Tuesday, September 27, 2011

Silence Therapeutics Signs Lung Delivery Deal with Mystery Partner

As Tekmira is struggling to regain possession over its delivery technology from mighty Alnylam, it is foremost Silence Therapeutics' business development that is benefitting from having one of the most advanced, clinically tested, and commercially uncontested systemic delivery technologies in RNAi Therapeutics. Less than a month after closing a deal with Dutch company InteRNA under which Silence’s AtuPLEX lipoplex delivery technology will be evaluated for the delivery of microRNA cancer therapeutics, the company has just announced another delivery collaboration, this time for the related DACC delivery system. Like AtuPLEX, DACC targets vascular endothelial cells, but unlike AtuPLEX it does so with a high preference for the vascular endothelia of the lung.

Curiously, the identity of the partner was not disclosed, although it was mentioned that it was a ‘Top 10 Pharma Company’. 'Top 10 Pharma Company'....didn't Takeda just become Number 10 with the acquisition of Nycomed? Moreover, the Nycomed acquisition included a fresh COPD drug, a pulmonary disease with an inflammatory component for which the DACC delivery system could very well be useful.

You can imagine that Takeda is a bit hesitant to talk about RNAi Therapeutics, maybe having overpaid a bit for what Alnylam really sold them, but with their significant investment in RNAi already it has every incentive to get things moving while Tekmira and Alnylam are fighting it out. Maybe following this rationale, Takeda and South Korean company Samyang announced earlier this year a somewhat surprising delivery collaboration.

The press release also noted that it is the partner that will provide the RNAi triggers. This pretty much excludes Silence’s existing Big Pharma partners AstraZeneca and Dainippon Sumitomo, the latter of which is not a Top 10 Pharma anyway. On the other hand, Takeda licensed RNAi triggers from Alnylam only for the metabolic and oncology fields, something that would probably add to the apparent sensitivities. I highly doubt that Takeda will hand over another $50M to Alnylam for pulmonary.

Of course, it is always possible that RNAi Therapeutics has gone so much out of fashion that Big Pharma companies are embarrassed to be publicly associated with it. Not only that, their investors shun the word ‘Research’ like the plague.

More seriously, the data that Silence reported for the DACC system has been quite impressive. Working on a model for acute lung injury, it has demonstrated potent and persistent gene knockdown in the pulmonary vascular endothelium following a single intravenous administration. While less is known about the clinical safety profile of DACC, it can be considered somewhat de-risked by the fact that its chemistry seems to be very similar to the clinically proven AtuPLEX system (see the highly encouraging safety profile of their phase I Atu027 clinical candidate so far).

Monday, September 26, 2011

RXi Pharmaceuticals to Write Off and Spin Out RNAi Assets

If you just blinked, you may have missed it: RXi Pharmaceuticals, now re-named Galena Biopharma, is to be a cancer vaccine company. As you may remember, when RNAi was still a hot technology in 2007, the parent company of RXi, small molecule biopharma CytRx, under the helm of corporate maverick Steven Kriegsman, acquired and then spun out RNAi assets in the form of RXi to be a pure-play RNAi Therapeutics company and cash cow for CytRx.

The financial details provided today on the transaction reveal that RXi has pretty much written off the value of its RNAi assets, chiefly among them the self-delivering RNAi trigger platform and the anti-scarring candidate RXI-109 which is about to enter clinical development, with the incoming investors taking over the lion's share of the company (83% of the shares) for their $9.5M in cash. Before RXi decided to be a cancer vaccine company, that is before the acquisition of Apthera in April, the then pure-play RNAi Therapeutics company had about 20 million shares outstanding, $10M in cash and was trading between $1.0-1.5, giving it an enterprise value of $10-20M. 5 months later, the net value of the same assets has become perhaps $2M.

On the other hand, the revaluation of the seemingly dead breast cancer vaccine candidate NeuVax was remarkably positive. From a value of essentially zero, it is now largely responsible for sustaining a market cap of ~$40M. Subtract about $20 in contributed cash, this still leaves a remarkable gain of ~100% for the asset (ignoring the value of the warrants and milestones). Having said that, it was definitely not the shareholders that profited from all that. Indeed, all these transactions make it difficult to follow where the money ended up.

For RNAi Therapeutics, there is still a hopeful message in all of this. The $9.5M in new investments is considerable. The confidence seems justified by the fact that RXi has found itself a nice niche by focusing on interesting self-delivering RNAi triggers, particularly for local and localized gene knockdown. The anti-scarring program also has potential to be an opportunity for the RNAi Therapeutics field to show relatively rapidly its clinical potential, especially since it can be measured against a promising late-stage antisense compound by ISIS satellite company Excaliard, EXC 001. So on the face of it the new investors seem to have gotten a good deal, although it is unclear how toxic the $45M in potential milestones to Galena are.

Today’s news shows how arbitrary the valuations of pre-clinical biotech assets can be and how fashion trends and promotion are often their main drivers. I’m so ready for the new season.

