Unraveling the mechanism of HIV drug resistance through protein structure

LA JOLLA (July 21, 2023)—Researchers from the Salk Institute, in collaboration with the National Institutes of Health, have discovered the molecular mechanism by which the human immunodeficiency virus (HIV) becomes resistant to Dolutegravir, one of the most effective antiviral drugs clinically used to treat HIV.

The new study, published July 21, 2023 in Science Advancesreveals how changes to the 3D structure of integrase, an HIV protein, can lead to Dolutegravir resistance and how other compounds can overcome this resistance.

“With HIV, one has to think two steps ahead of the virus,” said Salk Associate Professor Dmitry Lyumkis, one of the senior authors and the Hearst Foundation Development Chair. “We have now determined how the virus can continue to thrive against drugs like Dolutegravir, which is an important consideration for future therapeutic development.”

HIV infection relies on the virus’ ability to attach its own genetic material into the human cell’s genome, essentially hijacking the cell to become a virus-producing factory. Dolutegravir and related drugs work by blocking the integrase, a protein that is critical to the virus’ ability to integrate its own DNA into the host’s genome. Without a functioning integrase, HIV cannot effectively infect human cells. However, HIV is a rapidly mutating virus, and a growing number of HIV strains are resistant to Dolutegravir.

In the past, Lyumkis’ lab discovered the 3D structure of the integrase protein when it attaches to DNA as well as how exactly drugs like Dolutegravir bind to and block integrase. But the researchers weren’t sure how the structure of the integrase changed when the virus stopped responding to Dolutegravir.

In the new study, Lyumkis and collaborators from the National Institutes of Health created a version of the integrase protein with a mutation known to make HIV resistant to Dolutegravir. Then they determined the structure of each integrase mutant, uncovering why Dolutegravir could no longer bind and block each version of the protein. Scientists also evaluate the virus’ “fitness” (its capacity to produce infectious progeny) and enzyme activity to better understand what causes drug resistance in patients.

“We were quite surprised by how much resistance this integrase variant has,” said Lyumkis. “Dolutegravir’s ability to function is severely impaired.”

The researchers also tested the efficacy of an experimental HIV drug, 4d, to block the function of Dolutegravir-resistant integrase protein. 4d was developed by collaborator Lyumkis at NIH as a next-generation integrase-targeting drug and is currently in pre-clinical animal trials. In all variants, they found that 4d still blocked HIV’s ability to integrate its genes into human cells. This suggests that 4d or a variant of this compound could be used effectively to treat the virus in patients who have developed resistance to Dolutegravir.

Structural data on how 4d binds to the Dolutegravir-resistant integrase protein also hint at how the new drug might overcome drug resistance.

“4d is really just an example of how to fight drug resistance, but it gives us some basic principles that we can learn from to design other therapies,” said co-senior author Robert Craigie of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), part of the National Institutes of Health. “The way the sections of the 4d molecule stack like a flat sheet on top of the protein-DNA integrase assembly section can be replicated in other compounds.”

Next, scientists will study how integrase variants evolve—including those not yet seen in patients but possibly in the future—and how they affect response to the best clinically used drugs and HIV’s ability to infect humans.

Other authors include Dario Oliveira Passos, Zelin Shan, Avik Biswas and Timothy S. Strutzenberg of Salk; Min Li, Zhaoyang Li, Steven J. Smith, Xue Zhi Zhao, Terrence R. Burke, Jr. and Stephen H. Hughes of the National Institutes of Health; Qinfang Sun, Indrani Choudhury, Allan Haldane, and Ronald M. Levy of Temple University; Nanjie Deng of Pace University; and Lorenzo Brigantine and Mamuka Kvaratskhelia of the University of Colorado Anschutz Medical Campus.

This work was supported by National Institutes of Health (U01 AI136680, R01 AI146017, U54 AI170855, R35 GM132090), NIDDK Intramural Program, Margaret T. Morris Foundation, Hearst Foundation, NIH Intramural Program, Cancer Research Center, National Cancer Institute, NIH Intramural AIDS Targets Program, and Postdoctor F32 al Fellowship (GM148049).

The content in this release is the responsibility of the authors and does not represent the official views or imply enforcement of the National Institutes of Health.