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I was quoted in an article entitled “Bristol-Myers Squibb reaps biologics in ZymoGenetics windfall”, by freelance journalist Emma Dorey (Brighton, UK), in the November 2010 issue of Nature Biotechnology. The article focused on the acquisition of ZymoGenetics (Seattle, WA) by Bristol-Myers Squibb (BMS). To read the article, go to the Nature Biotechnology website.

Interestingly, I was also quoted in a Nature Biotechnology article on an earlier BMS acquisition–that of the monoclonal antibody (MAb) company Medarex–in September 2009. You can read our blog post that references that article, and which discusses the MAb sector in terms of technology strategy and innovation strategy, here.

The November 2010 Nature Biotechnology article discusses the acquisition in terms of the ZymoGenetics pipeline, the financial aspects of the deal, and the competitive landscape.

Most commentators believe that BMS’ main motivation for acquiring ZymoGenetics was to gain full ownership of ZymoGenetics’ pegylated interferon-lambda (Peg-IFN-λ) program for treatment of hepatitis C (HepC). The two companies had been been collaborating  to develop Peg-IFN-λ since January 2009.

HepC is a viral disease of the liver that in its chronic form can cause cirrhosis of the liver and other serious disease manifestations. The standard treatment is with a combination therapy of peginterferon-alfa-2a (Roche’s Pegasys) or peginterferon-alfa-2b (Merck’s PEG-Intron) plus ribavirin (generic). Approximately 50% of patients with chronic HepC do not respond to therapy, with patients infected with HepC virus (HCV) genotype 1 having the worst prognosis. The treatment also has significant adverse effects, ranging from flu-like symptoms to severe adverse events such as anemia, cardiovascular events and psychiatric effects such as depression and suicidal ideation. The disease therefore has a high unmet medical need.

The receptor for IFN-λ (which is designated as a type III interferon) has a more restricted cellular distribution than for type I interferons such as the interferon-alphas. The IFN-λ receptor is present on hepatocytes of the liver, so Peg-IFN-λ should be applicable to treatment of HepC. However, because of the more restricted distribution of its receptor, researchers hypothesize that Peg-IFN-λ should have fewer adverse effects than the peg-interferon-alphas.

The HepC field is very competitive. Companies with Phase III agents include Vertex, (Telaprevir, or VX-950, an oral protease Inhibitor, Phase III), and Merck (Boceprevir or SCH 5034, an oral protease inhibitor, Phase III). Vertex recently announced positive Phase III data for Telaprevir; it expects to file an IND later this year.

In addition to the collaboration with ZymoGenetics on Peg-IFN-λ, BMS had several small-molecule HepC drugs in development. None are more advanced than Phase II. Among these drugs are the protease inhibitor BMS-791325, and the RNA protease/helicase NS3 inhibitor BMS-650032. Perhaps the most interesting BMS HepC small-molecule drug is BMS-790052, an oral inhibitor of the HCV NS5A protein. NS5A has no known enzymatic function; thus BMS-790052 has a unique mechanism of action.

In in vitro studies, BMS-790052 appears to be the most potent HCV inhibitor reported so far. In published Phase I clinical results in patients with chronic HCV infection, this agent gave a 3.3-log reduction in mean viral load that was sustained over 120 hours in two patients. In the results of a Phase II clinical trial of a combination therapy of BMS-790052 with peginterferon alpha-2a and ribavirin (presented at the April 2010 meeting of the European Association for the Study of the Liver [EASL]), the three-drug combination therapy gave a significantly higher antiviral response than the standard therapy alone. The results support further development of BMS-790052 in combination with the standard therapy, and/or with other antivirals.

Other anti-HCV medications (e.g., protease and polymerase inhibitors, and the NS5A inhibitor) are intended to be administered together with the standard therapy. Peg-IFN-λ, however, is intended to replace the interferon-alpha component of the standard therapy.

The purchase of ZymoGenetics adds another promising drug to BMS’ hepatitis C portfolio, and allows it to be competitive with such rivals in the HepC market as Merck and Johnson & Johnson (Vertex’ principal partner for Telapravir).

ZymoGenetics and BMS completed and presented data from a Phase 1a study designed to evaluate the safety and tolerability of Peg-IFN-λ in healthy subjects. The data showed that Peg-IFN-λ was well-tolerated at pharmacologically active doses, supporting the decision to go forward and initiate studies in HepC patients. In November 2009, the companies presented final results from a Phase 1b study of Peg-IFN-λ as a single agent and in combination with ribavirin to assess safety and antiviral activity in patients with chronic genotype 1 HCV infection. In the study, Peg-IFN-λ demonstrated anti-viral activity at all dose levels tested in both relapsed and treatment-naïve HCV patients. A majority of patients across all treatment arms achieved a greater than 2 log reduction in HCV RNA.  Adverse effects appeared to be minor, at pharmacologically active doses below the limiting dose.

A Phase 2 study designated EMERGE is ongoing, in which Peg-IFN-λ and ribavirin are administered to treatment-naïve patients with chronic HCV infection. The EMERGE study began with a Phase 2a open-label study (which has been completed) that explored a range of doses to be tested in the second part of the study. In the second part of EMERGE, a still-ongoing Phase 2b randomized, controlled study, researchers are assessing the safety and antiviral efficacy of Peg-IFN-λ-ribovirin therapy as compared to the standard Pegasys-ribovirin therapy.

Enrollment was completed in the Phase 2b part of EMERGE on August 25, 2010. Thus the results of the Phase 2 trial will not be determined until well into 2011.