Friday, September 23, 2011

ISIS Files Aggressive Lawsuit against Santaris

It is not a big secret that antisense therapeutics companies ISIS and Santaris are fierce competitors. Today, ISIS filed an unusual, because rather aggressive lawsuit against Santaris Pharma that alleges the Danish company to be selling to the industry technology that is covered by at least two of ISIS’ literally thousands of patents. Because ISIS considers itself the gate-keeper of oligonucleotide therapeutics, and because some of the business development in RNAi Therapeutics has probably occurred under the mantle of the Research Exemption, a ruling in favor of ISIS Pharmaceuticals could have wide ramifications, actually well beyond oligonucleotide therapeutics.

Under the Research Exemption doctrine, the result of Merck vs Integra, it is generally assumed that patented technologies can be used for research purposes quite broadly as long as product, in this case drugs, are not marketed. Without this safe harbor, much of the preclinical pharmaceutical research and academic research would be a legal nightmare.

Nevertheless, ISIS believes this standard does not apply here, because Santaris in a way is selling ISIS technology as part of its platform partnerships. These include relationships with Pfizer, Enzon, GSK, and Shire. Moreover, it probably irks ISIS that Santaris has been rather successful in its business development efforts, and even had the guts to hire a former top ISIS executive, Art Levin, to set up a business development branch in ISIS’ backyard San Diego.

My impression is that Santaris’ LNA-based antisense compounds are more potent than ISIS’ generation 2.0 2’-MOE phosphorothioate gapmers, and this is why Santaris is likely to be the more attractive company to partner from a technical point-of-view. ISIS apparently has realized this as well as it is following Santaris' example in developing conformationally constrained (‘locked’) nucleic acid chemistries (expect Santaris to counter-sue ISIS on that). Anti-miR122 for the treatment of HCV infection is one example where Santaris’ data have been more promising than Regulus’ using ISIS chemistries. Ironically, GSK dumped Santaris’ stronger science on HCV in favor of Regulus for what had to be concerns about IP (I believe though that it was miR-122-specific IP, not antisense platform-related IP that was responsible for GSK’s move).

I don’t want to speculate whether Santaris in fact makes use of technology covered by ISIS patents or not. It is, however, a case worth watching for the entire pharmaceutical industry. Closer to home, it illustrates how aggressive, and so far successful ISIS is in using its sheer number of patents in ‘extorting’ concessions from other oligonucleotide therapeutics companies. Wherever you look, ISIS is getting a piece of the pie. I have been studying ISIS’ patents with regard to RNAi Therapeutics, and cannot really find anything of value there, except maybe if you are interested in using the 2’-fluoro modification which is useful, but dispensable. Still, ISIS was able to extract surprising concessions from Alnylam when Alnylam IPO’d a few years ago and has even called Alnylam a ‘satellite company’ without much public protest by Alnylam. Same story with the multi-million $ that Alnylam gave ISIS for the ill-fated single-strand RNAi collaboration. It goes to show that when it comes to public perceptions and business development, quantity and brand recognition often still trump quality and due diligence.

Post-scriptum (9 October, 2011): On October 7, Exiqon and Santaris on October 7, 2011, settled their legal differences that resulted from Santaris suing Exiqon for selling LNA-based reagents that were used for the development of drugs incorporating LNAs,,,and thus would not fall under the Research Exemption- an ironic twist of fate. In the settlement, Exiqon paid Santaris a minimal amount. It is difficult to conclude from this anything about the outcome of the ISIS-Santaris litigation.

Monday, September 19, 2011

Bass versus Tuschl: Patentability of 3’ Overhangs Could Depend on Meaning of ‘Person of Ordinary Skill in the Art’

2000-2001 was one of the most exciting, fast-moving periods in RNAi history. All the evidence from the various fields converged to unravel the central mechanisms of RNAi resulting, amongst others, in the discovery of how RNAi can be triggered in human cells. Plant scientists discovered that small RNAs were involved, a group in Cold Spring Harbor found that the 3’ overhang-generating enzyme Dicer played a role, fly biochemists, led by Tom Tuschl, found that synthetic siRNAs could induce RNAi first in fly extracts, and then also human cells. Eureka!

The discovery of RNAi in human cells would not have been possible without the contributions by so many other bright minds. In addition to the research publications, the scientific discourse that happens at conferences and the hypotheses put forward in review articles are a vital part of the scientific process. Everybody stands on the shoulders of others, but it is also acknowledged that the peer recognition belongs to the person/group that publishes first. It is this peer recognition more so than monetary compensation that is the satisfaction of many a scientist. If I’m honest, yours truly probably wasn’t all that different.

Tom Tuschl clearly deserves the scientific recognition. Being the first to demonstrate in a robust manner RNAi in a range of human cells in such a competitive field is no minor feat, nor did it come out of nowhere. Tuschl, partly in collaboration with Zamore, Bartel, and Sharp, did a considerable part of the groundwork leading up to the breakthrough. One should not forget that Brenda Bass, who (or is it really the University of Utah) contests the intellectual ownership over the 3’ overhang feature of the ‘Tuschl siRNA’, was in fact commenting on a paper involving Tuschl during his time as a post-doc in Cambridge, Mass, when she speculated about the possibility of 3’ overhangs in the Cell Review. The other discussions that she claims to have had with the Tuschl siRNA inventors and Zamore were also likely strongly influenced by that research…although I cannot say that for sure. In that sense Tuschl stood on the shoulders of many RNAi giants, Bass on top of Tuschl, and then (maybe) Tuschl again on top of Bass. You get the picture.

