RNAi Therapeutics Portfolio Review: Preparing for Novartis

As I am about to do some traveling over the next couple of weeks and won’t be able to monitor the markets closely, part of my preparations included a review and slight adjustment of my portfolio so as to position it well for what are likely to be turbulent weeks in RNAi Therapeutics. With the $100M Novartis decision coming up, a lot of the dust in the RNAi Trigger landscape about to settle, and share prices of a number of RNAi Therapeutics companies tumbling to mind-numbing levels, the number of companies was further reduced to more fully capture the upside from impending deal activity.

Rosetta Genomics and Benitec were sold as these two companies in the portfolio are probably the least exposed to the Novartis decision. The money was used to buy shares of RXi Pharmaceuticals that I had previously sold during the suspicious run-up to a financing round earlier this year which was followed by a steep 80% drop in RXII. The drop was exacerbated by the relentless selling of RXi shares by CytRx, the company from which RXi had been spun out. It is difficult for me to rationalize how the former parent of RXi could sell down their remaining shares in RXi without apparently any regard for the effect this would have on RXII. The sale of $5.1M worth of shares alone was directly responsible for a ~30% drop in RXII. The primary responsibility for the amateurish disposition of shares, of course, goes to CytRx. On the other hand, a company that cares about shareholder value would want to help and ensure that major stakes are disposed of in an orderly manner. Shareholders will find little consolation in the CEO’s comment on the CytRx issue during the recent quarterly conference call which described these stock sales as potentially beneficial for shareholders in the long run!

At the same time, the current share price of $1.75, which gives the company a market cap of slightly above $30M provides an opportunity to speculate on the company’s new focus on the highly modified and sufficiently differentiated ‘self-delivering rxRNAs’ which I believe to be quite compatible with the dermal and ocular disease areas that the company said it would concentrate proprietary pipeline efforts on.

After a string of technology development agreements with small and large companies alike, near-term upside in RXII will have to come from the company’s ability to execute on the long promised Big Pharma deal that would provide validation for the company’s position in self-delivering siRNAs and add non-dilutive capital. In terms of knockdown potency, the sd-rxRNAs appear to be at least on par with Alnylam’s (5-year-old) cholesterol conjugates and based on their structure should also work around most, if not all of Alnylam’s IP. It is here where the exposure to Novartis should come from, especially now that it has become a powerhouse in the ocular disease area with the Alcon acquisition.

Such a deal would need to be accompanied by the nomination of a serious development candidate to support the notion that the company is finally getting close to the clinic. It is my opinion that there are viable business strategies centered around early-stage RNAi technology development, but that such strategies are not appropriate for companies with RXi’s expense structure.

In addition to seeing validation that RXi has real clinical drive now and the Big Pharma deal, further investments in RXi critically depend management being on the side of the investors rather than pleasing a number of other constituencies as appears to have been the case. The times that public biotech companies were able to treat (retail) shareholders simply as a source of cash to keep management and employees in good stead are over now. If the pain is not truly felt and shares and options continue to be awarded regardless of performance and all the while share prices are tumbling, then such companies have no place to exist. Sadly, I can only say of Tekmira where I have seen an example of a company believing in its technology and managing it in a way to maximize shareholder value. Truly priceless as one can also see from its share price performance over the last 2-3 years.

With that we have arrived at Tekmira and Silence Therapeutics as the two other companies that are most likely to react with large percentage moves from Novartis-related deal activity. I have written a lot about why Tekmira is my favorite RNAi Therapeutics company, so I will only reiterate here my belief here that due to its its critical position in delivery, Tekmira should be The ‘in play’ company over the next couple of months. At the same time, it has now built a nicely diversified proprietary development pipeline consisting of TKM-ApoB for the treatment of hypercholesterolemia, TKM-PLK1 for non-liver solid cancers, and TKM-Ebola in the infectious disease area. The development candidates should make it easier for the market to assign a value to Tekmira, particularly once it lists on the Nasdaq. Importantly, although 3 development candidates may seem like quite a bit for a company the size of Tekmira, the related clinical expenses should be manageable and not overwhelm the pre-clinical research efforts that are aimed at expanding the utility of LNP-siRNA delivery, an area where it is positioned to create significant further shareholder value.

Silence Therapeutics should be the company second best positioned after Tekmira to benefit from the Novartis decision. Through its partner Quark Pharmaceuticals, companies like Pfizer and Novartis have now partnered products based on Silence Therapeutics’ RNAi trigger technology. In addition to the development milestones that Silence stands to collect and thereby extend the cash runway possibly into 2012, I would be surprised if Pfizer and Novartis had not considered Silence Therapeutics a less expensive alternative to Alnylam. Patent issuances for the Atu-siRNA structure and the Zamore RNAi trigger design rules should help Silence make its case.