Any small-molecule HepC drugs now in the clinic that achieve FDA approval will be approved for use in combination with a Peg-IFN-alfa and ribovirin. However, according to the Nature Biotechnology article, companies are also attempting to move toward therapies that combine two small-molecule drugs and do not include a pegylated interferon. For example, Vertex and Gilead are testing combinations of protease and polymerase inhibitors in Phase 2 clinical trials. The reason for attempting to develop interferon-free HepC therapies is that pegylated interferons are expensive, require subcutaneous injection, and at least in the case of pegylated interferon-alpha products, have significant adverse effects. If these small-molecule combination therapies prove to be safe and efficacious, they could limit the commercial potential of Peg-IFN-λ. However, BMS could also develop combinations of its small-molecule drugs as an alternative. Moreover, the safety and efficacy of any combinations of small-molecule drugs for treatment of HepC remains unproven.

As also discussed in the Nature Biotechnology article, ZymoGenetics has other pipeline drugs. These especially include interleukin-21 (denenicokin) for treatment of metastatic melanoma, which now in Phase 2b development. (Natural interleukin-21 is a regulator of natural killer cells and cytotoxic T cells.) According to the Nature Biotechnology article, interleukin-21 gave impressive results in an open-label Phase 2a trial in 39 patients with stage IV melanoma. The patients had a median overall survival of 12.4 months, and the percentage of patients surviving at 12 months was 53%. Some analysts. noting that BMS purchased ZymoGenetics mainly for its Peg-IFN-λ HepC program, say that BMS is getting ZymoGenetics’ other pipeline drugs and its marketed product (Recothrom, a recombinant thrombin product, for controlling bleeding after surgery) “for free”.

As we discussed in our September 2009 blog post on the BMS acquisition of Medarex, the BMS-Medarex acquisition represents part of a larger trend, the growing emphasis on biologics in large pharmaceutical companies, which have traditionally relied on small-molecule drugs. The acquisition of ZymoGenetics is also part of BMS’ efforts to expand into biologics. Biologics are a highly successful class of drugs that have mainly been developed by biotech companies. Big Pharma companies have been working to acquire biologics (and the companies that develop them) in order to stave off the depletion of their marketed and pipeline drugs by patent expiries and by clinical failures.

Mergers and acquisitions have been the major factor in the building of biologics franchises by large pharmaceutical companies. BMS refers to its strategy for moving into biologics (and innovative small-molecule drugs) via acquisition and partnerships as its “String of Pearls”strategy.  BMS has been forming a series of acquisitions, alliances and partnerships with biopharmaceutical companies, involving both small molecules and biologics. Medarex is the largest of these “pearls”, and ZymoGenetics is the newest. According to BMS, the String of Pearls strategy has enabled BMS to expand its pipeline by nearly 40 percent. About one-third of BMS’ pipeline drugs are biologics.

Interestingly, the 2010 BMS acquisition is not the first time that a large pharmaceutical company has acquired ZymoGenetics. ZymoGenetics was founded (as Zymos) in 1981 by three University of Washington professors. In 1988, the Danish pharmaceutical company Novo Nordisk acquired the company. For the next twelve years, it functioned as the US research arm of Novo Nordisk, and helped develop several Novo products, including ZymoGenetics products mentioned in the Nature Biotechnology article that are outlicensed to Novo (e.g, the insulin product Novolin and the Factor VIIa drug NovoSeven). In late 2000, Novo Nordisk spun out the company as ZymoGenetics, which completed an initial public offering in 2002.

That brings up the issue as to what BMS should do with ZymoGenetics. BMS might, having acquired ZymoGenetics for Peg-IFN-λ and other assets such as interleukin-21, liquidate ZymoGenetics, selling the Seattle location, offering some ZymoGenetics staff jobs at other BMS locations, and laying off the rest. Or it might realize that ZymoGenetics has proven to be an important drug discovery engine, from the days in which it was a division of Novo Nordisk, and continuing on into 2010. BMS might especially want the ZymoGenetics team to keep working on its partnered programs without interruption, bringing in milestone payments and royalties. In that case, BMS might keep ZymoGenetics as an R&D-oriented division in Seattle, only eliminating redundant functions and staff, and plan to reap any new drugs that ZymoGenetics might discover and take into the clinic. The latter strategy worked for Novo Nordisk. Might it work for BMS?

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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 contact us. We also welcome your comments on this or any other article on this blog.

Olaparib

In Part 1 of this series, we began a discussion of a new, disruptive strategy for clinical trials of oncology drugs, which had been outlined in a Perspective by Drs. Johann S. de Bono and Alan Ashworth, and published in the 30 September 2010 issue of Nature.

This strategy, which these authors call the personalized medicine hypothesis-testing strategy, is aimed at testing targeted drugs that have been developed via biology-driven drug discovery. Such a strategy begins with a strong biological hypothesis that a particular altered molecular target is critical for the malignant phenotype of a particular cancer. Based on this hypothesis, drug discovery researchers develop both targeted drugs that are specific for these altered targets, and biomarkers that can be used to determine which patients have tumors that express the target, and thus are most likely to benefit from treatment with the drug.

Following preclinical studies, clinical researchers test the drug in patients whose tumors express the target, aiming for proof of mechanism and proof of concept in early clinical trials. This involves the use of rapid dose escalation and adaptive trial design. Following these early trials, the researchers go on to conduct Phase 3 clinical trials, aiming at registration. This strategy is designed to reduce clinical attrition and the time and cost of clinical trials, and to develop superior, targeted drugs that provide greater patient benefit (in terms of progression-free survival) than the typical new oncology drugs that reach the market.

In the de Bono and Ashworth article, the authors provide several examples of successful hypothesis-testing clinical trials using this strategy. In this blog post, we discuss three of these examples, one of which is a “classic” that should be familiar to most of you, another which we have discussed in previous articles on this blog, and a third example that is based on Drs. de Bono and Ashworth’s own research.