Whether having earned the uncontested peer recognition will be followed by the issuance of strong patents, however, is an entirely different question, as I believe that there is merit to Brenda Bass’ contention that Tuschl was at least in part inspired by her work and ideas. On the other hand, I should repeat that because Bass chose to publicly disclose her ideas without filing for patent protection, her ideas became a free-for-all and part of the prior art so that trying to get her name on the patent would seem like inequitable conduct in broad daylight. Therefore, the consequences of the decision whether Bass was instrumental for Tuschl to choose the 3' overhangs in his siRNA design would seem one of patentability of 3’ overhangs, not ownership.

Why do I believe the University of Utah has a point with regard to Tuschl having been inspired by its very own Bass? Some evidence can be found in the commentary of the early papers themselves which I re-read with the question in mind of what gave Tuschl the actual impetus to choose the 3’ overhang feature.

Chapter 1: Long double-strand RNA is processed into small RNAs which direct RNAi in fly lysates (Zamore, Tuschl et al. Cell March 31, 2000)

In this paper, which is a central component of the Tuschl I patent application, Zamore and Tuschl studied the processing of long double-stranded RNAs in fly lysates and found that 21-23 nucleotide small RNAs were generated. They subsequently mapped the cleavage sites in the target mRNA and found that it was cleaved at 21-23 nucleotide intervals. Consequently, the authors suggest that the 21-23 nucleotide RNAs direct RNAi target cleavage- a hypothesis that would survive scientific scrutiny.

Of note, their proposed model of RNAi in Figure 7 shows siRNA without any evidence of 3’ overhangs.

Chapter 2: Bass proposes that small RNAs observed in Zamore et al. paper form 3’ overhangs (Cell April 28, 2000)

In this review in Cell, which shortly followed the Zamore et al. paper and which is a key exhibit in the Utah case, Bass proposes, for the first time, that since only RNase IIIs were known to be able to cleave double-stranded RNAs at specific sites, the small RNAs observed in the Zamore et al. studies ought to form 3’ overhangs as the typical feature of RNase III cleavage.

Importantly, she further speculates that the predicted instability of these 3’ single-stranded overhangs explains why Zamore et al. observed a mixture of small RNAs between 21 and 23 nucleotides, instead of small RNAs of a single size (i.e. 23 nucleotides) as one might have expected from the involvement of a single enzyme, since the single-stranded RNA 3’ overhangs of the initially generated siRNAs would be susceptible to degradation in the fly lysate. As we will see, this idea may have been picked up by Tuschl in his subsequent studies, providing additional support that he and his group indeed read this review very closely. Is Bass’ speculation in fact the reason why half the RNAi Therapeutics world and research/reagent providers still cling to the (actually largely useless, and sometimes indeed harmful) 3’ dTdT feature?

Chapter 3: First demonstration, by the Tuschl lab, that synthetic siRNAs, especially those with 3’ overhangs, can trigger RNAi (fly lysates; Elbashir et al. Genes and Development January 15, 2001)

Before the Tuschl group famously published in Nature on the finding that synthetic siRNAs with 3’ overhangs can trigger efficient RNAi in human cells, they published initial results with such siRNAs in fly lysates in Genes & Development. This paper is critical as it is the first use by the Tuschl group of siRNAs with 3’ overhangs. How would they explain the adoption of this feature for their RNAi trigger design?

In addition to mapping the RNAi cleavage sites in the target RNA, Elbashir and colleagues cloned the ~21-23nt small RNAs themselves. These were then analyzed for the modifications at the 5’ and 3’ ends, upon which they found that the small RNAs contained 5’ phosphates and 3’ hydroxyl groups. They then speculated that these termini indicate that they had been processed by RNase III as such ends are characteristic of cleavage by this enzyme. They then go on to show that synthetic siRNAs with 3’ overhangs were more efficient triggers of RNAi in fly lysates than the corresponding (blunt) RNAi triggers without them. The explanation for the choice of the 3’ overhangs was the RNase III speculation.

Importantly, Tuschl and colleagues acknowledge in their model at the end of the paper that Bass, in her 2000 Cell review, already proposed the involvement of an RNase III. I guess this is pretty good evidence that there was at least some inspiration, although they also suggested earlier in their description of the experimental results that this conclusion could also been drawn independently from the small RNA end modifications that they determined. Here, I would disagree with Tuschl and colleagues as there are other RNases that leave 5' phosphates and 3' hydroxyls, and it is really the understanding of a dsRNA expert like Bass that long double-stranded RNAs get processed by RNase III. That an RNase III was involved in RNAi was shown around the same time by the Hannon group in Cold Spring Harbor. But even if we assume that the conclusion of the RNase III involvement could have been drawn independently, the Bass review was part of the prior art at this point.

I was surprised that it was the RNase III speculation and not direct experimental evidence that led Tuschl and colleagues choose the 3' overhangs in this research. Without re-visiting this issue, I had been under the impression that it was the small RNA cloning results that allowed Elbashir et al. to reconstruct the 3' overhang siRNAs.