The impact of a Novartis option exercise on Alnylam’s share price is probably less certain. Because the market expects Novartis to exercise, this could limit the immediate upside, although I would certainly expect some increase in ALNY as it would remove lingering uncertainties and should be seen as a validation that Alnylam’s RNAi trigger position is not just slightly ahead of the competition. The exact extent of the upside, however, would likely depend on how much extra Alnylam can extract from providing Novartis with access to delivery. The Tuschl litigation in the US, and the Tuschl II and Kreutzer-Limmer patent exams in Europe also have to be closely watched as it will determine the extent to which Alnylam can control access to RNAi triggers. Fortunately, scientific progress reported at recent meetings suggests that despite the various legal battles Alnylam is fighting, there is actually some R&D happening, too. Long-term, this, and not trying to marginalize competitors at the cost of management attention, is really what will drive the value of ALNY.

In the short run, however, Alnylam needs one or two more significant platform deals. This is because a relatively early-stage pipeline would make it difficult to get the market cap back above $1B. Alnylam should be well positioned to get them done eventually given that many in Big Pharma do not have the luxury to delay RNAi Therapeutics forever. Sanofi-Aventis, GSK, and Pfizer are potential candidates. Intriguingly, Sanofi-Aventis will apparently occupy the first floor of the building where Alnylam is headquartered in Cambridge, MA, which is even more so curious given that Sanofi-Aventis will likely become Alnylam’s immediate neighbor anyway given their attempt to take over Cambridge-based Genzyme.

But as time progresses even the Tuschls and Kreutzer-Limmers will show their age and will decrease in value. Similar to monoclonal antibodies, what will count is the scientific quality of such triggers which will be more narrowly defined than just by the length or the blunt-endedness of an RNAi trigger. Alnylam is naturally best positioned to continue and lead the field here, but there is no reason to be complacent, especially as delivery, more than triggers is increasingly driving value in synthetic siRNA Therapeutics.

ISIS Pharmaceuticals, the remaining portfolio component, is currently recovering from the sell-off that followed the release of the last set of phase III results of lead candidate mipomersen. I believe the market almost assumes that an increase in liver fat equals liver toxicity. My view is that while liver fat increases can cause toxicity, by far most people with such increases do not go on to develop fibrosis and other complications and the clinical relevance of such cases is debatable. Supporting this view, cases of Hy’s Law, indicating actual liver toxicity, have yet to emerge (admittedly patient numbers are still somewhat limited). So if no further negative surprises emerge from upcoming data presentations of mipomersen, the stock should be attractive in the short run. In the medium-term, it will be important that the initial filing in 2011 will not be limited to the homozygous FH population. If so, it may be difficult for ISIS to sustain any upward momentum.

In conclusion, the second half of 2010 should be a good time to be invested in RNAi Therapeutics. Similar to the dogs in this picture, what may look like a languishing field based on share price performance, it actually has regained quite a bit of its scientific bite now and could come alive again faster than you’d think.

A comparison of Tekmira’s and AVI Biopharma’s Candidates for the Treatment of Ebola Virus

I was quite amused today, while driving a car on Borneo, the local radio report the headline ‘US scientists said that they are ready to start clinical trials for Ebola’. It was yet another reminder that oligonucleotide therapeutics, including RNAi is firmly emerging from the research stage, entering the medical arena and gaining more widespread attention.

As you may also have heard by now, 3 months after the impressive publication in The Lancet by Tekmira and collaborators that liposomal siRNA essentially cured non-human primates from otherwise lethal infections of Ebola virus, morpholino antisense company AVI Biopharmaceuticals followed up with results from their own Ebola non-human primate treatment studies in the equally prestigious journal Nature Medicine (Warren et al.: Advanced antisense therapies for postexposure protection against filovirus infections). Since both companies were recently awarded highly lucrative government contracts from the US Department of Defense to further develop these two oligonucleotide therapeutic candidates for the treatment of Ebola and therefore have to be considered competitors for further contracts, I will briefly compare and contrast the results from the two studies.

One remarkable benefit of having both lines of research enjoy funding from the DoD is that they have been highly standardized which makes them very comparable to the extent that even the animal laboratory was shared, I believe. So no excuses with 'in our hands' or the likes. In each case the goal was to evaluate the RNAi or antisense in a post-infection model whereby the oligo Rx was first given once 30-60min following intramuscular injection of rhesus macaques with 1,000 plaque forming units of the Zaire strain of Ebola, an amount many orders of magnitudes higher than needed to kill such an animal if left untreated.

