Wednesday, March 27, 2013

The Time for the U(nusual)siRNA Strategy Has Come

As Tekmira and Arrowhead Research will unveil their next RNAi Therapeutics development candidates later this year, an interesting question will be whether these will involve one of their RNAi trigger options that some consider to be unencumbered by fundamental IP related to traditional designs (esp. the Baulcombe and Tuschl II IP).  These decisions could have important strategic consequences for the competitive landscape, from targets and indications to Big Pharma involvement.   

Support for freedom-to-operate claim

One of these designs is the usiRNA from Marina Biotech.  These comprise at least one ‘unlocked’ nucleic acid monomer (UNA) in the double-stranded RNA molecule.  While I have reservations about the scientifically tenuous claim (see here why) that UNAs are not to be grouped with most of the other nucleotide modifications for RNAi use because they lack an intact ribose group, usiRNAs were held to be sufficiently non-obvious and of specific utility that the USPTO issued fairly broad claims in 2012.  Moreover, Marina Biotech once commissioned an external IP lawfirm perform a freedom-to-operate analysis on usiRNA, and (surprise, surprise) came to the conclusion that, indeed, usiRNAs have FTO.


Overcoming target picking limitations

This view seems to be shared also by others in the industry. Notably, Roche RNAi (now part of Arrowhead Research) in 2009 gained access to Marina’s usiRNAs, meroduplex siRNAs, and Dicer-substrate RNAi triggers.  This came as a surprise given that Roche had spent over $300M just two years earlier to gain access to RNAi trigger IP held by Alnylam.  Given that none of the three licensed RNAi trigger forms and related IP poses any FTO threat to traditional Baulcombe-Tuschl designs, the most likely explanation for the move is that it was about allowing the company to escape the target picking limitations under the license from Alnylam.  This included the 31 targets exclusively held by Novartis, some Tekmira exclusive target picks, and some targets pursued by Alnylam that Alnylam exempted from competition.  Whether the last of Alnylam’s Big Pharma licensees, Takeda, might pursue a similar strategy is an interesting question.


Facilitating platform partnerships

When Alnylam and ISIS sued Tekmira for infringing on their RNAi trigger IP by collaborating with Bristol-Myers Squibbs on RNAi delivery, it became a priority for them to have access to or control over non-Alnylam RNAi triggers.  As a consequence, they obtained an exclusive license to Halo-Bio’s multivalent RNAi triggers (more than two strands).  Subsequently, they gained access to Marina’s usiRNAs, including the ability to sublicense.   This now puts them in the position to engage in platform partnerships with Big Pharma companies that do not have access to Alnylam IP.
The same strategy would likely also apply to Arrowhead Research with its various RNAi trigger options that it inherited from Roche, especially if Alnylam provided Roche with only product-specific sublicensing rights, if at all.  As RNAi Therapeutics enjoys a return of pharmaceutical interest, this one-stop-shop option by the two leading delivery companies could be critical to bringing new companies into the space.

And for Alnylam, these developments would not only diminish the royalty it might earn from licensing its IP, they could undermine their own product candidates, including ALN-PCSK9 (hypercholesterolemia) and ALN-AT3 (hemophilia).  Accordingly, the preclinical data strongy suggest that subcutaneous DPCs can do everything that Alnylam’s GalNAcs can do, only much more potently and with less frequent dosing. 


 

Thursday, March 21, 2013

Whoa! AstraZeneca Pays RNA Therapeutics Start-Up Moderna $240M


In the age of rare/severe diseases in drug development and personalized medicine, RNA Therapeutics are enjoying broad interest like never before.  Following a series of RNaseH antisense, splice modulation, microRNAs, and RNAi Therapeutics deals with large pharmaceutical companies, the AstraZeneca-Moderna Therapeutics news today marks another high water mark in the deal-making.  According to their agreement, AstraZeneca will pay Moderna Therapeutics $240M in upfront alone for rights to Moderna’s technology in the cancer and cardiovascular/metabolic disease areas (40 targets).   


