Fundamental Baulcombe RNAi Patents Extend Reach

I just got notice of the September issuances of two additional US patents (US 8258285 and US 8263569) belonging to the Baulcombe IP estate.  As previously reported, a first patent (US 8097710) from this series was issued earlier this year and represented a mini-shock to the RNAi Therapeutics IP landscape as it sat smack on the sweet-spot of the prototypical Tuschl-type siRNAs: siRNAs with guide/passenger strands of 20-24 nucleotides in length.  Consequently, Alnylam obtained a non-exclusive license to ‘710 shortly thereafter.

‘569 extends coverage over Dicer-substrate RNAi triggers

The claims of the two newly issued patents extend the coverage of the Baulcombe patent estate in 2 important ways.  Firstly, the ‘569 patent is almost identical to the original ‘710 methods patent.  This time, however, the lengths of the guide/passenger strands can be up to 30 nucleotides in length (20-30 instead of 20-24).  This means that companies working with Dicer-substrates like Dicerna may want to take a license from PBL.  Similarly, the ~25bp dsRNAs previously reported on by RXi and Silence/Intradigm, which curiously did not function as Dicer-substrates, would also fall under this new patent.  The saving grace: like ’710, ‘569 is a methods patent.  Methods patents are often easier to work around.

‘285 is a solid composition-of-matter patent

Having said that, the new ‘285 patent essentially turns the ‘710 20-24nt methods patent into a composition-of-matter one.  There is one important exception though: 20mers have to be unmodified, leaving, de facto (because clinical synthetic RNAi triggers are modified), open important asymmetric designs like the 19/21 and 20/22 designs which have been reported to be even more efficacious in many cases than the classical Tuschl 21/21 design.  Nevertheless, the ‘710 and ‘285 together could pose significant headaches for those trying to find holes with traditional RNAi triggers designs. 

Another interesting question is whether Alnylam will have to seek an additional license to ‘285, as in the press release on the Baulcombe license, only the ‘710 was noted as the subject of the license.  My sense is that ‘285 will be included and that as a result PBL will get a slightly increased participation.

[Update September 17, 2012: in an email, PBL confirmed that the new patents are part of their non-exclusive agreement with Alnylam.]

Classical ddRNAi also impacted?

All 3 patents share claims directed towards DNA-directed RNAi (ddRNAi).  It is therefore possible that they will impact the freedom-to-operate of Benitec which practices short hairpin RNAs from which short RNAs are generated by enzymatic processing in the cell.  Accordingly, an important question will be whether the DNA-directed guide and passenger strands covered by the Baulcombe claims would have to be directly generated by the described vector or can also be provided for in the form of a shRNA-type precursor.  I would guess 'probably', because in the Hamilton et al. work, the small RNAs that were seen and form the basis of the claims were also only indirectly generated. 

In summary, the Baulcombe patents have, quite unexpectedly (because based on plant work), emerged as the strongest RNAi trigger IP estate.  Stronger than Kreutzer-Limmer and stronger than Tuschl I.  In many ways, very deservedly so.  The main limitation is though that they are rapidly ageing.   


Addendum: I reviewed some of the prosecution history of the Baulcombe patents and it seems that for '285 to be granted it had to overcome a 'Crooke' patent (in this case US 6,107,094).  I've always found it a travesty that the Crookes often get cited during RNAi trigger patent prosecutions- although they have no scientific relationship to the biological RNAi process.  It is thus pleasing to see that the Examiner in this case saw the light that a double-stranded RNA that directly inhibits an enzyme (i.e. a PROTEIN) does not represent prior art for a dsRNA that targets an mRNA.  Duh!

Brewed up in Seattle: Tekmira and Halo-Bio Seek to Capitalize on Multi-Targeting Potential of RNAi Therapeutics with Multi-Valent RNAi Triggers

It must have been over either coffee, the fuel of scientific discovery and frequent source of business development inspiration, or beer, a beverage that you may enjoy but not mix with business, that Seattlelites Mark Murray (CEO of Tekmira) and Todd Hauser (CEO/inventor of Halo-Bio) initially came up with the idea of joining forces to revolutionize one of the attractions of RNAi Therapeutics: Multi-Targeting, especially for the treatment of complex diseases, cancer and viral infections (see also previous blog entry on Merck’s hypercholesterolemia efforts; link to press release, here).

