Big Agriculture Bankrolling RNAi Therapeutics

After years of pouring millions, if not billions into RNAi-related intellectual property (IP) and the development of double-strand RNA delivery, the RNAi Therapeutics industry is now harvesting returns from an unlikely source: agricultural companies.

Most notably, Alnylam reported yesterday an IP license and collaboration agreement with Monsanto which is widely known for its transgenic seed business.  Particularly eye-catching was the $29.2M in upfront monies, an amount not seen in RNAi Therapeutics for a long time.

However, Alnylam is not the only RNAi company that has been approached by Big Ag.  Admittedly somewhat flying under my radar, Devgenclosed a similarly upfronted RNAi collaboration with Syngenta in May of this year.  Interestingly, that deal came after Devgen’s 4-5 year RNAi partnership with Monsanto had ended in 2011, earning the Belgian (ag) company tens of millions.  This suggests that there is an RNAi scramble in the Ag space reminiscent of what happened in RNAi Therapeutics in 2006-8.  Moreover, Marina Biotech, also in May, exclusively licensed RNAi IP to Monsanto, and Tekmira mentioned in their last two conference calls that it was undertaking evaluative work with a large agricultural company: Monsanto or Syngenta?

The fact that Tekmira is involved in this business development opportunity for RNAi Therapeutics companies suggest that general RNAi IP is only one reason for Big Ag’s approach.

At first, this left me scratching my head: how would you apply double-strand RNA delivery by LNP in a commercially meaningful way in agriculture?  After some research though, it became obvious that Monsanto, Devgen and Syngenta are interested in using orally ingested dsRNA to fight insect pests such as the Western corn rootworm (WCR).  The need of finding new solutions for WCR has dramatically increased as the long-standing transgenic Bacillus thurigiensis toxin-incorporating crop by Monsanto has been plagued by resistance.

Another compelling reason for using non-transgenic approaches in agriculture is the fact that it should speed up the regulatory process as RNA is Generally Regarded as Safe (GRAS) by the FDA. This much reduces the hurdles compared to transgenic plants which might spread in the environment and further express biologically active proteins.  Moreover, unlike a toxin like Bt, the RNAi trigger can be highly specific to the targeted pest species.

The question, of course, is whether this approach, despite its attractions is technically and financially feasible in the first place.  The seminal work by Devgen and Monsanto (Baum et al., Nature Biotech2007) suggests that this is in fact the case: sub-nanogram per cm2 amounts of relatively cheap T7 in vitro transcribed RNA were sufficient to specifically and effectively silence essential genes in the entire body (!!!).  As a result, the growth inhibition caused by the pest was much reduced after ingesting the RNA.  I guess that the delivery work is aimed at even further reducing the required amount of RNA by a log or two.

The mechanism of this amazingly efficient gene silencing is likely the same as the early finding in nematode worms (another group of agriculturally important pests no less) that feeding them with E. coli bacteria expressing dsRNAs can cause potent and long-lasting silencing.  This phenomenon is referred to as ‘systemic RNAi’ and involves RNA amplification.  Although such systemic RNAi is unlikely to operate at the same high efficiency in all pest species, harnessing it in a species like WCR would already be highly commercially lucrative.  Monsanto apparently is close to commercializing such an RNAi-based insectizide.

Transkingdom RNAi and ddRNAi

When thinking about RNAi in plants, DNA-directed RNAi (ddRNAi) usually comes to mind, the type of RNAi where long hairpin RNAs are expressed from a transgene inserted into the host genome.  Certainly, a ddRNAi approach e.g. in corn against the same transgenes is also possible and indeed this has proven to be equally effective when compared to sprayable RNAi in the 2007 Nature Biotech paper.  It should also be added that unlike in your typical protein-expressing transgenic crop, ddRNAi per se does not involve transgenic protein expression, thereby lowering the regulatory hurdles.

When thinking about oral RNAi, especially in light of the RNAi history of feeding dsRNA-expressing bacteria to nematode worms (the first ‘transkingdom RNAi’ example), one may also consider the ‘Transkingdom’ RNAi technology by Marina Biotech (originally from Cequent).  One can speculate that Monsanto’s interest in Marina Biotech is related to this as part of a wider RNAi initiative by the Ag giant. An issue of feeding pests with such bacteria, however, is that again you release transgenic organisms into the wild.  While this may not be so much an environmental or health problem, you know that there are many out there that are religiously against anything ‘GM’, smashed windows and all.

