War Against Hiv

At first it looked almost too easy. Emilio Emini had all the sophisticated tools of modern science to deploy against the virus. Tall, articulate, and energetic, trained in microbiology at Cornell University and able to muster the resources of one of the world’s leading research companies, he was in the prime of his scientific career in 1986 and was eager to meet the challenge. His opponent, identified only three years before, was a virus that needed to be in an animal to live, and even then half its population would die within a day. To win the struggle for survival against a host’s immune system, it had to reproduce extremely fast and, since it normally killed the infected animal, had to be able to move on to another host. HIV, the human immunodeficiency virus, had mastered both these requirements for survival. It had some other tricks too, as Emini would discover to his surprise and dismay. In the mid-1980s it also had the advantage of being very poorly understood. Neither Emini nor any other scientist knew much about HIV, but he and his colleagues were nevertheless convinced they could soon unmask its mysteries and find a way to defeat it.

After all, that was what had already been done against polio, mumps, hepatitis B, rubella, measles, and smallpox. There was no reason to think this new virus would be much different. It would take the scientists a few years to realize just how wrong they were.

All that was needed was an effective vaccine, and the Merck Research Laboratories, where Emini worked, had a long record of successful vaccine research and development. Many of the previous vaccines employed killed or weakened (socalled attenuated) viruses to elicit an immune response, teaching the body to recognize the dangerous virus—polio, for instance—and launch a powerful counterattack. The scientists had learned they could even avoid introducing a whole virus into the system, by using just the right fragment of one. A particle from the viral surface might elicit an immune reaction without the least danger of causing disease.

Merck’s new product Recombivax HB, the world’s first genetically engineered vaccine for humans, worked that way. Emini’s boss, Ed Scolnick, a widely respected virologist and the president of the laboratories, had taken the lead role in bringing out Recombivax, which protected against the hepatitis B virus. He and his team had been able to alter yeast cells genetically to make them produce the required surface particle of the virus; the transformed yeast cells could clone the particle in commercial quantities in fermentation tanks. Scolnick and the company’s chief executive, Roy Vagelos, agreed early on that Merck should attack HIV in the same way; the alternative, using a whole weakened or attenuated virus, seemed too dangerous. They assigned Emini and his colleagues to the job.

After setting up a containment laboratory to ensure the safety of the research teams, Emini and his crew started the search for the one crucial particle of protein from the virus’s surface that could arouse an immune response but be unable to start the deadly process of self-replication that defeats the immune system and leads to AIDS. This was the same track that most other researchers trying to develop an HIV vaccine were following in the late 1980s.

Collaborating with a small Massachusetts biotech firm, Repligen, and a group of academic scientists, Emini’s research team found a promising particle, a string of eight amino acids on HIV called the V3 loop. Their laboratory tests were encouraging, and so were the initial animal trials. Since their chosen particle could be reproduced in large quantities using recombinant DNA technology, Emini thought they might soon have in hand the Holy Grail of AIDS research, an effective vaccine that could be made available anywhere in the world.

The scientists wanted a vaccine that could be used not only in the United States but also in Africa, where public health officials were already warning that the virus was becoming the Black Death of the twentieth century. In subSaharan Africa public health experts anticipated that some countries might lose up to 30 or 40 percent of their populations if HIV couldn’t be stopped, and it has begun to happen. Even in the United States the predictions fell someplace between bad and horrendous, with no cure in sight.

At Merck everyone working on the project felt tremendous pressure build as the months passed and the pandemic spread. Emini and his fellow scientists grew much better acquainted with their opponent, but the more they learned, the worse the outlook became. The virus attacked the very cells that a vaccine would need to activate—CD4 cells, which play a central role in the immune system. Indeed, it turned these cells into tiny factories for reproducing HIV and relentlessly spreading the infection.

The researchers came up with a vaccine, but it became apparent by 1993 that it simply wouldn’t work. It was not exactly clear why this vaccine and all the others being developed at the time in labs around the world were failing, but the virus’s rapid rate of multiplication and mutation probably had something to do with it. The results were beyond question. Unable to elicit the necessary immune response, Emini and his fellow scientists reluctantly gave up after spending several years and many millions of dollars on vaccine research. Someday, they thought, science would open an entirely new avenue of research that would make a vaccine feasible; until then Merck would continue to conduct research, hut the vaccine program would no longer be a top priority.

Discouraged but still determined not to be defeated, Emini and his team shifted their attention to one of the other research paths Merck was exploring. Most promising was the hunt for a chemical that could prevent HIV replication. The virus reproduces at an astonishing pace by infecting a host cell, there transcribing its own RNA into DNA, and integrating this DNA with that of the host. Two enzymes in the virus play crucial roles in the process, one at the beginning, the other at the end. If either enzyme could be blocked, the immune system might be able to wipe out the virus as it routinely did less deadly infections. When a healthy person gets a bad cold, the immune system normally wins, and he or she goes back to work in a few days. With an HIV infection there is also an initial phase of feverish illness that passes, but the virus remains, fighting a war of attrition against the CD4 cells, the foot soldiers of the immune system.

