Biopharmconsortium Blog

Lumacaftor (Vertex’ VX-809)

I was quoted in an article in the March 11, 2013 issue of Elsevier Business Intelligence’s The Pink Sheet by senior writer Joseph Haas. The article is entitled “Cystic Fibrosis Market Snapshot: Disease-Modifying Drugs Elusive 24 Years After Discovery Of Root Cause”. A subscription is required to view the full text of this article.

The article focused on the newly-approved disease modifying drug ivacaftor (Vertex’ Kalydeco), as well as programs in drug discovery and development of disease-modifying drugs for cystic fibrosis (CF) at Vertex, PTC Therapeutics, Proteostasis Therapeutics, Pfizer, and Genzyme. It also discussed pipeline products aimed at treating or preventing life-threatening infections in CF patients at such companies as KaloBios, Insmed, and Savara.

Mr. Haas interviewed me for this article. Most of the content of our interview is available in our February 15, 2013 article on the Biopharmconsortium Blog. One company whose R&D program we did not cover in that article is Proteostasis. Proteostasis’ CF program, which is being carried out in collaboration with the Scripps Research Institute, is aimed at discovery and development of compounds that promote CFTR ΔF508 folding and trafficking. This program is in the research and lead optimization stage. We discussed R&D programs at other companies (Vertex, Pfizer) that are also aimed at correction of improper CFTR ΔF508 folding and trafficking in our February 15, 2013 article.

KaloBios’ KB001-A, a bacterial virulence factor-targeting agent

Among the agents aimed at ameliorating life-threatening infections in CF patients that were discussed in the Pink Sheet article is KB001-A, a monoclonal antibody (MAb) agent being developed by KaloBios (South San Francisco, CA). KB001-A is now in Phase 2 development for prevention of Pseudomonas aerguinosa infections in the lungs of CF patients. KB001-A targets an extracellular component of the bacterium’s type III secretion system. This system enables the bacteria to kill immune cells by injection of protein toxins into these cells.

The type III secretion system is an example of a virulence factor. Virulence factors are not expressed by a strain of pathogenic bacteria in vitro, but are expressed only when the bacteria infect a host. Once expressed, they enable the bacteria to colonize the host and cause disease.

In our June 11, 2012 article on this blog, we discussed an antibacterial drug discovery strategy aimed at targeting two related physiological systems that are important in the ability of pathogenic bacteria to cause disease, but are not essential for bacterial proliferation or survival. These systems are virulence factors and quorum sensing. At least by hypothesis, agents that disrupt these systems will prevent pathogenic bacteria from causing disease without selecting for resistant strains of the bacteria. This will give such agents an advantage over conventional antibiotics, which notoriously generate resistant strains when used to treat infections. According to the Pink Sheet article, KaloBios believes that P. aerguinosa bacteria will not develop resistance to KB001-A, which is in accord with this hypothesis.

Another issue with anti-infectives used to treat CF that is discussed in the Pink Sheet article is the definition of a “disease-modifying” agent for CF. We define disease-modifying agents as drugs that ameliorate or cure a disease by targeting the root cause of that disease. However, KaloBios considers KB001-A to be a disease-modifying agent. That is because the company believes that most CF patients die of the effects of P. aerguinosa infection, which causes deterioration of the patients’s lungs. Thus an effective anti-P. aerguinosa agent may produce dramatic increases in patients’ lifespans.

Perhaps the real issue is that one should not classify CF drugs as “disease-modifying” agent and agents that merely treat “symptoms” (as is done in the Pink Sheet article) but should define infections of CF patients as “complications” of the disease. Thus anti-infectives such as KB001-A may effectively treat a major life-threatening complication of CF, without modifying the underlying disease. Such an agent would result in increased lifespans (and improved quality of life) for CF patients, without affecting their underlying disease. As KaloBios asserts, anti-infective agents like KB001-A would be complementary to such disease-modifying agents as ivacaftor.

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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 an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Ivacaftor

In our January 24, 2013 article on this blog, we discussed the cases of two genetic diseases, sickle cell disease (SCD) and cystic fibrosis (CF). In both cases, the genetic cause of the disease was identified decades ago. However, no disease-modifying drugs for SCD have yet been developed.

In the case of CF, small-molecule disease-modifying drugs have only recently entered the pipeline. In one case, such a drug–ivacaftor (Vertex’ Kalydeco), was approved both in the U.S. and in Europe in 2012.

In this article, we discuss the development of small-molecule drugs for CF.

Cystic fibrosis

As we discussed in our earlier article, CF causes a number of symptoms, which affect the skin, the lungs and sinuses, and the digestive, endocrine, and reproductive systems. Notably, people with CF accumulate thick, sticky mucus in the lungs, resulting in clogging of the airways due to mucus build-up. This leads to inflammation and bacterial infections. Ultimately, lung transplantation is often necessary as the disease worsens. With proper management, patients can live into their late 30s or 40s.

The affected gene in CF and the most common mutation that causes the disease (called ΔF508 or F508del) were identified by Francis S Collins, M.D., Ph.D. (then at the Howard Hughes Medical Institute and Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI) and his colleagues in 1989. (Dr. Collins was subsequently the leader of the publicly-funded Human Genome Project and is now the Director of the National Institutes of Health, Bethesda, MD.)

The gene that is affected in cystic fibrosis encodes a protein known as the cystic fibrosis transmembrane conductance regulator (CFTR).  CFTR regulates the movement of chloride and sodium ions across epithelial membranes, including the epithelia of lung alveoli. CF is an autosomal recessive disease, which is most common in Caucasians; one in 2000–3000 newborns in the European Union is found to be affected by CF. ΔF508 is a deletion of three nucleotides that causes the loss of the amino acid phenylalanine at position 508 of the CFTR protein. The ΔF508 mutation accounts for approximately two-thirds of CF cases worldwide and 90% of cases in the United States. However, there are over 1500 other mutations that can cause CF.

CFTR is an ion channel–specifically a chloride channel.  Ion channels constitute an important class of drug targets, which are targeted by numerous currently marketed drugs, e.g., calcium channel blockers such as amlodipine (Pfizer’s Norvasc; generics) and diltiazem (Valeant’s Cardizem; generics). These compounds were mainly developed empirically by traditional pharmacology before knowing anything about the molecular nature of their targets.

However, discovery of novel ion channel modulators via modern molecular methods has proven to be challenging, mainly because of the difficulty in developing assays suitable for drug screening. In addition, development of suitable assays for assaying chloride channel function has lagged behind the development of assays for the function of cation channels (e.g., sodium and calcium channels).

Moreover the most common CFTR mutation that causes CF, ΔF508, results in defective cellular processing, and the mutant CTFR protein is retained in the endoplasmic reticulum. In the case of some other mutant forms of CTFR (accounting for a small percentage of CF patients), the mutant proteins reach the cell membrane, but are ineffective in chloride-channel function.

Vertex’ program for the development of small molecule CF drugs

Efforts aimed at the discovery of small-molecule drugs for CF began in 1998, when the nonprofit Cystic Fibrosis Foundation (CFF) established its Therapeutics Development Program. This included a drug discovery unit, through which CFF would support both academic and industrial research. An early recipient of CFF funding via this program was a small biotech company, Aurora Biosciences (San Diego, CA).  Aurora had developed technology for ultra-high-throughput screening in cellular assays, which they were applying to the discovery of small-molecule drugs for CF. In 2001, Vertex Pharmaceuticals (Cambridge, MA) acquired Aurora. Vertex then incorporated Aurora’s technology into its drug discovery programs, including its CF program. Vertex’ CF program received continuing support from CFF.

Vertex researchers screened thousands of drug-like and lead-like synthetic compounds in recombinant mouse cells expressing mutant human CFTR. Positive hits that met criteria for developability were further tested in a rat epithelial cell line that expressed the mutant CFTR. Compounds selected for further study were also tested for rescue of CFTR activity in cultured primary human lung airway epithelial cells from CF patients, which expressed the same mutant CFTRs studied in the recombinant cell assays. Performing the latter studies required isolating the epithelial cells from lung tissue of CF patients. The thick mucus found in CF lungs made this isolation very challenging. According to Vertex researcher and project head Fred Van Goor, researchers had to use tweezers to extract the mucus, in order to isolate the cells. It reportedly took all of 2003 to develop cellular assays (both in primary and recombinant cells) to conduct the drug discovery studies.

Vertex’ high-throughput screening studies resulted in the identifications of two types of lead compounds:

• CFTR potentiators, which potentiate the chloride channel activity of mutant CFTR molecules at the cell surface;
• CFTR correctors, which partially correct the folding and/or trafficking defect of such mutant CFTRs as ΔF508, thus facilitating exit from the endoplasmic reticulum and deposition of a portion of the mutant CFTR in the cell membrane.

Vertex’ ivacaftor, a CFTR potentiator

The Vertex screening studies discussed in the previous section, published in 2006, resulted in clinical candidates in both the potentiator and corrector classes. The company pursued development of one potentiator compound, ivacaftor (formerly known as VX-770) (Vertex’ Kalydeco). Ivacaftor is indicated only in patients with the G551D (Gly551Asp) mutation in CFTR, which only accounts for around 4% of CF patients.

Ivacaftor was discovered via high-throughput screening as described in the previous section, followed by lead optimization. The compound increased chloride channel function both in recombinant cells carrying mutant CFTR, and in cultured primary human lung airway epithelial cells from CF patients. Ivacaftor was found to be efficacious in opening both CFTR G551D and CFTR ΔF508 present in the cell membranes of recombinant cells. However, because of the retention of  CFTR ΔF508 in the endoplasmic reticulum in human lung airway epithelial cells, this compound is not efficacious in treating CF patients carrying this mutation. The lack of efficacy in patients homozygous for CFTR ΔF508 was confirmed in a subsequent clinical trial.

