A Lean RNAi Therapeutics Will Do Just Fine

The media coverage on Roche’s decision to ‘abandon’ all things RNAi Therapeutics almost makes one believe that we have just witnessed the demise of RNAi as a therapeutic modality. The naysayers of the technology had their heyday, apparently delighted by the that Roche's decision is absolute proof that RNAi has failed in its quest to improve human health. Nevermind that the Roche news has to be seen in the context of Big Pharma’s crisis of confidence in its own ability to innovate and investor pressure to cut almost everything that does not immediately produce positive cash flow. Even Roche has to admit that in the 3 years since it took the $300M+ license from Alnylam and the 2 years since it bought Mirus Bio for $125M, nothing fundamental has changed with the science, except for maybe that the potency of LNP delivery has improved by 100-fold for some applications.

On the other hand, it is also the time to acknowledge the significant financial support that Big Pharma, including Roche, has provided to RNAi R&D at times in the capital markets that were otherwise quite hostile for companies based on novel biotechnologies. I’m quite hopeful that measured investments in RNAi Therapeutics by larger pharmaceutical companies will continue, and even increase again in the not-so-distant future as results confirming gene-specific knockdown in Man emerge from a number of the ongoing clinical studies.

Unfortunately, the Roche news has done much damage to investor confidence. As valuations of RNAi companies have dropped to levels that may sicken some investors, companies in the space will have to change how they conduct business.

If done smartly, there is an amazing amount of progress to take advantage of, not only as described in the literally thousands and thousands of RNAi-related papers coming out at ever increasing speed, but also progress in disciplines as varied as human genetics, ‘omic’ technologies and bioinformatics, nucleic acid chemistry, and IT and how it has allowed for business models with increased capital efficiency. By judiciously combining the growing knowledge of human biology with technologies that lower the barriers of entry by the day, biotechnology in general is poised to become one of the major pillars in many of the world’s economies, similar to how the eroding cost of computing power has changed the way we lead our lives.

Not all companies, of course, will adapt equally well. Humble Tekmira, as the re-incarnation of Protiva, may serve as a great example in how it is possible to make speedy technology progress without having to throw millions at the wall and hope that something will stick, and without building corporate structures to rival that of Big Pharma. It is also my hope, and expectation, that chastised Alnylam will find back to its roots and put technology and clinical results front and center without letting empire building take primacy as I believe it did when Alnylam let go of its Kulmbach operations. A market cap of less than $400M for a company with a financial profile that is the envy of the biotech industry, and with a pipeline poised to yield critical proof-of-concept data for a potentially transformative technology…I would not have dreamt to see such bargain prices for ALNY again.

I will now take a little writing break. After a good year of re-commencing this blog, I am at the risk of repeating myself. As the RNAi research engine powers ahead just as swiftly without my commentary, I will dive into the literature and take a more detailed look at some of the technologies. It is truly amazing how far we have come in understanding human biology and rationally interfere with it, also for therapeutic purposes.

Merck: “Tekmira are Truly Experts [When It Comes to Formulating SiRNA-Liposomes]”

Roche’s decision this week to terminate in-house RNAi Therapeutics development is widely reported to be a vote of no confidence in the platform. The alternative interpretation, however, namely that it might reflect a vote of no confidence in the ability of Big Pharma to innovate from within receives little or no consideration in an online media world that, at best, gets compensated according to click number. Even more so in an environment that demands immediate financial results, they may prefer to play it ‘safe’ by buying innovation in later for hundreds of millions in the form of drug candidates that have already proven themselves in phase III studies or have even received regulatory approval.

In addition, it is widely understood that since Roche intended to use liposomal delivery for its first RNAi-based product candidates, Roche must have been disappointed with the performance of Tekmira’s LNP delivery technology. Again, I strongly disagree that this is necessarily the right conclusion, because for Roche the development of LNP-delivered siRNA therapeutics did not really require a large in-house RNAi Therapeutics development organization. One could even hypothesize that the collaboration with Tekmira and Alnylam opened Roche’s eyes just how difficult it is to develop cutting-edge technologies such as RNAi Therapeutics with the same efficiencies as pure-play companies can, at least within current organizational structures.

In this light, I found the presentation by Alan Sachs, Head of Merck's RNAi Therapeutics efforts, at the recent RNAi Asia meeting particularly telling as he went out of his way to complement Alnylam and particularly Tekmira for their pioneering work in RNAi Therapeutics. It almost appeared like Merck considered them less as competition and that Merck would stand to benefit from their success in developing the breakthrough technologies necessary for RNAi a therapeutic reality.

The number one example of how Merck, and Big Pharma in general is dependent on biotech innovation in the field of RNAi Therapeutics is siRNA delivery, in LNP-mediated delivery. The statement thus emphasizes that all liposomal siRNA formulations are not created equal. Failures that others see and report with their home-brew liposomal delivery methods cannot necessarily be applied to Tekmira’s LNP technology.

If the RNAi Asia meeting is any guide, then Tekmira’s LNP technology is the de-facto gold standard in systemic siRNA delivery, widely acknowledged by industry and academia. As the gold standard, of course, it is also exposed to a lot of criticism. An interesting dynamic that emerged in this meeting is that not only does liposomal siRNA delivery receive heaps of criticisms by those companies that develop competing delivery technologies, but that liposomal researchers themselves start criticizing it. Unfortunately, these are also the scientists that get approached by the investment community and pharmaceutical industry for their views on liposomal delivery.

As Alan Sachs put it: there are dozens of variables in formulating a liposomal siRNA nanoparticle. Slight variations can have large effects on shape, stability, and reproducibility of the process, all with important implications for the toxicity, potency, and commercialization of such therapeutics. It is formulation that Alan Sachs considers Tekmira to be ‘truly experts’ in. He goes on to say that the question of IP exclusivity is not really that relevant, what matters at the end of the day is really the know-how behind reproducibly formulating safe and efficacious LNPs, at commercial scale at that.

This, I guess, also addresses the claims by other company, valid or not, that they do not require Tekmira’s IP for their own liposomal siRNA delivery purposes. It is true that many groups can efficiently knock down genes in the liver, and some also in tumors in rodents. Some now also at quite low microgram per kg potencies. Transitioning from rodents to non-human primates, however, has proven to be a big hurdle for almost all of these groups.

And listening to the talks and reading the literature, it is not difficult to see why performances differ so widely. Often, lipid formulations are cooked up to superficially approximate what has been reported by Tekmira and their collaborators. However, because the formulation processes are typically not comparable and little effort is put into characterizing what particles have actually been generated, these particles will behave very differently to a Tekmira LNP, no matter how similar the lipid chemistries and molar ratios applied. In more extreme examples certain lipid components have been dropped out, or the particles are highly positively charged and unshielded and therefore prone to aggregate. Still, implications are directly drawn towards the safety of Tekmira’s LNP technology. Sometimes it appears that some research groups have only recently entered the field and are trying to re-invent the wheel by reporting what should have already be well known.

My cynical view is that pointing out such supposed safety issues, is what gets you research grants these days. Since Tekmira’s LNP technology is the gold standard, funding agencies are more likely to fund research into the safety of LNP technologies than on the safety of some obscure delivery technology.

I do not want to suggest that there are no safety concerns with LNP delivery, also as practiced by Tekmira. But from my perspective, I am more than encouraged by the clinical record so far: the Tekmira ApoB study went up to 0.6mg/kg and experienced (only) one case of apparent immune stimulation, and Alnylam’s ALN-VSP02 is still dose-escalating, having reached 1.5mg/kg. Before these programs went into the clinic, my biggest concern for Tekmira’s LNP technology had been immune stimulation at much lower dosages based on Protiva’s experience with the liposomal delivery of plasmids almost a decade ago.