Has Tekmira vs Alnylam been settled?

If we assume that LNP delivery is part of the package in the Alnylam-Monsanto deal and that Monsanto is the Ag company that has been working with Tekmira (until at least just two weeks ago), one can come up with at least three hypotheses for how the deal reflects on the Alnylam-Tekmira litigation:

1)     Tekmira and Alnylam competed, and Alnylam won;

2)     Monsanto will also tap Tekmira to cover all bases;

3)     There is an understanding that Alnylam will use the $30M to settle the lawsuit, and as part of the settlement/M&A, Monsanto will gain access to Tekmira technology.  Announcing the Monsanto deal before settlement is beneficial as it further bolsters Alnylam’s reputation and balance sheet. In that line of reasoning, the Regulus IPO should come SRTL.

The next weeks will tell.

Eventful Months for Tekmira

Last week, Tekmira reported its quarterly results and provided a corporate update.  With interim phase I results for its lead clinical candidate TKM-PLK1, well received clinical results by its licensee Alnylam, the Stop-Work Order from the Department of Defense, milestone payments from Talon and Alnylam, and the prospect of a jury trial following a key decision by the judge in the litigation with Alnylam, these certainly must have been one of Tekmira’s busiest 4 months ever.

TKM-PLK1 Results

20 months after trial start, Tekmira finally reported first data from its lead clinical program, TKM-PLK1 for advanced solid cancers.  The most informative data from this early-stage trial, as expected, related to safety/tolerability and pharmacokinetics. 

Accordingly, it appears that the maximally tolerated dose using an aggressive once-weekly dosing regime is 0.75mg/kg after encountering dose-limiting toxicities in the form of a case of transient thrombocytopenia and hypoxia/dyspnea each at 0.9mg/kg.  These data are in line with the clinical safety/tolerability data from other DlinDMA-based SNALP formulations (ALN-VSP02, ALN-TTR01) where the maximally tolerated dose was slightly higher, but which were dosed in in less aggressive schedules.  Although there seems to be a trade-off between dosing frequency and safety/tolerability, I would agree that for cancer applications where gene knockdown is targeted in rapidly dividing cells, more frequent dosing vs higher, but less frequent dosing may be desirable.  This is because the duration of gene knockdown is known to be largely inversely correlated with cell division frequency.   

Looking back at the overall DLinDMA results (ALN-VSP02, ALN-TTR01, TKM-PLK1), given the fairly uniform maximally tolerated doses, it is possible that lipid-specific toxicity can be as dose-limiting as siRNA sequence-specific immune stimulations.  It will therefore be interesting to see whether there will be a general shift in the maximally tolerated dose with SNALP formulations comprising different lipids.

While, as in many of these small, dose escalation trials, there were encouraging signs of therapeutic efficacy, here in the form of one partial response by RECIST and one stable disease, what excited me most about the released data was that this particular SNALP formulation achieved ‘several fold’ higher drug exposure levels than previous formulations (aka ALN-VSP02).  High/long exposure levels, of course, are thought to be critical for efficient drug delivery via the EPR effect.  The advance can be attributed to Tekmira’s rational SNALP design approach involving the use of a long-chain lipid-anchored PEG such that the cloak of invisibility is shed only after longer circulation times.  This is unlike in ALN-VSP02 (short chain anchor SNALP formulation) which exhibited short circulation times suitable for RNAi trigger delivery into various hepatic cell types.  Similar to ALN-VSP02 this time, further important pharmacokinetic data showed that the PK profile did not change upon repeat administration.  It is therefore unlikely that neutralizing antibodies are generated to the PEG component.  In certain old preclinical studies this had been shown to be an obstacle to repeat administration.

I look forward to learning about the more detailed clinical results.  In particular, I’d like to see not only the blood PK data, but possibly also the drug accumulations in tumor biopsies which could be compared to the ALN-VSP02 biopsy data.  By this, one would be able to model how exactly the higher blood exposure levels translate into tumor delivery benefits.  