On February 23, 2011, the CFF and Vertex announced that a Phase 3 trial of ivacaftor (then called VX-770) showed marked improvement in lung function in CF patients carrying the CFTR G551D mutation. Treated patients also had significant weight gain, showed reduced sweat chloride (a CF biomarker), and were less likely to have a pulmonary exacerbation. The results of this Phase 3 trial were published in the New England Journal of Medicine. Also in 2011, Vertex submitted a New Drug Application (NDA) for ivacaftor.  In January 2012, the FDA approved ivacaftor for treatment of CF patients carrying the CFTR G551D mutation. In July 2012, Vertex received European approval for this drug.

Vertex’ lumacaftor (VX-809) and VX-661, CFTR correctors

Vertex is currently developing the CFTR corrector lumacaftor (VX-809). The company has completed Phase 2 studies of a combination of ivacaftor and lumacaftor/VX-809 in CF patients who are homozygous for the CFTR ΔF508 mutation. It is now planning pivotal phase 3 trials of the combination therapy in this patient population. The rationale for the combination treatment is that VX-809 potentates the deposition of CFTR ΔF508 in the cell membrane, and invacaftor potentiates the function of cell-surface CFTR ΔF508.

Vertex is also conducting Phase 2 trials of another CTFR corrector, VX-661, alone and in combination with ivacaftor/VX-770 in CF patients homozygous for CFTR ΔF508.

The Cystic Fibrosis Foundation’s collaboration with Pfizer

The CFF has also been collaborating with Pfizer to discover drugs to treat patients carrying the the CFTR ΔF508 mutation. This collaboration began after the 2010 acquisition by Pfizer of FoldRX (Cambridge, MA). In November 2012, the CFF and Pfizer expanded their collaboration.

The Pfizer/CFF collaboration builds on FoldRx’s cystic fibrosis research program in collaboration with the CFF, which started in 2007. FoldRX (now a wholly-owned subsidiary of Pfizer) specializes in discovering and developing drugs to treat diseases of protein misfolding. The correction of protein misfolding clearly applies to CFTR ΔF508 protein.

Under the expanded six-year CFF/Pfizer collaboration, the CFF will invest up to $58 million to support and accelerate the discovery and development of disease-modifying therapies for CFTR ΔF508 CF. The goal of the collaboration is to advance one or more drug candidates into the clinic by the end of the six-year period. The CFF will provide scientific as well as financial support to help advance this discovery program.

Ataluren, for treatment of patients with CFTR nonsense mutations

Ataluren (formerly known as PTC124), is being developed by PTC Therapeutics for various genetic diseases caused by nonsense mutations in critical genes. The drug is currently being investigated for use in patients with nonsense mutation Duchenne/Becker muscular dystrophy (DBMD) and cystic fibrosis (CF). PTC Therapeutics’ efforts in CF are supported by a grant from the CFF.

Ribosomes normally translate messenger RNAs (mRNAs) into protein until arriving at a normal stop codon in the mRNA, at which point the ribosome stops translation, resulting in a functional protein. Nonsense mutations, however, create a premature stop signal in the mRNA coding sequence. This causes the ribosome to stop translation before a functioning protein is generated, creating a truncated, nonfunctional protein. This can result in disease.

Ataluren is designed to allow the ribosome to ignore the premature stop signal and continue translation of the mRNA, resulting in formation of a functioning protein. Ataluren does not cause the ribosome to read through the normal stop signal.

The results of clinical trials of ataluren in pediatric (Phase 2a) and adult (Phase 2) patients with nonsense-mutation CF showed that the drug resulted in production of functional CFTR protein and statistically significant improvements in CFTR chloride channel function. Ataluren treatment was also associated with significant reductions in cough frequency and trends toward improvement in pulmonary function tests.

Conclusions

As we discussed in our January 24, 2013 article on this blog, the 1989 identification of the genetic cause of CF did not immediately lead to the development of disease-modifying drugs. Bottlenecks in the pathway from genetic research to small-molecule drugs included understanding the different ways (e.g., deficiencies in chloride channel function, deficiencies in protein processing, blockages in protein translation due to nonsense mutations) in which the many mutations that can cause CF act, and the need to develop effective assays for use in drug discovery.

The 2012 approval of the CFTR potentiator ivacaftor (Vertex’ Kalydeco) in the U.S. and Europe represents a real milestone in CF drug development. Vertex and the CFF should be congratulated on their breakthrough CF R&D program, which required the willingness to pursue a long pathway to development.

Other compounds that target CFTR are in Phase 2 development. All indications suggest that treatment for CF will represent a case of “personalized medicine”, as befits a disease that is caused by multiple mutations that act at different levels of protein synthesis, processing, and function.

As is typical for personalized medicines that target rare diseases, Kalydeco is expensive. The drug reportedly costs upwards of $294,000 for a year’s supply. Vertex says that it will supply Kalydeco free to U.S. patients with no insurance and a household income of under $150,000.

With the interest of pharmaceutical and biotechnology companies in developing targeted therapies and therapies for rare diseases, the story of the development of small-molecule drugs for CF represents an important case study in drug discovery and development in the 2010s. According to the FDA, the emphasis on targeted drugs and rare diseases has also resulted in the the recent increase in FDA drug approvals; the agency approved 39 new drugs in 2012, which represents a 16-year high.
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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 an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

NBD1 of human CFTR. Source: PDBbot http://bit.ly/11UmpkS

A major objective of research in genomics is to identify mutations that cause genetic diseases. However, doing so does not necessarily directly enable researchers to discover and develop drugs to treat these diseases.

Two examples of genetic diseases whose causes were identified decades ago, without directly enabling the development of any disease-modifying drug, are sickle cell disease (SCD) (also known as sickle cell anemia) and cystic fibrosis (CF).

Sickle cell disease

The causative mutation of SCD was identified by protein researchers, decades before the era of genomics. Vernon M. Ingram, Ph.D. showed in 1957 that a glutamic acid to valine mutation at position 6 of the β-chain of hemoglobin was the sole abnormality in SCD. For this discovery, Dr. Ingram has been called The Father of Molecular Medicine. Dr. Ingram’s work was made possible by a 1949 study by Linus Pauling and his colleagues, which showed that SCD hemoglobin had a different electrophoretic mobility than normal hemoglobin. Thus the sickle cell trait was likely to be due to a mutation in the β-hemoglobin gene that changed its amino acid composition, as confirmed by Dr. Ingram.

Yet to this day, although SCD (which occurs in individuals who are homozygous for the sickle-cell mutation) can be managed by various treatments (such as hydroxyurea and blood transfusions and bone marrow transplants) that can result in survival into one’s fifties, there is no mechanism-based therapy for this disease. Thus the identification of the causative mutation of SCD has not led to any treatments.

The reason why discovery and development of drugs for SCD has been so very difficult is that the mutation that causes this disease affects an intracellular protein, hemoglobin, which is neither a receptor nor an enzyme. Unlike secreted proteins such as insulin, it is not possible to develop protein drugs to replace missing or defective hemoglobin. It is also not possible to replace the missing function of normal hemoglobin by treatment with a small molecule drug.

Diseases such as SCD–in which the function of an essential intracellular protein is defective or missing–have often been cited as candidates for gene therapy.

However, as we discussed in our October 11, 2012 and our November 8, 2012 Biopharmconsortium Blog articles, it is only this past fall that the first gene therapy was approved for marketing in a regulated market. As we discussed in the first of these articles, gene therapy has a history going back to at least the early 1970s. However, gene therapy has displayed the characteristics of a premature technology. Several notable failures, including some that caused the deaths of patients, put a severe damper on the gene therapy field. Only recently–between around 2003 and 2012–have researchers been developing more advanced gene therapy technologies and conducting clinical studies, with some success. Entrepreneurs have also been building gene therapy specialty companies to commercialize this research.

As also we discussed in our October 11, 2012 article, among the many companies that are developing gene therapies, bluebird bio (Cambridge, MA) has been singled our for special attention lately. Among the diseases being targeted by bluebird bio are SCD, and beta-thalassemias, which are also genetic diseases that affect hemoglobin. bluebird bio is in Phase 1/2 trials for its beta-thalassemia therapy, and in Phase 1 for its SCD program.

Cystic fibrosis

CF causes a number of symptoms, which affect the skin, the lungs and sinuses, and the digestive, endocrine, and reproductive systems. Notably, people with CF accumulate thick, sticky mucus in the lungs, resulting in clogging of the airways due to mucus build-up. This leads to inflammation and bacterial infections. Ultimately, lung transplantation is often necessary as the disease worsens. With proper management, patients can live into their late 30s or 40s.

The affected gene in CF and the most common mutation that causes the disease (called ΔF508 or F508del) were identified by Francis S Collins, M.D., Ph.D. (then at the Howard Hughes Medical Institute and Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI) and his colleagues in 1989. Dr. Collins was subsequently the leader of the publicly-funded Human Genome Project and is now the Director of the U.S. National Institutes of Health, Bethesda, MD.

The gene that is affected in cystic fibrosis encodes a protein known as the cystic fibrosis transmembrane conductance regulator (CFTR).  CFTR regulates the movement of chloride and sodium ions across epithelial membranes, including the epithelia of lung alveoli. CF is an autosomal recessive disease, which is most common in Caucasians; one in 2000–3000 newborns in the European Union is found to be affected by CF. ΔF508 is a deletion of three nucleotides that causes the loss of the amino acid phenylalanine at position 508 of the CFTR protein. The ΔF508 mutation accounts for approximately two-thirds of CF cases worldwide and 90% of cases in the United States. However, there are over 1500 other mutations that can cause CF.

