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.

Predicting the Outcome of Regulus HCV microRNA Therapeutics Study

Regulus Therapeutics is on track to reveal phase I results of its anti-HCV compound by the end of the year according to a presentation at last week's OTS.  Although the phase I study is largely a healthy volunteer dose-escalating safety study, it does involve a cohort of HCV patients to assess the viral knockdown kinetics following a single dose of anti-miR122 RG-101. 

MicroRNA-122 is a small RNA host factor that had been identified to play an important role in HCV replication.  As a therapeutic target it promises a low risk of viral resistance, pan-genotypic activity, and entirely novel mechanism of action making it suitable for combination therapy.

Based on the experience with an LNA-based competitor compound by Santaris/Roche (Janssen et al. NEJM 2013), I predict a 2 to 3 log viral knockdown, with a 3 log viral knockdown setting the scene for RG-101 as a single shot in a 4-week treatment regimen in combination with other oral direct-acting antiviral agents (DAAs).  If viral reductions were on the low end of my expectations, it may require 2 or 3 doses within 4 weeks for GalNAc, cET-enhanced RG-101 to facilitate such a short treatment period which is considered a necessary attribute of future treatment regimens in an increasingly competitive market.

Miravirsen comparison

Earlier studies by Regulus competitor Santaris/Roche largely form the basis for my predictions.  In particular, a phase II study of 5 weekly doses of miravirsen at 3, 5, and 7mg/kg yielded 1.2log (3mg/kg) and ~3log (5 and 7mg/kg) viral knockdowns.  Miravirsen is an LNA-based antisense compound whereas RG-101 involves the analogous high-affinity cET chemistry.  Conservatively, miravirsen has a slight (1-3x) potency advantage over RG-101 without the GalNAc conjugation when considering non-human primate and clinical AldoA and cholesterol results which reflect anti-miR122 activity.

However, the GalNAc conjugate in RG-101 is giving it a great 10-30x boost in potency, meaning that overall RG-101 should be 3-30x more potent than miravirsen.  It is because of this and considering that RG-101 is given at 2 and 4mg/kg in the phase I trial in HCV patients, that I arrive at a predicted 2-3 log HCV reduction in the phase I study.  This also makes the conservative assumption that 3log viral reductions is all that an anti-miR122 treatment strategy may achieve based on the apparent plateauing of miravirsen at 5mg/kg.  The 3 log prediction would require that a single shot of RG-101 can already achieve super-therapeutic tissue levels of the oligo.  This, however, cannot be assumed given that for non-ligand-targeted phosphorothioate antisense technology at least this would normally require a multi-dose loading schedule.

But isn’t RG-101 late to the HCV game?

It’s long been thought that it’s game over for RG-101 given the dynamics in the HCV markets.  In particular, the already approved and soon-to-be-approved all-oral DAAs which typically achieve cures in >90% of patients in 8-12 weeks in well-supervised clinical trial settings, would make newer agents like RG-101 seem outdated.  On the other hand, especially given cost pressures (~$100K per average treatment and ~4 million infected in the US alone), the uptake of the new treatments has been relatively slow with only 1-2% treated thus far (according to some of the analyst reports that I have read).  And even then, the sales have been spectacular: Sovaldi e.g. is on track to become the most successful drug launch ever being on track for more than $10 billion in sales in its first launch year!!!

It is the cost pressures (pricing per pill, not per cure) and improved adherence that make a shortened 4-week treatment period so desirable.  A single or two subcutaneous injections in the doctor’s office during routine check-ups where blood is taken anyway should add to compliance.  Holding the subcutaneous route of administration of RG-101 against the drug is therefore wrong in my opinion and the ‘all-oral’ notion, a misnomer really, has only been so attractive because the former subcutaneous standard of care, interferon, was so unpopular not because of the needle injections, but because of its side effects.

So place your bets.  I believe RG-101 has value and will not only be superior to the Santaris/Roche drug, but has pretty much caught up with it in development terms given that miravirsen has only been tested with a DAA (telaprevir) that is already long outdated.  As to the necessary Big Pharma/Biotech licensee, Johnson&Johnson tops my list.

Disclosure: Long RGLS as an RNA Therapeutics stock waiting to be re-discovered with an increasingly broad and clinical-stage pipeline and good financials.  The RG-101 results should only be the trigger for the re-discovery of this ~$300M market cap company.   

Roche Buys Santaris (Because It Could Not Buy ISIS)

Minutes ago, Roche announced the acquisition of Danish antisense company Santaris for $250M in upfront cash and $200M in contingent payment.  Given that Santaris only has a microRNA inhibitor for HCV in the clinical pipeline which many in the industry believe is outdated given recent successes in the treatment of HCV, this purchase is a big vote of confidence by Roche in the RNA Therapeutics platform.

This latest development comes after Roche struck a Huntington’s-based deal with ISIS Pharmaceuticals in April 2013 resulting in a development candidate as revealed today by ISIS in its earnings report.  Roche was fortunate to get that deal, because ISIS was about to strike a muchbroader neurology deal with BiogenIdec, leaving it hungry for all those other targets.  Apparently, Roche was happy with what it saw, also following a smaller deal with Santaris just in January this year on undisclosed targets.

This deal flow is reminiscent of what Roche did in RNAi Therapeutics in 2006/7.  After Merck took out Sirna Therapeutics, Roche saw a need to partner with Alnylam instead, at least this is how the narrative goes. 

You can bet your house that Roche at one point or another wanted to buy ISIS, but given its varied partnerships and general unwillingness to sell itself had to settle with archrival Santaris (--> ongoing litigation which perhaps Roche is more able to settle on ISIS' terms).  But, hey, maybe history is repeating itself and ISIS already signed itself away to AstraZeneca and we will hear about it soon.

PS: for the stock junkies (I know there are many here), this news also bodes well for Marina Biotech given its highly similar chemistry to that of Santaris: LNA and CRN.

GalNAc Advance by ISIS Means Oral Oligonucleotide Therapeutics around the Corner

Last week, the long-awaited first publication on ISIS’ GalNAc-targeted antisense oligonucleotides appeared in a ‘NAR Breakthrough Article’ (Prakash et al., 2014)  Living up to that label, the data with RNaseH antisense oligonucleotides (ASOs) conjugated to triantennary GalNAc sugars showed that this strategy increases potency by nearly an order of magnitude.  In combination with high-affinity chemistries (in this case cET) that facilitate the use of short (12-14nt vs ~20nt) oligonucleotides which has been shown to improve in vivo potency (Santaris research by Straarup et al., 2010), oral delivery for antisense modulation of hepatic gene expression has essentially been solved. 

Moreover, the lower dosages that can now be used in addition to the improved biodistribution profile that is now heavily slanted away from non-hepatocytic cell types in the liver and the kidney in favor of hepatocytes, means that the other major benefit of GalNAc-ASOs with immediate applicability is that the safety of therapeutic ASOs for liver-directed applications will be much improved.

The conclusion that oral antisense therapeutics are just around the corner is based on the observation that a relatively crude caprate-based phosphorothioate oligonucleotide formulation enabled a ~10% bioavailability following oral administration already (intravenous = 100%; Tillman et al., 2008).  This, in addition to some inter-subject variability that might have been linked to gastric emptying times, meant that too much oligonucleotide would have had to be administered orally with previous antisense oligonucleotides. 

Granted, this first piece of GalNAc-ASO literature did not explore oral delivery. The fact, however, that the combined use of GalNAc conjugation with high-affinity chemistry improved parenteral ASO potency by 60-fold is predicted to mean that oral GalNAc-cETs are already more potent (~6x) than subQ-administered 2^nd gen ASOs.  These have already produced impressive phase II data for targets such as Factor XI and ApoCIII.

The potency improvement in terms of oral delivery may actually be larger than 60-fold.  This is because oral delivery strategies such as caprate co-formulation which aim at increasing intercellular drug permeability are size dependent.  This means that there should be an added benefit of the smaller oligonucleotide size facilitated by cET chemistry with oral delivery.