Just as a reminder, in this treatment regimen, Tekmira’s intravenously administered SNALP-RNAi when given 3 times every other day or daily for 6 days following viral exposure rescued 2 of 3 and 4 of 4 animals, respectively.

In the AVI study, morpholino antisense molecules which have been slightly altered compared to previous studies to be positively charged to facilitate enhanced cellular uptake and improved target RNA binding, were also given daily, although in this case the follow-up administration period lasted for 10-14 days and the dosage was 40mg/kg compared to 2mg/kg siRNA. In addition to intravenous administration which the investigators refer to as the preferred route of administration for needle stick scenarios and the like, some studies involved simultaneous intraperitoneal and subcutaneous administrations.

Route of administration, however, did not seem to make much of a difference since in both cases around 60% of the monkeys were rescued from near-certain death: 5 of 8 in the subQ+i.p. regimen, and 3 of 5 in the intravenous regimen.

Put differently, the risk of dying from Ebola infection was 14% in the Tekmira study (1 out of 7 animals; 0 of 4 with the optimized protocol) compared to 39% in the AVI studies. Although the numbers are still small, this indicates an almost 3-fold risk reduction with SNALP-RNAi compared to morpholino antisense.

So while Tekmira’s SNALP-RNAi may in fact now lead the race towards a drug that can treat Ebola virus infection, it is far from over. AVI is apparently ready to move into safety studies with human (healthy) volunteers. In addition to such clinical studies, both companies and their collaborators will have to test in further non-human primate studies how long they can delay treatment after the initial infection, as ‘in the field’, as opposed to laboratory accidents and first responder situations, treatment will only begin after first symptoms emerge.

However, with the current efficacy of TKM-Ebola and what appears to be an already extensive pre-clinical safety database, if the initial human studies are uneventful, the case could be made that a first-generation Ebola standby for needle pricks and first responders in local outbreaks may be quite close indeed. In fact, researchers exposed to these viruses should be pushing for it, and the fact that the current SNALP-RNAi has to be administered intravenously should not be a problem for such purposes.

AVI’s antisense morpholino though may have some advantages over the SNALP-RNAi for wider outbreaks in that it may be administered subQ, although a pure subQ protocol has not been tested yet in the post-infection model and I am not clear about the practicalities of administering 40mg/kg x70kg= 2.8 grams (!) of oligonucleotides subQ. With the more potent, second generation SNALP-RNAi formulations ('LNP' is the official designation now), subQ administration of liposomal siRNAs should become more practical and I would not be surprised if some of the future Ebola contract funds were to be spent on further developing subcutaneous LNP administration.

While it was not obvious from the paper in The Lancet, reading the latest paper, it is quite clear that the 2 companies and probably even different groups within the Army that work on Ebola Rx are strongly competing with each other. It reminds me of the strategy of principal investigators of some ‘post-doc labs’ where at least 2 different post-docs are being competitively put on the same project. This way, the principal investigator increases his chances of timely success. Not being a military man myself, it would also make sense from a military point of view to even have 2 alternative Ebola Rx stockpiles, just in case one turns out to be more desirable than the other in a real emergency.

In the end, while the value of biodefense agents is often difficult to determine, the DoD Ebola program brings two significant benefits. One is that the program allows the involved companies plenty of room to develop their underlying platform technologies such as facilitating the scale-up of their manufacturing processes. The other is the images evoked by viruses such as Ebola and the attention it directs towards this rapidly growing area of oligonucleotide therapeutics. Even a remote island like Borneo is an escape from it no more.

Is Novartis' Kidney RNAi Drug Deal Part of its Grand RNAi Therapeutics Strategy?

In a reminder that the $100M adoption license option decision is coming close, Quark just announced that it has granted Novartis, for $10M in upfront and another $600M or so in potential milestones, the option to fully license Quark’s drug candidate QPI-1002, an siRNA targeting the famous 'guardian of the genome', p53. Delivered in its naked form intravenously, QPI-1002 is currently in phase I/II studies for the treatment of ischemia-reperfusion-related injuries of the kidney. While the deal is certainly supportive of Novartis’ interest in RNAi Therapeutics, questions remain whether this deal could reflect Novartis’ view of Alnylam’s RNAi trigger IP.

It is possible that this deal has indeed very little to do with Novartis’ general RNAi Therapeutics platform strategy and was largely driven by its therapeutic focus area and commercial groups that simply regarded this candidate as an interesting pipeline addition. As long as the underlying scientific data, market potential, the mechanism of drug action look attractive and the candidate is adequately protected by IP etc, Novartis may not care much about for example whether its core RNAi Therapeutics development group likes the Atu-siRNA structure or not. This would be somewhat reminiscent of the situation at Pfizer where the RNAi drug candidate licensing history does not seem to tell us much about its grand platform strategy.

