Biopharmconsortium Blog

Eltrombopag

On April 13, 2012, Informa’s Scrip Insights announced the publication of a new book-length report, Advances in the Discovery of Protein-Protein Interaction Modulators, by Allan B. Haberman, Ph.D.

Protein-protein interactions (PPIs) are of central importance in biochemical pathways, including pathways involved in disease processes. However, PPIs have been considered the prototypical “undruggable” or “challenging” targets. The discovery of small-molecule drugs that can serve as antagonists or agonists of PPIs, and which are capable of being successfully taken into human clinical trials, has been extremely difficult. Among the theoretical reasons for this is that contact surfaces involved in PPIs are usually large and flat, and lack the types of cavities present in the surfaces of proteins that bind to small-molecule ligands.

Nevertheless, over the last twenty years, researchers have developed a set of technologies and strategies that have enabled them, in a several cases, to discover developable small-molecule PPI modulators. One direct PPI agonist, the thrombopoietin mimetic eltrombopag (Ligand/GlaxoSmithKline’s Promacta/Revolade), has reached the market. The chemical structure of this compound is illustrated in the figure above. Several other small-molecule PPI modulators are in clinical trials. Despite this progress, the discovery and development of small-molecule PPI modulators has been one-at-a-time, slow and laborious.

The new strategic importance of protein-protein interactions as drug targets

Meanwhile, PPIs as potential drug targets have acquired a key strategic importance for the success of the pharmaceutical industry. Over at least the last decade, pharmaceutical R&D has failed to develop enough high-valued new drugs to make up for or exceed revenues from blockbusters that are losing patent protection. As we have discussed in previous publications and in articles on this blog, this low productivity is mainly due to pipeline attrition. There are several factors (ranging from target selection through drug design, preclinical studies, identification and use of biomarkers, and design of clinical trials) that can influence pipeline attrition.

However, increasing numbers of industry leaders and analysts identify target selection as the key factor that is limiting the productivity of pharmaceutical R&D. For example, I served as a workshop leader at Hanson Wade’s “World Drug Targets Summit”  last summer, which took that point of view. There are at least several such conferences throughout the year, which are organized at the request of industry leaders.

Industry experts who identify poor target selection as a major cause of pharma R&D’s productivity woes conclude that the main issue is that companies are running out of “druggable” targets that have not already been addressed by marketed drugs. As of 2011, only 2% of human proteins have been targeted with drugs. Most of the remaining disease-relevant proteins, including transcription factors and many other types of signaling proteins, work via interacting with other proteins in PPIs. Therefore, in order to reverse its R&D slump, the pharmaceutical industry needs to develop technologies and strategies to address PPIs and other hitherto “undruggable” targets.

Contents of the report

Our report discusses technologies and strategies that enable the discovery of drugs targeting PPIs, including both small-molecule and synthetic peptidic modulators. It includes case studies on the discovery of compounds that address specific target classes, with emphasis on agents that have reached human clinical studies. This includes addressing the issue of the need to produce PPI modulatory agents that have pharmacological properties that will enable them to be good clinical candidates.

The report also includes discussions of second-generation technologies for the discovery of small-molecule and peptidic PPI modulators, which have been developed by such companies as Forma, Ensemble, and Aileron, and by academic laboratories. The field of PPI modulator discovery has represented a “premature technology”, i.e., a field of biomedical science in which consistent practicable therapeutic applications are in the indefinite future, due to difficult technological hurdles. We have discussed premature technologies on earlier articles on this blog. The second-generation technologies are designed to overcome the hurdles and to thus enable a more accelerated and systematic approach to PPI drug discovery and development.

In part as the result of the development of these technologies, and of the increasing strategic importance of PPI modulator development, companies have been moving into the field. Examples include Bristol-Myers Squibb, Pfizer, Novartis, and Roche. A key issue is to what extent the new technologies for PPI modulator R&D will enable this area to be commercially successful, and to meet the strategic needs of the industry for expanding the universe of targets for which drugs can be developed.

For more information about Advances in the Discovery of Protein-Protein Interaction Modulators, or to order the report, see the Scrip Insights website.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

Atlas!

This is Part 2 of the article on RaNA Therapeutics that we began on March 29, 2012.

Jeannie Lee’s research and RaNA’s technology platform

Jeannie Lee’s laboratory focuses on the study of the mechanism of X-chromosome inactivation in mammals. In X-chromosome inactivation, one of the two copies of the X chromosome present in the cells of female mammals is inactivated. The inactive X chromosome is silenced by packaging into transcriptionally inactive heterochromatin.  X-chromosome inactivation results in dosage compensation, the process by which cells of males and females have the same level of expression of X-chromosome genes, even though female cells have two X chromosomes and male cells have only one. In placental mammals such as mice and humans, the choice of which X chromosome will be inactivated is random, but once an X chromosome is inactivated it will remain inactive throughout the lifetime of the cell and its descendants.

The Lee laboratory has focused on genes encoded by the X-chromosome whose actions coordinate X-chromosome inactivation. These genes  are contained in the 100 kilobase long X-inactivation center (Xic). One of these genes, Xist, encodes the lncRNA XIST, which as discussed in Part 1 of this article inactivates an X-chromosome by spreading along the X chromosome and recruiting the silencing factor PRC2. XIST is regulated in cis by TSIX, an antisense version of XIST which works to keep the active X-chromosome active. Tsix is in turn regulated by Xite (X-Inactivation intergenic transcription element), an upstream locus that harbors an enhancer that enables the persistence of TSIX expression on the active X chromosome. The mechanism by which Xite acts (including whether it acts via its RNA transcripts) is not clear. Xite and Tsix appear to regulate pairing between the two X chromosomes in a female cell, and determine which X chromosome will be chosen for inactivation. Several other recently discovered genes in the region of the Xic, which work via lncRNAs, also serve as regulators of XIST function. For example, the Rep A and Jpx genes, work via lncRNA transcripts to induce Xist. Thus Xist is controlled by positive and negative lncRNA-based switches–TSIX for the active X chromosome and JPX and REPA for the inactive X. Of these lncRNAs, REPA, XIST, and TSIX bind to and control PRC2.

In late 2010, the Lee laboratory published an article in Molecular Cell in which the researchers identified a genome-wide pool of over 9000 lncRNA transcripts that interact with PRC2 in mouse ES cells. Many of these transcripts have sequences that correspond to potentially medically-important loci, including dozens of imprinted loci (i.e., loci that are epigenetically modified such that only the paternal or maternal allele is expressed), hundreds of oncogene and tumor suppressor loci, and multiple genes that are important in development and show differential chromatin regulation in stem cells and in differentiated cells. The researchers obtained evidence that at least in one case, an RNAs works to recruit PRC2 to a disease-relevant genes, similar to PRC2 recruitment by XIST and HOTAIR. This case of specific PRC2 recruitment has not been previously known, suggesting that the researchers’ methodology could be used to discover new examples of PRC2 recruitment by lncRNAs.

Some of the PRC2-associated lncRNAs identified in the Molecular Cell report may be potential therapeutic targets and/or biomarkers. Overexpression of PCR2 proteins have been linked to various types of cancer, including metastatic prostate and breast cancer, and cancers  of the colon, breast, and liver. Pharmacological inhibition of PRC2-mediated gene repression was found to induce apoptosis in several cancer cell lines in vitro, but not in various types of normal cells. Induction of apoptosis in this system is dependent on reactivation of genes that had been repressed by PRC2. There is also evidence that PRC2-mediated gene repression may be linked to the maintenance of the stem-cell properties of cancer stem cells. These results suggest that at least in some cases, inhibition of PRC2-mediated gene repression–including via targeting lncRNAs that recruit PRC2 to critical genes–is a potential strategy for treating various types of cancer.

RaNA’s R&D strategy

Not much information is available about RaNA’s strategy.  However, according to the January 2012 Mass High Tech article, RaNA Therapeutics has licensed technology from Mass General Hospital based on Dr. Lee’s research. The company has also filed several patent applications, some of which are described as being very broad. This includes patent applications on the existence and method of use of thousands of lncRNA targets. However, Dr. Lee’s published patent applications currently include only three items involving the X-chromosome inactivation system or TERC. Presumably, the patent applications mentioned in the Mass High Tech article will be published at the end of the 18-month publication period for U.S. patent applications.

According to the Mass High Tech article, RaNA is in the process of narrowing down the diseases it will initially focus on. Likely areas will include genetic diseases, including diseases that result from haploinsufficiency. In haploinsufficiency, one allele of a gene is nonfunctional, so all of the protein coded by the gene is made from the other allele. However, this results in insufficient levels of the protein to produce a normal phenotype. RaNA intends to use its technology to increase expression of the functional gene, resulting in a adequate dosage of the protein for a normal phenotype.

RaNA intends to choose one indication out of a short list of 20 diseases for internal R&D, and to seek collaborations for other indications. Dr. Krieg says that he hopes to have a collaboration by the end of 2012, and also to have Investigational New Drug (IND)-enabling safety studies on its internal drug candidate by the end of the year as well.

As one might expect, RaNA will target the appropriate lncRNAs using oligonucleotides, similar to how RNAi companies target mRNAs. Dr. Krieg, an oligonucleotide therapeutic development veteran, recruited some of his old oligonucleotide team from Pfizer into RaNA, according to a Fierce Biotech article. Thus Dr. Krieg and his team can quickly get up and running in designing and testing oligonucleotide therapeutics, once RaNA selects the targets for its initial focus.

In the Mass High Tech article, Dr. Krieg says that he believes that “oligonucleotides are on the cusp of being recognized as the third leg of drug development,” along with small-molecule and protein therapeutics. However, as we discussed in our August 22, 2011 article on this blog, oligonucleotide drug development, as exemplified by RNAi and microRNA-based therapeutics, has run into several technological hurdles, especially those involving drug delivery. The August 2011 article cites an editorial by Dr. Krieg, in which he voices his optimism despite these hurdles.

Nevertheless, large pharmaceutical companies and investors have been moving away from the oligonucleotide field. This is exemplified by Alnylam’s January 20, 2012 restructuring, which cut one-third of its work force and focused the company on two of its Phase 1 programs. Having exhausted its ability to capture major Big Phama licensing and R&D deals, Alnylam has had to become a normal early-2012 biotech company and focus its strategy. (However, Alnylam did a $86.9 million public offering in February 2012.)