With regard to safety, Alan Sachs complemented Tekmira on putting patient safety first and making Tekmira’s whole-blood immune assay immediately available to the industry. Like Alnylam, Merck also quickly adopted/tested it. He added, however, that in Merck’s limited experience with the assay, results could vary quite a bit when using blood from different patients and that, as a result, the test cannot be considered to be reliable yet. My tendency, however, is to interpret the data to mean that the test is in fact very sensitive and reliable and that there may be some natural variability in how patients respond to LNPs. If a test like this can pick up some of these differences, then it should only contribute to the safety of LNP delivery. I’m sure Alnylam, and soon again Tekmira with TKM-PLK1, are busy collecting patient blood in an effort to determine the basis, maybe genetic, of such variability.

As an investor in Tekmira Pharmaceuticals, I must say that I do not really mind LNP formulation to be such a complex process. After all, one reason why the pharmaceutical industry is abandoning small molecules and flocking into biologics is that small molecules sales are easily canabilized by generic competition. A ‘naked’ antisense or siRNA that can be generated by straightforward chemical synthesis may face similar generic issues as small molecules. The story, however, would be quite different for an LNP-delivered RNAi Therapeutics with high technical barriers of entry.

In summary, in contrast to what seemed to be the message of an interview with Alan Sachs by Xconomy earlier this year, Merck appears to be as enthusiastic as ever about the potential of RNAi Therapeutics. Liposomal delivery won’t cure all diseases, but ‘even’ Merck considers it promising enough to focus most of their delivery efforts on this technology. As supported by Alan Sachs’ talk at RNAi Asia and the robust publication record by Merck RNAi scientists this year (at least 7 papers by my count), RNAi to Merck is not just about target discovery and validation. It’s much more, but since even with such an effort a Big Pharma like Merck expects to be dependent on sourcing RNAi innovation from the outside, it is best to lower, or ‘manage’ in the words of a Merck spokesperson, overall expectations and enjoy bargain prices.

Following Late-Stage Pipeline Setbacks, Roche Cuts In-House RNAi Research as Part of Large-Scale Corporate Restructuring

The writing has certainly been on the wall. First, in an August 2010 interview, Roche’s Head of Pharma Research and Early Development, Jean-Jaques Garaud, was a bit lukewarm about the maturity of RNAi Therapeutics. While acknowledging that ‘siRNA' was a 'hot field’, this Roche executive who assumed his current role in 2009 following the retirement of Jonathan Knowles, stated that RNAi Therapeutics was a ‘bit like science fiction right now’, but that within 2-5 years Roche should make progress in that direction. Then in September, a tight-lipped Roche informed development partner Tekmira that it won’t meet its earlier guidance of filing for an LNP-enabled RNAi Therapeutics IND before the end of the year.

Of course, 2-5 years in today’s pharma world, a world challenged by patent expirations, poor pipeline productivity, ailing healthcare systems, and an ultra-conservative FDA, equates to ‘not relevant to our bottom line’ and are considered an investment with expected negative returns. Roche in particular has been hit hard recently by setbacks in their late-stage pipeline, as well as several blows to their all-important Avastin franchise which now makes the Genentech acquisition look a bit pricey. This is in stark contrast to what appeared to be the healthiest pipeline in the industry in 2007 when it took a license to Alnylam’s RNAi Therapeutics IP and when it acquired RNAi delivery company Mirus Bio in 2008.

So as Roche struggles to meet earnings expectations for the coming quarters, it is maybe not that surprising that as it cuts costs where it can, its in-house ‘siRNA’ research in Kulmbach, Germany, and Madison, Wisconsin, have to go as part of the large-scale re-structuring of the Company announced today.

I have today returned from the RNAiAsia meeting in Singapore, and it was during this trip that I have been particularly struck by just how conservative Big Pharma has become again when it comes to new therapeutic modalities. Only 3 years ago Big Pharma seemed committed not to repeat its mistake of not having participated early on in the development of recombinant proteins and monoclonal antibodies and then pay a hefty premium for acquiring biologics companies later on in the game, yet today the same companies don’t even want to give the impression that they want to lead in the unchartered waters of RNAi Therapeutics. Potential and promise are just that, and it seems like that there is no way around the conclusion that proof-of-concept has to be provided by the smaller pure-play companies before Big Pharma (re-)commits in a big way.

In addition, despite some attempts to improve Big Pharma’s capacity to innovate by setting up pseudo-independent ‘Centers of Excellence’, Big Pharma seems to be fundamentally organizationally challenged in maturing cutting-edge technologies like RNAi Therapeutics as a result of inflexible bureaucracies and insufficient/inefficient communication between the relevant groups within sprawling organizations.

I do not want to deny that some of Roche’s RNAi expectations were probably disappointed, and not all of it is Roche's fault. I wonder how mature Roche considered dynamic polyconjugate delivery to be when it purchased Mirus for $125M, or what exactly it got from Alnylam in return for over $300M in 2007. Not to say that these were outrageously overvalued deals if put in the proper context, but Roche management, watching their peers pull back from RNAi Therapeutics, must feel a bit exposed now.

The full impact of Roche’s own pull-back from internal RNAi research on its RNAi Therapeutics partners Alnylam and Tekmira remains to be seen. After having spent north of $500M on RNAi Therapeutics, it is hard for me to imagine that Roche will write this investment off just like that.

It is possible that Tekmira and Alnylam get a shot at Roche’s RNAi assets, including the one candidate that seems pretty close to the clinic (Tekmira reported Roche revenues in the latest quarter of $0.7M, mainly for the development of this candidate). With Severin Schwan, Roche's CEO, stating that Roche may ‘spin off’ or ‘find a partner’ for its RNAi assets, one may even speculate as to whether Roche has plans to float its RNAi Therapeutics division on the stock exchange. These are strange times in RNAi Therapeutics and the pharmaceutical industry and stranger things have happened.

The Race between RXi, Marina, and Silence to Do Deal by Year-End (RNAi Therapeutics Portfolio Update)

It is not the first time in RNAi Therapeutics history that we hear of promises that cash-generating deals will be closed by the end of the year. This year is no different: RXi Pharmaceuticals, Marina Biotech, and to some degree Silence Therapeutics by disclosing an approach 2 months ago, all have the markets expect lucrative Big Pharma partnerships or even acquisitions as the year winds down.

Judging by the number of early-stage technology evaluations, there is good reason to believe that some partnerships will eventually materialize. However, because these 3 companies are likely to compete for a similar set of partners, the RNAi Therapeutics portfolio has been updated to take advantage of the recent increases in the shares of RXi and Silence Therapeutics, and after selling some of these shares add back Marina Biotech which is relatively attractively valued followed the share price decline ever since the merger with Cequent. Benitec was also added back following the re-grant of a fundamental ddRNAi patent in the US.

Marina Biotech

With the initiation of trials for the trans-kingdom RNAi Therapeutics candidate CEQ-508, Marina Biotech now sports a clinical program and that the Company may be able to develop all on its own. In addition, they have a good-quality program in synthetic RNAi trigger molecular biology and chemistry as exemplified by the recent publication on the utility of unlocked nucleic acids (UNAs), exclusively licensed from RiboTask, for siRNA trigger design. As previously indicated and supported by research from other groups, including Merck, these modifications can be used to abolish off-target effects mediated by the passenger strand. Even more importantly, UNAs can also mitigate microRNA-type off-targeting by the guide strand when judiciously placed in the seed region without compromising on-target RNAi-type silencing. Interestingly, inhibiting passenger strand incorporation by 5’ end UNA modification may simultaneously increase the potency of the guide strand. Hence, it fulfills is similar function as the Zamore thermodynamic end-stability rule.

While this molecular biology makes sense, the IP situation around ‘usiRNAs’ is less than apparent. I have long been puzzled by the usiRNA freedom-to-operate opinion that Marina had said a venerable intellectual property firm provided it with. I finally learned more about this during a Q+A session at an investor presentation by Marina where CEO Michael French answered this question as follows: usiRNAs are blunt-ended siRNAs with non-nucleotide 3’ overhangs (and thereby do not infringe the Tuschl-II 3' overhang IP)! Wow, somebody apparently got paid for this opinion. but who knows maybe Merck might subscribe to this interpretation of the scope of Tuschl-II should they lose access to it as a result of the Tuschl Litigation.