Ebola Stop-Work Order

Earlier this month, Tekmira and competitor Sarepta received Stop-Work Orders from the US Department of Defense relating to their Ebola biodefense programs.  Tekmira has greatly benefitted from the DoD contract- not so much in terms of making a direct profit from the contract, but in that it also provided funding for progressing its technology platform.  A significant number of employees would have to be laid off if the final decision on whether to continue with the program, expected by September 1, were negative.  Although the impact on Tekmira’s science would not be immediate, it would definitely impact the speed of Tekmira’s technology advances if no substitute funding was found soon (see litigation section).  What is particularly frustrating about this Order is that it comes in the middle of an ongoing phase I clinical trial (at least wait for the results before making a final decision) and because budgetary uncertainties, not scientific deficiencies apparently being the reason for it.  Ironically, therehave been two recent outbreaks of Ebola in Africa highlighting that Ebola is not just a bioterrorist, but also persistent public health threat.

Tekmira Partners Celebrate Successes, Company Collects Milestones

The recent past were particularly exciting for Tekmira’s technology licensees Alnylam and Talon Therapeutics.  As discussed on this blog before, the ALN-TTR02 knockdown results, critically enabled by Tekmira’s delivery technology, were very positively received by the biotech community, including investors.  These results also paved the way for the initiation of a phase II trial of ALN-TTR02 triggering a $1M milestone to Tekmira.  As important as the milestone is to Tekmira on the eve of the jury trial, once the company has fully recovered possession of its technology, the liver knockdown results should allow the company to turn many of those companies on the sidelines into willing customers once there is a resolution to the litigation.

A somewhat unexpected $1M milestone came from Talon Therapeutics, a small biotech company that had licensed early Tekmira small molecule liposomal drug candidates.  The milestone was triggered by the FDA approval of one of the licensed product candidates, Marqibo (liposomal vincristine), for the treatment of advanced Ph- ALL.  In addition, the company is entitled to receive sales milestones.   

All Set for a Jury Trial

Despite all the important events above, the most important news regarding the financial viability of the company came when the judge made the important decision to reject the delay and cost-intensifying tactic (here: Motion for Summary Judgment) by Alnylam paving the way for a jury trial at the end of October.  As the case will be tried on all counts and, according to Alnylam’s regulatory disclosure, could cost the company in excess of $1 billion, you would think that Alnylam has no choice but to settle the matter (or buy Tekmira).  The longer Alnylam waits, the more dearly it is likely to cost them.

In that light, the next 2-3 months should be even more exciting for Tekmira shareholders and hard-working employees.

The $28M AstraZeneca-Regulus MicroRNA Therapeutics Deal

Yesterday, it was announced that AstraZeneca is paying microRNA Therapeutics company Regulus $28M for three preclinical-stage microRNA targets.  This is certainly good news not only for the field of microRNA Therapeutics, but also oligonucleotide therapeutics in general which is well on the day to be the third major drug development engine after small molecules and monoclonal antibodies.  

After GSK and Sanofi-Aventis, it is the third of its kind for Regulus and there were similar ones between Miragen and Servier late last year and Santaris and GSK before that.  The number of such deals, each usually involving a number of microRNAs, illustrates how far the field of microRNA biology has come in just 10 years from the discovery of microRNAs in humans to yield promising therapeutic targets that number in the dozens.  In fact, microRNA Therapeutics has been more successful than the more straight-forward RNAi Therapeutics approach in attracting the partnering interests of Big Pharma lately.

On the other hand, it’s been now five years since the founding of Regulus Therapeutics, and still no program has made it into the clinic.  Such a performance is certainly not good enough to support an IPO these days for which the company, based on job postings, appears to have had ambitions for for some time now.  With remaining ~25M in cash and an annual burn rate of around that, the revenues recognized from the AZ deal may well be the substitute for a public offering.  

As it was not disclosed how much of the $28M was for equity in Regulus, other than the cash added to Regulus’ balance sheet it is really difficult to tell whether the dealmakers at Regulus will be all smiles about it.  What’s more, the miR-33 atherosclerosis program which had yielded exciting data (including in non-human primates) in enhancing reverse cholesterol transport with a subsequent reduction in plaque size seems to be spoken for already at this early stage (before the magical phase II value-inflection point).

It is unclear what is causing the apparent delay of Regulus progressing programs into the clinic.  Is it the complexity of microRNA biology where each microRNAs often has dozens of targets, or has it something to do with the concern that the 2'-fluoro modification initially favored by the company may be genotoxic?

AstraZeneca’s Return to ‘Proper’ RNA Therapeutics

When AstraZeneca, in its farewell to Silence Therapeutics in January, said that the Silence effort was ‘part of its overallstrategy to explore this important therapeutic approach [i.e. RNA Therapeutics]’, I took it to mean that the Silence projects may not be their top priority in this regard and that it already had other oligonucleotide technologies and companies in mind.  