The technology to which Tekmira acquired a worldwide exclusive license is referred to by Halo-Bio as multi-valent RNAs (mv-RNAs). It is a molecule that in its basic manifestation consists of three separate double-stranded regions, forming a structure similar to a Mercedes star. The RNAi machinery is thought to use each strand as a guide for the targeting of the same or, more interestingly, separate and independent genes.

Data from this technology is yet to emerge, although I would imagine that Tekmira has carefully evaluated mv-RNAs and various other RNAi trigger options before signing this deal given its increasing hints that it is looking at non-Alnylam RNAi triggers. It has become apparent that RNA interference is a robust naturally occurring process that it can harness various RNA molecules as substrates for efficient gene silencing. Of course, not all of them are created equal. Also worth noting in this context is that efficient RNAi largely depends on the 5’ end of the guide strand so that the 3’ end can function to satisfy complementarity requirements such as those for the formation of mv-RNAs.

Besides potency, additional practical and scientific questions remain to be answered. For example, the use of 3 RNA strands to generate one RNAi trigger may increase cost and quality. On the other hand, for those that follow the Tuschl II patent prosecutions in more detail or have seen the somewhat boring, yet useful study by Roche on the purity of annealed siRNAs, it should have occurred to a number of folks in the industry that strand annealing may not be the only way to generate double-stranded RNAs. Furthermore, even when using three strands (one and two may also be possible), the actual complexity may actually decrease compared to using 3 traditional RNAi triggers with 6 individual strands for targeting the same number of genes. Another question would be whether and which mv-RNAs are loaded directly into the RNAi RISC complex, or whether they require prior processing by other nucleases.

mv-RNAs may also have particular utility in lipo- and polyplex settings, or facilitate formulation of SNALP liposomes, because of their increased negative charge.

Of course, this deal also has to be seen in the context of the Tekmira-Alnylam feud. First of all, it is worth noting that Tekmira stated that mv-RNAs are an attractive alternative for multi-targeting RNAi Therapeutics. It still has the more traditional RNAi trigger options from Alnylam which, not least due to their simplicity, appear preferable over mv-RNAs for single-targeting applications.

The transaction also increases Tekmira's business development freedom from Alnylam. Due to the structural differentiation of mv-RNAs from traditional RNAi triggers, it is possible that certain of Alnylam's exclusive rights to Tekmira technology do not apply. In addition, mv-RNAs may also be sub-licensed independent of Tekmira's delivery technology.

Alnylam faces RNAi trigger uphill battle- even 3’ overhangs not safe

The worth of Alnylam’s RNAi trigger IP has deterioriated raplidly over the last two years and Tekmira may not require Alnylam IP even when using Tuschl siRNAs.

While Alnylam once had a decent shot at coming out as gate-keeping with Kreutzer-Limmer and Tuschl-I, failing in those patent prosecutions yet clinging on to ageing technology has meant that it failed to participate in RNAi trigger innovation, even if not gate-keeping. Anybody still remember Commodore or Atari or holds shares in Nokia and Research in Motion?

[correction 8/26/2011: I have re-read my entry and would like to clarify that Tuschl siRNAs are not 'out-dated' technology; it is more the underlying IP strategy that is failing].

Even as Max Planck, UMass, MIT, and Alnylam have just agreed to re-coordinate their Tuschl patent prosecution in the US, it is clear that the double-patenting issue was not the only issue preventing a strong Tuschl II from issuing. For example, by arguing that 3’ overhangs were implicit in T-I, yet T-I cannot claim this since it failed to recognize it, or by claiming 3' overhangs being obvious over other research on the discovery of Dicer in RNAi, the USPTO may have it both ways: deny a therapeutically useful T-I, yet reject T-II over obviousness involving T-I.