Whether you buy it or not, by committing itself to 3’ UNA overhangs, Marina consciously compromises siRNA activity, especially with 3' UNAs in the guide strand (typically some reduction in activity). UNAs in the passenger strand 3’ overhan, however, appears to make scientific sense and it will be interesting to see whether Marina will adopt asymmetric overhang designs in the future.

With CEQ-508, and maybe also relatively soon the topical bladder cancer candidate, Marina has bought itself some time to try and catch up on the systemic delivery front where it still seems to be stuck at the rodent stage and behind the likes of Tekmira and Alnylam.

As the number one wheeling-and-dealing company in the space, Marina Biotech has to be considered a serious contender in the race to find a partner by year-end.

Silence Therapeutics

Following the exciting news of a possible takeover, I am getting a bit concerned that the longer a deal takes to materialize, the weaker the negotiating position for Silence Therapeutics and the more complex for the company to secure alternative capital. In light of the recent positive development in Silence’s share price, it might not be a mistake to reduce the exposure should no deal materialize any time soon.

On the IP front, it appears that one can now expect more of the same also for Zamore: patent litigation galore. At least it shows that somebody, I wonder who, considers Zamore to be a threat. It cannot be Alnylam, of course, since it stated that the Zamore end-stability rule patents are of no concern at all. I guess the RNAi trigger players harvest what they sow. In the big picture, everybody could benefit from preserving IP around the fundamental discoveries in RNAi biology.

RXi Pharmaceuticals

My view on their technology hasn’t changed, but as the clock runs down one is reminded by RXi’s history of missed partnership promises. Whether Pfizer’s recent comments that intravenous delivery is not a viable delivery route makes a deal with RXi more or less likely is an open question. Since RXi has a new CEO, however, I will give him the benefit of the doubt.

Tekmira

Hopefully a highlight for the RNAi Therapeutics portfolio for the rest of the year will be the NASDAQ listing of Tekmira. With Tekmira being a well recognized player in RNAi Therapeutics, the US listing and a share price above $5 could mean that US institutions like Fidelity take meaningful positions in the company.

Tekmira under its new leadership is the only company in the space that has never explicitly promised a partnership and also happens to be the only 2^nd tier RNAi Therapeutics company that does not desperately need a deal at this moment. In recent weeks I am starting to get the impression that Alnylam understands the value of an amicable relationship with Tekmira. On the other hand, this could mean that upcoming deals will have to be Roche-like deals, possibly with Novartis and Takeda, deals that are focused on developing specific LNP-formulated candidates.

OK, it’s now time for the companies to wow us with scientific results and the promised deals. No pressure, of course. RXi, Marina, Silence…which one is most likely to close a deal by year-end? Have your say by participating in the poll on the top right hand side.

Notice: None of the above is meant as investment advice, and as always, do your own due diligence before considering an investment in RNAi Therapeutics. Also, please read the important disclaimer at the bottom of this blog page.

Alnylam Escalates Liver Cancer Drug Candidate to Dose Levels Predicted to Yield Meaningful Knockdown

Alnylam provided an update on the ongoing phase I clinical studies for their RNAi Therapeutics candidate ALN-VSP02 for liver cancer. Clinical data such as these are widely anticipated by investors and potential partners alike, and Alnylam with recent comments have left themselves little choice but to be measured against the quality of the data.

The presentation provided at the Chemotherapy Foundation Symposium held this week in New York City follows a June 2010 presentation at the prestigious ASCO meeting at which point 19 patients had received the liposomal formulation containing siRNAs directed against VEGF and kinesin spindle protein (KSP) up to a dose level of 0.7mg/kg. The importance of the new data is that the trial has now reached a dose of 1.25mg/kg, a dose that based on pre-clinical studies for VSP02 is predicted to start to yield meaningful and widely distributed gene knockdown in the liver (compare ASCO pharmacokinetic data with AACR 2009 animal data). However, for VSP02 to reach a dose of at least 1.5mg/kg would be even better.

The ASCO data included preliminary data from 19 patients and strongly suggested that VSP02 has anti-angiogenic activity as measured by reduced blood-flow in the tumors and as might be expected from reduced VEGF activity. This response, however, was not dose proportional which could be due to small numbers. As to safety in this quite sick and heavily pre-treated patient population as of ASCO, the one patient death was remarkable, an event that was deemed possibly due to study drug. Since this patient had an extensive liver tumor burden it had been decided to exclude patients of comparable or worse cancer burden for the remainder of the studies.

Achieved dose bodes well for the entire LNP pipeline

The good news is that the 0.7mg/kg dose has been overcome and that there have been no dose-related elevations in liver enzymes, the expected dose-limiting toxicity for most LNP applications. If we assume that such general liver toxicity and potency of LNPs are independent parameters, in the case of the ionizable LNPs I believe a valid assumption, then the fact that 1.25mg/kg has been achieved in this challenging patient population, challenging especially in terms of liver health, this should bode well not only for VSP02, but also for the other D-Lin-DMA-based LNP drug candidates currently in clinical trials or close (ALN-TTR01, TKM-PLK1, and TKM-EBOLA), and even more so for the 2^nd gen LNP formulations with up to 100x increased potency for liver gene knockdown.

Among the 9 patients recruited since ASCO, one patient experienced transient grade 3 thrombocytopenia at 1.25mg/kg, a dose-limiting toxicity that necessitated a confirmation of the safety of 1.25mg/kg. Again, given the nature of the patient population and the importance of the liver also for platelet function, I would not read too much into this adverse event. With 6 patients in this cohort having been initiated on the drug, it looks like 1.5mg/kg is realistic.

Some patients have now received quite a number of LNP administrations, up to 13 (up to 5 at ASCO), and 3 with stable disease have entered the extension phase of the study. A trend towards increased disease stabilization with dose was noted. While this is promising, I would again caution that we are dealing here with very limited number of patients in an uncontrolled trial, and also the fact that some of this analysis could be confounded by the fact that a slightly different patient population is now being recruited at the higher dosages following the 0.7mg/kg adverse event. No tumor responses were reported.

In summary, the update is very encouraging for the success of VSP02, and even more so for the entire LNP pipeline. The next major milestone will be the presentation of biopsy data, possibly at ASCO 2011, which should critically tell us whether the drug is doing what it’s supposed to do (RNAi cleavage assay; mono-aster formation; RNA/protein knockdown etc). Beyond that, it will be interesting to speculate on the nature of the next clinical studies. A combination of VSP02 with a microtubule-targeting chemotherapeutic could be promising with VSP02 functioning as a sensitizer, thereby opening up MT cancer drugs also for liver cancer. Combinations trials with DNA-damaging agents often used for liver cancer would also appear to be reasonable to investigate.

Next stop for the clinical data-flow: Results from the ongoing ALN-TTR01 studies- this time hopefully with knockdown data.

Update on Silence Therapeutics

Yesterday seemed to be RNAi Cancer Therapeutics Awareness Day, with Silence Therapeutics highlighting a publication related to their lead candidate Atu-027, also in phase I studies for solid cancers. The publication concerns the activity and potential mechanism of action of the PKN3-targeting lipoplex formulation in mouse models for (hematogenous) lung metastases.

I would categorize these studies as being consistent with the previous scientific reports by Silence Therapeutics that suggest pleiotropic mechanisms to be responsible for the observed pre-clinical activity of Atu-027. Importantly, the results further seem to indicate that we may not see a response in the form of existing tumor shrinkage in the phase I studies as Atu-027's main activity appears to be in preventing the spread and seeding of new metastases. Similar to ALN-VSP02 the maximum tolerated dose will be the primary focus of the phase I trial with Atu-027.

Shareholders, albeit apparently pleased by the publication of these studies, will be even more interested in a Calando or Alnylam-like clinical update for Atu-027. And even more than that (!), they will want to know whether a takeover offer is finally forthcoming. In any case, it may be advisable to become more concrete about short-term financial plans in order to avoid a situation like last year when Silence Therapeutics was forced to merge with Intradigm as it was running out of funds.