Confusingly, half a year before that AstraZeneca entered into a ‘small molecule RNA Therapeutics’alliance with PTC.  Beware of companies, particularly prevalent in the (cancer) stem cell field it seems, which claim to be pursuing new platforms and treatment paradigms, when the innovation actually rests on just tying pre-existing molecules to new biological rationalizations.  

Classic Big Pharma I thought then: advertising innovation, but really sticking to its old, rusty guns; and if AstraZeneca is widely thought to have the industry’s worst productivity, you have to look no further for its causes.

Yesterday’s news was therefore quite encouraging in that AstraZeneca has not given up on developing ‘proper’ RNA Therapeutics by which I mean that nucleic acids are the therapeutic agents.  Whether the stream of positive clinical results in oligonucleotide therapeutics (and vaccines) have provided AZ encouragement to go down this path is unclear, but they certainly did not hurt.  Maybe it will even make AZ re-energize its RNAi Therapeutics efforts (e.g. for oncology or respiratory disease).

Want to learn more about microRNAs?  Register for the 2012 Janssen Award Symposium in New York.

Next post: Tekmira's very busy quarter.

As MicroRNAs Make First Clinical Impact, Janssen Prize 2012 Awarded for Their Discovery

20 years ago, Gary Ruvkun and Victor Ambros made the startling discovery that a tiny noncoding RNA, lin-4, could be a key regulator of C. elegans development by downregulating messenger RNAs through Watson-Crick base-pairing.  What for a number of years seemed like an oddity of worm biology has become the first example for a whole new fundamental class of biological molecules, rivaling in importance messenger RNAs: essentially every biological pathway is regulated by a microRNA.     

Not only have microRNAs fundamentally re-shaped our thinking about molecular biology, they have also made quick inroads into the clinic.  Even before RNAi Therapeutics, microRNA-based diagnostics are already making a clinical impact today.  Half a dozen such tests have been commercially launched.  The currently arguably medically most impactful among them, mirViewMets(2) for the diagnosis of Cancers of Unknown Primary by Rosetta Genomics received Medicare coverage in May of this year.  This in the diagnostics is tantamount to the regulatory approval of a drug candidate in the therapeutics space.

On the microRNA therapeutics front, the miR-122 inhibitor by Santaris for the treatment of HCV infection is the most advanced.  Studies with this antisense inhibitor have yielded intriguingclinical data, including the suppression of viral loads to undetectable levels. A number of other miRNA drug candidates are in late preclinical development.

Considering the general biological importance of microRNAs and their rapid translation into the clinic, it is not all that surprising that Gary Ruvkun and Victor Ambros were recognized with the 2012 Dr. Paul Janssen Award for Biomedical Research.  This prize is one of the premier accolades in biomedical research for inspirational scientists that have undertaken ground-breaking science with great medical impact.  Surely, the discovery of microRNAs and their discoverers fit that bill.  Without lessening the importance of the prize and the contributions of corporate sponsor J&J, many of these prizewinners will go on to win the Nobel Prize.  I fully expect Ambros and Ruvkun to do so, too.

Daring Resesarch on the Cutting Edge

One cannot overestimate the scientific accomplishment of the work by Ambros and Ruvkun.  At the time, the notion of small RNAs as genetic regulators was simply unheard of.  It was thus the accomplishment of the Ambros group to embrace the possibility that their odd genetic mapping results during a worm developmental timing project pointed towards such a class of molecules. 

The lab-books around the world are littered with curious findings that never get followed up on because we think that they are likely caused by some experimental artifact and we would no get anything else done if we chased after each of them.  And even when the evidence is so clear before your eyes (e.g. that band in the low molecular weight range), the conditioned eye will simply ignore it.  In this case, the initial disbelief was only overcome by sequencing and re-sequencing before Ambros and colleagues had to finally accept that the mutation was indeed in a region without a proper open-reading frame (= protein).  Moreover, the recognition that a small RNA was the molecule affected by the mutation required that RNAs of all sizes were considered despite the fact that at the time small RNAs were not meant to be captured by the laboratory gels.  And when they accidentally were, such small RNAs surely were artefactual junk.

