Black Box Therapeutics Finds Small Molecule Cure for Spinal Muscular Atrophy

After curing Cystic Fibrosis and Duchenne Muscular Dystrophy with nonsense drug ataluren, PTC Therapeutics is moving on to relieving the sufferings of many more children afflicted with severe genetic diseases.  This time it is spinal muscular atrophy (SMA).  In a publication that recently appeared in SCIENCE, PTC Therapeutics has stumbled upon another orally bioavailable small molecule that is claimed to modulate an RNA processing event for therapeutic purposes.

The reason why I’m interested in the PTC story is that their small molecule approach to RNA modulation is counter-intuitive as it instinctively calls for a nucleic acid-based solution.  On the other hand, an oral alternative to what are usually more invasive routes of administration could have certain advantages such as patient convenience and access.

Naryshkin paper

The paper by Naryshkin and colleagues is on the discovery of RG7800, a compound partnered with the new LNA antisense owner Roche.  It is an illustration of the general strategy taken by PTC Therapeutics of finding RNA sequence-specific small molecule modulators of genes of interest. 

In this example, the company began the panning process by hooking up RNA elements from the SMN2 gene that are involved in the splicing of an exon of interest with a luciferase reporter gene so as to enable large-scale small molecule library screening.  If left untouched, this reporter construct will produce very little light emission due to luciferase expression.  On the other hand, if the small molecule is successful in biasing splicing towards the inclusion of exon 7, the intended outcome of this particular SMA treatment approach, then light is produced.

As one might expect there are numerous ‘hits’ that come out of such primary screens.  In this case, 2000 small molecules from the library increased luciferase expression.  Since such expression changes can be due to a myriad of causes, selected candidates were put through a number of tests such as whether the increase was dependent on the SMN2 sequence elements (reporter constructs without the SMN2 sequences would take care of this), whether the selected small molecules change the expression or splicing of other RNAs (à off-targets; e.g. by RNA seq) etc.

RG7800 apparently survived all these tests and was found to increase the desired SMN2 splice form by about 70% in a number of cell models (including patient-derived cells) and in a mouse model.  It also has entered clinical development.

Comparison with ISIS drug

Since RG7800 is in direct competition with antisense drug candidate ISIS-SMNRx by ISIS and Biogen as both aim to increase SMN2 exon inclusion, a brief comparison is warranted.

While RG7800 has the obvious advantage of being orally bioavailable versus the need for intrathecal administration of ISIS-SMNRx, in terms of molecular outcome, exon inclusion in spinal motor neurons, it appears to be lacking: a ~70% increase compared to ~100-150% increases in the good SMN2 isoform achieved by ISIS-SMNRx in two clinical trials in SMA infants and children, and even more than that in rodent studies before (Passini et al. 2011).    However, RG7800 achieves SMN2 splice modulation not just in the motorneurons of the CNS, but in many other places, in and outside the CNS. 

There is ongoing debate as to whether such body-wide modulation is required, a question also prompted by a study by ISIS and collaborators on the systemic/subQ application of the antisense drug (Hua et al. 2011).  Parenthetically, this also means that if ISIS/Biogen wanted global SMN2 regulation, they have an option with subcutaneous administration in addition to intrathecal administration.  Interestingly, with the subcutaneous administration of ISIS-SMNRx, the mice lived much longer than when the oligo was given intrathecally (days/weeks versus months).  Indeed, consistent with those studies, the PTC small molecule also prolonged the lives of SMA mice considerably.  

I guess it will have to be the clinical trials which will be most informative as to whether this is an artefact of the mouse model or not.  If so, systemic drug exposure would add no benefit and only increase the risk of adverse events from off-targeting.

At the end of the day, what I find remarkable is that it is apparently possible to find small molecules that can modulate gene expression in a fairly sequence-selective manner.  While I don’t doubt that you can change splicing with small molecules, it is the apparent specificity of a simple molecule such as RG7800 that perplexes me.  

PTC Therapeutics did not disclose how many compounds they had to sift through to find RG7800.  If they really just picked one or a few after the initial screen that yielded ~2000 hits and then got lucky, I’d be quite skeptical.  Adding to my skepticism is that drug concentrations in the CNS were reported that greatly (>10x) exceeded those in the plasma (supplementary figure S7).  I’m no small molecule guy, but for an oligo guy who has been following drug development in general, that seems very unique. The blood-brain-barrier apparently does not exist for PTC.  

As a result, and also given the controversy around the discovery of ataluren (artefact or not) and the fact that PTC Therapeutics itself can only remotely speculate on the mechanism of action of RG7800, I acknowledge the publication as interesting, but am not ready to jump on board just yet.