Of course, the data leave open some questions.  My most pressing, applicable to both oral and non-oral uses of GalNAc-ASOs is how the rodent data translate into non-human primates and ultimately humans.  This is because for unconjugated phosphorothioate oligonucleotides, the potency on a mg/kg basis improves with the size of the organism.  The discussion above is based on an assumption that GalNAc-targeting will not change that.  I have been unable to make a determination yet as to whether this should hold true or not.

Other than that, the antisense weather forecast is blue skies ahead, though with a chance of thunderstorms in the form of IP skirmishes with their good friends over at Alnylam as they have pioneered GalNAc conjugation in oligonucleotide therapeutics, but may now be ironically penalized for it from a competitive point of view.  Alnylam is not the type of company that just lets competitive threats happen to them.

Imetelstat Off-Target Mechanism Might Be Its Therapeutic Mechanism of Action

This morning’s biotech news featured a clinical hold on Geron’s imetelstat, a 13-mer lipid-conjugated N3’-P5’ thio-phosphoroamidate oligonucleotide telomerase inhibitor.  Since maintaining chromosome ends by telomerase is important for repeated cell replication, it is not surprising that the company is aiming this compound at proliferative disorders such as cancers and essential thrombocythemia (ET).  The latter is a condition in which there are too many platelets.

The clinical hold imposed by the FDA relates to apparent liver toxicity.  Liver toxicity as evidenced by elevated liver enzymes has been a known side effect of imetelstat with 90% of subjects in the phase II trial of imetelstat exhibiting low-grade elevated liver enzymes.  What is more, about 30% of the subjects had concurrent increases in bilirubin.  Taken together this strongly smells like cases of Hy’s Law, the nuclear liver tox bomb of drug development.

No wonder the alarm bells at the FDA are ringing.  According to the press release by Geron this morning, the agency is concerned about the reversibility of these elevations.  If not reversible, chronic liver disease, if not failure might ensue.  

I am not too surprised by these developments.  What surprises me is that the stock market apparently has not picked up on the concurrent liver enzyme/bilirubin increases since these had already been known.

The reason why I am not surprised is that phosphorothioate oligonucleotides can be expected to result in liver injury at the ~10mg/kg very high dosages given in the ET trial (dosage similar to the 640mg phase III prostate cancer trial of OncoGeneX discussed yesterday).  Note that ISIS Pharmaceuticals generally settles with 200mg, at most 300mg of systemically administered phosphorothioates and Santaris had to terminate two candidates targeting genes expressed in the liver due to liver tox.

It should be added here that the Geron, ISIS, and Santaris chemistries are slightly different, but share the phosphorothioate modification which in my opinion is what is causing these toxicities.

Given that the half-lives of phosphorothioate oligonucleotides in the liver are about 1 month, one would expect the low-grade liver enzyme elevations to go away with time and they might not be a show-stopper for non-chronic applications of imetelstat.   

That’s the somewhat good news.

The bad news: applying a phosphorothioate oligonucleotide-based telomerase inhibitor for the treatment of cancer and increases in platelet counts sounds like a bad joke.  Thrombocytopenia (decreases in platelet counts) and anti-proliferative immunostimulation are well known side effects of large doses of phosphorothioate oligonucleotides.  In light of that, claiming that imetelstat works via telomerase inhibition seems a bit optimistic to put it kindly.

Oligonucleotide Therapeutics Companies Crowding into GalNAc-Conjugation

Following Alnylam’s achievement of making subcutaneous administration work for RNAi gene knockdown in the liver by conjugating RNAi triggers to the GalNAc sugar, antisense companies have started to copy the approach.  As RNAi Therapeutics have made great progress in targeted delivery, antisense companies are starting to realize that in order to stay competitive and improve the safety of systemic uses of antisense, they need to get away from the notion of 'naked'/unformulated delivery that relies on swamping the body with phosphorothioated oligonucleotides.

This has become apparent at the AsiaTIDES meeting here in Tokyo where both Santaris and ISIS Pharmaceuticals disclosed their great interests in GalNAc conjugation.

In collaboration with Axolabs (the part of Roche RNAi Therapeutics that was not acquired by Arrowhead Research and that had familiarity with GalNAcs), Santaris presented phosphorothioate-LNA Factor VII (liver) knockdown data showing 80% gene knockdowns in mice following a single dose of 0.1mg/kg.  Even more potent knockdowns were seen at 0.25mg/kg and above. 

In another presentation by ISIS Pharmaceuticals on their cardiovascular franchise, the company noted that they will follow up on their initial Apo(A) (‘little A’) candidate with a GalNAc-conjugated version.  With this, they expect to increase potency by up to 10-fold, thus allowing for 10-30mg (~0.15-0.45mg/kg) dosing.

This illustrates the utility of the GalNAc receptor (ASGPR) and how the competing RNAi and antisense technologies are fertilizing each other.

Regulus Therapeutics, of course, is the first antisense (anti-miR) company of sorts that has adopted GalNAc conjugation for their liver-directed programs, most notably anti-miR122 for HCV that is about to enter clinical development.  Regulus obviously has a license to GalNAc from Alnylam.  Whether this also applies to ISIS Pharmaceuticals, remains to be seen.  The word on the lab floors is that GalNAcs per se are not patent-protected, so ISIS may use an entirely different linker strategy to Alnylam just as Arrowhead Research does with its GalNAc-targeted DPCs.

What it means for Tekmira and Marina Biotech

Since some of you are following my investment strategy, here is what I think this means for the liver-directed efforts by Tekmira and Marina Biotech (both of which I own). 

Marina Biotech could obviously follow the same path as ISIS Pharmaceuticals and Santaris in adopting GalNAc conjugation with its CRN technology.  As such, there should be no change in the competitive value of CRN compared to Santaris and ISIS antisense.  It could also attach GalNAcs to their liposome-based SMARTICLES for which delivery to the liver remains to be demonstrated.  To do all this, however, Marina Biotech needs to grow and establish in-house R&D.  

For Tekmira, it means that RNaseH antisense are getting close in potency for gene knockdown compared to the 2^nd gen MC3 SNALP LNPs (85-90% TTR gene knockdown in humans at 0.3mg/kg).  With the 3-fold more potent 3^rd generation SNALP LNPs which should enter the clinic this or early next year (TKM-ALDH2, TKM-HBV), Tekmira should stay well ahead of its competition with the most potent gene knockdown technology for the liver.  This means more addressable diseases and in most cases higher treatment effects as well.   And if it incorporated GalNAc-conjugated lipids into their liposomes, too, maybe that would extend that lead even further.

If gene knockdown in the liver is not a great example for why you need a competitive free market economy, then I don’t know what is. And, of course, there is no better example of why you need a lab ;).

Big Pharma Panic over Nucleic Acid Therapeutics

News this week of Roche licensing antisense technology from Santaris 3 years after having written down a related $500M+ investment in RNAi Therapeutics, is symptomatic for the apparent panic and resulting schizophrenic behavior that grips Big Pharma when it comes to Nucleic Acid Therapeutics (NATs).  Can NATs help rekindle their flagging discovery efforts or will NAT companies leave them in the dust as they advance to the top of the Pharma food chain?   

Meanwhile, Big Biotech in the form of BiogenIdec has also recognized that NATs are critical for their growth in the form of a partnership with Zinc Finger Nuclease specialist Sangamo Biosciences for the treatment of red blood cell disorders (sickle cell and beta-thalassemia).  This follows significant (~$150-200M) recent investments in ISIS’ antisense technology for diseases of the CNS and a deal with microRNA Rx company Regulus Therapeutics.

If you sit back and consider the clinical and preclinical developments in the space (look out for the upcoming RNAi Therapeutics Investment Guide 2014), there can be no doubt that nucleic acid therapeutics (including oligonucleotide therapeutics) are about to materialize as the 3^rd major chemical class of drugs following small molecules and recombinant proteins.  In fact, their mechanistic versatility (gene up- and down-regulation, modulation of RNA processing etc) means that in a few decades, there will be many more NAT-based new molecular entities than small molecules and recombinant proteins combined, in many cases for genetically defined patient populations.  

