Tuesday, July 31, 2007
When Alnylam and the medical device company Medtronic announced their initial partnership in 2005, the plan was to evaluate Medtronic’s CNS drug delivery devices for use with RNAi Therapeutics (see July 22, 2007 Blog: “Looking Ahead: Alnylam-Medtronic Alliance Stop-Go Decision Expected Soon”), and a joint decision on whether to continue pursuing such drug-device combinations would then be made in 2007.
Yesterday, the companies announced that the progress to date, particularly in their pre-clinical program for Huntington’s disease, warranted a continuation of their partnership. Simultaneously, the original terms of the agreement were amended as a 50:50 relationship in the US, while Medtronic will be solely responsible for development and commercialisation in Europe. It is not clear, however, whether Medtronic will make a $1-8M equity investment in Alnylam as under the original agreement. If not, the new deal structure might reflect the greater flexibility gained by Alnylam through their strong financial position, especially in the wake of the Roche alliance 2 weeks ago.
Such details should become available during next week’s Q2 conference call. Meanwhile, the decision to pursue this alliance further speaks to the promise of RNAi Therapeutics for the treatment of neurodegenerative diseases.
In a similar development, Silence Therapeutics announced a deepening of their existing partnership with Quark Biotech. Quark Biotech, which only very recently dropped their ambitious plans to go public, has two ongoing clinical programs with siRNAs licensed from Silence. In the new agreement, Quark obtains non-exclusive rights to develop RNAi Therapeutics for three gene targets using Silence Therapeutics’ AtuRNAi platform. Details of the deal were not available, but it does not appear to involve a significant upfront cash payment to Silence. Although the deal sizes by Silence Therapeutics pale in comparison to those of Alnylam, at least some of their partners appear to be convinced that Silence’s AtuRNAi technology is sufficiently distinct from Tuschl’s siRNAs to be worth paying money for. It could also mean, however, that some are unwilling or unable to meet the terms that Alnylam can ask for now.
Wednesday, July 25, 2007
The most promising delivery technologies so far (next to gene therapy vectors such as AAV which I will not discuss here) involve liposomes such as the SNALP particles which were first pioneered by Protiva scientists and subsequently became the subject of intense legal battles involving Protiva, Tekmira, Sirna Therapeutics, and Merck. While facilitating highly efficacious gene knockdown, toxicities such as liver enzyme elevations and non-linear relationships between knockdown and siRNA dosage have been repeatedly reported with these chemistries. While the toxicities were observed at relatively high dose levels, non-linear dose responses complicate the choice of the right dose for entering clinical trials.
One step in the right direction was taken when Daniel Anderson from the MIT reported earlier this year at the Keystone meeting the identification of a slightly different class of compounds which they termed “lipidoids”. Importantly, this class of chemistries appear to efficiently promote RNAi gene knockdown with little if any apparent toxicities and linear dose responses.
The just released paper by Rozema and colleagues from Mirus Bio Corporation (Rozema et al. PNAS Early Edition 24 July 2007: Dynamic PolyConjugates for targeted in vivo delivery of siRNA to hepatocytes) sheds light on some of the issues above and holds out a new paradigm for achieving safe and efficacious therapeutic RNAi knockdown in select cell populations of the liver. Rather than regarding drug delivery to the liver as a passive process given that the bulk of intravenously injected drugs will pass through it with a relatively high chance of entering resident cells there, the present approach involves attaching a simple galactose-derived ligand thereby actively targeting asialoglycoprotein receptors (ASGPr) displayed on hepatocytes.
Knockdown of ApoB100 and microscopic analysis of fluorescently tagged small double-stranded nucleic acids confirmed that hepatocytes were indeed efficiently transfected. Equally important, however, was their observation that Kupffer cells, a major population of macrophages in the liver that are implicated in many cases of drug-related liver toxicities, did not take up the siRNA mimicks, whereas non-ASGPr targeted particles were able to transfect surrounding cells, including Kupffer cells.