The T-II patents that have issued in the US are not that strong as they involve methods of synthesizing two RNA strands and annealing them to form double-stranded RNAs with 3’ overhangs. It is somewhat surprising that such a annealing method would have been granted a patent, and there are signs that the patent offices are starting to realize this.

Coffee or Beer? Have your say in whether you think the Tekmira-Halo deal is a hare-brained idea or stroke of genius by participating in the survey on the upper right hand corner of the blog.

Silence Therapeutics Issued Important Zamore siRNA Design Rule Patent

Silence Therapeutics announced yesterday the issuance of a United States patent related to the design of gene silencing siRNAs. This is the second such patent issuance in little more than a month for which Intradigm, Silence’s merger partner earlier this year, had exclusively licensed from the University of Massachusetts and that is based on fundamental work by the Zamore lab on the enzymology of RNAi. These and other recent patent issuances related to sequence/gene-specific siRNAs address some of my concerns that I had with regard to Silence’s RNAi trigger strategy that I felt was at the risk of being too narrow and, as a consequence, becoming outdated. They should complement Old Silence's lipoplex delivery technology for vascular endothelia with valuable siRNAs in the fields of oncology and retinal disorders. Together, these developments provide evidence that the merger is starting to prove synergistic, with Silence providing the technical know-how and Intradigm complementary IP.

The two Zamore patents that were recently issued in the US relate to guidelines on how to design siRNAs with increased efficacy and selectivity. The first one, announced last month (US patent 7732593) teaches the use of mismatches between the 3’ end of the siRNA guide strand with the target mRNA so as to enhance the ability of the RNAi gene silencing complex RISC to detach from a target mRNA once cleaved and seek out new target mRNAs (note: one of the reasons RNAi is so potent is because one siRNA can destroy many mRNAs). The biochemical experiments on which these claims are based have well stood the test of time. The value of this particular patent for Silence Therapeutics is that it gives them and potential partners optionality for eventually replacing the somewhat restrictive Atu-siRNA design with next-generation siRNA structures based on solid scientific evidence. It has to be said, however, that while many current siRNAs have in fact two such mismatches, or ‘non Watson-Crick base pairs’, namely the classical Tuschl dTdT overhang that was originally conceived as stabilizing the siRNA from exonucleolytic degradation, the claims specify at least three such mismatches in the last five nucleotides of the guide strand. Moreover, the benefit of such mismatches in living cells remains to be determined, as some of the helicases and nucleases that may facilitate RISC detachment from a cleaved target mRNA in living cells may have been missing in the test tube experiments by the Zamore lab.

So while US7732592 is certainly a quite useful patent to have control over, it is the Zamore patent US7750144 of which the issuance was announced yesterday (‘Methods and Compositions for Enhancing Efficacy and Specificity of RNA Silencing’) that should provide for some interesting discussions. This patent is based on one of the classic findings in RNAi molecular biology, namely that the efficacy and selectivity of small duplex RNAs, both siRNAs and miRNAs, is critically determined by the relative thermodynamic stabilities of the two ends of an siRNA (Schwarz et al., 2003: Asymmetry in the assembly of the RNAi enzyme complex). Accordingly, it is the strand of which the 5’ end is less stably base-paired that is preferentially loaded into the RISC gene silencinng complex to become the guide strand, while the non-incorporated strand is discarded as the 'passenger strand'.

This has a few implications for siRNA design. First of all, it increases the absolute loading and consequently silencing efficacy of an siRNA. Secondly, by preferentially loading just the desired strand to become the guide, the potential undesired/off-target activity of the passenger strand can be virtually eliminated. These asymmetry rules have also been extensively validated in living cells and are part and parcel of most siRNA design strategies and algorithms. They are also consistent with structural X-ray crystallographic findings that show that the 5’ end of a guide strand within RISC is unpaired. As a result, it is very likely that a number of siRNA therapeutic candidates currently in the clinic could be interpreted to fall within the scope of this patent. This should also encourage some of the research & reagent companies that sell synthetic siRNAs to take a license from Silence Therapeutics.