Interestingly, in 2013, only 2 monoclonal antibody new molecular entities (NMEs) received marketing authorization by the FDA (see here).

Investors do not have to take such a very long view as a number of commercially attractive Oligonucleotide Therapeutics are gearing up to enter the market, including for TTR amyloidosis, Hepatitis B infection, spinal muscular atrophy, and hypertriglyceridemia.

For those interested in the more particular relevance of yesterday’s deals to RNAi Therapeutics stocks, the Roche-Santaris deal ($10M in upfront plus the usual biobucks and royalties) represents another blow to ISIS’ claim that it owns the IP in the space, especially in light of the ongoing litigations and patent battles between the companies and the fact that not long ago, Roche partnered with ISIS on Huntington’s Disease.  This should provide further comfort to those, including myself, speculating that Marina Biotech’s CRN chemistry is a valid equivalent, if not superior alternative to the ISIS and Santaris antisense chemistries.  Regarding the deal between Sangamo and BiogenIdec ($20M upfront plus the usual biobucks and royalties), it is a validation of the attractiveness of the hemoglobinopathy market that forms an important part of Alnylam’s pipeline options.

In additional RNAi Therapeutics developments...

Bad news for Benitec

In a recent paper by Lisowski et al. from Stanford (Kay lab) which appeared in Nature, very strong evidence was presented that the AAV8 serotype is far from ideal when it comes to transducing human hepatocytes.  This is in contrast to preclinical results mainly in mice that have shown highly efficient, almost 100% transduction of hepatocytes, the transduction level probably needed to achieve an RNAi cure of HepC.

Based on the preclinical work, the AAV8 serotype was readily embraced by gene therapists and adopted for various liver-related clinical studies. Surprisingly, however, the data so far in hemophilia did not support a significant advantage of AAV8 over the old AAV2 workhorse.

The study by Lisowski et al. shows that this is very likely the result of poor AAV8 transduction of human hepatocytes.  Among the multiple striking results, in mice with chimeric human/mouse livers, basically only the murine hepatocytes could be transduced whereas the adjacent human hepatocytes were not.

This is an unfortunate development that Benitec cannot be held responsible for.  It could be a double-whammy though for the company as in addition to the commercial concerns about the HepC indication for TT-034, results from the ongoing phase I study may not even support the delivery technology for other liver applications.  There is, however, light at the end of the tunnel as there are plenty new AAV serotype that appear to be as good in transducing human hepatocytes as AAV8 is in transducing murine hepatocytes.

ISIS Demonstrates Wider Utility of RNaseH ASOs for Nuclear Targets

While research astounds us on a daily basis with unexpected discoveries, sometimes it is what we don’t know and haven’t bothered to ask is what is astounding.  One example of the latter in the field of Oligonucleotide Therapeutics is the poor understanding of which tissues and cell types and therefore disease indications are most appropriate for a particular (delivery) approach based on the ability to engage targets there.   

Antisense Therapeutics, over 30 years in the making, has been the biggest violator of this principle.  Smug in the belief that delivery is not necessary, the approach has been to just apply the oligonucleotide and then pray that it will go to the right place and work its magic, especially in cancers.  Only after decades, the field through much clinical trial and error has come to the realization that the liver and kidney may be pharmacologically favored target organs.

In a long overdue tour-de-force, Hung and colleagues from ISIS Pharmaceuticals recently published in the journal Nucleic Acid Therapeutics a detailed investigation of the global biodistribution and RNaseH knockdown efficacy of phosphorotioate antisense chemistries (PS-ASO) following systemic application: Characterization of target mRNA reduction through in situ RNA hybridization in multiple organ systems following systemic antisense treatment in animals. This parallels a similar study for the direct application of this chemistry to the CNS presented at this year's OTS meeting which has yielded the surprising insight of the broad CNS distribution of PS-ASOs following focal administration. 

As a result of the latest research, a roadmap of target organs was created.  Importantly, through the application of newer RNA immunohistochemistry methods rather than the old harvesting and mashing up organs, the study looked at the specific cell types within an organ that were amenable to RNaseH knockdown.  This is important in at least two ways.  Firstly, it allows us to reject a potential target in organs where bulk knockdowns have shown a rather deep knockdown, but where the detailed organ analysis shows that the particular cell type in which one desired the knockdown does not show such a knockdown (e.g. kidney).  Secondly, it allows one to reconsider targets and cell types within organs for which bulk knockdowns have not been observed (e.g. the small intestines).

Another valuable piece of insight of the study was that it compared the old, second-generation 2’ MOE chemistry with the higher affinity locked nucleic acid chemistry version pioneered by Santaris (in this case the cET ISIS knock-off version of LNAs).  In addition to increasing the knockdown potency in traditional tissues such as liver, kidney, and adipose tissue, the chemistry allows for appreciable knockdowns in some less traditional tissues such as muscles.  Unfortunately, the direct comparison between 2’ MOE and LNAs was only performed in mice and at the very high 50mg/kg dose.  In the non-human primate study, also at a very high (35mg/kg) dose, no such direct comparison was  performed and from this, it seems that the new organs enabled by the higher-affinity chemistries were limited to the muscle and lung.

Why Marina Biotech could be the 2014 high-flyer

Regular readers will notice that I have shifted some of my investment attention to Marina Biotech.  The main reason for this is that this company which is considered by many to be dead, actually owns the rights to a high-affinity ASO chemistry (CRN) of a potency that is equivalent to Santaris’ LNAs and probably superior to ISIS’ cET while the market cap of Marina is just one-thousandth that of ISIS Pharmaceuticals.  Even when one considers that the in vivo safety (especially) and potency evaluations lag behind the others due to the budget constraints of Marina Bio, I believe it is a risk worth taking given the enormous valuation gap and the fact that CRN PS-ASO biodistributions and activities can be assumed to be similar to the competing chemistries.

What is more, Marina Bio is pursuing a program in type I myotonic dystrophy which represents the sweet spot of indications uniquely facilitated by these chemistries: muscle as a new druggable target organ and still shielded from superior RNAi competition; a rare, severe orphan disease; and a toxic nuclear RNA.

Largely depending on the recapitalization strategy (partnering first before capital raise or vice versa), this program together with SMARTICLE RNAi delivery and access to usiRNAi triggers, has made me accumulate 1.5% of the company with the intention of increasing my position.  Of course, financial success can only happen if other investors share my view that we should therefore give Marina Bio another chance.  As always, invest at your own risk and according to your unique financial circumstances.

A shameful title

If you re-read the title of the paper and even the entire publication, you may be forgiven for going away with the impression that it is open season for RNaseH knockdown in muscles and other tissues and organs.  This is far from the truth as the ‘exemplary’ target chosen in the study was the nuclear non-coding RNA MALAT.   This is because a high-profile Nature publication by ISIS Pharmaceuticals itself (Wheeler et al. 2012) has shown that whereas largely cytoplasmic m-e-s-s-e-n-g-e-r RNAs (i.e. RNAs encoding for proteins as even a decent high-school kid will know) expressed in muscles were entirely recalcitrant to RNase H knockdown, the mutated nuclear retained DMPK underlying myotonic dystrophy was susceptible to such action.  Curiously, while Wheeler et al. was cited in the Hung paper, the authors failed to point out this important and very obvious caveat.

