Exploring Pharmacological Space

RESEARCH HIGHLIGHTS

INFORMATICS Exploring pharmacological space

What can we learn from the data are at a much earlier stage, and how the ligand properties of known integration of vast collections of at present most such data are widely active compounds for protein targets pharmacological data? Can we ration- spread among research papers, patents can be used to derive probabilistic ally expand the search for new drugs and proprietary screening databases. approaches to determining ‘degrees’ of beyond compounds that affect single So, Paolini et al. set out to create a druggability, relative to oral drug space. targets in the ‘druggable genome’? single integrated database, including The analysis also highlights the Insight into key questions such as ~4.8 million compounds and potential for more rational investiga-

these has been provided by a recent ~600,000 SARs (for example, IC50 tion of an issue that has attracted extensive analysis, described in Nature values) for ~3,000 protein targets from much interest in drug discovery Biotechnology, which integrates several published and proprietary sources, recently: the notion of polypharma- large sources of structure–activ- with the aim of better understanding cology or ‘dirty drugs’. So far, such ity relationship (SAR) data from ‘pharmacological space’ — the parts drugs, whose therapeutic activity is medicinal chemistry efforts. of chemical space that contain thought to depend on their ability Although databases containing biologically active small molecules. to modulate multiple targets — for protein sequence and structure data In total, the authors identified example, neurotransmitter receptors are well established and widely avail- 529 proteins encoded in the human in the case of several major antipsy- able, analogous resources for SAR genome for which there is at least one chotics — have had a fairly limited compound with a binding affinity amount of rational input in their dis- <100 nM that also satisfies the covery. However, the mapping of poly- Lipinski rule-of-five (the standard pharmacology networks as described criteria for likely oral drug absorp- by Paolini et al. should facilitate the tion). At least one small-molecule development of rational design strate- ‘chemical tool’ (binding affinity <10 gies for selectively promiscuous drugs. μm, but not necessarily satisfying the And overall, increased application rule-of-five) has been identified for of predictive models based on such 836 human proteins. analysis in the assessment of other Several issues that could have important factors in drug discovery considerable significance for future such as druggability and attrition risks drug discovery efforts were also inves- could lead to significant improvement tigated by the authors. For example, in the success rate of the process. they show how a large-scale integrated Peter Kirkpatrick chemogenomics database can be used to build Bayesian models to predict ORIGINAL RESEARCH PAPER Paolini, G. V. et al. compound activity across a virtual Global mapping of pharmacological space. Nature Biotechnol. 24, 805–815 (2006) screening bank of more than 600 FURTHER READING Lipinski, C. & Hopkins, A. protein targets. Furthermore, the Navigating chemical space for biology and authors propose a refinement of medicine. Nature 432, 855–861 (2004) | Hopkins, A. L. & Groom, C. R. The druggable the concept of druggability beyond genome. Nature Rev. Drug Discov. 1, 727–730 (2002) Lipinski’s rule-of-five, by considering

RESEARCH HIGHLIGHTS ADVISORS ERIK DE CLERCQ F. PETER GUENGERICH MADS KROGSGAARD THOMSEN CHRISTOPHER LIPINSKI Katholieke Universiteit Leuven, Belgium Vanderbilt University Nashville, TN, USA Novo Nordisk, Bagsvaerd, Denmark Pfizer Global Research and Development, RODERICK FLOWER FRANZ HEFTI HUGO KUBINYI Groton, CT, USA William Harvey Research Institute, QMW, Rinat Neuroscience Corporation, Palo Alto, University of Heidelberg, Germany TOMI SAWYER London, UK CA, USA ROBERT LANGER Massachusetts Institute of Ariad Pharmaceuticals, Cambridge, MA, USA YOSHIJI FUJITA JOAN HELLER BROWN Technology Cambridge, MA, USA JANET WOODCOCK Clinical Proteome Center, Tokyo Medical University of California San Diego, JULIO LICINIO University of California Los Food & Drug Administration, Rockville, University CA, USA Angeles, CA, USA MD, USA

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The idea that endogenous progenitor Encouragingly, such progenitors NEUROLOGICAL DISORDERS cells might be harnessed to replace have been identified in the SNc, and neurons lost in neurodegenerative previous work has demonstrated that