The actual issued claims relate to a method of decreasing passenger strand activity by introducing one or more changes in the interaction between the 5’ end of the guide strand with the passenger strand such that the loading of the guide strand is enhanced. The broadest interpretation, and the one that I would expect Silence will take, is that any siRNA containing such a modified nucleotide or mismatch in the specified region (the first 5 nucleotides of a guide strand) would infringe. Most siRNAs should fall within this definition. In some cases, such modifications may have in fact been motivated by other things like stabilizing an siRNA against degradation or reducing innate immune responses, but this remains to be tested, unless the companies involved choose to settle without resorting to yet more exhausting and extremely tedious legal battles. I should note here that when one follows the patent prosecutions especially in Europe, there does not seem to be a single patent that gets issued that will not be opposed by the other party, no matter the scientific merits (my personal opinion). It is enough that some in Big Pharma routinely abuse the patent system to bully smaller competitors into bankruptcy, essentially a way of doing business, and pure-play RNAi Therapeutics companies should be smart enough to know that by adopting these practices they only destroy the size of the shared pie they all depend on: patent-protected innovation. But I digress...

In summary, the recent events have lessened my concerns that it was largely Intradigm that was the beneficiary of the merger as their historical focus on IP is now bearing fruit in the form of some quite fundamental patent issuances and should nicely complement Silence’s strength in the science and clinical translation of RNAi which I had considered to be the stronger of the two. So while I still await data that similarly support the company’s claim that the merger also brought synergies in siRNA delivery, the combined company appears to be quite undervalued here with a market cap of around $20M. The patent issuances should also bode well for the extension of the RNAi trigger-focused part of Silence’s relationship with AstraZeneca. Because of this and because the markets appear to be on summer vacation with the stock virtually unchanged following such strategically important patent news for the company, I’ve decided to buy a few shares of Silence here.

PS: For the various reasons that you can also find in Silence’s regulatory filings, investments in RNAi Therapeutics in general and Silence Therapeutics in particular have to be considered very high risk. Moreover, although I consider myself fairly familiar with the molecular biology of RNAi, I am not trained in intellectual property and my interpretations of the Zamore patents have to be read in this light. Please also read the disclaimer at the bottom of the page.

Alnylam Wins Important Battle in Kreutzer-Limmer Patent Fight

The Kreutzer-Limmer (KL) patent estate, exclusively owned by Alnylam and very broadly claiming double-stranded RNAs (dsRNAs) for gene silencing in human cells (up to 15-49 base pair dsRNAs), won an important battle at an oral hearing last week at the European Patent Office. This comes after Kreutzer-Limmer has suffered a number of setbacks at the EPO about one and a half years ago. The resuscitation of KL means that Alnylam may leverage this patent as potentially gate-keeping as it looks to enter additional non-exclusive licensing partners for its dominant RNAi Therapeutics patent portfolio, also as a potential backstop in the unlikely event that Alnylam loses the fight for the key Tuschl inventions.

The decision reversed an earlier rejection based on technical objections, mainly by Sirna/Merck and Silence Therapeutics, that some of the claims in the daughter application at issue had been incorrectly drawn from the parental application. In general, the main claim describing the structure of gene silencing short dsRNAs are somewhat clumsily constructed and not as straight-forward as one might imagine. This could be the result of having to take into account the embodiments underlying this claim.

If it were not be so important, reading the deeply philosophical arguments of what it means to be 'double-stranded' can be quite amusing, but unfortunately also very time-consuming and distracting, as are these drawn-out patent back-and-forths. Especially for smaller companies like Silence Therapeutics it may actually be worth focusing on developing the enabling delivery technologies and their therapeutic pipelines instead of having their lead scientists waste their creative juices taking part in these battles.

It is likely that the patent will go back again, but this time to be challenged on other issues such as novelty. Regardless, Alnylam should benefit from last week's decision to uphold Kreutzer-Limmer in that it adds to the appearance that, no matter how the individual patent chips fall, Alnylam has so many patent options that making some kind of licensing arrangement with the company would be required if one wanted to securely develop RNAi Therapeutics. Recent progress in systemic delivery should add to the urgency and may even make waiting for the outcome of the Tuschl Tussle a difficult decision.