Taken together with the SNALP and lipidoid data, this study supports the hypothesis that Kupffer cells may act as a sink for certain siRNA formulations such as SNALPs, thereby not only causing non-linear dose responses, but also an immunogenic response and related toxicities. It also shows that it should be possible to design simple and small siRNA nanoparticles for RNAi delivery from relatively cheap materials. Although lipidoids appear to be a clinically viable technology already, it is comforting to know that alternative routes exist and gratifying to see almost daily improvements being made in the RNAi delivery field.
PS: An interesting aspect of this publication was data the authors obtained on ApoB knockdown. In addition to serving as a target for early proof-of-concept studies for systemic RNAi delivery, ApoB has been a favourite for treating hypercholesterolemia using both antisense and RNAi. ISIS Pharmaceuticals in particular has an anti-ApoB antisense compound in late phase II clinical trials. However, only a month ago, Alnylam reported that in their hands ApoB knockdown led to unacceptably high levels of fat accumulation in the liver (fatty liver phenotype), a finding that was confirmed in the present study. Moreover, both reports indicate that this was a siRNA sequence specific effect and was achieved using two different delivery methods. This physiologic response makes a lot of sense, since ApoB’s main role is in the export of cholesterol and triglycerides from the liver. Failure to export them should accumulate them in the liver.
This is a good example where RNAi can serve both as a target validation tool AND a platform for developing innovative drugs. Consequently, I fully support Alnylam’s decision to target PCSK9 in their hypercholesterolemia program instead, which is a genetically well validated target for reducing LDL-cholesterol and heart disease (see also Blogs from 6 May, 2007: “Preventing Heart Disease with RNAi Therapeutics”, and 9 May, 2007: “ISIS Copies Alnylam’s Heart Disease Strategy“). It is curious then that ISIS maintains and has published the absence of such a phenotype. For the sake of patients and stakeholders in ISIS, I can only hope they are right. The explanation for the apparent discrepancy? I cannot really offer a good one except to speculate on a fortuitous ISIS 301012 antisense off-target effect.
Sunday, July 22, 2007
According to regulatory filings, the original decision making due date was April 2007, but was then postponed to July 2007. It is interesting to speculate that this delay may have been either caused by scientific uncertainties or is the consequence of drafting a comprehensive and therefore complicated co-operation agreement. Certainly, in development time-frames, 3 months do not seem to be sufficient to reasonably expect major new breakthroughs had there been fundamental scientific problems.
Medtronic realised early on the potential of RNAi as a new class of drugs that could be used with their drug delivery devices. Only shortly before the 2005 agreement, in August 2004, Medtronic published a patent on the treatment of neurodegenerative diseases such as Parkinson’s, Alzheimer’s, and Huntington’s, through intracranially delivered siRNAs using Medtronic’s implantable catheters (United States Patent 20040162255). Two years later, a similar patent was published for the treatment of neuropathic pain.
While pertinent in vivo data are lacking in these patents, it is clear that Alnylam already has amply tested Medtronic’s devices. Josephine Lai from the University of Arizona Health Sciences Center in Tucson, a Alnylam collaborator, for example has published strong in vivo data on intrathecally delivered siRNAs [Luo et al. Mol. Pain 1: 29 (2005)]. It is also of note that in this study, siRNAs were most efficient when formulated in the liposomal i-Fect transfection reagent from Neuromics. The same reagent was also successfully applied in rescuing mice from lethal flavivirus infection of the CNS [Kumar et al. Plos Med. 3: e96 (2006)].