Final Chapter 4: Synthetic 3’ overhang siRNAs trigger RNAi in human cells (Elbashir et al. Nature May 24, 2001)

This is the famous paper where Elbashir and colleagues from the Tuschl lab showed for the first time RNAi gene silencing in human cells, using synthetic 3’ overhang siRNAs. Unlike the preceding Genes&Development paper, this one discloses the exact nature of the overhangs. With the exception of one siRNA, all of them contained a dTdT in the overhang (deoxy-ribose, not ribose). This immediate adoption of deoxy would seem strange initially, because the siRNAs that are generated from long dsRNAs would have ribonucleotides in their overhangs and why risk a loss of silencing activity by substituting them with deoxy? The cited reason was that it would reduce the cost of synthesis, and probably also stabilize them from degradation. The synthesis cost argument clearly is not a valid reason for using deoxy for a basic science study such as this one, so it makes sense that it was actually instability that was on their mind, an instability first suggested by Bass in her review.

In light of the evidence in the above publications alone, I believe that it will be very difficult to make the argument that Bass did not influence the 3’ overhang feature in Tuschl’s siRNA design. Nor do I see much evidence that Tuschl made an effort to hide this and quite fairly referenced the Bass review in the Genes & Development paper. I have seen much worse examples of groups deciding not to cite the work of others because it may take away from the novelty of their research. And furthermore, if the Bass review was prior art, why didn’t others jump on the idea and published before Tuschl? Was it because he had an unusual understanding of what was going on in the field and the Bass review, presentations, and discussions only gave an extraordinary person like Tuschl the right insights, or was it ‘just’ because he was already set up to do the experiments and that there would have been many others that were inspired by Bass and would have come up with the 3’ overhang siRNAs if Tuschl had gotten into a bad accident.

The decision whether a person in the art of ordinary skill would have been able to exploit Bass’ speculations to come up with the 3’ overhang siRNAs, similar to how it apparently influenced Tuschl and colleagues, is one of the critical questions challenging the patentability of the 3’ overhang feature, possibly the only RNAi trigger feature of relatively broad scope and value that Alnylam can still hope to control.

Monday, September 12, 2011

Impressions from the Abstracts of the 7th Annual Meeting of the Oligonucleotide Therapeutics Society (Part 2)

The OTS Meeting has just finished and it looks like it was a success in that meaningful progress, especially on delivery, but also specific development candidates was presented. As the press releases by Tekmira and Alnylam today showed, the abstracts do not necessarily reflect the full progress of the respective studies as these have been submitted months ahead of the conference and also because some groups may want to hold back with the most exciting data points.

For this reason, I will first summarize what I consider to be the highlights of today’s press releases, and then complete my review of the abstracts following a blog post from last week.

Tekmira and SomaGenics report ~300-fold knockdown of HCV in chimeric mouse model

In last week’s post I had mentioned that Tekmira and SomaGenics reported in their abstract #30 the successful use of 'short shRNAs' together with SNALP LNP delivery technology in a model of HCV. This model comprised of an HCV-luciferase reporter gene driven by a liver-specific promoter which is delivered on a plasmid before the application of the LNP-formulated shRNAs. A 90% knockdown at 2.5mg/kg was noted with these somewhat unorthodox RNAi triggers. This type of system is somewhat similar to knocking down a 'normal' gene in the liver, and as such the abstract did not suggest that studies were also performed in the context of real viral replication.

Today’s press release, however, revealed that the companies went an important step further, namely that they applied LNP-shRNAs in a chimeric mouse model for HCV infection. As a reminder, animal models of HCV infection are hard to come by. The best system may be the chimpanzee model, but it is obvious that this system does not lend itself to large numbers, is very costly, and it has been challenging also for ethical reasons to conduct these types of studies. More recently, chimeric mice have been developed in which the mouse liver is repopulated by transplanted human cells under selection pressure. Unlike the hepatocytes of mice and almost all other animals, these chimeric livers can sustain a form of HCV replication.

Having demonstrated 2.0-log and 2.5-log HCV viral knockdowns following one and two administrations of LNP-shRNAs, respectively, is therefore intriguing news. Similar to Santaris’ anti-miR122 antagonist, such a treatment should have significant potential to increase cure rates in treatment failure patients and those patients with genotypes not served well by current therapies.

Alnylam reports more potent LNPs and liver cell-targeted GalNac-siRNA conjugates

Alnylam issued an OTS-related press release today on three different lines of RNAi delivery research, two concerning LNPs, one to siRNA conjugates. As ionizable SNALP LNPs already incorporate a hepatocyte-targeting mechanism (ApoE), the interesting aspect of the GalNac-siRNA conjugates (Abstract #32) is that they may better lend themselves to subcutaneous administration compared to the mostly intravenously delivered LNPs- although this may be less so if the LNP delivery efficiencies are in the single to low double-digit micrograms per kg. The 5 mg per kg ED50 of GalNac-siRNAs puts them right around where some of today’s RNaseH antisense technologies are just in terms of amount of oligonucleotides administered.

Alnylam claims that these numbers make GalNac-siRNA conjugates serious candidates for clinical development. Still, because of the superior, 1000-fold increased efficacies of LNPs and the less frequent dosing that can be achieved with them, this comment may be Alnylam trying to portray themselves as having multiple realistic delivery options, when in fact they are relying for essentially all of their relevant pipeline candidates on Tekmira’s LNPs- my prediction is also that the 5th and final 5x15TM candidate will be SNALP delivered. This cautionary note may also apply to the reported 0.002mg/kg ED50 MD1 lipidoid formulation, developed in collaboration with Professor Dan Anderson from the MIT, although I have yet to see the lipid structures and formulations to really conclude this.