AstraZeneca’s Externalized RNA Therapeutics Efforts

The deal with an innovative biotechnology start-up while in the process of shedding yet another few thousand employees, particularly in internal R&D, illustrates AstraZeneca’s R&D externalization trend.  RNA Therapeutics here seem to play a key role as supported by additional recent multi-million dollar deals in the space with ISIS Pharmaceuticals (December 2012) and PTC Therapeutics (June 2011) in oncology.  Unfortunately for RNAi Therapeutics though, it has been left out so far from the AZ’s deal bonanza.  Only in 2011, it wrapped up a collaboration with UK-based Silence Therapeutics.  Still, as AstraZeneca faces the challenge of how to deliver messenger RNAs to the liver and cancer, I expect RNAi Therapeutics delivery companies to financially benefit from AZ's mRNA investment soon (not just for mRNA, but also for RNAi delivery).


Moderna’s Technology

Moderna’s approach is a gene therapy one.  However, while classical gene therapy involves the use of DNA vectors for expressing therapeutic proteins, Moderna aims to circumvent the need for DNA, which have certain regulatory and safety drawbacks, and deliver instead messenger RNAs encoding for the same proteins.  This, in fact, is not a new idea and particularly popular in the immunotherapy field (albeit delivered ex vivo here, by electroporation). Duke University for example had a clinical RNAi Therapeutics program that involved the transfection of mRNAs along with siRNAs (cancer vaccine).

A 2013 Nature Protocols paper by the company’s scientific co-founder Derrick Rossi also leaves me scratching my head as to why AstraZeneca concluded that Moderna’s IP was worth $240M to them.  According to the protocol, the mRNAs are generated by normal in vitro phage polymerase transcription as you would do in the lab using Life Technology’s MEGAscript kit.  The only difference from the standard protocol may be that modified CTPs and UTPs were included.  This is supposed to mitigate the immunostimulatory potential with RNAs just as in RNAi Therapeutics and also contribute to the stability of the long RNAs.  

Based on the fact that neither the concept of mRNA Therapeutics are novel nor the RNA modification strategy unexpected, I expect that Moderna has yet to come out with their secret sauce and that the Nature Protocol may be misleading.  I therefore look forward to studying the patent applications, two of which curiously just published today.  It must be the IP that explains why AZ took a $240M license, to get a sense of the secret sauce.  But still, given the hundreds of nucleotide modifications available, it seems hard to fathom that Moderna's a blocking IP position, and why pay $240M if not a blocking one?

Need for Delivery

In addition to AstraZeneca’s interest in cardiovascular/metabolic disease and cancer, the state of the RNA(i) delivery technologies explains their choice.  Compared to RNAi Therapeutics where small RNAs are involved, the longer mRNAs face an even steeper cytoplasmic delivery challenge.
The liver, of course, is a key target organ for metabolic and cardiovascular disease.  Among Arrowhead’s DPCs, Alnylam’s GalNAcs, and Tekmira’s SNALP, the most advanced RNAi delivery technologies for the liver, it is essentially only Tekmira’s SNALP technology which I regard to be readily applicable to mRNA delivery (also for cancer delivery).  Conjugate approaches such as DPCs and GalNAcs are disadvantaged for mRNA delivery because they would provide no extra protection to the long, fragile mRNAs.  Liposomes by contrast provide such protection by wrapping around the RNA.

I expect to hear more about Moderna’s and AstraZeneca’s mRNA delivery strategies soon.  I, for one, do not believe that Tekmira’s shares are trading up by 8% on strong volume on the back of a SeekingAlpha article.






Other evidence that RNA Therapeutics (and Gene Therapies) Are Hot

ISIS Pharmaceuticals yesterday presented phase I data for their spinal muscular atrophy (SMA) splice modulation drug candidate at the annual AAN meeting.  This compound is partnered with BiogenIdec.  The results from the single-dose PK-oriented study suggest that fully 2’-MOE phosphorothioate oligos are well tolerated in the CNS and that a once-a-year/once-every-half-year dosing regimen may be possible: phosphorothioate oligos sit like a rock in the CNS when intrathecally administered.  In addition to the hints of clinical efficacy at the highest dose level (9mg) presented at the conference, what makes me optimistic about this program is that relatively little (compared to RNaseH) phosphorothioate molecules seems to be required based on the pre-clinical results.