One potential limitation with the local delivery of siRNAs and shRNA vectors such as AAV, however, is to achieve sufficient diffusion of the RNAi inducing agent to its target cells. That diffusion of macromolecules in the dense matrix of the CNS may also be an issue with a device from Medtronic similar to the one Alnylam is evaluating, is suggested by the failure of a phase II clinical experience of the neurotrophic factor GDNF for Parkinson’s [Salvatore et al. Exp. Neurol. 202:497 (2006)]. This particular experience, however, has to be taken with a grain of salt, as there appears to be some controversy about the interpretation of the trial results [Slevin et al. Annals Neurol. 59:989 (2006)]. A positive announcement on the Medtronic-Alnylam alliance may therefore indicate that it is possible to achieve sufficient siRNA diffusion.
Nevertheless, local delivery may not be sufficient for diseases where the whole brain has to be targeted, such as in viral infections and brain tumours. Here, systemic delivery solutions are needed. While the blood-brain barrier has historically been regarded as a major obstacle to achieving that goal, targeted approaches such as the rabies-peptide conjugation approach that I have highlighted in my June 19 Blog (“New Breakthrough in the Systemic Delivery of RNAi for the Brain”) and similar efforts make me hopeful that a range of both local and systemic delivery strategies will eventually prove successful in addressing a number of diseases of unmet medical need. These issues also highlight once more, that it will be critical to carefully tailor the delivery of an RNAi Therapeutic to its disease application.
Blog Watch: The ‘Old Vic’ blog talks about a possible takeover or significant RNAi Therapeutics alliance involving Silence Therapeutics: http://www.sharescity.com/2007/07/silence-therapeutics-takeover-rumours.html
Sunday, July 15, 2007
Currently, the only effective drugs in addressing RSV are neutralising antibodies that were developed by MedImmune (now AstraZeneca). These monoclonal antibodies (MAb) are directed against the F-protein on the surface of RSV and block cellular entry of the virus. Importantly, whereas these MAbs are used for the prevention of RSV infection in a small at-risk population, premature infants, ALN-RSV01 is geared towards the treatment of RSV.
Numerous studies have shown that the effect of RNAi, and probably any type of drug, on viral replication is most potent when given around the time of infection. I therefore wondered why ALN-RSV01 should succeed in the treatment of RSV when other drug classes such as MAbs have failed. Indeed, my own literature research confirms that MAbs have been tested in animal models for the treatment of RSV, but were found to lack sufficient therapeutic activity.
A study by Mejia et al. [Antimicrobial Agents and Chemotherapy 49: 4700 (2005)] compares 50mg/kg of the latest generation of anti-RSV MAbs when given either before or after viral infection in mice, and finds that on almost all accounts (viral load, inflammation, lung pathology) MAbs were only effective when given shortly (24 hours) before infection. The only assay that showed an effect when MAbs were given 48 hours after infection was a viral plaque forming assay which may reflect the presence of neutralising antibodies in the assay.
Bitko et al. [Nature Medicine 11:50 (2005)] on the other hand showed in an almost identical mouse model that intranasally delivered siRNAs had a profound effect on RSV replication even when given after viral infection. Moreover, 3.5mg/kg doses already proved very effective. Importantly, siRNAs were able to limit viral replication even when given up to 5 days after viral infection, the time when the acute phase of RSV peaks in this particular model. This is crucial in the clinical setting where the treatment benefit will likely be optimal if RNAi therapy can be initiated before acute infection has peaked. The authors then go on to show that on a number of counts (respiratory rate, pathology score, leukotriene production), anti-RSV siRNAs almost abolished any pathological signs of the disease.
These results suggest that while current MAbs are potent in reducing the initial infection by neutralising the interaction of the virus with the host cell, they are ineffective in preventing the subsequent spread of the virus. This could be due to the kinetics of viral re-infection in close proximity to the next host cell. By contrast, unless they target host surface receptors, siRNAs will not be able to prevent viral infection. The can, however, prevent and limit the ability of the viral genomic RNA to replicate and/or inhibit virion formation. Although Bitko et al. have not measured viral RNA levels directly, it is very likely that these were also reduced, and treatment with siRNAs even after the acute phase of infection may have a clinical benefit on RSV co-morbidities such as asthma/wheezing later in life.