This includes reporting milestones it is currently receiving, such as from Quark. Alnylam reported a Q3 increase in InterfeRx revenues of about $2M which I speculate largely comprises the Quark payment related to Quark granting Novartis an option on their kidney drug candidate. I speculate that Silence received a similar amount from Quark.

Alnylam Green Shoots After Corporate Restructuring

The latest quarter must have been the best quarterly performance by Alnylam in the last 3 years. After going through a rough patch that culminated in Novartis not adopting a widely expected $100M platform license with the attendant lay-off of a third of its staff, the results and also tone of the conference call struck me as if the company had re-discovered its old enthusiasm for RNAi Therapeutics drug development and is intensely focused on creating value by providing additional clinical proof-of-concept data over the coming months.

There is reason to be cautiously optimistic about the upcoming clinical data. For one, dose escalation for the liver cancer candidate ALN-VSP02 seems to have progressed beyond the magic 1mg/kg mark and is still ongoing! First generation or not, the fact that patients have now received and tolerated this kind of dosage, and on a repeat basis, is major de-risking for all of Alnylam’s, but also Tekmira’s pipeline candidates which involve LNP delivery (almost all of them). Similarly encouraging, ALN-TTR01 dosing is also ongoing and with 3 centers in Europe recruiting now, results may not be that far off (28 patients anticipated in this phase I study).

Although the first generation LNPs appear to be well tolerated, Alnylam seems to be even more excited about a potential quantum leap in LNP delivery: LNPs containing the next-generation MC3 lipid which not only silence in the unprecedented single micro-gram per kg range for gene targets in the liver, but also appear to be very well tolerated in animals. The MC3 lipids are derived from the DLin-KC2-DMA ionizable lipids developed by Tekmira, results from which were published earlier this year in Nature Biotech.

Besides the science, financials seem to be in better-than-expected shape, and I believe is what underlies today’s jump in share price (you can assume that the stock market wouldn't pay much attention to MC3). With over $370M cash/equivalents on the balance sheet, Alnylam is poised to close the year with well over the previously guided $325M cash/equivalents. Having slashed the work force, albeit probably at considerable personal cost, thus buys the company strategically valuable breathing room. In addition, there were a number of positive one-offs this quarter, including $2M for the successful award of 8 federal grants, a Quark milestone, and increased activities related to Novartis finalizing its 31 target picks. And with Novartis' relationship with Alnylam settled now, it should become easier to talk to other companies about partnerships and further add to the strong financial position.

Alnylam and Medtronic also stand to receive very significant funding from the Huntington’s Disease Foundation (CHDI), likely totaling over $10M, some of which has already been earned (agreement is retro-active). Somewhat dampening the excitement around that program was news that ALN-HTT is now a 2012 goal for entering the clinic, while LNP-delivered ALN-TTR02 and PCSK9 (both probably MC3) are poised to be the Company’s 2011 new clinical candidates.

An interesting tidbit on PCSK9 is that, faced with numerous competition from mainly monoclonal antibody candidates against the same target, some of which have already entered the clinic, it appears to be now Alnylam’s strategy to emphasize the fact that with RNAi you down-regulate both intra- and extracellular PCSK9 levels, which therefore is closest to recapitulating human genetics which has been driving the adoption of PCSK9 as a drug target for hypercholesterolemia in the first place. A good argument indeed.

Overall, my most important take-home was that this seems to be a re-energized company, and with some of the right clinical news, there may soon be a second honeymoon between Alnylam and its shareholders (of whom I’m btw not one of…yet).

Big Pharma Interest in RNAi Therapeutics Often Poor Indicator of the Science

The current perception is that large pharmaceutical companies have become quite a bit more conservative in their approach towards RNAi Therapeutics. This stands in stark contrast with only 3 years ago when some of the same companies topped each other in their efforts to securing a piece of the RNAi Therapeutics action. Clearly, given that the development of any new class of drugs is a gradual process and facts do not change as fast, Big Pharma must have been very wrong not too long ago, or it is now. So today I try to put Big Pharma’s mood swings into the perspective of the big picture progress in the underlying science.

In brief, while some players in the RNAi Therapeutics sector are partly responsible for the current Big Pharma RNAi conservatism, a lot can be explained by the herd mentality prevalent in Big Pharma where the actions of a fellow company rather than the primary scientific data guide the decision making, since standing up for your beliefs and out from the crowd has rarely proven to be good for climbing the corporate ladder. At the moment, the overpowering mantra in Big Pharma from which RNAi suffers from as being considered too early to know is that, with the exception of diagnostics, investments in R&D and especially innovative technologies generate deficits. This is not helped by the fact that the healthcare sector does face a few economic uncertainties leading to a state of paralysis where RNAi clinical development is put on hold and investments in RNAi technology development are reduced to rather mundane pharmacological assay development projects instead of real enabling technology development.

The 2006-2008 gold rush

About 4 years ago, Merck set on a collision course with Alnylam and bought rival Sirna Therapeutics for more than a billion US dollars. Now, RNAi Therapeutics was firmly on the radar of Big Pharma with Roche firing the next volley through a $300M+ platform deal with Alnylam the following July, the same month that Silence entered into a relatively broad RNAi development deal with AstraZeneca. Heightening the excitement was the Nobel Prize to Fire and Mello later that year for having discovered, only a decade earlier, that it is double-stranded, not single-stranded antisense RNA that triggers highly potent homology-dependent, post-transcriptional gene silencing.

Consequently, and despite the cracks in the economy that were starting to surface then, Takeda spent $150M for limited access to Alnylam’s IP estate, to at least secure an RNAi leadership position among its fellow Japanese pharma companies. All this left Pfizer scrambling not to be left behind in RNAi. Pfizer made the unorthodox decision to acquire Coley Pharma, which was working on TLR therapeutics and with which Pfizer had a collaboration, and use their oligonucleotide therapeutics expertise to form the basis for Pfizer’s RNAi platform effort. In addition, Pfizer also licensed a ddRNAi Therapeutics candidate for HepC from Tacere. The price tag: $164M for Coley alone. Despite all these investments, Pfizer has not formulated an outwardly cogent RNAi Therapeutics strategy, with no significant access to leading delivery technologies (this after having lost Mirus to Roche in 2008) and RNAi trigger IP.

Now, do I believe that Big Pharma overpaid for RNAi Therapeutics in that period? If you consider how RNAi has already revolutionized biomedical research and feel, as I do, that it also has the potential to do the same as a therapeutic platform, then the multi-million dollar deals should not come unexpected. I do believe, however, that some of these investments certainly did not find the right targets, the Sirna Therapeutics acquisition probably being the most egregious example. In addition, when it came to delivery, Big Pharma largely behaved penny-wise, pound-foolish, treating it almost the necessary evil of RNAi Therapeutics, or worse, ignoring it altogether. Why for example would anybody want to spend over a billion dollars for essentially RNAi triggers only, when delivery had only just reached the non-human primate stage (Alnylam-Tekmira 2006 Nature SNALP/LNP paper)? And even for LNP delivery then, scale-up, immune stimulation and the ability to repeat administer were still very much in doubt. Like building an aircraft and forgetting that you need fuel to fly it.

So RNAi Therapeutics investments at that time had still to be regarded visionary investments that could pay off hugely, driven by the belief that humanity would not fail to exploit such an elegant natural gene-regulatory pathway for therapeutic purposes, and I am convinced that Roche and Merck conducted some careful analysis of whether the attributes of RNAi Therapeutics would fit into the pharmaceutical business model of the future (‘personalized medicines’). Nevertheless, the actual trigger for the nature and timing of these investments in many cases must have been some mild panic of maybe missing the RNAi Therapeutics train about to leave the station, a technology that may have come around just in time to help the industry through the worst of the patent cliff that it was just starting to face. And if Merck invests $1.1B in the technology, maybe they know something we don’t know?