In other news, cancer drug developer Celgene will work with gene therapy company bluebird bio on cancer gene therapy.  Although financial details were not disclosed, they were probably substantial (wild guess: $20M) given the broad nature of the collaboration (multi-year, multiple targets). 

Thursday, March 14, 2013

Over 90% Viral Knockdown in HBV-Infected Chimpanzee with DPC Delivery


Arrowhead Research today provided a little appetizer ahead of its analyst event for ARC520, its candidate for the treatment of chronic hepatitis B (profiled here).  The press release stated that with a single injection of the DPC formulation, serum HBV DNA levels in a chronically infected chimpanzee were reduced by ‘greater than 90%’.  This suggests that the knockdown of the direct target, HBV mRNAs (incl. for the critical HBsAg), was on the same order.  Although the knockdown number here refers to a replicating virus, they are consistent with the high potency of DPC seen in other monkey studies.

The obvious limitation of the present study is that only one animal was treated.  Infected chimpanzee studies are almost impossible to conduct these days, and I am curious how the company got access to the animal in the first place.  The study is being conducted at the Texas Biomedical Research Institute and was led by Robert Lanford.  Dr. Lanford is well known for his chimpanzee work for viral infections, including proof-of-concept for miR-122 inhibition for the treatment ofHepatitis C (Santaris program) and, more recently, chronic HBV studies for Gilead’sTLR7-agonist GS-9620.

Nevertheless, as the animal served as its own control and HBV DNA levels do not fluctuate much from day-to-day, obtaining a credible >90% knockdown without being able to rely on a proper dose-finding study, is remarkable and suggests that more potent results would have been obtained with higher and more frequent dosing.

More about the clinical dosing plans and additional data on the chimpanzee, esp. the HBsAg knockdown data that are so critical to the immune reconstitution hypothesis central to ARC520 (read here for why), should be forthcoming at the March 25 analyst meeting.  Mark your calendars.

Wednesday, March 13, 2013

ISIS-CRP Phase I Results: The Decreasing Competitiveness of RNaseH Antisense for Liver Gene Knockdown

To maintain is positive trajectory of the recent comeback, it is important for RNAi Therapeutics to firmly claim gene knockdown in the liver for itself.  This is because liver gene knockdown is the lowest hanging fruit for the technology, yet RNaseH antisense has proven to be capable of gene knockdown there as well.   If RNaseH were to crystallize as the preferred technology, it would jeopardize a considerable portion of the near to midterm market potential of RNAi Therapeutics.  Just think of Alnylam's 5x15(TM) portfolio of drug candidates.

As I have explained before, dose/tissue oligonucleotide concentrations and, related to that, safety/tolerability will determine which technology will win the competition.  Although the odds seem in favor of RNAi Therapeutics, ISIS Pharmaceuticals keeps promising that improved chemistry and screening methods will improve upon the modest potency (~30-35% ApoB knockdown) of and the safety concerns with mipomersen.  Due to the importance of liver gene knockdown to RNAi Therapeutics, this blog will continue to comment on the respective data points as they come in.


RNaseH Antisense CRP Phase I Data

Today, ISIS Pharmaceuticals announced phase I knockdown data from its c-reactive protein (CRP) program, ISIS-CRPRx.   CRP, a gene expressed by the liver, is believed (by some, not all) to act as a central player in a host of inflammatory diseases such as atrial fibrillation and rheumatoid arthritis.  Phase II studies for these indications are ongoing.

The phase I study tested whether ISIS-CRPRx can blunt CRP induction upon inflammatory stress.  Accordingly, healthy volunteers were dosed 6 times over 3 weeks with either 400mg or 600mg of the phosphorothioate antisense molecule against CRP.  Following that, subjects received endotoxin, a common laboratory reagent that is interpreted by the body as an infection.

Subjects treated with placebo saw an approximately 30-fold increase in CRP levels due to endotoxin.  When pre-treated with 400mg and 600mg, however, the induction was reduced by 36% and 63%, respectively.
 
Although the study succeeded in showing that ISIS-CRPRx could blunt CRP induction, it is much less clear whether ISIS-CRPRx makes for a viable therapeutic.  A 63% knockdown knockdown may be OK for some indications, but intuitively one has to wonder whether to stop an acute inflammation in its tracks you need to step much harder on brakes like CRP.  Indeed, the press release proclaimed, as a testament to the specificity of the drug candidate, that ‘other important immune modulators’ were not changed- somewhat puzzling given that CRP is thought to play such a central role in inflammation.