The emergence of RaNA, and its $20.7 million funding, thus swims against the tide of the general pessimism about oligonucleotide therapeutics of Big Pharmas, investors, and stock analysts. However, at least some oligonucleotide therapeutics will eventually emerge onto the market, and lncRNA regulation is likely to be crucial to many disease pathways. RaNA is thus the pioneering company in this field.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

XIST Source: Alexbateman http://bit.ly/GZNTZg

On January 18, 2012, start-up company RaNA Therapeutics (Cambridge, MA) emerged from stealth mode with 20.7 million in cash. The Series A venture funding was co-led by Atlas Venture, SR One, and Monsanto, with participation of Partners Innovation Fund.

RaNA will work on developing a technology platform that involves targeting long noncoding RNA (lncRNA), in order to selectively upregulate gene expression.

Arthur Krieg, M.D. will serve as RaNA’s President and CEO. He is the former Chief Scientific Officer of the now-closed Pfizer Oligonucleotide Therapeutics Unit, who later became an Entrepreneur in Residence at Atlas Venture (Cambridge, MA). Dr. Krieg was mentioned in two of our previous Bippharmconsortium Blog articles, dated February 15, 2011 and August 22, 2011.

Atlas quietly nurtured RaNA while working to complete the Series A venture round. According to a January 18, 2012 article in Mass High Tech, the company plans to move into about 9,000 square feet of space “somewhere in Cambridge” in early 2012.  RaNA has approximately a dozen employees.

According to the Mass High Tech article, RaNA’s platform is based on technology developed by scientific founder Dr. Jeannie Lee (Massachusetts General Hospital/Howard Hughes Medical Institute, Boston MA).  Drs. Lee and Krieg and Atlas Ventures are cofounders of RaNA.

This is Part 1 of our discussion of RaNA Therapeutics.

RaNA and “junk DNA”

RaNA’s focus is related to what has traditionally been called “junk DNA”. As shown by work on the Human Genome Project and other genomics studies, only about 2-3 percent of the human genome consists of protein-encoding genes. Genomics researchers had not been able to identify a function for most of the remaining 97-98% of the human genome. This gave rise to the idea that these sequences consisted of parasitic DNA sequences that had no function whatsoever. Most researchers thus called these sequences “junk DNA”. Some of the leading lights of the genomics field gave presentations in which they dismissed this DNA as “junk”, and they even proposed models for how this “junk DNA” might accumulate during evolution. Then they would go on to discuss the “interesting” 2-3 percent.

However, the “junk DNA” concept was not really established science, but a hypothesis. I–among a few others–would call these sequences “DNA of unknown function”.

In more recent years, many researchers showed that at least the vast majority of DNA of unknown function was transcribed. Then researchers found a function for a relatively small percentage of these sequences–they are precursors of microRNAs and other small regulatory RNAs. These RNAs are related to the phenomenon of RNA interference (RNAi), which has been the subject of much basic research, including the Nobel Prize-winning research of Drs. Andrew Fire and Craig Mello. RNAi is the basis for various therapeutic RNAi drug discovery and development efforts at such companies as Alnylam, Silence Therapeutics, Quark Phamaceuticals, Dicerna, and Santaris, as well as several large pharmaceutical companies.

The majority of DNA sequences of unknown function, however, are transcribed into lncRNA. As exemplified by the first article ["Quantity or quality?", by Monika S. Kowalczyk and Douglas R. Higgs (University of Oxford)] in a point/counterpoint Forum published in the 16 February 2012 issue of Nature, many researchers postulate that at least most of these transcripts are nonfunctional. Transcription of these sequences might be, for example, at a low level, as the result of experimental artifacts or of exposure of sequences to the transcriptional machinery due to changes in chromatin during such processes as cell division or expression of nearby genes. This point of view moves the “junk DNA” hypothesis to the RNA level–now one might speak of “junk RNA”.

However, in the second article in the Nature Forum ["Patience is a virtue", by Thomas R. Gingeras (Cold Spring Harbor Laboratory)], the author counsels “patience” in carefully unraveling the function, one by one, of each noncoding RNA (ncRNA) transcript. According to Dr. Gingeras’ article, there are currently some 161,000 human transcripts, 53% of which are ncRNAs. About 2% of these ncRNAs are precursors to microRNAs. Approximately 10% of the transcripts are lncRNAs that map to intergenic and intronic regions, and many of these transcripts have been implicated in regulation — both of locally and at a distance— of developmentally important genes. Another 16% of the ncRNAs are transcripts of pseudogenes — genes that appear to have lost their original functions during evolution. Some of the pseudogene transcripts have been shown to regulate gene expression by acting as decoys for microRNAs. Despite this progress in assigning functions to ncRNAs, no function has yet been found for the majority of these transcripts. However, these are early days in the ncRNA field, so patience and openness to new discoveries is advisable.

The same 16 February 2012 issue of Nature contains a “Nature Insight” supplement on “Regulatory RNA”. Of particular interest with respect to the functions of lncRNAs is the review by Mitchell Guttman (Broad Institute and MIT, Cambridge MA) and John Rinn (Broad Institute and Harvard, Cambridge MA), entitled “Modular regulatory principles of large non-coding RNAs”. Among the lncRNAs discussed in that review are the X-inactive specific transcript (XIST) (see the figure above) and the telomerase RNA component (TERC). Both of these lncRNAs were identified and their functions determined in the 1990s–XIST in 1991  and TERC in 1995. XIST is expressed exclusively from inactive X chromosomes and is required for X inactivation in mammals. TERC is an essential RNA component of telomerase, the enzyme that replicates chromosome ends (telomeres). At the same time as the functions of XIST and TERC were beginning to be unraveled, most researchers were continuing to dismiss ncDNA as “junk”. Should they have known better?

The Guttman and Rinn review discusses several other lncRNAs with known, important functions, all of which were discovered since the pioneering work on XIST and TERC. Among the genes that encode these lncRNAs are HOTAIR and HOTTIP, which affect expression of the HOXD and HOXA gene family, respectively. HOX genes are a superfamily of evolutionarily conserved genes that are involved the determination of the basic structure of an organism. They encode transcription factors that regulate target genes by binding to specific DNA sequences in enhancers. The large intergenic non-coding RNA-RoR (lincRNA-RoR) modulates reprogramming of human induced pluripotent stem cells (iPS cells, which were discussed in earlier articles on this blog). The lncRNA NRON regulates transcription factors of the NFAT (nuclear factor of activated T-cells) family, which are involved in regulating the immune response, as well as in the development of cardiac and skeletal muscle, and of the nervous system. These genes have also been implicated in breast cancer, especially in tumor cell invasion and metastasis.

A common theme in the function of several lncRNAs, as highlighted in the Guttman and Rinn review, is association of the lncRNA with a chromatin-regulatory protein complex. The lncRNA serves to guide the regulatory protein complex to specific regions of chromatin. The protein complex then modifies specific histones in the chromatin regions, resulting in silencing of target genes.

In particular, HOTAIR serves as a molecular scaffold that binds to two protein complexes. A 5′ domain of HOTAIR binds polycomb repressive complex 2 (PRC2), and a 3′ domain of HOTAIR binds the CoREST–LSD1 complex. This enables the targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation by PRC2 and histone H3 lysine 4 demethylation by LSD1. Both are required for proper repression of HOX genes.

XIST has at least two discrete domains, one involved in silencing (RepA) and the other in localization (RepC) of the XIST molecule on the X chromosome. The silencing domain RepA binds to PRC2, and the localization domain RepC binds to the YY1 protein and heterogeneous nuclear ribonucleoprotein U (hnRNP U).

The cases of HOTAIR and XIST are examples of how lncRNAs may function as molecular scaffolds of regulatory protein complexes. This may be general phenomenon, since a recent study by Drs. Guttman and Rinn and their colleagues indicates that about 30% of lincRNAs in mouse embryonic stem (ES) cells are associated with multiple regulatory complexes. In this study, the researchers found that RNAi knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of specific differentiation programs. Thus lincRNAs appear to have important roles in the circuitry controlling the pluripotent state of ES cells, and in commitment to differentiation into specific lineages.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

Salinomycin

On November 3, 2011, Cambridge MA biotech firm Verastem announced that it was filing a prospectus for an initial public offering (IPO). At that time, the company was 15 months old.

Verastem is led by Christoph Westphal, MD, PhD, a founder and the former CEO of Sirtris and a veteran entrepreneur and venture capitalist. The IPO has been underwritten by UBS, Leerink Swann, Lazard Capital Markets, Oppenheimer & Co., and Rodman & Renshaw.

On January 27, 2012, Fierce Biotech reported that Verastem had announced the previous night that its IPO raised $55 million from the sale of 5.5 million shares at $10 apiece. This price fell exactly in the middle of its expected $9 to $11 price range, and the company had even increased the offering by a million shares over what had originally been planned.

On the same day, Verastem’s stock opened at $11 a share on the NASDAQ, up from its initial public offering price of $10.

Verastem not only has Christoph Westphal as its Chairman and CEO, but is also based on science from eminent MIT researchers Robert Weinberg, Ph.D. and Eric Lander, Ph.D., and has several other well-respected academic researchers (including Nobelist Phillip Sharp, Ph.D.) plus biotech industry drug discoverers Julian Adams, Ph.D. (MIllennium’s Velcade) and Roger Tung, Ph.D. (Vertex’ Lexiva and Agenerase) on its Scientific Advisory Board. The company has had considerable fundraising success prior to its IPO, including raising $32 million in venture capital  in July 2011.

However, Verastem has not one lone drug in human clinical trials, its most advanced compounds are in the preclinical stage, and the company does not plan to file an IND until 2013! Thus Verastem has successfully gone public, in an era in which even most private biotech companies with drugs in late-stage clinical trials are finding it very difficult to do so, despite its lack of any clinical-stage drugs.