The Ripple Effects of the Dark Days of 2008-9 Still Being Felt Today

The worst financial crisis in decades was made worse still for the industry as it became clear that some of the early results that may have led Merck to believe that RNAi was quite close to reality, particularly in the antiviral, wet AMD, and cancer areas, were indeed too good to be true. Innate immune stimulation reared its ugly head, and soon every in vivo efficacy result was assumed to be an immunostimulatory artefact. Could innate immune stimulation be the fatal fundamental flaw of RNAi Therapeutics?

Here, the industry proved resilient and some high-quality studies came out that showed that in vivo efficacy can be achieved in the absence of immune stimulation and rules how to avoid them emerged. I would like to highlight here the efforts by Tekmira which in many ways have proven to be the forward-looking savior of the industry a) by developing the most advanced systemic delivery technology, and b) for having addressed immune stimulation almost as soon as they entered the field. In early 2009, Silence Therapeutics also provided high-quality pre-clinical proof-of-concept for non-immunostimulatory RNAi for cancer in various animal models. This was nice also because this validation occurred outside the Alnylam-Tekmira space.

Still, Big Pharma interest in RNAi Therapeutics as a platform hit a low. Merck-Sirna Therapeutics strangely made it their PR policy to question the platform, Roche after their merger with Genentech became noticeably more cautious about RNAi Therapeutics (also probably due to a change in personnel), and Pfizer just last week said that maybe, although we still have to test it, antisense is great after all? Contrary possibly to Pfizer, I had always believed in investing in drugs for diseases where treatment decisions are not influenced by whether having to go for a half-hour infusion every 2-4 weeks is sufficiently convenient to patients. With all due respect, I don’t understand a number of comments that were published in an interview on Pfizer’s RNAi efforts last week.

Considering the publications and conference abstracts from Big Pharma, one may speculate that Big Pharma’s PR strategy for RNAi Therapeutics may be considerably informed by lack of access not only to IP, but especially enabling delivery technologies. Lack of access not because such IP and technologies don’t exist, but because they cost something. Moreover, RNAi champions within these organizations are likely frustrated by being held on a short corporate leash due to the general economic uncertainties of the pharmaceutical industry and the fundamental loss of Big Pharma’s confidence in the power of innovation. This means that Big Pharma’s internal efforts in RNAi Therapeutics are largely limited to more mundane pharmacologic assay development, which albeit certainly useful, cannot substitute for investments in delivery technologies with essentially all the innovative, ground-breaking work happening outside their walls.

This situation is not helped by the fact that the high-ranking decision-makers are typically too busy to read the scientific literature to properly inform their own opinion and instead rely on the conventional wisdom which at the moment says that RNAi has disappointed as a therapeutic modality and now it needs to prove that it is more than just a useful laboratory tool. And it does not matter whether the current scientific literature has well moved past this existential angst phase.

I know that this is a rather scathing critique of Big Pharma’s RNAi Therapeutics philosophy, one driven by herd instinct and PR rather than an open-minded assessment of the latest primary data. There must be many scientists in Big Pharma, too, that are frustrated by the constraints and lack of scientific leadership in those companies. In a way, I sometimes feel sorry for the criticism that Merck gets for its $1.1B purchase of Sirna Therapeutics. Others are now well aware of the consequences of sticking out from the crowd as RNAi visionaries.

It is now up to the industry to carefully manage its way through this funding desert and, over the next 12 months provide a series of human proof-of-concept data with Alnylam’s ALN-TTR01 and ALN-VSP02 coming up first, then followed by Silence Therapeutics’ Atu-027 phase I results in H2 2011. In addition, there should much to be gained for the negotiating position of pure-play RNAi Therapeutics companies by aligning some of the fundamental IP and pushing back efforts by Big Pharma to talk down the price of RNAi.

(Very) Broad Zamore End-Stability Patent Issued in Europe

Last week, Silence Therapeutics announced that the European Patent Office has granted a patent from the Zamore RNAi trigger design IP estate (EP 1633890 B1). This follows the issuance of related patents over the summer in the US. This IP is assigned to the University of Massachusetts and exclusively licensed to Silence Therapeutics.

What is newsworthy in this latest patent issuance is that very broad claims were allowed which would almost require a company with RNAi Therapeutics platform ambitions to take a license. As I have discussed here before, Zamore made the highly influential finding that it is both the absolute and relative base-pairing strength (relative to the base-pairing strength on the other end of an siRNA duplex) at the 5’ end of the guide strand that determines its RNAi effector complex (RISC) incorporation as well as discourages passenger strand incorporation. Accordingly, the rules have implications for both efficacy and specificity of RNAi gene silencing. It has to be assumed that the end-stability rule figures in one form or another into the siRNA design algorithms used by companies as part of the siRNA screening process, and it should also be an important guiding principle in optimizing an initial candidate siRNA.

A strong patent, of course, does not necessarily follow such fundamental biological insights. In this instance, it could well turn out to be the case. The US claims cover methods focussed on the reduction of off-targeting effect, including first assessing the off-targeting of a first siRNA, and then changing it according to the end-stability rules. As the recent Merck paper illustrates, companies in the field undertake such modification-RISC incorporation studies. Since a given siRNA structure can theoretically be arrived at via a number of different routes, such methods papers are more difficult to enforce. In addition, the direct value of the US claims may somewhat affected as they emphasized the reduction of off-targeting aspect of the design rules rather than the enhanced efficacy aspect which might be considered the more attractive feature of the invention.

What is therefore different in the European patent issuance is that not only does it emphasize the efficacy aspect, but it also importantly includes very broad composition of matter claims relating to the structure of an siRNA. It should be very straight forward to enforce these.

The breadth of the claims is striking: siRNAs with small features already that lessen the base pairing at the 5’ end of a guide RNA are covered in these claims. This can be a mismatched base pair, relatively widely employed for example at the very 5’ end of the guide RNA, or a single nucleotide modification. One of the methods claims even covers siRNAs solely characterized by having fewer G:C base-pairs at the guide strand 5’ end compared to the 3’ end. I would expect many if not most siRNAs to fall into that bucket.

In a phone conversation last night with Phil Haworth, the CEO of Silence Therapeutics said that Silence Therapeutics are naturally excited of having been granted these broad claims. When asked, he added that similar efficacy and composition of matter claims derived from the original Zamore patent application are also being considered in the US (note: due to a restriction requirement, the off-target reduction elements of the invention were initially pursued in the US and the efficacy aspects put on the back-burner). I also agree with him that given the strength of the claims and because this is a European patent prosecution, competing RNAi Therapeutics companies can be expected to challenge the validity of the patent. This should also be a good indicator whether Alnylam really meant what it said when it stated that it saw nothing of value in the Zamore siRNA design IP estate.

Given the importance of the siRNA end-stability rules and broad-ening claims, will we therefore see Silence Therapeutics soon swim in cash? Here, Phil Haworth was a bit more cautious and said that Silence’s RNAi trigger IP estate would be just one element in the discussions they are having right now with pharmaceutical companies.

As you will be aware, Silence Therapeutics has been ‘approached’ by a company a few weeks ago, an approach that could lead to an offer, and Dr. Haworth confirmed that these discussions were still ongoing. Without going into any more details, he also said that they are conducting a number of platform partnership talks in parallel and that the ‘approach’ and platform conversations would be separate discussions.

Phil Haworth did not disagree when I speculated on the potential strategic value of the Zamore end-stability IP to particularly Merck, given the one billion dollar+ Merck spent on Sirna Therapeutics for access to the 3’ overhang IP which it now stands to lose (see coverage on the 'RNAi Litigation Blog'). He emphasized, however, that the company does not spent much time speculating internally what other companies might be scheming and instead focus their limited resources on building strong science and IP. In the end, the value of the Zamore siRNA design rules will be closely tied to advancements in the delivery of RNAi triggers and in that regard they are pleased with the continued dose escalation of Silence’s first clinical candidate Atu-027 (6^th of planned 11 dose cohorts ongoing).

