Researchers Find New Clues to AIDS Virus Replication

A team of Harvard researchers has developed a new portrait of how HIV, the virus that causes AIDS, reproduces itself in a development that may provide clues for future drug treatments.

Through a collaboration between the Department of Chemistry and Chemical Biology and the Department of Molecular and Cellular Biology, researchers were able to take a snapshot of a stage of the mechanism by which the enzyme reverse transcriptase (RT) works on a strand of viral DNA to make new copies.

Understanding this mechanism may help researchers make new drugs that will serve as options in the drug cocktails--mixtures of three or four drugs--that have resulted in far more effective treatment of AIDS.

RT, one of several major proteins in the AIDS virus, is one of the most important enzymes in the replication of HIV, performing various functions at different stages of replication.

Currently, one major class of drugs that fights AIDS, called RT inhibitors, tries to interfere with RT. These drugs range from AZT to DDI to DDC.

But mutations in RT--which lead to mutations in HIV--sometimes make these drugs ineffective, said Huifang Huang, a post-doctoral fellow in the Department of Molecular and Celluar Biology who served on the research team.

"The virus finds a way to evade the action of the drugs that we come up with to fight it," said David D. Ho, a Harvard Overseer who won Time Magazine's Man of the Year Award in 1996 for AIDS research.

With an understanding of the mechanism, researchers said they have made another important step in combating AIDS, which killed 2.3 million people worldwide last year.

Higgins Professor of Biochemistry Stephen C. Harrison, who worked with the research team, said that while this is not "some major breakthrough...in the history of AIDS research," it is certainly an advance.

"Here's one more small step in the direction of trying to make this process faster, better, more rational, more effective," Harrison said. "[And] it's a contribution I'm very proud of, incidentally," he added.

"That's how science is done," Ho said. "Little by little."

A Good Shot

The group's research, published in an article in Science entitled "Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Nucleoside-Analog Drug Resistance," represents years of efforts aimed at understanding RT.

In the late 1980's Harrison and colleagues at other schools began uncovering the structure of RT. But until recently, researchers still did not know much about the mechanisms by which RT worked.

Then several years ago, Harrison joined forces with Professor of Chemistry Gregory L. Verdine and Huang. Rajiv Chopra, another post-doctoral fellow, joined the effort soon after.

According to Harrison, when HIV enters a human cell, it uses RT and RNA to form a new strand of viral DNA. Then this strand is used to make another one,which when joined with the first, forms the fameddouble helix.

Researchers pinpointed a moment in the encodingof the second strand of viral DNA at which one newbuilding block of DNA, known as a nucleotide, isadded.

"What we wanted to do was get a snapshot in aparticular stage of the reaction cycle," Harrisonsaid. "In other words, trap the enzyme in action."

The moment at which a nucleotide is added isimportant because it is the same instant at whichmany HIV drugs inhibit RT--or fail to, if RT hasmutated.

RT inhibitors attempt to act as a stop valve,inserting defective nucleotides that are unable tobind with other molecules, thus ending the growthof a new chain of DNA and preventing thereproduction of HIV.

Getting a freeze frame of the mechanism was anextremely difficult task because of the alarmingrate at which HIV grows, Harrison said.

Huang was the one who found a way to look atthe molecules for only an instant.

"If you're a child who cannot sit still youbasically bind this child to a chair," Huang said.

Developing a model of the structure of themolecule at the particular instant was also madepossible by X-ray crystallography--Chopra'sspecialty--which provided the necessary data.

The model the researchers built of RT--placedon computer generated diagrams--resembles a handmoving along a stand of DNA.

All of this research is important not only forsolving the riddle of HIV, but also for purelyscientific reasons, Harrison said. The work willhelp scientists understand how enzymes such asRT--called polymerases--work "in general," henoted.

Huang said it is difficult to quantify howsignificant the new work is, but he said that itsappearance in Science places it at the forefrontof scientific research.