Alnylam Granted Expanded Kreutzer-Limmer Patent Series in Germany, Signals Its Intention to Enforce Dominant IP Position

Yesterday, Alnylam announced issuance of the new Kreutzer-Limmer patent series in Germany, covering double-stranded RNAs of 15 to 49 base-pairs for gene silencing in mammals. This is quite significant and Alnylam’s accompanying press release made it clear that this should be understood as a watershed event, sending a stern signal to companies like Silence Therapeutics, RXi, Nastech, Dicerna and others that thought to have identified Kreutzer-Limmer as a potential loop-hole in Alnylam’s IP strategy by employing double-stranded RNAs (dsRNAs) longer than Tuschl’s 19-23 base-pair siRNAs and/or making them blunt-ended to emphasize an apparent difference to the classical Tuschl siRNA that features 3’ overhangs. These patent workaround efforts seemed to bear first fruits last year when the original Kreutzer-Limmer I patent series was restricted by the European Patent Office to covering siRNAs between 15 and 21 base-pairs in length (opposing parties: Sirna [now Merck], AstraZeneca PLC, Atugen [now Silence Therapeutics], Janssen Pharmaceutica N.V., and Sanofi-Aventis).

From a partnering perspective, this seemingly small development could have important implications for striking the next major deal, since which company would feel comfortable paying hundreds of millions of dollars for a technology license that appears to be circumventable.

Kreutzer-Limmer was Alnylam’s first line of defense against such blunt-end siRNAs and siRNA precursors longer than 23 base-pairs (aka Dicer substrates) given that, depending on the explicitly granted range of double-stranded RNA lengths, Kreutzer-Limmer would directly cover such structures. Its short-coming, however, is that in 1999, Kreutzer and Limmer did not understand well how these dsRNAs exactly caused gene silencing, which is what Tuschl II is famous for. While I consider Tuschl II, in addition to the ubiquitous Fire-Mello patent, as the fundamental patent series for therapeutic RNAi, due to its excruciatingly detailed explanation of what it takes to effect efficient RNAi in mammalian cells, it is the early priority date of Kreutzer-Limmer’s invention that makes this patent so potentially valuable and dangerous, and explains why Alnylam saw it necessary to remove any uncertainty and obtain exclusive access to it by acquiring Ribopharma AG in 2003.

I found it curious that a number of companies have chosen to take licenses to Kreutzer-Limmer, but not Tuschl II. While that may be interpreted as reflecting the fundamental importance of Kreutzer-Limmer, it was as if by pursuing this strategy, it is almost made implicit that as soon as the scientifically less detailed Kreutzer-Limmer series were curtailed in scope due to heavy opposition, the field for newly patentable RNAi inducers would be wide open. In this case, Alnylam would probably have argued in a second line of defense that, although not spelt out letter by letter, Tuschl II would also cover Dicer-substrate and other RNAi inducers that obviously function either as siRNA precursors (= pro-drugs) or are derived from it, for example 3-stranded siRNAs (meroduplexes). This argument becomes particularly relevant in the case of a weakened Kreutzer-Limmer as this ironically would directly strengthen Tuschl II. In this way, Alnylam holds all the cards and may play them as they wish.

Silence Therapeutics, in particular, will not be very happy with the outcome in Germany, not only because it and others, myself included (to be explained in my next posting), sees itself as a major force in RNAi in Europe, but also since their blunt-end, modified dsRNA is not only the size of the classical Tuschl siRNA, but with Kreutzer-Limmer any gene silencing dsRNA, modified or unmodified, is covered. Silence Therapeutics’ approach could be likened to first taking an invention (here: Tuschl’s siRNAs), then impair its function (here: by flushing the ends blunt), and finally rescue some of the original function by adding further changes (here: by introducing a pattern of RNA modifications). Certainly original, in its own complicated way.