This can be no innocuous omission as ISIS Pharmaceuticals in one of their patent applications has expressed the striking difference between mRNA and nuclear RNA druggability by PS-ASOs as follows (highlights are mine):

Reduction of Nuclear-Retained RNA

Data provided herein demonstrates that sensitivity to cleavage by ASOs is dramatically increased for a nuclear-retained RNA making it possible to reduce nuclear-retained targets in tissue that has low uptake of oligonucleotide by a pharmacologically relevant amount. For example, out of the more than 4,000 transcripts that Isis has targeted by antisense, MALAT1, a non-coding, nuclear-retained RNA, is demonstrated to be one of the most sensitive targets for antisense oligonucleotide/RNase H inhibition. The data demonstrate a great number of oligonucleotides targeting over the majority of the transcript that inhibit by more than 50% in vitro. The data also demonstrates very low IC50 values in multiple cell types. Half-life studies have also shown that the MALAT1 is stable over a period of at least 10 hours. Subcutaneous administration of oligonucleotide targeting MALAT1 at doses commensurate with other oligonucleotide drugs (e.g., liver targeting drugs) achieved pharmacologically relevant reduction of MALAT1 in skeletal and cardiac muscle. Dosing at 50 mg/kg biweekly for 3.5 weeks achieved a 89% and 85% reduction in gastrocnemius and quadriceps, respectively, and 54% reduction in heart (as compared to 95% reduction in liver). Pharmacologically relevant reduction of MALAT1 has also been achieved in tumor xenograft models.

As a member of the Oligonucleotide Therapeutics Society, it greatly saddens me that the related journal is letting ISIS Pharmaceuticals get away with the highly misleading, and simply wrong title.  There is no arguing around it.  Followers of the competitive oligonucleotide therapeutics investment arena know that the game here is to make RNaseH antisense appear much more widely applicable than it actually is.  What is more, it was at the 2011 OTS meeting in Boston where the ISIS CEO Stan Crooke in his keynote made the ignonimous statement that ‘mipomersen has no side effects’.  

I strongly suggest to the society and the journal Nucleic Acid Therapeutics which are supposed to foster the development of the technology broadly to keep a watchful eye on the growing corporate influence, especially by 'generous sponsors' ISIS and Alnylam Pharmaceuticals.   

ISIS Pharmaceuticals Next-Gen cET Technology on Shaky Grounds

As I was listening to a presentation by ISIS satellite company Regulus Therapeutics at the Future Leaders in the Biotech Industry Conference last week, I noticed that the fight between ISIS/Regulus and Santaris over intellectual property has increased in bitterness. On the same day, Santaris announced that the USPTO had rebuffed the second patent challenge concerning its conformationally constrained nucleotide technology (LNA).  As ISIS and Regulus have decided on making the LNA-derived cET technology their next-generation antisense technology, the increased aggression (including an ongoing gapmer patent infringement suit brought by ISIS against Santaris) may indicate that also ISIS sees cET technology on shaky IP grounds.

Thanks for the Validation!

Even during the hard-fought Tekmira vs Alnylam battle, the participants largely refrained from making direct snarky comments.  This, however, cannot be said of last week’s presentation by Regulus, when it sarcastically thanked Santaris for being years ahead in their miR-122 HCV program and doing all the clinical validation- for them.  The comment obviously refers to the fact that Stanford University had licensed the seminal Sarnow patent related to miR-122 inhibition for HCV therapy to Regulus, not Santaris.  It is also what made GSK dump Santaris and partner with Regulus on the program instead.  I would agree that Regulus has a strong case in this matter, but the unmitigated sarcasm was remarkable.

Is it all about cET?

When ISISfirst reported on their next-generation (gen 2.5 that is) nucleotide modification, it (cET) was explicitly derived from LNAs.  The rationale was that although LNA is the most potent antisense technology around, it suffered from poor safety (as supported by the premature termination of the PCSK9 and ApoB programs by Santaris).  Consequently, additional moieties were incorporated into the bridge that fixes the conformation of the backbone ribose in place.  As a result, the high affinity of the parent LNA was retained, but the safety issues were apparently overcome.

As a LNA-derived technology, the obvious question is whether Santaris, which controls fundamental LNA patents, has IP rights in cET.  Given the importance of cET to ISIS Pharmaceuticals and Regulus such uncertainty is intolerable.  Hence, it would make sense for ISIS and Regulus to attack Santaris and its LNA patents, which is exactly what ISIS has been doing.  Two such pre-emptive strikes, however, have failed according to last week's news.  And as a pre-emptive reminder on my part, a patent only gives you the right to exclude, not freedom-to-operate.

The gapmer patent infringement suit against Santaris may thus be viewed as an effort to get Santaris to the negotiating table.  The miR-122 situation, albeit unrelated to the LNA issue, would be further ammunition to ISIS and Regulus in that effort.

Expect the confrontation to get heatier still, as Santaris should strike back as the overall strategy by ISIS Pharmaceuticals, which is continuing to closeone deal after the other, seems to be working despite the lost patent re-examination battles last week, and is taking away the financial oxygen from Santaris.

Register for the GTC RNAi Research and Therapeutics meeting in San Francisco today (June 20-21).  Get a free RNAi Therapeutics blog T-shirt and 20% discount on registration by entering discount code 'RNABLG13'.

ISIS Claims Scalp of Santaris CEO

After noticing that the former President of the US operations of Danish LNA antisense company Santaris, Art Levin, had just joined muscle microRNA Therapeutics company miRagen, I was alerted that this has been in the wake of a major shake-up at Santaris. Most notably, it appears that the CEO of Santaris, Soren Tulstrup, either handed in his resignation, or, more likely, was let go.


Privately-held Santaris, of course, has been a fierce rival of ISIS for supremacy in the antisense space.  Having former ISIS insider Art Levin join Santaris 2 1/2 years ago was in fact a bit of a coup for that company.  Its LNA technology is probably the most potent/high-affinity in the space for many applications.  ISIS, however, has had the benefit of increased financial might and having built a large patent estate that it is (ab-)using to sue, preferably smaller competitors with the obvious intention of making it difficult, if not impossible for those to raise capital and pursue business development opportunities.  It is rumored that ‘partner’/satellite company Alnylam has probably paid the price in the tens of millions for the privilege of going public.   


Not long ago, ISIS sued Santaris for unduly hiding under the Research Exemption in its various relationships including Pfizer, Enzon, GSK, and Shire.  In parallel, ISIS and microRNA spin-off Regulus have been haunting Santaris by questioning Santaris’ ability to develop its exciting lead candidate, miravirsen, a miR-122 antagonist for the treatment of HCV.  As a result, Santaris was dumped by GSK in favor of Regulus’ miR-122 program despite having the superior data package, which is also born out by the clinical data so far (here for the latest update at EASL).


Regulus announced this week that it was awarded another HCV miR-122 patent, in Japan, concluding with the remark that it was continuing to pay 'attention to hepatitis C'- somewhat ironical given that its clinical entry seems to be delayed forever.  Seeing that announcement, I had thought that this was one of the unnecessary PRs that I often take as a sign of weakness. In hindsight, it was probably just a case of adding insult to injury.


I myself have had reservations about the wisdom of building the company’s financial future on a program for which it may be lacking access to some of the key patents in the space.  Although one may assume that in the wake of its scientifically leading efforts in miR-122/HCV, Santaris will have in turn built IP to which Regulus would need access if it were to develop its own miR-122 antagonist,  such a strategy has been a high-stakes gamble for sure.  Along with the ISIS lawsuit questioning Santaris’ fundamental business development strategy, I would therefore not be surprised if the CEO had faced some tough questions by Santaris' investors about his decisions and consequently was ousted. 


Clearly, an exit in the form of an IPO or takeover had long been overdue for that company.  The company’s technology, pipeline, and relationships, also in light of what’s out there already (i.e. ISIS and AVI Biopharma), should have easily supported this, if not for the lawsuit and threats thereof.

SNALP RNAi versus RNaseH Antisense for Gene Knockdown in the Liver

Following recent phase I results from ISIS Pharmaceutical’s Factor XI (ASH abstract 12999; addendum: PR on phase I data reported on December 12) and Apo C III programs, there is little doubt left that phoshorothioate-based RNaseH antisense as developed by this company and Santaris can mediate target-specific gene knockdown in the liver in Man. These results confirm the clinical experience with the registrational hypercholesterolemia candidate mipomersen and are corroborated by the impressive HCV results obtained by Santaris’ with its anti-miR122 HCV candidate. Beyond the liver, RNaseH efficacy has been demonstrated for solid cancer (custirsen) and possibly Excaliard’s (now Pfizer’s) anti-scarring candidate. On the other hand, the recent trial termination(s) by Santaris, and the safety profiles of mipomersen and OncogeneX' custirsen highlight some of the challenges facing phosphorothioate antisense technology.

