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United States Patent Application

View the Complete Application at the US Patent & Trademark Office
Compounds that are inhibitors of the unfolded protein response and endonuclease IRE1 are provided, together with compositions comprising such compounds, and methods for their use in the treatment of various disorders, such as cancer, autoimmune disorders, and diabetes. Also provided are packaged pharmaceuticals comprising these compositions. The compositions may be administered in combination with another therapeutic agent.
Koong, Albert C. (Los Altos, CA), Feldman, Douglas E. (Mountain View, CA)
The Board of Trustees of the Leland Stanford Junior University (Palo Alto CA)
13/ 764,200
February 11, 2013
STATEMENT OF GOVERNMENTAL SUPPORT [0001] This invention was made with government support under contract 1R01CA112108-01A1, awarded by the National Institutes of Health. The government has certain rights in the invention. CROSS-REFERENCE TO RELATED APPLICATIONS [0002] This application is a divisional application of U.S. patent application Ser. No. 12/280,793 filed on Jan. 9, 2009, which is U.S. Pat. No. 8,372,861, which is a national stage application of PCT International Application No. PCT/US07/062,917, filed Feb. 27, 2007, which claims priority of U.S. Provisional Application No. 60/777,458, filed Feb. 27, 2006, all of the preceding disclosures of which are hereby incorporated by reference in their entirety. REFERENCE TO SEQUENCE LISTING, COMPUTER PROGRAM, OR COMPACT DISK [0003] In accordance with "Legal Framework for EFS-Web," (6 Apr. 11) Applicants submit herewith a sequence listing as an ASCII text file. The text file will serve as both the paper copy required by 37 CFR 1.821(c) and the computer readable form (CRF) required by 37 CFR 1.821(e). The date of creation of the file was Feb. 11, 2013, named 3815.sub.--69.sub.--2_seq_list.txt, and the size of the ASCII text file in bytes is 9,520. Applicants incorporate the contents of the sequence listing by reference in its entirety. BACKGROUND OF THE INVENTION [0004] 1. Field of the Invention [0005] The present invention relates generally to compounds, compositions, and packaged pharmaceuticals useful in the treatment of disorders characterized by cell growth in hypoxic conditions, such as cancers, in particular solid tumors. More specifically, the invention relates to compounds, compositions, and packaged pharmaceuticals that inhibit the activity of IRE1. The invention also relates to methods for inhibiting the unfolded protein response, for inhibiting IRE1, and for treating or preventing disorders associated with the unfolded protein response. [0006] 2. Related Art [0007] Presented below is background information on certain aspects of the present invention as they may relate to technical features referred to in the detailed description, but not necessarily described in detail. The discussion below should not be construed as an admission as to the relevance of the information to the claimed invention or the prior art effect of the material described. [0008] A defining feature of solid tumors is their capacity to divide aggressively and disseminate metastases under conditions of nutrient deprivation and limited oxygen availability. These severe stresses arise from inadequate perfusion as the primary tumor rapidly outgrows its initial blood supply, and from dramatic structural abnormalities of tumor vessels that can lead to disturbed microcirculation (Hockel and Vaupel, Semin. Oncol. 28(2 Suppl 8):36-41, 2001; Vaupel, et al. Med. Oncol. 18:243-59, 2001). As a result, regions of low O.sub.2 tension, or hypoxia, are heterogeneously distributed within the tumor mass. While tumor hypoxia is a physiological barrier to cell survival, it paradoxically drives malignant progression by imposing a powerful selective pressure for cells that can best adapt to this stress and subsequently resume cell division. [0009] Tumor hypoxia also correlates with a more aggressive disease course and increased failure following radiation and chemotherapy. The presence of hypoxia has been demonstrated in a wide variety of human cancers, including cervix, breast, lung, brain, pancreas, head and neck, and prostate (Evans S., & Koch C. Cancer Lett. 195:1-16, 2003). Many of these tumors contained regions of severe hypoxia (<5 mmHg oxygen). Clinically, the duration of disease- and