By David N. Leff

Science Editor

A 31-year-old homosexual man – identity withheld – may have to be thanked some day for the first effective vaccine against the AIDS virus. For six years, this putative benefactor had been infected with HIV, while remaining free of symptoms.

This contrarian standoff led scientists at the Scripps Research Institute in La Jolla, Calif., to speculate that the unscathed individual’s immune system had beaten his human immunodeficiency virus to a draw. He willingly donated bone marrow, from which the researchers extracted the genes for every antibody deployed by his immune defenses. One monoclonal antibody in particular, named b12, displayed strong reactivity against the virus’ prime antigenic target – glycoprotein 120 (gp120).

It’s gp120 that breaks and enters the immune system’s T cells. The passkey that gp120 pilfers is CD4, a receptor protein that sits on the surface of those cells. Once an HIV particle has violated a T cell, it hijacks that cell’s DNA, multiplies mightily, and wastes the victim’s immune defenses – en route to AIDS.

Today’s Science, dated Aug. 10, 2001, reports: “Crystal structure of a neutralizing human IgG [immunoglobulin] against HIV-1: A template for vaccine design.” The paper’s first author is Scripps X-ray crystallographer Erica Ollmann Saphire, a research associate at the institute.

“The trouble with HIV,” Saphire told BioWorld Today, “is its ability to rapidly mutate. Whatever your immune system comes up with to counterattack HIV, the virus changes its isolates – and escapes. Several years ago,” she recalled, “Scripps immunologists discovered in the anonymous donor’s bone marrow that his b12 antibody can inactivate about 75 percent of HIV strains – including American, European, African and Asian isolates.

“That’s extraordinarily rare,” Saphire continued.” In fact it’s one of only two antibodies against HIV that is capable of neutralizing such a broad array of viruses. The ideal vaccines would generate antibodies like that. So what we did was determine the atomic structure of that b12 antibody. Now we can tackle the question: How can we use its shape and fit on HIV’s gp120 epitopes in order to design a vaccine that’s going to elicit antibodies like b12 in a vaccinated person?”

First-Ever Human Antibody Structure

“The significance of these findings,” Saphire went on, “is twofold: One – a bit lost in the Science paper – is the fact that this was the first-ever structure of an entire human antibody. And the second is its powerful activity against HIV. There are two vaccine-promising antigenic proteins on the surface of HIV,” she pointed out, “gp120 and gp41. Each has two highly effective antibody docking sites. AIDS immunologists over the years have probably identified many, many antibodies against these two proteins, but only four are broadly reactive and potent – two against a protein called gp41 and two against gp120. So the significance of our work so far is that obtaining this atomic structure of antibody b12 gives us a model to work from, to try to design an effective vaccine against the majority of HIV’s different strains.”

To accomplish this structural analysis, Saphire explained, “I grew crystals of the antibody, and put them in an X-ray beam. The crystals scattered the beam, and the scatter made spots. The pattern of spots was determined by the atomic structure of the object in the crystal. So we could see at the atomic level what the antibody looked like. It binds to the same place on gp120 as does the human receptor CD4. So when HIV infects human cells, gp120 binds to CD4, and that’s its way in.

“Here’s the key important thing: If HIV wants to go on being infective, the region that binds CD4 can’t really mutate to the same extent as other places in gp120,” she said. “So b12 is hitting a place on gp120 where the cells are conserved. And that’s one reason why the b12 antibody is so effective. CD4’s structure has been known for a few years. It’s just a fragment of gp120 that the CD4 receptor binds to. Gp120 is almost completely covered with sugar – glycoprotein – except for one portion, and CD4 binds into that portion.

“In the part that binds CD4, and isn’t cloaked with sugar,” she went on, “there’s a recessed cavity – one of the distinguishing features of that antigenic region. And we think the b12 antibody binds into that cavity. The antibody’s most outstanding feature,” Saphire recounted, “is a very prominent finger-like projection that rises out of b12’s center – the site in the antibody that binds gp120. This 18-amino-acid-long loop pokes into the cavity in that protein, where it seems to makes a very snug fit – like the fingers in a kid glove.”

Crystallographers, Immunologists Team Up

If enough antibody makes its way into the viral antigen’s cavities, it could spell the HIV particle’s death sentence. “Each virus is a membrane-coated sphere,” Saphire pointed out. “Coming out of the sphere are spikes that look a little like mushrooms. The precise number of these gp120 or gp41 spikes is under debate. People think that each HIV is studded with about 70 or 72 spikes, each of which has three epitopes. If you put in at least one entire antibody per spike, that significantly disarms the virus. Two antibodies per spike almost completely defang it.”

With a view toward a future AIDS vaccine, Saphire and her co-authors “have identified portions of gp120 that are in contact with the b12 antibody. And we’ve done extensive mutagenesis, tinkering with each one of those little amino acid pieces to see which part is critical for b12 binding.”

How does Saphire explain the fact that apparently no AIDS vaccinologist has yet used the atomic structure approach to HIV antibodies. “I think in the past,” she surmised, “crystallographers were not immunologists, and immunologists were not crystallographers. And I believe a new generation of science will be able to incorporate both of these skills. The reason why this is necessary for HIV,” she added, “is that this virus is uniquely difficult. Other viruses don’t change as much. HIV is so changeable, we’ll really have to go about it in a much smarter way.”

So besides both persuasions of scientists in-house at Scripps, she concluded, “in developing an AIDS vaccine, we’ll have collaborations across the U.S. and in Europe.”