The human immunodeficiency virus (HIV) is a
clever virus that has learned to evade even some of the best drugs on the
Salk Institute scientists have solved the atomic structure of a key
piece of machinery that allows HIV to integrate into human host DNA and
replicate in the body, which has eluded researchers for decades. The
findings describing this machinery, known as the "intasome," appear in Science
and yield structural clues informing the development of new HIV drugs.
‘The atomic structure of a key piece of machinery that allows HIV to integrate into human host DNA and replicate in the body has been solved by Salk scientists.’
"We're particularly excited about the ability to understand and
combat mechanisms of viral resistance," says the study's senior author
Dmitry Lyumkis, a Helmsley-Salk Fellow at the Salk Institute. "Understanding the mechanisms of viral escape and developing
more broadly applicable drugs will be a major direction in the future."
Currently, a class of drugs called integrase strand transfer
inhibitors (INSTIs) targets the intasome and are already approved to
treat HIV in the U.S. and Europe. Despite being some of the best drugs
available, scientists have only gained a limited understanding of the
precise mechanism of action of INSTIs, and how the virus mounts
resistance, by the inference of structures of a similar retrovirus
(called the prototype foamy virus or PFV). That's because the HIV
intasome itself has been notoriously difficult to study at the atomic
"Now we have the very first native blueprint in the context of HIV
for studying the mechanisms of INSTIs," says Lyumkis. He and his
collaborators are already using the discovery to try to improve the
ability of INSTIs to block the virus-"and industry researchers will
likely do the same," he adds.
As a retrovirus, HIV inserts a DNA copy of its RNA genome into the
host's DNA using the intasome, which cuts and pastes viral DNA using
enzymes called integrases. In 1994, scientists determined the structure
of a small part of the integrase enzyme. Since then, biologists have
solved several other pieces of the HIV integrase, as well as the
intasomes from other retroviruses. But the entire structure of the HIV
intasome remained difficult to solve using conventional techniques.
In the new study, Lyumkis and colleagues used a cutting-edge imaging
technique called single-particle cryo-electron microscopy (cryo-EM),
which has increasingly allowed scientists to image large, complex and
dynamic molecules (see Lyumkis's previous development in this area
here). The team attached a specific protein to improve the intasome's
ability to dissolve in liquid and bathed the intasome in a syrup-like
liquid called glycerol, with loads of salt added to prevent it from
clumping. These are extreme conditions for a cryo-EM sample, but they
were necessary in the case of the HIV intasome. Then, building upon
novel technical advances in the field, the scientists cranked up the
cryo-EM machine to spray even more electrons at their sample than usual.
All retroviral intasomes have core structural components that
perform the integration function. The group noticed some differences
when they compared the enzyme cores of HIV with those of PFV. "Although
these variations are minor, they could be a big deal for drug
development and for understanding mechanisms of drug resistance," says
the study's first author, Dario Passos, a senior research associate in
To the group's surprise, HIV intasomes are also more intricate and
complex than other retroviruses. Scientists already knew that they had a
four-part core, but the new study finds that HIV intasomes have many
more units, what they call "higher-order" species. Evidence suggests
that more complex versions of the intasome serve a purpose in helping
HIV integrate itself within the host genome.
Lyumkis says the HIV intasome's complexity hints at how nature has
shaped its evolution from simpler retroviruses, which are considerably
smaller, yet still use the same core pieces of enzyme. HIV can perform
functions that its relatives can't, such as gain access to the cell's
nucleus through active transport rather than having to wait for the cell
to divide. "HIV is like the luxury car whereas other retroviruses are
the economy models-they're both cars, but the HIV intasome contains
important upgrades to do different jobs," he adds.
Based on the different structures present in the samples, the team
thinks that the HIV intasome could take multiple routes for assembly.
"That's speculative at this point, but it's an intriguing possibility
and would build upon mounting evidence that certain macromolecular
machines take different routes to assemble the final product," Lyumkis
says. (Another large molecular machine called the ribosome also
assembles in different ways, according to a separate cryo-EM study by
The current study focused on intasomes after they assemble on host
DNA, but future work will study the structures prior to their landing on
the host genome and in the context of bound drugs. To this end, the
group is also working to push the resolution of their structures higher,
from ~4 Angstrom resolution in the new study to ~2 Angstrom, which
would allow them to see the chemical bonds in water molecules for
example, proving crucial insight for drug discovery and development.
"Taking the car analogy further, if you really want to understand
how the car works in order to modify its performance, you can't just
look at a whole engine. You have to take it apart and dig inside to
really understand it inside out," Lyumkis says.
"We must do the same with these complex molecular structures to better understand-and target-viruses," adds Passos.