Biopharmconsortium Blog

Expert commentary from Haberman Associates biotechnology and pharmaceutical consulting.

Monthly Archives: March 2010

Some notes on this blog

We started the Biopharmconsortium Blog in July of 2009, so it is relatively new. Since that time, we have posted 21 articles (not including this one), 7 of which were posted in 2010.

The blog has gradually been picking up a following, and it recently made a “Top 50 Biotech Blogs” list. Thanks to Medicareer for honoring our blog in that way. (Haberman Associates has no business or financial relationship with Medicareer, nor do I even know the people there.)

The 21 articles now posted on the blog may at first glance seem to be on random subjects—commentary on recent news and/or recent published scientific reports or business articles, and a few announcements and commentaries on Haberman Associates publications or events. However, there is a strong theme of R&D strategy—especially productive R&D strategies—running through the whole blog.

When we first began the blog, the masthead at the top read “Your place for discussion of scientific and business issues in the biotechnology, pharmaceutical, diagnostics, and research products industry”. Earlier this month, we changed the masthead to read “Expert commentary from Haberman Associates biotechnology and pharmaceutical consulting.” The new heading better reflects what the blog has become since we started it, and also reflects the fact that it is a business blog. Nevertheless, our blog is also a service to the life science community, including companies, academic institutions, and disease organizations and patient advocates. We continue to welcome your comments and discussions of our articles.

“Animal Models for Therapeutic Strategies” published by Cambridge Healthtech Institute

On March 5, 2010, Cambridge Healthtech Institute (CHI) announced the publication of our new book-length report, Animal Models for Therapeutic Strategies. This new Insight Pharma Report discusses the use of animal models to develop new paradigms for drug discovery and development in important human diseases. The report also discusses strategies for developing more predictive animal models of drug efficacy. Poorly predictive animal models are a major reason for Phase II and Phase III pipeline drug attrition. Thus this new report complements our May 2009 Insight Pharma Report, Approaches to Reducing Phase II Attrition.

We have an article, published in Genetic Engineering News in 2004, on the use of animal models in developing novel therapeutic strategies for the treatment of Alzheimer’s disease (AD), available free on our website. This article, based on our 2004 animal models report that is now out of print, gives examples of the use of animal models (the mouse, C. elegans, Drosophila, and the zebrafish) in developing therapeutic strategies. These animal model studies were key to the eventual development of nearly all the pipeline drugs now in the clinic for AD, as well as the development of alternative hypotheses to the dominant amyloid hypothesis (and therapeutic strategies based on them).

The 2010 report includes discussions of using animal models to develop therapeutic strategies for such diseases as Parkinson’s disease, polycystic kidney disease (PKD), autism, and various types of cancer. It also includes discussion of development of emerging animal models, from fish to frogs to mammals.

In the “emerging mammalian model systems” chapter, we include a discussion of the “reemergence” of the laboratory rat, an old animal model that had been eclipsed by the mouse in the era of knockout mice and genomics. Many of you have no doubt seen the ads from SAGE Labs (Sigma Advanced Genetic Engineering) in scientific and trade journals, announcing that “knockout rats are finally here”. Some of you may also have seen the Nature news article Return of the rat. We cover the technologies behind the reemergence of the rat, and the companies and research groups that are driving this development, in our report. As we also discuss in the report, some of the new technologies used in developing rat models are also being applied to other mammalian species.

The report also covers the issue of why it is so difficult to model the complex diseases that are the major focus of current drug discovery and development efforts in the pharmaceutical/biotechnology industry, and strategies that researchers are using to develop more predictive animal models, especially more predictive mammalian models.

For more information on the report, or to order it, see the CHI Insight Pharma Reports website.

Plexxikon’s discovery of PLX4032, a selective targeted therapeutic for metastatic melanoma

In our March 2, 2010 blog post, we focused on a Phase I clinical trial of Plexxikon/Roche’s PLX4032, in which clinical researchers led by Keith T. Flaherty achieved a dramatic breakthrough in treatment of metastatic melanoma. Now we shall discuss the discovery of the drug itself, PLX4032.