In the case of CF, the affected protein, CFTR, is an ion channel–specifically a chloride channel.

Ion channels constitute an important class of drug targets, which are targeted by numerous currently marketed drugs, e.g., calcium channel blockers such as amlodipine (Pfizer’s Norvasc; generics) and diltiazem (Valeant’s Cardizem; generics). These compounds were mainly developed empirically by traditional pharmacology before knowing anything about the molecular nature of their targets. However, discovery of novel ion channel modulators via modern molecular methods has proven to be challenging, mainly because of the difficulty in developing assays suitable for drug screening. In addition, development of suitable assays for assaying chloride channel function has lagged behind the development of assays for the function of cation channels (e.g., sodium and calcium channels).

Moreover the most common CFTR mutation that causes CF, ΔF508, results in defective cellular processing, and the mutant CTFR protein is retained in the endoplasmic reticulum. In the case of some other mutant forms of CTFR (accounting for perhaps 5% of CF patients), the mutant proteins reach the cell membrane, but are ineffective in chloride-channel function.

Given these difficulties, researchers first attempted to develop gene therapies for CF. Genzyme (a Sanofi company since 2011) has been a leader in developing gene therapy for CF, and has been conducting research in this area since the 1990s. However, as with most gene therapies, development of treatments capable of reaching the market has been elusive.

Genzyme is still researching gene therapies for CF, as are others. An academic group in the U.K., known as the U.K. Cystic Fibrosis Gene Therapy Consortium is working to develop CF gene therapies, using Genzyme’s nonviral cationic lipid vector GL67 (Genzyme lipid 67) as the delivery vehicle. GL67 is the current “gold-standard” for in vivo lung gene transfer. Recently, the Consortium received funding from the U.K. Medical Research Council and National Institute of Health Research to continue its Phase 2B trial of its CF gene therapy product,GL67A/pGM169. This is a combination of GL67 and plasmid DNA expressing CFTR (pGM169).

Very recently, R&D on disease-modifying small-molecule drugs for CF has begun to bear fruit. In January 2012, the FDA approved the first such drug, ivacaftor (Vertex’ Kalydeco.) In July 2012, Vertex received European approval for this drug. Ivacaftor only works in patients with the G551D  (Gly551Asp) mutation in CFTR, which only accounts for around 4% of CF patients. Vertex and other companies–including Genzyme–are working on development of other small-molecule disease-modifying drugs with the potential to treat greater numbers of CF patients.

We shall discuss the new wave of disease-modifying CF drugs, including ivacaftor, in a later post on this blog.

Conclusions

SCD and CF are two examples of cases in which the identification of the genetic or molecular cause of a disease did not directly lead to new treatments. In the case of SCD, even though over 55 years have elapsed since the identification of the genetic cause of the disease, no therapy had yet emerged from this discovery. In the case of CF, it took over two decades from the identification of the molecular cause of the disease to the approval of the first disease-modifying drug.

Many other cases in which molecular targets involved in disease have been identified also lack disease-modifying treatments because the targets are “undruggable”. This especially applies to protein-protein interactions (PPIs). However, PPIs have assumed increasing strategic importance in drug discovery and development in recent years, and researchers and companies have been developing new technologies and strategies to discover  developable drugs that address PPIs.

Back in the early 2000s, researchers and commentators hailed the sequencing of the human genome as heralding a new era in drug discovery and development. However, the “industrialized biology” approach that grew out of the genomics of that era gave very few successes in terms of drug development. Now–a decade later–we have next-generation sequencing and  are approaching the “$1000 genome.” Once again, at least some commentators are expecting immediate breakthroughs in therapeutic development to come out of these breakthroughs in sequencing technology. Others, such as CFTR gene discoverer Francis Collins, believe that we can “speed the development of genetic advances into treatments” by more rapidly weeding out “what turn out to be..nonviable compounds.”

However, in the case of CF there were barriers to drug discovery, such as limited understanding of disease biology and difficulties in assay development, that were the true causes of lack of progress in developing disease-modifying genes. Moreover, once they had good assays, researchers needed to come up with effective strategies to develop small-molecule drugs for CF. In the case of SCD, because of the nature of the target, only gene therapy–with its manifold difficulties–had any hope of addressing the disease. In the case of PPIs, there was the need to discover new breakthrough strategies to address these “undruggable” targets.

Thus, despite breakthroughs in sequencing technologies, determining of disease-related sequences is likely to only be the first step in effective discovery of disease-modifying drugs. And there may continue to be a considerable time lag between sequence determination and drug development.

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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 an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Neurofibrillary tangle.

In August and September of 2012, we published three articles on Alzheimer’s disease on the Biopharmconsortium Blog:

• New genetics study supports the amyloid hypothesis of Alzheimer’s disease–but the drugs still don’t work! (August 19, 2012.)
• Here we go again–Lilly’s Alzheimer’s drug solanezumab fails to show efficacy in Phase 3, but company is “encouraged” by secondary analysis. (August 28, 2012.)
• Alzheimer’s disease–where do we go from here? (September 20, 2012.)

Subsequent to the publication of our articles–on 21 November, 2012–the Wellcome Trust announced the identification of a novel pathway involved in the pathogenesis of Alzheimer’s disease (AD). This research was led by Professor Simon Lovestone and Dr Richard Killick (Kings College, London U.K.), and was published in the online edition of Molecular Psychiatry on 20 November 2012. The Wellcome Trust helped to fund the research.

As we have discussed in earlier articles on this blog, the dominant paradigm among AD researchers and drug developers is that the disease is caused by aberrant metabolism of amyloid-β (Aβ) peptide, resulting in accumulation of neurotoxic Aβ plaques. This paradigm is known as the “amyloid hypothesis”. AD is also associated with neurofibrillary tangles (NFTs) which are intracellular aggregates of hyperphosphorylated tau protein. In contrast to the amyloid hypothesis, some AD researchers have postulated that NFT formation is the true cause of AD. The new research links amyloid toxicity to the formation of NFTs, and identifies potential new drug targets.

The new study is based on the discovery of the role of clusterin–an extracellular chaperone protein–in sporadic (i.e., late-onset, non-familial) AD. The gene for clusterin, CLU, has been identified as a genetic risk factor for sporadic AD via a genome-wide association study published in 2009. Clusterin protein levels are also increased in the brains of transgenic mouse models of AD that express mutant forms of amyloid precursor protein (APP), as well as in the serum of humans with early stage AD.

The researchers first studied the relationship between Aβ and clusterin in mouse neuronal cells in culture. Aβ rapidly increases intracellular concentrations of clusterin in these cells. Aβ-induced increases in clusterin drives transcription of a set of genes that are involved in the induction of tau phosphorylation and of Aβ-mediated neurotoxicity. This pathway is dependent on the action of a protein known as Dickkopf-1 (Dkk1), which is an antagonist of the cell-surface signaling protein wnt. The transcriptional effects of Aβ, clusterin, and Dkk1 are mediated by activation of the wnt-planar cell polarity (PCP) pathway. Among the target genes in the clusterin-induced DKK1-WNT pathway that were identified by the researchers are EGR1 (early growth response-1), KLF10 (Krüppel-like factor-10) and NAB2 (Ngfi-A-binding protein-2)–all of these are transcriptional regulators. These genes are necessary mediators of Aβ-driven neurotoxicity and tau phosphorylation.

The researchers went on to show that transgenic mice that express mutant amyloid display the transcriptional signature of the DKK1-WNT pathway, in an age-dependent manner, as do postmortem human AD and Down syndrome hippocampus. (Most people with Down syndrome who survive into their 40s or 50s suffer from AD.) However, animal models of non-AD tauopathies (non-AD neurodegenerative diseases associated with pathological aggregation of tau, and formation of NFTs, but no amyloid plaques) do not display upregulation of transcription of genes involved in the DKK1-WNT pathway, nor does postmortem brain tissue of humans with these diseases.

The Kings College London researchers concluded that the clusterin-induced DKK1-WNT pathway may be involved in the pathogenesis of AD in humans. They also hypothesize that such strategies as blocking the effect of Aβ on clusterin or blocking the ability of Dkk1 to drive Wnt–PCP signaling might be fruitful avenues for AD drug discovery. According to the Wellcome Trust’s 21 November 2012 press release, Professor Lovestone and his colleagues have shown that they can block the toxic effects of amyloid by inhibiting DKK1-WNT signaling in cultured neuronal cells. Based on these studies, the researchers have begun a drug discovery program, and are at a stage where potential compounds are coming back to them for further testing.

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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 an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Agios Germanos, Greece. Source: http://bit.ly/YRDIBJ

I was quoted in an article in the November 19, 2012 issue of Chemical & Engineering News (C&EN) by senior editor Lisa M Jarvis. The article is entitled “Agios Takes A Long View In Cell Metabolism.”

The article focuses on Agios Pharmaceuticals’ (Cambridge, MA) strategy for building a company that can endure as an independent firm over a long period of time, and that can also demonstrate sustained performance.

This contrasts with the recent trend toward “virtual biotech companies”–lean companies with only a very few employees that outsource most of their functions, and that are designed for early acquisition by a Big Pharma or large biotech company. The virtual company strategy is designed to deal with the inability of most young biotech companies to go public in the current financial environment. Without the ability to go public, young companies cannot provide early-stage venture capital investors with a profitable exit within a few years after launching the company. Virtual companies typically have a few assets, such as molecules that are ready for preclinical studies or early clinical trials. The goal is to obtain enough evidence that their compounds can become drugs to interest a Big Pharma.