diseases is popular, but requires the activation of D3 dopamine receptors New neurons repair development of methods to stimulate stimulates neurogenesis in this region their proliferation and differentia- in healthy adult rats. Parkinson’s brain tion. Hopes for this approach have The new study demonstrates the now received a boost from a study effects of a preferential D3 agonist, by Van Kampen and Eckman, show- 7-OH-DPAT, in a common rat ing that activation of a particular model of Parkinson’s disease, the dopamine receptor subtype stimu- 6-hydroxydopamine model. By label- lates neurogenesis and functional ling cells undergoing DNA synthesis, repair in a Parkinson’s disease model. the researchers showed that chronic Parkinson’s disease involves the drug treatment increased prolifera- degeneration of dopaminergic neu- tion in the SNc. Many new-born cells rons in the nigrostriatal tract, which subsequently expressed proteins projects from the substantia nigra pars typically found in mature dopamin- compacta (SNc) in the midbrain to the ergic neurons. To achieve functional striatum and is essential for the con- recovery and repair of the nigrostriatal trol of movement. Current treatments tract, these newly generated neurons that boost striatal dopamine levels must generate new projections to have adverse side effects, lose efficacy the striatum. This was assessed by over time and do not alter the under- injecting a fluorescent tracer into the lying pathology, making cell-replace- striatum. After retrograde transport ment strategies desirable. Utilizing of the tracer to the SNc, increased endogenous progenitor cells for this numbers of neurons with axons pro- purpose could have advantages over jecting along this tract were revealed. invasive transplantation strategies. Finally, two different behavioural tests

prolonged imatinib therapy — IRE1 can KINASE INHIBITORS and dilated endoplasmic reticulum (ER), which are signs of stress. signal cell death by activating the pro- To investigate this further, the authors death JNK pathway. The authors found treated healthy mice with imatinib that JNK was activated in the hearts Stressed out hearts and saw similar structural changes in of imatinib-treated mice and that this the mouse hearts. Doses of imatinib activation was reduced by treatment Imatinib mesylate (Gleevec) potently given to produce blood concentrations with salubrinal, a small-molecule inhibits the kinase activity of the comparable to those in humans led to inhibitor of EIF2α dephosphorylation. oncogenic fusion protein BCR–ABL and These findings left ventricular dysfunction. Imatinib Furthermore, the inhibition of either is an effective treatment for chronic seemed to cause necrotic cell death EIF2α dephosphorylation with myeloid leukaemia. Although imatinib suggest that (as seen by the dose-dependent salubrinal or JNK activity with a peptide seems to be well tolerated by most clinical trials collapse of mitochondrial membrane inhibitor rendered cardiomyocytes patients, more than 60% of patients of new agents potential, release of cytochrome c and resistant to the imatinib-induced on imatinib in clinical trials develop pronounced cytosolic vacuolization) collapse of mitochondrial membrane peripheral oedema, a possible sign of that target rather than apoptosis. Gene transfer potential and cell death. Therefore, the cardiotoxicity. However, heart function ABL should of an imatinib-resistant mutant of ABL imatinib-mediated induction of the ER was not assessed in any of the clinical prospectively inhibited the imatinib-induced release of stress-response pathway leads to cell trials with this agent. Thomas Force and cytochrome c and conferred protection death through the activation of JNKs. colleagues report that 10 patients who assess left against cell death. This suggests that These findings not only suggest that previously had normal heart function ventricular the inhibition of ABL by imatinib is the patients who are on imatinib should developed severe heart failure after the function. mechanism of cardiomyocyte toxicity. be monitored closely for signs of left initiation of imatinib therapy. They found What are the mechanisms ventricular dysfunction, but also that that imatinib is not directly toxic, but that regulate imatinib-induced clinical trials of new agents that target that the inhibition of one of its targets, cardiomyocyte death? Because of ABL should prospectively assess left ABL, triggers the stress response in the observed ER dilation, Force and ventricular function so that rates of cardiomyocytes and induces cell death. colleagues investigated the ER stress- cardiotoxicity can be determined. Myocardial biopsy samples taken from response pathway and found that Ezzie Hutchinson, patients showed prominent membrane imatinib activated both the EIF2α and Nature Reviews Cancer whorls in the myocytes, an abnormality IRE1 parts of this pathway in imatinib- that is a characteristic of toxin- treated mice. Although this response is ORIGINAL RESEARCH PAPER Kerkelä, R. et al. Cardiotoxicity of the cancer therapeutic agent induced myopathies. The cells also initially protective, if the inducing stress imatinib mesylate. Nature Med. 12, 908–916 (2006) showed pleiomorphic mitochondria to cells is not relieved — as occurs with

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were used to demonstrate recovery of CANCER motor function in the treated animals. These effects lasted several months after treatment ended, providing Stress can fuel tumour angiogenesis further evidence of changes in the underlying neuronal pathways. These findings show that endogenous progenitor cells can be stimulated to contribute to the functional repair of damaged neuronal tracts, providing hope for neurodegenerative disease therapy and giving further support for targeting the D3 receptor as a therapeutic strategy for Parkinson’s disease. Several