Discovering microRNAs as a whole new class of key genetic regulators was just one accomplishment.  Another one was deciphering their mechanism of action.  As long-time fellow researchers of worm development, Ruvkun and Ambros were familiar with the genetic interactions of the lin-4 mutant.  One gene in particular, protein-coding gene lin-14 appeared to be suppressed by lin-4.  A deletion mutant in the 3’ UTR of lin-14 found by the Ruvkun group abolished this genetic interaction.  Noticing that there was sequence complementarity between lin-4 and the missing lin-14 3' UTR fragment, it dawned upon the two scientists almost in unison that lin-4 must be interacting with lin-14 through Watson-Crick base-pairing, thereby silencing it post-transcriptionally.

Award Symposium in New York

If you want to learn more about the discovery of microRNAs, their biology and medical importance, and also meet the scientists, you can register for the Dr. Paul Janssen Award Symposium to be held on September 7, 2012 at the New York Academy of Sciences.  It will be a great opportunity for both academic scientists and the biotech crowd to leave the lab bench and trading desks behind them for a few hours and reflect on the importance of basic research, in model organisms as seemingly obscure as the worm, for advancing medicine.

The RNAi Therapeutics Blog is a proud promotional partner of the Symposium.

Shoppers- Attention Please! Marina Bio High-Affinity Nucleotides On Sale

Why pay tens of millions to ISIS Pharmaceuticals or Santaris for modified nucleic acid chemistry when you can get the same, if not better from Marina Bio for just a million?

This is the question that Novartis probably was answering when they non-exclusively licensed CRN technology (for single and double-strand oligo Rx) from Marina Bio for just $1 million in upfront considerations.  CRN stands for conformationally restricted nucleotides, similar in shape and thermodynamic behavior to Santaris’ LNA technology, a technology that is also being researched by ISIS Pharmaceuticals.

To me, CRN has been the best bet for Marina Bio's corporate survival.  The reason is that selling a nucleotide modification, especially for antisense therapeutics should be fairly straight-forward: there is no formulation involved requiring support by a functioning laboratory, just include it in standard phosphorothioate oligos like everybody else.  This comes in handy when you have become a largely virtual, IP-based biotech company like $3M market cap Marina Bio.   

I had wondered whether the reason why Marina Bio had not been able to capitalize on this opportunity so far was either due to IP uncertainties or manufacturing issues with this novel nucleotide.  The latter issue seemed to have been resolved when Marina in May of this year struck a cGMPsupply agreement with Girindus. The IP issue I have to admit I have not researched in too much detail, but suffice it to say that my understanding of Santaris’ and ISIS’ CRN patents is that they are quite structure-specific which would move the IP issue more to questions surrounding their use in general (e.g. in gapmers and the like).  

Today’s announcement also confirms that Novartis is still in the game of oligonucleotide therapeutics after picking their 30+ targets from Alnylam and a product-specific deal on an RNAi Therapeutics from Quark.  Although $1M is not much to a Big Pharma, nobody wants to part just like that with a million, even if it means being able to rescue old friend Michael French (now for the second time after the 2009 mdRNA cash crunch, Marina Bio’s predecessor).

Today’s deal further fuels the rekindled fire of commercial small RNAs:

1)      impressive clinical results by Alnylam facilitated by Tekmira’s technology;

2)      penny stock investors multiplying their money following the Medicare coverage announcement for Rosetta Genomics' Cancer of Unknown Primary miRNA diagnostics;

3)      Rosetta Genomics gearing up for the commercialization of the test in what is a whopping $>25M offering for the company;

4)      new investors in Silence Therapeutics doubling and tripling their money overnight in a new share offering;

5)      and the Tekmira-Alnylam trade secret theft show-down coming to a widely followed climax.

Big investors may be jeering at such nanocap biotech companies, but it is a fact of life that most small silencing RNA companies have become pennystocks, which also means that their resuscitation could make for some nice investment returns.

Short Alnylam

Biotech shorts and event traders rejoice.  The Tekmira-Alnylam litigation is coming close to a jury trial.  This opens up a few interesting trading opportunities.

As evidenced alone by Alnylam’s delay and cost-intensifying tactics in both the main litigation with Tekmira and the VSP patent interference, Alnylam’s views its strong balance sheet and market capitalization (arguably partly built on the back of Tekmira) key advantages in their alleged attempt to misappropriate SNALP technology from Tekmira.  Why sweat the merits of a case when you think that you can financially outlast your opponent?

At the same time, following a number of positive clinical results, enabled by the contested technology no less, Alnylam the stock has soared over 200% in less than a year.  But as the big showdown with Tekmira approaches (at the end of October in front of a jury) the stock has become a near-perfect short. 