Only one or two pure research articles areplaced in the magazine each week, he added. "Theyhave limited space," Huang noted. "[The research]must be pretty good."

Ho said he has not yet read the article, but hepraised the group of researchers. "I just knowthat group generally does beautiful work and I'vesure they've done the same," he said.

What Now?

Though new AIDS drugs could mean a mountain ofmoney, Huang said he and his fellow researcherswill probably not be involved in drug development.

A handful of researchers can only do so muchcompared to larger corporations, especiallybecause of the complications of finding drugs thatare safe, Huang said.

"In order to design [it] as a drug, it needs tobe a massive force like a pharmaceutical company,"Huang said. "Don't expect much from us."

But by publishing their research, Huang saidthey are providing the starting block for futureefforts.

"We are not going to hold back information," hesaid.

Huang said the group's success was acombination of luck and determination. The rightgroup of people and the right circumstances madethe work possible, he said.

But the team has also been burning the midnightoil for the past several years. Huang said heoften works long hours, remaining at the lab past10 p.m.

"We will work 11 hours a day. Almost novacation," Huang said. "I don't have much patienceto wait very long."

All that work seems to be finally paying off.

"I'm very happy," Huang said. "I feel lucky andat the same time very happy."

Chopra and Verdine could not be reached forcomment

Researchers pinpointed a moment in the encodingof the second strand of viral DNA at which one newbuilding block of DNA, known as a nucleotide, isadded.

"What we wanted to do was get a snapshot in aparticular stage of the reaction cycle," Harrisonsaid. "In other words, trap the enzyme in action."

The moment at which a nucleotide is added isimportant because it is the same instant at whichmany HIV drugs inhibit RT--or fail to, if RT hasmutated.

RT inhibitors attempt to act as a stop valve,inserting defective nucleotides that are unable tobind with other molecules, thus ending the growthof a new chain of DNA and preventing thereproduction of HIV.

Getting a freeze frame of the mechanism was anextremely difficult task because of the alarmingrate at which HIV grows, Harrison said.

Huang was the one who found a way to look atthe molecules for only an instant.

"If you're a child who cannot sit still youbasically bind this child to a chair," Huang said.

Developing a model of the structure of themolecule at the particular instant was also madepossible by X-ray crystallography--Chopra'sspecialty--which provided the necessary data.

The model the researchers built of RT--placedon computer generated diagrams--resembles a handmoving along a stand of DNA.

All of this research is important not only forsolving the riddle of HIV, but also for purelyscientific reasons, Harrison said. The work willhelp scientists understand how enzymes such asRT--called polymerases--work "in general," henoted.

Huang said it is difficult to quantify howsignificant the new work is, but he said that itsappearance in Science places it at the forefrontof scientific research.

Only one or two pure research articles areplaced in the magazine each week, he added. "Theyhave limited space," Huang noted. "[The research]must be pretty good."

Ho said he has not yet read the article, but hepraised the group of researchers. "I just knowthat group generally does beautiful work and I'vesure they've done the same," he said.

What Now?

Though new AIDS drugs could mean a mountain ofmoney, Huang said he and his fellow researcherswill probably not be involved in drug development.

A handful of researchers can only do so muchcompared to larger corporations, especiallybecause of the complications of finding drugs thatare safe, Huang said.

"In order to design [it] as a drug, it needs tobe a massive force like a pharmaceutical company,"Huang said. "Don't expect much from us."

But by publishing their research, Huang saidthey are providing the starting block for futureefforts.

"We are not going to hold back information," hesaid.

Huang said the group's success was acombination of luck and determination. The rightgroup of people and the right circumstances madethe work possible, he said.

But the team has also been burning the midnightoil for the past several years. Huang said heoften works long hours, remaining at the lab past10 p.m.

"We will work 11 hours a day. Almost novacation," Huang said. "I don't have much patienceto wait very long."

All that work seems to be finally paying off.

"I'm very happy," Huang said. "I feel lucky andat the same time very happy."

Chopra and Verdine could not be reached forcomment