Imatinib (Novartis’ Gleevec/Glivec)

The “classic” example of the use of a personalized medicine hypothesis-testing strategy is the development of imatinib (Novartis’ Gleevec/Glivec).  This drug was originally designed as a specific inhibitor of the ABL tyrosine kinase, which is stuck in the activated conformation in the BCR-ABL fusion protein. BCR-ABL is the “driver” mutation in Philadelphia chromosome-positive chronic myeloid leukemia (CML). Imatinib was also found to be specific for two other tyrosine kinases, c-Kit and the platelet-derived growth factor receptor (PDGFR); these findings have led to the use of imatinib to treat other cancers, especially gastrointestinal stromal tumors (GIST). We discussed the role of Dr. Brian Druker (Oregon Health Sciences University in Portland) and Nicholas B. Lydon (then at Novartis) in the development of imatinib in an earlier blog post.

The 2001 published Phase 1 clinical trial of imatinib in CML led by Drs. Druker and Lydon, and clinician Charles L Sawyers, M.D. (Memorial Sloan-Kettering Cancer Center/Howard Hughes Medical Institute) is what Drs. de Bono and Ashworth called “a landmark paper” in the use of a personalized medicine hypothesis-testing strategy to demonstrate the efficacy and safety of a targeted oncology drug. The development of imatinib for CML was made possible by basic research that showed that the BCR-ABL fusion protein (which is generated as the result of the translocation that produces the Philadelphia (Ph) chromosome, the characteristic genetic abnormality of CML) alone was sufficient to cause CML, and that the tyrosine kinase activity of the ABL moiety of the protein was required for its oncogenic activity. Researchers then discovered a compound, imatinib, that was highly specific for BCR-ABL, c-kit, and PDGFR.

The Phase I clinical trial (which took place in 1999) was a dose-escalation trial of imatinib in 83 patients with chronic-phase CML in whom treatment with interferon-alpha had failed. The primary endpoint of the trial was the safety and tolerability of the drug; efficacy was a secondary endpoint. Imatinib was found to be well-tolerated, and a maximum tolerated dose was not identified in this trial. Complete hematological responses (defined by reductions in the white-cell and platelet counts) were seen in 53 of 54 patients who received 300 mg per day or more of imatinib; these responses typically occurred in the first four weeks after initiating treatment. Cytogenetic responses were defined by the percentage of blood cells in metaphase that were positive for the Ph chromosome, ranging from major responses (zero to 35% of Ph chromosome-positive cells) to minor responses (36-65% positive) to no response (over 65% positive). Of the 54 patients treated with doses of 300 mg or more, 29 had cytogentic responses, including 17 with major responses; seven of these patients had complete cytogenetic remissions (durable zero percent Ph chromosome positive).

Blood samples were taken to determine whether BCR-ABL tyrosine kinase activity had been inhibited by in vivo treatment with imatinib. The researchers observed dose-dependent inhibition of BCR-ABL tyrosine kinase activity. This constituted proof of mechanism of the drug, while the antileukemic activity of imatinib in the trial constituted proof-of-concept.

The researchers then conducted Phase 2 clinical trials, which confirmed and extended the results seen in Phase 1. The FDA approved imatinib in May 2001, less than three years after initiation of clinical trials. This rapid approval was made possible by the FDA granting imatinib a Fast Track designation and Accelerated Approval, which allowed approval of the drug based on Phase 2 trials using surrogate markers (in this case, cytogenetic responses).

As imatinib gained approval as frontline therapy for treatment of Ph chromosome-positive CML, resistance to imatinib became an important issue. Researchers found that this resistance was usually due to mutations in BCR-ABL that interfere with imatinib binding. Two companies therefore designed inhibitors that can bind to and inhibit these resistant BCR-ABL proteins and thus successfully treat imatinib-resistant CML–dasatinib (Bristol-Myers Squibb’s Sprycel) and nilotinib (Novartis’ Tasigna). This is an example of the use of reiterative translational studies to determine mechanisms of drug resistance, and the design of second-generation drugs to combat this resistance. This type of follow-up strategy was discussed in the de Bono and Ashworth article and in our previous blog post.

Only a few years ago, many industry commentators were of the opinion that the development of imatinib to treat CML was a unique case, and development of other personalized biology-driven drug discovery-based cancer medicines would not be successful. However, the examples discussed in the de Bono and Ashworth article (and elsewhere) show that that is not true.

Roche/Plexxikon’s PLX4032

The second example of successful use of the hypothesis-testing clinical trial strategy is the development of Roche/Plexxikon’s PLX4032 for metastatic melanoma. This compound is exquisitely specific for B-Raf carrying the V600E mutation B-Raf(V600E). This is the most common somatic mutation found in human melanomas, and is a “driver mutation” that is particularly critical for the malignant phenotype of human metastatic melanomas that carry the mutation.

We have discussed PLX4032 in three articles on this blog in 2010, published on March 2, March 10, and August 27.

As in the case of imatinib, researchers achieved proof-of-mechanism and proof-of-concept for PLX4032 in a dose-escalation Phase 1 trial in patients who were preselected for carriers of the B-Raf(V600E) mutation. The Phase 1 trial took place in 2008/2009. This was followed by an extension phase in which patients were given the maximum tolerated dose of the drug. Patients showed an 81% response rate (i.e, a partial or a complete response). The estimated median progression-free survival among all patients was over 7 months, as compared to less than 2 months in large numbers of advanced melanoma patients as determined by historical analysis. Oncologists had never seen such a dramatic response in treatment of metastatic melanoma.

