Press Archive

SDSC Resources Help Scientists Identify Possible Source of HIV Drug Resistance

Published 03/25/2004

Protein Science - April 2004, Volume 13, Issue 4, 1108-1123

In just over two decades, the death toll from AIDS has passed twenty million. And the AIDS crisis continues with the disease infecting people around the world, including millions of children. In the late 1980s and early 1990s, after years of frustration, AIDS researchers succeeded in developing a class of drugs known as protease inhibitors that proved to be highly effective against AIDS. By blocking the activity of the viral enzyme HIV protease, which is essential for the virus to reproduce, protease inhibitors brought greatly extended life-spans to patients who had previously faced early deaths.

In recent years, however, mutant strains of HIV have shown increasing resistance to some or all of these formerly effective drugs. Now, scientists in the McCammon research group at University of California, San Diego have used molecular simulations to take an important step forward in the fight against AIDS. In research using the facilities of the San Diego Supercomputer Center (SDSC), the researchers have identified a potential mechanism underlying the drug resistance of the worst mutant HIV strain. In the same research, reported as the cover article in the April 1 Protein Science journal, the scientists also identified a separate region of the protease enzyme that might serve as a new target for drugs that could restore the effectiveness of today's protease inhibitor drugs and also help block the reproduction of HIV by themselves.

HIV-1 Protease
This enzyme, which essential for HIV to reproduce, is the target of successful AIDS drugs known as protease inhibitors. Emerging mutant HIV strains are showing resistance to these drugs. The wild type protease is shown in green, and the drug-resistant double mutant in purple, with the mutant side chains shown as red sticks. Analyses of the structural dynamics of these molecules, including the flaps that form the top of the binding site, and the "Ear to Cheek" region, have led researchers to a possible explanation for the mutant's drug resistance as well as a potential new target site for new drugs.

"The first step in overcoming the drug resistance of the mutant HIV strains is to understand the resistance mechanism," explained Alexander Perryman, first author of the paper and a graduate student in the research group of Professor J. Andrew McCammon of the Biomedical Sciences Program at UCSD. "The results we've obtained, if confirmed, can give important guidance in searching for new drugs to restore the effectiveness of today's protease inhibitors and help fight HIV." For their simulations, the researchers chose one of the worst mutants, the V82F/I84V double mutant of HIV-1 protease, which is between 11 and 2,000 times less likely to bind with current protease inhibitor drugs, significantly weakening their effectiveness in treating HIV.

"We hope that these results will have significant practical importance in the fight against AIDS," said McCammon, a Howard Hughes Medical Institute investigator and UCSD professor of Pharmacology who holds the Joseph Mayer Chair of Theoretical Chemistry at UCSD. "At the same time, they're also an important demonstration of the power of computational science and technology for rapidly advancing our understanding of both fundamental biology and rational drug design." The research team also included Jung-Hsin Lin, an Assistant Professor in the School of Pharmacy at National Taiwan University.

The research is part of a broad program of computational science by the McCammon group that can help guide or in some cases replace costly lab methods that require thousands of trials of different molecules. The computationally intensive research makes use of SDSC supercomputers, including the Meteor Cluster, the Keck satellite clusters, operated by SDSC, and the largest-scale machines such as Blue Horizon, the TeraGrid, and DataStar. In addition, the researchers store data in SDSC's High Performance Storage System, the world's largest academic production storage archive. "Having access to the cutting-edge facilities at SDSC is a key factor in making our research program feasible, as we work to understand the underlying biology and enable rational drug design," said McCammon.

Drugs are typically small molecules that bind tightly to a target receptor protein, either inhibiting or enhancing the protein's activity. Modern drug designers usually begin with a crystallized sample of the receptor protein. But as the HIV research community has sought to find the mechanisms that underlie the growing resistance of mutant strains of HIV, the traditional method of looking at static crystal structures has yielded little insight. This can be because such methods typically treat the crystal structure as a rigid object, when in reality the HIV protease molecule is always undergoing complex changes in shape at room temperature.