Wednesday, July 11, 2007
In the proposed COBALT study, Cand5 (bevasiranib), an unmodified siRNA against VEGF, will be given once every 8 or 12 weeks in patients with wet age-related degeneration (AMD). The goal is to assess its safety and, more importantly, whether it has equivalent efficacy compared to a the currently leading wet AMD drug Lucentis, which is another VEGF inhibitor that is given once every 4 weeks by needle injection.
Although the sweet spot for RNAi Therapeutics are targets that are otherwise undruggable by small molecules and monoclonal antibodies, Opko is one of a handful of companies targeting the VEGF pathway for AMD and diabetic retinopathy (see “RNAi and the Eye” post on May 1, 2007). This is in spite of the fact that other widely prescribed drugs, namely the monoclonal antibody Lucentis and the RNA aptamer by OSI Pharmaceuticals already serve this market. While this may reduce development risk and function as a proof-of-concept, RNAi Therapeutics for these applications will have to compete directly with such therapies in terms of safety and tolerability, potency, and duration of efficacy.
The reason why Opko wants to challenge Lucentis on duration is because each needle injection carries a risk of damaging the eye and causing discomfort to the mostly elderly patients. This becomes a particularly pressing issue for a repeat-administered therapy such as for wet AMD. Therefore, being able to reduce the frequency of injections by half or even more without a loss in efficacy would make an RNAi Therapeutics a very attractive treatment option. Indeed, pre-clinical studies published last year on the silencing of liver-expressed ApoB100 by systemic administration (Zimmermann et al. (2006) Nature 441: 111-4) support the notion that RNAi Therapeutics may have comparable or even better pharmacokinetics compared to what is usually observed for therapies such as monoclonal antibodies
While a positive outcome would certainly help the field of RNAi Therapeutics, there is cause to be skeptical. In particular, bevasiranib is an unmodified siRNA that is given without a particular performance enhancing formulation. This may result in suboptimal gene silencing due to RNA instability issues and inferior cell delivery and ultimately exhibit poor pharmacokinetics. Indeed, results from the C.A.R.E. phase II studies in 129 wet AMD patients were mixed and did not show statistically significant evidence for improvement of acuity. Opko clearly sees the need for optimizing RNAi delivery and have two years ago formed an alliance with the RNAi nano-delivery company Intradig to develop topical and other formulations for Cand5. Whether this will directly impact the current studies is unclear.
I am therefore more optimistic about the approach taken by Merck (formerly Sirna Therapeutics) and their partner Allergan to develop a slow-release formula of a modified siRNAs against the VEGF-receptor that when combined may significantly reduce the need for frequent needle injections. Phase II studies for that trial have started earlier this year.
Monday, July 9, 2007
Roche may use this license to discover and develop RNAi Therapeutics in four out of 20 Alnylam defined therapeutic focus areas: oncology, respiratory, metabolic disease, and non-viral liver diseases. This excludes, however, gene targets that have already been exclusively licensed to other 3rd party licensees or are covered by Alnylam’s own gene-target specific IP. Further reasonable milestone payments could top $1billion with additional royalties on any product sales.
This landmark agreement could significantly speed up the whole field of RNAi Therapeutics by bringing into the fold a highly resourceful biopharmaceutical company with a proven track-record in bringing innovative medicines to patients (see Roche’s Genentech alliance). Moreover, Alnylam, which has a promising RNAi Therapeutics candidate for RSV in phase II clinical trials, will now have all the financial resources it needs to greatly expand and accelerate its own proprietary pipeline and may never need to raise cash through dilutive secondary offerings. What is more, similar deals could follow as Alnylam is free to issue similar non-exclusive licenses, including in the 4 fields covered today, for similar, if not better conditions. The interest should only increase as more partnerships are being announced and players still outside of Alnylam’s umbrella IP estate may now rush to become licensed before their competitors will claim some valuable gene targets of interest.