PLX4032 is on an accelerated path to potential registration, and parallel Phase 2 and Phase 3 clinical trials are in progress in previously treated and previously untreated patients, respectively, all who have metastatic melanoma carrying the B-Raf(V600E) mutation.

Despite the dramatic regressions and increased survival seen in the Phase 1 trials, all the patients apparently eventually suffered relapses. As stated in the article on PLX4032 in the 30 September 2010 issue of Nature, researchers are therefore doing reiterative translational studies to determine the mechanisms of resistance to PLX4032 in cases of tumor regrowth after treatment with the drug. Proposed strategies include the development of combination therapies that include PLX4032 and other targeted drugs, immunotherapeutic agents, or chemotherapy. Given the promising efficacy and safety profile of PLX4032, researchers believe that the drug has the potential to enable the development of such combination therapies.

In conjunction with the early clinical trials of PLX4032, researchers developed a real-time polymerase chain reaction (PCR) assay to assess B-Raf(V600E) mutation status. The assay has the potential to be used as a companion diagnostic in treatment with PLX4032.  As stated in the 30 September article, researchers are assessing the reliability of the PCR assay In the ongoing concurrent Phase 2 and Phase 3 clinical trials of PLX4032.

A synthetic lethal therapeutic strategy using KuDOS/AstraZeneca’s olaparib

The third example of successful use of the hypothesis-testing clinical trial strategy is taken from Drs. de Bono and Ashworth’s own work. The therapeutic strategy in this example is fundamentally different from the cases of imatinib and PLX4032, both of which are exquisitely targeted drugs that inhibit specific mutated versions of oncogenes. Instead, this example involves the use of synthetic lethality in the design of an anticancer therapeutic strategy. Based on classic studies in yeast and Drosophila, synthetic lethality is defined as a situation in which mutation in either of two genes individually has no effect, but simultaneous mutation in both genes is lethal. In cancer, if one gene in a synthetically lethal pair is defective (and especially if this defect is involved in the malignant phenotype) targeting the other gene with a drug should be selectively lethal to the tumor cells but not to normal cells. If this works, it should result in a large therapeutic window for treatment with the drug.

Women with a germline mutation in one BRCA1 or BRCA2 allele have a high risk of developing breast and ovarian cancer; BRCA1 or BRCA2 carrier status in men also carries an increased risk of developing prostate cancer. Via the process of loss of heterozygosity, cells of carriers of loss-of-function mutations in BRCA1 or BRCA2 can lose the wild-type allele, resulting in cells that lack BRCA1 or BRCA2 function. The products of the two BRCA genes are both involved in the pathway for DNA repair via homologous recombination. Loss of a functional homologous recombination pathway results in the development of genomic instability that can lead to carcinogenesis. Moreover, since BRCA-negative tumor cells cannot repair their DNA via homologous recombination, they are dependent on an alternative pathway of DNA repair, which involves the enzyme Poly(ADP) ribose polymerase (PARP). Since the average cell must repair its DNA thousands of times a day, researchers hypothesized that BRCA-negative tumor cells should be uniquely vulnerable to drugs that inhibit PARP. In contrast, normal cells are able to utilize the homologous recombination pathway, and should not be affected by PARP inhibitors.

Alan Ashworth and his colleagues developed and published this synthetic lethality strategy for therapy of BRCA-negative breast cancer in 2005. They showed that cells deficient in BRCA1 or BRCA2 were about 1,000-fold more sensitive to a class of PARP inhibitors developed by AstraZeneca (AZ) subsidiary KoDOS Pharmaceuticals (Cambridge, MA) than cells with BRCA1 and BRCA2 function. Treatment of BRCA-deficient cells with the PARP inhibitors resulted in chromosomal instability and cell cycle arrest, followed by apoptosis. The efficacy and specificity of the PARP inhibitors for BRCA-deficient cells also carried over to in vivo studies in mouse models. These cell culture and animal studies constituted the generation of a strong hypothesis that this synthetic lethal therapeutic strategy would be useful in developing antitumor treatments for patients with BRCA-negative breast cancer.

In 2006 and 2007, Drs. Ashworth, de Bono, and their colleagues (including researchers from KuDOS and AZ) conducted a Phase 1, hypothesis-testing clinical trial of KuDOS/AZ’s potent, orally-active PARP inhibitor olaparib (AZD-2281; formerly known as KU-0059436). The study enrolled a total of 60 patients with a variety of types of solid tumors, including 22 who were confirmed BRCA1 or BRCA2 mutation carriers and one patient with a strong family history of BRCA-associated cancer but who declined mutation testing. The study was published in July 2009 in the New England Journal of Medicine. The trial was a dose-escalation study–the dose was increased from 10 mg daily for two of every three weeks to 600 mg twice daily. A reversible dose-limiting toxicity was seen in one of eight patients receiving 400 mg twice daily, and in two of five patients who received 400 mg twice daily. Based on these results, the researchers established 400 mg twice daily as the maximum tolerated dose. They then enrolled a new cohort of carriers of a BRCA1 or BRCA2 mutation; these patients received a dose of 200 mg twice daily.

As a Phase 1 trial, the primary objectives were to determine safety, adverse effects, the dose-limiting toxicity and maximum tolerated dose, and the pharmacokinetic and pharmacodynamic profiles. Once these were established, the aim was to test the hypothesis that patients’ BRCA1 or BRCA2 mutation-associated cancers would show an objective antitumor response to olaparib as a single agent. In terms of safety, adverse effects were generally mild. There were two patients deaths due to infectious disease that were deemed not to be drug related. There was also no difference in adverse effect profiles between known BRCA1 and BRCA2 mutation carriers and other patients.