2 Short Stories: An siRNA Delivery Paper by Merck, Pharmaceutical Interest in Silence’s Gene Target

The most enjoyable part in following RNAi Therapeutics is to look at the rich stream of scientific data and determine the absolute maturity and competitive position of the technologies and companies involved, as well as getting a glimpse at relationship dynamics. I therefore thought to share today two examples of this that I picked up recently. One is a paper by Sirna Therapeutics/Merck shedding some light on their approach towards RNAi pharmacology and RNAi trigger design. The other is some intriguing evidence that Silence Therapeutics’ most important gene target, PKN3, is gaining traction in the pharmaceutical space.

Studying the pharmacology of siRNA delivery

Pei and colleagues from Merck published in RNA a nice paper on better understanding the pharmacology of siRNA delivery [Pei et al. (2010). Quantitative evaluation of siRNA delivery in vivo]. Unlike small molecules or even antibodies, the pharmacology of RNAi Therapeutics is more complex as simply measuring the raw tissue abundance of an RNAi trigger is a poor indicator of successful RNAi delivery. This is because functionally inactive siRNAs may vastly outnumber the active siRNAs loaded into the mammalian Argonaute 2 protein (Ago2), the nuclease responsible for seeking out and destroying complementary target messenger RNAs.

Not surprisingly, the Merck researchers employed the LNP/SNALP delivery technology in rodents and monkeys as their system of choice. After intravenous delivery of these LNPs, siRNA abundance was determined by quantitative PCR both at the tissue (mainly liver) and Ago2 level.

For the LNP aficionados among you, the 1mg/kg ED50 lipid nanoparticle used in this study still involved the CLinDMA lipid that was shown previously by Merck to be associated with immunostimulation (Abrams et al. 2010), something that Tekmira has interpreted as being the result of the strong positive charge of such LNPs.

Although playing too many number games carries the risk of missing biology sometimes, a number of quite interesting findings were made. One is that the vast amount of siRNA in the liver (>99%) is lost in the first 24 hours upon which a slower tissue elimination phase sets in that is apparently dominated by the turnover of guide strand incorporated in Argonaute.

It is generally thought that the longevity of gene silencing often seen in vivo, often on the order of 1-2 months following a single administration, is due to the stability of this complex. Despite that, there was still an approximately 3-5 fold decrease in the abundance of such complexes over a week. Not too fast, but fast enough to make it worthwhile studying in more detail whether the stability of these complexes is limited by Argonaute protein half-life or by a selective removal of the guide strand. If the latter, siRNA structure-chemistry may be able to increase silencing duration still. Such studies should also shed light on what pharmacological advantages siRNA depots might have which could be of particular interest to ocular and oncology applications.

Merck employed Zamore rule in siRNA design

The paper also allowed for some interesting insights into the siRNA trigger design process employed by Sirna/Merck. Supporting the importance of the Zamore end-stability patent recently issued in the US and exclusively licensed to Silence Therapeutics (Intradigm) from UMass [note: this corrects an earlier version that improperly stated the IP had been assigned to Silence], the authors first determined the relative Ago2 incorporation efficiencies of guide and passenger strands and then studied how this was changed following chemical modification of the same sequence. As a reminder, achieving a high ratio of guide to passenger strand in RiSC is widely considered to be beneficial both for reducing passenger strand-mediated off-targeting as well as enhancing siRNA efficacy.

Indeed, the authors find that chemical modification changed (in this case enhanced) guide strand incorporation over passenger strand incorporation. However, the authors argued that this was not due to the application of the Zamore rules, but due to having added inverted caps to the ends of the passenger strand. I agree that since the 5’-modification of the guide strand plays a major role in Argonaute loading, these caps, as also employed e.g. by mdRNA, should have a considerable effect on loading the passenger strand. However, since the modified siRNA with which the comparison to the unmodified siRNA was undertaken contained additional modifications besides the caps, it is not possible to argue that it was only the caps that had the effect on differential loading. In fact, the differential strand loading efficacies of 2 modified siRNAs, distinguished only by the nature and position of backbone modifications, differed by a factor of 2, clearly indicating that siRNA modifications besides the cap have a major influence on differential strand loading.

Wyeth/Pfizer shows interest in PKN3 in cancer

I had always considered it the wrong strategy for Silence, even more so before their merger with Intradigm, to focus so much of the company’s resources on a single drug target: PKN3. One reason is that Silence claims to be an RNAi platform company, and resources would have been better spent on building on their early pioneering position in siRNA design which then seemed to be at the risk of getting stuck in an early 2000’s 'dead-end'.

Even more worrisome is that Silence was essentially the only group really working on the PKN3 gene, and at that early stage it is always a very real possibility that it might turn out to be a useless artifact of no commercial value. However, the scientists stuck to their guns and it now seems that additional data confirms PKN3 to be an interesting oncology target in the angiogenesis field with the rest of the pharmaceutical world slowly paying attention.

Curiously, it is research by Wyeth, now part of Pfizer (!), that confirms that PKN3 plays a role in endothelial biology and that it is upregulated in a number of cancers. Even more intriguing is the fact that one of the co-discoverers of PKN3 as a cancer drug target (Anke K.-G.) is also named as an inventor in a PKN3-related patent application by Pfizer published this year (WO 2010/105128 A2). This patent application is about methods of using PKN3-containing protein complexes for cancer diagnostic purposes, e.g. determining patients with high PKN3 levels which would be candidates for a PKN3-targeting drug just like Silence’s Atu-027 (this candidate has been reviewed here with Tobias Wolfram). A nice validation of Silence’s own results and demonstrating just how close Pfizer’s PKN3 science seems to be to that of Silence is that a number of experiments described in the patent application were based on the same rodent cancer models previously employed by Silence showing that PKN3 silencing leads to an inhibition of tumor growth in mice.

With the PKN3 gene patented by Silence as a cancer drug target, it would make sense for Pfizer to gain access to Silence’s IP and maybe even take on the clinical development of Atu-027 itself for which Pfizer could use their methods as a response biomarker. Maybe Silence’s belief in PKN3 will be financially rewarded after all, and it might also explain why Alnylam seems to be so keen in weakening Silence’s PKN3 patent estate. Until now, I had come to believe that the only purpose of fighting that patent estate was to frustrate Silence by engaging them in yet another patent skirmish. It is interesting to speculate that the strength of PKN3 science and IP could critically inform whether Pfizer will partner with Silence or Alnylam.

Tuschl Litigation Decidedly Shifting into Max Planck-Alnylam’s Favor

As often in life, involve money, and you will soon see who your true friends are. This rule also seems to apply to the fate of the Tuschl patent applications which more and more seem to go in Max Planck/Alnylam’s favor, and against the interests of UMass and Sirna Therapeutics/Merck, according to the latest coverage on the Tuschl Litigation Blog.

It has always been a mystery to me why Whitehead and the MIT would want to side with UMass in the first place, since as parties to the Therapeutic Use agreements between Max Planck, MIT, and Whitehead, Whitehead and MIT had nothing to gain, actually much more to lose, from UMass’ decision to go it alone and license the therapeutic rights to their part in the Tuschl invention to Sirna Therapeutics (now Merck) and to some degree also RXi Pharmaceuticals. Even more so given that Zamore's assignment of his interest in Tuschl-I to UMass is questionable in the first place.

It has equally been a mystery to me why Wolf Greenfield & Sacks, the patent law firm engaged by Whitehead to prosecute the Tuschl-I patent application on the behalf of Whitehead, Max Planck, MIT and UMass would seek to gain the benefit of inventive subject matter that obviously belonged to Max Planck only.

It is therefore no surprise then that MIT, Wolf Greenfield & Sacks, and finally The Whitehead have all decided after all that the legal exposure from the Tuschl Litigation does not make it worth to them any more to continue to support UMass' insistence on ownership over the use of 3’ overhangs in RNAi triggers and the discovery of efficient RNAi gene silencing in mammalian cells using short double-stranded RNAs by claiming the benefit of the '325 priority application filed by Max Planck in Europe.