Nevertheless, given the timing of the license, it is interesting to think that the various departments at Novartis in fact talk to each other occasionally. Such a conversation would probably have been centered around the siRNA structure and IP as well as delivery.

In terms of siRNA structure, QPI-1002 is a 19bp blunt-ended Atu-siRNA that is protected under licenses from both Silence Therapeutics and Alnylam. Since it is an Atu-siRNA structure and patents have actually been issued on this in major markets, there is little question about the need for the license from Silence Therapeutics which it obtained in 2005. In 2006, however, Quark also struck a license with Alnylam for additional patent protection. Because of its size and blunt-endedness, I would agree that such protection may be indeed required due to Kreutzer-Limmer in Europe (15-21bp), although the eventual outcome of the opposition proceedings remains to be seen. Consequently, I expect a decent portion of the Novartis payments to flow to Silence Therapeutics (10%?) and probably also to Alnylam.

In pre-clinical studies reported last year, QPI-1002 demonstrated decent potency with an IC50 of 230pM in tissue culture experiments. Potency has been my biggest concern when it comes to Atu-siRNAs. While I still believe that the rigid Atu-siRNA design makes it quite a bit more difficult to find potent RNAi triggers, at least this study is further support that Atu-siRNAs of clinically relevant potency, let's say an IC50 of less than 50nM, can be found.

The heavily modified Atu-siRNA structure makes QPI-1002 also very stable in biological fluids which is presumably required for the type of naked delivery approach that Quark has taken. Which gets us to the question of delivery.

All of Quark’s RNAi drug candidates are unformulated siRNAs. This raises, of course, a lot of skepticism about their scientific soundness. Quark counters that it just looks at where the naked siRNA goes after various routes of administrations and then select the indication accordingly. Since naked siRNAs following their unformulated administration quickly accumulate in the proximal tubule where the process of the re-uptake of the bulk of the primary urine begins, and since apoptosis in that area is believed by some to be important for the type of kidney injury Quark is targeting, it may explain why the company may have seen success whereas others have apparently failed.

In general, when it comes to target selection, I also like the approach where you carefully match pathophysiology, target, and siRNA pharmacology, instead of having a fixed idea of the target and cell at the start of your project and desperately try and find a suitable delivery technology for it.

Nevertheless, how the siRNA escapes into the cytoplasm of the proximal tubular epithelial cells still remains a mystery although it is always possible that cells in general, especially those with high membrane dynamics, have a general leakiness that allows some siRNA to get through the lipid bilayer when siRNA concentrations are very high. And because siRNAs can be highly potent, this would be sufficient to prompt knockdown.

Similar reasonings may apply to Quark’s eye drugs, one of which, another Atu-siRNA structure, has been licensed to Pfizer and the other one Quark is apparently out to license, too. I guess being too productive in entering the clinic may not be the best way to build value if you are a small and private company.

Overall, this deal is good for the RNAi Therapeutics field as it shows that it is yielding candidates in various therapeutic areas that can attract serious funding by the industry. Not that I need to be convinced of this, but headlines like this should encourage further investments in the space. We shall soon see how this investment will look like in more detail for Novartis. One thing is for sure: delivery has to be a critical part of that equation, and this creates a number of interesting scenarios. I guess I was not the only one wondering about those when I first heard of the news.

Zamore Design Rules not Essential, but Highly Desirable and Strategically Important

As Silence Therapeutics is being issued one patent after another from the Zamore siRNA design rule patent families in the US, and possibly also soon in Europe, there has been some confusion about their value, both scientific and strategic. Silence claims that they are highly valuable additions to the RNAi Therapeutics toolbox; Alnylam dismisses them as something they chose to pass on as worthless. This controversy is part of the general debate of how easy it is to work around Alnylam’s historically strong IP position in RNAi triggers at a time that the Tuschl Tussle and a hearing on Tuschl II in Europe in early December are set to provide much-anticipated clarification of the RNAi trigger IP playing field.