The researchers established three types of biomarkers. The predictive biomarker was the presence of BRCA1 or BRCA2 loss-of-function mutations, as determined by standard sequencing methods in patients with a family history of BRCA-associated cancers. The pharmacodynamic biomarker was the inhibition of PARP enzymatic activity in peripheral blood mononuclear cells and in tumor biopsies taken before and after olaparib treatment, and the formation of double-strand DNA breaks in hair follicle tissue. The intermediate endpoint biomarker consisted of radiological determination of tumor shrinkage and biochemical tests for serum tumor markers.

Using the pharmacodynamic biomarker, the researchers showed that inhibition of PARP was over 90% in peripheral mononuclear cells in patients treated with 60 mg or more of olaparib twice daily. Determination of PARP activity in tumor biopsies before and after 8 days of treatment showed that drug treatment inhibited PARP in tumor tissue. Pharmacodynamic studies in samples of plucked eyebrow hair follicles showed that induction of formation of double-strand breaks occurred within 6 hours of olaparib treatment. These studies constitute proof-of-mechanism of olaparib in humans.

In studies to determine whether olaparib treatment induced antitumor responses, the researchers found that such responses only occurred in patients with confirmed BRCA1 or BRCA2 mutation carrier status, except for one patient who declined mutational testing but had a strong family history of BRCA mutation-related cancer. 23 patents who were confirmed or (in the one case) deemed to be BRCA mutation carriers were treated. Of these 23 patients, two could not be evaluated. Two of the remaining patients had tumors not typically associated with BRCA mutations, and neither received clinical benefits from drug treatment.

Of the remaining 19 patients (who had ovarian, breast, or prostate cancer), 12 exhibited clinical benefits from olaparib treatment, with either tumor responses (determined radiologically or via serum tumor markers) or stable disease for a period of four months or more. Nine BRCA carriers had a tumor response. Eight patients with advanced ovarian cancer had a partial response (determined by radiology), and six of these had a greater than 50% tumor response based on tumor marker assays. Of the three patients with advanced BRCA2 breast cancer, one had a complete remission lasting for over 60 weeks, and another had stable disease for 7 months. The other breast cancer patient, who had refused mutational testing, had a decline in metastases and an over 50% decline in serum tumor markers. The patient with BRCA2-related castration resistant prostate cancer has an over 50% reduction in PSA levels, and resolution of bone metastases. He had been participating in the study for over 58 weeks at the time of the cutoff date, and for more than 2 years since that date.

The above efficacy data constitutes proof-of-concept, and confirms the hypothesis that BRCA-associated cancers can be addressed by a synthetic lethal therapeutic strategy based on the use of the PARP inhibitor olaparib. Olaparib also has a satisfactory adverse effect profile, and lacks the toxicity typically seen with cancer chemotherapy. Since this Phase 1 clonal trial, AZ had taken olaparib into Phase 2 clinical trials in advanced BRCA-related breast and ovarian cancer. Olaparib has continued to demonstrate efficacy and a relatively mild adverse effect profile in these trials, as shown here and here, and as also discussed in a July 2010 Medscape article.

Dr. Ashworth and his colleagues noted that not all cancers in BRCA1 or BRCA2 carriers respond to olaparib. They hypothesize that different BRCA1 or BRCA2 mutations may result in different defects in homologous recombination, which may cause variations in sensitivity to PARP inhibition. Moreover, certain secondary BRCA2 mutations may restore BRCA function, which may cause resistance to PARP inhibition. They see the need to develop assays for homologous recombination proficiency, which might be used in reiterative translational studies to determine causes of resistance to olaparib.

Synthetic lethal therapy with PARP inhibitors such as olaparib may be applicable to other types of cancers that have defects in DNA repair by homologous recombination. These may include sporadic breast and ovarian cancers that acquire loss of function of BRCA1 or BRCA2 via somatic genetic or epigenetic events, and other sporadic cancers that develop loss of function (via somatic genetic or epigenetic events) of other proteins involved in the homologous recombination DNA repair pathway.

Dr. Ashworth and his colleagues have also shown that loss of function of DNA damage signaling proteins (e.g., ATM, ATR, CHK1, CHK2), and of Fanconi anemia proteins, can induce sensitivity to PARP inhibition. Loss of function in these pathways may be relatively common in other sporadic cancers. It will be essential to develop biomarkers for loss of function of these DNA repair proteins in order to design hypothesis-testing clinical trials to investigate the potential of olaparib (or other PARP inhibitors) to treat this broader class of cancers.

As show by these three examples–and the other examples discussed in the 30 September 2010 de Bono and Ashworth Perspective (see Box 5 in that article)–researchers have been using the personalized medicine hypothesis-testing strategy to develop exciting new oncology drugs to treat disease in specific classes of patients. However, except for the case of imatinib, all of the drugs are still in clinical trials and have not yet achieved registration, which is the real test of the success of this strategy. Moreover, as we discussed in the first article in this series, the personalized medicine hypothesis-testing strategy is a work in progress. For example, biomarker identification and qualification/validation, which is a critical need for further development and utilization of this new clinical trial strategy, is an early-stage area of science and technology. Nevertheless, the personalized medicine hypothesis-testing strategy for cancer drug development provides a means to extend biology-driven drug discovery into the clinic, to decrease the time and cost of clinical trials, and to develop anticancer drugs that should be superior to both conventional chemotherapy and to early-generation targeted drugs.

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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 contact us. We also welcome your comments on this or any other article on this blog.

The 30 September issue of Nature included a major emphasis on translational research in cancer. Featured articles included an editorial, a Perspective, and a research report. There was also an online “Specials” archive on translational cancer research, containing many recent research reports, all with free access to nonsubscribers.

