A common hallmark of viral genome replication is a high mutation rate, which can aid in their ability to evade new treatments and acquire resistance to once-effective antiviral medications. Now, a new study uncovers one of the mechanisms herpes simplex virus (HSV) uses to become resistant to treatment. Using cryogenic electron microscopy (cryo-EM), researchers revealed how conformational changes in the viral DNA polymerase alter the virus’s susceptibility to drugs.
The new findings further the understanding of how alterations in the conformation of a viral protein fuel drug resistance and may be relevant for understanding drug effectiveness and drug resistance in other viruses, the researchers noted. It also answers long-standing questions about why certain viruses, and not others, are susceptible to antiviral medications and how viruses become impervious to drugs.
“Our findings show that we have to think beyond targeting the typical drug-binding sites,” said Jonathan Abraham, PhD, associate professor of microbiology at Harvard Medical School and HHMI investigator. “This really helps us see drug resistance in a new light.”
The findings are published in Cell in the paper, “Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance.”
HSV, estimated to affect billions of people worldwide, is well known as the cause of cold sores and fever blisters, but it can also lead to serious eye infections, brain inflammation, and liver damage in people with compromised immunity. Additionally, HSV can be transmitted from mother to baby via the birth canal during delivery and cause life-threatening neonatal infections.
It is well known that DNA polymerases are important drug targets. In addition, there has been a lot of work done to capture them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational dynamics on drug resistance has been lacking.
The HSV polymerase is the target of acyclovir, the leading antiviral drug for treating HSV infection, and of foscarnet, a second-line drug used for drug-resistant infections.
Abraham’s group sought to understand how alterations in the polymerase render the virus impervious to normal doses of antiviral drugs and, more broadly, why acyclovir and foscarnet are not always effective against the altered forms of the HSV polymerase.
“Over the years, the structures of many polymerases from various organisms have been determined, but we still don’t fully understand what makes some polymerases, but not others, susceptible to certain drugs,” Abraham said. “Our study reveals that how the different parts of the polymerases move, known as their conformational dynamics, is a critical component of their relative susceptibility to drugs.”
Structural analysis paired with computational simulations suggested that several mutations that are distant from the sites of drug binding confer antiviral resistance by altering the position of the polymerase fingers responsible for closing onto the drug to halt DNA replication.
The finding was an unexpected twist. Up until now, scientists have believed that polymerases closed partially only when they attached to DNA and closed fully only when they added a deoxynucleotide. It turns out, however, that HSV polymerase can fully close just by being near DNA. This makes it easier for acyclovir and foscarnet to latch on and stop the polymerase from working, thus halting viral replication.
“I’ve worked on HSV polymerase and acyclovir resistance for 45 years,” noted Donald Coen, PhD, professor of biological chemistry and molecular pharmacology at HMS. “Back then I thought that resistance mutations would help us understand how the polymerase recognizes features of the natural molecules that the drugs mimic. I’m delighted that this work shows that I was wrong and finally gives us at least one clear reason why HSV polymerase is selectively inhibited by the drug.”