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Therefore, as RNAi Therapeutics have progressed from the basic discovery of its mechanism in mammals 10 years ago to solid proof-of-concept gene knockdown in the form of the ALN-TTR01 results 2 weeks ago, it may be a good time to compare and contrast these two technologies also in light of the fact that, after the RNAi Therapeutics backlash, there is a clear trend towards Big Pharma (and other pharmaceutical companies) opening themselves up again towards antisense, meaning that the 2 technologies are competing for precious non-dilutive funding. For this purpose, I will focus on the liver as the best developed target organ for both these technologies.

20 to 100-fold more antisense required

An obvious advantage of antisense, with about 3x the age of RNAi Therapeutics, is that more is known about its clinical pharmacology. As such, there is good visibility as to how much antisense will be needed to achieve the kind of 50-75% knockdown that will be required for therapeutic outcomes in most cases. Dose has important implications particularly in terms of safety and cost.

Current ‘2^nd gen’ molecules (fully phosphorothioated gapmers) like mipomersen require 200mg oligonucleotide per week. Actually, if 300-400mg would have been better tolerated, the higher dosages would have enhanced the commercial profile of mipomersen considerably. Let’s therefore say 1000mg per month for 2^nd gen RNaseH antisense.

With the higher-affinity ‘2.5 gen’ technologies that are starting to move into the clinic, best exemplified by Santaris’ LNAs which in fact may also symbolize the most potent version, it is expected that clinical dosages can be further reduced. Based on the non-human primate data and clinical dosage regimes, I expect that dosages of around 100mg/week or 500mg per month are feasible in the foreseeable future. Also because of the modifications involved, I would be therefore very surprised if the cost of oligonucleotides for treating a patient over a year would be below $15,000 even at commercial scale.

By contrast, it can be expected that it will take about 0.15mg/kg of siRNA formulated in the ‘2^nd gen’ SNALPs that are now moving into the clinic to achieve the type of once-a-month pharmacology that Tekmira and its licensees are aiming for. If you do the math, that translates into about 10mg per month of siRNA oligonucleotides. Give and take the added costs of the lipids and formulation process, but cheaper nucleotide chemistries involved, this translates into a maybe 50-fold cost of goods difference alone. For some diseases and in some countries, this may be less of an issue, but it will be a factor for others.

Safety

The even larger implications of dosage is the related safety. Although clinical repeat-administration studies with SNALP have yet to be conducted, it seems that with the 2^nd gen SNALP formulations, the main safety challenge with SNALP will be in managing acute hypersensitivity reactions around the time of drug administration. Based on similar issues with intravenously administered biologics such as monoclonal antibodies where e.g. transient immune suppression with steroids is routine (and widely accepted), I believe that infusion-related acute toxicities will be manageable.

What is nice with the pharmacology of SNALP RNAi Therapeutics is that the bulk of the drug that does not hit the target, i.e. gets incorporated into the RISC silencing complex, is rapidly turned over by the body, meaning that drug exposure levels between drug administrations will be extremely low. It is because of this that I am hopeful that the risk of causing liver toxicity, long believed to be the main toxicity challenge for SNALP, is quite limited at dosages of 0.15mg/kg/month.

By contrast, RNaseH antisense do not harness a natural gene silencing mechanism and, in the case of the phosphorothioate-based gen 2 and gen 2.5 antisense, work by saturating the target (and off-target) organs with high levels of the ‘sticky’ phosphorothioated oligonucleotides so that mass action carries enough of them into the cells. Consequently, the exposure of the body to the antisense drug is significantly higher compared to SNALP-delivered siRNAs. Assuming ~100-300mg of antisense oligonucleotide per kg of liver or kidney tissue (e.g. ISIS TTR patent application US 2011/0294868) and single-digit microgram siRNA oligonucleotide per kg of liver tissue (e.g. Landesman et al. 2010), you could argue that the real difference in bioburden between antisense and SNALP RNAi is about ten thousand fold. It also does not take into account that it is the sticky phosphorothioate chemistry that is thought to be responsible for much of the toxicity (interactions and turnover) whereas RNAi triggers employ more natural chemistries. On the other hand, double-strand RNAs are recognized by more innate immune receptors than highly modified, single-stranded oligonucleotides.

Route of administration

Although the subcutaneous administration of SNALPs has been demonstrated (see e.g. Tekmira's ApoB patent) and may become practical with the higher potencies of SNALPs and extracellular matrix-degrading technologies as developed e.g. by Halozyme, antisense is currently more amenable to subcutaneous administration whereas SNALP have to be infused in an institutional setting. This means that, as is the case for essentially all monoclonal antibody drugs, SNALP drugs have to address diseases of considerable unmet medical needs where patients do not perceive a once-a-month trip to the infusion center a huge burden. Maybe Pfizer can't, but I can think of many such diseases. Infusion in an institutional setting also has the advantage that acute toxicities, the main safety challenge for SNALPs, can be well managed through professional supervision, whereas patients that inject themselves with antisense at home may be slightly panicked on seeing redness develop at the injection site or on experiencing ‘flu-like symptoms’ that have been reported to occur at high frequency with antisense (often 1/3 to 1/2 of patients), but has surprisingly been little discussed by ISIS Pharmaceuticals.

Manufacturing

Like route of administration, manufacturing is considered to be a practical advantage of antisense over SNALP RNAi. I agree…in purely practical terms. What is, however, entirely forgotten is that as long as you can deal with the manufacturing complexities, it suddenly gives you an invaluable competitive advantage. How about unlimited market exclusivity? Isn’t one of the lessons that Big Pharma should have learned from the current patent cliff that simple small molecule chemistries are highly vulnerable to generic competition? Isn't this also a major reason for why everybody obsesses about monoclonal antibodies these days, yet is often strangely held against SNALP RNAi? To my knowledge, there are no generics of a nanoparticle-formulated drug.

So in summary, as antisense has reached an inflection point as a slew of clinical data is confirming the early clinical results with mipomersen from 6-7 years ago which demonstrated gene knockdown in the liver, SNALP RNAi is making even faster progress with many of its theorized advantages, especially related to the amount of oligonucleotide required and pharmacology, turning into clinical reality quickly. The race is on. The most likely winners meanwhile are the patients.

RNAi Therapeutics Investors Hoping for a Merry Christmas

I’ve just come back from working at the Starbucks across my street which strongly reminded me that Christmas was just around the corner. Christmas this year in RNAi Therapeutics is synonymous with data releases by Alnylam from its transthyretin amyloidosis (ALN-TTR01; data presentation November 20-22 in Japan) and hypercholesterolemia (ALN-PCS02; release of top-line results by year-end) phase I clinical trials. These have the potential to demonstrate, for the first time, direct and physiologically meaningful target gene knockdown following systemic RNAi delivery, and thereby have the potential to turn around still negative RNAi Therapeutics sentiments and depressed valuations.

Some of the anticipation can already be felt in the form of appreciating share prices of Alnylam and Silence Therapeutics, together with Tekmira the companies most directly exposed to the current RNAi Therapeutics dataflow, and the financial analyst-investment community which have turned noticeably bullish on Alnylam. Only Tekmira, the inventor of SNALP technology that powers ALN-TTR01, ALN-PCS02 and 5 other candidates in or close to clinical development, has not participated in the rally by failing to find investors willing to defend its stock after taking on well-connected Alnylam.

