Controlling DNA Scanning Machines to Slow Expansion of CAG Repeats

A team of scientists have discovered small molecules that block the DNA repair protein MSH3, thought to be a key driver of repeat expansion in Huntington’s disease (HD). Although still at an early stage, this work opens the door to a new kind of therapeutic strategy: slowing down HD before symptoms begin. Let’s get into what they found. 

Unstable C-A-Gs

HD is caused by an extra-long stretch of DNA C-A-G letter repeats in the huntingtin gene. The longer the repeat, the earlier symptoms tend to begin. But it’s not just the inherited repeat length, also called a CAG number, that matters. These DNA repeats can grow even longer during a person’s lifetime in some cells in the body by a process called somatic instability. Many researchers are working to understand how expanding DNA repeats contribute to disease. A leading hypothesis is that faster repeat expansion may lead to faster disease progression.

This idea is supported by findings from large-scale genetic studies in people with HD, which have identified additional genes, beyond the huntingtin gene, that influence when symptoms begin. Many of these so-called modifier genes are involved in a biological process called DNA repair that keeps unwanted DNA changes in check. Of particular interest to HD researchers are the DNA repair modifiers involved in the pathways thought to drive and control somatic instability. 

A new drug target: MutSβ and MSH3

One of these DNA repair modifier genes encodes the protein MSH3. MSH3 is an attractive possible drug target because it plays a central role in recognising DNA errors that lead to CAG repeat expansions. Importantly, blocking it from working is thought to be unlikely to raise cancer risk, unlike some of the other modifiers found so far.

MSH3 teams up with another protein, MSH2, to form a complex called MutSβ (pronounced mute S beta). The MutSβ molecular machine uses energy in the form of ATP, a type of cellular “fuel”, to scan DNA for mistakes. 

Although MutSβ normally helps cells by spotting and fixing certain kinds of DNA errors, in the case of HD it can actually make things worse. The MutSβ machine can mistakenly act at CAG repeats in the huntingtin gene and rather than protecting DNA, causing repeats to get longer over time through somatic instability. 

So, while MutSβ is generally “helpful” for DNA repair, in the special context of CAG repeats its activity can backfire. The scientists reasoned that if small molecules could block how MutSβ uses the ATP fuel, they might be able to stop this molecular machine from working. This might then help reduce CAG repeat expansions, which could delay when signs and symptoms of HD begin.

A needle in a haystack

The research team developed a sensitive test to measure how well MutSβ was working in a test tube and then screened an enormous library of almost one million different chemical compounds to see which might stop it working. 

In this first round of screening, they identified thousands of candidate molecules, but most turned out to be false positives or weak inhibitors.

The team improved their screening methods to weed out artifacts. This included things like “sticky” molecules that get stuck on lots of different proteins, not just MutSβ. After these filtering steps, just 11 promising compounds remained.

With this shortlist, the team looked at exactly how they stuck to MSH3, compared to other related proteins. They found several compounds only stuck to MSH3 and not closely related proteins like MSH2 or MSH6, reducing the risk of possible cancer-related side effects.

Seeing the molecules at work

The researchers didn’t just stop at finding hits. They used special microscopes and other tools in the lab to see exactly how the small molecules stuck to MSH3 in atom-by-atom resolution. 

These structural snapshots confirmed that the compounds act in the expected way, by blocking the ATP fuel from being used by MutSβ. By “seeing” exactly how the compounds work, the scientist can now make informed decisions about how they can make them even better in the future. 

Why this matters for HD

These results are an early but exciting step toward drugs that could slow or prevent CAG repeat expansions, potentially delaying HD onset. 

The identified molecules are a long way from being ready for the clinic. Their properties would have to be substantially improved to ensure they worked inside cells and eventually in people, rather than just in a test tube. 

But thanks to the data shared by this team, scientists in this group and drug hunters from around the world can make rational decisions about how best to do this as quickly and as efficiently as possible. 

The road ahead

This study shows that MSH3 can indeed be drugged, and it provides the first molecular blueprints for exactly how to do it. 

There’s still a lot to do to improve the drug-like properties of these compounds and make sure they don’t have any unwanted side effects. Even then, we don’t yet know for sure if blocking MSH3 with this type of therapeutic will actually reduce somatic instability in cells or animal models of HD, or most importantly, whether this will slow or halt the signs and symptoms of HD in people.

The good news is that there are a lot of different teams working in this space to try and solve these problems. This includes the biotech company, Loqus23 ,and the pharma company Pfizer, as well as lots of academic teams of scientists. 

Together, their efforts are steadily advancing the search for therapies that target a possible genetic driver of HD progression.

Summary 

• CAG DNA repeats expand in some cells over the lifetime of someone with HD through a process called somatic instability.
• The DNA repair protein MSH3, part of the MutSβ complex, is a driver of repeat expansion and an attractive drug target.
• Scientists screened nearly one million compounds and identified a handful that specifically block MSH3 from working. 
• These molecules are early-stage tools, but provide the first blueprints for drugging MSH3 to potentially treat HD. 

Learn more

“Orthosteric inhibition of MutSβ ATPase function: First disclosure of MSH3-bound small molecule inhibitors”, (paid access).