In light of this, Alnylam’s share price which shot up over 50% today should have much room to extend its rally. Today’s closing price of $23.12, giving the company a market capitalisation of around $900M with over $500M in cash or cash equivalents, could easily be seen as a very attractive bargain. Still below its all-time high set in the wake of Merck’s acquisition of Sirna Therapeutics last year for $1.1billion, it would not be surprising to see the stock extend its rally considerably as the wider financial community comes to grasp with the magnitude of today’s events.
I congratulate John Maraganore and his team at Alnylam for today’s accomplishment. This astounding deal gives me time to pause and rethink my long-held dogma that turning the promise of RNAi Therapeutics into reality is a largely science-driven endeavour. What we have witnessed today will bring some hope into the lives of many patients and relatives suffering from a range of serious diseases. It may not be this, the next, or even the year thereafter, but possibly sooner rather than later.
Friday, July 6, 2007
The AtuRNAi platform is at the heart of Silence Therapeutics. AtusiRNAs are blunt-ended, double-strand oligos with a particular 2’O-methylation pattern that induce post-transcriptional gene silencing. Silence believes that its AtuRNAi platform sufficiently differentiates it from competing RNAi platforms, most notably Tuschl siRNAs, to be considered proprietary. Indeed, the European Patent Office has been a good ally of the company by granting them a core patent relating to this technology earlier this year and restricting the scope of the competing Kreutzer-Limmer patents before that. This has allowed Silence to attract a number of reputable collaborators even before today’s deal with AstraZeneca.
It will be interesting, however, to see whether the value of the AtuRNAi patents are as significant as is claimed, since the seminal Tuschl II patent series demonstrates the use not only of 3’ overhang siRNAs, but also those without such overhangs. It should be noted that while retaining RNAi activity, blunt-ended siRNAs have been shown to be less potent than 3’ overhang siRNAs. Moreover, Tuschl II, to which Alnylam Pharmaceuticals holds exclusive rights, covers siRNA modifications in general and 2’O-methylations in particular. Only last week, Alnylam has strengthened this position by securing exclusive rights to ISIS’ fundamental nucleic acid modification patents for the use in RNAi Therapeutics.
Indeed, at least one licensee appears to have started to doubt the strength of the AtuRNAi IP position. After it had licensed two AtuRNAi agents from Silence that have entered phase I clinical studies this year, Quark subsequently decided to be covered through Alnylam’s InterfeRx siRNA licensing program as well.
However, unless Alnylam feels threatened in its ability to negotiate high-value collaborations due to secondary RNAi IPs such as the AtuRNAi platform, I do not expect them to resort to legal measures at this point. Today’s deal should be seen as yet another validation for the RNAi Therapeutics platform and the considerable funding stream flowing in should strengthen the whole field. Silence has certainly proven its business savvy, now is the time for them to show that they can also execute on their own cancer focussed clinical programs.
Sunday, July 1, 2007
In an interesting twist, Alnylam announced at the Beyond Genome conference held last week in San Francisco the use of MIT’s lipidoid technology for their first systemic RNAi programs. These formulations will be used for knocking down PCSK9 for the treatment of hypercholesterolemia and the dual siRNA cocktail ALN-VSP01 for liver cancer. This was somewhat surprising, following a proof-of-concept Nature study last year that demonstrated efficient systemic RNAi delivery in primates using cationic liposomes. These were developed by Protiva/Tekmira, and Alnylam consequently established a broad alliance with Inex Pharmaceuticals, now Tekmira, that comprised an exclusive license to Alnylam to Tekmira’s liposomal delivery IP estate. It was therefore largely expected that Alnylam would use Tekmira’s cationic liposome SNALP technology in their systemic RNAi programs which are scheduled to enter the clinic by the end of this year.