Here is why.

First of all, there seems to be little risk of a catalyst ahead of this key event which could significantly jolt the stock to the upside.  This is because the clinical results with the SNALP-based drug candidates have been reported (ALN-TTR01, ALN-TTR02, ALN-PCS02) and Alnylam will not be able, in light of the Tekmira litigation, close any meaningful product-based partnership, much less close a platform-based deal for any upfront that would move the needle of this billion dollar market cap company.    

The recent run-up in the stock, the early-stage pipeline plus the absence of catalysts make the stock an attractive short based on technicals alone.  A simple analyst downgrade which may come any day could easily knock down the stock by a double digit percentage.  The big short opportunity, however, lies in the increasing likelihood that Alnylam has no choice but to settle the legal matter as the judges in both cases are getting visibly annoyed by Alnylam’s tactical games.  For example in the VSP patent interference, Alnylam got reprimanded for filing motions belatedly and manipulating history by adding claims to an ex parte patent applications; or in the words of the  judge in the main litigation: ‘I conclude that the proposed motions are not only unlikely to eliminate any issues but they would at the same time be extremely costly for the parties to litigate and distract them from preparing for and focusing the issues for trial.'

In fact, I am surprised by how well the judges have picked up on Alnylam’s smugness with all of the important decisions in both cases so far going in Tekmira’s favor.  Note that I did not expect this for the VSP Interference where I had seen the situation more balanced before Alnylam and their lawyers bungled the case.  Unless the bitterness of the dispute has led Alnylam’s management to actually believe in their case, settling the matter ahead of the trial would seem a foregone conclusion.     

Lose, lose big; win, get your money back

A settlement, of course, is likely to be expensive to Alnylam and should pressure the stock as it should consume a good part of their $300M+ cash position.  Tekmira is asking for a billion dollar in compensation, a number that sounds outlandish at first glance, but maybe not so considering that Alnylam has earned over half a billion in non-dilutive partnership funding which would have been impossible without Tekmira’s technology.

Even assuming the best outcome for Alnylam, namely an outright win at the trial, this would be unlikely to have much of a positive effect on the stock at current valuations (~$18.6/share).  In fact, there may be a sell-on-the-news as this legal uncertainty disappears and the biotech analysts/stock market have largely disregarded the Tekmira litigation in their estimates.   

And if it comes to trial and Alnylam loses, well, this could get real ugly for the stock.  But again, I do not believe that Alnylam management and BoD wish to expose themselves to the inevitable shareholder class action lawsuits that would surely follow and therefore settle.

Tekmira Long as an Alternative

With a market cap of merely $30-40M and a potential, if not likely, multimillion dollar windfall, a Tekmira long would be the obvious trading alternative.  If they lose the trial and technology, it would likely destroy the company through endless rounds of dilutions at low share prices.  Consequently, unlike you are me and strongly believe in the merits of the case and have held the stock for close to four years now, I would not hold an outsized Tekmira long position relative to your personal wealth based on the simple mathematical rule that anything multiplied by zero equals zero.  The anemic trading volumes in the stock would also argue against taking a large position, although a slow accumulation strategy and strong trading volumes on the event may allow for that.

Addendum: It would seem that Alnylam management agrees with the above short thesis.  The company's CSO and CFO were quick to act by exercising options and selling the respective shares on the recent ALN-TTR02 data spike.  The CSO made around 350K in profits, the CFO around 100K.

Disclaimer: The above is my personal opinion only.  If you intend to trade stocks based on the account above, it is entirely at your own risk.

MC3 Authorship Discrepancies Increase Suspicions of Cover-Up

Last week was a tumultuous one in RNAi Therapeutics and in the relationship between Alnylam and Tekmira.  

On the positive side, results from the ALN-TTR02 phase I study revealed that highly potent knockdowns for liver-expressed genes are possible in Man.  Although solid knockdowns had been demonstrated before using the same delivery formulation for the hypercholesterolemia-related PCSK9 (ALN-PCS), the latest results demonstrate the most potent and prolonged knockdowns in RNAi Therapeutics history.  Thus, this should be reproducible for most liver-expressed genes as long as highly efficient RNAi triggers are selected, further substantiating the claim that RNAi trigger potency matters.