The present study has successfully harnessed computer simulations to analyze the dynamic properties and changing shapes of the protease molecule as it wiggles and jiggles. The researchers performed molecular dynamics simulations of both wild type (un-mutated) and mutated HIV-1 protease for a period of 22 nanoseconds - 22 billionths of a second, enough time for many thousands of oscillations in the fast-paced world of a protein molecule. To build a comprehensive ensemble or array that represents the range of motion in the molecules important for drug binding, they sampled 11 million slightly different shapes of each protease molecule, analyzing 22,000 of those conformations from each system.

Drug Resistance and Increased Flap Opening
Simulations of the molecular dynamics of HIV protease have yielded evidence that the growing resistance of mutant HIV strains to today's most effective drugs may be related to increases in the opening behavior of the flaps forming the top of the drug binding site. This image shows the most open configurations of both the wild type (purple) and mutant (red) compared to their initial shapes. Green shows the configuration when the simulations began. Note that both of the mutant's flaps opened up much further than the wild type's flaps.

New Drug Target
The most open flap configuration (purple, red) and the most closed flaps (green) in the wild type simulation. The researchers noticed that the closed flaps occur in correlation with an expanded Ear to Cheek peripheral region (green ribbon on the right), and the open flaps correlate with a pinched Ear to Cheek region (red and purple ribbons on the left). This relationship suggests the Ear to Cheek region as a potential target for new types of drugs that could regulate flap opening and closing, possibly restoring the effectiveness of today's drugs and acting as treatments in themselves.

The binding site on HIV protease for the current drugs has "flaps" that open and close, and the simulations revealed that the drug-resistant mutant displayed more rapid and more frequent curling behavior of the tips of the flaps, and that the binding site's flaps also tend to open more. As a consequence, when an AIDS drug is in the process of binding to the mutant HIV protease, the drug must pay a larger energetic penalty to force the flaps to close. This may explain why that mutant is able to resist all of the different protease drugs currently used, since there is a far steeper "energy hill" for the drug molecule to climb for successful binding to the mutant strain of HIV.

In addition to shedding light on the question of how the mutant HIV so effectively resists a number of different drugs, by observing the coordinated dynamics of the protease molecule the researchers were also able to locate a new site on the surface of HIV protease that has the potential to serve as a target for drugs known as allosteric inhibitors. Allosteric inhibitors work by causing changes at a different region of the HIV protease from where they bind.

"We realized that this result points to two new possible types of drugs that would bind to the newly identified site on the protein," said Perryman. "One new drug could keep the flaps open, and the other could keep the flaps closed." Such drugs have the potential both to improve the effectiveness of the protease drugs currently given to HIV patients as well as to be useful drugs by themselves. "This is very exciting," Perryman explains. "Our research can provide valuable guidance in developing these new allosteric inhibitor drugs, which could help humanity evade the drug-resistant strains of HIV now casting a shadow over the lives of so many infected individuals around the world."

The research was supported by the Howard Hughes Medical Institute, the National Science Foundation (NSF), the National Institutes of Health, the W. M. Keck Foundation, the National Biomedical Computation Resource at SDSC, and Accelrys, Inc. Alex Perryman is a Howard Hughes Medical Institute Pre-doctoral Fellow.

The mission of the San Diego Supercomputer Center (SDSC) is to innovate, develop and deploy technology to advance science. SDSC is involved in an extensive set of collaborations and activities at the intersection of technology and science whose purpose is to enable the next generation of scientific advances. Founded in 1985 and primarily funded by the National Science Foundation (NSF), SDSC is an organized research unit of the University of California, San Diego. With a staff of more than 400 scientists, software developers, and support personnel, SDSC is an international leader in data management, grid computing, biosciences, geosciences, and visualization. For more information, visit

Related Links

The McCammon research group at UCSD -
The Biomedical Sciences Graduate Program -
National Biomedical Computational Resource (NBCR) -
Howard Hughes Medical Institute (HHMI) -
San Diego Supercomputer Center (SDSC) -
Background on HIV-1 Protease -