The theme of these articles was the development of novel strategies for accelerating the translation of research on cancer biology into safe and efficacious therapies.

The Perspective, entitled “Translating cancer research into targeted therapeutics”, by British researchers Johann S. de Bono, M.D., Ph.D. and Alan Ashworth, Ph.D., outlines a novel disruptive clinical trial strategy for accelerating the translation of biology-driven oncology drug discovery into the clinic, with an early determination of proof of concept. This new strategy is designed  to ameliorate the high levels of Phase 2 and Phase 3 attrition of cancer drugs, as well as to lower the cost of clinical trials and to shorten the time from preclinical studies to the approval and marketing of oncology drugs that successfully emerge from clinical trials. It also is designed to aid in the development of therapies that provide greater patient benefit (in terms of progression-free survival) than the typical new oncology drugs that reach the market.

We have discussed clinical trial strategies of this type in two of our publications–our 2009 book-length report Approaches to Reducing Phase II Attrition (available from Cambridge Healthtech Institute, and our 2009 article published in Genetic Engineering and Biotechnology News, “Overcoming Phase II Attrition Problem” (available on our website). The de Bono and Ashworth article provides a more detailed and specific presentation of this strategy with respect to oncology drug development, and provides several examples of its successful application.

In the traditional Phase 1/Phase 2/Phase 3 format of cancer drug development, clinical studies focus on treating patient populations with advanced cancers that have not been characterized in terms of their genetics and molecular biology. The trials culminate in large, pivotal randomized Phase 3 trials that typically last several years, and are aimed at regulatory approval. In most cases, new drugs that emerge from Phase 3 trials and win approval only improve survival by a few months. Patients who participate in Phase 1 and Phase 2 clinical trials usually derive little or no benefit, and a high proportion of drugs fail in Phase 2 or Phase 3. This clinical trial format determines how well a particular drug or drug combination works for the average patient. However, that treatment might not be the best for a given individual patient.

As basic researchers have advanced the study of molecular genetic pathways of cancer, drug discovery researchers have been developing targeted therapies for cancer. These drugs–such as monoclonal antibodies (MAbs) like trastuzumab (Genentech/Roche’s Herceptin) and kinase inhibitors like imatinib (Novartis’ Gleevec/Glivec) work by modulating specific biomolecules (e.g., overexpressed or mutated oncogenic proteins) that are critical for the malignant phenotype. Population-based clinical trials of unselected patients make little or no sense in developing targeted therapies. Instead, clinical researchers need to first select groups of patients whose cancers express the biomolecule to be targeted, and preferably whose cancers are driven by that particular biomolecule. This way of thinking leads to the formulation of a new clinical trial strategy, as outlined in the Perspective.

Drs. de Bono and Ashworth call this strategy a personalized medicine (or “stratified medicine”) hypothesis-testing approach. The first step in this strategy is to develop a strong biological hypothesis that a particular altered molecular target is critical for the malignant phenotype of a particular cancer. This hypothesis is usually generated as the result of laboratory and clinical studies. Researchers need to show that blocking of the function of the altered target results in a lethal or cytostatic effect in cancer cells that express the the target, but not in normal cells that do not. It is also preferred that resistance to agents that block the target is not easily gained.

In the discovery stage of this strategy, researchers need not only to identify and optimize clinical candidate drugs that modulate the target, but also biomarkers that can be used to identify patients whose tumors express the altered target and are therefore likely to benefit from treatment. These biomarkers are called “enrichment biomarkers”, and have the potential to become predictive biomarkers. (Predictive biomarkers may also be the basis for the development of companion diagnostics). It is also important to identify pharmacodynamic biomarkers (biomarkers that can be used to determine target occupancy by the drug) and intermediate endpoint biomarkers (which can assess antitumor activity of the drug–for example, radiological assessment of tumor regression). Identification and qualification/validation of biomarkers is a work in progress, and is a critical need for further development and utilization of the personalized medicine hypothesis-testing clinical trial strategy.

Once targets and drugs that modulate them have been identified, they must be validated in animal models. The issue of the inadequacy of current mouse models of cancer–mainly xenograft models in which human cancer cell lines are transplanted into immune deficient mice–to predict drug efficacy is important both in the traditional cancer drug development strategy and in the novel strategy discussed in the de Bono and Ashworth article. We have discussed development of improved animal models for cancer drug development in an earlier blog post. de Bono and Ashworth note that there is an urgent need to develop such improved animal models. Nevertheless, as discussed in the de Bono and Ashworth article, there are examples of the successful implementation of the personalized medicine hypothesis-testing strategy of cancer drug development that have used traditional animal models in the preclinical phase.

In the personalized medicine hypothesis-testing strategy, clinical trials have the same three phases as in traditional trials. However, the trials involved stratification of patients using biomarkers, such that clinical studies are done in patients whose tumors express the target of the drug. Trial design is also more flexible and adaptive, and is contingent on obtaining key clinical data. The trials focus on determining the following as early as possible:

• Proof of mechanism: determining a dose range and dosing schedule under which the drug achieves sufficient target occupancy for long enough, using biomarker-based pharmacodynamic assays.

• Proof of concept: Determining that once sufficient target occupant is achieved, the drug exhibits antitumor activity, as determined using intermediate endpoint biomarkers.

In first-in-human clinical trials, in addition to determining safety and tolerability and evaluating pharmacokinetics and pharmacodynamics as in traditional Phase 1 trials, researchers also pursue rapid dose escalation, until proof of mechanism is achieved, using the appropriate biomarkers. Researchers then move on to proof of concept hypothesis testing, at doses and dosing schedules (ideally, the maximum tolerated dose) that are sufficient to address the target for long enough to have a biological effect. Ideally, researchers should move seamlessly from determination of proof-of-mechanism to assessment of antitumor activity, via adaptive trial design and patient selection using enrichment biomarkers.

