Targeting RNA – Lessons Learned from Oligos

Arrakis’s mission is to drug the transcriptome.  The ability to modulate RNA biology using drug-like small molecules – we call them rSMs – will open up a vast, previously undruggable, target space.  New therapeutic capabilities will include altering the expression of proteins that cannot be targeted directly with conventional small molecules, as well as modulating the regulatory activities of noncoding RNAs.  While Arrakis is young, the vision of targeting the transcriptome is not new.  Roughly four decades ago, the desire to drug RNA led to the birth of the oligonucleotide therapeutics field.  We have learned a great deal through that field’s strategies, technical challenges, failures, and successes.

The concept underpinning oligonucleotide therapeutics is simple and powerful.  Short synthetic nucleic acids are produced that are complementary in sequence to a region of a target RNA.  The first wave of oligonucleotide therapeutics were single-strand antisense oligos (ASOs) intended to degrade target mRNA.  These are designed as “gapmers”, consisting of modified RNA nucleotides on each side of a central DNA sequence.  The RNA provides stability and high affinity, while the DNA portion, when the oligo is bound to its target RNA, creates a substrate for degradation of the target RNA by RNase H.  Later, double-strand oligos (siRNA) that knock down gene expression through the RNAi mechanism were developed.

Nucleic acids, however, do not have favorable drug-like properties.  They are considerably larger than SMs and highly charged. Consequently, they are not orally available and don’t easily enter cells. In addition, nucleic acids are labile.  They are rapidly degraded in blood and cells.  Thus, getting sufficient drug to the target mRNA is an immense challenge.

These limitations have been addressed through the chemical modification of oligos to protect them from nuclease digestion and by packaging them in a form more amenable to biodistribution and cellular uptake. Cellular uptake has been enhanced by the use of lipid nanoparticles (LNP) and chemical ligands that mediate uptake via cell surface receptors.

When administered by intravenous or subcutaneous injection, a large proportion of the oligo distributes to the liver. Delivery to the liver, and in particular, uptake by hepatocytes, has been improved by the conjugation of N-acetylgalactosamine (GalNAc) to the oligos.  GalNAc enables efficient uptake via the asialoglycoprotein receptor which is expressed at high levels on the surface of hepatocytes.  GalNAc conjugation has enabled the effective use of oligo drugs for targets in the liver.

Oligos in the clinic: Signs of success and challenge

We are now starting to learn how these molecules perform in the clinic. Mipomersen (Kynamro; Ionis Pharmaceuticals) is an ASO that decreases ApoB expression to reduce LDL cholesterol levels. It was the first systemically administered oligo to obtain FDA approval.  Mipomersen has not been commercially successful. SM alternatives, such as lomitapide (Juxtapid; Novelion Therapeutics) which lowers ApoB secretion, are more widely used.

One area where oligos have excelled is modulation of pre-mRNA splicing. Eteplirsen (Exondys 51; Sarepta Therapeutics), an ASO that induces exon-skipping in the dystrophin pre-mRNA, was approved for the treatment of Duchenne muscular dystrophy. Nusinersen (Spinraza; Ionis Pharmaceuticals and Biogen), which promotes the inclusion of an SMN2 exon that is normally skipped, was approved in 2016 for the treatment of spinal muscular atrophy. These exciting drugs are the first approved treatments for these difficult childhood genetic diseases. But, like mipomersen, they may eventually be displaced by small molecule alternatives. In SMA, for example, both Novartis and Roche/PTC are developing small molecules drugs with a similar mechanism of action as nusinersen.

The first RNAi drug, Patisiran (Alnylam Pharmaceuticals), is nearing approval. Patisiran, which is an LNP formulation that selectively targets the liver, reduces production of mutant TTR protein as a treatment for transthyretin amyloidosis. Patisiran reduced TTR expression in a sustained manner and met its endpoints in a phase 3 clinical trial.

But the jury is still out on the effects of long-term chronic dosing of oligos.  Thrombocytopenia (low platelet counts leading to increased risk of bleeding) has been observed in multiple trials, suggesting it may be a class effect.  Trials of three advanced oligo drugs – Inotersen (single-strand ASO to TTR; Ionis Pharmaceuticals), Revusiran (another Alnylam RNAi targeting TTR), and Volanesorsen (ASO to APOC3; Ionis Pharmaceuticals and Akcea) have exhibited promising clinical activity but also worrying signs of safety issues.

Lessons for rSMs

The discovery and development of oligonucleotide drugs for targeting RNA has been an undeniable breakthrough, recognized by the Nobel Prize in 2006. It is gratifying to all of us in the field to see the fruits of this discovery now reaching patients – and a tribute to the painstaking effort of scientists all over the world, but particularly at Alnylam and Ionis, who relentlessly worked to turn this approach into real medicines.

What lessons do we draw here at Arrakis?

First, the successes of oligos drugs validate RNA as a target. We knew this had to be so, but having real data is better.

Second, for all of their therapeutic firepower, these drugs still have significant limitations. They require administration by injection, they are complicated and expensive to manufacture and formulate, their use is largely limited to liver or local delivery, and their long-term safety profile is still unknown. Consequently, if alternatives are available, patients and physicians are likely to favor them.

Targeting RNA with small molecules (rSMs) offers the opportunity to access all of the biology of RNA but with few of the limitations of oligo drugs. Perhaps the most important consideration is that we have a long history with small molecule drugs. We understand how they work and, generally, how they can go wrong. We know how to test them, manufacture them, formulate them, and distribute them. We have a robust set of tools in place to optimize their efficacy and safety. Importantly, small molecules typically distribute broadly in the body, allowing RNA targets to be accessed wherever they live. Here at Arrakis, we have a strong interest in cancer and diseases of the brain, which have been traditionally difficult areas for oligo drugs to access.

We are excited by the new world of medicines we can create by accessing the RNA world with small molecule drugs.