I should disclose here that I largely agree with Alnylam’s view of their IP position and have invested in this company, but at this time I particularly felt like speaking out on all these confusing claims about proprietary RNAi compositions that threatened to hurt investments in RNAi Therapeutics. The acquisition of Sirna Therapeutics by Merck was certainly triggered in part by Sirna’s IP claims which now appear to be weaker than originally hoped for by the buyer and has escalated into a costly and time-consuming mess for a number of companies. In the same vein, I should also emphasize that I am likewise invested in companies that I have strongly criticized in this and other contexts and that I am therefore not wed to any company’s view of the space. It is in this spirit that I hope that Alnylam does not use their IP position to block the evaluation of RNAi inducers that differ from the classical siRNA design in more than just a modification here or an overhang there. Financial incentives should therefore be created for investments in such start-ups without requiring a $1 billion upfront license fee.

PS: In my next posting, barring further developments, I would like to provide the promised company-by-company overview.


Two additional recent developments that I would like to briefly comment on:

1) The FDA removed the clinical hold on Targeted Genetics’ rheumatoid arthritis AAV gene therapy that had been suspected to have played a role in the unfortunate death of a clinical trial participant. I am relieved by this judgment since there was just no good scientific evidence that the gene therapy caused or was associated with the fatality. AAV vectors are currently probably the most potent method to deliver RNAi in vivo and there are a number of indications where AAV-RNAi may be years ahead of synthetic siRNA strategies, and where the benefits outweigh the real risks of gene therapies. One such indication would be AAV-RNAi for treating Huntington’s Disease, where published and orally presented data so far suggests superiority of the AAV approach compared to siRNAs and that Targeted Genetics should now be in a better position to pursue in collaboration with Sirna Therapeutics/Merck and Bev Davidson’s group in Iowa.

2) At a recent symposium on RNAi and its targeting in Sonoma, California, Ian MacLachlan from Protiva presented more data on the efficacy of SNALP-siRNA delivery in non-human primates. According to the abstract, more than 90% gene silencing of ApoB, with silencing lasting for several weeks, could be achieved by single-dose intravenous administration. These are impressive numbers and the task is now to minimize the toxicities associated with cationic liposomes. I am quite impressed by Protiva’s past work not only on RNAi delivery (in collaboration with Sirna Therapeutics and Alnylam), but also on dissecting the causes for the toxicity, and would expect them to be the first to find a solution for this problem. Unfortunately, the ownership and know-how of SNALP delivery technology is highly contested and I can only urge the involved parties to consider working together on this promising technology. During a recent conference call by Tekmira it was apparent that a lack of suitable scientists caused delays in the development of SNALP technology. I would even venture as far and propose that Alnylam’s delays on their systemic delivery programs have probably cost the company more in terms of reagent, labor, time and market cap than the combined market cap of Tekmira and Protiva.

The Confusing World of AtuRNAi, Stealth siRNAs and mdRNAs (Part I)

“Next-generation” RNAi is all the rage in the world of the ambitious RNAi start-up. The definition (note that everything is allowed under the guise of the satire): “An RNAi-inducing molecule derived from the classical Tuschl siRNA design, however with a magical pattern of modifications and variations in the exact length of the RNA duplex, sometimes an NA duplex, with overhang or not. As important as the chemistry that may sound impressively inventive to the lay (investing) public is that a proper name is chosen to further accentuate its apparent uniqueness. This is intended to suggest freedom-to-operate with the ultimate aim of attracting investments from people hoping the company will eventually catch up to the market cap of Alnylam (why would you invest in any of their direct rivals otherwise?).”

Considering that it has become commonplace to hear CEOs talk about their RNAi being so unique and advanced that they are now operating in parallel universes, the staid Tuschl siRNA must have really lost its relevance for the development of RNAi Therapeutics. While I think that some select siRNA derivatives given names such as StealthTM RNAi or Dicer-substrate definitely warrant further investigation, as it is yet unclear how well they will perform relative to the simple, but fundamental siRNA design, what I would like to do is to cut through the marketing fog and provide a brief overview of the types of RNAi inducers currently being used at the bench or in the clinic and how I think they relate to each other in terms of IP. In this post I will lay the foundation by giving a summary account of the history of RNAi as a tool, including some of the fundamental patents (and applications), before dissecting some of the Next-generation siRNA designs in a follow-up posting.