As I have detailed before, I personally believe that while one of the Zamore patent families related to enhancing RISC turnover (mismatches between the 3’ end of guide and target mRNA) is quite useful and probably still widely underappreciated, it is the differential end-stability patent family that should be of Alnylam’s concern. Sure, going forward, you can easily get around it by simply not using the covered methods, but ignoring one of the most impactful siRNA design rules would be very much at the considerable expense of the siRNA discovery efficiency. Also, there is a good likelihood that some of the current RNAi clinical candidates have employed these rules and would require licenses at some point. Ask a handful of RNAi molecular biologists and I bet 4 or 5 out of 5 will attest you the importance of the end-stability rules which are quite comprehensively covered by the issued claims. Here is an exemplary main claim:

1. A method of producing a dsRNAi agent having decreased off-target silencing activity, the method comprising:

(a) identifying an off-target silencing activity mediated by a sense strand of a first dsRNAi agent, wherein the first dsRNAi agent directs cleavage by a RISC complex at a phosphodiester bond within a desired target mRNA; and

(b) synthesizing a substituted dsRNAi agent comprising one or more substituted base pairs with respect to the first dsRNAi agent, wherein the substituted dsRNAi agent comprises a sense and an antisense strand, each strand having a 5′ end and a 3′ end, wherein the substituted dsRNAi agent directs cleavage by the RISC complex at the same phosphodiester bond within the desired target mRNA, wherein the one or more substituted base pairs are within about 5 base pairs from the 5′ end of the antisense strand (AS 5′) and the 3′ end of the sense strand (S 3′) and are selected from the group consisting of a mismatched base pair, a wobble base pair, a base pair comprising a rare nucleotide and a base pair comprising a base-modified nucleotide, such that the sense strand of the substituted dsRNAi agent is less effective than the sense strand of the first dsRNAi agent at entering the RISC complex;

You will see that it is a claim on a method detailing specific steps taken to increase the specificity of an siRNA, and in order to enforce it you would probably need to have insight into the development history of individual RNAi Therapeutic candidates. Since I was therefore curious as to how Silence thinks it may enforce such claims, I recently spoke about it to the CEO of Silence Therapeutics, Phil Haworth, on the phone.

Dr. Haworth stated that Silence’s current strategy was to raise awareness of the Zamore patents and have companies decide for themselves whether they ought to get a license to it or not, implying that getting a license now would be cheaper than waiting until products are close to commercialization. He agreed that it may be impossible to prove without doubt that the Zamore rules had been employed without direct insight into the RNAi trigger lead development of the various companies. He added, however, that after Silence Therapeutics and Intradigm merged earlier this year, they found that Silence Therapeutics would indeed have infringed the Zamore design rules. Although only an n=1, this is consistent with the notion that particularly the end-stability rules find wide application in the industry.

I also asked whether we may see composition of matter patents issued covering the end-stability rules, particularly since they may be more straightforward to enforce. For reasons that are not fully clear to me without studying the status of the entire patent family in detail, Dr. Haworth wished to leave this an open question. So it’s possible, I guess, and Silence may want to retain the thunder for any such issuance.

Whatever the case, I feel Silence has a strong case that it is likely that Big Pharma will license some of the Zamore rules on a non-exclusive basis, either broadly for companies interested in RNAi Therapeutics as a platform (Merck, Roche, Novartis probably highest on the list) or on a case-by-case basis.

Alnylam may be in a more tricky situation. Although they would probably also be invited to take a license, such rights are unlikely to come together with rights to sub-license the Zamore rules to Alnylam platform licensees. As such, these potential partners may now feel that even if they pay for a RNAi trigger license from Alnylam, they still would not have all the desirable siRNA design tools at their disposal. Silence, of course, is in a somewhat similar situation, namely that while they can probably work around Alnylam’s RNAi triggers, particularly for blunt-ended dsRNAs 22 base-pairs and longer with some related composition of matter patents to boot ('AtuRNAi'), potential partners may not want to sacrifice on the use of 3’ overhangs that, although dependent on the Tuschl litigation, are likely to be controlled by Alnylam in the future.

Alnylam is arguably in the better position. It could just continue and bury the $20M market cap Silence Therapeutics under patent litigation costs and diverted management attention. One example that struck me here particularly was Alnylam’s opposition to Silence’s PKN3 patent which I feel is built on solid data and given the 20000 or so genes available, Alnylam should have no reason to oppose except to hold up Silence’s efforts with IP costs. On the other hand, as its investors grow impatient about long-promised deals, Alnylam does not have the luxury of there being increased uncertainties not only on its gate-keeping position, but also whether the scope of its freedom-to-operate is scientifically satisfactory. There is, of course, also the distinct possibility that Merck may see Zamore a relatively cheap way to gain leverage over Alnylam and may therefore choose to be Silence’s white knight. With Silence at a $20M market cap and Alnylam having $400M in cash waiting to be invested in RNAi Therapeutics instead of litigation, you’d think Zamore would be a good investment for Alnylam to make.

