Unraveling HIV’s Resistance to Dolutegravir

The study, led by Salk associate professor Dmitry Lyumkis and his colleagues at the National Institutes of Health, focuses on understanding how changes in the three-dimensional structure of integrase, an essential HIV protein, contribute to resistance against dolutegravir. Integrase plays a critical role in the virus’ ability to insert its genetic material into human cells, allowing it to replicate and spread. Dolutegravir and similar drugs block integrase, preventing HIV from effectively infecting human cells.

Past research from Lyumkis’ lab has provided crucial insights into the structure of the integrase protein and how drugs like dolutegravir interact with it. However, until now, the specific structural changes that occur when the virus becomes resistant to dolutegravir were unknown.

Unveiling the Structural Changes in Integrase

In their new study, Lyumkis and his team engineered different versions of the integrase protein with known mutations that confer resistance to dolutegravir. By analyzing the structure of each mutant protein, the researchers discovered the precise reasons why dolutegravir could no longer bind to and inhibit the function of integrase. This structural understanding provides valuable insights into how the virus evolves to escape the effects of the drug.

Furthermore, the researchers assessed the “fitness” of the dolutegravir-resistant virus strains by measuring their ability to produce infectious offspring. They also examined the enzyme’s activity to gain a better understanding of the factors that contribute to drug resistance in patients.

Unexpected Resistance and Promising Alternatives

One surprising finding of the study was the magnitude of resistance observed in the integrase variants. Lyumkis explains, “Dolutegravir’s ability to function was completely compromised.” This emphasizes the urgent need for novel therapies to combat drug resistance in HIV.

Fortunately, the researchers also tested the efficacy of an experimental HIV drug called 4d, which was developed by Lyumkis’s colleagues at the NIH and is currently undergoing preclinical animal trials. The results were promising, as 4d was able to effectively block the function of dolutegravir-resistant integrase proteins across all tested variants. This suggests that 4d or its derivatives could be potentially used to treat patients who have developed resistance to dolutegravir.

The structural insights gained from studying how 4d interacts with dolutegravir-resistant integrase proteins also provide valuable clues for the development of new drugs that can overcome drug resistance. The researchers observed an intriguing stacking mechanism between a section of the 4d molecule and a section of the integrase protein-DNA assembly. This structural motif could serve as a blueprint for the design of future compounds.

Implications and Future Directions

The research conducted at the Salk Institute and the NIH represents a significant step forward in our understanding of HIV drug resistance. By unraveling the molecular mechanisms behind dolutegravir resistance, this study provides vital insights for the development of new therapies and treatment strategies.

Looking ahead, the next focus for the scientists involved will be investigating how integrase variants continue to evolve. This research will aim to anticipate and understand the emergence of new resistant strains that may appear in the future. By studying these variants and their effects on patients’ responses to clinically used drugs, researchers hope to gain a comprehensive understanding of how HIV evolves and adapts.

Conclusion

The recent breakthrough at the Salk Institute and the NIH holds tremendous promise for the future of HIV treatment. The discovery of the molecular mechanisms underlying HIV resistance to dolutegravir provides a solid foundation for the development of new antiviral therapies and the fight against drug resistance.

As we continue to deepen our understanding of the complex interplay between HIV and antiviral drugs, researchers like Lyumkis and his colleagues pave the way for innovative approaches to combat the virus and offer hope to millions of individuals affected by HIV worldwide.

The new study, published on July 21, 2023 in Progress of sciencereveals how changes in the 3D structures of integrase, an HIV protein, can lead to resistance to dolutegravir and how other compounds can overcome this resistance.

“With HIV, you have to think two steps ahead of the virus,” says Salk associate professor Dmitry Lyumkis, co-senior author and chair of development at the Hearst Foundation. “We have now determined how the virus could continue to evolve against drugs such as dolutegravir, which is important to consider for the development of future therapies.”

HIV infection depends on the virus’s ability to paste its own genetic material into the genomes of human cells, essentially hijacking the cells to turn them into virus-producing factories. Dolutegravir and related drugs block integrase, a protein critical to the virus’s ability to integrate its own DNA into the host’s genome. Without a functional integrase, HIV cannot effectively infect human cells. However, HIV is a rapidly mutating virus and an increasing number of HIV strains are resistant to dolutegravir.

In the past, Lyumkis’ lab has discovered the 3D structure of the integrase protein as it binds to DNA, as well as exactly how 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 colleagues at the National Institutes of Health created versions of the integrase protein with mutations known to make HIV resistant to dolutegravir. They then determined the structure of each mutant integrase, revealing why dolutegravir could no longer bind to and block each version of the protein. The scientists also tested the “fitness” of the virus (its ability to produce infectious offspring) and the enzyme’s activity to better understand what leads to drug resistance in patients.

“We were quite surprised by the magnitude of the resistance that these integrase variants had,” says Lyumkis. “Dolutegravir’s ability to function was completely compromised.”

The researchers also tested the efficacy of an experimental HIV drug, 4d, in blocking the function of dolutegravir-resistant integrase proteins. 4d was developed by Lyumkis’s collaborators at the NIH as a next-generation integrase-targeted drug and is currently in preclinical animal trials. Across all variants, they found that 4d still powerfully blocked HIV’s ability to integrate its genes into human cells. This suggests that 4d or variants of this compound can be used effectively to treat the virus in patients who have developed resistance to dolutegravir.

The structural data on how 4d binds to dolutegravir-resistant integrase proteins also hinted at how new drugs might overcome drug resistance.

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

Next, the scientists will study how integrase variants evolve, including those that have not yet been seen in patients but may occur in the future, and how they affect response to the best clinically used drugs, as well as the ability of HIV 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 Choudhuri, Allan Haldane, and Ronald M. Levy of Temple University; Nanjie Deng of Pace University; and Lorenzo Briganti and Mamuka Kvaratskhelia of the University of Colorado Anschutz Medical Campus.