TSRI scientists devise new way to boost RNA treatment potency

JUPITER, Fla.— While targeting DNA has been used as atherapeutic strategy against cancer, few similar approaches have been attemptedfor disease-associated RNAs. Scientists from the Jupiter, Fla. campus of TheScripps Research Institute (TSRI) are changing that with the publication of astudy describing a novel way to dramatically raise the potency of drugcandidates targeting RNA, resulting in a 2,500-fold improvement in potency andsignificantly increasing their potential as therapeutic agents.

The study, "Induction and Reversal of Myotonic DystrophyType 1 Pre-mRNA Splicing Defects by Small Molecules," was recently publishedonline ahead of print by the journal AngewandteChemie, and confirms for the first time that a small molecule actuallybinds to a disease-causing RNA target—a breakthrough that should helpscientists identify precise RNA targets within living cells, profile theirinteractions and predict drug candidates' side effects, according to MatthewDisney, a TSRI associate professor who led the research.

"Many people think RNA is an undrugable target," Disneysays. "The main focus of our lab is to demystify this and develop rationalmethods to target RNA with small molecules."

In the lab's most recent work, Disney and his colleaguesreport on two small molecules that induce or ameliorate alternative splicingdysregulation. The ability to control pre-mRNA splicing with small moleculescould facilitate the development of therapeutics or cell-based circuits thatcontrol gene function. Pre-mRNA splicing defects cause a wide variety ofdiseases, including beta-thalassemia, inherited breast cancer, fragileX-associated tremor ataxia syndrome (FXTAS) and myotonic dystrophy types 1 and2.

In particular, myotonic dystrophy type 1 involves a type ofRNA defect known as a "triplet repeat," a series of three nucleotides repeatedmore times than normal in an individual's genetic code. In this case, therepetition of the cytosine-uracil-guanine (CUG) in the RNA sequence leads todisease by binding to a particular protein, MBNL1, rendering it inactive andresulting in a number of protein-splicing abnormalities.

Disney's lab created a small molecule that binds to thegenetic defect in RNA that causes myotonic dystrophy type 1 and improvesassociated defects in cell culture.

"We didn't choose myotonic so much as it chose us," Disneynotes. "We have been studying myotonic for a long time, and we got into thisarea of research by establishing a database of RNA-folding small-moleculeinteractions. It turned out that this was one small molecule with the highestaffinity, which presented a bottom-up way of designing drugs."

They then attached a reactive molecule (a derivative ofchlorambucil, a chemotherapy drug that has been used to treatment a form ofleukemia) to the small molecule they had identified. The new compound bound tothe target, but more importantly, became a permanent part of it—and onceattached, it switched off the CUG defect and prevented the cell from turning itback on.

"I was shocked by the 2,500-fold increase," Disney says,"but it was extremely gratifying."

The new compound, known as 2H-4-CA, is the most potentcompound known to date that improves DM1-associated splicing defects.Importantly, 2H-4-CA does not affect the alternative splicing of a transcriptnot regulated by MBNL1, demonstrating selectivity for the CUG repeat andsuggesting that it might have minimal side effects.

According to Disney, this approach can be used to attachreactive molecules to other RNA-targeted small molecules.

"We're trying to take the genomics-to-therapeutics approachfull cycle," Disney says. "Our main goal is to develop tools that allow us totarget the RNA that cause disease, and quickly and effectively develop drugs totreat those diseases."

Disney anticipates a follow-up paper describing the designof RNA-targeted small molecules in cancer cells will be published soon.

The study was supported by the U.S. National Institutes ofHealth.