In 2002, a research consortium based at the Wellcome Trust Sanger Institute in the U.K. found B-Raf somatic missense mutations in 66% of malignant melanomas (as well as in a subset of other cancers). V600E (valine substituted by glutamic acid at position 600) accounted for 80% of these mutant forms of B-Raf. The V600E mutation causes destabilization of the inactive conformation of B-Raf kinase, shifting the equilibrium toward the catalytically active conformation.

B-Raf is a serine/threonine protein kinase that is a component of an intracellular pathway that mediates signals from growth factors. B-Raf is regulated by binding to Ras. In turn, B-Raf activates MEK (mitogen-activated protein kinase kinase), which activates ERK (extracellular signal-regulated kinase). Activated ERK goes on to upregulate transcriptional pathways that promote cellular proliferation and survival.

Growth factors → →Ras→ B-Raf→ MEK→ ERK→ →upregulation of cell proliferation and survival

Growth factor signaling via Ras also controls other signaling pathways that upregulate cell proliferation, notably the PI3K-Akt (phosphatidylinositol-3-OH kinase-Akt) pathway.

The Sanger researchers found evidence that cells carrying B-Raf(V600E) no longer require Ras function for proliferation. This would mean that melanoma cells carrying this mutation could proliferate independently of growth factor signaling, resulting in the runaway proliferation characteristic of the malignant phenotype.

These results suggested that B-Raf(V600E) would be a good target for novel kinase inhibitors to treat malignant melanoma. The first such kinase inhibitors to be developed, although they had inhibitory activities at low nanomolar concentrations against B-Raf (both wild-type and mutant), were not successful in the clinic, due to their inhibition of multiple nonspecific targets and/or their poor bioavailability. Plexxikon researchers therefore set out to discover inhibitors that are highly selective for B-Raf(V600E). The result was the discovery of PLX4032.

The discovery of PLX4720 (a tool compound or chemical probe related to PLX4032) by Plexxikon researchers and their academic colleagues, and its preclinical validation, is described in a 2008 publication, Tsai et al. Plexxikon used its proprietary “scaffold-based drug design” technology platform to discover PLX4720. Scaffold-based drug design involves synthesizing sets of low-molecular weight “scaffold-like’” compounds. These compounds interact (typically at low affinity) with many members of a protein family by targeting their conserved regions.

In the B-Raf study, the researchers identified protein kinase scaffolds by screening a select library of 20,000 150-350-dalton compounds for inhibition of a set of three structurally characterized protein kinases at a concentration of 200 micromolar (μM). Of this library, 238 compounds were selected on the basis of their inhibition of the kinases by at least 30% at the 200 μM concentration. Each of the compounds was cocrystallized with one if the three kinases, Pim-1. Using this method, the researchers found that 7-azaindole bound to the ATP-binding site of Pim-1 kinase. They further modified this compound by adding side chains on the 3 position of 7-azaindole, resulting in a “scaffold candidate” with increased affinity for the ATP binding site of PIm-1 and other kinases. The researchers further modified this scaffold, based on structural data from other kinases. Ultimately, they cocrystallized their modified compounds with wild-type B-Raf and B-Raf(V600E), and optimized the structure of their compounds to give a compound, PLX4720, with selectivity for B-Raf(V600E) and against wild-type B-Raf and other kinases. This process (including the relevant chemical and protein structures) is illustrated in Figure 1 of Tsai et al.

In biochemical assays, the researchers found that PLX4720 inhibited B-Raf(V600E) at low nanomolar concentrations, and was 10-fold more selective for B-Raf(V600E) than for wild-type B-Raf, and was even more selective for B-Raf(V600E) than for other kinases.

Surprisingly, in cellular assays, PLX4720 is over 100-fold (not 10-fold) more selective in inhibiting proliferation of tumor cell lines that bear B-Raf(V600E) as compared to those that bear wild-type B-Raf. Moreover, as first found by researchers at Pfizer and their academic collaborators, a specific inhibitor of MEK (Pfizer’s CI-1040) is also similarly selective for tumor cell lines bearing B-Raf(V600E). This suggests that the B-Raf-MEK-ERK pathway is critical for the proliferation of B-Raf(V600E) cells, but not for cells bearing wild-type B-Raf. [For example, tumor cells that bear wild-type B-Raf might use the PI3K-Akt pathway to upregulate pathways that control cell proliferation independent of ERK signaling, while tumor cells that bear B-Raf(V600E) cannot.]

