Friday, March 27, 2015

FDA Hard-Pressed to Approve Biomarin, But Not Sarepta Drug

When Biomarin late last year bought Prosensa for its experimental exon skipper drisapersen for the treatment of Duchenne Muscular Dystrophy (for $680M plus potential milestones), it exuded confidence about the likelihood of getting approval for the 2’-O-methyl phosphorothioate antisense molecule.  This, despite of the fact that drisapersen failed in a pivotal phase III trial of 186 patients which prompted the old partner GSK to dump the drug and walk away.

Tenuous early evidence for drisapersen in earlier trials

The confidence is largely based on some supposedly successful earlier trials, especially a multi-center, randomized, blinded 53-patient phase II study which had seen improvements in the 6 minute walk distance (6MWD) at week 25, the primary endpoint of the study (Voit et al. 2014).  

This, however was statistically significant only the case in the subgroup of patients that received drisapersen continuously (à treatment in 10 out of 10 weeks with 6mg/kg), but not in patients which were treated identically, except for the small difference in skipping the last week in a 10-week treatment cycle.

At week 49, the difference with placebo failed to reach statistical significance and Prosensa had to resort to pooling both subgroups to claim victory for that time point. Similarly, drisapersen failed in obtaining statistically significant outcomes for other muscle function endpoints.

Since the mechanism of action for the DMD exon skipping candidates is to change splicing of the mutated dystrophin transcript to a form in which the reading frame is restored with recovery of partial activity, it is important to understand the relationship between drug treatment and dystrophin production.

Here, too, the evidence was less than robust.  For example, even when applying the sensitive immunofluorescence technique, no increase or even a decrease in dystrophin was seen in almost half of treated subjects.  With the less sensitive Western blot, an increase in dystrophin was seen in only a third of treated subjects (0 for placebo).

Therefore, given the failed phase III trial and the less than robust earlier evidence in favor of the drug, I struggle to understand Biomarin’s confidence in obtaining approval in 2016.   

The importance of dystrophin as a surrogate endpoint

Part of the difficulty of obtaining statistically significant results for muscle function endpoints is most likely due to the small patient size (orphan disease affecting ~1 in 3500 male births) and the consequent need to pool boys at various stages of the disease together in a given trial.  It would thus not be surprising if say obtaining 10% levels of normal or Becker-type dystrophin will translate into very meaningful clinical benefit in some, but not other boys.

This will be an even more challenging problem for the DMD subgroups that are not amenable to exon 51-based exon skipping which is targeted by drisapersen.  Probably insurmountable for first-generation chemistries like drisapersen.

Accordingly, in both the drisapersen and the competitive PMO-based eteplirsen trials, it has not been possible to correlate dystrophin production with functional outcomes.

For that reason, I strongly support the importance of establishing reliable, quantitative methods to measure dystrophin in clinical trials (there was an FDA workshop related to this last week).  Dystrophin-dependent markers may also be acceptable if they can be measured by means that do not involve taking painful muscle biopsies.  For example, serum-based microRNAs as developed by Rosetta Genomics and Marina Biotech would be of interest here.

Eteplirsen before drisapersen

I thus find it difficult to grasp the notion of rejecting the current crop of exon skippers like drisapersen or eteplirsen should they be found to produce functional dystrophin with few side effects.  After all, it is the loss of dystrophin function that causes Duchenne Muscular Dystrophy and one has to wonder how generating additional dystrophin cannot be beneficial to patients, especially since the principle behind drisapersen and eteplirsen is strongly supported by human genetic evidence (à Becker’s Muscular Dystrophy).

In this world, it has got to be eteplirsen that should be first in line for regulatory approval.  This is because there is overwhelming evidence (e.g. Heemskerk et al., 2009; Sarepta's Barclays presentation March 12, 2015) that the PMO-based drug is much more potent than drisapersen which, let’s face it, is based on stone-age antisense chemistry (2’-O-methyl phosphorothioate).  Such chemistry is characterized by minimal efficacy and dose-limiting toxicities, especially renal in the case of drisapersen.