As noted in the Fierce Biotech article, Dr. Westphal as well as other venture capital funders of Verastem agreed to buy up to $16.3 million of the IPO. This in part explains the success of the IPO. As also noted by Fierce Biotech, with over 19 million common shares outstanding, the offering valued Verastem at $192 million.

We discussed Verastem in our August 2, 2011 Biopharmonsortium Blog article entitled “Development of personalized therapies for deadly women’s cancers”. Verastem focuses on discovery and development of drugs to target cancer stem cells. Its technology is based on a strategy for screening for compounds that specifically target cancer stem cells, developed by Drs. Weinberg, Lander, Piyush Gupta (MIT and Broad Institute) and their colleagues.

Cancer stem cells are best known in acute myeloid leukemia (AML), but their existence in other cancers (especially solid tumors) is controversial, as discussed in our article. Whether cancer stem cells are involved in the pathobiology of solid tumors (or a particular type of solid tumor) or not, the biology of the putative cancer stem cell phenotype can be important in certain subtypes of cancer. Cancer stem cells are characterized by the epithelial-mesenchymal transition (EMT). In the Cell paper, the researchers screened for compounds that specifically targeted breast cancer cells that had been experimentally induced into an EMT, and which as a result exhibited an increased resistance to standard chemotherapy drugs.   They identified the compound salinomycin (now being marketed as a generic veterinary antibiotic) as a drug that specifically targeted these cells, as well as putative cancer stem cells from patients.

As we discussed in our article, triple-negative (TN) breast cancer cannot be treated with standard receptor-targeting breast cancer therapeutics (e.g., tamoxifen, aromatase inhibitors, trastuzumab) but must be treated with cytotoxic chemotherapy. It is generally more aggressive than other types of breast cancer, and even treatment with aggressive chemotherapy typically results in early relapse and metastasis. However, TN breast cancer includes two experimentally defined subtypes that have gene expression signatures related to the EMT. One or both of these subtypes might therefore be expected to be sensitive to compounds that specifically target putative breast cancer stem cells. This may be true whether the cancer stem cell hypothesis applies to TN breast cancer or not. Verastem is focusing on TN breast cancer as its first therapeutic target.

Verastem’s VS-507, a proprietary formulation of salinomycin, is being developed to treat TN breast cancer. The company is also screening for additional compounds, including New Chemical Entities (NCE) that can achieve stronger intellectual property protection than a salinomycin formulation. Verastem had not chosen a lead compound as of the middle of 2011. The company is now reported to be doing preclinical studies on three of its compounds, and also plans to create diagnostic tests to identify patients that could benefit from its treatments. (As we discussed in our article, biomarker-based tests will be critical in making such therapies work.)

As one can discern from our blog article, we are intrigued by Verastem’s approach to cancer treatment, and especially its approach to TN breast cancer. The science behind Verastem’s drug discovery strategy, developed by 2011 ASCO award-winning oncogene and cancer stem-cell pioneer Bob Weinberg, is very compelling. We would love to see Verastem’s therapeutic strategy succeed.

However, as virtually all pharmaceutical and biotechnology R&D researchers well know, it is difficult to translate even the most compelling science developed by the most brilliant researchers into the clinic. Even therapeutic strategies with an excellent scientific rationale that have achieved proof of principle in the best animal models can result in clinical failure, especially with the first compound tested in proof-of-concept studies in human patients. The cancer stem cell hypothesis remains controversial. Moreover, diseases such as TN breast cancer are complicated, they may have mechanisms of resistance to a new experiential therapy that no one knows about, and our understanding of disease biology is limited.

Thus at least until Verastem’s therapies achieve proof of concept in human studies, purchase of Verastem stock is risky indeed. Moreover, there are other risks involved other than technical and clinical risk–especially competition for developing cancer stem cell-based therapies by other biotech/pharma companies. Venture capitalists (and certain knowledgeable individual investors and funds) are in the business of taking on high-risk investments for the sake of potential large rewards, but ordinary retail investors in the public markets are not. Therefore, it seems too early for Verastem to go public, even if it has founders and investors with enough clout to make an IPO successful.

Expert analysts in the IPO field, as stated in the Fierce Biotech article, are puzzled by the rationale for Verastem going public at this time. The financial news and services website “TheStreet.com” agrees. Our own sense of puzzlement is symbolized by the interobang (‽) in the title of this article.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

RNase/RNase inhibitor protein-protein interaction. Dcrjsr http://bit.ly/zRrlaz

We mentioned Forma Therapeutics in two previous articles on this blog. In one article, we focused on Forma’s R&D efforts in discovering small-molecule inhibitors of protein-protein interactions (PPIs).  The other article included a discussion on Forma’s efforts in cancer metabolism.

This month–January 2012–when the new year had barely started–Forma signed two new Big Pharma alliances, covering both of these areas.

On January 5, Forma announced that it had entered into an R&D collaboration with Boehringer Ingelheim, focusing on discovery and development of small molecule drugs to address oncology-relevant PPIs. Under the terms of the agreement, Forma will receive a total of $65 million in up-front payments and research funding, and could be eligible for up to $750 million in pre-commercial milestone payments for development programs resulting from the collaboration.

As with the Genentech deal in cancer metabolism that we discussed in an earlier article, the new Boehringer Ingelheim agreement provides Forma and its shareholders several opportunities to realize early return through assets developed under the collaboration. However, details of how this might occur were not disclosed. According to a January 6, 2012 article in BioWorld Today, flexibility and liquidity (without the need for a IPO or an acquisition) are importance goal of Forma’s business development activity in general. Nevertheless, Forma CEO Steven Tregay does not rule out a future acquisition, and says that large pharmaceutical companies are interested in such a deal.

On January 10, 2012, Forma announced an exclusive alliance with Janssen Biotech (a Johnson & Johnson company), in which the companies will collaborate on the discovery, development and commercialization of novel small molecule drug candidates that target mechanisms of tumor metabolism.

Under the terms of the agreement, Forma will discover and develop drugs against a panel of tumor metabolism targets. Forma may receive up to $700 million in project and milestone funding. In addition, FORMA may receive royalties on revenues from products commercialized as a result of the collaboration. Moreover, if certain milestones are achieved during the initial phase of the collaboration, FORMA will have the opportunity to co-develop and maintain North American commercial rights to one program selected by Janssen. The two companies may also expand the collaboration to include other targets, including those in areas beyond tumor metabolism.

Once again, Dr. Tregay sees the opportunity to maintain North American rights to a product resulting from the collaboration as in line with the company’s strategy to create long-term shareholder value within Forma.

In December 2011, Forma moved its operations from Cambridge MA to Watertown MA, in the process gaining double the amount of space it had before. This will allow for the company’s growth in new internal and partnered R&D projects, and for the growth in staff that this will entail.

As we discussed in earlier articles on this blog, PPIs have been considered “undruggable” targets. However, given that researchers have been able to discover and in at least one case develop small-molecule agents to address this class of targets, it is best to think of this area as a premature technology. As discussed in our July 27, 2011 article, Forma believes that it has developed a set of enabling technologies to move the PPI field up the technology curve, similar to what happened to the monoclonal antibody field in the 1990s. Apparently, several partner organizations–not only Boehringer Ingelheim, but also Novartis and the Leukemia & Lymphoma Society–agreed with Forma enough to invest in partnerships in this area.

Forma is not the only Boston-area biotech to have a major program in discovery of drugs that modulate PPIs. Ensemble Therapeutics (Cambridge, MA), has internal programs and partnerships in discovery of small-molecule compounds that target PPIs, and Aileron Therapeutics (Cambridge, MA), which we discussed in our November 27th 2009 and our August 24th 2010 blog articles, is developing peptide compounds designed to target PPIs in internal and partnered programs.

As for cancer metabolism, Forma is once again not the only Boston-area biotech to have major programs in drug discovery in this area. We have discussed Agios Pharmaceuticals, which specializes in that area, in our December 31, 2009, April 23, 2010, and November 30, 2011  Biopharmconsortium Blog articles.

In our December 22, 2010 blog article, we discussed the field of intermediary metabolism, asking “Will intermediary metabolism be a hot field of biology again?” In the 1920s through the 1950s, intermediary metabolism was a hot field of biology, but the field was eclipsed by molecular biology starting with the Watson and Crick paper in 1953. However, largely as the result of research that combines intermediary metabolism and molecular biology, metabolism is coming to the forefront of biomedicine again. In the area of cancer metabolism, researchers such as signal-transduction pioneer (and Agios scientific founder) Lewis Cantley have been combining the two fields in order to understand cancer disease pathways, with implications for drug discovery and development.

All of the companies mentioned in this article are research-stage companies, with no drug candidates yet beyond the preclinical stage. The strategies of these companies, and the compounds that have resulted from them, thus must be validated in clinical studies. Nevertheless, we are encouraged by these companies’ success so far, and the interest show in them and their science and technology platforms by large pharmaceutical companies. The success of these companies also provides an object lesson–premature technologies and neglected fields may at least in some cases provide opportunities for drug developers.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

Blood cells

Our November 25, 2011 article on this blog focused on Ralph Steinman, one of the three winners of The Nobel Prize in Physiology or Medicine for 2011. That article focused on dendritic cell-based vaccines for cancer, and the application of this area of science and technology to treating Dr. Steinman’s own pancreatic cancer. Dr. Steinman died on September 30, 2011 after a four-and-a-half year battle with his disease, and was awarded the Nobel Prize three days later. He is the only person to ever have been awarded a Nobel Prize posthumously.

Now comes a Nobel Prize Essay, in the December 9, 2011 issue of Cell, entitled “Bridging Innate and Adaptive Immunity”, written by William E. Paul (Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH”). It is immediately followed by an obituary for Ralph Steinman, written by Antonio Lanzavecchia and Federica Sallusto (Institute for Research in Biomedicine, Bellinzona, Switzerland).

The Nobel Prize in Physiology or Medicine for 2011 was divided, one half awarded jointly to Drs. Bruce A. Beutler (Scripps Research Institute, LA Jolla, CA and University of Texas Southwestern Medical Center, Dallas, TX) and Jules A. Hoffmann [National Center of Scientific Research (CNRS), Strasbourg, France] “for their discoveries concerning the activation of innate immunity” and the other half to Dr. Ralph M. Steinman (Rockefeller University, New York, NY) “for his discovery of the dendritic cell and its role in adaptive immunity”. So the focus of this year’s Nobel Prize in Physiology or Medicine is on the two arms of the immune response–innate and adaptive immunity, and the relationship between the two.

