Technology Trends: MicroRNA Inhibitors and Single-Strand RNAi

There have been developments in the areas of microRNA inhibition and single-strand RNA-mediated RNAi that might have strategic implications for delivery technologies and RNAi Therapeutics, respectively.

MicroRNA inhibition: naked antisense no more?

Currently, all development-stage anti-miR programs to my knowledge envisage the use of unformulated phosphorothioated antisense molecules with various high-affinity modifications such as LNA/LNA-type conformationally restricted nucleotides or 2’F and 2’MOE. To some degree, antisense and certain microRNA companies are making a living out of advertising that, unlike (most) RNAi Therapeutics, no intravenous administration was required.

At the same time, it is becoming clear that more complex structures such as Dharmacon’s miRIDIAN hairpin microRNA inhibitors or the tough decoys (also the synthetic versions that were newly developed in collaboration with Japanese RNAi behemoth Kyowa Hakko: Haraguchi et al. 2012) are considerably more potent on a per molecule basis. Because of their structural complexity, however, they would require delivery formulations for therapeutic use. It remains to be seen how often such formulations would need to be applied, but the early research by Haraguchi in tissue culture shows that the anti-miR effect with these structures can be relatively long-lived. Nevertheless, the in vivo pharmacology of these structured anti-miRs remains to be better explored, but I could imagine that especially for antiviral or oncology applications, the more rapid onset of action and the potentially improved targeting due to the delivery technology could yield positive surprises.

Single-strand RNAi Therapeutics: Stable 5’ phosphate and 2'F

A little more than a year after ISIS and Alnylam ended their ssRNAi Therapeutics collaboration (for which I believe Alnylam had greatly overpaid), ISIS and Merck have made progress in the area.

It had been well known based on particularly protein structural work that the 5’ phosphate modification in the guide strand is important for incorporation in the RNAi effector complex RISC. There has also been corresponding early evidence in ssRNAi research (Martinez et al 2002) that ssRNAs with a 5’ phosphate are more efficient inducers of RNAi, albeit at much lower efficicay compared to dsRNAi triggers. Notably, in the case of double-strand RNA-induced RNAi, prior 5’ phosphorylation is not necessary as this is efficiently accomplished inside the cells.

Based on work by ISIS presented at the Keystone conference in January it now seems that lability of the 5’ phosphate is partly responsible for the reduced efficacy of ssRNAi. Using a new 5’ phosphate mimic (and some other lipophilic modification strategies) that is much more stable than the natural counterpart, it was now possible, following subcutaneous administration, to achieve solid knockdown in rodents. However, the cumulative dose required to get there is still very high, in the range of 2^nd generation RNaseH antisense.

ssRNAi work just published by Merck (Haringsma et al. 2012) confirmed that the 5’ phosphate modification was important, but more importantly worked out the beneficial role of the sticky 2’-fluoro (2’F) modification in ssRNAi. The impressive efficacy-enhancing activity of the 2’-F modification (for which, I believe, Alnylam holds rights to an important patent via a license from ISIS, but a modification that has also raised genotoxicity concerns) was found to apply to both tissue culture and animal settings [Note: an earlier version mistakenly stated that the IP belonged to Alnylam]. Unlike the ISIS work, however, Merck studied ssRNAi in mice using SNALP-like liposomal delivery. It therefore seems as if Merck would need to extra work on adding chemistries such as phosphorothioates or conjugates so that its ssRNAi technology can be used in the ‘naked’ form. This is because the prospect of using ssRNAi in the naked versus formulated form would really be the only motivation for pursuing ssRNAi.

2010 in RNAi Therapeutics Starts Off with Big Pharma Validations

If the first week is any guide, 2010 could develop into one of the most interesting years in RNAi Therapeutics history and comes after a somewhat lackluster 2009. Both the Dicerna-Kyowa Hakko platform collaboration announced earlier this week and the pre-IND milestone payment Alnylam received today from Big Pharma partner Roche are important proof-points that Big Pharma/Biotech (BBP) continues to invest in RNAi Therapeutics.

The Roche payment due to the initiation of IND-enabling studies marks the first time that a BBP is close to entering the clinic with its in-house developed RNAi Therapeutics candidate. The strength and clinical value of Alnylam’s strategy to further monetize on its mainly RNAi trigger IP has been increasingly questioned by skeptical investors as around half a billion dollars in realized IP funding has apparently not been enough thus far for one of its BPP partner to enter the clinic. This event should also be a boost to Tekmira Pharmaceuticals both in terms of platform validation and financially, as Roche has stated before that its first 2 RNAi Therapeutics INDs will involve SNALP delivery and Tekmira stands to collect ~$9M for each of the 2 candidates it helps Roche to get to the IND stage. For speculations about the indication of Roche’s first RNAi Therapeutics candidate, read the recent blog entry here.

While the Roche news is a definite plus for Alnylam, the Dicerna news has somewhat negative implications as it could be interpreted that BPP is becoming more hesitant to pay the Alnylam premium for what had been considered a toll-gate into RNAi Therapeutics. This is particularly so because Kyowa Hakko once paid Alnylam $15M upfront for Asian rights for Alnylam’s lead RNAi Therapeutics program for the treatment of RSV infection, and very little has been heard about the Kyowa relationship after ALN-RSV01 has been dropped as a candidate for development in pediatric populations. [update] However, as a reader rightly points out in the comments section, Kyowa's 'slight' may also simply reflect the fact that Takeda is Alnylam's exclusive Asian platform partner until 2013 and that Kyowa Hakko was sufficiently eager to speed up the development of its internal RNAi Therapeutics efforts by partnering with a pure-play RNAi Therapeutics company such as Dicerna.