progression-free survival correlates inversely with the degree of tumor hypoxia. For example, in patients with squamous carcinoma of the head and neck, the one year disease-free survival was 78% for patients with median tumor pO2 >10 mm Hg but only 22% for median pO2 <10 mm (Brizel, et al., Int. J. Radiat. Oncol. Biol. Phys. 38:285-9, 1997). Hypoxic cells also exhibit increased resistance to standard radiation and chemotherapy treatment programs, as these cells are relatively isolated from the blood supply and because radiation and chemotherapy preferentially kill rapidly dividing cell populations. Collectively, these findings provide strong evidence that hypoxia has a profound impact on tumor growth and clinical outcome. [0010] Hypoxia dramatically reshapes cellular physiology, causing cell cycle arrest, a shift in energy production to glycolysis, elevated secretion of survival and pro-angiogenic factors, expression of genes involved in drug resistance, and increased cell motility and invasion. A watershed discovery linking these profound changes to the control of gene expression was made with the identification of hypoxia-inducible factor (HIF), a heterodimeric transcription factor that exerts control over a broad range of cellular pathways including glycolysis, angiogenesis and erythropoiesis (Semenza, Trends Mol. Med. 2002 8(4 Suppl):S62-7, 2002; Semenza, Nat. Rev. Cancer 3:721-32, 2003). [0011] While HIF controls the expression of more than 60 genes and constitutes a key node in cellular stress signaling, HIF activation alone cannot account for the full repertoire of changes that occur intracellularly as oxygen becomes limiting. The hypoxic cell also elicits additional, HIF-1-independent, adaptive responses that contribute to increased survival under low oxygen conditions. For example, an immediate reaction to hypoxia is a reduction in the rates of global protein synthesis, which reduces energy demands when oxygen and ATP levels are low (Hochachka et al., Proc. Natl. Acad. Sci. USA, 93:9493-8, 1996). Further, hypoxia causes a sharp increase in the expression of molecular chaperones, which assist in protein refolding and in the degradation of terminally misfolded conformers. Underlying these changes is a coordinated cellular program called the unfolded protein response (UPR) that serves as a master regulator of cellular homeostasis and which plays a fundamental cytoprotective role during cellular stresses such as hypoxia. [0012] The endoplasmic reticulum (ER) is an extensive intracellular membrane network that extends throughout the cytoplasm and functions primarily to process newly synthesized secretory and transmembrane proteins. Accumulation of unfolded proteins in this compartment causes ER stress, with prolonged ER stress resulting in cell death. The cellular response to ER stress consists of at least two coordinated pathways: 1) rapid translational arrest mediated by PERK (pancreatic ER kinase or PKR-like ER kinase); and 2) transcriptional activation of unfolded protein response (UPR) target genes (Ron D. J. Clin. Invest. 110:1383-1388, 2002; Harding H., et al. Annu. Rev. Cell. Dev. Biol. 18:575-599, 2002; Feldman D. E., et al. Mol. Cancer. Res. 3:597-605, 2005). In addition to solid tumors, the UPR has been implicated in diseases such as conformational diseases, diabetes, cardiovascular disease, atherosclerosis, viral infection, and cerebrovascular disease (Schroder M., et al. Mutat. Res. 569:29-63, 2005; Kaufman R. J. Clin. Invest. 110:1389-1398, 2002). [0013] During normal embryonic development, activation of the UPR is essential for the maturation of secretory cells in the liver and pancreas, and drives an expansion of the ER in antibody-secreting B lymphocytes to accommodate increased secretory load. Iwakoshi et al., Immunological Reviews 194: 29-38 (2003); Harding et al., Molecular Cell 5: 897-904 (2000); Shaffer et al., Immunity 21: 81-93 (2004); Reimold et al., Genes Dev 14: 152-157 (2000). Several lines of evidence have also implicated the UPR in various disease processes, such as diabetes and cardiovascular disease, and as a survival mechanism underlying tumor growth and the adaptation of malignant cells to hypoxic stress. Ma and Hendershot, Nat Rev Cancer 4: 966-977 (2004); Feldman et al., Mol Cancer Res 3: 597-605 (2005); Koumenis, Curr Mol Med 6: 55-69 (2006). [0014] A critical feature of malignant tumors is their capacity to survive