The news on the ‘3rd generation reLNPs’, probably belonging to the SNALP line of research, similarly relates to further increases in LNP potencies. Here, a ~10-fold increase was reported in therapeutic window over ‘2nd generation LNPs’, including those containing the contentious MC3 lipid, with an ED50 of below 0.005mg/kg and being well tolerated at the much higher 10mg/kg dosage. Whether Tekmira has a claim also on reLNPs remains to be seen.

Abstract #35: Preclinical development of sd-rxRNAs for fibrosis and retinal disorders (RXi Pharmaceuticals)

RXi Pharmaceuticals reports interesting progress with their self-delivering siRNA for dermal scarring with more than 2 weeks of CTGF gene silencing following single intradermal administration. Also based on Excaliard’s antisense work, CTGF seems to be a quite promising gene target for an orphan indication of solid market potential. RXi Pharmaceuticals would probably aim to improve upon Excaliard’s candidate by increasing the extent and duration of CTGF knockdown, making it potentially a once or twice drug administration approach instead of one involving multiple administrations every couple of days.

RXi expects to file the corresponding IND later this year.

Abstract #43: Characteristic aspects of skeletal muscle as a target organ for siRNA (Dainippon Sumitomo and Koken, both Japan)

I found this abstract particularly interesting because it indicates that Japanese pharma company Dainippon Sumitomo has a quite broad interest in RNAi Therapeutics. As a reminder, Dainippon Sumitomo is one of Silence Therapeutics’ larger RNAi target and delivery collaborators and we should hear about that particular relationship soon.

Koken meanwhile is a company which has an interest in providing delivery solutions for RNAi Therapeutics using its collagen-derived atelocollagen formulation.

Abstract #59: Dicer-substrate siRNA exhibit improved guide strand selection and stronger RISC Loading Complex formation compared to canonical siRNA (Rossi lab, City of Hope)

This study concerns the molecular comparison between Dicer-substrate RNAi triggers, as also practiced by Dicerna, and more conventional (Tuschl-type) RNAi triggers. The abstract suggests that Dicer substrates were more potent and more specific than the competition. A big sweeping comparison between these structures remains to be performed and published to put this issue to rest.

Abstract #69: Glucan particles for selective delivery of siRNA to phagocytic cells in mice (University of Massachusetts)

Glucan-encapsulated siRNA particles (GeRPs) made headlines and raised a few eyebrows a few years ago when a study published in Nature claimed these to be a viable oral delivery technology for targeting gene knockdown in phagocytic cells throughout the body. RXi was the licensee to that technology.

The present update concerns combining GeRP-like particles with the Endoporter peptide-based delivery system. The micrometer-sized GeRP particles are meant to be taken up by phagocytes with the amphiphilic Endporter chemistry supposed to overcome the ‘last mile’, that is RNAi trigger escape into the cytoplasm which has been a challenge especially with phagocytic cells. In principle, these ‘first-localize, then escape’ two-component formulations are reasonable to develop. Whether this particular one can solve the problem, again, remains to be seen. It is probably noteworthy that the present abstract does not mention the oral delivery of these particles.

Abstract #72: RNA-based pancreatic cancer therapy by local delivery of ant K-RASMT siRNA (Silenseed, Israel)

The Israeli company Silenseed has been quietly pursuing the development of its siG12D LODER slow-release siRNA matrix for the local treatment of pancreatic cancer (gene target: mutated KRAS). This candidate is unique in the clinical RNAi Therapeutics staple in that it uses a biodegradable polymer matrix to locally deliver siRNA not at once, but over a sustained period of about 8 weeks. The matrix is placed into the pancreatic tumor mass by ultrasound-guided procedure.

While the concept is sound in principle, it is still not clear whether Silenseed has considered all of its technical requirements such as the intracellular delivery of the RNAi trigger following its local release and distribution. It would not appear an insurmountable challenge, but I have seen groups pursuing promising concepts, but really addressing half the technical requirements only.

Abstract #97: miRNA turnover in Dicer knockout cells (Monash University, Australia and IDT)

This is an interesting abstract as it addresses the inherent stability of small silencing RNAs in mammalian cells. This stability is responsible for allowing us to often observe 4 weeks and more of RNAi gene silencing in non-dividing tissues after single RNAi trigger administration in vivo. With the more potent LNPs, every two months (intravenous) dosing is already within reach.

In this particular system, the authors removed the critical microRNA enzyme Dicer by genetic ablation in mouse embryonic fibroblast. With this, the observed decline in miRNA abundance reflects the decay of the largely RISC-incorporated single-stranded miRNAs following Dicer knockout. An average miRNA half-life of ~5 days was observed this way. It is likely that knocking out the microRNA pathway upstream of Dicer at the Drosha step would have yielded even slightly prolonged half-lives and this would have better reflected the fate of double-stranded RNAi triggers. It will be critical to find out by how much these half-lives can be further increased using siRNA chemistry, as Merck has done, and how much of it is determined by the protein turnover of the RISC complex which ultimately may be a rate-limiting step difficult to meddle with.