Innate and adaptive immunity in the early to mid-20th century

Dr. Paul’s essay is a historical exposition of how researchers came to understand the basis of the innate and the adaptive immune responses, and how they work together as a coherent system. Adaptive immunity focuses on the ability of a vertebrate organism to “learn” to respond to a specific new antigen, and to “recall” and respond to an antigen that it had been exposed to in the past. Innate immunity focuses on the ability of nearly all multicellular life forms, including plants, to respond rapidly to protect themselves against pathogens, using the inflammatory system.

The essay begins with the first ever Nobel Prize given for a discovery in immunology, in 1908. This was shared by two pioneers in the field–Paul Ehrlich and Ilya (or Élie) Metchnikoff. Ehrlich pioneered the study of what is now called adaptive immunity. His work in immunology focused on the ability of humans and animals to develop specific antibodies to toxins such as tetanus toxin and diphtheria toxin. Metchnikoff pioneered the study of what is now called innate immunity. His work resulted in the discovery of phagocytosis, the process by which certain white blood cells can ingest and destroy harmful microbes.

As outlined in Dr. Paul’s article, most of the attention of immunologists between the awarding of the 1908 Nobel Prize and the modern era was on adaptive immunity, focused on the clonal selection theory of immunity and on discoveries in the the cellular (e.g., T cells) and humoral (e.g., antibodies) arms of adaptive immunity. A key practical application of the study of adaptive immunity–from Ehrlich’s day to the present–has been the development of vaccines.

Adjuvants and Charles Janeway’s pattern recognition hypothesis

However, mid-20th century immunology had a “dirty little secret”. Immunization with a pure antigen produces either a very weak immune response, or immune tolerance. In order to obtain a strong immune response, it is necessary to co-inject an adjuvant along with the antigen. The creation of adjuvants–which is involved not only in experimental immunology, but in such practical applications as vaccines–has been something of a black art. Adjuvants used in vaccines include  oil emulsions (which are thought to serve as depots for an antigen) and aluminum hydroxide (which is thought to act as an irritant). The most famous adjuvant in experimental immunology is complete Freund’s adjuvant, a strong adjuvant that consists of killed Mycobacteria tuberculosis bacteria in a water-in-oil emulsion. (Complete Freund’s adjuvant is too toxic for use in humans.)

In 1989, the late Dr. Charles Janeway (Yale University, New Haven, CT) proposed a hypothesis to explain the need for adjuvants; this hypothesis was very fruitful in stimulating further research on the immune response. Dr. Janeway hypothesized that the immune system required both an antigen/receptor interaction (as in classic adaptive immunity) and a recognition of pathogen-associated molecular patterns (PAMPs). PAMPs would be recognized by “pattern-recognition receptors” (PRRs), which would be broadly expressed by immune and inflammatory cells. Recognition of PAMPs by cells carrying PRRs would result in an innate immune response, which would be interpreted by cells of the adaptive immune system, the lymphocytes, as “permission” to mount an adaptive response when they recognized a specific antigen. In vaccination, the function of an adjuvant would be to provide the needed PAMPs.

Drs. Hoffman and Beutler and innate immunity

Beginning in 1996, Jules Hoffmann and his colleagues elucidated the innate immune response pathway in the fruit fly Drosophila, which enables the fly to produce the antifungal peptide drosomycin, and thus to become resistant to fungal infection. This pathway is initiated by the cell surface receptor Toll, and is homologous to the interleukin 1 (IL-1)/NF-κB signaling pathway, which is a key pathway in vertebrate immune and inflammatory responses.

Dr. Janeway and his colleagues then followed up on this study, in order to identify the corresponding microbial sensors in humans. They first scanned a molecular biology database, and identified a transcript that encoded a human homologue of Drosophila Toll, which they named a “Toll-like receptor” (TLR). Since Dr. Janeway and his colleagues did not know the ligand for their TLR, they constructed a chimeric molecule in which the extracellular domain of CD4 was linked to the cytoplasmic domain of the TLR. They expressed this chimera in a human monocyte cell line. When the chimera was crosslinked with an anti-CD4 antibody, NF-κB was activated, resulting in the production of the proinflammatory cytokines IL-1, IL-6, and IL-8. This showed that humans had at least one Toll homolog (Dr. Janeway’s TLR turned out to be TLR4) and that it controlled a signaling pathway similar to those controlled by Drosophila Toll or human IL-1. The ligands for human TLRs remained unknown, as did whether TLRs were the microbial sensors/PRRs postulated by Dr. Janeway had postulated.

It was Bruce Beutler who first determined the nature of TLR recognition specificity. In the 1990s, he worked to identify the genetic defect that rendered some mice unresponsive to lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, which acts as an endotoxin in humans and other mammals. He used two closely related mouse strains, one of which was responsive to LPS (the “wild type” strain), and the other that was unresponsive (the “mutant” strain). Upon stimulation with LPS, macrophages from the wild type mouse produced tumor necrosis factor alpha (TNFα), while macrophages from mutant mice did not. Dr. Beutler used positional cloning to determine the gene that was mutant in the LPS unresponsive mice. In 1998, he and his colleagues reported that that gene was Tlr4, which codes for the very same TLR identified by Dr. Janeway and his colleagues a year earlier. Dr. Beutler’s study indicated that LPS was a direct or indirect ligand for TLR4. It also showed that one type of molecule that would fulfill the criteria for a “PAMP”, namely LPS, working via TLR4 as a “PRR”, could activate the NF-κB-IL-1 pathway.

Since the initial identification of TLR4 by Dr. Beutler and his colleagues, other researchers have identified numerous other TLRs, which are activated by a variety of bacterial and viral molecules. These include such types of molecules as single- and double-stranded RNAs, CpG oligodeoxynucleotides, bacterial flagellin, lipopeptides, and zymosan, all of which fit with Dr. Janeway’s PAMP hypothesis. Different TLRs occupy different subcelluar locations–some are on the cell surface, others in intracellular vesicles. In addition to TLRs, other types of molecules may also act as PRRs.

Dr. Steinman, dendritic cells, and the unification of innate and adaptive immunity

Now we come to the work of Ralph Steinman and his colleagues on the role of dendritic cells in adaptive immune responses, and their relationship to innate immunity.

Antibodies (whether free antibodies or antibodies on the surface of B cells) can recognize molecules on the surface of pathogens. T cell receptors, however, recognize small antigenic peptides carried by major histocompatibility complex (MHC) molecules on the surface of antigen-presenting cells (APCs). This recognition, together with the activity of other signaling molecules on APCs, results in the activation of the T cell.

The requirement for an APC in T-cell activation was first recognized in the late 1960s and early 1970s. At that time, immunologists generally believed that macrophages and perhaps B cells were the major APCs. In 1973, Ralph Steinman and Zanvil Cohn identified mouse dendritic cells, which are rare cells in the spleen and lymph nodes that have a stellate morphology. In 1978, Dr. Steinman and his colleagues published evidence that dendritic cells had potent immunostimulatory activity, and were over 100 times as effective in immunostimulation as macrophages and B or T cells.

Researchers were initially skeptical about Dr. Steinman’s studies, largely based on the widely held view that the far more numerous macrophages were the major APCs. However, a series of studies by Dr. Steinman and his colleagues showed that dendritic cells are the key APCs for nearly all aspects of T cell activation, and that the potency of dendritic cells as APCs far exceeds that of macrophages and B cells.  Indeed, modern techniques that led to the deletion of dendritic cells result in a profound inability to mount adaptive immune responses.

Dendritic cells are found in perhaps every type of tissue, where they exist in an immature state. For example, the population of immature dendritic cells in the skin are known as Langerhans cells–these cells are illustrated in the figure at the top of our November 25, 2011 article. Immature dendritic cells in tissues act as sentinels of microbial infection, and function to capture antigens (e.g., antigens from pathogenic microbes, or from cells infected by viruses or bacteria). They also express TLRs.

When tissue dendritic cells are stimulated via their TLRs (e.g., by TLR4 binding to bacterial LPS), the dendritic cells change to a mature phenotype, which is specialized in antigen presentation. These mature dendritic cells migrate from the tissue into the draining lymph node. The stimulated dendritic cells in the lymphoid system upregulate class II MHC molecules and other cell surface molecules involved in antigen presentation, and they also produce cytokines involved in T cell activation. The dendritic cells thus activate T cells, and the antigens presented on their surface, as well as the pattern of cytokines they produce, determine the specificity and the type of activated T cells that will result from their actions.

Thus, the work of Dr. Steinman and his colleagues serves to integrate studies of innate and adaptive immunity, and to elucidate how these two branches of the immune system work together to enable humans and other vertebrates to mount immune responses against pathogens and other insults such as tumors.

Despite the major advances in the relationship between innate and adaptive immunity that have been made in recent years, their are still many unknowns. For example, there are minority types of T cells such as natural killer T (NKT) cells and gamma-delta (γδ) T cells, which are conventionally thought to be involved in bridging innate and adaptive immunity. However, their functions are not well understood. Moreover, there are also numerous subsets of dendritic cells, and the functions of these subsets is also not well understood. These cell types, and other unknowns in the relationship between innate and adaptive immunity might, for example, be involved in the pathogenesis of steroid-resistant asthma, the most serious type of asthma.

Implications for drug discovery and development

Our previous article on Ralph Steinman and dendritic cells emphasized the development of dendritic cell vaccines, especially those for cancer. However the broad area of the relationship between innate and adaptive immunity has been and is expected to be a major factor in discovery and development of many types of drugs, vaccines, and immunotherapies.

• Numerous cytokine-based therapies (e.g., interferons, interleukins, and TNF-related therapeutics) have already been developed and marketed. Dr. Beutler himself was the co-discoverer of TNFα in 1985,  and now there are several types of TNF inhibitors on the market.

• In the vaccine area, Dr. Steniman’s work may allow researchers to design more effective adjuvants, a key need in the design of novel anti-viral and anti-cancer vaccines.