At the same time, the results once again brought into focus the hard-fought battle for this most valuable RNAi Therapeutics delivery asset: SNALP.  On the celebratory conference call, Alnylam’s management was more aggressive than ever in claiming that this ‘second-generation LNP’ technology was entirely theirs: ‘Proprietary!’  Of course, this makes little sense for the reason alone that the composition and formulation method of these particles clearly identify them as SNALPs which belong to Tekmira.  Just as a reminder, there is an important distinction between an exclusive license and owning something.

Not only does it reveal that Alnylam management is apparently unable to grasp this very basic concept of property rights, well captured by John Maraganore's statement 'you pay for it, you own it', Tekmira alleges that what enabled this improvement in liver gene knockdown potency over the ‘first-generation’ liposomal formulations and which is the basis for Alnylam’s ‘proprietary’ statement, namely the MC3 ionizable lipid, was stolen from them in a covert operation.  This operation apparently happened at the end of a series of actions to not only appropriate valuable SNALP technology on which Alnylam has come to essentially wholly rely upon (despite its recent attempts to claim that it employs four different delivery approaches), but also marginalize, and ultimately destroy Tekmira.

The reason why I strongly believe that Tekmira is not making up these shocking allegations, is not just based on the fact that Alnylam’s PR strategy has been so obviously aimed at wrestling away from Tekmira its reputation as THE liposomal RNAi delivery company (see the promotion of the clinically unfit lipidoids to a point where many observers believe that the clinically employed liposomal technology originated at MIT; Alnylam oligonucleotide chemists prominently listed on liposomal patents; or back-handed compliments in the context of ‘1^st-generation’ technology).  No, it is also because all of the evidence and accounts that I have gathered in my investigations were consistent with Alnylam having had little respect for Tekmira and thought their financial might and influence can be used to take full possession of SNALP technology and leave Tekmira in the dust. 

MC3 Origins

Probably the most telling of these acts concerns the origin of the MC3 lipid.  This lipid is an important component in ALN-PCS and ALN-TTR02 which have attracted so much attention recently, and which forms the basis for Alnylam’s ‘proprietary’ claim.  Briefly, Tekmira alleges that former employees of the company were hired by Alnylam (first as consultants, and then as employees at pseudo-independent Alnylam Canada, pardon me, AlCana) and were supposedly struck by genius essentially the moment they had left the company's premises (and apparently finished downloading the files) to come up with MC3, ownerhip of which was duly transferred to Alnylam.

Alnylam claims that MC3 was an ‘independent’ lipid and thus would fall under the scope of the Supplemental Agreement.  Based the above timelines alone, it seems that Alnylam management must have very low expectations for the IQ of the jury that they will be facing in late October.  Moreover, it is obvious that MC3 was part of a series of lipids that these employees had started work on as full Tekmira employees.  Note: although they may have been the rightful inventors of the MC series of lipids and may even hate their former employer for personal reasons, the fact remains that they did so when employed by Tekmira.  Consequently, the lipids and related trade secrets are not theirs.  Moreover, the key insight in the 2010KC2 Nature Biotechnology paper by the same authors (when employed by Tekmira) was that changing the length of the linker between the lipid headgroup and tails had a profound impact on performance.  Hence, developing new lipid scaffolds and then start testing series thereof with variable linker lengths was Tekmira's trade secret until then.  And that, of course, is what got them to discover MC3 (from the recent Jayaraman et al): 'In the second group, the dimethylamino moiety is maintained but the distance between the ester and the amine is varied from one to five methylene units to generate lipids with pKa values ranging from 4.17 to 7.16.'

Too bad for Alnylam that ‘rational’ appears in the title of that key Nature Biotechnology paper (Rational design of cationic lipids for siRNA delivery) as it will be Alnylam’s strategy at the trial to convince the jurors that successful lipid discovery is an extremely unlikely chance event, further hoping that the jurors won’t be able to make the distinction between unpredictability in terms of how many carbon atoms exactly would yield the most useful lipid and unpredictability in terms of which search strategy (Tekmira know-how) would likely yield such a lipid.

It is also curious that the research organizations of Tekmira and Protiva had been kept separate until in late 2008.  Supposedly, Alnylam demanded this as a precondition to blessing the Protiva-Tekmira merger so as to keep Merck from getting their hand on certain Old Tekmira’s technology.  Whether true or not, it likely also had the effect that not only Merck, but also Old Protiva were left in the dark on these trade secrets (although they belonged to the combined company).   This darkness was then allegedly exploited to get MC3 ownerhip transferred to Alnylam and to obtain a broad covenant not to sue from Tekmira that according to Alnylam’s interpretation would also absolve it from IP and trade secret theft.