and seed distant metastases under conditions of nutrient deprivation and limited oxygen availability. Hockel and Vaupel, Seminars in Oncology 28: 36-41 (2001); Vaupel et al., Methods in Enzymology 381: 335-354 (2004); Subarsky and Hill, Clin Exp Metastasis 20: 237-250 (2003). Intratumoral hypoxia arises solid tumors through severe structural abnormalities of tumor vasculature and disturbed microcirculation, resulting in tissue regions of extremely low O.sub.2 partial pressures distributed heterogeneously within the tumor mass. Vaupel et al., Methods in Enzymology 381: 335-354 (2004); Hockel and Vaupel, Journal of the National Cancer Institute 93: 266-276 (2001); Vaupel et al., Medical Oncology 18: 243-259 (2001). Since the delivery of oxygen and nutrients to the tumor is determined by fluctuating blood flow, different regions of the tumor must constantly adjust to varying degrees of nutrient deprivation. The tumor microenvironment thus imposes a strong selective pressure for cells best adapted for survival under these stresses. Adaptation to hypoxia contributes to the diminished apoptotic potential of tumor cells and accounts for many of the clinical consequences of malignant progression, including locoregional tumor recurrence and distant metastases. Evans and Koch, Cancer Letters 195: 1-16 (2003); Le et al., Cancer Metastasis Rev 23: 293-310 (2004). Hypoxia-mediated clonal expansion of cells with diminished apoptotic potential has been demonstrated in vitro, and hypoxic cells exhibit increased metastatic potential. Erler et al., Nature 440: 1222-1226 (2006); Graeber et al., Nature 379: 88-91 (1996). Importantly, depletion of molecular oxygen or glucose impairs the posttranslational modification and oxidative folding of secretory proteins, providing a direct biochemical link between nutrient deprivation in tumors and activation of the UPR. Tu et al., Science 290: 1571-1574 (2000); Koumenis et al., Molecular & Cellular Biology 22: 7405-7416 (2002). [0015] PERK, an ER transmembrane protein, was first identified as regulating translational attenuation during ER stress through the phosphorylation of translation initiation factor eIF2.alpha.. While most mRNA translation is repressed following phosphorylation of eIF2.alpha., activating transcription factor 4 (ATF4) is selectively translated during ER stress leading to increased expression of chaperones, foldases, and downstream targets such as CHOP/GADD153, a pro-apoptotic gene. Koumenis et al demonstrated that translational control of protein synthesis during hypoxia also occurs through the activation of PERK. These investigators showed that PERK-/- MEFs where unable to phosphorylate eIF2.alpha. and had decreased survival after exposure to hypoxia compared to the wild-type MEFs. They concluded that PERK plays an important role in hypoxia-induced translation attenuation, further supporting a role for hypoxia in the development of ER stress (Koumenis et al., Mol. Cell. Biol. 22:7405-7416 (2002)). A rapid decrease in de novo protein synthesis upon exposure to hypoxia has also been observed (Chen et al., Cancer Res. 64:7302-7310 (2004)). Downstream of PERK, ATF4 is also activated by hypoxia in a HIF-1 independent manner. One consequence of ATF4 activation is induction of a GADD34 which feeds back to desphosphorylate eIF2.alpha. and release cells from translational inhibition. [0016] In coordination with the inhibition of protein synthesis, the UPR is also responsible for the transcriptional activation of a discrete set of genes. These genes function to increase the cellular folding capacity through the induction of ER chaperone proteins and folding enzymes. The UPR is a conserved stress response and many of its downstream target genes have been characterized in yeast and mammalian cells. In mammalian cells, activating transcription factor 6 (ATF6) and X-box binding protein (XBP1) are critical regulators of the transcriptional response to ER stress. [0017] The ER resident transmembrane protein IRE1 is conserved in throughout eukaryotic phylogeny and functions as both a proximal sensor of ER stress and as a critical UPR signal transducer via its dual cytoplasmic kinase and endoribonuclease domains. Tirasophon et al., Genes Dev 12: 1812-1824 (1998). Mammalian IRE1.alpha., the major functional homolog of yeast IRE1.alpha., excises a 26-nucleotide intron from the mRNA encoding the bZIP transcription factor