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.