In contrast, there are a few young  “platform companies” that are built on a broad technology platform, which aim to address important areas of biology and potentially to develop numerous products with the potential to address important areas of unmet medical need. One of these is Agios.

“Built to Last” in the current biotech ecosystem

In the C&EN article, I was quoted as saying that only a few platform companies have been launched in recent years. In the Boston area, in addition to Agios, such companies include Forma Therapeutics and Aileron Therapeutics. I was further quoted as saying “These companies are built to last.”

That brings up the old business paradigm from the 1990s and early 2000s–“Built to Last” versus “Built to Flip”. Those involved in building virtual biotech companies–especially venture capitalists and angel investors–do not like the use of “Built to Flip” to characterize their companies. And there are some fine virtual biotechs–some, such as Energesis and Zafgen–which we have covered in our blog.

(Plexxikon, the developer of targeted melanoma drug vemurafenib, also operated as a virtual company. However, it had a technology platform, and had the potential to become an independent biotech with marketed products. Thus Plexxikon did not fit the usual “virtual biotech model”. Nevertheless, it was acquired by Daiichi Sankyo in 2011.)

However, some industry commentators believe that “Built to Flip” is an appropriate designation for virtual biotech companies, and that the virtual model is likely to be detrimental to drug discovery and to the biotech/pharma industry as a whole.

Meanwhile, the 2012 BIO International Convention in Boston had a session entitled “Moving the Goal Posts: How to Build a Free-Standing Biotech from Scratch in Today’s Environment.” This session focused on how to build the “next Vertex or even the next Genentech” (i.e., a “Built to Last” biotech company) in today’s environment. John Evans, the Vice President of Business Development & Operations of Agios was a speaker at that session. The session was moderated by Bruce Booth of Atlas Ventures. Thus, despite the preference for lean virtual biotech companies in the current funding environment, there is an interest in the entrepreneurial and venture capital communities for how free-standing biotechs might emerge under current conditions.

How to build a young platform biotech company

The Biopharmconsortium Blog has included three articles about Agios:

• Cancer metabolism as a target for drug discovery: Agios Pharmaceuticals (December 31, 2009)
• Agios Pharmaceuticals partners with Celgene (April 23, 2010)
• Cancer metabolism specialist Agios Pharmaceuticals continues its spectacular fundraising success (November 30, 2011)

These articles, as well as the November 19 2012 C&EN article, outline how Agios has been building a free-standing biotech in today’s unfavorable environment. Agios’ strategy is based on three elements:

• A stellar group of scientific founders–Drs. Craig B. Thompson, Tak W. Mak, and Lewis C. Cantley.
• A strong proprietary technology platform based on cancer metabolism
• A financing strategy that includes both venture capital and partnerships with established companies. In the case of Agios, their partner is Celgene. The Agios/Celgene partnership provides Agios with $150 million, and allows Agios to maintain control over the direction of its early stage research.

As stated in the C&EN article, the financial security gained via Agios’ funding by its venture investors and by Celgene enables Agios to work on multiple potential targets, with the goal of dominating the field of cancer metabolism. Agios focuses on two types of targets: metabolic enzyme species that are found only in cancer cells, and enzyme species on which a cancer cell has become dependent. Agios researchers intend to develop drugs against targets for which their are predictive biomarkers that identify the right patients for clinical studies.

New developments outlined in the November 19, 2012 C&EN article

Both the November 19, 2012 C&EN article and our Bipharmconsortium Blog articles outline Agios’ program to target a mutated form of isocitrate dehydrogenase 1 (IDH1), which together with mutated IDH2 has been implicated in 70% of human brain cancers. As stated in the C&EN article, Agios researchers have recently reported a series of compounds that selectively inhibit the mutant form of IDH1. This research had been carried out in collaboration with researchers from Ember Therapeutics (Watertown, MA). As we stated in another Biopharmconsortium Blog article, Ember specializes in targeting beige adipocytes for treatment of metabolic diseases.

As we noted in our November 30, 2011 Biopharmconsortium Blog article, Agios had slated a portion of the $78 million that it raised in its Series C financing 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 rare metabolic diseases have a high level of unmet medical need.

As outlined in the C&EN article, Agios’ work with mutant IDH1 and IDH2 is serving as a bridge to the company’s programs in IEMs. IDH2 mutations have been found in a class of children with 2-hydroxyglutaric aciduria, a rare inherited neurometabolic disorder that can cause developmental delay, epilepsy, and a set of other pathologies.

According to the C&EN article, IEMs are of special strategic interest to Agios. Agios CEO David Schenkein stated that expanding the company’s R&D efforts into IEMs helps the company to manage the risk profile of its portfolio. In the case of cancer, Agios researchers must identify and validate targets involved in the pathobiology of these diseases, and then to find drugs that modulate these targets. In the case of IEMs, disease biology is already validated by genetics.

Moreover, IEMs have small patient populations. Thus only small clinical trials are needed to bring a drug to market. Agios therefore believes that it can bring drugs for these diseases to market on its own, without the need for a larger partner such as Celgene or a Big Pharma.

As we discussed in a Biopharmconsortium Blog article on improving the clinical trial system, although rare diseases only require small clinical trials, finding and recruiting patients for the trials is made more difficult because of the very small number of patients with a particular disease. One solution is to work with patient advocates and “disease organizations”, some of which have patient registries. In the case of 2-hydroxyglutaric aciduria and other organic acidemias, a “disease organization” exists–the Organic Acidemia Association (OAA). Perhaps Agios will find it fruitful to work with the OAA in its patient recruitment efforts.

Currently, Agios is focused on getting compounds into the clinic–both for IEMs and for cancer. Looking down the road, the company’s $180 million war chest should enable Agios to put several compounds through proof-of-concept studies, according to Dr. Schenkein. (This is besides any cancer drug candidates that are licensed by Celgene.) Despite Agios’ strategy of conducting small trials for IEM drug candidates, Dr. Schenkein said that the company will eventually need to go public to achieve its strategic goal of dominating the cancer metabolism 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 an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail.  We also welcome your comments on this or any other article on this blog

New Alzheimer’s disease model, the CVN mouse

Our August 19, 2012 and our August 28, 2012 articles on this blog focused on the latest developments in Alzheimer’s disease (AD) drug development. To summarize the conclusions of the articles:

• The results of a new genetic study by DeCode Genetics and its collaborators strongly support the amyloid hypothesis of AD, and especially the hypothesis that reducing the β-cleavage of APP [e.g., by use of an inhibitor of β-secretase (also known as the β-site APP cleaving enzyme 1, or BACE1)] may protect against the disease.

• Nevertheless, in Phase 3 trials of two anti-amyloid monoclonal antibody (MAb) drugs in patients with mild to moderate AD–Pfizer/Janssen’s bapineuzumab (often called “bapi” for short) and Lilly’s solanezumab–the drugs failed their primary cognitive and functional endpoints.

• Roche/Genentech, as well as two academic consortia, have begun clinical trials of anti-amyloid MAb drugs in asymptomatic patients with mutations that predispose them to develop AD, or in asymptomatic patients with amyloid accumulation. These studies are based on the hypothesis that the reason for the failure of anti-amyloid MAb drugs in clinical trials has been that the patients being treated had suffered extensive, irreversible brain damage. Treating patients at a much earlier stage of disease with these agents might therefore be expected to be more successful.

Analyses of the data from the Phase 3 studies of both bapi and solanezumab will be presented in scientific meetings in October 2012. An academic research consortium will present its independent analysis of the data from the EXPEDITION studies of solanezumab at the American Neurological Association (ANA) meeting in Boston on October 8, 2012, and at the Clinical Trials on Alzheimer’s Disease (CTAD) meeting in Monte Carlo, Monaco, on October 30, 2012.

According to a September 11, 2012 news article in Drug Discovery & Development, researchers who conducted the Phase 3 trials of bapi found evidence that the drug stabilized amyloid plaque in the brain and may have ameliorated further nerve damage in patients treated with the drug. This finding is among the results to be presented in the October meetings.

Development of BACE1 inhibitors

Strictly speaking, the results of the DeCode Genetics study most strongly support the development of BACE1 inhibitors. In our August 28, 2012 article, we link to a 2010 review that includes a discussion of companies developing BACE1 inhibitors. However, we also note that the development of BACE1 inhibitors has been elusive. This is because of medicinal chemistry considerations. Specifically, it has been difficult to design a specific, high-affinity inhibitor of the BACE1 active site that can cross the blood-brain barrier and which has good drug-like ADME (absorption, distribution, metabolism and excretion) properties. Nevertheless, recently progress has been made in developing such compounds, and several companies are developing BACE1 inhibitors and have entered them into early-stage clinical trials.

Among the companies developing BACE1 inhibitors, as listed in a recent post on Derek Lowe’s In The Pipeline blog are CoMentis/Astellas, Merck, Lilly, and Takeda.

Satori Pharmaceuticals is developing γ-secretase inhibitors

Developing γ-secretase inhibitors has been abandoned by the vast majority of companies, because of the essential role of these enzymes in the Notch pathway and other pathways involved in normal physiology. As a result, development of γ-secretase inhibitors for AD has not progressed beyond the preclinical stage.