Listening to some of Alnylam’s recent comments, especially its more frequent comparisons of RiSC vs Dicer-substrates, it also appears that Alnylam is not claiming to control the IP around Dicer-substrates. dsRNAs of 25bp and longer may therefore be a tempting, cheaper alternative into RNAi Therapeutics. I still believe that while Dicer-substrates are of comparable potency to Tuschl-type siRNAs, they are more complicated and therefore more costly to develop (especially innate immunity and more restricted chemical space due to requirement for Dicer-cleavage), although they these should not be considered show-stoppers and Dicer-substrates may actually allow for unique delivery strategies and in that regard may be considered complementary. The relatively early stage of Dicer-substrates, however, may explain why the immediate financial benefit to Dicerna was limited ($4M upfront, the rest biotech bucks), but should help the VC-stage company to raise further funds.

Price competition in RNAi trigger IP in the face of financially struggling competitors such as Dicerna, recent IP uncertainties, and the relatively increasing value attached to delivery vs RNAi trigger IP may indeed be responsible for Alnylam’s missed guidance of two major deals in 2009. While SNALP/LNP delivery is making great progress, Alnylam may have to offer more high-quality delivery options to further command terms similar to the Roche and Takeda collaborations. The decision of Novartis, which is about to spend $50B on eye-care provider Alcon, to pay Alnylam ~$100M this year for the broad adoption of Alnylam’s full RNAi Therapeutics IP, will be a good indication of the perceived strength of Alnylam’s IP if not the maturity of the technology.

Both the Alnylam-Roche and Dicerna-Kyowa news further underline the strong momentum of liposomal delivery and RNAi Therapeutics for cancer as also indicated by the Silence-Intradigm merger. Liposomal and lipid-based deliveries were highlighted in the delivery capabilities of Kyowa Hakko and Dicerna, respectively, and the first target picked by Kyowa was for oncology. Antibody-directed targeted delivery, also seems to gather pace as Kyowa Hakko further high-lighted such capabilities in the press release ('POTELLIGENT').

The two news items thus should be a good prelude to two other events this quarter that could decisively shift sentiment on the RNA Therapeutics sector into positive territory, namely the clinical trial results from Tekmira and ISIS Pharmaceuticals on their respective ApoB-lowering drug candidates.

Some RNAi Therapeutics Trivia: Dicerna almost appropriately means 'digested' in the Malay language.

Alnylam Starts Monetizing RSV Drug Candidate, but Keeps Options Open

As the biotech world is gathered at the BIO 2008 in sunny San Diego, Alnylam announced today the licensing of Asian rights to their lead, early phase II, RNAi Therapeutics program ALN-RSV01 for the treatment of RSV infection, to Kyowa Hakko, a Japanese company with an increased focus on biotech drug development. The deal involves an upfront $15M cash payment to Alnylam, with additional development and commercialization milestones of up to $78M and remarkable double-digit sales royalties.

Earlier this year, ALN-RSV01 has demonstrated proof-of-concept antiviral activity in an experimental infection model in healthy adult volunteers. This deal therefore comes at a reasonable value inflection point for the drug. Since the Asian rights for ALN-RSV01 were explicitly excluded from the platform licensing deal with fellow Japanese company Takeda, last month, today’s announcement may not come as a surprise to some observers. However, it shows that, supported by the strength of the RNAi platform, IP, and know-how, Alnylam management has executed on yet another strategic corporate goal. The exact timing may have to do with the convenience of signing contracts while assembled at the BIO, by the way taking place not too far away from where not only Kyowa Hakko’s parent company Kirin, but also Takeda have US operations, but possibly (pure speculation) also with the achievement of some clinical milestone (patients dosed in the current lung transplant trial etc.).

Importantly, while Alnylam is thus starting to monetize ALN-RSV01 thereby lowering the risk that its broad RNAi Therapeutics platform may be unduly predicated on this first-generation RNAi Therapeutics candidate, this arrangement leaves Alnylam almost all options open with regards to ALN-RSV01. It leaves them with the clinical development responsibility which is a good thing for a company that aims to become a vertically integrated drug company and, despite its young age, may be the best to shepherd such an RNAi drug candidate through clinical development due to its intimate familiarity with the technology. On the other hand, should one of Alnylam’s upcoming programs for hypercholesterolemia, liver cancer or Huntington’s Disease, show even more promise than ALN-RSV01 early on in the clinic, Alnylam may decide to lower their exposure to ALN-RSV01 through further partnering, potentially on even more lucrative terms following results from ongoing phase II studies. If not, Alnylam may decide to invest more and thus retain most of the rights to ALN-RSV01 for itself.

The terms of the agreement are very favorable indeed and illustrate the virtue of developing innovative therapeutics based on novel mechanisms of actions for diseases of high unmet medical needs- one of the attractions of RNAi Therapeutics. By this, even programs that may ultimately fail in the clinic could actually pay for themselves. The deals just keep coming, and it is only a question of time until even Wall Street realizes that as Alnylam starts paying taxes on the resulting profits, that this is actually part of a sustainable business strategy.