If the above early-stage strategy results in a strong determination of proof of concept, this provides the basis for moving on to Phase 3 trials in patients selected using enrichment/predictive biomarkers, with the goal of drug registration. Such Phase 3 trials should have a higher probability of success than traditional Phase 3 trials in unselected patient populations, with less than adequate demonstration of proof of concept in Phase 2.

However, in the personalized medicine hypothesis-testing strategy, there is also the need for reiterative translational studies, between the laboratory and the clinic and back to the laboratory. Such studies should be designed as early as possible in clinical development. For example, clinical trials might allow researchers to obtain tumor samples to determine mechanisms of drug resistance. Such studies might form the basis for generating further hypotheses that are relevant to reversing drug resistance, via such means as development of combination therapies or of second-generation drugs.

The personalized medicine hypothesis-testing strategy is a work in progress. However, as we shall discuss in Part 2 of this series, there are examples of its successful implementation. And this strategy provides a means to extend biology-driven drug discovery, arguably the most successful drug discovery strategy of the past decade, into early and mid-stage clinical trials, thus increasing the probability of clinical success.

Nevertheless, it must also be emphasized that our understanding of disease biology (especially cancer biology) is limited, thus limiting our ability to successfully carry out biology-driven drug discovery in all cases. However, as our understanding of disease biology grows–in an incremental manner–as the result of basic research mainly in academic laboratories, we should be able to utilize this research to develop novel, breakthrough treatments via biology-driven drug discovery and personalized medicine hypothesis-testing clinical trials.

B-Raf

In March 2010, we published two articles on this blog relating to Roche/Plexxikon’s PLX4032 for metastatic melanoma. The first article, dated March 2, described a Phase I clinical trial of the drug, based on an article about this trial in the New York Times (NYT). The second article, dated March 10, described Plexxikon’s discovery of PLX4032, using its proprietary “scaffold-based drug design” technology platform. The latter post is among the most popular articles on this blog.

Now the results of the Phase I trial of PLX4032 has been published in the August 26, 2010 issue of the New England Journal of Medicine (NEJM). (A subscription is required to read the full article.)

As we discussed in our previous articles, PLX4032 is a B-Raf (called “BRAF” in the NEJM paper and in some other publications) kinase inhibitor that is exquisitely specific for B-Raf carrying the V600E mutation. B-Raf(V600E) 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. B-Raf(V600E) is constitutively activated, and melanomas carrying this mutation can proliferate independently of growth factor signaling, resulting in the runaway proliferation characteristic of the malignant phenotype.

The clinical trial described in the NEJM article was carried out by researchers at Plexxikon and Roche, in collaboration with academic researchers at five institutions in the United States and Australia. The trial was led by Keith T. Flaherty, M.D. (then at the University of Pennsylvania in Philadelphia, and now at the Massachusetts General Hospital Cancer Center [where he is Director of Developmental Therapeutics] and the Dana-Farber Cancer Institute in Boston) and Paul B. Chapman, MD (Memorial Sloan-Kettering Cancer Center).

As discussed in the NEJM article, the researchers conducted a multicenter Phase I dose-escalation trial of PLX4032 (which is orally available), followed by an extension phase in which patients were given the maximum dose that could be administered without adverse effects (960 mg twice daily). (The latter dose is the recommended Phase II dose.) A total of 55 patients (49 of whom had melanoma) were enrolled in the initial, dose-escalation portion of the trial. 32 additional patients, all of whom had metastatic melanoma with the B-Raf(V600E) mutation, were enrolled in the extension phase. Patients were given the drug twice a day until they had disease progression.

In the dose-escalation phase, among the 16 patients with melanoma carrying the B-Raf(V600E) mutation and who were receiving 240 mg or more of PLX4032 twice daily, 10 had a partial response (i.e., tumor shrinkage of at least 30%) and 1 had a complete response. Among the 32 patients in the extension cohort, 24 had a partial response and 2 had a complete response. The latter figure represents an 81% response rate. The estimated median progression-free survival among all patients was over 7 months.

Dose-limiting adverse effects included rash, fatigue, and joint pain.

The published results of this Phase I trial elicited great enthusiasm in the popular press and in such industry media as Fierce Biotech and BioWorld Online, and by oncologists who were interviewed for these articles. The oncologists said that they had never seen such a dramatic response in treatment of metastatic melanoma.

Because PLX4032 is targeted to a specific oncogenic mutation, Plexxikon and several industry commentators refer to the use of the drug as an example of personalized medicine. In parallel with development of PLX4032, Plexxikon and Roche Molecular Systems are developing a DNA-based companion diagnostic to identify patients whose tumors carry the B-Raf(V600E) mutation.

PLX4032 is on an accelerated path to potential registration. Parallel Phase II and Phase III clinical trials are in progress in previously treated and previously untreated patients, respectively, all who have metastatic melanoma carrying the B-Raf(V600E) mutation.

Meanwhile, the results of a Phase III trial (in 676 patients with advanced melanoma) of Medarex/Bristol-Myers Squibb’s (BMS’s) ipilimumab were published in the August 19, 2010 issue of the NEJM.  Ipilimumab, unlike the targeted therapeutic PLX4032, is an immunomodulator that blocks cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) to potentate an antitumor T-cell response. Ipilimumab is a monoclonal antibody, unlike PLX4032 which is a small-molecule compound. In this NEJM article, the researchers reported that ipilimumab–given with or without the gp100 peptide vaccine–showed a median overall survival of 10 months, as compared to 6.4 months in patients receiving gp100 alone. Ipilimumab treatment also gave improved one-year survival compared with gp100 alone–46% versus 25%. Two-year survival was 24% in the ipilimumab group and 14 percent in the gp100 group. BMS has filed a Biologics License Application (BLA) for ipilimumab, and earlier this month (August 2010) received fast-track status from the FDA for the drug.