Nevertheless, Satori Pharmaceuticals, a Cambridge, MA venture capital-backed biotech company, is now actively involved in developing γ-secretase inhibitors. Satori’s γ-secretase inhibitors are based on a proprietary scaffold derived from a compound isolated from the black cohosh plant (Actaea racemosa). The company utilized modern synthetic and medicinal chemistry to derive compounds based on this scaffold that they believe are suitable for long-term oral therapy for AD in humans. Satori’s lead compound, SPI-1865, is a potent γ-secretase modulator that decreases levels of the amyloidogenic Aβ42 peptide as well as Aβ38, increases levels of Aβ37 and Aβ39, but does not affect Aβ40. Researchers believe that decreasing Aβ42 levels in favor of shorter, less amyloidgenic A-beta forms is beneficial in treatment of AD. SPI-1865 is also selective for Aβ42 lowering over the inhibition of Notch processing, and appears to be free of any other off-target activities.

In animal models [e.g., wild type mice and rats, and transgenic mice (Tg2576) that overexpress APP and thus have high levels of Aβ peptides] orally-administered SPI-1865 has been found to lower brain Aβ42. SPI-1865 has good brain penetration in these models, and a long half-life that should permit once a day dosing in humans.

SPI-1865 is now in the preclinical stage. Satori plans to file an Investigational New Drug (IND) Application with the FDA in late 2012 with the goal of enabling initial human testing to begin in the early part of 2013.

The overall strategy of Satori Pharmaceuticals is to develop novel and proprietary oral small-molecule drugs that are designed for chronic dosing, and can be used to treat patients with early-stage (or presymptomatic) AD for years or decades. Such a strategy will require compounds that are efficacious and exceptionally safe. Satori expects that its unique γ-secretase inhibitors will have these properties. However, this needs to be shown in human clinical trials. Moreover, this strategy–as with all strategies that involve treating AD in its earliest stages–will involve the development of reliable biomarkers and companion diagnostics.

A new mouse model for AD

As Derek Lowe says in an August 31, 2012 post on “In the Pipeline” with respect to Lilly’s AD drugs, anti-amyloid MAbs, BACE1 inhibitors, and γ-secretase inhibitors are “some of the best ideas that anyone has for Alzheimer’s therapy”. Given the APP processing pathway as illustrated in the figure at the top of our August 28, 2012 article, these are the “sensible” and “logical” alternatives.

Nevertheless, there is the nagging feeling among many AD researchers that we do not understand the causes of AD, especially sporadic AD, which represents around 95% of all cases of the disease. Sporadic AD occurs in aging individuals who have normal genes for the components of the APP processing pathway. Not only do we not understand the pathobiology of sporadic AD, but we have little understanding of the normal physiological function of APP and of APP processing. Processes that may be involved in the initiation of sporadic AD may include not only those involved in Aβ production, but also those involved in Aβ clearance.

An important tool in understanding the pathobiology of AD, and potentially in developing novel therapies for the disease, would be an animal model that recapitulates the human disease as closely as possible. We published an article on AD mouse models that were designed to more closely recapitulate human AD than the most commonly used models in the September 15, 2004 issue of Genetic Engineering News. However, since the publication of our article, Carol A Colton, Ph.D. (Duke University Medical Center, Durham, NC) and her colleagues have published on their research aimed at producing an even better mouse model, known as the CVN mouse. They published their research in two articles, one in PNAS in 2006 and the other in the Journal of Neuroscience in 2008.

Charles River Laboratories (CRL) (Wilmington, MA) now offers the CVN mouse to researchers who might wish to employ it in their AD research. CRL has also recently produced a webinar (with the participation of Dr. Colton) on the CVN mouse, entitled “CVN Mouse: A More Translatable Alzheimer’s Efficacy Model”. You may access this webinar by registering at http://www.criver.com/thesource.

Genome-wide association studies (GWAS) in humans, as well as various functional studies, have implicated variants in genes involved in inflammation and immune responses in susceptibility to late-onset, sporadic AD in humans. The Colton group, noting that commonly-used mouse models of AD recapitulated human disease very poorly, looked for differences between mice and humans in innate immunity. The biggest difference they found was that expression of nitric oxide synthase 2 (NOS2) the inducible form of nitric oxide synthase, is high in mice and low in humans. NOS2 is an enzyme that produces nitric oxide (NO), a highly reactive oxidant that can serve in signal transduction, neurotransmission and in cell killing by macrophages. Microglia, the macrophages of the brain, express NOS2 and NO. The Colton group has been studying the role of microglia and oxidants and antioxidants in microglia that can produce oxidative stress in the brain in normal aging and in AD.

Because of the striking difference in NOS2 expression between mice and humans, the Colton group created a transgenic mouse AD model by crossing mice that  expressed a mutant form of human APP known as APPSwDI (APP Swedish Dutch Iowa) with NOS2 knockout (NOS2 -/-) mice. The APPSwDI transgenic mouse, a well-characterized standard AD mouse model, was chosen because it expresses low levels of APP and high levels of Aβ peptides in the brain. The APPSwDI/NOS2 -/- mouse is the CVN mouse that is available from CRL.

Unlike APPSwDI mice and other standard AD mouse models, the CVN mouse recapitulates many features of human AD as the animals age, including AD-like amyloid pathology (starting at 6 weeks of age, which is early), perivascular deposition of amyloid, AD-like tau pathology (including aggregated hyperphosphoryated tau), AD-like neuronal loss, and reduction in interneuron numbers (including NPY interneurons). Age-related cognitive (learning and memory) loss (as assessed by the radial arm water maze test) was also seen. The researchers also saw increases in immune activation and inflammation (e.g., microglial activation) over the course of the disease; this appeared to be dependent on increases in Aβ and in tau.

The researchers also used the mouse to study changes in immune-related proteins over the course of the disease. Several protein that are encoded by genes that have been associated with sporadic AD via GWAS change over time in this mouse model, including APOE (which has been known to be important in AD for a long time) and BIN1. Other proteins that change over the course of disease include the complement component C1QB, and the centrosomal protein ninein. Immune activation genes such as those that encode IL-1α and TGF-β also show changes over the course of disease in these mice. The Colton group will soon publish their work on changes in these proteins and genes in the CVN mouse in a peer-reviewed journal.

In summary, the CVN mouse more faithfully models AD-like progression than other mouse models that have been used to study AD, including those that have been used in preclinical studies of such failed drug candidates as solanezumab, bapineuzumab, Flurizan (tarenflurbil), and Alzhemed (3-amino-1-propanesulfonic acid). It also allows researchers to study the role of genes and proteins such as those identified in GWAS studies in AD, and especially in sporadic AD. (However since the CVN mouse expresses a mutant form of APP, it can not be used to study all aspects of the pathophysiology of sporadic AD, especially the initiation of the disease process.) The CVN mouse can also be used in drug discovery and preclinical studies.

One example of such drug discovery studies is being carried out by the Colton group. They have recently been studying small APOE mimetic peptides in CVN mice. The subcutaneously administered APOE mimetics were reported to significantly improve behavior, while decreasing the inflammatory cytokine IL-6, as well as decreasing neurofibrillary tangle-like and amyloid plaque-like structures. These improvements are associated with apoE mimetic-mediated increases in protein phosphatase 2A (PP2A) activity. [Decreased PP2A levels in AD may be involved in formation of neurofibrillary tangles (NFTs) which are aggregates of hyperphosphorylated tau; PP2A may also be involved in the production of Aβ peptides. The APOE mimetic are thus potential AD therapeutics.

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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.

Is beige the new brown?

This is an update to our recent discussion on targeting the physiology of brown fat [or brown adipose tissue (BAT)], in developing novel antiobesity therapies. It is based on a research article published in the July 20 2012 issue of Cell by Dr. Bruce Spiegelman (Dana-Farber Cancer Institute and Harvard Medical School, Boston MA) and his colleagues.

As we discussed in our May 23, 2012 blog article, Dr. Spiegelman, a leading metabolic disease researcher, is a founder of Ember Therapeutics. Ember is working to develop novel metabolic disease therapeutics based on Dr. Spiegelman’s work on BAT physiology and on novel insulin sensitizers.

In the work described in the new Cell article, Dr. Spiegelman and his colleagues showed that the white adipose tissue (WAT)-derived “brown fat-like cells” that they had been studying are actually a new type of cells known as “beige adipocytes”.

Other researchers had previously described a class of “brite” or “beige” adipocytes, which were induced in WAT depots that have been chronically treated with the peroxisome proliferator-activated receptor γ (PPARγ) agonist rosiglitazone. Brite/beige adipocytes expressed UCP1 (uncoupling protein 1) and had high levels of mitochondria as do brown adipocytes but lacked expression of certain characteristic brown fat-specific genes. UCP1 is the key mitochondrial protein that makes the process of thermogenesis (i.e., production of heat by oxidizing fat rather than storing it) possible. As shown previously by Dr. Spiegelman and his colleagues, BAT is derived from  a myf-5 muscle-like cell lineage, via the action of the transcriptional regulator PRDM16. However, beige cells are not.

Beige precursor cells in murine subcutaneous white fat depots

In the new Cell publication, Dr. Spiegelman and his colleagues carry these earlier studies further by cloning murine beige fat cells and describing their unique gene expression signature. They first isolated adipocyte precursors from mouse subcutaneous WAT (specifically, the inguinal fat depots). These precursors are found in the stromal-vascular fraction of the adipose tissue. The researchers immortalized stromal vascular fraction (SVF) cells from subcutaneous WAT of the 3T3 mouse by passaging them in culture, similar to the classic derivation of 3T3 fibroblast cell lines by Todaro and Green 49 years ago. They cloned the resulting immortalized cells via limiting dilution, and selected the 20-some odd cell lines that could be readily differentiated (via standard differentiation protocols) to adipocytes. For purposes of comparison, the researchers also derived multiple adipogenic clones from the SVF cells of the interscapular brown fat depot.

