RNA drugging strategies beyond oligos shaping up

Pers / media: OverigPopular


A Polish/Dutch team of investigators has reported new insights into the structure of the SARS-CoV-2 genome that suggests it could be amenable to both small-molecule and oligonucleotide drugs. The work, which was published in the November 10, 2020, issue of NucleicAcids Research, is part of a growing body of work that suggests small molecules could be a broadly useful approach to targeting RNA.

The studies focused purely on the structural features of the SARS-CoV-2 genome and did not attempt to find either small molecules or ASOs that could bind the sites that looked to be druggable.

But co-corresponding author Danny Incarnato, who is an assistant professor at the University of Groningen, noted in a prepared statement that if such small molecules can be identified, they might be useful beyond SARS-CoV-2.

"A number of the structures are conserved between different coronaviruses, meaning that a successful drug targeting SARS-CoV-2 could also be effective against future new virus strains," he said.

The most striking aspect of RNA, and DNA, is its sequence, or secondary structure. Finding a sequence that is specific to a disease, and targeting that sequence via a nucleic acid with a complementary sequence, is a way to precisely target nucleic acids that is straightforward in principle.

Tertiary structure, or the shapes that RNA folds into, have received much less attention overall. Partly, this is because those shapes are typically less stable than in proteins. Another reason is that binding pockets, which account for some of the greatest successes of small molecules, are not as common in RNA molecules. Nor does RNA function as receptors -- another protein structure where the targeting abilities of small molecules can shine.

As a result, using small molecules to target RNA has long been "an afterthought," Matthew Disney told BioWorld Sciencerecently. Disney is a professor of Chemistry at Scripps Research Institute, Florida Campus, where his work focuses on identifying RNA-targeting small molecules and developing methods that are suited to identifying drug-like RNA-small molecule interactions.

The first such small molecule targeting RNA was approved by the FDA in September 2020. Evrysdi (risdiplam; Roche) is an orally available drug approved for the treatment of spinal muscular atrophy.

The ability to target RNA with small molecules has the potential make an enormous difference in the fight against infections cause by RNA viruses. Because RNA replication lacks some of the error correction machinery of DNA replication, such viruses can mutate rapidly, making them extremely challenging as far as both drug and vaccine development are concerned.

The most striking current example is, of course, SARS-CoV-2 and the COVID-19 pandemic. Even as vaccines are being developed at record speed, estimating how long their protection will last remains impossible at this point.

Influenza and HIV are two other examples of single-stranded RNA viruses whose rapid mutations are part of the reason they remain formidable challenges in terms of vaccine and therapeutics development.

Strong foundation for finding weaknesses

Targeting structural features of the genomes, rather than the rapidly mutating genome sequence or the resulting rapidly mutating proteins, could be a useful strategy against single-stranded RNA viruses.

Because they are single-stranded, such viruses are able to fold back on themselves and bind to complementary sequences in distant parts of their genome, forming stable structural features. The authors of the new Nucleic Acids Research publication wrote in their paper that such structures "have been proven essential for viral replication, protein synthesis, packaging, immune system evasion and more."

Furthermore, "certain RNA structures formed in the context of viral RNA genomes are well conserved... in spite of changes in the underlying encoded amino acid sequence, making them valuable therapeutic targets."

In their work, the team used a method called selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) combined with mutational profiling to look at the structure of the entire SARS-CoV-2 genome, which, at more than 30,000 bases, is large as RNA viral genomes go.

In both in vitro studies and studies in infected cells, the team identified nearly 90 stable tertiary structures, which could in principle be druggable by small molecules. Several of those structures formed binding pockets.

The team also identified regions of the virus that do not hybridize with other regions. Because such regions are permanently single-stranded, they would be accessible to antisense oligonucleotides (Manfredonia, I. et al. Nucleic Acids Res 2020, Advanced publication).