Salk scientists’ breakthrough in understanding HIV genetic structure

Originally published in the La Jolla Village News.

Dmitry Lyumkis’ lab at the Salk Institute for Biological Studies serves numerous purposes. Still, one of their main goals is to determine complex viruses' structure and genetic makeup. Recently, advances in technology, especially molecular 3D imaging, have allowed Lyumkis and his team to reconstruct the composition and density of HIV cells.

Although the team published their findings in early January, this information required years of research at Salk and other institutions to achieve this breakthrough.

The critical issue at hand was the building up of intasomes, the molecular machinery that enables HIV to irreversibly integrate its genetic material into host immune cells in the body. Salk researchers captured the structure of the complex intasome that lets HIV and similar viruses establish permanent infection in their hosts. The intasome hijacks host genetic material and irreversibly inserts viral DNA.

While other researchers have come close to mapping out these structures before, it took significant increases in biochemistry and technology to view these molecular compositions in the third dimension.

“This is truly the first atomic-level blueprint for understanding how intasomes target host cells,” said Lyumkis, a Helmsley Fellow at the Salk Institute. “Furthermore, this allows us to modify treatments or understand how the HIV virus learns to evade current therapies.”

Lyumkis explained that before the breakthrough, their working understanding of HIV was derived from another retrovirus, the prototype foamy virus (PFV).

“In solving the HIV intasome, essentially we are completing the atomic blueprint of the viral machinery,” Lyumkis said. “What we need to do, is understand this structure at the molecular level. Now, with our data, we can better understand how drugs targeting intasomes work. This way, we can create new drugs or improve existing ones.” 

Currently, there are existing treatments on the market, as seen in a class of drugs called integrase strand transfer inhibitors (INSTIs). This drug targets the intasome and has already been approved to treat HIV in the U.S. and Europe.

Although these drugs work, scientists have only been able to gain a “limited understanding” of the mechanism of action of INSTIs, and how the virus mounts resistance by the interference of structures of the similar retrovirus, PFV. In their most recent study, the Lyumkis team utilized a cutting-edge imaging technique called “single-particle cryoelectron microscopy (cryo-EM).”

This technology has allowed scientists to create images of large, complex and dynamic molecules. In their comparison of HIV with PFV enzyme cores, the original author and senior researcher, Dario Passos, commented: “Although these molecular variations are minor, they could be a big deal for drug development and understanding drug resistance.”

Lyumkis further notes that while some effective drugs are already on the market, they aim to find those with very low-resistance profiles. He says several compounds are already under development in collaborating labs. When it comes to the third-dimensional characterization of the molecular machinery within the HIV-1 virus, Lyumkis says that his team uses “many different” programs, which can be divided into two general classes.

These classes are comprised of programs that recover the 3D density of the molecular complexes and those that build and refine atomic coordinates into the density. Once all of this data is mapped out in a high-definition model, they can view the virus's molecular components in their natural state.

To the group’s surprise, they discovered that HIV intasomes are “much more intricate and complex than other retroviruses.” Lyumkis notes that the HIV intasome’s complexity hints at how nature shaped its evolution from simpler retroviruses. Although HIV intasomes are much larger, they all use core pieces of a similar enzyme.

“HIV is like the luxury car, whereas other retroviruses are the economic models,” said Lyumkis. “They’re both cars, but the HIV intasome contains necessary upgrades to do different jobs.Taking the car analogy further, if you want to understand how the car works to modify its performance, you can’t just look at a whole engine. You must take it apart and dig inside to understand it inside out.”