They then differentiated the WAT-derived adiopogenic clones to adipocytes, and treated them with forskolin [an agent that raises intracellular levels of cyclic AMP (cAMP)]–increases in cAMP levels activate expression of UCP1 in the mitochondria of brown fat cells. They then determined the gene expression pattern of the differentiated and forskolin-stimulated WAT derived clones. The clones clustered into two groups, one of which had a gene expression pattern more similar to BAT cells than the other group. These two groups appeared to represent beige and white adipocytes, respectively. Comparison of these two groups of cells to BAT cells revealed that the presumptive beige adipocytes had gene expression patterns that were similar, but not identical to, those of brown adipocytes.

Further characterization of the three types of cells indicated that beige cells have characteristics of both white and brown adipocytes. Both white and beige adipocytes have low basal levels of UCP1, while brown adipocytes have higher levels. Upon cAMP stimulation, however, the beige adipocyte lines responded with a very large induction of UCP1 gene expression, reaching similar UCP1 levels to that observed in the brown adipocyte lines. White adipocyte cell lines showed little UCPI induction. These characteristics of beige and white adipocyte cell lines also were seen in in vivo studies.

Still further characterization of the three types of cell lines revealed that beige and brown fat cells have related but distinct gene expression profiles. These include a set of beige-selective genes that can distinguish beige fat cells from both brown fat cells and white fat cells. Protein expression was highly concordant with mRNA expression. Since some of the beige-selective markers are cell surface proteins, and since antibodies to these proteins are commercially available, this allowed the researchers to use fluorescence-activated cell sorting (FACS) to isolate primary beige precursor cells from the SVF of mouse inguinal fat.

Murine beige fat precursors–not white fat or brown fat–are targets of the hormone irisin

In our May 23, 2012 blog article, we discussed the myokine hormone irisin, which was recently discovered by the Spiegelman group. As we discussed, irisin is produced by muscle cells and increases with exercise. It has little or no effect on classic brown fat found in the interscapular depot. However, It acts on subcutaneous white adipose cells in culture and in vivo to stimulate what appears to be development into brown fat-like cells. Specifically, irisin stimulates expression of UCP1 and an array of other brown fat genes, producing a thermogenic effect.

In the study reported in the July 20 2012 Cell paper, the researchers used FACS to sort primary inguinal precursor cells into white and beige preadipocytes, and studied the effects of two forms of recombinant irisin on these cells during adipogenic differentiation. All cells treated either with vehicle or irisin showed good adipocyte differentiation. Both forms of irisin, but not vehicle, induced the expression of brown fat-like genes such as UCP-1 in beige cells, but had little effect on white cells. This suggests that irisin works on white fat depots in vivo by inducing brown-like gene expression in the beige cell component of preadipocytes in these depots.

Adult human “brown fat” is really beige fat

As we discussed in our blog articles of November 17, 2010 and May 23, 2012, and as illustrated in the figures at the top of each of these articles, adult humans possess what appears to be reservoirs of brown fat in the neck region and other areas of the upper body as well as in skeletal muscle.

In the study reported in the July 20 2012 Cell paper, the researchers preformed BAT biopsies from two independent cohorts of human subjects, and analyzed their gene expression signatures based on the findings of the studies of mouse brown, beige, and white adipocytes. They found that the UCP1-positive “BAT” cells from the human biopsies had gene expression signatures that resembled those of murine beige adipocytes more closely than they resemble classic brown fat or white fat. As a result of this finding, several popular articles written about the new Cell paper are entitled “Beige is the New Brown”.

Conclusions

Although additional research is needed to fully characterize beige fat physiology, the picture that emerges from the above study is that beige fat cells exist in subcutaneous fat mainly in a basal, unstimulated state, in which their phenotype resembles that of white fat. Once stimulated, however, beige cells activate expression of a brown fat-like thermogenic program, including expression of levels of UCP1 similar to those of brown fat cells. Thermogenesis of beige fat cells is induced by such stimuli as 1. β-adrenergic activation; 2. the myokine irisin; and 3. other polypeptide hormones, such as fibroblast growth factor 21 (FGF21), and atrial natriuretic peptide (ANP). The role of FGF21 in inducing UCP1 and the thermogenic program in adipose tissues was elucidated by Dr. Spiegelman and his colleagues. This was described in a February 2012 report in Genes & Development.

The above scenario is mainly based on studies in mice. However, as discussed earlier, humans also have what appear to be beige cells, which may be amenable to induction by irisin or other agents, thus giving rise to a thermogenic program that might be utilized to combat obesity and type 2 diabetes. Classical interscapular brown fat in humans, however, although it is present in infants, disappears as humans mature. This it is likely that beige fat will be the target such agents as irisin, which are aimed at overcoming metabolic disease via increasing energy expenditure.

Long before researchers obtained evidence for “browning” of white fat as a potential mechanism for induction of a thermogenic program, the pharmaceutical industry had a long history of attempting to develop β3-adrenergic agonists as therapies for metabolic diseases.  Many agents were entered into clinical trials by numerous companies, but all failed, either due to lack of efficacy or to averse effects due to activation of β-adrenergic receptors in other tissues. An important underlying factor in the failure of these studies was the lack of understanding of brown (or beige) fat physiology in humans, including whether brown fat existed in adult humans at all. Of course, beige fat was completely unknown.

In our May 23, 2012 blog article, we discussed several young companies that are working to develop novel approaches to treating obesity based on brown-fat physiology and/or other non-CNS pathways involved in increasing energy expenditure. Among these companies are Ember Therapeutics. As we discussed in the May 2012 article, Ember entered into an exclusive license agreement with Dana-Farber Cancer Institute for the irisin technology, and is optimizing and developing a proprietary molecule based on this technology. This research constitutes the company’s lead BAT biology program.

More recently, Ember completed a licensing agreement with the Dana-Farber for intellectual property related to Dr. Spiegelman’s beige fat discovery. As discussed earlier, beige fat cells are specifically targeted by irisin, which induces the thermogenic program in these cells. Especially in adult humans, which appear to lack classic brown fat, beige adipocytes and/or their precursors are the true target of irisin, and any program to develop irisin-like protein drugs for metabolic disease will need to focus on the effect of such products on beige cells. Moreover, Ember’s programs to develop small molecules via screening for compounds that activate pathways specific to the “brown fat” cell lineage will need to focus specifically on pathways involved in induction of the thermogenic program in beige adipocytes.

In contrast to Ember’s R&D programs, which must focus on beige adipocytes, Energesis Pharmaceuticals’ R&D programs focus on brown fat “stem cells” from skeletal muscle. This research thus has to do with classical BAT, which is derived from a skeletal muscle-like lineage, as opposed to beige adipocytes, which are not. Thus Ember’s and Energesis’ R&D programs represent completely different approaches to developing antiobesity agents that work to increase energy expenditure. Among the other companies mentioned in our May 2012 article, Zafgen’s R&D programs represent still another completely different approach, involving targeting the liver. Acceleron Pharma’s approach, however, probably involves targeting beige fat. In fact, Dr. Spiegelman has been a collaborator in some of their research.

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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.

Keynote speaker, Bob Langer of MIT

2nd Annual Partnership Opportunities in Drug Delivery

October 1st and 2nd 2012

The Boston Park Plaza Hotel & Towers
50 Park Plaza at Arlington Street
Boston, MA, 02116-3912

Keynoted by Dr Robert Langer of MIT, this is a strategic level event designed with two purposes:

1. To present a strategic level event for pharma and biotech business development and external licensing professionals with a thorough overview of the latest drug delivery technologies available along with an update on deals and opportunities to enhance patients, therapies and the life cycle of a drug.

2. To provide drug delivery and specialty pharmas with a platform to present their technologies and get the latest insights from both established pharma and biotechs as well as start up companies on what the delivery and formulation needs are.

15% discount for Biopharmconsortium Blog readers with code BPCON

For more information, see http://www.poddconference.com

I am registered to attend this conference, and hope to see many of you there.

Macrophages attack a cancer cell

An article in the June 2012 issue of OncologyLive, authored by the publication’s senior editor, Anita T. Shaffer, reviews cancer immunotherapies now in late-stage clinical trials, and discusses the prospects for the field.

The article begins with a discussion of the recent renaissance of cancer immunotherapy, as exemplified by the April 2010 FDA approval of Dendreon’s Sipuleucel-T (APC8015, Provenge) and the March 2011 FDA approval of Ipilimumab [Medarex/Bristol-Myers Squibb’s (BMS') Yervoy]. It then went on to discuss the exciting Phase 1 results with Medarex/BMS’ anti-PD-1 MAb, which we featured in the June 28, 2012 article on the Biopharmconsortium Blog.

But the bulk of the article was a discussion of the current late-stage (Phase 3) active immunotherapy pipeline. The article’s table lists 14 such agents. If one eliminates Cel-Sci/Teva’s Multikine (which is a mixture of cytokines), that leaves 13 agents, at least most of which can be described as therapeutic cancer vaccines. These products range from dendritic cell vaccines to tumor cell-based vaccines and viruses that encode tumor antigens.

For example, Argos Therapeutics‘ AGS-003 (Arcelis) is an autologous dendritic cell vaccine loaded with the patient’s own messenger RNA (mRNA). This vaccine is in Phase 3 clinical trials in patients with newly diagnosed metastatic renal cell carcinoma (mRCC). We mentioned Argos and its technology in our November 25, 2011 article on the late Ralph Steinman, MD, who had discovered the dendritic cell and elucidated its central role in the immune system. Dr. Steinman was a cofounder of Argos. Patient mRNA in Argos’ cellular immunotherapy product encode tumor antigens, which are expressed on the surface of the dendritic cells. The dendritic cells then potentiate the production of tumor antigen-specific T cells which attack the patient’s tumor.