In a paper comparing 2’-O-methyl to PMO chemistry for DMD exon skipping conducted by researchers close to eteplirsen, it was found that at same doses in mice, PMO chemistry is moderately to vastly more potent than 2’-O-methyl phosphorothioate antisense compounds of a size comparable to drisapersen.  The extent of the difference depended on whether the human or mouse dystrophin were targeted and the target sequence.   Unsurprisingly given the acrimonious competition between the two parties, Sarepta has also picked up on this and continued along these lines by showing that in addition to chemistry, eteplirsen has the edge over drisapersen in terms of the targeted sequence:

Sure, there is the theoretical caveat that PMO and 2’-O-methyl scale differently from mice to humans and that what is the most potent target sequence for one chemistry does not necessarily have to be the most potent one for the other.  Intuitively, however, the differences are too big for these factors to compensate the preclinical evidence.  Also, keep in mind that in the clinic, eteplirsen is being given at 5 to almost 10-fold increased doses than drisapersen and, on top of that, is much safer and better tolerated than drisapersen.

Because of this and the competition, it is not surprising and disingenuous when Biomarin would now suddenly like to de-emphasize the importance of dystrophin as a surrogate biomarker (see last week's workshop).

Dear regulatory agency, if you approve drisapersen, you cannot deny eteplirsen.  Sure, drisapersen has been tested in more patients than eteplirsen and Sarepta has conducted a clinical trial in the worst possible manner and probably ‘embellished’/overstated some of their results, including the dystrophin evidence.  However, given that eteplirsen almost certainly generates more dystrophin than drisapersen, the highly favorable side effect profile of eteplirsen (also in comparison to drisapersen), and in light of the 6MWD issue that applies to both drug candidates, the question is whether the bureaucratic application of rules should trump scientific evidence and patient interests.

Disclosure: I am long SRPT based on the notion that Biomarin, with its orphan disease savvy, will turn out to be the biggest supporter of eteplirsen getting approval this time around.  Additionally, the agency is partly responsible for the long duration of the ongoing eteplirsen trial (close to 4 years soon) and the repeated taking of muscle biopsies, and after all this taking away hope from patients and their close ones is difficult to fathom.

Tuesday, March 24, 2015

Isis Pharmaceuticals and Roche/Santaris About to Settle Patent Dispute

According to court documents dated March 20, 2015, it looks like Isis and Roche, the new owner of the original defendant Santaris, are about to settle the RNaseH antisense patent infringement suit brought by Isis.  A settlement would have important implications for the future of Antisense Therapeutics. 

To wit, in 2011 Isis sued Santaris for infringing its RNaseH gapmer patents by Santaris signing on Big Pharma partners regarding RNaseH Therapeutics development.  Isis viewed this as a form of monetizing their IP and consequently sued.  If decided in Isis’ favor, the case would have been a notable departure from the long-held practice of shielding preclinical business and drug development under the safe harbor of the Research Exemption

As such, the case could have had a chilling effect on particularly small innovative biotech companies seeking to improve upon existing technologies, but by this using aspects of those technologies.  Big Pharma, after all, do not rely on partnerships to finance technology development and can thus go on using and improving the IP of other companies in their own labs impugned.
Although one could have thus taken the view that losing the case would have been in Roche’s interest in a perverted sort of way, it could also have more immediately jeopardized the value of their acquisition of Santaris (USD 250M) in addition to payable damages.  For example, Roche might have been ordered to cease any RNaseH work in the US which may be impractical for a global research organization like Roche.

Since I cannot imagine that Isis would tolerate Roche to challenge their control over RNaseH antisense gene knockdown and compete for pretty much the same targets, I expect the settlement to take the form of a significant broadening of the companies’ existing relationship around Huntington’s Disease in the form of additional target picks in exchange for a sizeable upfront fee. 