Ipilimumab treatment is associated with autoimmune toxicities (especially enterocolitis), which can be severe. These are usually reversible by treatment with high-dose steroids.

Decision Resources published our report on development of immunomodulators in treatment of cancer in 2007. This report includes a discussion of ipilimumab, and provides further information on its mechanism of action, adverse effects, etc., as well as on other immunomodualtors for treatment of cancer, some of which are now on the market.

We believe that it is important to pursue development of both targeted therapies and of immunomodulators for metastatic melanoma. This may provide oncologists a range of therapeutics (and of combinations of therapeutics) to treat this disease, which now has very few treatment options and a very poor prognosis.

The results with both PLX4032 and ipilimumab provide hope for better treatment of at least some classes of metastatic melanoma in the near future. However, as discussed in our March 2010 articles, even in the case of PLX4032 treatment of melanoma carrying the B-Raf(V600E) mutation, it will most likely be necessary to develop combination therapies in order to achieve long-lasting remissions or cures.

On December 31, 2009, we posted an article on this blog about Agios Pharmaceuticals (Cambridge, MA). Agios is a private research-stage biotech company that is developing a pipeline of oncology drugs based on targeting metabolic pathways in cancer cells. In our article, we focused on Agios’ research on mutations in the metabolic enzyme cytosolic isocitrate dehydrogenase (IDH1) as a causative factor in gliomas and glioblastomas. We also mentioned Agios’ research on pyruvate kinase M2 (PKM2) and aerobic glycolysis in cancer.

On April 15, 2010, it was announced that Agios and Celgene Corporation (Summit, NJ), a public biotechnology company with marketed products, had formed a strategic collaboration in the area of cancer metabolism.

Celgene markets Thalomid (thalidomide), which is approved by the FDA for treatment of multiple myeloma (MM). Thalidomide was notorious for causing birth defects in the late 1950s and early 1960s. However, beginning in the late 1990s, this drug has undergone a rehabilitation, provided that proper precautions are maintained to prevent its use in pregnant women and women who may become pregnant. Celgene has also been developing a class of thalidomide-derivative immunomodulatory drugs (IMiDs), which are designed to have greater efficacy against cancer and lesser toxicity than thalidomide. Of these drugs, Revlimid (lenalidomide) is approved by the FDA for treatment of MM and myelodysplastic syndromes (MDS) (life-threatening diseases of the bone marrow in which abnormally functioning immature hematopoietic cells are made; MDS can progress to acute myeloid leukemia in a substantial percentage of patients.) Celgene is researching additional indications for lenalidomide, and is also developing other IMiDs for various indications in cancer and inflammatory and neurodegenerative diseases.

Celgene’s Vidaza (azacitidine), a nucleoside metabolic inhibitor, is also indicated for the treatment of MDS. Celgene acquired Vidaza via its 2007 acquisition of Pharmion (Boulder, CO), which had developed the drug. Vidaza is an inhibitor of DNA methyltransferases (DNMT), which are enzymes that methylate DNA at specific sites and are important in epigenetic regulation. It was the first approved drug that works via an epigenetic mechanism. (Epigenetics is the study of heritable changes in gene function that do not involve changes in the nucleotide sequence of DNA. Major epigenetic processes include DNA methylation, modification of histones in chromatin, and RNA interference.)

Since Vidaza’s approval in 2004, two histone deacetylase (HDAC) inhibitors, which also modulate epigenetic regulation, have been approved. In late 2009, Celgene acquired the HDAC inhibitor romidepsin (Istodax) [approved in 2009 for the treatment of cutaneous T-cell lymphoma (CTCL)], via its acquisition of Gloucester Pharmaceuticals (Cambridge MA).

Celgene is also developing several other anti-inflammatory drugs and kinase inhibitors.

The goal of the Agios/Celgene collaboration is to discover, develop, and commercialize novel oncology therapeutics based on Agios’ innovative cancer metabolism platform. Celgene sees the potential for early drug development opportunities in Agios’ IDH1 and PKM2 programs, as well as future opportunities based on new targets expected from Agios research programs. Celgene also sees opportunities to harness Agios’ R&D to expand its own pipeline in cancer and other diseases.

Under the terms of the agreement, Agios will receive a $130 million upfront payment, including equity. In return, Celgene will receives an initial period during which it will have the exclusive option to develop any drugs resulting from the Agios cancer metabolism platform. Celgene may also extend this exclusivity period through additional funding. Agios will lead discovery and early development for all cancer metabolism programs. During the period of exclusivity, Celgene will have an exclusive option to license any clinical candidates at the end of Phase I, and will lead and fund global development and commercialization of licensed programs. On each program, Agios may receive up to $120 million in milestones as well as royalties, and may also participate in the development and commercialization of certain products in the United States.

The Celgene collaboration continues Agios’ record of success in fundraising, and in gaining the recognition of the scientific and corporate communities. Despite the generally unfavorable financial environment for young biotech companies, Agios has raised, through alliances and investments, over $163 million in less than two years. This is despite the fact that the company has not one drug in the clinic. Agios expects to have a lead compound in the clinic some time in 2010, however. As is always the case, the validation of Agios’ innovative biology-driven platform awaits the results of human clinical trials and the attainment of regulatory approval.