D3 receptor agonists are already in use for Parkinson’s disease, which could encourage the development of similar therapeutics and lead to a better understanding of the underlying molecular pathways, revealing further therapeutic targets. β Katherine Whalley The possible effects of stress on cancer are a 2-adrenoceptor-deficient ovarian cancer cell matter of hot debate. While most studies line variants, and tumour cells in which the ORIGINAL RESEARCH PAPER Van Kampen, J. M. investigating this connection focus on the β -adrenoceptor was knocked down by small & Eckman, C. B. Dopamine D3 receptor agonist 2 delivery to a model of Parkinson’s disease restores dampening effects of stress on the immune interfering RNA, were ‘immune’ to the stress the nigrostriatal pathway and improves locomotor response to arising tumours, a more direct link effect, further confirming the central behaviour. J. Neurosci. 26, 7272–7280 (2006) has now been uncovered. Reporting in Nature importance of this receptor. Downstream of β Medicine, Thaker et al. demonstrate that stress the 2-adrenoceptor, it was found that hormones can accelerate cancer progression catecholaminergic stimulation induces expression by affecting tumour angiogenesis, thereby of vascular endothelial growth factor (VEGF) via a enhancing tumour growth and metastasis, cyclic AMP–protein kinase A-dependent pathway. in mouse models of ovarian cancer. The resulting elevated levels of VEGF led to To investigate the stress–cancer link, immune- increased tumour vascularization — and the deficient ‘nude’ mice were inoculated into the ovarian cancer cells seem to exploit this pathway peritoneal cavity with human ovarian cancer cell to boost their own blood supply. lines after one week of experimental stress. This Although the effects of stress on immuno- was induced using a physical restraint system, in logical, neurochemical and endocrinological which periodic immobility induces high levels of functions are well known, this is the first report hypothalamic–pituitary–adrenal and sympathetic to demonstrate that the neuroendocrine stress nervous system activity that is characteristic of response can also directly affect the growth and chronic stress. Two weeks after tumour activity of malignant tissue via hormone receptors inoculation, there was a marked difference in on tumour cells. If this mechanism is confirmed in tumour aggressiveness: stressed mice had two- the human setting, it could have exciting to threefold more tumour nodules, with similar therapeutic implications for the management increases in tumour weight gain, compared with of ovarian cancer and possibly other types of ‘unstressed’ controls. Furthermore, whereas in cancer — especially as beta-blockers are safe control mice tumours were confined to the and readily available. The authors also peritoneal cavity, tumours had spread to the liver speculate that other neuroendocrine signalling and spleen in 50% of the stressed mice. Similar pathways might modulate tumour cell biology experiments with a different ovarian cancer cell under other circumstances, implying that line and in an orthotopic breast cancer model interventions targeting neuroendocrine function showed that these stress effects were evident in at the level of the CNS could represent a new a wide range of tumour cell lines. strategy to protect patients from the At the molecular level, this effect was found detrimental effect of stress on the progression to be conveyed by stress-induced tissue of malignant disease. β catecholamines activating 2-adrenoreceptors on Alexandra Flemming tumour cells, a receptor overexpressed in most ovarian cancer cell lines. The effect of stress could ORIGINAL RESEARCH PAPER Thaker, P. H. et al. Chronic stress be mimicked with β -adrenoceptor agonists, and promotes tumor growth and angiogenesis in a mouse model of 2 ovarian carcinoma. Nature Med. 12, 939–944 (2006). blocked with the beta-blocker propanolol. Natural

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IN BRIEF CARDIOVASCULAR DISEASE

OBESITY SNP to the rescue?