Unlike Isis’ more recent Big Pharma deals with J&J, GSK, BiogenIdec, and AstraZeneca, however, I expect this to involve less early development work by Isis as some of this would be the obvious job of the former Santaris crew.

Sunday, March 22, 2015

Follow-Up to Simplified GalNAc-RNAi Trigger Discussion

Just days after the Matsuda et al. publication on simplified, non-triantennary GalNAc-RNAi triggers (the subject of the previous blog entry), another related paper from Alnylam came out (Rajeev et al. 2015). 

The Rajeev et al. publication further supports that monomeric GalNAc designs as pioneered by Arrowhead Research for the use in RNAi Therapeutics and others (e.g. Matulic-Adamic et al., 2002) before for non-RNAi Oligo Therapeutics applications allow for effective ASGPR receptor recognition and subsequent gene silencing.  

The main difference to the Matsuda paper was that instead of GalNAc-modified nucleotide monomers, non-nucleosidic GalNAc monomers were employed (note: the Matulic-Adamic et al. also explored both nucleoside- and non-nucleoside-based monomeric clustering GalNAc strategies). They, however, were also appended to the 3’ end of the passenger strand as part of the phosphoramidite-based RNA synthesis.

The use of non-nucleosidic phosphoramidite monomers further simplifies the chemistry demands and thus cost of goods of GalNAc-siRNAs.

Ironically, not only does this paper also fail to cite the seminal Arrowhead and Matulic-Adamic research, this significant effort to get away from the apparently costly triantennary design is also at odds with Alnylam’s claims in July 2014 that a patent covering bi- and triantennary conjugates designs ‘broadly cover[ed] conjugate-based delivery of RNA Therapeutics’.

Obviously, if non-bi- and triantennary designs work, then one cannot consider the issued patent to broadly cover conjugate-RNAi triggers.

It will now be interesting to see how broad the claims will be that the patent offices will grant related to the simplified designs.  The re-writing of history effort obviously is not aimed at impressing investors or enabling the field, but part of a GalNAc IP landgrab effort, ideally resulting in the issuance of claims covering any monomeric GalNAc designs.

The one thing that I would like to give Alnylam credit for is that they will put significant resources behind the technologies they consider promising- whether they invented, own, or have a license to them or not- and thus advance RNAi Therapeutics as a field.

Tuesday, March 17, 2015

Alnylam’s Scientifically Dishonest GalNAc Claims

Arrowhead Research, as the successor of Mirus Bio, can regard itself as the father of GalNAc-conjugated RNAi delivery.  Accordingly, in 2007, Rozema and colleagues published a seminal paper in which a multivalent polymer-conjugated GalNAc construct was utilized for the hepatocyte-specific delivery of RNAi gene silencing.

In 2015, Alnylam likes to be recognized as the inventor of GalNAc-oligonucleotide Therapeutics, with competitors like Isis Pharmaceuticals and Solstice Biologics playing the roles of copy-cats, and Arrowhead Research failing to get much mention at all.

This, however, is as noted in the introduction far from the truth, and a recent paper on ‘sequentially assembled’ GalNAc-RNAi triggers by Alnylam (Matsuda and colleagues, 2015) is yet another example for how they would like to re-write history to suit their (IP) goals.  History repeating itself you might think after all we’ve been through with SNALP LNP.

Matsuda re-discovering Rozema

Alnylam likes to laugh off Arrowhead’s GalNAc approach by claiming that you need a magic triantennary GalNAc ligand design with highly specific geometry to achieve tight ASGPR target receptor binding and subsequent cellular internalization.  By contrast, Arrowhead Research would be only using monovalent GalNAc which are known, in isolation, to be much poorer ASGPR binders.

The existence of the triantennary design obviously has not evaded Arrowhead Research.  Nevertheless, they have opted for monovalent GalNAcs most likely for their chemical simplicity and therefore reduced cost of goods.

The apparently high cost of triantennary GalNAc synthesis was acknowledged in the Matsuda paper and was said to be the motivation for testing RNAi triggers in which instead of a single triantennary ligand, monovalent GalNAcs were distributed along the RNAi triggers.