Be that as it may, what the press release did not mention was the side effect profile seen in the ISIS-CRPRx phase I study; to wit, safety and tolerability is the primary objective of any phase I study.  What concerns me is that mipomersen is 200mg weekly and causes injection side reactions, flu-like symptoms, and indications of chronic inflammation which are likely the result of the elevated steady-state tissue concentrations required for RNaseH antisense efficacy.  In the CRP study, 2- to 3-times more phosphorothioate antisense molecules were given.  Although the side effect profile of an RNaseH antisense molecule is also sequence-dependent, doses of 400mg and higher have historically been associated with toxicity/tolerability considered unacceptable outside of cancer.   

My prediction is that due to the poor efficacy-dose relationship, ISIS-CRPRx will not go into phase III.  We have to see whether the gen2.5 cET chemistry brings any significant increases in clinical potencies as inherent molecular potencies as measured in cell culture studies may not take into consideration other pharmacological rate-limiting factors.  If gen2.5 can lower liver tissue concentrations required to obtain 50% gene silencing into the low single-digit microgram/g range, RNaseH would become more interesting again for the liver.  Otherwise, it seems that more fertile hunting grounds for antisense technologies may be found in the areas of noncoding RNAs (e.g. microRNAs and lincRNAs) and therapeutic splice regulation, especially when the target molecules have a long nuclear residence time.  With ISIS about to present phase I data for its spinal muscular atrophy splice modulation drug candidate at next week’s AAN meeting, a next step into that strategic re-direction may be taken.

Thursday, March 7, 2013

Cancer RNAi Therapeutics Moving On

As RNAi Therapeutics targeting genes expressed in the liver, especially for orphan indications, have captured much of the recent interest in the technology, it is time to once again pay closer attention to RNAi Therapeutics in the oncology space.

Atu027 and TKM-PLK1 Moving into Phase II
Silence Therapeutics have just announced that they got the green light from the German regulators to test Atu027 in combination with small molecule gemcitabine in pancreatic cancer.  Following a short phase Ib to establish the safety of the combination (note: the original phase I was a monotherapy trial), the plan is to rapidly move into phase II which will aim at establishing proof of concept for efficacy.  Depending on the funding situation, it is possible that the company will expand Atu027 into other indications in phase II, possibly in collaboration with private investigators in the UK.
Clearly, the strength of Atu027 is its safety profile so far, one that has surpassed my own expectation for this positively charged lipoplex formulation.  The clinical attraction meanwhile is that Atu027 aims at a quite novel anti-cancer mechanistic approach by inhibiting metastatic spread by fortifying the vascular endothelia. 
The challenge with Atu027, however, is that the gene target, PKN3, remains a relative black box.  This not only demands a certain leap of faith in mechanistic terms, but also complicates the clinical development as biomarkers and other tools are not readily available.
This is quite different from TKM-PLK1, the cancer RNAi Therapeutics by Tekmira.  Polo-like kinase 1 is a hot target, but specificity/safety issues have so far dogged drug development efforts with small molecules, most notably represented by Boehringer-Ingelheim.  By contrast, the SNALP RNAi delivery approach promises to be more cancer tissue targeted and consequently should avoid some of the dose-limiting toxicity observed so far, especially the hematologic ones.
TKM-PLK1 has flown a bit under the radar and the phase I update late last year did not capture much attention.  This is probably because the response rate did not seem too much to get excited about.  However, as Ian MacLachlan, the CSO of Tekmira, pointed out at the AsiaTides meeting last week, it was a small dose-escalating phase I trial (20-30 patients) in advanced solid cancer patients and only four patients actually received TKM-PLK1 for two or more cycles (6 infusions over 2 months) at 0.6 mg/kg or above, dose and durations you would think would be required for advanced cancer patients to get a chance to respond in the first place. Notably, two out of those four showed signs of efficacy: one partial response and one with stable disease after more than 6 months on study drug.
In light of that, the phase I profile of TKM-PLK1 supports my view that it could be the foundation for an exciting PLK1-related cancer franchise for Tekmira and I look forward to seeing the full results presented at the upcoming AACR meeting.  My attention will be particularly focused at any direct measures of target knockdown.  Beyond that, with the company’s healthy financial situation, I look forward to a rich phase II strategy involving a number of solid cancers and innovative study designs such as patient selection based on genetic criteria.  As good as Tekmira's science is, they now also need to be as proactive and innovative on the clinical front.