Unless Zamore’s testimony will shock the field of RNAi, the testimonies of the 2 more impartial inventors named in Tuschl-I, namely Sharp and Bartel, make it clear that the 3’ overhang work was the accomplishment of Tuschl after he set up his lab at the Max Planck. This is also consistent with my view of RNAi history that is not only based on the publication history and authors on key papers, but has also been critically influenced by how the RNAi field in general has always felt about who was to be acknowledged for that body of work: Tuschl. Science is such a gossipy endeavor after all that I would have expected to have heard rumors if Tuschl wasn't the inventor of the 3’ overhung siRNA.

So now it seems like UMass is the last man standing, and unable to move forward with the Tuschl I patent application. The fact that UMass has not surrendered yet let’s me speculate that not only do they stand to lose future benefits under the Tuschl patents, but that they feel considerable pressure from Sirna Therapeutics-Merck. Understandably, given that the $1.1B value Merck placed on Sirna Therapeutics much depended on perceived access to the mammalian and 3’ overhang data. Should UMass never have been allowed to license IP which erroneously cross-referenced the patent application of another party? Or might the pressure be one day on former Sirna Therapeutics, many of who have left Sirna after the acquisition, should Merck believe that they have been misled?

A less conspirational explanation for this mess, of course, would be honest human mistakes, such as misunderstanding the rules for citing priority documents or scientists signing off on legal declarations that they do not have the time to read, much less fully understand. But with billions of dollars at stake, what started as honest mistakes may quickly become interpreted as, and actually also have led to ‘malpractice’ and ‘deceptive behavior’. Money.

RNAi Delivery to Vascular Endothelium Increasingly Validated

Less than a month after Napoleone Ferrara from Genentech was recognized with a 2010 Lasker Prize for identifying VEGF as the central actor in blood vessel formation, a prize widely regarded as the stepping stone towards the Nobel Prize in Physiology or Medicine, a press release by Alnylam seems to suggest that RNAi delivery to the vascular endothelium is appropriately reaching critical mass. Before that, the most important body of work in this area probably came from Silence Therapeutics, which, despite its apparent quality, got me a bit worried given what I perceived as a certain lack of enthusiasm in the commercial RNAi Therapeutics space and, more importantly, third party scientific validation.

It is particularly exciting that the silencing of endothelial gene markers following a single dose persisted for two months. Since the duration of silencing is critically dependent on the cell type, for example its proliferation rate, this bodes very well for all delivery technologies targeting the vascular endothelium.

Alnylam mentions that the new LNPs (liposomal nanoparticles) that work for endothelial siRNA delivery stem from their collaboration with the MIT which as we know has involved positively charged ‘lipidoids’. Seen in light of the data by Silence (cationic lipid-siRNA)/Intradigm (RGD-targeted PEI polymers), the picture that is emerging is that LNPs that comprise positively charged lipids have a natural propensity of being taken up by vascular endothelial cells. Although I haven’t seen the details yet, it is to be expected that a number of parameters beyond positive charge, such as the method of formulating the particles, e.g. SNALP-like siRNA encapsulation versus Atuplex-like lipoplex formation, determine the efficiency of the functional uptake of these particles.

Beyond Alnylam and Silence Therapeutics, which with Atu-027 already has an endothelial cell-targeting RNAi Therapeutics in the clinic, Tekmira should also have considerable expertise in this area. Similar to optimizing LNP delivery to the liver, leadership in endothelial RNAi will depend on first empirically determining the structure-function relationships of these particles and then the biological pathway by which the uptake occurs. To my knowledge, it is still unclear whether receptor-mediated uptake, non-specific macropinocytosis ('cell drinking'), or the limited capacity of endothelial cells for phagocytosis is involved. This will also be important to understand as more targeted technologies will be developed.

One trade-off that current technologies might suffer from is that their positive charge at physiological pH may cause them to be slightly more toxic compared to negatively or neutrally charged formulations. This may also tie in with Phil Haworth’s comments in my last interview with him that Silence Therapeutics will initially focus on acute indications with high unmet needs. But again, everything is toxic at sufficiently high concentrations and it is encouraging that Atu-027 is still in its dose-escalating phase according to the last clinical update by the company.

Progress also reported for systemic RNAi delivery to immune cells

Following up on their declared pursuit of vaccine opportunities, Alnylam also highlighted progress in the systemic delivery of siRNAs to immune cells. Previously, LNPs comprising lipids derived from the KC2 series of next-generation ionizable lipids had been described to silence the immune cell marker CD45 with an ED50 of approximately 1mg/kg following intravenous administration (see RNAi delivery roundtable). The new report suggests some improvement over those formulations, stating that a 95% knockdown of CD45 was achieved, with an ED50 of as little as 0.2mg/kg. It will be very interesting to see the scientific details and discussions on these experiments (note: this last paragraph was corrected from an earlier version that mistakenly stated that the 95% knockdown was achieved with 0.2mg/kg).

Uptake of RNAi triggers by immune cells per se is not entirely new. It is a case of turning lemons into lemonades, as the non-specific uptake of nanoparticles by phagocytic cells has been long lamented. However, these cells play a central role in at least as many important diseases as endothelial cells do- so why not harness the efficient uptake of particulates in those cells for therapeutic purposes? Sure, being taken up and being functionally released into the cytoplasm are 2 separate issues, but Tekmira’s Ebola work has shown already that LNPs can trigger gene silencing in macrophages. Again, it will be important to delineate the functional uptake pathways and to employ chemistry to increase the efficiency with which LNPs can harness them.

Once thought of as liver-only formulations, LNPs are showing more and more their considerable versatility. I remember well a talk given by Tekmira’s CSO Ian MacLachlan at Stanford two years ago when he demonstrated that by even only slightly changing the formulation parameters, strikingly different patterns of biodistribution can be achieved. Now it ‘only’ takes one of the LNP/SNALP programs in the clinic to show some efficacy, and the pharmaceutical industry to change its approach towards drug target selection, for the liposome to finally shed its image as the unloved, but necessary stepchild of the industry.

RNAi Therapeutics Still Challenged with Re-Educating Pharmaceutical Industry

Judging from the body language of RNAi Therapeutics companies, it seems that they are still fighting a wide-spread perception, also in Big Pharma, that systemic siRNA delivery is limited to targeting genes in the liver and that as a result the current commercial opportunities are relatively small. To quote from Alnylam’s press release yesterday, on research presented at the 8^th International M. Judah Folkman Conference ‘The new research demonstrated effective silencing of target genes in distinct cell types and tissues beyond the liver with systemic delivery of RNAi therapeutics’ [emphasis mine]

To me this is frustrating as it should be obvious to any modern biologist that a strategy of selecting drug candidates starting with the characteristics of delivery systems that already show much promise for clinical development should yield a rich pipeline. Just think about 'only' the liver and how it affects a range of diseases in therapeutic areas ranging from metabolic, to cardiovascular, and even neurological diseases.

Or take systemic delivery to endothelial cells as another example. First pioneered in the commercial realm by Silence Therapeutics with their positively charged siRNA-lipoplexes (see Atu027 clinical candidate for solid cancers) which, as Alnylam rightly points out, has implications for diseases such as ‘atherosclerosis, diabetes, inflammation, and cancer’. Consequently, companies like Silence Therapeutics and Tekmira have made it a high priority to demonstrate the wider applicability of their delivery technologies.

This to me indicates that the established pharmaceutical industry may be even slower in adjusting their thinking than I originally imagined. One can only hope for both RNAi Therapeutics and Big Pharma that the transition from therapeutic franchise-driven to technology-driven drug development will be realized sooner rather than later. To put it bluntly, the franchise-driven strategy worked in an era where sales and profits were more a function of the number visits paid by large salesforces to primary care physicians and the number of drugs in a given franchise the salesperson was able to pitch in a single visit, rather driven by the data underlying an approved drug.

But with small molecule generics eroding Big Pharma's profit base, this has more and more become a losing proposition, and the focus has rightly shifted to advanced and highly targeted technology platforms having hopefully larger impacts on the diseases they address and akso being less easy to copy. Because such therapeutics can command high prices, this allows for a model in which only small, well trained and educated salesforces are needed to address very specialized markets.