To stop that war, Merck scientists were already looking for a chemical that would hlock the first stage in the virus’s replication. They decided to target the reverse transcriptase enzyme, the one controlling the RNA-to-DNA conversion. AZT, which was made by Burroughs Wellcome and had been introduced in 1987, was a reverse transcriptase inhibitor, but it had two major problems: serious side effects and resistance arising from viral mutations. Merck’s scientists began to run what seemed after a while to be an endless series of tests, called assays, to find an inhibitor that would lock up the reverse transcriptase enzyme and effectively protect the immune system. They expanded the laboratory. Needing more room, the company invested in a new building for the research teams. During the next two years, from 1988 to 1990, the labs screened 23,000 compounds before finally finding a promising one. Medicinal chemists synthesized four varieties of that compound’s active substance, and Merck brought each of the four successfully through safety tests and launched the first phase of clinical testing in human patients. Emini, Scolnick, and the hundreds of Merck researchers now focusing on HIV finally had reason for real hope.

Then the virus demonstrated once again just how devious it could be. Replicating at its tremendous rate, it produced mutations that couldn’t be stopped by any of Merck’s four reverse transcriptase inhibitors. The viral target was moving and changing. The drug was actually working, killing some of the strains of HIV and eliminating all but the most successful mutants. Those few mutants that were impervious to the reverse transcriptase inhibitors quickly replicated and became the dominant strain of the infection. Emini and the other Merck scientists had hoped they had finally found a way to hit their moving target. But they hadn’t.

That was hard to admit after four years of intensive research. It was especially hard to explain to the deeply disappointed AIDS activists with whom Merck had opened Communications. Emini and others had been explaining what the company was doing to confront the pandemic, but by then the number of infected persons worldwide was estimated to be somewhere between six and ten million, and in the United States the number of reported AIDS cases had increased more than fivefold. If Emini and Scolnick now had any reason for hope, it was that by 1990 they had learned a great deal about the virus, not only from their own failed efforts but also from research being conducted by thousands of scientists at universities, at the National Institutes of Health, and at other pharmaceutical firms. So far, however, none of them had very much to show for their efforts.

Fortunately, Merck and a small number of other laboratories were conducting research down a third pathway. Looking to the final stage of replication, scientists had found the other major enzyme, the protease, that was crucial to the final assembly of new virus in the infected CD4 cells. The protease enzyme guided the division of viral proteins into what would become a new generation of infectious virions; the virions then attacked other CD4 cells, carrying forward the replication process while impairing the host’s immune system.

At Merck, Dr. Irving Sigal had led the early research on the protease, but in an ugly twist of fate, he had been killed in 1988 in the explosion of Pan Am Flight 103 over Lockerbie, Scotland. Not long after his death Merck’s first protease inhibitor, known as L-689,502 (or simply 502), had failed to pass its safety tests. “The chemists were so depressed,” Ed Scolnick said, “that I stopped having weekly meetings because I knew they couldn’t handle it. I really backed off.”

Not for long, however. Merck was too deeply committed to let go. Besides, the news in 1991 that a major competitor, the Swiss firm Hoffmann-La Roche, might have a successful protease inhibitor sent a tremor through the Merck laboratories. Learning from their competitor and their own unsuccessful approaches, Merck’s scientists once again accelerated the search for an inhibitor that the virus couldn’t defeat.

They stitched together the parts of 502 they thought would be useful and some elements from Hoffmann-La Roche’s new chemical, hoping to create a drug more effective than either. They were helped by a crystallographer named Paula Fitzgerald, who showed that the protease enzyme was essentially symmetrical, which is unusual; this gave them greater flexibility in building crystals. And Kate Holloway, in molecular modeling, was able to construct threedimensional representations of the compounds they came up with and help them work toward one that would have a tight fit with the binding site.

Before long a chemist named Bruce Dorsey developed an especially promising compound. Young and ambitious, he had gotten his Ph.D. in chemistry in 1987 and joined Merck in 1989. He started off in a new direction by changing the compound’s basic ring system, in hopes of increasing bioavailability, the amount of the drug that could reach its target and act. “You can look at it like a tree that has a root system,” he later said, “and only one of the roots is going to get to the water that’s underneath this tree. When you’re going down the trunk, you don’t know which direction is going to lead you to the water source. And so the best thing to do is to be going down in about four or five different directions.” His new direction soon led to the water. Then Dorsey, Scolnick, Emini, and the entire team held their breath while the compound slowly passed through the tests that would tell them whether it would be safe and effective.