ALN-VSP02 and CALAA01 Falling Behind
As TKM-PLK1 and Atu027 are moving into phase II, fellow early movers in oncology RNAi ALN-VSP02 and CALAA01 are falling behind. 
The next step for ALN-VSP02 will be a phase I in hepatocellular carcinoma (‘real’ liver cancer) in China under a license by Alnylam to Ascletis.  As noted by Patrick Lu of Sirnaomics at AsiaTides though, it would be a mistake to believe that the Chinese regulatory environment is any less demanding than in the West.  Au contraire, it seems that much more paperwork is required to file an RNAi-realted IND as the authorities there are keen on building their expertise in this new technology.  Expect a delay of at least 6 months from IND application to the green light to go ahead, after all the paperwork has been submitted.  For Tekmira watchers, I expect the $5M milestone thus in 2014, not in 2013.
While ALN-VSP02 still has a pulse, despite of the fact that it lacks the long circulation thought to be necessary for cancer uptake (note: delivery to liver cancer is a very different animal from delivery to normal liver; TKM-PLK1 is a long circulating SNALP), RIP CALAA-01 by Arrowhead Research.  Having said that, the value of CALAA-01 to Arrowhead Research has not been lost entirely as the company has filed for a patent covering a low/high dose strategy of minimizing immune stimulation.  

As the recent high-profile pulling from the market of a pegylated peptide (Omontys by Affymax) due to hypersensitivity, even anaphylactic reactions demonstrate (and also the infusion reactions reported by Alnylam in their SNALP RNAi Therapeutics trials), administration-related hypersensitivity reactions are an issue for the entire drug development arena.  In order to rescue the value of a number of blockbuster franchises, I expect that changing administration schedules could be one area attracting increased attention.  A patent here could have unexpected value.   

A New Crop of Cancer RNAi Therapeutics
Behind TKM-PLK1 and Atu027, a new crop of cancer RNAi Therapeutics is emerging.   Dicerna has signaled that it will finally move into clinical development (Q1 2014) with a liposomal Dicer-substrate formulation with a focus on liver cancer.  Of note, the liposomal formulation process is quite distinct from that of SNALP involving sequential core and envelope formation steps, potentially amenable to ligand-directed targeted delivery.
Another program worth following is another one for liver cancer, the subject of a collaboration of Korean company Bioneer andSanofi-Aventis.  The attraction of that program is that the nanoparticle here, SAMiRNA, comprises a single molecule, even to the extent that the RNAi trigger and delivery components can be manufactured on a single column.  Although I’m opposed to the fundamental notion that the ease of route of administration and the manufacturing process should drive drug development, don’t underestimate the attraction of meeting idealistic product profile when it comes to partnering with Big Pharma.    

The efforts above are a reminder that cancer could be an even bigger commercial opportunity for RNAi Therapeutics than liver-related indications.  The genome-wide targeting opportunity with RNAi Therapeutics has not been lost.  The pharmaceutical industry is watching.

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'.

Friday, March 1, 2013

Functional Cure of Chronic Hepatitis B: RNAi Therapeutics May Be the Only Game in Town (Part II)


Today, I will explain why I believe that ARC520, the chronic HBV drug candidate by Arrowhead Research, is particularly well suited to exploit the unique potential of RNAi to deliver a functional cure for many people suffering from chronic HBV.   For the basic rationale of using RNAi gene silencing to treat HBV, the reader is referred to the previous blog entry.


