop-derived peptides DP32 (HIV-1 MN-derived as 302-334) and C53 (HIV-1 IIIB-derived as 304-318). The same sera also reacted against the HIV-unrelated peptide necdin. Moreover, sera from BALB/c mice injected with LPS presented antibodies reacting against both HIV-related and -unrelated peptides, suggesting that similar mechanisms are shared in alloimmune and LPS-treated mice. A similar analysis was then performed on the sera of patients affected with beta-thalassemia major, receiving at least 10 blood transfusions/year. In particular, 15 of 58 (26%) sera from HIV-uninfected thalassemic patients showed a significantly reactivity against the HLA/gp 120-derived peptides. Moreover, 22 of 58 (38%) sera from the same cohort showed a significant reactivity against DP32 peptide. This reactivity was related to a polyclonal activation mechanism since the DP32-reactive sera significantly bound a panel of HIV-unrelated peptides, as observed by testing 22 sera against necdin, 21 against HSP65 kDa, 21 against amyloid-1, and 17 against MAGE-1 peptides. Moreover, a significant increase of IgG concentration was also observed in all thalassemic sera, when compared to healthy controls, without regard to the anti-gp120 antibody reactivity. Taken together, these results indicate that (i) allogeneic stimuli may induce anti-gp120 antibodies in CBA and in 38% of polytransfused patients and (ii) this reactivity is related to a polyclonal activation mechanism but not to a heightened concentration of IgG.

Further evidence for the relationship of HIV-1 gp120 V3 loops with Ig superfamily members: similarity with the putative CDR3 region of T-cell receptor delta-chains

Twenty-five V3 loops of envelope gp 120 extracted from 30 HIV-1 isolates were compared with T-cell receptor (TCR) subunits variable (V) portions using pairwise alignments of 11-residue peptides. The results indicate that, in comparison with random sequences, the analyzed V3 loops, unlike control (unrelated) sequences, display highly significant local similarity with TCR V delta (p approximately 10(-20)). However, pattern-matching searches were performed on a much larger number of V3 loops (484). In particular, selective pattern TR * * * NT * K * I is shared by V delta from human T-cell line KT19E and 230 HIV-1 V3 loops (N-terminal portion). Pattern RA * YT * * * I * G is common for V delta chain isolated from T-cell line DS6 of an immunodeficient patient and 69 V3 loops (C-terminal portion). The presented delta-chain portions of sequence similarity with the V3 loops overlap the putative complementarity-determining region (CDR3), thus possibly indicating functional similarity too.

Deceptive imprinting in the immune response against HIV-1

The clonal profile of anti-HIV-1 antibodies is established at the time of infection as part of a vigorous immune response against HIV-1, and remains stable during the infection process. This bias towards antibodies specific for the initially infecting clonal virus population, termed imprinting, is inappropriate for attempts of the infected host to control viral variants that subsequently emerge. Here, Heinz Köhler, Sybille Müller and Peter Nara argue that immunodominant epitopes on viral variants or recombinant proteins are selected that induce and maintain this deceptive state, and thereby remain unrecognized through a functional and cross-reactive hole in the B-cell repertoire.

Improbability of harmful autoimmune responses resulting from immunization with HIV-1 envelope glycoproteins

Autoimmunity mediated by cross-reactive antibodies, elicited by HIV-1 envelope glycoproteins gp120/gp160, has been postulated to contribute to the pathogenesis of AIDS. Partial amino acid sequence homology between gp120/gp160 and several human host proteins, including MHC antigens and immunoglobulins, has been perceived as the basis for immunological cross-reactivity. Binding of antibodies from sera of HIV-1-infected individuals to selected host proteins and/or to synthetic peptides derived from them and the inhibitory activity of such sera in assays measuring the functional activity of T cells provided apparent support for the autoimmunity hypothesis, which is also relevant to the issue of safety of anti-HIV-1 vaccines. Considering the possibility that the detected autoantibodies may arise for reasons other than antibody responses to gp120/gp160, the immunological cross-reactivity between gp120/gp160 and the relevant host proteins was investigated using hyperimmune rabbit anti-gp120/gp160 and monoclonal antibodies. As determined from dilution end-point comparisons for polyclonal anti-gp120, the cross-reactivity of anti-gp120 with CD4 was undetectable (< 10(-5)%). The cross-reactivity of anti-gp120/gp160 with HLA-I and HLA-II antigens was also undetectable (< 4 x 10(-4)%) and that with other human proteins reported to have partial sequence homology with gp120/gp41 was < or = 0.013%. Anti-gp120/gp160 did not have detectable inhibitory effects in functional assays measuring proliferative T cell responses. Therefore, immunization with gp120/gp160 is unlikely to elicit harmful autoimmune responses.

Potentially negative effects of AIDS vaccines based on recombinant viruses carrying HIV-1 derived envelope gene. A warning on AIDS vaccine development

Various candidate AIDS vaccines based on HIV-1 envelope glycoprotein (gp120/160) are currently under clinical trials (phase 1 and 2) in healthy, HIV-negative volunteers, as well as in HIV-infected persons. Most of these vaccines use recombinant viral vectors carrying the HIV-derived gp120/160 gene. Possible negative effects of recently reported sequence and gene similarities between HIV-1 gp120 and the variable region of human immunoglobulins on further development and current application of such AIDS vaccines are discussed.

Spectral and sequence similarity between vasoactive intestinal peptide and the second conserved region of human immunodeficiency virus type 1 envelope glycoprotein (gp120): possible consequences on prevention and therapy of AIDS

Recently, in sera of HIV infected individuals, antibodies recognizing nonimmunogenic C-terminal domain of the second conserved region of HIV-1 gp120 were identified (1). These antibodies are significantly more prevalent in asymptomatic carriers than in AIDS patients (1). Here we reported striking spectral and sequence homologies between human vasoactive intestinal peptide (VIP) and the conserved peptide derived from HIV-1 gp120 which binds these antibodies. The possible consequences of these findings on therapy and prevention of AIDS are discussed.

Comparison and fine mapping of both high and low neutralizing monoclonal antibodies against the principal neutralization domain of HIV-1

Monoclonal antibodies raised against viral lysate of HIV-1 (strain LAV-1) and against recombinant gp 160 of HIV-1 (strain HTLV IIIB) which neutralized HIV-1 in a type specific manner were mapped with the aid of peptides (Pepscan analysis). Each of these monoclonal antibodies bound to peptides located on the principal neutralizing domain (PND) of HIV-1. We found that the antigenic sites of the MAbs described in this paper are represented by linear peptides of at least 10 amino acids long. The affinity of the MAbs is high for these peptides and in the same order of magnitude as for native gp 160. The fine mapping of the epitopes may reflect structural features of the PND, for instance which amino acid side chains are exposed and which are buried in the protein. Furthermore the fine mapping of the epitopes explained the HIV type-specific neutralizing activity of the MAbs. Antibodies that bound to the tip of the loop (amino acids QRGPGRAF) have a higher neutralizing activity than antibodies that bound to amino acids towards the N-terminal side of the loop (amino acids KSIRI). Furthermore, MAbs that bound to virtually the same amino acids on the tip of the loop (amino acids IQRGPGRAF and RGPGRAFV) had different neutralizing activities due to different affinities for native gp 160. These data reveal that neutralizing activity not only is determined by the affinity of an antibody to the neutralizing site but also by its fine binding specificities to the V 3 loop of gp 120.