• Several companies are developing TLR modulators as drugs or vaccine adjuvants. These include TLR agonists and antagonists. For example, Pfizer is developing the oligonucleotide TLR9 agonist vaccine adjuvant CpGTLR9 (in Phase 3 trials with GlaxoSmithKline’s MAGE-A3 melanoma vaccine), and another oligonucleotide TLR9 agonist product agatolimod, in combination with trastuzumab (Genentech/Roche’s Herceptin) in treatment of breast cancer (Phase 2). [Pfizer's TLR agonists were originally developed by Coley Pharmaceuticals (Cambridge, MA), which Pfizer acquired in 2008.] TLR antagonists in development include Eisai’s eritoran tetrasodium, a TLR4 antagonist in Phase 3 trials for the treatment of sepsis and septic shock.

• Research on the role of various immune cell populations that are thought to link innate and adaptive immunity (e.g. Th17 cells, NKT cells, and γδ T cells) in steroid-resistant asthma may lead to the design of new medicines to treat this serious condition.

There are likely to be numerous other drug discovery and development applications of research on the relationship between innate and adaptive immunity that will emerge as work in this very complex area continues.
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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

Agios Nikolaos, Crete http://bit.ly/uNaFMW

On November 17, 2011, Agios Pharmaceuticals (Cambridge, MA), arguably the leader in cancer metabolism R&D, secured $78 million in an oversubscribed Series C financing.

The company intends to use the proceeds of this financing to advance its preclinical cancer metabolism therapeutics into the clinic, and to expand its R&D efforts into inborn errors of metabolism (IEMs). IEMs comprise a large class of inherited disorders of metabolism, most of which are defects in single genes that code for metabolic enzymes. These conditions have a high level of unmet medical need.

Investors participating in this round included Agios’ existing strategic partner Celgene, existing investors ARCH Venture Partners, Flagship Ventures and Third Rock Ventures, and several new, undisclosed investors, including three leading large public investment funds. In conjunction with the new financing, Perry Karsen, COO of Celgene, joined Agios’ Board of Directors.

Despite being only a preclinical-stage biotech company, and despite the tough early-stage biotech venture capital market, Agios has done very well in fundraising.  In April 2010, as discussed in a Biopharmconsortium Blog article, Agios secured a $130 million upfront payment in a strategic collaboration with Celgene. In October 2011, Celgene extended its collaboration with Agios from three to four years, including making an additional $20 million payment to Agios. According to a November 11, 2011 Fierce Biotech article, Agios has secured a total of over a quarter of a billion dollars in financing, beginning with its $33 million Series A round in July 2008.

Also according to Fierce Biotech, by bringing in public investors in its new financing round, Agios has taken a financing route that has enabled other biotechs to go public. For example, Ironwood Pharmaceuticals took this route. Agios’ CEO, David Schenkein, told Fierce Biotech that his management intends to build an independent company for the long term, including securing an investor base that could support a public offering.

The Biopharmconsortium Blog has been following Agios since December 2009. See our December 31, 2009 and April 23, 2010 articles. Also see our December 22, 2010 article on the reemergence of intermediary metabolism as an important field of biology, which highlighted the role of Agios in developing applications of this field to oncology therapeutics.

Recent research at Agios

More recently, Agios researchers and academic collaborators led by Agios Scientific Advisory Board member David Sabatini M.D., Ph.D (Whitehead Institute and Massachusetts Institute of Technology, Cambridge MA) published a study in the 18 August 2011 issue of Nature. In this study, the researchers demonstrated that 70% of estrogen receptor (ER)-negative human breast cancers exhibit amplification and elevated expression of the gene for phosphoglycerate dehydrogenase (PHGDH). PHGDH catalyses the first step in the serine biosynthesis pathway, and breast cancer cells with high PHGDH expression have increased flux through this pathway. This in turn results in increased levels of α-ketoglutarate, which is a tricarboxylic acid (TCA) cycle intermediate. (The TCA cycle, the central pathway in intermediary metabolism, was illustrated in the figure at the top of our December 22, 2010 blog post).

Suppression of PHGDH [via RNA interference (RNAi)] in breast cancer cell lines with elevated PHGDH expression, but not in those without, causes a strong reduction in cell proliferation, a reduction in serine synthesis, and a reduction in levels of α-ketoglutarate. This result indicates that most ER-negative breast cancers are dependent on deregulation of the serine synthesis pathway, and that targeting this pathway may provide a novel therapeutic strategy for this subset of breast cancers.

In the September 2011 issue of Nature Genetics, Agios founder Lewis C. Cantley, Ph.D., and Agios advisor Matthew Vander Heiden, M.D., Ph.D., (Beth Israel Deaconess Medical Center/Harvard Medical School and MIT, respectively) published a report that provides further evidence that amplification of PHGDH and deregulated activity of the serine pathway are linked to the growth and survival of certain cancers, especially melanoma and subtypes of breast cancer. This study was carried out using a novel research method called metabolic flux analysis, which is an important component of Agios’s technology platform in cancer metabolism.

These studies provide additional validation for the field of cancer metabolism as a source of novel therapeutic strategies.

Pharmaceutical industry interest in cancer metabolism

Agios is not the only company that is active in the field of cancer metabolism. For example, Forma Therapeutics (Cambridge, MA) is also conducting R&D in this field. According to an article in XConomy Boston, Forma entered into a collaboration with Genentech in cancer metabolism on June 27, 2011. Under the agreement, Genentech will receive exclusive rights to acquire one of Forma’s early preclinical-stage cancer metabolism drugs. In return, Forma will receive an upfront payment, research support, R&D milestone payments, and development funding for that drug. If Genentech decides to acquire the drug after it has met its development goals, Forma will forgo any royalty payments. Instead, Genentech will make an asset buyout payment, which will be distributed to Forma’s investors. In addition, Forma will receive milestone payments on sales of the drug.

Thus Forma’s investors will receive a return on their investments, without the need for an acquisition or an initial public offering. Forma will thus remain an independent company, free to develop its other pipeline drugs, including any other of the approximately 8-10 cancer metabolism drugs that it has already discovered.

This deal, which is made possible by the industry’s keen interest in cancer metabolism-based therapeutics, suggests that Forma, like Agios, intends to remain an independent company over the long haul. Forma has raised over $50 million in venture capital so far, and has revenue-producing alliances with Novartis, Cubist, and the Leukemia & Lymphoma Society as well as Genentech.

Conclusions

Agios is leveraging the strong biotech/pharma industry interest in cancer metabolism, and its own leadership in the field, to build and to finance its R&D programs, and also its corporate development. However, as always, all will depend on the performance of the company’s compounds in the clinic. Dr. Schenkein is providing no information on the timeline for entry of Agios’ drugs into clinical trials. However, he says that the funding secured by Agios will provide the means to get its lead drugs through proof-of-concept studies in humans.

Interestingly, Agios Pharmaceuticals’ founders and management have a particular fondness for the Greek language. At the apex of Agios’ values is arete (ἀρετή), an ancient Greek word that connotes virtue, excellence, and courage and strength in the face of adversity. CEO Schenkein also adds another meaning, “living up to ones potential”.

“Agios” itself is a Greek word (Άγιος), which means “holy” or “Saint”. This is why I chose the figure at the top of this article. It is a photo of the town of Agios Nikolaos (Άγιος Νικόλαος), Crete, which is named for Saint Nicholas.
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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

Dendritic cells in skin

Ralph M. Steinman, MD of the Rockefeller University (New York, NY) the discoverer of the dendritic cell and its central role in the immune system, died on September 30, 2011 at age 68 after a four-and-a-half year battle with pancreatic adenocarcinoma. On October 3, 2011, he was awarded half of the The Nobel Prize in Physiology or Medicine for 2011 “for his discovery of the dendritic cell and its role in adaptive immunity”. (The other half of the Prize was shared between Bruce A. Beutler and Jules A. Hoffmann “for their discoveries concerning the activation of innate immunity”.)

Previously, in 2007, Dr. Steinman had been awarded an Albert Lasker Basic Medical Research Award for the discovery of dendritic cells.

Dendritic cells are the principal antigen-presenting cells (APCs) in the immune system. They process antigenic material (for example, from invading bacteria and viruses, and from cancer cells), and present antigens on their surfaces to other types of immune cells, especially T cells. This results in antigen-specific activation of the T cells. Dendritic cells thus serve as the principal link between the innate and the adaptive immune system.

Nobel Prizes are not awarded posthumously, but the Nobel Committee was not aware that Dr. Steinman had died when they made the award. So the award still stands. Dr. Steinman thus has the distinction of being the only person to be awarded a Nobel Prize posthumously. The Nobel Foundation said, after reviewing the case, “The decision to award the Nobel Prize to Ralph Steinman was made in good faith, based on the assumption that the Nobel Laureate was alive.”

Nature published a “News in Focus” article on Dr. Steinman in its 13 October 2011 issue, written by Lauren Gravitz, a freelance writer and editor based in Los Angeles, California. The article details the attempt by Dr. Steinman and his colleagues to use dendritic cell-based immunotherapy to treat Dr. Steinman’s own cancer.

Ms. Gravitz met Dr. Steinman during her two-year tenure as a science writer in the Rockefeller University communications department.  While she was there, Dr. Steinman educated her on the complex field of dendritic cell biology. It was also during her time at Rockefeller that Dr. Steinman was diagnosed with advanced pancreatic cancer (in March 2007). Starting at the time of his diagnosis, Dr. Steinman and his colleagues began developing and using their experiential immunotherapies against that cancer. Thus Ms. Gravitz has been following this story from the beginning, and the October 2011 Nature article is the result.

An approved and marketed dendritic cell-based immunotherapy

Only one dendritic cell-based immunotherapy, Dendreon’s Sipuleucel-T (APC8015, Provenge) for treatment of advanced prostate cancer, has been approved by the FDA. The FDA approved it on April 29, 2010, and it is considered the first approved and marketed cancer vaccine. Sipuleucel-T was the first therapeutic cellular immunotherapy for cancer to demonstrate efficacy in Phase 3 clinical trials; this led to the FDA approval. However, Sipuleucel-T only extended mean survival by four months as compared to placebo in Phase 3 clinical trials. And the treatment is expensive, costing a total of $93,000 for the full treatment of three infusions.