Short story short, having GalNAcs conjugated on 3 sequential nucleotides or every other nucleotide did not impact potency much compared to the triantennary 'parent' design.  In other words, the benefit from multivalent binding can be achieved by bringing monovalent GalNAcs together in space.

This, of course, is the same principle behind the Arrowhead approach, where GalNAcs are added to the free amines along a polymer/peptide (an RNAi trigger is just another polymer).  In the case of the melittin-like peptide, I have highlighted the basic amino acids to which GalNAcs are expected to be conjugated:


As you can see, towards the C-terminus (right hand side) of the peptide, there is a cluster of 4 positively charged amino acids that is expected to generate a multivalent ASGPR binder (note that 3 and 4 GalNAcs have similar binding affinities).

Shockingly, while masquerading as the inventors of GalNAc Oligonucleotide Therapeutics with statements like these…

The triantennary GalNAc ligand was subsequently used for hepatocyte-specific delivery of antisense oligonucleotides and short interfering ribonucleic neutrals (siRNNs) in mice, and anti-microRNA therapeutics in humans, confirming the value of the parent trivalent design.’

…they failed to even cite the Rozema paper and went on to say that now (i.e. for the first time) they were going to test the hypothesis that sequential monovalent GalNAcs could do the same job.  This obviously is a clear case of willful scientific dishonesty in their campaign to re-write GalNAc history.

Silence Therapeutics not even a pimple

While the Matsuda paper is geared towards claiming the sequential GalNAc assembly idea and is an affront to Arrowhead Research, it is also a reminder that Silence Therapeutics has been similarly treated with disregard in Alnylam’s ‘invention’ of ‘enhanced’ GalNAc-siRNAs. 

This is because (like Arrowhead Research actually), Alnylam, at least in essentially all RNAi trigger examples in the Matsuda paper, uses the AtuRNAi trigger design, US patents of which claim 2’-O-methylation every other base with a staggered pattern as it regards the annealed guide and passenger strands.

It therefore looks more and more like Alnylam will have to approach Silence Therapeutics for a license sometime before enhanced GalNAc-siRNAs hit the market (at least 2 by 2020 according to Alnylam’s 2020 guidance), if not ALN-TTRsc already (~2017-8).  If Alnylam will have to approach Arrowhead Research for a license regarding GalNAcs, I do not know, but given Alnylam’s noise, worth paying attention to the intricacies of the various IP estates. 

Thursday, March 5, 2015

Arrowhead Acquires 30 Alnylam Exclusive, Priority Target Picks and Plus More from Novartis

Arrowhead Research keeps mopping up the billions of Big Pharma dollars spent on RNAi Therapeutics R&D and IP.  After acquiring the Roche assets for dimes on the dollar in 2011, heralding Arrowhead Research becoming a real biotech company, it is now Novartis’ turn to give their RNAi assets to dedicated RNAi hands.

What Arrowhead bought

For $10M and $25M in cash and stock, respectively (representing a dilution of ~5%), Arrowhead research acquired

1)      new Novartis RNAi trigger chemistry that the company claims to fall outside competing RNAi trigger IP (thus avoiding milstone and royalty obligations);

2)      intriguing new RNAi trigger chemistry that supposedly enhances RISC RNAi effector loading of RNAi triggers in the cytoplasm and which  could enhance the potency and duration of gene silencing; and

3)      the RNAi-related IP rights that Novartis acquired from Alnylam in 2005, most notably the 30 target picks.

Arrowhead in the house

10 years ago, Novartis made headlines by getting access to 30 exclusive target picks under Alnylam RNAi trigger IP.  For the privilege of picking targets not only ahead of Alnylam, but also excluding Alnylam from these targets, Novartis paid $10M in cash and made a $58M equity investment at a 16% premium to the ALNY trading price back then (so say $20M overall), plus the usual biotech milestone (up to $700M) and royalty obligations.