As I pointed out in some of my earlier blogs, I was concerned that Alnylam’s plans to move into systemic clinical trials so quickly were too aggressive. This concern was largely based on the considerable, albeit transient elevation in liver enzymes, a measure of liver toxicity, at the 2.5mg/kg dose range reported in last year’s Nature study. Moreover, combined with the non-linear dose response for cationic liposomal siRNA delivery that Alnylam reported at the Keystone RNAi meeting earlier this year, this made choosing the right dose range for human studies less than certain.
Interestingly, at the same Keystone meeting, Dan Anderson together with Rob Langer, a world authority on drug delivery and scientific advisor for Alnylam, presented impressive systemic delivery data using so called “lipidoids”. “Lipidoids” were discovered as part of a library approach as an apparently new class of lipid-like molecules that were very effective in delivering siRNAs systemically to the liver and were structurally sufficiently distinct to conventional lipids and cationic polymers to give it a new name. Only a few months after that, Alnylam and the same groups at MIT announced a broad systemic RNAi delivery initiative in which Alnylam would fund 10 post-doctoral researchers for 5 years in return for exclusive rights to the lipidoid technology and an exclusive option for any new RNAi delivery technologies resulting from the sponsored fellowships.
Importantly, the tiny lipidoid formulations were reported to have a favourable safety profile and showed dose-dependent gene suppression without compromising RNAi knockdown efficacy.
In hindsight, it is very reassuring to see that Alnylam did not go out on a limb by promising an aggressive systemic RNAi timeline and gamble an early program on a potentially unsafe delivery technology. It speaks to the quality of the management and Alnylam’s reputation as the leader in RNAi Therapeutics that it always had valid options outside cationic liposomes.
Where does this leave the Tekmira-Alnylam alliance? Although “lipidoids” appear to be somewhat distinct to cationic liposomes, it is certainly a good insurance to be covered by Tekmira’s important IP estate in the field of liposomal drug delivery. Moreover, as part of the alliance Alnylam invested in Tekmira’s manufacturing capabilities, and it appears this investment will pay off as Tekmira is manufacturing the lipidoid-siRNA formulations for the PCSK9-hypercholsterolemia and liver cancer trials. According to David Bumcrot of Alnylam, IND-enabling studies for these programs are well underway.
PS: In another interesting twist, David Bumcrot noted that part of Alnylam’s decision to target PCSK9 in their hypercholesterolemia program is due to a fatty liver problem seen in targeting the former front-runner ApoB100. This appears to be a target-specific phenotype as this phenomenon has been seen with a number of siRNAs targeting ApoB100. Interestingly, ISIS Pharmaceuticals which has an ApoB100 antisense compound in late phase II trials, but has not reported on that problem has followed Alnylam’s lead in targeting PCSK9 in a new hypercholesterolemia program (see May 9, 2007 post). Once again, Alnylam has demonstrated a characteristically circumspect development approach that includes bringing together the best scientists in a given disease area to carefully characterise RNAi knockdown phenotypes.
[Update May 1, 2008: According to a report by RNAiNews , an Alnylam spokesperson indicated that the company had not given guidance on the specific liposome formulations to be used for their hypercholesterolemia and liver cancer clinical programs. This is in contrast to an earlier report by RNAiNews from last year’s Beyond Genome conference in San Francisco which indicated that Alnylam had chosen “choose lipidoids over SNALPs” for these indications (also discussed in a blog entry here). It therefore seems that Protiva/Tekmira's 0.1mg/kg IC50 liposomal nanoparticle formulations may be the current frontrunners in entering the clinic (see also a recent PR).
The sometimes imprecise use of the terms SNALPs and lipidoids may be partly to blame for the confusion. SNALP refers to a liposomal formulation technique, while lipidoids are a new class of lipids generated by combinatorial chemistry which can now be evaluated for liposomal drug delivery. As such, lipidoids could be used within the context of SNALPs, and both of these approaches are therefore complementary to each other.]
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