Since Sipuleucel-T must be prepared specifically for each patient, using the patients own dendritic cells, a discussion of this product is relevant to the case of Dr. Steinman’s experimental treatment, which also involved autologous dendritic cells.

To prepare Sipuleucel-T, a patient’s autologous dendritic cells are purified from his or her blood. The cells are then sent to a Dendreon site, where they are incubated with a fusion protein, consisting of two moieties–the antigen prostatic acid phosphatase (PAP), which is present in 95% of prostate cancer cells, and a granulocyte-macrophage colony stimulating factor (GM-CSF) moiety, which is an immune cell activator. The resulting product, APC8015 or Sipuleucel-T, is returned to the infusion center and infused into the patient. The goal is to stimulate an immune response to tumor cells carrying the PAP antigen.

Although Sipuleucel-T is the the first therapeutic cellular immunotherapy for cancer to demonstrate efficacy in Phase 3 clinical trials in terms of overall survival, neither it, nor other cancer vaccines in clinical trials, gives complete responses. In our April 27, 2011 blog post, we discussed another therapeutic cellular immunotherapy for cancer, known as adoptive immunotherapy, which does give some complete responses in metastatic melanoma. However, this therapy is experimental and difficult to standardize, and has thus attracted no commercial interest. It is not approved by the FDA, and will not be covered by third-party payers. Thus the emphasis on dendritic cell vaccines.

Using dendritic cells to stimulate immune responses to Dr. Steinman’s pancreatic cancer

There are no approved cancer vaccines for pancreatic adenocarcinoma, which has a poor prognosis (survival measured in weeks or a few months in advanced cases). The disease is generally treated with the cytotoxic drug gemcitabine (Lilly’s Gemzar). However, this treatment appears to be mainly palliative in patients with advanced pancreatic cancer, giving an improved quality of life and a 5-week improvement in median survival. Most patients soon develop resistance to treatment with this agent. Thus, when Dr. Steinman (with the help of his colleagues) attempted to treat his own pancreatic cancer, he was venturing into the unknown.

According to Ms. Gravitz’ article, Dr. Steinman had a meeting with two immunotherapy researchers who had formerly been members of his lab–Michel Nussenzweig of Rockefeller and Ira Mellman of Genentech, shortly after he had been diagnosed with pancreatic cancer. The three planned a strategy to design potential therapies for Dr. Steinman’s cancer.  Dr. Nussenzweig would implant some of the tumor as xenografts in mice so that there would be enough material to work with. Dr. Mellman would start a cell line, so that drugs could be screened for activity in killing the cells. Other colleagues would look for mutations in tumor cell DNA that could be used to design drug treatments, and another would isolate surface peptides from the tumor cells so that they could be used as the basis of a vaccine. Meanwhile, Dr. Steinman would undergo conventional chemotherapy with gemcitabine  in combination with whatever experimental therapies that might be deemed to have potential to treat the cancer.

Dr. Steinman tried eight experimental therapies, one at a time. For each of these treatment, he and his colleagues submitted a single-patient, compassionate-use protocol to the FDA, and received approval from the agency. Among these treatments were three cancer vaccines. One of them was a form of BioSante’s GVAX. The product GVAX Pancreas for pancreatic cancer (which is now in clinical trials) is based on human pancreatic cell lines that have been engineered to secrete GM-CSF, and have then been lethally irradiated. In the case of Dr. Steinman’s treatment, cells from his own tumor were used instead of cell lines.

The other two cancer vaccines were dendritic cell-based immunotherapies, and used dendritic cells isolated from Dr. Steinman’s own blood. The first of these immunotherapies was developed by Argos Therapeutics (Durham, NC), of which Dr. Steinman was a cofounder. It involved transfecting Dr. Steinman’s dendritic cells with RNA derived from his own tumor. The resulting dendritic cells expressed tumor antigens on their surfaces, and were injected back into Dr. Steinman’s blood to potentiate the production of tumor antigen-specific T cells. The second immunotherapy, developed by researchers at the Baylor Institute for Immunology Research (Dallas, TX) involved loading Dr. Steinman’s dendritic cells with peptide antigens from the surface of his tumor. These were also injected back into Dr. Steinman’s blood, in order to potentiate a tumor-specific immune response.

Dr. Steinman also wanted to try combination therapies with ipilimumab. Dr. Steinman tried ipilimumab as a monotherapy, but never got the permissions needed to try the combination therapy. Ipilimumab is an immunomodulator that blocks cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) (a cell surface protein that transmits an inhibitory signal to T cells) to potentate an antitumor T-cell response. The FDA refused permission for the combination therapy despite his belief, and that of other leading immunologists, that the cancer vaccines were likely to work better in combination with ipilimumab. Ipilimumab (Medarex/Bristol-Myers Squibb’s Yervoy) was approved by the FDA in March 2011, and clinical trials of combination therapies of ipilimumab and dendritic-cell vaccines are in early stages.

The course of Dr. Steinman’s disease

Patients with advanced pancreatic adenocarcinoma typically have a poor prognosis. The median survival for locally advanced and for metastatic pancreatic cancer (advanced pancreatic cancer represents over 80% of individuals diagnosed with the disease) is about 10 and 6 months respectively. For all stages of pancreatic cancer combined, the 1- and 5-year relative survival rates are 25% and 6%, respectively.

However, Dr. Steinman survived for four-and-a-half years!

Did any of the treatments that Dr. Steinman received extend his life? No one can know, since with a one-patient experimental treatment there are neither controls nor statistical data as in properly controlled clinical trials.

Dr. Steinman appeared to be much more responsive to gemcitabine than is usually the case. And he had a measurable antitumor immune response, since approximately 8% of his cytotoxic T cells targeted his cancer. Was this due to his natural immunity, or due to the dendritic cell immunotherapies and/or other treatments that he received? Did Dr. Steniman’s antitumor immune response make his cancer more susceptible to gemcitabine than is usually the case? There is no way to know.

The implications of Dr. Steinman’s one-patient experimental treatment

According to Lauren Gravitz’ article, despite these unanswerable questions, Dr. Steinman’s treatment helped move the cancer vaccine field forward. For example, it showed that the leaders in the cancer vaccine field can work together as a team to design and carry out therapies. It also showed that conventional chemotherapy can be given in combination with cancer vaccines. And it also bolstered Dr. Steinman’s passionate belief that it is vitally important to move beyond in vitro studies and animal models into human studies of dendritic cell vaccines, especially given the limitations of animal models.

With respect to animal models and dendritic cell vaccines:

• Dendritic cell immunotherapies designed for use in humans cannot be directly tested in standard animal models. For example, species specificity issues made direct testing of Sipuleucel-T in rodents impossible. Therefore, in preclinical studies researchers constructed “rodent equivalents” of Sipuleucel-T. These consisted of rodent APCs loaded with fusion proteins composed of either rat PAP (rPAP) fused to rat GM-CSF (rPAP•rGM-CSF) or human PAP (hPAP) fused to murine GM-CSF (hPAP•mGM-CSF), and these surrogate versions of Sipuleucel-T were tested in rodents.

• Autologous dendritic cell immunotherapies have proven to be “remarkably safe” in human studies. Therefore, it may not be necessary to test for safety in animal models.

• Dendritic cell biology is complicated. For example, researchers are still attempting to identify human dendritic cell subsets that correspond to known mouse dendritic cell subsets, especially subsets that appear to be the most promising for vaccine design. Therefore, the results of studies carried out in mice may not be directly applicable to humans. Moreover, the use of rhesus macaques for translational studies of vaccines based on dendritic cell biology is expensive.

Should autologous dendritic cell immunotherapies/vaccines for cancer be tested directly in humans, without the use of animal models for preclinical studies? In the case of the treatment of Dr. Steinman, the FDA allowed this to happen. Authorities in the field and regulatory agencies need to continue to discuss this issue.

Meanwhile, as stated at the end of Ms. Gravitz’ article, Anna Karolina Palucka of Baylor, a researcher who had been involved in Dr. Steinman’s treatment, says that she and her colleagues at Baylor are developing an immunotherapy program against pancreatic cancer based on the data from Dr. Steinman’s one-person trial. And Baylor will honor Dr. Steinman by opening a Ralph Steinman Center for Cancer Vaccines. This will be one of many tributes to a pathbreaking physician/scientist.
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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

http://bit.ly/dGrWW3

In recent months, there have been quite a few articles on the need to fix the clinical trial system. Among the most recent articles is the one by Boston-based Nature writer Heidi Ledford, Ph.D. published as a News Feature in the 29 September issue of Nature. In my humble opinion, this is the best article on the subject among those that have been published recently.

The pharmaceutical/biotechnology industry is frustrated with the increasing expense and the low output of the clinical trial system. This low productivity is economically unsustainable. The current clinical trial paradigm is over 50 years old. Back in the 1960s, the norm was to conduct single trials at single sites, each designed to answer a single question.

Nowadays, the norm is the large, multicenter clinical trial, especially for Phase 3 trials. “Multicenter” means that a trial is conducted at multiple sites, often in different countries, and could involve thousands of investigators and staff members. As pointed out in Dr.Ledford’s article, the large trials are mandated by the need in our more risk-adverse world to detect safety issues that occur in only a small percentage of patients, and to obtain good statistics for drugs that confer only a small benefit over the standard of care. However, certain major diseases require large trials of long duration even for drugs that may confer large benefits. For example, because the percentage of patients per year in cardiovascular disease (CVD) trials who experience cardiovascular events is small, these trials must be large and multiyear, in order to see any benefit even for a breakthrough drug.

The advent of personalized medicine–developing drugs and combinations of drugs that are specific for the molecular mechanism behind a patient’s disease–has put additional burdens on the clinical trial system. A disease may be found to be a collection of rare diseases in terms of mechanistic subtypes, each of which affects only a small number of people. This makes patient recruitment difficult.

As stated by Dr.Ledford, “Solving the problem may require fundamental changes to the clinical-trial system to make it faster, cheaper, more adaptable and more in tune with modern molecular medicine.”

Don’t use an “e-commerce” approach to determining drug efficacy!