ARC520 is Highly Potent

As illustrated in this week’s publication of preclinical data on ARC520 (Wooddell et al. 2013), ARC520 promises to be a particularly potent example for therapeutic RNAi gene knockdown.  90% and more knockdowns were routinely observed for all HBV proteins.  What is more, the protein for which knockdown is most important according to the underlying immune reactivation hypothesis, the Hepatitis B surface Antigen (HBsAg), seems exceptionally susceptible to RNAi with multi-log gene knockdowns for this target.  Equally important, the masked melittin-like peptide component of DPC, expected to be dose limiting, was very well tolerated at 10mg/kg in non-human primates, the highest dose tested in the publication.  Such an amount was considerably more than what was required for achieving maximal knockdowns.

HBV is also an example for which the high knockdown potency of DPC (and SNALP) sets it apart from other potential competing RNAi Therapeutics approaches for HBV, including a GalNAc-siRNA conjugate-based one, which lack knockdown potencies adequate for such a viral applications.   At this moment, I do not exclude Tekmira to become interested in HBV as well, especially with their UsiRNAs and MV-RNAs which they probably consider to be free from the Alnylam-imposed target restrictions.


ARC520 Fits into Current Standard of Care

At the AsiaTides meeting in Tokyo that I have just attended (btw, you’d be amazed how much serious RNAi Therapeutics development work is going on in Japan, China, and South Korea), Dr. Lewis from Arrowhead Research presented drug-drug interaction data for ARC520 and Entecavir, the current standard of care Nuc for HBV.  These interaction studies performed in mouse models of HBV are important since ARC520 would initially likely be used in combination with current standard of care (probably also interferons).  In fact, the distinct mechanisms of actions of Nucs, interferons and RNAi Therapeutics would neatly complement each other.  Importantly, ARC520 did not impair Entecavir-mediated suppression of viral replication nor did Entecavir impair the 2-3 log-fold viral protein suppression by ARC520.

Moreover, the data which include 80% knockdown following a single administration after 3 months in non-human primates (Factor VII surrogate gene), clearly support once-monthly dosing.  Given that ARC520 is not intended as a chronic therapy, it should thus easily fit into current treatment regimes. 


ARC520 May Be Foundation for HBV Franchise

ARC520 is administered by intravenous infusion.  In terms of dose escalation and achieving maximal potency, this is positive since solubility and injection volume issues do not apply.  However, there is the obvious opportunity for Arrowhead to enhance the value of their HBV franchise by developing a subcutaneously administered follow-on candidate, thus capitalizing on their progress with the protease-sensitive DPCs.  This would broaden the target population and extend market exclusivities.


Risk-Reward

For a small biotech company like Arrowhead Research, the enormity of the HBV opportunity also comes with its challenges.  The complex course of chronic HBV and probably also the various genotypes mean that clinical development will be equally complex- and costly.  I have followed with horror the many billions Vertex Pharmaceuticals invested on developing their HCV drug after the first exciting phase I proof-of-concept data were reported.  Ultimately, Vertex shareholders that had invested before the phase I validation, only made a 3x return taking on all the risk, and those that jumped onto the bandwagon after the results did not see much appreciation after 6-7 more years, despite of the fact that clinically pretty much everything went according to plan.

Part of the expense, however, was also driven by the fear of the emerging competition in HCV leading to a capital intensification of clinical development.  Except for competing RNAi Therapeutics candidates enabled by similarly potent liver-directed knockdown technologies (perhaps SNALP), I do not see such intense competition emerging for ARC520. 

Another risk for Arrowhead is that while the immune reactivation hypothesis is attractive and supported by clinical data correlating HBsAg seroconversion with preceding loss of HBsAg, the remaining uncertainty may make ARC520 unsuitable for a small platform company to wager its entire future on it.  By contrast, a Big Pharma may be willing to take on the risk if it agrees with the hypothesis simply because the market opportunity is so large.  Witness how much capital is being spent on the amyloid hypothesis in Alzheimer’s Disease or the good HDL-cholesterol hypothesis in cardiovascular disease.

Therefore, at the right time and for the right price, also depending on factors such as clinical data, share price performance, and the availability of non-dilutive funding opportunities, the HBV franchise should be partnered.  The issuance of the patentcovering the protease-sensitive DPCs which are amenable to subcutaneous administration could be an important piece in this puzzle.  After all, with manufacturing much less of an issue with DPC 2.0, you don’t have much to sell unless you control the IP. 
By Dirk Haussecker. All rights reserved.

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