HARVARD GAZETTE ARCHIVES

New Structure Helps Explain AIDS Drug Resistance

By William J. Cromie
Gazette Staff

Working with Gregory Verdine (left), Huifang Huang captured the AIDS virus in the act of reproducing itself in a human blood cell.

Researchers at Harvard University have crystallized part of the AIDS virus at work inside a human blood cell, and they now can see more clearly how the virus makes itself resistant to drugs.

The stop-action structure reveals how a protein, known as RT or reverse transcriptase, goes about making more of the virus. It also shows how mutations of RT prevent drugs now in wide use from slowing down this process.

"With this sort of information, drug companies are better equipped to develop improved RT inhibitors," says Gregory Verdine, a professor of chemistry. "It took years to solve the puzzle of how mutations in the virus allow it to counter the activity of first line drugs such as AZT [zidovudine]. Now, the whole thing makes sense."

Details of the breakthrough are reported in the current issue of the journal Science. The new knowledge is of major importance; last year 5.6 million people worldwide became newly infected with the virus, and 2.3 million died from the incurable disease it causes.

Stephen Harrison (right) and Rajiv Chopra check a computer simulation of a protein from the AIDS virus copying its genes (center red spot).

Productive Teamwork

Stephen Harrison, Higgins Professor of Biochemistry at Harvard and investigator in the Howard Hughes Medical Institute, began studying the structure of RT in the late 1980s, but a picture of how RT actually works eluded him and other scientists working on the problem. Such proteins don't remain still for even a fraction of a second; they constantly move and change shape as they go about their work.

Seeking more expertise in chemistry, Harrison started a collaboration with Verdine. They persuaded Huifang Huang, a post doctoral fellow who works in both their labs, to join them. Huang soon found that RT has what Verdine calls an "attention deficit."

When the virus invades a blood cell, its RT begins to copy the viral genes so the virus can reproduce itself. To do this, it must attach to a specific position on the viral DNA. But when this reaction is reproduced in the lab, RT often tries to fasten itself to various wrong places. Huang figured out a way to bind RT to the correct end of the DNA, so researchers could see things as they are when the action begins.

"It was a heroic piece of work," Verdine comments. "The guy's amazing."

Huang was then able to crystallize the first complex of RT and DNA that he managed to capture. At this point, he teamed with Rajiv Chopra, a post-doctoral fellow in biology. Together, they worked out the atom-by-atom structure of the complex using a technique known as X-ray crystallography.

"Chopra is a remarkably insightful researcher," Harrison says. "He quickly recognized that RT undergoes an important structural change in its active state."

The picture Chopra built shows the viral RT gripping one end of the DNA like a closed hand. The hand gradually works its way along the DNA, copying it into a new set of genes that allows the virus to reproduce itself.

Drugs that slow this process interfere with the grip and movement along the DNA. But the viral genes, which control the structure of RT, can undergo mutations that change the shape of the "hand."

You can think of it as a drug trying to loosen RT's grip, while the mutations tighten it. When the mutations win, the virus becomes resistant to the drug.

Future Directions

"An important organizing principle is now available to us," Verdine notes. "We can see what's possible and what's not in terms of determining how resistance to RT inhibitors can be thwarted."

The full picture is, however, more complicated. Many AIDS patients take an expensive "cocktail" of three drugs, which include RT inhibitors and so-called protease inhibitors that work on a protein other than RT. Details of how the latter drugs work are not revealed in the new structural pictures.

The Harvard team intends to examine a series of RT inhibitors to determine how they might be changed for the better. They also intend to improve the resolution of their crystal structures. "At the present resolution, some features are rendered like those in an Impressionist painting; they aren't clearly defined," according to Verdine. The goal is to see every atom in any RT-DNA-drug complex.

"The virus mutates so rapidly, it seems unlikely that we can design a perfect RT inhibitor, one that never generates resistance," Verdine admits. "But the new information may enable scientists to develop better types of inhibitors."

"The insights we have gained," Harrison adds, "are also likely to increase our understanding of how similar proteins from other viruses become resistant to drugs."