Other commentators have recently noted the need to make clinical trials “faster, cheaper, and more adaptable.” Several of them have suggested bringing in strategies from other industries, especially e-commerce and social media.

For example, in an editorial published in the 23 September issue of Science, Andrew Grove, the former Chief Executive Officer of Intel, proposes moving towards an “e-trial” system, based on such large-scale e-commerce platforms as that of Amazon.com. Under the proposed e-trial system, the FDA would ensure safety only, not efficacy, and would continue to regulate Phase 1 trials. Once Phase 1 trials have been successfully completed, patients would be able to obtain a new drug through qualified physicians.

Patients’ responses to a drug would be stored in a database, along with their medical histories. There would be measures to protect a patient’s identity, and the database would be accessible to qualified medical researchers as a “commons.” The response of any patient or group of patients to a drug or treatment could then be tracked and compared to those of others in the database who were treated in a different manner or were untreated. These comparisons would provide insights into a drug’s efficacy, and how individuals or subgroups (perhaps defined in part via biomarkers) respond to the drug. This would liberate clinical trials from the “tyranny of the average” that characterize most trials today. As the database grows over time, analysis of the data would also provide information needed for postmarketing studies and comparative effectiveness studies.

Dr. Grove’s proposal is one of several in which the mandate of the FDA (and regulatory agencies in Europe, Japan, etc.) is to regulate safety only (via Phase 1 clinical trials) not efficacy. Efficacy is then determined via some sort of open system, with information gathered and provided to patients and physicians electronically, via systems reminiscent of e-commerce or social media.

We are opposed to removing efficacy from the oversight of the FDA and other regulatory agencies. There are two reasons for this, both of which are illustrated graphically in Box 1 of Dr. Ledford’s article, entitled “the clinical trial cliff”. Approximately half of Phase 2 clinical trials between 2008 and 2010 failed due to inability to demonstrate efficacy. (Around one-third of Phase 2 failures were due to safety, and the remaining failures were mainly due to strategic decisions to terminate a drug.) Among Phase 3 failures between 2007 and 2010, around two-thirds were due to efficacy, and around one-quarter were due to safety. These results indicate that the majority of drugs entered into clinical trials lack efficacy.

The second reason is that many safety problems–especially the rarer safety issues that occur in only a small percentage of patients–are typically not detected in Phase 1, but in Phase 3 and even the postmarking period.

Reduce clinical attrition with new trial designs and improved animal models

Dr. Ledford’s proposals for fixing clinical trials leave regulatory agencies in charge of overseeing both safety and efficacy. They mainly focus on improving clinical trials by reducing “attrition”–i.e., failure of drugs in the clinic, especially in Phase 2 and Phase 3, and on improving patient recruitment. Haberman Associates has produced publications–as well as articles on this blog–during the 2009-2011 period that provide a more in-depth discussion of strategies for reducing attrition than is possible in a 3-page article such as Dr. Ledford’s.

Two of Dr. Ledford’s strategies involve modifications of clinical trial design. Both of these are discussed in Chapter 6 of our book-length Cambridge Healthtech Institute (CHI) Insight Pharma Report, Approaches to Reducing Phase II Attrition. The first is the “Phase 0″ trial. This is a type of pre-Phase 1 clinical trial, which uses microdoses of a drug to assess such parameters as pharmacokinetics and target occupancy. As Dr. Ledford suggests, in some cases Phase 0 trials can reduce or eliminate pharmacological testing in animals, and allow researchers to get human data more quickly.

The other trial design strategy mentioned in Dr, Ledford’s article is the use of adaptive clinical trials. This type of trial allows researchers to change the course of a trial in response to trial results. For example, this may mean assigning new patients to specific doses, changing the numbers of patients assigned to each arm of a trial, and changes in hypotheses or endpoints. Monitoring and changing the trial is typically done by an independent data monitoring committee [DMC] so that ideally, double-blind conditions are maintained.

As Dr. Ledford states, adaptive clinical trials may result in shortening the time and cost of the clinical trial process. But, as with Phase 0 microdosing trials, there are many controversies surrounding adaptive clinical trials. Both of these strategies are works in progress.

The other strategy for reducing attrition discussed in Dr. Ledford’s article is to use improved animal models (i.e., animal models designed to more faithfully model human disease) in preclinical studies. We discussed this strategy in Approaches to Reducing Phase II Attrition, and in greater detail in another book-length report, Animal Models for Therapeutic Strategies. I also recently led the workshop “Developing Improved Animal Models in Oncology and CNS Diseases to Increase Drug Discovery and Development Capabilities” at Hanson Wade’s 2011 World Drug Targets Summit.

Several articles on our Biopharmconsortium Blog also focus on improved animal models for predicting efficacy of drug candidates in discovery research and in preclinical studies. Our April 15, 2010 blog post, based on an article in The Scientist, focused on “co-clinical mouse/human trials”. This type of clinical trial was developed by Pier Paolo Pandolfi, MD, PhD (Director, Cancer and Genetics Program, Beth Israel-Deaconess Medical Center Cancer Center and the Dana-Farber/Harvard Cancer Center) and his colleagues.

These trials utilize genetically engineered transgenic mouse strains that have genetic changes that mimic those found in specific human cancers. These mouse models spontaneous develop cancers that resemble the corresponding human cancers. In the co-clinical mouse/human trials, researchers simultaneous treat a genetically engineered mouse model and patients with tumors that exhibit the same set of genetic changes with the same experimental targeted drugs. The goal is to determine to what extent the mouse models are predictive of patient response to therapeutic agents, and of tumor progression and survival. The studies may thus result in validated mouse models that are more predictive of drug efficacy than the currently standard xenograft models.

The new Ledford Nature article discusses co-clinical trials as a means to develop more predictive animal model studies–not only using improved, potentially more predictive animal models, but also treating these animals in similar way (in terms of doses, formulations, schedules of medication, etc.) to the humans in the parallel human clinical trial.

The Ledford article mentions the animal-model portion of a co-clinical trial, which was published in January 2011. This trial utilized two genetically-engineered PDGF (platelet-derived growth factor)-driven mouse models of the brain tumor glioblastoma multiforme (GBM), one of which has an intact PTEN gene and the other of which is PTEN deficient.

Unlike the “standard” mouse xenograft models, these models more closely mimicked the human disease, including growth of tumors within the brain, not subcutaneously. Thus any drug administered to these mice systemically (e.g., intraperitoneally, as was done in this study) had to cross the blood-brain barrier (BBB), as in the case of human clinical trials. This would not be the case with a standard xenograft model, which is one deficiency of these models for brain tumors such as GBM.

GBM is both the most common and the most malignant primary brain tumor in adults. It has a poor prognosis. PDGF-driven GBMs, which results from deregulation of the PDGF receptor (PDGFR) or overexpression of PDGF, account for about 25-30% of human GBMs. These mutations result in the activation of the phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway. These tumors may also exhibit mutation or loss of heterozygosity of the tumor suppressor PTEN, which also upregulates the PI3K/Akt/mTOR pathway.

The researchers tested the Akt inhibitor perifosine (Keryx Biopharmaceuticals, an alkylphospholipid) and the mTOR inhibitor CCI-779 (temsirolimus; Pfizer’s Torisel; originally developed by Wyeth prior to the Pfizer merger and approved for treatment of renal cell carcinoma), both alone and in combination, in vitro and in vivo. Specifically, the drugs and drug combinations were tested in cultured primary glioma cell cultures derived from the PTEN-null and PTEN-intact mouse PDGF-driven GBM models, and in the animal models themselves.

The studies showed that both in vitro and in vivo, the most effective inhibition of Akt and mTOR activity in both PTEN-intact and PTEN-null cells or animals was achieved by using both inhibitors in combination.  In vivo, the decreased Akt and mTOR signaling seen in mice treated with the combination therapy correlated with decreased tumor cell proliferation and increased cell death; these changes were independent of PTEN status. The co-clinical animal study also suggested new ways of screening GBM patients for inclusion in clinical trials of treatment with perifosine and/or CCI-779.

According to Dr. Ledford’s Nature article, the National Cancer Institute (NCI) invested $4.2 million in Dr. Pandolfi’s co-clinical trials in prostate and lung cancer in 2009. In addition to the co-clinical trials with genetically-engineered mouse models run by Dr. Pandolfi and others, researchers at the Jackson Laboratory are conducting co-clinical trials with mouse xenograft models that receive tumor cells from patients to be treated in human clinical trials.

Use patient registries in recruitment of patients for clinical trials

In Dr, Ledford’s article, she discusses a crucial factor other than clinical attrition that hinders progress in conducting clinical trials–patient recruitment. According to the article, at least 90% of trials are extended by at least six weeks because of failure to enroll patients on schedule. Only about one-third of the sites involved in a typical multicenter trial manage to enroll the expected number of patients. As a result, clinical trials are longer and more expensive, and some of them are never completed.

Personalized medicine, in which researchers use biomarkers or other criteria to determine what fraction of patients with a particular disease are eligible for a trial (e.g., cancer patients with an activating mutation in a kinase that is the target of the drug to be tested), makes recruitment harder. That is because researchers must screen large numbers of patients to identify the fraction of patients that would be eligible for the trial. So they need to recruit (and screen) a much larger number of patients than in conventional clinical trials with no patient stratification.

Therefore, researchers, “disease organizations”, and patient advocates are devising new strategies to facilitate recruitment of eligible volunteers. Dr. Ledford cites the example of the Alpha-1 Foundation (Miami, Florida), a “disease organization” that focuses on the familial disease alpha-1 antitrypsin deficiency. (This disease renders patients susceptible to lung and liver diseases.) This foundation has  created a registry of patients with alpha-1 antitrypsin deficiency who are willing to be contacted about and to participate in clinical trials.

There are also cancer registries. Dr. Ledford mentions the Total Cancer Care program run by the Moffitt Cancer Center (Tampa, Florida). This program, which involves 18 hospitals, compiles medical history, tissue samples (stored for future analysis) and genetic information about each patient’s tumor. Patients can consent to doctors contacting them about trials. There are other similar programs being developed in the Netherlands and elsewhere. Dr.Ledford mentions the difficulty in negotiating agreements between institutions, and the need for adequate, ultra-secure networks to support registries that connect multiple hospitals and research centers.