In assessing the data, a primary focus will be on whether dose escalation was able to proceedeup to the highest planned doses (1.0mg/kg for ALN-TTR01 and 0.25mg/kg for ALN-PCS02) and whether, despite the small number of patients at the high dose levels, there are clear signs for target gene knockdown. 50% target gene knockdown in both cases would be reasonable goals, and probably also necessary ones to have the desired impact. In the case of ALN-PCS02 there should also be at least a 30% reduction in ‘bad’ LDL-cholesterol, the intended pharmacologic outcome of a PCSK9-targeting agent. In terms of safety, the absence of grade 3 adverse events or worse would be highly welcome, of course, as we would be the absence of consistent and clinically meaningful innate immune activations.

Santaris’ anti-miR122 HCV Drug Continues to Impress

MicroRNA Therapeutics seems to have found its poster child already with Santaris’ miR122 LNA antagonist for the treatment of HCV. In an oral presentation at The Liver Meeting which is just wrapping up in San Francisco, the company reported robust dose-dependent anti-HCV activity in a phase IIa study, with close to a 3-log mean reduction of HCV RNA from baseline and viral load below detection in 4 of 9 patients at the highest dose of miravirsen (7mg/kg). The corresponding abstract marking a milestone in microRNA Therapeutics by reporting first clinical activity of an microRNA Therapeutic was released in early October (click here for commentary). There is no doubt that this drug candidate works as expected/hoped for, and unless the future of HCV treatment is in all-oral combos, anti-miR122 with its uniquely differentiated mechanism of action looks like a valuable addition to the fast-moving field of HCV care.

Santaris Terminates PCSK9 Hypercholesterolemia Trial

Antisense company Santaris seems hardly able to catch its breath these days. After being sued by ISIS Pharmaceuticals for patent infringement, reporting first clinical proof-of-concept for a MicroRNA Therapeutic, it has now been revealed that the company prematurely terminated a phase I trial of its PCSK9 phosphorothioate LNA RNase H antisense inhibitor SPC5001 for the treatment of hypercholesterolemia. This study had been initiated in May of this year with an estimated enrollment of 40 healthy and familial hypercholesterolemia subjects.

Reasons for the trial termination were not revealed. However, since this was a phase I safety trial, it is likely that the trial termination was due to some safety issue. Supporting this is that, coinciding with the PCSK9 trial termination, enrollment has been halted in another phase I hypercholesterolemia trial sponsored by Santaris, this time targeting ApoB (SPC4955).

Consequently, after the premature trial termination last year of BMS/ISIS’ phosphorothioate 2’ MOE RNase H PCSK9 antisense inhibitor (BMS-844421), Alnylam’s SNALP-delivered ALN-PCS has suddenly taken the lead in the race to develop a PCSK9-targeting RNA Therapeutic, pitting it against the monoclonal antibodies by the likes of Regeneron and Amgen.

Without explanations for the trial terminations, it is difficult to pin down the exact cause(s) of the presumed toxicities. What the compounds by Santaris and BMS/ISIS Pharmaceuticals obviously share is that they both use phosphorothioate chemistries and work via an RNaseH mechanism. Phosphorothioates are widely used in antisense development because they bind to proteins in the plasma and various tissues, thereby allowing one to achieve tissue concentrations high enough such that mass action will allow for cell penetration and target gene knockdown. In my opinion, phosphorothioate oligonucleotides are promising for a number of local applications. The problem with systemic applications, however, is that the high concentrations reached in tissues such as liver, spleen, and kidney, ultimately limit their therapeutic window. Some industry experts have referred to this issue as the ‘hazardous waste’ problem of systemic phosphorothioate oligonucleotides.

ISIS supporters will point out that Santaris’ specific LNA chemistry is the most likely culprit, whereas ISIS’ chemistries are relatively safe as supported by ISIS’ comparative studies. Of course, these studies were published to make Santaris look bad, just as the recent lawsuit was aimed at blunting Santaris’ competitive threat. Conspiracy theorists may even suspect that the sudden turmoil around Santaris is no coincidence and was orchestrated to inflict maximum damage at a time that Santaris seemed to be on a roll with a number of trial initiations, positive HCV data, and depriving RNAi Therapeutics of a deal with Pfizer (Pfizer apparently being attracted to ‘naked’ oligonucleotide approaches over RNAi nanoparticle ones). However, if Santaris intended to go public to satisfy its increasing cash needs (maybe less so with the trial terminations), it can probably scratch that now.

RNA Therapeutics is intensely competitive as they compete for pretty much the same investment dollars. Investors, including Big Pharma, are easily influenced by public opinions and fashion trends. 4 years ago it was all about the fear of being left behind in RNAi Therapeutics, with little attention being paid to true enablement and expertise in a noisy field. This made antisense look like the ugly cousin. In the last 2 years, however, antisense has regained favor as the RNAi delivery ‘problem’ became widely publicized which made antisense look deceptively simple. Santaris especially made a living of that by advertising, e.g. at conferences and press releases, the delivery problem of RNAi Therapeutics and getting a few laughs by stating their motto of 'staying naked’ and ‘staying short’.

Needless to say, my favored technology is RNAi Therapeutics: ‘natural’ and ‘potent’ is my motto. The hypercholesterolemia arena will be a particularly good battleground for antisense and RNAi Therapeutics to test their metals: same targets, easy biomarkers, chronic applications. The next chapter will be top-line data from Alnylam’s ALN-PCS phase I trial which are expected by year-end.

Santaris Reports Clinical Efficacy of Anti-miR122 Treatment for HCV

Santaris reported yesterday intriguing antiviral HCV efficacy results from an ongoing phase IIa study of miravirsen, Santaris’ LNA-based antisense inhibitor of microRNA-122 (miR-122), miravirsen, an important host factor in HCV replication. Full interim results will be presented in a late-breaking oral session at the upcoming AASLD, The Liver Meeting.

The phase IIa study investigates 3, 5, and 7mg/kg of miravirsen, given weekly to treatment-naïve HCV patients subcutaneously for 29 days. According to the abstract, with the study now in the 3^rd and last dose cohort, patients in the second, 5mg/kg cohort showed very encouraging mean reductions in viral plasma RNA levels from baseline of up to 2.5logs when miravirsen was given as a single agent compared to placebo control. 5 of the 9 miravirsen subjects had reductions of more than 2 logs (>100-fold) with viral RNA in one patient becoming undetectable 10 weeks after the dose. Although the cohorts were relatively small, 9:3 drug:placebo, almost all efficacy measurements reached statistical significance.

What was interesting is that the decline in viral titers was quite prolonged, with the biggest viral reductions being observed after treatment had finished. While having prolonged drug activity per se is positive, the gradual decline is not optimal as it increases the chance of selecting for escape mutants, a major issue in HCV treatment in general and reason why the industry is busy developing new HCV treatment options to be added to the arsenal. In fact, a recent study out of Denmark showed that it is possible to select for HCVs that do not require miR-122 for replication, at least in tissue culture systems. On the other hand, given that miravirsen is targeted at a host factor and since the miR-122-viral interaction occurs at conserved sites, it may be relatively more difficult for the virus to develop such resistance as compared to for example direct antivirals. I would expect the company to report sequencing data at the conference next month.

Irrespective of the viral escape issue, slow clinical responses may also make it somewhat more difficult to integrate miravirsen into the newly emerging treatment paradigms, one aim of which is the reduction of treatment times. Here, RNAi Therapeutics would have an obvious advantage over miravirsen by acting much more rapidly than phosphorothioate antisense oligos which rely on tissue enrichment over time. This is also supported by the data that were recently reported by SomaGenics in collaboration with Tekmira and Roche.

On the safety front, the abstract noted the absence of drug-related serious adverse events. It did, however, note that among the supposed biomarker signals for anti-122 efficacy was an elevation of alkaline phosphatase (ALP) levels. ALP elevations are normally considered a marker of liver injury similar to ALT/AST, so I am not really sure how why this is not considered a safety signal. We will therefore have to for the conference presentation to learn more about the safety profile of miravirsen.

Overall, with the demonstration of antiviral activity and reductions in cholesterol levels which further support functional inhibition of miR-122, the abstract marks an important milestone in the development of microRNA Therapeutics: The first unambiguous demonstration of MicroRNA Therapeutic activity in Man.