SNALP Delivery Taking Off

Just like SNALP delivery has become a staple of this blog, Alnylam has been investing aggressively into its development as exemplified by the one dozen or so presentations by the company and a whole range of collaborators, most notably the University of British Columbia and Old Tekmira spin-off Alcana, at the recent International Liposome Research Days at the world capital of liposomal nucleic acid delivery, Vancouver. It illustrates a theme that I believe we will see repeated over the next decades of RNAi Therapeutics drug development where, once in a while, there will be these pockets of tremendous value creation driven by a few key technical breakthroughs. SNALP is the first of this kind and will be critical for the valuation of the RNAi Therapeutics field over the next 5-10 years.

Seemingly ever increasing potencies with ED50s for knockdown of genes in the liver now in the single-digit microgram (not milligram) per kg range is only one side of the story.

Mechanistic understanding to drive next phase of SNALP development

In fact, more so than ever more potent and smarter lipids, at this point it is the mechanistic understanding of SNALP delivery, together with the ability to sculpt SNALP formulations at will, that will drive the adoption of SNALP for extra-hepatic applications such as in cancer, immune and infectious-related applications, in addition to further improving the overall safety profile.

One important finding, first published earlier this year in Molecular Therapy, is that much of the potency of ionizeable SNALPs can be explained by ApoE association and cellular uptake via the LDL-receptor. Based on this, it is now possible to re-direct SNALP particles from the liver by for example abolishing ApoE association which can be done through increasing the PEG density on the outside. The attachment of targeting ligands can then facilitate the uptake in cells bearing cognate receptors. Combine that with long circulation times and we will see more and more examples of SNALP-RNAi for non-liver tissues. Similar to what has been the case for the ApoB and TTR programs this also means that there will for example soon be cancer formulations that are more potent and selective than Tekmira’s SNALP-PLK1 for which an IND has just been filed. Again, a good problem to have and probably a much better strategy than the one taken by Merck which, after $1.5B or so spent, is to constantly admonish the field of the dangers of innovative drug development while procrastinating forever before collecting valuable clinical data.

So while SNALP potency for the liver is starting to scratch at theoretical limits, based on the rapid progress we’ve been witnessing there is no sign that SNALP technology will have fulfilled its inherent potential any time soon. Alnylam has to be given credit that in the case of SNALP it chose to lead the translational science instead of entirely relying on outside help, and now has results to show.

Given that RNAi Therapeutics in 30 years or so is likely to comprise a number of delivery platforms, is this the right level of investment, or does it risk neglecting potentially complementary delivery technologies that Alnylam likes to emphasize they are investigating, too? From the perspective of the net present value of the pipeline alone, ignoring partnership appeal etc, I believe it is. As an analogy, if you are looking to enter a little explored area at the cutting edge of academic science, it often happens that you will be tapping in the dark for the longest time, and while picking up an interesting signal here or there, this period is very costly if you think in terms of numbers of publications (= clinical candidates). However, once or so often you encounter a strong, robust signal and if you are wise enough you will drop everything to extensively feel out what you’ve just found in a phase that should be very productive. Artefacts (= delivery dead-ends) don’t lend themselves to that type of productivity.

Despite the wealth of exciting data, SNALP delivery probably still has many more skeptics than enthusiastic supporters like myself. I believe this is largely due to the perception that SNALP suffers from many of the same problems that other liposomal nucleic acid delivery platforms suffer from, a perception curiously widespread even among those that get identified as liposomal experts by those undertaking due diligence of the technology, but have yet to read a single paper or patent related to the technology. Immune stimulation, clotting abnormalities and liver toxicity are some of the challenges frequently cited, of course also by a number of competitors.

The reason, however, why competing groups struggle to reach the non-human primate stage while SNALP is enabling now one clinical candidate after another is that these are precisely the areas where Tekmira and Alnylam have invested and made key advances, many of them formulation and process-related, the benefits of which have been now amplified with the more potent lipids. Moreover, with shelf-lives of at least 2 years in the fridge and the improvement in potency decreasing cost of goods and paving the way towards new routes of administration, including subcutaneous, the commercial (and also biodefense) appeal of the technology grows.

Somewhat similar to Alnylam when it talks about the other delivery technologies in its stable, Marina Biotech and Silence Therapeutics are often also keen to stress that lipid-mediated siRNA delivery is not everything, cautioning against making a single technology platform, i.e. [SNALP], fit for various therapeutic applications, although it is quite clear from their own activities that liposomes/lipoplexes play a very critical role for these companies, too. Just recently, Marina Biotech bought the IP for Novosom’s amphiphilic liposomal delivery platform and they also presented improvements in liposome potency at the Vancouver meeting with ED50s down to 80ug/kg in rodents.