Patient registries that are designed to proactively support recruitment for clinical trials have some resemblance to a “social media” approach to recruitment. However, there is a big difference–the need to secure the privacy of patient records. The current trend in social media (and in some e-commerce platforms) is anti-privacy. This is yet another important reason why a social media or e-commerce approach to clinical trials or other aspects of biotech/pharma R&D is not a suitable model. (To his credit, Dr. Grove mentions the need to maintain patient privacy and confidentiality. But this is not the norm with e-commerce and social media.)

Cutting red tape for faster and cheaper clinical trials

Dr Ledford also mentions ways to deal with more bureaucratic issues that can slow down or block the progress of clinical trials. The NCI is now initiating a data-management system that will standardize data entry across all 2,000 sites that conduct NCI-sponsored trials. This should help reduce costs and cut down on record-keeping errors and omissions.The FDA is also looking into ways to reduce reporting requirements and paperwork. so that investigators can submit summaries of case reports rather than each individual document.

To adapt to the multicenter nature of clinical trials, the US Office for Human Research Protections (Rockville, Maryland), which oversees NIH-funded human studies, has proposed changes to its guidelines that would require designation of a single review board for each project. This may greatly improve the current situation, in which multicenter trials must get approval from each center’s institutional review board. This can take months or even years. Despite the definite advantages of more centralized review, individual research centers may be reluctant to give up their direct oversight of clinical trials.

Something important was not in Dr. Ledford’s article

The space limitations for Dr. Ledford’s “News Feature” article, plus its strict focus on clinical trials per se, did not permit her to include something of crucial importance to reduce clinical attrition. That is utilizing such strategies as biology-driven drug discovery in the research phase of drug development. These strategies are designed to select the best targets and to discover drugs that are more likely to be efficacious in treating a particular group of patients. These research strategies are then coupled with early development strategies that emphasize designing clinical trials aimed at obtaining rapid proof of concept in humans. Such trials typically involve the use (and often the discovery) of biomarkers.

We discussed these issues extensively in our report, Approaches to Reducing Phase II Attrition, as well as in an article published in Genetic Engineering and Biotechnology News (and available on our website) “Overcoming Phase II Attrition Problem“. We also discussed a specific case of the use of this strategy in our October 25, 2010 article on this blog.

Conclusions

Given the low productivity of pharmaceutical R&D, it is tempting to take an envious look at the success of e-commerce and social media, and to attempt to devise strategies that apply methodologies from these industry sectors to the biotech/pharmaceutical industry. We should remember, however, that not so long ago some pharmaceutical executives attempted to apply methodologies from such industries as aerospace, computer hardware, and the auto industry to pharma R&D. Not only did that not work too well for the pharmaceutical industry, but as we all know, the industries that served as a model for these approaches haven’t done very well in recent years either.

In contrast, pharmaceutical and biotechnology companies that have formulated strategies that embrace the uniqueness of biology, such as Novartis and Genentech (the latter now merged with Roche), have done a lot better.

There are other strategies for making clinical trials faster, cheaper, and better that are now under discussion in the biotech/pharma industry and the FDA.  These strategies are based on clinical experience, not e-commerce. We shall discuss them in further blog posts.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.

PPARγ

This article is an update of a three-part series on insulin sensitizers for treatment of type 2 diabetes that was published on this blog in August and September of 2010.

Summary of our August/September 2010 blog articles on insulin sensitizers

In part 1 of the series (posted August 23, 2010), we focused on safety issues with the two marketed thiazolidinedione (TZD) peroxisome proliferator-activated receptor gamma (PPARγ) agonists–rosiglitazone (GlaxoSmithKline’s Avandia) and pioglitazone (Takeda’s Actos). Both of these insulin sensitizing, antidiabetic agents induce weight gain, and carry an increased risk of edema and heart failure. In addition, rosiglitazone carries an increased risk of myocardial infarction. On September 23, 2010, the FDA restricted access to Avandia, and the European Medicines Agency (EMA) recommended that the drug be pulled from the market.

In part 2 of the series (posted on August 29, 2010), we discussed a breakthrough discovery by Bruce Spiegelman (Dana-Farber Cancer Institute and Harvard Medical School, Boston MA) and his colleagues, published in the 22 July 2010 issue of Nature. It was the Spiegelman group that originally identified PPARγ as the master regulator of adipocyte biology and differentiation, which eventual led to the development of the TZD drugs.

In that research, the Spiegelman group found evidence that the insulin sensitizing and antidiabetic effects of PPARγ agonists may not be due to the agonistic effects of these compounds on PPARγ, but to their ability to inhibit phosphorylation (at Ser 273) of PPARγ by the enzyme cyclin-dependent kinase 5 (CDK5). A weak PPARγ agonist, the benzoyl 2-methyl indole (non-TZD) MRL24, inhibits CDK5 phosphorylation of PPARγ as well as rosiglitazone, and also has very good antidiabetic activity.

CDK5 phosphorylation of PPARγ does not change the ability of PPARγ to upregulate transcription of genes involved in adipocyte differentiation. However, it inhibits the ability of PPARγ to upregulate transcription of a set of genes, including the gene for the adipokine adiponectin, that induce insulin sensitivity and resistance to obesity. Although both rosiglitazone and MRL24 inhibit CDK5 phosphorylation of PPARγ, treatment with the strong agonist rosiglitazone results in upregulation of both the adipogenic and the pro-insulin resistance sets of genes, while treatment with MRL24 results only in upregulation of the pro-insulin resistance set.

Researchers hypothesize that it is the upregulation of the adipogenic gene set that is responsible for the adverse effects of strong agonists of PPARγ–weight gain, edema, and the risk of heart failure. In contrast, the upregulation of adiponectin and the other members of the pro-insulin resistance gene set is thought to be responsible for the desirable, antidiabetic effect of PPARγ agonists.

In part 3 of the series (published on September 16, 2010), we discussed two essays, also published in the 22 July 2010 issue of Nature, that discuss using the new breakthrough results of the Spiegelman group to discover and develop improved insulin sensitizers. These essays recommended that researchers screen for compounds that inhibit CDK5 phosporylation of PPARγ rather than those that are strong PPARγ agonists. We also discussed the prospects for early-stage non-TZD partial or selective agonists of PPARγ, which might constitute second-generation insulin sensitizers.

New research from the Spiegelman group based on their 2010 breakthrough result

On September 4, 2011, Nature published, as an “advance online publication”, a new paper [subsequently published in Nature's 22 September 2011 print edition] by Bruce Spiegelman, Patrick R. Griffin and Theodore Kamenecka (Scripps Research Institute, Jupiter, Florida) and their colleagues on discovery of novel compounds that bind to PPARγ and block its phosphorylation by CDK5, and which completely lack PPARγ agonist activity. (These compounds are thus neither full nor partial/selective agonists of PPARγ.)

One of these compounds, SR1664, exhibited potent antidiabetic and insulin sensitizing activity in two mouse models of obesity-associated type 2 diabetes. However, unlike full agonists such as rosiglitazone, it did not cause fluid retention and weight gain in these animal models. Fluid retention and weight gain are major adverse effects of TZDs in their own right, and are also thought to be related to the even more serious cardiovascular adverse effects of TZDs. Moreover, SR1664 did not interfere with bone mineralization in cultured osteoblasts; this assay is a model for the loss of bone mineral density and increase risk of fracture seen with TZDs.

The researchers developed SR1664 by starting with a partial agonist of PPARγ developed by GlaxoSmithKline, known as compound 7b. Using compound 7b as a scaffold for chemical modification, the researchers optimized for (1) high binding affinity for PPARγ, (2) blocking of CDK5-mediated PPARγ phosphorylation and (3) lacking classical agonism. The structure of two resulting compounds, SR1664 and SR1824, are given in the new Spiegelman/Griffin paper.

Although the new study suggests that SR1664 may be as efficacious an insulin sensitizer as TZDs without inducing their major adverse effects, the safety of these compounds in humans (as opposed to the mouse models) remains unproven. Moreover, SR1664 has unfavorable pharmacokinetic properties and is thus not a good candidate for development as a drug. According to a press release, Dr. Griffin’s molecular therapeutics group and Dr. Kamenecka’s medicinal chemistry group at Scripps have been using S1664 as a molecular scaffold for the discovery of derivatives with improved pharmacokinetic properties. They are advancing such newer compounds into additional studies.

Why develop new insulin sensitizers rather than depending on current antidiabetic drugs?

In Heidi Ledford’s commentary published in the 22 July 2010 issue of Nature, the author points out that some observers believe that pharmaceutical companies will be reluctant to attempt to develop new insulin sensitizers that target PPARγ, given the checkered history of that class of drugs. And other medical authorities believe that the older, inexpensive, and well proven type 2 diabetes drugs–insulin, metformin, and sulfonylureas–are adequate for the treatment of type 2 diabetes.

However, there remain important unmet needs in the treatment of type 2 diabetes. These especially include dealing with the relentlessly progressive nature of type 2 diabetes–for example, even patients who initially succeed in reaching glycemic goals with only diet/exercise and metformin will eventually need multidrug treatment, including insulin. Progression of type 2 diabetes is mainly due to the loss of pancreatic beta-cell function, which results in increased impairment of a patient’s ability to produce insulin in response to increased blood glucose.

Despite the major safety issues with TZDs, there is both animal model and human evidence that these agents may work to preserve and/or enhance beta-cell function. It will be important to determine if nonagonist second-generation insulin sensitizer candidates, such as those being developed by the Spiegelman and Griffin groups, also have the beta-cell preserving or enhancing effects of TZDs.

The Harvard/Scripps efforts to discover safer insulin sensitizers illustrate the potential role of academia (based on breakthrough science) in areas of drug discovery and development that industry is reluctant to undertake. However, although these academic groups might potentially take the nonagonist insulin sensitizers through lead optimization and preclinical studies, eventually industry (whether a biotech company or a pharmaceutical company) will need to take the compounds through clinical trials in order for any drugs to reach the market.
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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please click here. We also welcome your comments on this or any other article on this blog.