Roche AASLD RNAi Therapeutics abstracts: HCV and LNP

Roche will present at the AASLD meeting on two RNAi Therapeutics studies. Both studies involve LNP01, which I assume involves ‘lipidoid’ LNP delivery chemistry. In one study, Roche and their academic collaborators targeted a host factor believed to be involved in the development of HCV drug resistance, especially to the interferons which are at the risk of becoming replaced and, unsurprisingly, Roche would like to revive that franchise. The abstract, together with the recent SomaGenics/Tekmira revelations, further demonstrates that Roche had been quite interested in RNAi Therapeutics for HCV. It also makes me think that maybe Novartis has not picked HCV as a target under Alnylam IP which would e.g. allow Tekmira to step into the void- well, if it saw any reason to do so, maybe out of strategic considerations.

The other abstract concerned potential innate immune stimulation elicited by LNPs. Consistent with what had already been known or suspected, TLR7/8 are the major innate immune receptors and cause of LNP hepatotoxicity, and this can be alleviated by simple 2’-O-methylation as demonstrated before by Tekmira before. What was particularly nice though in this particular study was that with the use of TLR3 knockout mice, TLR3 can now essentially be excluded as a significant tox factor for LNP delivery.

Read also: Miravirsen shows efficacy in HCV chimpanzee models.

ISIS Files Aggressive Lawsuit against Santaris

It is not a big secret that antisense therapeutics companies ISIS and Santaris are fierce competitors. Today, ISIS filed an unusual, because rather aggressive lawsuit against Santaris Pharma that alleges the Danish company to be selling to the industry technology that is covered by at least two of ISIS’ literally thousands of patents. Because ISIS considers itself the gate-keeper of oligonucleotide therapeutics, and because some of the business development in RNAi Therapeutics has probably occurred under the mantle of the Research Exemption, a ruling in favor of ISIS Pharmaceuticals could have wide ramifications, actually well beyond oligonucleotide therapeutics.

Under the Research Exemption doctrine, the result of Merck vs Integra, it is generally assumed that patented technologies can be used for research purposes quite broadly as long as product, in this case drugs, are not marketed. Without this safe harbor, much of the preclinical pharmaceutical research and academic research would be a legal nightmare.

Nevertheless, ISIS believes this standard does not apply here, because Santaris in a way is selling ISIS technology as part of its platform partnerships. These include relationships with Pfizer, Enzon, GSK, and Shire. Moreover, it probably irks ISIS that Santaris has been rather successful in its business development efforts, and even had the guts to hire a former top ISIS executive, Art Levin, to set up a business development branch in ISIS’ backyard San Diego.

My impression is that Santaris’ LNA-based antisense compounds are more potent than ISIS’ generation 2.0 2’-MOE phosphorothioate gapmers, and this is why Santaris is likely to be the more attractive company to partner from a technical point-of-view. ISIS apparently has realized this as well as it is following Santaris' example in developing conformationally constrained (‘locked’) nucleic acid chemistries (expect Santaris to counter-sue ISIS on that). Anti-miR122 for the treatment of HCV infection is one example where Santaris’ data have been more promising than Regulus’ using ISIS chemistries. Ironically, GSK dumped Santaris’ stronger science on HCV in favor of Regulus for what had to be concerns about IP (I believe though that it was miR-122-specific IP, not antisense platform-related IP that was responsible for GSK’s move).

I don’t want to speculate whether Santaris in fact makes use of technology covered by ISIS patents or not. It is, however, a case worth watching for the entire pharmaceutical industry. Closer to home, it illustrates how aggressive, and so far successful ISIS is in using its sheer number of patents in ‘extorting’ concessions from other oligonucleotide therapeutics companies. Wherever you look, ISIS is getting a piece of the pie. I have been studying ISIS’ patents with regard to RNAi Therapeutics, and cannot really find anything of value there, except maybe if you are interested in using the 2’-fluoro modification which is useful, but dispensable. Still, ISIS was able to extract surprising concessions from Alnylam when Alnylam IPO’d a few years ago and has even called Alnylam a ‘satellite company’ without much public protest by Alnylam. Same story with the multi-million $ that Alnylam gave ISIS for the ill-fated single-strand RNAi collaboration. It goes to show that when it comes to public perceptions and business development, quantity and brand recognition often still trump quality and due diligence.

Post-scriptum (9 October, 2011): On October 7, Exiqon and Santaris on October 7, 2011, settled their legal differences that resulted from Santaris suing Exiqon for selling LNA-based reagents that were used for the development of drugs incorporating LNAs,,,and thus would not fall under the Research Exemption- an ironic twist of fate. In the settlement, Exiqon paid Santaris a minimal amount. It is difficult to conclude from this anything about the outcome of the ISIS-Santaris litigation.

Impressions from the Abstracts of the 7th Annual Meeting of the Oligonucleotide Therapeutics Society (Part 1)

The Annual Meetings of the Oligonucleotide Therapeutics Society are among the best on the conference circus related to, well, oligonucleotide therapeutics drug development. One benefit of bringing together RNAi Therapeutics, traditional RNaseH and steric block antisense, aptamers, and a few other oligo-based approaches is that researchers can benefit from sharing lessons in safety, how pharmacology relates to chemistry and formulation, manufacturing etc. Remember, it is the experience with older oligonucleotide technologies that allowed RNAi Therapeutics to take 10, instead of 20 or 30 years, to get to where it is today: over a 1000 patients and healthy volunteers dosed with more than a dozen of RNAi candidates exhibiting a decent, and improving safety profile; the ongoing Atu027 and ALN-TTR01 trials having reached dose levels where, based on sound science, robust target gene knockdown, technologically the primary objective, can be expected. Moreover, data from hypercholesterolemia, solid cancer, ocular and respiratory disease studies have provided evidence of dose-related therapeutic efficacy.

Not able to attend the 7^th Annual Meeting to be held this week in Denmark myself, I eagerly went through the abstract book to learn of new developments and trends. Here are my thoughts on a few select abstracts that I thought might be of interest to the readers of this blog (presented in the order they appear in the book). Note that if you are a Tekmira investor, keep reading until the end. Part 2 of the discussion can be found here.

Oral presentation: Expanding the structural diversity repertoire of siRNAs (Dong-Ki Lee, Sunkyunkwan University, Korea)

This presentation highlights the realization that a number of non-Tuschl RNAi trigger structures are not just IP workarounds, but can be used to achieve novel biological outcomes such as targeting multiple genes with one RNAi trigger molecule (multipodal structures), inducing select innate immune stimulation while at the same time silencing genes (long siRNAs), and reducing off-targeting (asymmetric siRNAs and ‘wobbly’ siRNAs).

Oral presentation: Activation of RNA interference in animals with single-stranded oligonucleotides (Erice Swayze, ISIS Pharmaceuticals)

For some indications, the intravenous application of the nanoparticle RNAi formulations which are leading in terms of in vivo RNAi gene silencing potency may be a commercial drawback (for the purpose of long market exclusivities, I believe it is a widely underappreciated benefit). ISIS Pharmaceuticals, until recently in collaboration with Alnylam have been working on naked single-strand RNAi (ssRNAi) solutions that can be administered subcutaneously.

It has been long known that ssRNAs can induce RNAi gene silencing, just 100-1000 less efficiently, which is not surprising since RNAi has evolved as a dsRNA-induced mechanism. The abstract claims that using fully modified, partially phosphorothioated ssRNAs, they were able to come within 5-fold of the potency of corresponding double-stranded structures. The initial animal experiments, however, seem to have failed due to ssRNA instability, but after further modifications they have now achieved activity at ‘pharmacologically relevant doses with subcutaneous administration in saline formulations’.

Certainly an interesting abstract and it remains to be seen just how pharmacologically relevant these doses are and the related safety profile. Similar, or better to their current RNaseH antisense? ssRNAi...ISIS’ antisense 3.0? Another interesting question is at what point did Alnylam drop the ball on ssRNAi after considerable investments- before or after the initial animal experiment failures?