All the time the new drug, indinavir sulfate, first known as L-735,524 and later given the trade name Crixivan, was being tested, Emini was wracking his brain over the resistance problem. It could well be safe (it was) and more effective than AZT (it was). It could have the significant advantage of being available in pills instead of shots (it was). But if the virus could successfully mutate around the drug—as it eventually did around AZT and every other drug then available—all their efforts would be in vain. Crixivan worked by binding with the protease enzyme and thus preventing the final stage of viral replication. Suppose a mutant form of the virus no longer needed the protease to reproduce. They would have spent hundreds of millions of dollars and years of laboratory time developing a new drug no better than the products already on the market.

There were other potential problems with Crixivan: It was devilishly complex, and difficult and expensive to make even in the relatively small amounts needed for safety assessment and clinical testing. Creative engineering got it over that hump; someone in the Process Research Department later remarked that they got the job done by running on “Crixivan time.” But as Emini knew, the resistance problem was still someplace down the road. At some time before they received FDA approval to market the drug in the United States, they would know whether the virus had won another battle.

Emini began to discuss HIV resistance with Jon Condra, a biologist. Condra had joined Merck in the early 1980s, after spending several years at the Laboratory of Molecular Genetics in the National Institutes of Health. The two men were a study in contrasts, Emini dark and bearded, his new partner fair and clean-shaven; Emini effusive, Condra reserved. The latter brought to the partnership a dedication to Darwinian biology that bordered on the religious. Thinking about HIV, he anthropomorphized the virus, trying to imagine what it would do to survive if it had a brain and could deliberately try to avoid Merck’s new drug.

After digging into the molecular dynamics of HIV resistance for several years, he concluded that the virus might well develop resistance to Crixivan. He had been surprised to learn how rapidly HIV replicated; it was producing a minimum of a billion new virions a day in an infected person. During the first burst of infection, HIV inserted itself into the chromosomes of the host cells; then, since the immune system couldn’t entirely eradicate it, a long, slow struggle followed, often lasting many years. While this was happening, the patient’s body was producing about the same number of new CD4 cells—a billion—every day. It was during that struggle, initially and erroneously labeled the “latent phase,” that the virus had manifold opportunities to generate mutations, some of which Condra and Emini thought would probably be resistant to Crixivan.

When the clinical trials began, they had a chance to discover if their concerns were realistic. Apparently they weren’t. According to Merck’s tests, the amount of virus in the patients on Crixivan dropped to an astonishingly low level and stayed there for weeks. Condra was suspicious. “Something’s wrong,” he said. “Something’s got to be wrong, you know. It can’t work this well. Nothing works this well. … HIV’s not going to roll over and play dead like that.”

He was right. In the midst of a brutal ice storm in January 1994, he went to the lab in his fourwheel-drive vehicle and, all alone, carefully studied the clinical results from a new, more sensitive test. There were ambiguities in the clinical results that would have to be explained, but the statistics told him that HIV was prevailing.

Eight years and hundreds of millions of dollars into the research, the virus was winning what might well be the last round in Merck’s fight against it. As Condra knew, the laboratories at Hoffmann-La Roche were likely to have a protease inhibitor ready to go shortly, and other pharmaceutical scientists, including those at Abbott Laboratories, were headed down the same trail, looking for a molecule that would bind with the protease enzyme. Condra called Emini and explained what he’d discovered. A thick blanket of gloom settled over their conversation. Emini reached Scolnick at home and gave him the bad news. Scolnick, unable to eat dinner after he heard Emini’s report (his wife said, “I’ve seen you like this before. Just go do whatever it is you want to do.”) and unwilling to admit defeat, called the country’s leading authority on HIV, Anthony Fauci at the National Institutes of Health. Scolnick said, “We have these crazy results,” and described the findings. “Ed,” Fauci said bluntly, “you’ve got resistance.”

A whirlwind of discussion swept through the Merck laboratories starting the next day. From Condra’s perspective, the data on resistance provided a case of “straight Darwinian evolution, the survival of the fittest.” The virus was sloppy. Lacking a “proofreading” enzyme—that is, an enzyme that monitored the reproduction process and eliminated mutant virions—it kept producing errors or mutations as it replicated. These mutations were, as Condra saw it, the virus’s search mechanism as it tried to find a way to survive Crixivan. Relentless replication equaled relentless mutation—and eventually a drug-resistant form of HIV.

When Emini arrived at his first meeting that day, he was so concerned that he began talking even as he entered the conference room. There were anomalies in the data that still had to be explained, he said. While the viral load, the amount of virus in the blood, was increasing, the number of CD4 cells was also remaining high. The immune system wasn’t being weakened in proportion to the increase in the viral load. This hadn’t happened with the previous drugs.