A company that I consider to be torn between the franchise vs technology strategy is BiogenIdec. This is a company that much values their franchise in multiple sclerosis, and is rightly also proud of its capabilities in protein engineering. As a result of trying to marry both worlds, they seem to be paying the price of having to in-license drug candidates for the MS franchise which limits their profit growth. Proteins/antibodies alone seem to miss important opportunities in MS. However, considering all types of technologies for a given franchise appears to be too tall an order for a mid-sized company. And when that company has an opportunity in protein therapeutics, but outside its core franchises, no matter how exciting financially, it is faced with a real communication challenge (see BiogenIdec’s recent hemophilia roundtable).

It is my thesis that the use of the new platform technologies demands a re-thinking of what ought to be driving the selection of development candidates. It is for example clear that candidates based on RNAi Therapeutics depend heavily on having extensive RNAi expertise. Knowing the capabilities of the technologies, especially the tissues and cell types that they can address and pharmacology involved, one may then go out and consult with disease specialists in the various areas to discuss specific treatment strategies.

A model that is more likely to work for large companies is therefore to establish those Centers of Technology Excellence and have them interact with the more disease-oriented people in the rest of the company. Hardly a new concept and it is certainly also happening to some degree in the RNAi Therapeutics space, examples here being Roche Kulmbach, Merck Sirna Therapeutics, and Pfizer Coley/RTC. Nevertheless, despite these encouraging signs, even in those cases I’m still not sure whether the dynamics within those companies are conducive to RNAi technology-driven drug development.

Opko Health and its RNAi Therapeutics candidate (for wet AMD) is probably a good example of where an RNAi Therapeutics drug development project was run largely by disease specialists. Since I could never understand how a group without much of a track record in RNAi could possibly come up with the first RNAi Therapeutics candidates, it did not come as a surprise to me that that candidate eventually failed. I am also worried that when Pfizer and Novartis decided to license certain RNAi Therapeutics candidates from Quark, these were decisions largely made by the particular disease focus groups in those companies instead of being integral to those companies’ RNAi Therapeutics efforts.

Ironically, this situation can be partly attributed to the fact that RNAi has to a certain degree allowed for the democratization of drug development by facilitating translational research: I could teach any semi-bright 12-year-old in a day design an RNAi molecule that will knock down a gene. This, however, does not mean that it will make for a suitable development candidate.

So yes, it is worth reminding Big Pharma and investors that systemically delivered RNAi Therapeutics are on the horizon, not only for gene targets in the liver, but also beyond. The mere fact, however, that it is still necessary to emphasize this constantly tells me that a slow-moving pharmaceutical industry leaves a lot of RNAi Therapeutics value unlocked. Liver, cancer, endothelial cells, phagoctytic cells, sites of inflammation, the retina, neuronal cells…put a dozen RNAi scientists, another dozen geneticists and two dozen experts in the pathophysiology of important diseases in a room for a week, and you may end up with more interesting development projects based on currently available RNAi technologies than you have the manpower to pursue.

After this more general critique of the pharmaceutical industry, I will try and shed some light about the particular advances highlighted in the Alnylam press release in my next blog entry.

RXi Pharmaceuticals Still Confident About Outstanding 2010 Goals

A week or so ago, I had the opportunity to talk by phone to the CEO and CSO of RXi Pharmaceuticals, Noah Beerman and Anastasia Khvorova respectively, about the company's scientific and business development strategy. Overall, they were quite upbeat about the prospect of turning around the perception of a company aimlessly wandering around in early technology development and increase shareholder value by finally moving their technology into the clinic and raise the promised non-dilutive capital. Specifically, they did not flinch when asked about their belief whether they were still on track to achieve their outstanding 2010 goals: the selection of their first development candidate (anti-scarring) for which an IND would be expected in 2011, and establishing their first major partnership.

Painfully aware that RXi has a history of promising lucrative partnerships, not one of which has yet to come to fruition, I specifically wanted to confirm that the stated partnership goal is yet to be reached and is not accounted for by the recent string of deals where RXi evaluates whether its self-delivering siRNAs ('sd-rxRNA') have utility in conjunction with technologies provided by partners small and large. While definitely the right approach to explore the wider potential of sd-rxRNAs (note that they have 6-12 month milestone goals), these deals lack the traditional upfront monies and royalties/milestones which would make a world of a difference in limiting shareholder dilution until the company’s own product candidates will allow it to raise capital on the risk-averse financial markets on favourable terms. And yes, Noah Beerman left no doubt that the company has no intention of letting the technology development deals serve as a substitute for that partnership goal.

Yet the exact nature of such a deal was left an open question. It seems that the company is still debating internally about issues such as whether such a deal ought to involve its strategic areas or its core focus areas in ocular and dermal disease. I can understand if a potential partner wanted to benefit from the company’s technology for ocular disease in particular, but that RXi might feel that it should get a better valuation for that at a later point. On the other hand, with self-delivering rxRNAs having potential for direct and localized RNAi applications beyond their core focus areas, such as in certain cancers (e.g. cervical, bladder, breast, maybe liver), respiratory disease, and disorders of the CNS, there could be demand for the technology in non-focus areas, too. This would be mutually beneficial, since these investments would help develop sd-rxRNAs in areas, many of which very attractive financially, for which RXi with its 32 employees and less than $10M in cash realistically wouldn’t have the resources to pursue on its own and the potential value of which would eventually have to be written down. Accordingly, it seemed that CNS and oncology could indeed be high-traffic areas for partnership discussions.

Do I believe that RXi’s sd-rxRNAs have the potential to form the basis for a decent Big Pharma deal (what follows in the next two paragraphs are my speculations only, not management’s guidance)? Based on conference presentations and the company’s patent application for the technology, I do believe that it has such value simply because unformulated siRNAs should eventually occupy a niche in RNAi Therapeutics and RXi can be considered a, if not the emerging leader in this area. Alnylam (of cholesterol-siRNA conjugate fame), naturally, and Dharmacon (Accell siRNAs) can probably be considered the two closest competitors. While Alnylam seemed to have the early lead in the area (2004 Nature and 2007 Nature biotech papers), it is not clear to me what their current stage of the technology is. It seems like the comparative data slightly favors sd-rxRNAs, but in order to command favourable economics, one has to assume that RXi has now amassed, through sheer focus and some siRNA chemistry genius of Dr Khvorova, such a toolbox of diverse chemistries and know-how in designing potent sd-rxRNAs such that candidates with IC50 potencies in the low nanomolar range can be found routinely in passive tissue culture uptake studies, instead of the 500nM-10uM potencies commonly observed with first-generation lipophilic-siRNA conjugates. In this regard, I am concerned that the patent applications that provide RNAi trigger screening examples for a number of genes, do not support that. However, RXi may have chosen, for trade secret purposes, not to provide the best mode in the patent application, but modes of applications sufficiently advanced to get patents issued.

If the technology has indeed advanced over what is publicly available and a deal were to involve the core area of ocular disease, I could imagine a drug discovery deal in which RXi gives away a handful of targets in return for ~$20M in upfront plus the usual milestones and royalties. If CNS or oncology, a deal involving a similar number of drug candidates with a $10M upfront plus an equity investment at a premium would appear reasonable.

As we concluded the talk, I had to ask about how to interpret parent company CytRx' aggressive selling of RXi stock, very disconcerting indeed given the already depressed share price (RXII) at which some of these purchases happened, a financial position by CytRx that does not appear too distressed and the fact that the CEO of CytRx, Mr. Steven Kriegsman, sits on RXi’s Board of Directors. It was apparent that this must be a question that RXi is often asked, and while Noah Beerman did not want to speak on behalf of CytRx, he told me to listen to Mr. Kriegsman’s own words on the RXi stock issue. So I did. What Mr. Kriegsman said in conference presentations (paraphrasing now) is that isn’t it nice to be able to use RXi as a piggy bank, but isn’t it also nice at the same time to be still the largest owner of RXII shares (~17% of outstanding) in case that RXII goes up for a change. Since RXi has strictly served CytRx as a piggy bank thus far, RXi shareholders will hope that the rest of the comments were not but some empty words.