It is still unclear to me whether this communication strategy is simply to reach out to Big Pharma to whom the supermarket concept appeals, or whether they have actually made internal progress with other delivery platforms to back up such statements. Anything else would be either corporate suicide or trying to mask deficiencies in formulation and scale-up, areas where Tekmira dominates and (still) enjoys a gate-keeping position. I say ‘still’ because it is obvious that since Alnylam has moved so close to Tekmira’s quarters, it may be a question of time until sufficient know-how has moved over to Alnylam’s allies in Vancouver to make Alnylam’s SNALP efforts independent that of Tekmira’s at least in terms of know-how. Instead of an adversarial relationship, one may also speculate that such a transfer of know-how would make sense if Alnylam and Tekmira were scheming to sell Tekmira as part of a larger Alnylam alliance, in which case Alnylam would want to make sure that it can stand on its own SNALP feet first.

Of course, advertising their RNAi capabilities, particularly in delivery, to potential platform collaborators is one aim when Alnylam impresses at a meeting like this with a full range of presentations. Notably, the accompanying press release states (paraphrasing now) that progress such as this will form the basis for future platform partnerships as, I’m convinced, it has for the Roche and Takeda relationships. Within 2 months or so, we should know how much in particular SNALP delivery is worth to Novartis after exercising the $100M adoption license option or whether it will adopt a different approach to RNAi Therapeutics drug development altogether.

Mipomersen Efficacy Surprises to the Upside, on Track to Become First Commercially Meaningful Antisense Therapeutic

ISIS Pharmaceuticals and co-development partner Genzyme reported today top-line data from the final 2 out of 4 phase III studies with the ApoB-targeting antisense compound mipomersen for the treatment of hypercholesterolemia. The efficacy results came in above my lowered expectations and support mipomersen to be an attractive treatment option for the many patients with severe hypercholesterolemia for which current care is still inadequate and who are therefore at a high risk of suffering cardiovascular events. Further studies, however, will be needed to better understand the clinical relevance of the observed liver enzyme and fat elevations.

As I wrote earlier this year, the first 2 phase III studies in patients with homozygous (25% LDL-cholesterol reductions) and heterozygous (28% LDLc reductions) familial hypercholesterolemia raised concerns that the efficacy of mipomersen could be less than one might have expected based on the initial phase I/II trial results. Couple this with a number of safety and tolerability issues such as elevated liver enzymes, fat accumulation, plus wide-spread injection site and flu-like reactions, the overall profile may not have looked that attractive. The 36-37% reductions in LDLc reported today for the severe hypercholesterolemic and high-risk/high-cholesterol patient populations, however, put efficacy concerns to rest, and it is possible that intact LDL-receptor function contributes to LDLc lowering, somewhat similar to statins.

Actually, due to the high drop-out rates in the latest studies (31-41% for those on drug), the LDLc reductions are likely to be quite a bit higher, at least on par or superior to LDL-apheresis which many of these patients are eligible for, but not widely used due to cost and safety/tolerability/patient convenience reasons. Moreover, the on-target efficacy, and not 2^nd gen antisense as a class, may indeed be responsible for some of the safety issues as the companies strongly suggest that the liver enzyme and fat elevations were in fact correlated with the speed and degree of the LDLc reductions. In some cases apparently more than 80% reductions in LDLc were achieved!

If this were the case, one can easily imagine that in real life, patients could be simply monitored for liver enzymes and fat content as they go on drug, similar to what is already routine for other widely used drugs such as warfarin. Although clearly something that regulatory agencies will want to see studied further (e.g. the ~200 persons that have received full 26-week course of drug may alone not be sufficient to argue against liver tox based on Hy’s Law), at this point it is actually not clear to what degree ApoB knockdown-related enzyme and fat elevations would be clinically relevant. The strategy of the companies to pursue a step-wise filing strategy starting with the highest risk patient populations (planned for early 2011) before seeking to expand the label is therefore very reasonable. For commercial success, the severe hypercholesterolemia population should be key and could already be part of the first filing cohort.

SNALP-ApoB in light of mipomersen data

Now a few words on how the mipomersen results may impact Tekmira’s RNAi Therapeutics candidate SNALP-ApoB which targets the same gene as mipomersen for the treatment of hypercholesterolemia. Assuming that liver enzyme and particularly fat elevations are indeed a function of ApoB knockdown, then some of the same strategies such as gradual dose adjustments may be applicable. In general, as the runner-up, Tekmira has a lot of valuable lessons to learn from mipomersen especially with regard to its regulatory path.