At the time, Alnylam was criticized for selling much of the farm.  This is because 30 target picks might have been too much given the state of RNAi delivery technology at the time.  Archrival Sirna Therapeutics gloated that it would never enter into such broad sweeping deals and consequently started to win business from other Big Pharma names, culminating in the $1B acquisition by Merck in 2006.

Novartis had time until October 2010 to officially nominate its target picks. At the time, SNALP LNP delivery to the liver was the only game in town for clinically relevant RNAi delivery.  Therefore, if Novartis had any brains, it would have spent some of the picks on the juiciest liver targets in addition to their oncology dreams.  

Usually, I don’t give much credit to the critical thinking ability of Big Pharma, but given that a number of Novartis RNAi folks came from Sirna Therapeutics and had worked on liver targets such asHBV early on, it is a good assumption that, yes, a few targets are aimed at the liver.

Note also that Alnylam never entered the HCV drug development race, instead pointing to their unwillingness to compete with its microRNA joint venture Regulus Therapeutics for the target.  I never bought that argument and instead suspected that Novartis was on HCV.

This, of course, adds an interesting facet to the somewhat uneasy relationship between Arrowhead Research and Alnylam and how today's deal impacts Alnylam’s 3 STAr franchises, namely viral hepatitis, cardiometabolic, and orphan diseases.

Value of Novartis RNAi assets in the eye of the beholder

I fully expect the usual suspects to spin today’s news as Arrowhead Research (once again!!) acquiring assets that a Big Pharma had put on hold (in the case of Novartis in early 2014) and nobody else allegedly wanted.  This may be partly true given that Novartis did not appear to be successful at developing strong RNAi delivery technologies.  So the Novartis RNAi assets in isolation may not have been worth that much.

Arrowhead, however, is in a different position given that its DPC delivery technology is being validated in the clinic.  I expect the ARC-AAT results towards the end of the year to remove any doubt about that.  Moreover, Arrowhead is on track to commit its subQ DPC version into clinical development, instantly increasing the value of any cardiometabolic targets that Novartis may have picked.

This illustrates that for Arrowhead Research today was about expanding its RNAi trigger IP leverage in addition to increasing its chances of finding the best possible RNAi trigger against a given target from its broad stable of RNAi trigger structures and chemistries (usiRNAs, Dicer-substrates, canonical), and finally adding a unique RNAi pharmacology trick to its toolbox.  All of this to be married with its DPC delivery technology so that the result would be worth far more than the sum of its parts.

Today, we have only glimpsed part of the strategic and technological importance of the deal. Stay tuned as the movie unfolds.  Kudos to Arrowhead Research for making the bold, but mostly right strategic decisions.

Monday, March 2, 2015

RNA Therapeutics Are Back in the Cardiometabolic Game

In the mid- to late 2000s, in the wake of Vioxx, I remember sounding the alarm bell on developing RNAi Therapeutics for cardiometabolic indications.  The FDA would simply refuse to approve cardiometabolic drugs even when strong data on widely accepted biomarkers such as blood glucose in diabetes and LDL-cholesterol levels in cardiovascular disease suggested that they should be efficacious.  Instead, the agency was demanding ridiculously expensive outcome trials for even the most underserved patient population, making cardiometabolic drug development difficult to justify financially.

Regulatory and technology changes

10 years later, the situation has changed dramatically due to a confluence of regulatory and technology changes.  In the regulatory arena, the staged approval process which involves a fast-to-market strategy for high unmet need orphan populations based on surrogate markers followed by the roll-out in larger patient populations, partly supported by the clinical experience gathered from the orphan indications, has been successful at rekindling interest in cardiometabolic drug innovation in general.

In terms of technology, both RNAi and antisense technologies have matured to a point that the risk:reward proposition looks highly promising not only for the most severe patient populations, but suitable for even the more general population.  The Old is exemplified by gen 2.0 RNaseH antisense oligonucleotide mipomersen for which it will be very difficult to break into markets beyond the ultra-orphan homozygous familial hypercholesterolemia one due to its weak drug activity and considerable side effects. 