MicroRNA Therapeutics Company InteRNA Technologies Selects Clinically De-risked AtuPLEX Delivery Technology

Silence Therapeutics and InteRNA Technologies announced today the signing of a collaboration agreement following which the companies will use the endothelial cell-directed AtuPLEX gene knockdown delivery technology for the development of microRNA cancer therapeutics.

The news comes as Atu027, Silence’s RNAi Therapeutics candidate in oncology which also uses AtuPLEX delivery technology, is about to wrap up phase I studies (enrolment to complete by year-end at current rate of recruitment, with follow-up putting data announcement 3 or 4 months after that). Importantly, this study suggests a quite promising safety profile for AtuPLEX with apparently no dose-limiting toxicities so far as doses reach levels where meaningful gene knockdown in endothelial cells can be expected based on the pre-clinical rodent and non-human primate studies.

The deal makes sense to both Silence Therapeutics and InteRNA Therapeutics.For Silence Therapeutics, it is a quite obvious and facile monetization opportunity of its already established AtuPLEX technology with a nucleic acid payload (microRNA mimics discovered by InteRNA) where it does not have a core interest. For InteRNA, it promises to speed up its clinical development efforts as the safety of AtuPLEX has been considerably de-risked by now in the clinic and a lot of the learnings of AtuPLEX, also with regard to regulatory issues, should be applicable to the envisaged microRNA Therapeutics. In this regard, InteRNA may be different from some other microRNA Therapeutics companies that intend to do the heavy lifting of bringing a new small silencing RNA systemic delivery technology into the clinic.

Consequently, I consider this collaboration a win-win for both companies, even more so in financially constraint times. There is considerable synergies to be gained if companies would think more about how they could use their respective strengths to help each other develop promising therapeutic candidates instead of trying to do everything themselves and replicate the mistakes of others.

Thursday, September 8, 2011

Tekmira’s SNALP Delivery Technology Yields yet another Development Candidate: ALN-APC for Hemophilia

You will see this theme continue: Systemic RNAi delivery technologies that have proven themselves in non-human primate and clinical studies will continue to yield pipeline candidates and attract potential partners. Today’s announcement by Alnylam at the Annual OTS Meeting that it has chosen SNALP-enabled ALN-APC targeting the liver-expressed Protein C in hemophilia as its 5x15TM development candidate no. 4 confirms this.

As a reminder, and despite of Alnylam’s claims of SNALP being only one of its many systemic delivery options, all four of Alnylam’s nominated 5x15TM candidates are based on Tekmira’s SNALP technology, which also means that 5 out of 6 of Alnylam’s development candidates are SNALP-based (in temporal order): ALN-VSP02, ALN-TTR, ALN-PCS, ALN-HPN, ALN-APC. Only Alnylam’s (historical) first candidate, the aerosolized naked and unmodified ALN-RSV01 is not a SNALP product. Add to this Tekmira’s own TKM-ApoB, TKM-PLK1, and TKM-EBOLA development candidates, and one can see the promise of RNAi Therapeutics become reality [correction September 9, 2011: the Huntington's program should have been noted here, although that one in some regards is quite similar to ALN-RSV01].

ALN-APC is indicated for the treatment of hemophilia patients, especially those that have developed resistance to their first-line therapy in the form of inhibitory antibodies against their recombinant protein replacements. As activated Protein C shifts the hemostatic balance towards bleeding, knocking this exclusively liver-expressed gene down is predicted to reduce the propensity of hemophilia patients to bleed. This, importantly, is also suggested by human genetics as there are apparently hemophilia patients that have a genetic resistance against or deficiency in Protein C, and consequently have less frequent bleeding compared to hemophilia patients without these concomitant mutations. Boding well for the safety of this approach, especially a concern when one starts to meddle with coagulation, these patients do not have a known increased risk of thrombosis.

Tekmira’s SNALP technology, as predicted based on strong science, is leading the way in this pipeline expansion paradigm by targeting particularly liver, but also solid tumor-expressed genes in a variety of diseases. The only other systemic RNAi delivery technology that has about reached the stage where one can feel comfortable similarly entering new pipeline candidates is Silence Therapeutics’ Atuplex technology for knocking down genes in vascular endothelial cells.

RNAi Therapeutics development does not have to be complicated. The simple trick is to let science lead the way…

Wednesday, September 7, 2011

Impressions from the Abstracts of the 7th Annual Meeting of the Oligonucleotide Therapeutics Society (Part 1)

The Annual Meetings of the Oligonucleotide Therapeutics Society are among the best on the conference circus related to, well, oligonucleotide therapeutics drug development. One benefit of bringing together RNAi Therapeutics, traditional RNaseH and steric block antisense, aptamers, and a few other oligo-based approaches is that researchers can benefit from sharing lessons in safety, how pharmacology relates to chemistry and formulation, manufacturing etc. Remember, it is the experience with older oligonucleotide technologies that allowed RNAi Therapeutics to take 10, instead of 20 or 30 years, to get to where it is today: over a 1000 patients and healthy volunteers dosed with more than a dozen of RNAi candidates exhibiting a decent, and improving safety profile; the ongoing Atu027 and ALN-TTR01 trials having reached dose levels where, based on sound science, robust target gene knockdown, technologically the primary objective, can be expected. Moreover, data from hypercholesterolemia, solid cancer, ocular and respiratory disease studies have provided evidence of dose-related therapeutic efficacy.