At the same time, to differentiate itself in the market, Tekmira may also want to take advantage of some of the challenges that mipomersen is encountering when it comes to drug tolerability, particularly the injection site reactions and flu-like symptoms that appear to be responsible for quite a few of the study drop-outs and where I believe that SNALP-ApoB could do better. Although I had never thought that being intravenously administered as opposed to the subcutaneous administration of mipomersen would be a major issue, competitive or otherwise, for the high-risk patient populations we are talking about, the fact that ISIS and Genzyme are now considering daily injections as an option to address the injection site reactions even makes intravenous infusion every 2-4 weeks look like a competitive advantage now.

Meanwhile, due to the satisfactory efficacy of mipomersen and the fact that you probably don’t want to overdo it with lowering ApoB as long as it is in the 32-40% range, efficacy should not be too much of a differentiating factor.

All of this is in no way to suggest that the current value of SNALP-ApoB is comparable to ISIS’ mipomersen. Tekmira has yet to enter the clinic with its improved SNALP-ApoB candidate and we all know that clinical development is fraught with surprises. In any case, it is quite satisfying to see oligonucleotide therapeutics progress in the clinic on so many fronts and I wish ISIS and Genzyme well for the commercialization of mipomersen as it would also reflect well on the commercial value of the entire space in general.

Studies on siRNA Stability to Increase Adoption of RNAi Therapeutics

A study by the Zamore group published in Science (Ameres et al.: Target RNA-directed Trimming and Tailing of Small Silencing RNAs) provides intriguing insights into an important mechanism impacting siRNA stability by showing that guide strands that are perfectly complementary to their target mRNAs are subject to tailing and subsequent degradation. By better understanding siRNA stability, such work has the potential to decrease the frequency and dose with which synthetic siRNAs have to be administered, thus improving the overall clinical and commercial profile of this class of RNAi Therapeutics.

Actually, siRNA Therapeutics turned out to have a better pharmacokinetic profile than I had thought when I first started to work with siRNAs in late 2002. Most experiments in these early days for mammalian RNAi were conducted in rapidly dividing tissue culture systems where, somewhat depending on the natural turnover of the target mRNA/protein, silencing would be maximal between day 1-3 after siRNA administration and then quickly subside by ~day 5. Luckily, it was then found that it is cell division that is responsible for the relatively rapidly diminishing silencing effect observed in many tissue culture systems by diluting the siRNA-loaded RISC silencing complex between daughter cells. By contrast, silencing in non-dividing tissues, particularly in whole organisms typically persists for about 2-4 weeks after single administration- and on top of it is btw also typically more potent there on a per molecule basis as well!

Especially since many of the first batch of RNAi Therapeutics are likely to be intravenously and intravitreously (needle injection into eye) administered, the longer the interval between drug administrations, the broader the adoption of the technology should be, particularly for non-lethal, chronic diseases. 2-4 weeks is at the lower-to-mid-range for what is practiced for many monoclonal antibodies (subQ and IV) and in my opinion quite acceptable for most diseases where it is worth going to seek treatment for. On the other hand, extending this to something like 6-10 weeks, could in some cases quite significantly impact the adoption of RNAi Therapeutics, especially in situations where the administration procedure itself is associated with cumulative risk e.g. as is the case for the intravitreous route. This realization should also be the motivation for the recently formed collaboration between ophthalmic drug company Surmodics and Egen for ocular controlled-release siRNA formulations.

What Ameres and colleagues show in their paper is that small RNAs such as microRNAs and siRNAs are destabilized in the presence of target mRNAs with perfect complementarity, especially with regard to the 3’ end of the guide strand. For reasons that remain to be determined, the cell somehow recognizes this configuration triggering a polymerase to add a few nucleotides to the guide strand 3’ end which in turn is recruits the ubiquitous RNA degradation complex, the Exosome.

This finding has direct practical implications for the design of siRNAs. Because RNAi gene silencing molecules tolerate mismatches towards their target mRNAs without losing efficacy, especially at the 3’ end, it should be possible to increase siRNA stability by introducing such mismatches. Incidentally, such mismatches should have the added benefit of increasing RISC turnover rates, a finding made by the same group earlier and covered by the first Zamore siRNA design rule patent issued in the US a few months ago and exclusively licensed to Silence Therapeutics.

It is, however, also likely that instead of introducing 3’ mismatches, (blocking) nucleotide modifications at the guide RNA 3’ end would have the same effect by not being suitable substrates for the polymerase.

It will now be important to test how these findings translate to silencing in large animals and develop in vitro assay systems that faithfully recapitulate such small RNA destabilization. If the stability of the guide strand within the RISC complex is indeed a major determinant of the gene silencing longevity in mammals (rather than stability of Argonautes e.g., in which case slow-release strategies would gain in relative attractiveness), then this line of work should have significant potential for improving the eventual clinical and commercial profile of RNAi Therapeutics.