In RNAi Therapeutics, the Old was represented by the need for intravenous administration with the former gold standard in RNAi delivery, 1st and 2nd generation SNALP liposomal nanoparticles (LNP), and their confounding effect on lipid metabolism (see the need for various normalizations in the phase I results of ALN-PCS02).  

Today, however, we not only have improved SNALP LNPs and 2nd generation RNaseH antisense (2.2), but more importantly GalNAc-targeted RNAi and antisense technologies by Arrowhead Research, ISIS Pharmaceuticals, Regulus Therapeutics, and Alnylam.  Importantly, due to their highly specific targeting of hepatocytes in the liver, the therapeutic window has been widened considerably.  In addition, the surprisingly long duration of target engagement makes monthly, if not quarterly dosing conceivable, therefore not only erasing, but surpassing oral small molecules in terms of patient convenience.  And we have not even considered the superior therapeutic utility that they promise by their ability to go after all conceivable targets- individually or in combination.  This, after all, is what we all should care about most.

The attraction of cardiometabolic applications is also reflected by the recent establishments of related franchises by Alnylam (cardiometabolic STAr) and ISIS Pharmaceuticals (Akcea lipid commercial subsidiary), with development programs targeting ApoCIII (ISIS Pharmaceuticals), PCSK9 (Alnylam/The Medicines Company), Lp little a (ISIS Pharmaceuticals), and ANGPTL3 (ISIS/Alnylam) looking already very favorable.  In addition, ISIS Pharmaceuticals sports a couple of interesting diabetes-focused programs (targets: PTB, GCGR, GCCR) which are showing novel therapeutic/safety profiles that could be suitable for specific sub-populations in the enormous, but equally complex diabetes market (e.g. insuling sensitization, reduction of glucose production).

Competitive outlook
As ISIS Pharmaceuticals and Alnylam compete for some of the same targets, the most common pattern you will likely see is that ISIS has a first-mover advantage (à IP and experience) with non-GalNAc generation 2.2 candidates due to their formerly somewhat fool-hardy, but now genius-looking pursuit of the cardiometabolic area.  When there is direct competition, the gen2.2-based drugs will likely be outcompeted by Alnylam’s GalNAc-siRNA conjugates due to their a) longer duration of action, and b) their possibly superior safety profile.

However,  as ISIS Pharmaceuticals is giving their cardiometabolic franchise a GalNAc overhaul, the company will also likely have the once monthly dosing frequency and a safer alternative turning it into a head-to-head race between Alnylam and ISIS Pharmaceuticals with winners that could differ from target to target.  Long-term, ISIS Pharmaceuticals may another ace in the competitive race as the single-stranded phosphorothioate oligonucleotide approach currently seems more amenable to oral dosing than double-stranded RNAi approaches.
While Tekmira’s SNALP LNP technology may be competitive when it comes to multiplexing targets, it is Arrowhead Research that is best positioned to surpass both Alnylam and ISIS Pharmaceuticals should they succeed in progressing their single-molecule subQ DPC technology into the clinic as indicated in last quarter’s conference call.  The endosomal release chemistry gives it a potency, and potentially also dosing frequency advantage over Alnylam’s simpler GalNAcs. 

Expect the CEO of Alnylam to increasingly attack the Arrowhead competition by raising safety concerns as he did in the recent RBC Healthcare conference presentation. I find this remarkable given that Arrowhead Research has not released the full safety data from its phase I study of ARC520.  But if you don't think you can win on potency, it may be best to sow seeds of safety doubt based on innuendo.

So watch this space. Next up are results from ISIS-GCCRRx (diabetes) and ISIS-ANGPTL3Rx (lipid disorders), clinical results from which are imminent.  Head-turning ALN-PCSsc results could be out in Q3. 
By Dirk Haussecker. All rights reserved.

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