The B-Raf-MEK-ERK pathway dependence of B-Raf(V600E) cells may in part be related to feedback inhibition of B-Raf (and other isoforms of Raf). Activated ERK can phosporylate wild-type Raf isoforms at specific inhibitory sites. This results in downregulation of signaling via the Raf-MEK-ERK pathway. However, in cells bearing B-Raf(V600E), this feedback inhibition is disabled, resulting in uncontrolled signaling.

The Plexxikon researchers (Tsai et al.) tested PLX4720 against tumor xenograft models. Oral administration of PLX4720 blocked tumor growth, and in 4 out of 9 cases caused tumor regressions, in mice with tumor xenografts bearing B-Raf(V600E). Treatment with PLX4720 was well tolerated, and showed no adverse effects. Growth of tumor xenografts bearing wild-type B-Raf was not affected by PLX4720. In mice with tumors bearing B-Raf(V600E), PLX4720 blocked B-Raf-MEK-ERK pathway signaling, as demonstrated by immunohistochemical assays.

The exquisite specificity of PLX4720/PLX4032 for B-Raf(V600E) as compared to wild-type B-Raf was made possible by Plexxikon’s structure-guided “scaffold-based drug design” technology. Other structure-guided drug design technologies, such as fragment-based lead design, as is carried out in several companies, might be used to design comparably specific drugs.

The discovery of PLX4720/PLX4032 is an example of the use of new-generation chemistry technologies (or the revival of the old, and now disused natural products chemistry approach), coupled with biology-driven drug discovery strategies, to discover promising new drugs. We have discussed this strategy in several articles on this blog. (For example, see here and here).

Despite the promising results seen in Phase I clinical trials of PLX4032, it must be emphasized that the establishment of the efficacy and safety of this compound awaits the completion of the ongoing Phase III trials. Moreover, despite the dramatic regressions and increased survival seen in the Phase I trials, all the patients apparently eventually suffered relapses. Dr. Flaherty, as discussed in our earlier blog post, sees the need for combination therapies to effectively combat metastatic melanoma. In early 2009, Dr. Flaherty and his colleague Keiran S Smalley published a mini-review on potential strategies for developing such combination therapies.

Bringing targeted therapy of metastatic melanoma into the clinic–the crucial role of translational researchers

During the week of February 22, 2010, the New York Times (NYT) ran a three-part series on a Phase I trial in 2008/2009 of a targeted therapy for metastatic melanoma, a disease that is almost always fatal within a year. The trial was led by Keith T. Flaherty, M.D. (then at the University of Pennsylvania in Philadelphia, and now at the Dana-Farber Cancer Center in Boston). The drug was PLX4032, developed by Plexxikon, which is co-developing the compound with Roche. PLX4032 is a kinase inhibitor, which specifically targets the V600E mutant of the B-Raf oncoprotein. This is the most common somatic mutation found in human melanomas. Researchers believe that B-Raf(V600E) is a “driver mutation” that is particularly critical for the malignant phenotype of human metastatic melanomas that carry the mutation. PLX4032 entered Phase III clinical trials in 2009.

The NYT series, authored by Amy Harmon, focused on the stories of several patients, and on the dogged efforts of Dr. Flaherty to help his patients and to prove the value of targeted therapy. Although the targeted kinase inhibitor imatinib (Novartis’ Gleevec/Glivec) produces complete responses in the majority of treated patients in the chronic phase of CML (chronic myelogenous leukemia) and long-lasting remissions in many of these patients, many researchers believe that this is a special case, and they cite evidence that targeted therapy, especially in solid tumors, almost never produces durable responses. But Dr. Flaherty pressed on with his quest to prove the value of targeted therapy, despite this skepticism.

A key point in the story was when the original formulation of PLX4032, at the highest dose that patients could absorb, produced neither adverse effects nor clinical responses. Because of his belief in targeted therapy, and in this particular drug, Dr. Flaherty convinced Roche to reformulate the drug to enable patients to absorb a higher dose. With the higher doses of the drug made possible by the new formulation, the researchers saw dramatic clinical responses in the great majority of patients whose tumors contained B-Raf(V600E). Responses lasted an average of nearly 9 months, a dramatic breakthrough in treatment of metastatic melanoma.