MC3 Authorship Discrepancies

Over a year ago, when the lawsuit broke, it bothered me that in the MC3 patent application (now issued patent US8158601), the key ex-Tekmira employees which should have been the real inventors behind MC3 according to my logic described above, i.e. Madden, Hope, and Semple, were missing as listed inventors.  M. Hope, importantly, was the senior author of the KC2 Nature Biotech paper, which served as the blueprint for the MC series.  Instead, a slew of Alnylam oligonucleotide chemists are listed as if the synthesis of an extra carbon in the linker group here and there was an inventive contribution. Surely not.

This to me strongly smelled like part of the cover-up.  Read for yourself my speculations at the time:

'But looking at the (published) patent application, all these key people are actually missing as named inventors. I would identify these key scientists as Thomas Madden, Sean Semple, and Michael Hope and it would have been natural for Tekmira to have non-compete arrangements in place for these individuals. Importantly, these are also the senior authors on the KC2 Nature Biotech paper from January 2010, a lipid from which MC3 is derived (see also e.g. slide 28 in August 4, 2010, presentation by Alnylam at the International Liposome Research Days held in…Vancouver).

However, despite of Alnylam’s assertions that it was the fired Tekmira employees now working, for apparently legal purposes, at AlCana (but practically for Alnylam) that invented MC3, the published patent application only lists Alnylam employees (and maybe some consultants) as inventors and Alnylam as the applicant: Akinc, Dorkin, Qin, Cantley, Manoharan,Kallanthottathil, Narayanannair, Jayaraman; and (for US purposes only) Chen, Ansell. (the latter two being the two ex-Tekmira employees, but no mention of AlCana).

You would think that, as the inventors of KC2, the inventive contributions by Madden, Semple, and Hope would have played an important role in MC3, much more so than the number of trained oligonucleotide chemists from Alnylam listed as inventors on the application. Given that the Response admits that Alnylam hired the ex-Tekmira employees that would eventually form AlCana as consultants, it seems highly unlikely that Madden, Semple, and Hope played no role in the MC3 patent application.'

12 days ago then finally appeared the peer-reviewed publication concerning the discovery of MC3 (actually a long time after the 2009 patent application).  I could not believe my eyes when the list of authors indeed revealed Michael Hope as the senior author on the paper (highlighted in red along with Thomas Madden):

Muthusamy Jayaraman,* Steven M. Ansell, Barbara L. Mui, Ying K. Tam, Jianxin Chen, Xinyao Du, David Butler, Laxman Eltepu, Shigeo Matsuda, Jayaprakash K. Narayanannair, Kallanthottathil G. Rajeev, Ismail M. Hafez, Akin Akinc, Martin A. Maier, Mark A. Tracy, Pieter R. Cullis, Thomas D. Madden, Muthiah Manoharan, and Michael J. Hope*

For those unfamiliar with how authors are listed on papers in the biomedical sciences, the last author is the senior author with responsibility for the overall study.

I have only four possible explanations for this:

1)      Sheer stupidity/carelessness on the part of Alnylam and their lawyers- this would not be a first considering the VSP Interference history alone;

2)      This hypothesized cover-up had so many tracks to conceal that some of them would always make it through to the daylight;

3)      For scientists which see their future in the academic sciences, it is publish-or-perish and Michael Hope and Thomas Madden insisted being on the paper for this reason (note that also the academic Pieter Cullis from the University of British Columbia is on the paper, likewise absent on the patent);

4)      Alnylam knows that the evidence is such that the involvement of Hope and Madden will be revealed anyway, and trying to further conceal the fact would make it look even worse.  Now, they may claim that the omission of Madden and Hope was an honest mistake and they may file for a correction of inventorship on the patent (otherwise they risk the patent becoming invalid due to Inequitable Conduct).

Personally, I favor a combination of 1) and 2).  Alnylam and their lawyers have surprised me a number of times already with their carelessness, a carelessness that is possibly born out of arrogance.  This arrogance may very well be its downfall.  There are only three months to go until the trial and it looks like, despite of Alnylam's delay and cost-intensifying tactics, as if the jury will have it!

Next up: Judge in Tekmira-Alnylam case orders no more delays and why I believe Alnylam is a highly attractive short here...