According to a July 2 2012 company news release, AGS-003 is a fully personalized immunotherapy that preferentially targets mutated tumor antigens, which drive disease progression. Patient T cells recognize these antigens as foreign. This enables AGS-003 to direct a specific and potent anti-tumor immune response, without attacking normal tissues.

In a Phase 2 study of a combination of AGS-003 and sunitinib (Pfizer’s Sutent, the standard of care for mRCC), researchers demonstrated a statistically significant correlation between the number of anti-tumor T cells induced and overall survival in mRCC patients receiving AGS-003. Adding AGS-003 to sunitinib doubled overall survival for these patients compared to historical results for unfavorable risk patients treated with sunitinib alone. Over 50 percent of patients in the study survived longer than 30 months after initiating therapy, which is four times the expected rate for sunitinib.

Another type of cancer vaccine is based on modified cancer cells. In our Steinman article, this strategy is represented by BioSante’s GVAX cancer vaccines. One such vaccine, GVAX Pancreas for pancreatic cancer (which is now in clinical trials) is based on human pancreatic cancer cell lines that have been engineered to secrete the immunostimulant granulocyte-macrophage colony-stimulating factor (GM-CSF), and have then been lethally irradiated. Since the most advanced GVAX products are in Phase 1 and Phase 2 clinical trials, GVAX was not covered in the OncologyLive article. However, other more advanced immunotherapies, such as NewLink Genetics‘ HyperAcute Pancreas cancer immunotherapy (in Phase 3 trials), also consist of modified cancer cells. HyperAcute Pancreas consists of equal parts of two separate allogeneic pancreatic cancer cell lines engineered to express α-galactosidase (an enzyme that is not expressed by natural human pancreatic tumors).

Another type of cancer vaccine is based on viruses that encode tumor antigens. For example, Bavarian Nordic A/S’ PROSTVAC, a treatment for prostate cancer, is a  sequentially dosed combination of vaccinia and fowlpox poxviruses that encode an altered, more immunogenic form of prostate-specific antigen (PSA) plus three immune enhancing costimulatory molecules ( B7.1, ICAM-1, and Lfa-3).

The late-stage immunotherapies listed in the table in the OncologyLive article include cancer vaccines that represent several design strategies other than the three mentioned here.

Some good news about sipuleucel-T

The OncologyLive article also referred to an abstract presented at the 2012 American Society of Clinical Oncology (ASCO) meeting, which suggests that the survival advantage for prostate cancer patients treated with sipuleucel-T was significantly greater than the 4.1-month benefit reported in the Phase 3 trial that led to approval of the agent. The analysis reported in this abstract indicates that the overall survival treatment benefit with sipilleucel-T ranged from 4.1 months to  7.8 months.

Conclusions

As illustrated by the number of late-stage cancer immunotherapies in development, as well as the approval of two drugs in 2010 and 2011, cancer immunotherapy is here to stay. One question in the use of such immunotherapies, as highlighted in the OncologyLive article, is how they will be integrated with such established modalities as cytotoxic chemotherapy, radiation therapy, and targeted cancer therapies.

Another factor is cost. A course of treatment with sipuleucel-T costs $93,000, and the cost of a course of treatment with ipilimumab is $120,000. However, as pointed out in the OncologyLive article, the total cost of treatment with other modalities that may continue for months or years may be higher. Nevertheless, the cost of cancer therapies, especially those that only increase overall survival by a few months, is a great concern to patients, physicians, and payers.

It must be remembered, however, that nearly all cancer therapies, when first introduced to the market, gave only slightly enhanced survival over older treatments. However, as oncologists learned how to use the therapies better (e.g., with changes in dosing, use in other groups of cancer patients, and/or use in combination therapies), numerous therapies eventually gave long-term remissions or even cures and proved to be cost-effective indeed.

Another issue with the cancer immunotherapy field, as pointed out in the OncologyLive article, is the difficulty of raising capital for cancer immunotherapy specialty companies. This is especially true in the current market, where most biotech companies have difficulty in raising capital. However, what venture capitalists and Big Pharma consider to be “premature technologies” or “unproven” emerging early-stage areas, as is usually the case, have particular difficulty in attracting investment.

Nevertheless, if and when additional late-stage cancer immunotherapy agents successfully complete Phase 3 trials and gain approval, this may demonstrate to investors that cancer immunotherapy has graduated from the premature-technology stage. In that case, cancer immunotherapy specialty companies may find it easier to attract capital, and large pharmaceutical companies may wish to acquire some of these companies. Since Big Pharma already is involved in developing such immunotherapies as anti-PD-1 and anti PD-1L, and ipilimumab is already a marketed Big Pharma drug, that should not be much of a stretch.

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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.

Quorum sensing synthetic biology project http://bit.ly/LO1ynR

Way back in May 2000, Decision Resources published my short report entitled “New approaches to small-molecule antibacterial drug discovery” as part of its Spectrum Life Sciences series. As might be expected, the report is now out of print.

The report was a brief review of then-novel approaches to antibacterial drug discovery, in the face of the increasing level of antibiotic resistance in pathogenic bacteria. These approaches included genomics and such technologies as high-throughput screening against bacterial-specific targets.

However, the most interesting part of the report was a section on using the study of bacterial physiology to identify targets that are important for the ability of bacteria to cause disease, but are not essential for bacterial proliferation or survival. The hypothesis behind these studies was that it might be possible to develop compounds that prevent these bacteria from causing disease, without selecting for resistant strains of the bacteria.

Antibiotics typically kill or prevent proliferation of bacteria by targeting biomolecules involved in such essential processes as cell wall synthesis, DNA proliferation, or protein synthesis. Treating large populations of bacteria with such agents inevitably selects for a few resistant mutant cells. These proliferate, mutate further, and give rise to antibiotic resistant populations. However, if a therapeutic targets a nonessential pathway that is involved in pathogenesis, resistant populations might not be selected for. That was the hypothesis.

This field of bacterial physiology for drug discovery focused on two related areas–virulence factors and quorum sensing. Virulence factors are not expressed by a strain of pathogenic bacteria in vitro, but are expressed only when the bacteria infect a host. Once expressed, they enable the bacteria to colonize the host and cause disease. Examples of such virulence factors include secretion systems that deliver bacterial effector proteins into host cells. These effector proteins may, for example, kill host cells, inhibit cytokine production or phagocytosis, or may mediate bacterial entry into the host cells.

Quorum sensing is a system by which certain bacteria can monitor their own population density. They accomplish this by secreting specific autoinducer molecules. When the concentration of an autoinducer reaches a critical threshold value (as the result of an increase in bacterial population density), it triggers specific response systems, causing the induction of sets of genes that are only expressed at high population density.

For example, many gram-negative bacteria (e.g., Pseudomonas aeruginosa, Vibrio cholerae, and Escherichia coli) use specific acyl homoserine lactones (AHSLs) as their autoinducers. P. aeruginosa has two quorum sensing systems that use the AHSL autoinducers butyrylhomoserinelactone and 3-oxododecanoylhomoserinelactone, respectively. These systems (operating via specific receptors for the auotoinducers and interacting with each other) control the induction of several genes, some of which are virulence factors. Some of these genes enable the bacteria, when they are at sufficient density, to form biofilms (slimy mats of bacteria and polysaccharide matrix).

P. aeruginosa is an opportunistic pathogen, causing infection in the lungs of people with cystic fibrosis, burn patients, and other hospitalized patients. These infections cause death in over 80% of cystic fibrosis patients. The ability to form biofilms renders the bacteria resistant to antibiotics and to the patient’s own immune system.

Other gram-negative bacteria that form biofilms have been implicated in dental caries, peridontitis, osteomyelitis, and numerous nosocomial infections. Bacterial biofilms can also form on the surface of implanted medical devices, such as catheters and mechanical heart valves, and cause device-related infections.

The gram-positive human pathogen Staphylococcus aureus also has a quorum sensing system. However, it does not use an AHSL as an autoinducer. The S. aureus autoinducers are peptides that contain an unusual thiolactone structure (i.e., a thol ester-linked cyclic structure). The S. aureus quorum sensing system controls the synthesis of virulence factors responsible for the pathogenicity of this organism in vivo. Although specific peptides induce virulence factors in a given strain of S. aureus, there are other specific peptides that inhibit the induction of virulence in strains of the organism other than the one secreting the inhibitory peptides. That finding suggested that researchers should be able to develop specific agents to shut down S. aureus pathogenesis by targeting the quorum sensing system.

Interestingly, quorum sensing-based systems have been used in projects for the International Genetically Engineered Machine (iGEM) competition, an annual undergraduate synthetic biology competition. See the figure above, which was taken from the 2009 Chiba University (Japan) iGEM project.  [http://2009.igem.org/Team:Chiba/Project/Signaling-system]

Quorum Sciences and Vertex Pharmaceuticals’ research on quorum sensing

At the time of the writing and publication of our antibacterial drug discovery report, there was a company, Quorum Sciences (Iowa City, IA) that had been established to commercialize the findings of leading researchers on bacterial quorum sensing. As the result of two successive acquisitions in 2000 and 2001, Quorum Sciences passed into the hands of Vertex Pharmaceuticals (Cambridge, MA). In 2006, Vertex researchers and their academic collaborators published a report on the discovery of novel specific inhibitors of the P. aeruginosa quorum sensing system. The last author of this report was quorum sensing pioneer E. Peter Greenberg, formerly of the University of Iowa and chief scientific officer at Quorum Sciences, and from 2005 to the present at the University of Washington School of Medicine. The compounds identified in the 2006 report, discovered via high-throughput screening of a diverse 200,000-compound chemical library, resembled the natural AHSL that binds to the P. aeruginosa quorum sensing receptor LasR. (LasR is a transcription factor that when bound to its specific AHSL, mediates the expression of a set of downstream genes, including those that encode virulence factors.) The researchers concluded that the novel quorum sensing inhibitors might be useful chemical tools, but not drug leads.

