Whitehead Structural Biologists Discover Vulnerable Region in HIV Envelope Protein

CAMBRIDGE, Mass. — For the first time scientists have a high-resolution picture of the protein fragment that enables HIV (the AIDS virus) to invade human cells—work that has immediate implications for new drug design. In the April 18 issue of Cell magazine, Dr. Peter S. Kim and his colleagues at the Whitehead Institute for Biomedical Research and the Howard Hughes Medical Institute present the crystal structure of a key fragment of the HIV envelope protein.

"The envelope protein resides on the surface of the virus and plays a crucial role in HIV infection," says Dr. David Chan, first author of the Cell paper and a postdoctoral fellow in the Kim lab. "One part of the protein, known as gp120, allows the virus to bind to human cells. Another subunit, gp41, mediates fusion of the viral membrane and the cell membrane—it initiates entry of the virus into the cell. We have determined the core structure of gp41 using X-ray crystallography."

The striking images produced by the Whitehead scientists reveal a compact, six-helix bundle punctuated by deep cavities. "Until we saw the images, we didn't know that these cavities existed," Dr. Kim says. "They could be key targets for the development of new antiviral drugs."

Despite its importance, there are no antiviral drugs that target the envelope protein, in part because the virus is extraordinarily clever at changing the pieces of the protein it presents to the outside world. Experimental evidence indicates, however, that the cavity structure revealed by the Whitehead scientists may not be so amenable to change, and therefore drugs directed towards this region may be effective against many HIV strains.

Dr. Kim adds, "The importance of identifying drugs that block the HIV envelope protein is underscored by the recent success of combination drug regimens for the treatment of AIDS. It would be extremely useful to add to this arsenal a drug directed against the membrane-fusion machinery."

To speed the process of drug discovery, the Whitehead scientists will make the precise, three-dimensional information about the fusion structure accessible to all scientists through the Protein Data Bank at the Brookhaven National Laboratory. In addition to Drs. Kim and Chan, the authors of the Cell paper are Dr. James Berger, a Whitehead Fellow, and Ms. Deborah Fass, a graduate student in the Kim laboratory.

Protein Dissection

Scientists have tried for almost a decade to determine the physical structure of gp41 with little success. Rather than examine the whole molecule, the Whitehead researchers used a strategy called protein dissection. They broke gp41 into pieces and then selected for study two key fragments known through other methods to play a central role in the fusion process. Biophysical studies indicated that the two fragments, labeled N36 and C34, interacted with each other in the fusion-active form of the molecule.

To understand this interaction, Dr. Chan grew crystals from a solution containing a mixture of N36 and C34, and then bombarded the crystals with X-rays (using both the W.M. Keck Foundation X-ray Crystallography Facility at the Whitehead Institute and the Howard Hughes Medical Institute beamline at the National Synchrotron Light Source at Brookhaven National Laboratory).

Dr. Berger explains, "X-ray crystallography is based on the observation that X-rays striking a well-formed protein crystal will scatter in a pattern that is unique for that protein or protein fragment. Structural biologists then use computational and biochemical methods to decode the pattern and determine the exact location of individual atoms in the crystal. We convert this information into images that reveal the detailed three-dimensional structure of the protein."

Fusion Structure Is 'Striking'

"Images of the N36/C34 complex revealed a structure that was strikingly familiar," Dr. Kim says.

Several years ago, Whitehead scientists predicted the fusion structure of the flu virus as a three-part coiled-coil (resembling three intertwined springs). Other laboratories later confirmed this prediction. The HIV fusion protein looks very similar. Three helices of N36 cling together in a tightly wound coiled coil (indicating that gp41 functions as a trimer—three gp41 molecules come together to initiate the fusion reaction). The outside of this coiled coil bears three deep grooves; these are filled by helices of C34 that wind around and support the N36 coil.

The one element that surprised the Whitehead scientists was the presence of a deep cavity or pocket at the base of each groove in the N36 coiled coil. In the active structure, each cavity is filled by a knob-like protrusion from C34.

Ball-and-Socket Arrangement

"This ball-and-socket arrangement of C34 and N36 could be an ideal target for drug design or discovery," Dr. Kim says. "Our structure, combined with data from other laboratories, suggests that a small molecule constructed specifically to block this interaction could stop fusion and prevent the virus from entering cells."

Dr. Kim, who is a member of the AIDS Vaccine Research Committee of the National Institutes of Health, gives three reasons for this optimism:

First, test tube studies have shown that fragments, or peptides, of gp41 encompassing or overlapping with N36 or C34 have potent anti-viral activity. However, peptides generally make poor drugs because they are poorly absorbed and the body breaks them down almost immediately. A small molecule targeting just the cavity structure could escape this fate.

Another reason for optimism, Dr. Kim says, is that the inhibitors derived from the C and N peptides are effective in the test tube against a wide range of HIV strains, including patient isolates and laboratory-adapted strains. By contrast, neutralizing antibodies and drug candidates designed to block the binding activity of the envelope protein are typically effective against only a limited subset of HIV strains.

Finally, other workers have shown that alteration of the walls of the N36 cavity can block the fusion reaction, indicating that the ball-and-socket arrangement of N36 and C34 must be preserved to obtain viral infection. In addition, the protein building blocks that make up the walls are highly conserved among HIV strains and between HIV and SIV, the virus responsible for AIDS in monkeys. This suggests that the virus cannot tolerate much change in this region, and that HIV may have more difficulty developing resistance to a cavity-blocking drug than to many other compounds.

"In addition to providing new opportunities for drug development, the gp41 core structure serves as a crucial starting point for exploring the mechanism of HIV entry into cells," Dr. Kim concludes. "Also, the similarity between the fusion mechanisms in HIV and flu—two viruses with no known evolutionary links—suggests that the knowledge we acquire in our research will have broad implications for other viral diseases."

This work was supported by the Howard Hughes Medical Institute and by fellowship support to Dr. Chan from the Jane Coffin Childs Memorial Fund for Medical Research.

Citation: Chan, D. et al.  "Core Structure of gp41 from the HIV Envelope Glycoprotein." Cell. April 18 1997. 89:263-273.