The discussions kept returning to Patient 142, whose viral load had dropped below the level of detection and never increased. For all practical purposes Patient 142 appeared to be cured. If they could do that for one patient, Scolnick said, they could surely do it for others. But unfortunately they didn’t know why the viral load for this one patient had remained so low while it increased for everyone else in the trial.

Emini, Condra, and the rest of the team probed the details of the resistance studies. It was obvious that the virus responded differently to Crixivan than it had to earlier compounds. HIV was at least finding it more difficult to survive. The process of producing a successful mutation had become incremental. Even with replication occurring at the usual high rate, HIV was requiring more than one sequence of genetic mutations to yield a high level of resistance. The scientists had thrown up a barrier, a genetic barrier, to resistance. The virus was now paying a price in efficiency for these changes in its genetic makeup, a fact that helped explain the anomalous findings. As the clinical trials indicated, the drug was giving a boost to the immune system and the vital CD4 cells.

What the team would now have to do, they realized, was make it even more difficult for the virus to complete the process of genetic mutation that was leading to resistance. How? First, by increasing the dosage of Crixivan. Among the patients then in clinical trials, that alone created a higher genetic barrier, making it impossible for the virus to develop resistance in about one-third of those taking the new drug. Sensing that they had at last found where HIV was vulnerable, the Merck team continued down that path.

“Why not,” they asked, “raise the barrier even higher?” They had increased the dosage of Crixivan as much as possible, so they looked elsewhere for help. Perhaps, they decided, they could raise the barrier by adding other antiviral drugs to the treatments. Clinical trials with combination therapy were already under way using other drugs, including AZT and 3TC, two reverse transcriptase inhibitors. By adding Cixivan to the combinations, they would create a more potent “cocktail,” one that made it extremely difficult for the virus to develop drug-resistant strains. To succeed, the virus would have to produce a mutation that could bypass both the reverse transcriptase enzyme and the protease enzyme, a challenge even for HIV.

They were right. By hitting more than one enzyme at once, the new cocktail brought viral loads below the level of detection and kept them there in as many as 85 percent of the patients. As Emini said, “It’s the oncology paradigm. You hit it hard. You hit it up front.”

Out of these experiments, the elaborate clinical trials, and the discussions that swirled about them for many months, Emini, Condra, and the other scientists arrived at three major conclusions by the late summer of 1995. First, a new treatment paradigm was needed for HIV, one that approached the disease as an active persistent infection that could be controlled without being eliminated. Second, combination therapy that attacked the virus at two sites of replication must be more successful than any form of treatment with a single drug. Third, a protease inhibitor like Crixivan or either of two similar drugs approved in 1995 and early 1996 (Roche’s Invirase and Abbott’s Norvir) would play a central role in controlling the disease. Since the protease inhibitors made the virus go through multiple successive mutations to become resistant, physicians could now control that process in most of their patients infected with HIV. They could delay progression to AIDS, perhaps indefinitely.

Announced in early 1996, this new paradigm and the new drugs revolutionized the treatment of HIV and AIDS in the developed world. A full year before that had happened, Merck and its new chief executive, Ray Gilmartin, had already invested the $200 million needed to build a pair of factories to make Crixivan. The drug was difficult to manufacture and would have to be taken in large amounts—probably for a lifetime. Merck would have to produce a million pounds of it a year. The company waded into this challenge even before the clinical trials were over (but not before activists publicly worried Merck wasn’t doing all it could). As Emini put it, “We went out on a limb big time on this one.”

Subsequent events proved it well worth the risk. In the United States a dramatic decline in death rates followed the introduction of combination therapy employing Crixivan and other protease inhibitors. In Europe, too, the new drug cocktails and new concept of treatment produced almost unbelievable results. People who had been preparing their affairs for an imminent death were instead resuming their normal lives. This was happening not just to a handful of the fortunate few but to large numbers of those suffering from AIDS. Those whose infections had not progressed to AIDS now had hope their immune systems could control the infections indefinitely.

Problems still abounded. The search for a vaccine continued at Merck and other laboratories as the pandemic cut an even larger swath through African, Latin American, and Asian populations. The vast majority of those infected in the poorer nations would never be able to afford drug therapy; in some countries they did not even have fresh water, let alone the expensive medical infrastructure required for successful combination treatment. The cost of the new drugs in the United States and elsewhere drew vociferous complaints from activists, physicians, and public health authorities. Meanwhile, the Darwinian struggle for survival continued, and Emini and Condra worried that the virus might someday develop resistance even to the cocktails.

The viral target was still moving. But they could be satisfied for the moment that they and their hundreds of coworkers had hit it squarely, disrupting its smooth progress decisively—at least in the developed world. Ten years of research had yielded a new product, a new therapeutic paradigm, and new hope for millions of patients. That was enough to steady them for the next round in a fight that may never end.