Neuronal PTP1B regulates body weight, adiposity and Can a common single nucleotide polymorphism (SNP) have sufficient impact to leptin action. affect therapeutic targeting in heart disease? This possibility has recently been Bence, K. K. et al. Nature Med. 16 July 2006 (doi:10.1038/mm1435) raised in a paper by Liggett and colleagues, who showed that a polymorphism β β Protein tyrosine phosphatase (PTP) 1B is a potential therapeutic in the 1-adrenergic receptor ( 1AR) altered cardiac function and response to target for obesity and type 2 diabetes. To investigate how PTP1B the adrenergic receptor antagonist bucindolol in human heart failure. affects adiposity, Bence and colleagues generated mice with β Clinical trials of 1AR antagonists in heart failure have often revealed tissue-specific deletions of Ptp1b in brain, muscle, liver or fat. substantial interindividual variability in outcomes, which the authors Only mice lacking neuronal PTP1B were resistant to high-fat considered could be due to differences in the β AR gene. Indeed, the Liggett diet-induced obesity and were protected from developing leptin 1 resistance. Neuronal PTP1B also regulated adipocyte leptin group had previously found a common non-synonymous SNP that results in β production and insulin sensitivity independent of changes in either Arg or Gly being encoded at amino-acid position 389 of the 1AR. β β body weight. So, it seems for effective obesity and type 2 diabetes Compared with Gly- 1AR, Arg- 1AR displayed increased stimulation of therapy, PTP1B inhibitors should be directed to the brain. adenylyl cyclase in transfected fibroblasts, enhanced contractility in transgenic mouse hearts and caused a larger increase in left ventricular ejection fraction β ANTI-INFECTIVES after 1AR antagonist administration in human studies. The authors therefore set out to investigate the relevance of this SNP for The protozoan inositol phosphorylceramide synthase; β AR antagonist therapy in heart failure by using bucindolol, a a novel drug target which defines a new class of 1 drug that has previously failed to show efficacy in clinical sphingolipid synthase. trials. Ventricular tissue from failing and non- Denny, P. W. et al. J. Biol. Chem. 22 July 2006 (doi:10.1047/jbc. failing human hearts was used to investigate M600796200) β the impact of 1AR genotype on contractile Infections caused by kinetoplastid protazoan parasites are responses. In both heart types, Arg prevalent in developing countries, but treatments are often toxic. Denny and colleagues identified and characterized a protozoan homozygotes displayed fourfold larger inositol phosphorylceramide (IPC) synthase, an enzyme essential agonist-promoted contractility than Gly for the synthesis of cell-membrane sphingolipids. Because this carriers. In transfected fibroblasts enzyme has no mammalian equivalent, it raises the possibility of β expressing 1ARs of either genotype, developing antiprotozoal drugs with reduced side effects. β those expressing the Arg- 1AR displayed a substantially greater degree of BIOTECHNOLOGY noradrenaline-stimulated cAMP accumulation, and bucindolol showed a larger Stem cell-derived erythroid cells mediate long-term absolute cAMP-lowering effect in these cells systemic protein delivery. β compared with those expressing the Gly- 1AR. Chang, A. H. et al. Nature Biotechnol. 16 July 2006 (doi:10.1038/nbt1227) β To understand the clinical implications of the 1AR SNP, the authors Chang and colleagues have developed a novel method of long- β undertook genotyping of the 1AR allele in patients who had taken part in a term, systemic therapeutic protein delivery by exploiting the large placebo-controlled clinical trial of bucindolol for the treatment of globin-synthesis system in erythroid cells. By targeting human clotting factor IX expression to late-stage erythropoiesis, high- moderate and severe heart failure. Each patient cohort consisted of >200 level secretion of clotting factor IX was achieved in a murine subjects, grouped by treatment and genotype. No outcome was associated model of haemophilia B, resulting in phenotypic correction of with genotype in the placebo group, indicating little impact on the natural the coagulation disorder. Advantages of this method include course of heart failure. However, Arg homozygotes treated with bucindolol had resistance to transcriptional silencing, induction of immune an age-, sex- and race-adjusted 38% reduction in mortality and 34% reduction tolerance and a reduction of the risk of insertional oncogenesis. in mortality or hospitalization compared with placebo. In contrast, Gly carriers had no change in clinical response to bucindolol compared with placebo. TARGET VALIDATION The therapeutic advantage of Arg homozygotes was due to the degree of Expression of mammalian GPCRs in C. elegans adrenergic activity that could be antagonized by bucindolol. generates novel responses to human ligands. Although it has yet to be shown whether these results can be β Teng, M. S. et al. BMC Biol. 20 July 2006 (doi:10.1186/1741-7007-4-22) extrapolated to other 1AR antagonists with differing pharmacological Current in vitro methods used to study mammalian G-protein- properties to bucindolol, this study has shown that a drug that was not coupled receptor (GPCR)–ligand interactions might not efficacious in a mixed patient population displayed greater efficacy in accurately reflect in vivo interactions. Teng and colleagues patients of a specific genotype, and so could set the stage for genetic-based have developed a simple in vivo method to study and screen treatments in heart failure. GPCR ligands using the nematode Caenorhabditis elegans. Charlotte Harrison In an avoidance assay, C. elegans expressing either mammalian somatostatin-2 receptor (Sstr2) or chemokine-5 receptor ORIGINAL RESEARCH PAPER Liggett, S. B. et al. A polymorphism within a conserved β1-adrenergic in gustatory neurons were able to detect and respond to receptor motif alters cardiac function and β-blocker response in human heart failure. Proc. Natl Acad. Sci. USA appropiate agonists. Pre-exposure to ligand led to receptor 103, 11288–11293 (2006) FURTHER READING Weinshilboum, R. & Wang, L. Pharmacogenomics: bench to bedside. Nature Rev. Drug desensitization and behavioural adaptation, and structure– Discov. 3, 739–748 (2004) function relationships could be established for Sstr2 ligands.

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