In 2010, other academic researchers published a report on the discovery of novel antagonists and agonists of the P. aeruginosa quorum sensing receptor LasR, which were of lower molecular weight and otherwise structurally distinct from the natural P. aeruginosa AHSL. However, these compounds were still deemed to be scaffolds for chemical tools, not drug leads. Nevertheless, the researchers speculated that the compounds “could, with further development, provide a pathway for the design of novel antivirulence agents”. Other researchers are continuing studies aimed at discovery of quorum sensing receptor antagonists, whether synthetic organic molecules or natural products. These involve studies with quorum sensing systems of both gram-positive and gram-negative bacteria.

The 2006 report appears to be the last Vertex publication on quorum sensing. However, Vertex continues to conduct research on antibacterial agents. And the company has a facility in the University of Iowa BioVentures Center (Coralville, IA),  which is a continuation of the old Quorum Sciences Iowa facility. As of 2009, Vertex’s Iowa-based team consisted of seven full-time scientists, working on development of antibacterials, and agents to treat hepatitis C and cystic fibrosis, among other areas. The Iowa group participated in the development of Vertex’ now-marketed anti-hepatitis C virus (HCV) agent Incivek (telaprevir).

The May 2012 article “Freezing Time” in The Scientist, and discovery of novel quorum sensing inhibitors

The May 2012 issue of The Scientist contains an article entitled “Freezing Time”, by Vern L Schramm, Ph.D. (Albert Einstein College of Medicine (Bronx, NY). The article focused on design of “transition state analogues”, i.e., compounds with a chemical structure that resembles the transition state of a substrate in an enzyme-catalyzed reaction. Transition state analogs usually act as enzyme inhibitors by blocking the enzyme’s active site. They are exquisitely potent and specific inhibitors, which act at extremely small doses. This makes these compounds potentially attractive as drugs.

A transition state analogue inhibitor that was designed by Dr. Schramm and his colleagues in the early 2000s as an early proof-of-concept molecule is immucillin-H, or forodesine. This is a transition-state analog inhibitor of purine nucleoside phosphorylase.  Forodesine is being developed by BioCryst Pharmaceuticals for treatment of relapsed B-cell chronic lymphocytic leukemia, and the results of a Phase 2 trial were published in 2010.

As described in Dr. Schramm’s May 2012 article, his laboratory has been applying their transition-state analogue technology to the field of quorum sensing in bacteria. Instead of targeting the recognition of AHSLs by quorum sensing receptors such as LasR, the researchers targeted the key enzyme in the AHSL biosynthesis pathway in gram-negative bacteria, known as 5′-methylthioadenosine nucleosidase (MTAN). The biosynthetic pathway for the production of AHSLs, including the key role of MTAN, had been elucidated by Dr. Greenberg and his colleagues in the late 1990s.

Dr. Schramm and his colleagues published the results of studies of three transition state analogues that potently inhibited MTANs of gram-negative bacteria. For example, they inhibited the Vibrio cholerae MTAN with dissociation constants of 73, 70, and 208 pM, respectively. They inhibited MTAN in cell of a virulent strain of V. cholerae with IC50 values of 27, 31, and 6 nM respectively, disrupting autoinducer production in a dose-dependent manner without affecting bacterial growth. The compounds were also potent inhibitors of autoinducer production in an enterohemorrhagic strain of Escherichia coli. The transition-state analogues did not inhibit growth in either V. cholerae or E. coli, but one such compound reduced biofilm production by 18% in E. coli and 71% in V. cholerae.

Moreover, the MTAN inhibitors did not appear to select for bacterial resistance in vitro. When V. cholerae bacteria were grown for 26 generations in the presence of a large excess of MTAN inhibitors, subsequent generations of these bacteria were equally sensitive to inhibition by these compounds as bacteria that had not been previously exposed to the inhibitors. These results are consistent with the hypothesis that agents that inhibit targets that are important in the ability of bacteria to cause disease, but are not essential for bacterial proliferation or survival might not select for drug resistance.

As Dr. Schramm said in the May 2012 article in The Scientist, it remains to be seen whether the MTAN-targeting transition-state analogs developed in his laboratory can translate into novel antibiotics that do not select for resistant pathogens. As of March 2009, Dr. Schramm’s team had developed over 20 potent MTAN inhibitors, which will be specific for bacteria and should have no effect on human metabolism. These compounds have been licensed to Pico Pharmaceuticals (Melbourne, Australia), which plans to develop and initiate clinical trials. Dr. Schramm is a Pico Pharmaceuticals co-founder and chairman of its scientific advisory board. Pico claims that one of its quorum sensing inhibitors, designated as PC0208, has demonstrated proof-of-concept in preclinical studies, and now has “pre-IND” status.

Lessons from these studies

Dr. Schramm’s discovery of novel quorum sensing inhibitors was made possible by a strategy that involved a combination of biology-driven drug discovery and sophisticated chemistry technology. The biology-driven drug discovery strategy involved a combination of 1. Building on the quorum sensing studies of Dr. Greenberg and others, and adopting the strategy, as reviewed in our 2000 Spectrum report, of targeting the quorum sensing system in order to discover agents that would have the possibility of not triggering resistance, and 2. Targeting a critical, bacterial-specific pathway enzyme that is upstream of the recognition of AHSLs by quorum sensing receptors (the usual target of most researchers in this area). This enzyme, MTAN, has a key role in the biosynthesis of AHSLs.

The sophisticated chemical technology employed by Dr. Schramm and his colleagues was of course the transition state analogue technology developed in his own laboratory. Combined with the biology-driven strategy described in the last paragraph, Dr. Schramm’s approach has succeeded in the discovery of compounds that are potential drug candidates, while approaches based on high-throughput screening for AHSL antagonists have so far failed to produce any such compounds. Dr. Scharamm’s laboratory has also obtained evidence that treatment with their compounds should not result in the selection of resistant strains of pathogenic bacteria.

It is possible that other chemistry approaches might be successfully employed to discover quorum sensing inhibitors, both for gram-negative bacteria and gram-positive organisms such as S. aureus.

As we have discussed in numerous articles on this blog, biology-driven drug discovery strategies, often coupled with innovative approaches to chemistry (in the case of small-molecule drug discovery) are applicable to very many different targets involved in a whole range of human diseases. (Biology-driven drug discovery has also been central to discovery and development of many successful large-molecule drugs.) The quorum sensing case study in this article is a simple, understandable, and elegant example of such a strategy.

In addition to the scientific, clinical, and medical aspects of antibacterial drug discovery, the other major issue is the business of antibacterial discovery and development. The economics of drug discovery and development have shifted pharmaceutical industry investment away from the development of drugs targeting short course therapies for acute diseases (such as antibacterials) and towards long-term treatment of chronic conditions.  At the same time, discovery of novel antibacterials has gotten more difficult. As a result, during the 2000-2010 period, such companies as Wyeth, Aventis, Eli Lilly, GlaxoSmithKline, Bristol-Myers Squibb, Abbott Laboratories, Proctor & Gamble, and Merck have either deprioritized anti-bacterial R&D or left the field altogether. Meanwhile, antibiotic resistance, which was a problem in 2000, has become an even greater problem in 2012, in some cases reaching crisis proportions [e.g, methicillin resistant S. aureus (MRSA) that is also resistant to the drug of last resort, vancomycin].

As a result of these economic, scientific, and medical challenges, a €223.7 consortium of five pharmaceutical companies and leading academics, called NewDrugs4BagBugs (ND4BB) was launched in Europe in May 2012. The program is envisioned  to involve a three-stage approach – to improve the understanding of antimicrobial resistance, to design and implement efficient clinical trials, and finally, to take novel drug candidates through clinical development.

And at least one venture capitalist has observed that biotechs that specialize in antibacterial drug development (as well as those that specialize in other areas that have been deemphasized by Big Pharmas) have provided “contrarian opportunities” in biotech venture. According to a June 2 2012 article by Bruce Booth of Atlas Venture published in Forbes, what has been deprioritized by some (or several) Big Pharmas, are likely be re-prioritized by others several years later. Such antibacterial drug developers as Calixa, Cerexa, Novexel, Neutec, Paratek, Pennisula, Protez, and Vicuron have produced some of the best returns in biotech venture capital from merger/acquisition exits. These biotechs included companies that were built around compounds outlicensed from Big Pharma, and others that conducted new research on novel targets, especially for MRSA and other resistant bacteria.  By taking advantage of a strategic depriorization in Pharma, these biotechs and their venture backers were able to create considerable value in the past decade out of antibacterial drug development.

Meanwhile, antibiotic specialist Cubist Pharmaceuticals (Lexington, MA) remains an independent, and profitable, biotech company that is continuing to conduct R&D, including on discovery and development of agents to treat pathogens that are resistant to current antibiotics. It has expanded into development and marketing of peripheral mu-opioid receptor antagonists (including via acquisition of Adolor in 2011), and has recently expanded its R&D facilities.

Can Pico Pharmaceuticals (which has oncology programs in addition to antibacterials) experience similar success?

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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.