BioWorld International Correspondent

LONDON - The crystal structure of the complex between an antibody that can neutralize several different strains of HIV-1 and the viral protein to which it binds has been solved.

The structure provides a framework for studying the molecular basis of HIV-1 neutralization, said the researchers who carried out the work.

They hope it also would help in the search for molecules that would be even more effective at inhibiting HIV-1, and for antigens to include in vaccines to protect against the virus.

Andrea Carfi, group leader at the Institute for Research for Molecular Biology P. Angeletti, in Rome, told BioWorld International, "This antibody has the potential to be used against a large number of HIV-1 strains because the region it recognizes is very conserved on the protein in different strains of HIV-1."

Carfi, together with colleagues in Rome and collaborators at Merck Research Laboratories in West Point, Pa., reported the study in a paper in Nature Structural and Molecular Biology, published online July 23, 2006. Its title is "Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody."

Many studies have shown that neutralizing antibodies raised against a particular strain of HIV-1 can protect against subsequent challenges with that strain - but not against others. Many researchers therefore have been searching for new targets on HIV-1 that could be used to generate broadly neutralizing antibodies, effective against many different strains.

In order to infect a human cell, a protein on the surface of HIV-1 - gp120 - must first bind to a receptor on the cell surface, such as CD4. The viral protein gp120 is closely associated with another viral protein, gp41. The latter is responsible for bringing about the fusion of the viral and cell membranes. Only after that has happened can the virus insert a DNA copy of its genome into the host's DNA - a necessary prerequisite for making more viruses.

After gp120 has bound to the cell-surface receptor, gp41 undergoes a series of conformational changes. They ultimately lead to fusion of the two membranes, but en route, gp41 forms an intermediate, known as the "pre-hairpin intermediate."

Carfi and his team decided to examine what epitopes (small parts of antigens) became exposed during the entry process, including the formation of the "pre-hairpin intermediate." Certain small molecules that effectively can inhibit HIV-1 entry into cells were known to target that intermediate.

One small molecule, called C-peptide T-20, or enfuvirtide, is already being used to treat people infected with HIV-1 who have strains that are resistant to many different anti-retroviral drugs.

Such observations, Carfi and his colleagues wrote in their paper, "together with the functional and sequence conservation of gp41 among HIV-1 primary isolates, make the . . . gp41 inner-core fusion intermediate an appealing antigen for the elicitation of broadly neutralizing antibodies."

The team recently found that a human monoclonal antibody called D5 could neutralize a range of clinical isolates of HIV-1.

In the Nature Structural and Molecular Biology paper, Carfi and his colleagues reported on the X-ray structure of D5 with a molecular mimic of the crucial part of gp41. Their studies show that a loop from D5 protrudes into a conserved hydrophobic pocket on gp41. In addition, a large pocket on D5 surrounds part of the core of gp41.

Further experiments suggest that it is crucial for D5 to be present in the fusion intermediate molecule for neutralization to take place.

Carfi said: "D5 recognizes a region of the viral protein that is very conserved among different strains. This region is normally not exposed, but it becomes exposed during the process of infection. It is therefore key to the function of gp41. We can conclude that it will presumably also be very difficult for the virus to produce an escape mutant without impairing the function of gp41."

Data presented in the paper suggested that altering the interactions between the proteins to improve the strength with which they bind to each other could make D5s neutralizing powers even more potent.

As well as improving the potency of D5, Carfi and his colleagues also plan to produce peptide sequences representing the epitope to which D5 binds. "It will be very important to assess the effect of including this epitope in candidate vaccines for HIV-1," Carfi said.