Not able to attend the 7th Annual Meeting to be held this week in Denmark myself, I eagerly went through the abstract book to learn of new developments and trends. Here are my thoughts on a few select abstracts that I thought might be of interest to the readers of this blog (presented in the order they appear in the book). Note that if you are a Tekmira investor, keep reading until the end. Part 2 of the discussion can be found here.

Oral presentation: Expanding the structural diversity repertoire of siRNAs (Dong-Ki Lee, Sunkyunkwan University, Korea)

This presentation highlights the realization that a number of non-Tuschl RNAi trigger structures are not just IP workarounds, but can be used to achieve novel biological outcomes such as targeting multiple genes with one RNAi trigger molecule (multipodal structures), inducing select innate immune stimulation while at the same time silencing genes (long siRNAs), and reducing off-targeting (asymmetric siRNAs and ‘wobbly’ siRNAs).

Oral presentation: Activation of RNA interference in animals with single-stranded oligonucleotides (Erice Swayze, ISIS Pharmaceuticals)

For some indications, the intravenous application of the nanoparticle RNAi formulations which are leading in terms of in vivo RNAi gene silencing potency may be a commercial drawback (for the purpose of long market exclusivities, I believe it is a widely underappreciated benefit). ISIS Pharmaceuticals, until recently in collaboration with Alnylam have been working on naked single-strand RNAi (ssRNAi) solutions that can be administered subcutaneously.

It has been long known that ssRNAs can induce RNAi gene silencing, just 100-1000 less efficiently, which is not surprising since RNAi has evolved as a dsRNA-induced mechanism. The abstract claims that using fully modified, partially phosphorothioated ssRNAs, they were able to come within 5-fold of the potency of corresponding double-stranded structures. The initial animal experiments, however, seem to have failed due to ssRNA instability, but after further modifications they have now achieved activity at ‘pharmacologically relevant doses with subcutaneous administration in saline formulations’.

Certainly an interesting abstract and it remains to be seen just how pharmacologically relevant these doses are and the related safety profile. Similar, or better to their current RNaseH antisense? ssRNAi...ISIS’ antisense 3.0? Another interesting question is at what point did Alnylam drop the ball on ssRNAi after considerable investments- before or after the initial animal experiment failures?

Oral presentation: Delivery of Nucleic Acids (Muthiah Manoharan, Alnylam)

Alnylam’s oral presentation will be, you already guessed, about RNAi delivery. By listing 25 papers on two pages without any meaningful comment or discrimination, the abstract obviously wants to make the point that Alnylam is the leader also in RNAi delivery. Somewhat reminiscent of Alnylam’s press releases that used to list seemingly all their RNAi trigger-related patents, no matter how relevant to their gate-keeping potential which was the reason for listing them in the first place. As such, the abstract carries the dubious distinction of being the longest one of the conference, but the one with arguably the least content.

It is not the amount of money spent, the numbers of patents (‘thousands’), or papers published that makes you a leader in RNAi Therapeutics.

Oral presentation: Non-covalent peptide-based delivery systems (Divita, CRBM-CNRS-UMR5237, Montpellier, France)

This abstract concerning a non-covalent cell penetrating peptide-siRNA systemic delivery technology to me has firstly sentimental value. This is not a specific criticism of the work to be presented, a body of work that is buttressed by some credible data, but the abstract still reminds me of the early days when RNAi Therapeutics was hot…hot, hot, and all kinds of, sometimes wild, delivery claims were made: oral, blood-brain, all organs to name a few keywords.

While I wished that there was more excitement around RNAi Therapeutics right now as the negativity, particularly in the commercial arena, threatens to choke deserving technologies, the one benefit of RNAi being less hyped and exploited for fund-raising purposes by the biotech promotion machinery is that the overall scientific credibility index has increased. This can also be seen from the abstracts at this year’s OTS meeting.

Oral presentation: Investigating the potential of therapeutic oligonucleotides for pulmonary diseases (Clark, GSK)

GSK and AstraZeneca are probably the two Big Pharma companies most interested in RNAi/oligonucleotide Therapeutics for pulmonary diseases. This is an area with high unmet medical needs and new therapeutic approaches are needed here more than anywhere else. There are fundamentally two different approaches to knocking down genes in the respiratory tract: local delivery by aerosol inhalation, or through systemic delivery. Based on the abstract, GSK seems to be primarily interested in inhalation methods.

Among the companies having explored inhalation are Alnylam, ISIS’ respiratory disease spin-off Altair, and most recently Tekmira. It has become obvious that Alnylam’s naked siRNA approach (e.g. in ALN-RSV01) is sub-optimal and conjugation plus chemical modifications need to be applied to give such ‘semi-naked’ routes a chance. Altair meanwhile has closed down following phase II results with their naked MOE gapmer antisense candidate for asthma. Based on Tekmira’s track record of publicizing only meaningful scientific progress, Tekmira's aerosolized LNP approach is to be considered a serious contender for the leadership position in gene knockdown in the respiratory epithelium. Tekmira this year has presented data that its aerosolized LNPs retain the ability to knockdown genes in tissue culture. It is quite possible that GSK was/is the undisclosed Big Pharma collaborator for this program.

