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.
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| 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.
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"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.
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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. |
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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.
ABOUT SDSC
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 http://www.sdsc.edu/.
Related Links
The McCammon research group at UCSD - http://mccammon.ucsd.edu/
The Biomedical Sciences Graduate Program - http://biomedsci.ucsd.edu/
National Biomedical Computational Resource (NBCR) - http://nbcr.sdsc.edu/
Howard Hughes Medical Institute (HHMI) - http://www.hhmi.org/
San Diego Supercomputer Center (SDSC) - http://www.sdsc.edu/
Background on HIV-1 Protease - http://www.rcsb.org/pdb/molecules/pdb6_3.html