Studies on RNAi-related gene silencing really started in the early 90’s in plants with the observation of co-suppression whereby genes that share sequence similarity inhibited each others’ expression. Usually, this was triggered by the inappropriate processing of one of the gene products, typically from an introduced designer gene that is recognized as aberrant and therefore as a threat by the plant RNAi surveillance system. While the mechanism by which this occurs is a scientifically very interesting question, it cannot be used for gene silencing in humans and therefore has little or no relevance to RNAi Therapeutics IP. Parallel work on gene silencing in worms by Fire and Mello, of course, discovered that it was long double-stranded RNA (dsRNA) that was central to inducing RNAi and patents were filed covering dsRNAs longer than 25 base-pairs for gene silencing. This patent can be licensed non-exclusively by almost anybody that wants it, and despite it being based on work in worms and the long dsRNA nature in the stated claims, it is nevertheless considered to be a license that you should add to your IP portfolio anyway, I guess just because it has proven so fundamental to the understanding of RNAi in general and nobody would want to argue that. I also think this highlights the fact that real fundamental scientific insight will be credited by the patent courts even if the exact length of the duplex or modification pattern was not spelt out in the claims letter by letter.

Shortly after Fire and Mello published their research, Kreutzer and Limmer from the University of Bayreuth in Germany reasoned that short dsRNAs may have similar gene silencing effects in mammalian cells. This prediction, as we know, turned out to be true and now forms the basis of the Kreutzer-Limmer patents claiming short dsRNA of around 15-49 base-pairs for the induction of gene silencing in mammalian cells, although the exact length is the subject of patent challenges, including Merck’s opposition in Europe. This early work was considered important enough by Alnylam for them to acquire Ribopharma AG, the company founded on the Kreutzer-Limmer patents. Although I consider Tuschl’s subsequent work to be quite a bit more fundamental to the use of RNAi in mammals, Alnylam understood that it was important to remove any uncertainty as to the dominance of their RNAi IP position given the relative timing and overlapping content of Kreutzer-Limmer and Tuschl.

Around the same time, Hamilton and Baulcombe discovered that small RNAs were generated during plant RNAi. While they were prescient in predicting that these may mediate RNAi, they did not formally prove it and the structure of the siRNA that was detected in those experiments remained unknown. A world away, in Australia, DNA-directed hairpin vectors for reliably inducing RNAi were being described by Waterhouse and colleagues from the CSIRO. Based on the utility and impact of these vectors on plant research, the patents derived from these studies should give the CSIRO a strong position in the agricultural uses of RNAi. In many ways, the commercial development of plant RNAi is more progressed than therapeutic RNAi as traits can now be altered relatively quickly without having to resort to lengthy breeding and selection. I guess the most important question will be how uniform these knockdown phenotypes will be across a field of crops. The CSIRO patents also form partly the basis for Benitec’s claims to the therapeutic uses of DNA-directed hairpin RNAs. The Graham patents form the other pillar of Benitec’s contested patent estate describing the use of DNA cassettes driving the expression of various forms of dsRNAs, although I find these patents to be quite theoretical in nature and wonder whether most of the described non-Pol III expression cassettes would actually work for gene silencing in most mammalian cell types (to be continued…).


Two noteworthy developments last week that I would briefly like to comment on:

1) ISIS released further phase II data for their ApoB-targeting antisense compound mipomersen. The 200mg/week dose reduced by about half the level of bad cholesterol in patients already on stable statin therapy. This looks quite impressive and if no safety issues come up in the larger phase III trials, then this has the potential to become a blockbuster. I’ve been quite critical about mipomersen in the past, particularly due concerns about fatty liver which many scientists in the field would have expected to observe following ApoB knockdown. Safety data for the 200mg dose, based on liver enzyme measurements, however do not indicate this to be a problem. Ultimately, the proof is in the pudding and I would be happy to ultimately have to admit to have been wrong on this issue. ISIS explains the absence of fatty liver due to transcriptional compensatory changes in fat metabolism. Overall, these data augur well for the development of all RNA-targeting platform technologies, including RNAi Therapeutics, as it suggests that minor off-targeting should be well tolerated in many cases.