Silence Therapeutics, probably more by necessity than choice, takes a systemic approach towards gene knockdown in the lung using their intravenously administered lipoplexes (DACC). Actually, since Silence’s and Tekmira’s technologies may be best suited for endothelial and epithelial cell knockdown, respectively, the two approaches are complementary. It would make sense if AstraZeneca had some familiarity with Silence’s DACC technology.

Abstract #9: [3H]-radiolabeling of siRNA (Christensen, Novartis)

Abstract #86: Characterization of side reactions during the annealing of siRNA (Noll, Roche)

I list the two abstracts from Novartis and Roche here together because I believe they illustrate the cultural differences between Big Pharma and pure-play RNAi companies. While pure-play companies emphasize biology and developing new RNAi trigger and delivery solutions, the established pharmaceutical companies are apparently more concerned about manufacturing and pharmacology methods. It is obvious that manufacturing and pharmacology is an essential part of the game, and such work is also happening at pure-play companies and their outsourcing partners, but such work obviously does not address the rate-limiting challenges and Big Pharma, perhaps with the exception of Merck, willfully relies on accessing that from the pure-play companies.

Abstract #16: Inhibition of complement C6 synthesis in the liver using antisense oligonucleotides affects neuro-regeneration (Fluiter, Academic Medical Center, Amsterdam, Netherlands)

This abstract highlights that by knocking down a gene in the liver, one can have therapeutic benefits for a wide range of non-liver diseases, such as neurodegenerative diseases. This is not really surprising given that all organs almost exclusively depend on their development and function on what they are provided for by the blood. Proteins made in the liver constitute the majority of free proteins in the blood and consequently impact all organs. Complement proteins which play a critical in immunity are one example of such proteins. As most diseases contain a complement-related immune/inflammatory component, RNAi Therapeutics could be a tool for modulating a wide range of autoimmune and other hypersensitivity disorders.

This principle of inhibiting a target in one organ to address disease in others (see e.g. transthyretin amyloidosis) is in contrast to other, post-translational therapeutic drug modalities that target the liver for which the therapeutic benefit is almost always restricted to the liver. As such, the medical and commercial potential of RNAi delivery technologies that work well for gene knockdown in the liver is larger than widely appreciated.

Abstract #27: Thirteen week non-clinical testing of miravirsen in cynomolgous monkeys (Hildebrandt-Eriksen, Santaris)

This abstract concerns the toxicological evaluation of Santaris’ exciting phase II LNA anti-miR122, a LNA-modified phosphorothioate steric block antisense, for the treatment of HCV infection. Despite the successes of the recently approved protease inhibitors for genotype 1 HCV, there is still considerable unmet medical need, including for those with less drug-responsive genotypes or those high-risk patients that have failed on established therapies.

Presenting on home soil, the reported toxicities were in line with expected class effects of phophorothioate oligonucleotides, including slight, but relatively persistent clotting abnormalities which was not judged an adverse side effect because of the apparently small extent of the increase; reversible kidney toxicities at doses above 10mg/kg (the effective dose of miravirsen is likely between 2 and 5mg/kg); and finally some enlargements in macrophages which does not appear to be of too much concern. Note that because miravirsen is not intended for chronic use, this safety profile may be adequate. In addition to liver toxicity, it appears however that the kidney toxicity will be something to watch out for in the development of miravirsen.

The first phase II study of miravirsen has just completed enrolment according to clinicaltrials.gov and I look forward to learning about the results in due course.

Abstract #30: Lipid nanoparticle formulations of minimal-length shRNAs show potent inhibition of HCV-driven, liver-specific gene expression in mice (Johnston, Somagenics- in collaboration with Tekmira)

This abstract concerns the evaluation of 40-50 nucleotide hairpin RNAs with Tekmira’s LNP delivery technology for liver gene knockdown (in this case using HCV as a model system). It is not a surprise that the abstract shows that Tekmira’s LNP technology works with various RNAi triggers. The real new insight for Tekmira investors, however, is that Tekmira did not go into this litigation in a way that its access to payloads would be threatened as a loss of access to Alnylam’s RNAi triggers may very well be one of the outcomes that could facilitate a settlement. Instead, Tekmira must have been evaluating various RNAi trigger structures and presumably other nucleic acid payloads as well, and when it chose to exclusively license Halo-Bios multivalent RNAi triggers one has to assume that this was after an extensive evaluation of their safety and potency.

Whether there will be a similar arrangement with SomaGenics remains to be seen. Synthetic shRNAs are credible RNAi triggers and may in fact have some advantages over two-stranded approaches, e.g. highly efficient unimolecular annealing. However, their development has been held back by increased cost of goods associated with such long oligonucleotides and concerns about clogging up the RNAi enzyme Dicer (probably not an insurmountable challenge). A licensing decision may also depend on how broad SomaGenics' intellectual property is with regard to shRNAs. It is highly unlikely that SomaGenics has any gate-keeping claim in this area, and partnering with them would have to be driven by their shRNA-related know-how.

To be continued...(for part 2 click here)

By Dirk Haussecker. All rights reserved.

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