As the series ended, Dr. Flaherty was working with his colleagues and the pharmaceutical industry to find ways to enable the testing of combination therapies of targeted drugs (including PLX4032) that might result in long-lasting remissions in patients with metastatic melanoma. Meanwhile, Plexxikon and Roche have taken PLX4032 into Phase II clinical trials and now into Phase III.

The NYT series is essentially a human-interest story. I commend it to all researchers, executives, and consultants in the industry whose work does not involve contact with patients, since creating products that can help patients is what our work is all about.

Dr. Flaherty reminds me, and others who have commented on this story, of Brian J. Druker, M.D. at the Oregon Health Sciences University in Portland. It was Dr. Druker’s efforts, centered on helping patients and proving the value of targeted therapy, that was the driving force behind the development of imatinib (Novartis’ Gleevec/Glivec). Without this effort (conducted in collaboration with biochemist Nicholas B. Lydon, then at Novartis), the whole field of kinase inhibitors for targeted therapy of cancer would not have emerged. Dr. Flaherty, as well as several other oncologists, is continuing this worthy tradition.

As pointed out to me by a leading Boston-area academic researcher in a cancer-related area, the NYT series did not give credit to the academic researchers who identified the role of B-Raf in cancer, and especially the role of B-Raf(V600E) in human melanoma. (For that matter, it did not credit the Plexxicon researchers who discovered PLX4032.) She said that the series sounded as if only one person, Dr. Flaherty, was responsible for the development of PLX4032. Moreover, the development of imatinib was made possible by decades of academic research on the target of the drug, Bcr-Abl, a fusion protein formed as the result of a chromosomal translocation. Drs. Druker and Lydon thus were not solely responsible for the development of imatinib either.

The academic researcher has a point. However, some industry commentators take a contrary point of view, downplaying the role of academic researchers in the drug discovery/development process and giving most of the credit to industry.

For years, we have taken the point of view that biology-driven drug discovery and development (arguably the most successful drug discovery/development strategy in the post-genomic era) requires the contributions of both academia and industry, and that more effective collaboration between academia and industry would result in more effective drug discovery and development. (See also my 2005 letter to the editor of BusinessWeek.)

It is basic research, usually in academic laboratories, that has resulted in the very best validated targets. Basic research on a particular target typically takes years or even decades (as in the case of Bcr-Abl). Many of the breakthrough drugs that have emerged in the past 10-15 years (as well as numerous promising pipeline drugs now in clinical testing) were made possible by this research. In contrast, large-scale “target validation” testing in industry more often than not results in targets whose role in normal physiology and in disease is poorly understood. This is an important cause of clinical attrition in drug development.

Nevertheless, it is industry, not academia, which uses this basic research to create drugs. In particular, it is industry that bears the enormous economic risk of drug development, especially of late-stage clinical trials.

Translational researchers, who are involved in taking the results of academic research and/or of discovery research in industry, and translating them into therapies that benefit patients, are—or should be—a key component of the drug discovery-development process. Drs. Druker and Flaherty are two outstanding examples.

However, at least some sectors of academia (and of governmental policy-makers and the media) are suspicious of the type of closer industry-academic collaboration that is needed to produce more effective translation of basic and drug-discovery research into the clinic. An editorial in the 25 February issue of Nature notes that there has been criticism of the recent hiring of William Chin, Lilly’s senior VP for discovery and clinical research, to be the executive dean for research at Harvard Medical School. The critics charge that strong research collaborations between academia and industry will inevitably result in conflicts of interest. The Nature editorial supports institutional policies that require disclosure of links between academic researchers and industry, but deplores the views of influential critics who believe that any collaboration between academic researchers and industry “corrupts” the academic research enterprise.

In addition to Nature, some leading academic researchers say that it is time for industry and the academic medical community to fight back against the critics, rather than appeasing them with ever more restrictive conflict-of-interest policies. These researchers note that the main purpose of medical research is not to publish scientific papers, but to translate this knowledge into therapies that benefit patients. This requires effective collaboration between academia and industry. We agree.