2) Pfizer announced the acquisition of Coley Pharmaceuticals for almost triple of Coley’s market cap before the offer. Coley Pharmaceuticals is an oligonucleotide therapeutics company that exploits the immunostimulatory properties of oligonucleotides for applications such as boosting vaccines or in the fight against cancer. Actually, I’ve been quite impressed by their OTS presentation in Berlin, particularly their vaccine program. This comes only days after a blog this month where I asked the question when Pfizer will make its big move in RNAi Therapeutics (11 Nov 07 Blog: “When Will Pfizer Finally Make its Big Move in RNAi Therapeutics?”). It is notable that Coley is a Massachussetts company and I would like to think that the proximity to Alnylam will not be an impediment to Pfizer’s new biotech initiative that also appears to more and more focus on oligonucleotide therapeutics. With the new oligo expertise in-house (note that Alnylam does not have another subsidiary to throw into the next deal) and plans to add more staff to a research facility in Cambridge (the headquarters of Alnylam) in addition to a possible biotech incubator near Boston, the plot thickens.

The RNAi Patent Landscape

Patents are essential for drug development as they protect the significant investments that have to be made in order to obtain marketing approval from the relevant regulatory agencies. Common estimates put the cost of successfully developing a drug at around $1 billion. A whole technology platform such as RNAi would suffer and be unable to attract sufficient funding if the scientific discoverers and institutions failed to file patents and license them to organisations capable of taking RNAi to the clinic. Luckily, fundamental patents have been filed and have been either exclusively or non-exclusively licensed. What are they?

According to folklore, Fire and Mello, the discoverers of RNAi in worms, had to be “encouraged” by the NIH to spend the time to file a patent for RNAi. This resulted in the Fire and Mello patents that can be non-exclusively licensed by almost whoever wants to for a nominal fee. While their science was impeccable, commercially their patents suffer from the fact that originally the dsRNA inducer length was defined as 25bp and above. Additionally, even if efforts to bring this size down to the relevant 21 and upward size succeed, this will not give licensees automatically the freedom to operate as it does not claim the use as a therapeutic. For this, the Tuschl patent series are essential. These are based on Tuschl’s seminal and non-obvious discovery that small double-stranded RNAs (siRNAs) of 19-23 base-pair length are the mediators of RNAi gene silencing. It appears that Alnylam, of which Tuschl is a co-founder, can claim rights to most of the claims in the series, although the Tuschl I series can be claimed by Alnylam, Sirna Therapeutics (now a Merck subsidiary), and CytRX alike. This is because one of the four academic institutions involved in the licensing of Tuschl I decided to go it alone and license it to CytRX and and Sirna in addition to Alnylam. It seems strange to me that one institution alone can do this without the apparent support of the other parties, but I will leave this to the lawyers. The Kreutzer-Limmer patents, covering double-stranded RNAs for the purpose of gene inhibition, may also turn out to be an important piece of the puzzle and were acquired early on by Alnylam through its acquisition of Ribopharma AG.

There are a number of other pending and granted patents in the RNAi field, including siRNA manufacturing and modification patents that will be important in the actual drug development process. However, I view them as secondary albeit important and meritorious patents when measured on an innovation scale. Efforts are also being made to circumvent the need for prototype siRNAs by using either their biological precursors or even variants such as blunt-ended small double-stranded RNAs (apparently it works!), however their exact merit remains to be evaluated. In this context, I am encouraged by recent Supreme Court decisions that emphasise the importance of innovation and non-obviousness in a patent.

Note: The discussion did not cover DNA-directed RNAi that do not involve synthetic siRNAs.