Oral presentation: Delivery of Nucleic Acids (Muthiah Manoharan, Alnylam)

Alnylam’s oral presentation will be, you already guessed, about RNAi delivery. By listing 25 papers on two pages without any meaningful comment or discrimination, the abstract obviously wants to make the point that Alnylam is the leader also in RNAi delivery. Somewhat reminiscent of Alnylam’s press releases that used to list seemingly all their RNAi trigger-related patents, no matter how relevant to their gate-keeping potential which was the reason for listing them in the first place. As such, the abstract carries the dubious distinction of being the longest one of the conference, but the one with arguably the least content.

It is not the amount of money spent, the numbers of patents (‘thousands’), or papers published that makes you a leader in RNAi Therapeutics.

Oral presentation: Non-covalent peptide-based delivery systems (Divita, CRBM-CNRS-UMR5237, Montpellier, France)

This abstract concerning a non-covalent cell penetrating peptide-siRNA systemic delivery technology to me has firstly sentimental value. This is not a specific criticism of the work to be presented, a body of work that is buttressed by some credible data, but the abstract still reminds me of the early days when RNAi Therapeutics was hot…hot, hot, and all kinds of, sometimes wild, delivery claims were made: oral, blood-brain, all organs to name a few keywords.

While I wished that there was more excitement around RNAi Therapeutics right now as the negativity, particularly in the commercial arena, threatens to choke deserving technologies, the one benefit of RNAi being less hyped and exploited for fund-raising purposes by the biotech promotion machinery is that the overall scientific credibility index has increased. This can also be seen from the abstracts at this year’s OTS meeting.

Oral presentation: Investigating the potential of therapeutic oligonucleotides for pulmonary diseases (Clark, GSK)

GSK and AstraZeneca are probably the two Big Pharma companies most interested in RNAi/oligonucleotide Therapeutics for pulmonary diseases. This is an area with high unmet medical needs and new therapeutic approaches are needed here more than anywhere else. There are fundamentally two different approaches to knocking down genes in the respiratory tract: local delivery by aerosol inhalation, or through systemic delivery. Based on the abstract, GSK seems to be primarily interested in inhalation methods.

Among the companies having explored inhalation are Alnylam, ISIS’ respiratory disease spin-off Altair, and most recently Tekmira. It has become obvious that Alnylam’s naked siRNA approach (e.g. in ALN-RSV01) is sub-optimal and conjugation plus chemical modifications need to be applied to give such ‘semi-naked’ routes a chance. Altair meanwhile has closed down following phase II results with their naked MOE gapmer antisense candidate for asthma. Based on Tekmira’s track record of publicizing only meaningful scientific progress, Tekmira's aerosolized LNP approach is to be considered a serious contender for the leadership position in gene knockdown in the respiratory epithelium. Tekmira this year has presented data that its aerosolized LNPs retain the ability to knockdown genes in tissue culture. It is quite possible that GSK was/is the undisclosed Big Pharma collaborator for this program.

Silence Therapeutics, probably more by necessity than choice, takes a systemic approach towards gene knockdown in the lung using their intravenously administered lipoplexes (DACC). Actually, since Silence’s and Tekmira’s technologies may be best suited for endothelial and epithelial cell knockdown, respectively, the two approaches are complementary. It would make sense if AstraZeneca had some familiarity with Silence’s DACC technology.

Abstract #9: [3H]-radiolabeling of siRNA (Christensen, Novartis)

Abstract #86: Characterization of side reactions during the annealing of siRNA (Noll, Roche)

I list the two abstracts from Novartis and Roche here together because I believe they illustrate the cultural differences between Big Pharma and pure-play RNAi companies. While pure-play companies emphasize biology and developing new RNAi trigger and delivery solutions, the established pharmaceutical companies are apparently more concerned about manufacturing and pharmacology methods. It is obvious that manufacturing and pharmacology is an essential part of the game, and such work is also happening at pure-play companies and their outsourcing partners, but such work obviously does not address the rate-limiting challenges and Big Pharma, perhaps with the exception of Merck, willfully relies on accessing that from the pure-play companies.

Abstract #16: Inhibition of complement C6 synthesis in the liver using antisense oligonucleotides affects neuro-regeneration (Fluiter, Academic Medical Center, Amsterdam, Netherlands)

This abstract highlights that by knocking down a gene in the liver, one can have therapeutic benefits for a wide range of non-liver diseases, such as neurodegenerative diseases. This is not really surprising given that all organs almost exclusively depend on their development and function on what they are provided for by the blood. Proteins made in the liver constitute the majority of free proteins in the blood and consequently impact all organs. Complement proteins which play a critical in immunity are one example of such proteins. As most diseases contain a complement-related immune/inflammatory component, RNAi Therapeutics could be a tool for modulating a wide range of autoimmune and other hypersensitivity disorders.

This principle of inhibiting a target in one organ to address disease in others (see e.g. transthyretin amyloidosis) is in contrast to other, post-translational therapeutic drug modalities that target the liver for which the therapeutic benefit is almost always restricted to the liver. As such, the medical and commercial potential of RNAi delivery technologies that work well for gene knockdown in the liver is larger than widely appreciated.

Abstract #27: Thirteen week non-clinical testing of miravirsen in cynomolgous monkeys (Hildebrandt-Eriksen, Santaris)

This abstract concerns the toxicological evaluation of Santaris’ exciting phase II LNA anti-miR122, a LNA-modified phosphorothioate steric block antisense, for the treatment of HCV infection. Despite the successes of the recently approved protease inhibitors for genotype 1 HCV, there is still considerable unmet medical need, including for those with less drug-responsive genotypes or those high-risk patients that have failed on established therapies.

Presenting on home soil, the reported toxicities were in line with expected class effects of phophorothioate oligonucleotides, including slight, but relatively persistent clotting abnormalities which was not judged an adverse side effect because of the apparently small extent of the increase; reversible kidney toxicities at doses above 10mg/kg (the effective dose of miravirsen is likely between 2 and 5mg/kg); and finally some enlargements in macrophages which does not appear to be of too much concern. Note that because miravirsen is not intended for chronic use, this safety profile may be adequate. In addition to liver toxicity, it appears however that the kidney toxicity will be something to watch out for in the development of miravirsen.

The first phase II study of miravirsen has just completed enrolment according to clinicaltrials.gov and I look forward to learning about the results in due course.

Abstract #30: Lipid nanoparticle formulations of minimal-length shRNAs show potent inhibition of HCV-driven, liver-specific gene expression in mice (Johnston, Somagenics- in collaboration with Tekmira)

This abstract concerns the evaluation of 40-50 nucleotide hairpin RNAs with Tekmira’s LNP delivery technology for liver gene knockdown (in this case using HCV as a model system). It is not a surprise that the abstract shows that Tekmira’s LNP technology works with various RNAi triggers. The real new insight for Tekmira investors, however, is that Tekmira did not go into this litigation in a way that its access to payloads would be threatened as a loss of access to Alnylam’s RNAi triggers may very well be one of the outcomes that could facilitate a settlement. Instead, Tekmira must have been evaluating various RNAi trigger structures and presumably other nucleic acid payloads as well, and when it chose to exclusively license Halo-Bios multivalent RNAi triggers one has to assume that this was after an extensive evaluation of their safety and potency.

Whether there will be a similar arrangement with SomaGenics remains to be seen. Synthetic shRNAs are credible RNAi triggers and may in fact have some advantages over two-stranded approaches, e.g. highly efficient unimolecular annealing. However, their development has been held back by increased cost of goods associated with such long oligonucleotides and concerns about clogging up the RNAi enzyme Dicer (probably not an insurmountable challenge). A licensing decision may also depend on how broad SomaGenics' intellectual property is with regard to shRNAs. It is highly unlikely that SomaGenics has any gate-keeping claim in this area, and partnering with them would have to be driven by their shRNA-related know-how.

To be continued...(for part 2 click here)