XBP-1. This introduces a translational frame shift downstream of the splice site to generate XBP-1s, a potent transcription factor. Yoshida et al., Cell 107: 881-891 (2001); Calfon et al., Nature 415: 92-96 (2002); Lee et al., Genes & Development 16: 452-466 (2002). XBP-1s drives an expansion of ER capacity through the increased expression of molecular chaperones and components of the ER-associated protein degradation (ERAD) machinery that is required for the clearance of terminally misfolded proteins. Schroder and Kaufman, Mutation Research 569: 29-63 (2005); Lee et al., Molecular & Cellular Biology 23: 7448-7459 (2003). IRE1.alpha. is extensively activated in hypoxic regions of human tumor xenografts throughout tumorigenesis (Feldman et al., Mol Cancer Res 3: 597-605 (2005)), and transformed mouse fibroblasts genetically deleted for XBP-1 exhibit increased sensitivity to hypoxia and fail to grow as tumors when implanted into immune-deficient mice (Romero-Ramirez et al., Cancer Research 64: 5943-5947 (2004)). Activation of IRE1.alpha. by ER stress triggers multiple signaling outputs that extend beyond the splice-activation of XBP-1, including IRE1.alpha. endonuclease-mediated cleavage of a subset of mRNAs encoding secretory proteins (Hollien and Weissman, Science 313: 104-107 (2006)), and activation of autophagy and apoptosis pathways through the IRE1.alpha. kinase domain and its downstream effectors caspase-12, ASK1, and JNK1 (Ogata et al., Mol Cell Biol (2006); Urano et al., Science 287: 664-666 (2000)). Thus IRE1.alpha. may participate in both cytoprotective and pro-apoptotic pathways. [0018] A schematic of the UPR pathway is shown in FIG. 1. In this model, GRP78 regulates each of the major branches of the UPR by direct association with ATF6, IRE1 and PERK. Given its importance in regulating the UPR, GRP78 levels can be increased by downstream signaling from each of these pathways, indicating that significant overlap occurs in activation of the UPR. [0019] The functional link between the UPR and hypoxia was found through studies on GRP78, a critical regulator of the UPR. Expression of the glucose regulated family of proteins (GRPs) within solid tumors was recognized more than a decade ago. These experiments indicate that glucose starvation and hypoxia were physiologically relevant stresses occurring during the growth of solid tumors (Cai J., et al., J. Cell. Physiol. 154:229-237, 1993). Furthermore, cells in which GRP78 expression was inhibited through an antisense strategy exhibited increased sensitivity to hypoxia compared to the parental wild-type cell line (Koong A., et al., Int. J. Radiat. Oncol. Biol. Phys. 28:661-666, 1994). [0020] Other UPR regulated genes such as GRP94 and protein disulfide isomerase (PDI) have also been implicated in mediating neuronal survival after ischemia/reperfusion injury (Sullivan D., et al., J. Biol. Chem. 278:47079-47088, 2003; Bando Y., et al., Eur. J. Neurosci. 18, 2003.). Similarly, oxygen regulated protein 150 kDal (ORP150, also known as GRP170), another ER chaperone protein, protected neurons from ischemic stress in a cell culture model and reduced the cerebral infarct area after middle cerebral artery occlusion in a transgenic mouse model (Tamatani M., et al., Nat. Med. 7:317-323, 2001). [0021] These studies indicate that the UPR has a broad range of functions during hypoxia including promotion of cell survival and regulation of angiogenesis. Given its role in regulating survival under hypoxia and its requirement for tumor growth, targeting XBP-1 may be an effective therapeutic strategy. However, there are currently few examples of anti-cancer drugs that can effectively inhibit transcription factor activation. There thus remains a need for compositions that may be employed to inhibit the activity of XBP-1 and thereby prevent or inhibit tumor growth. [0022] Identification of compounds capable of inhibiting the activity of XBP-1 and thereby capable of preventing or inhibiting tumor growth would be facilitated by assays suitable for use in high throughput screens. Direct measurement of XBP-1 levels in cells is not easily automated. Convenient and easily detectable substrates for the endonuclease or kinase activities of IRE1 are currently unavailable. US Patent Application No. 2003/0224428 reports methods purportedly useful in screening inhibitors of IRE1-mediated processing of untranslatable XBP-1 mRNA. The reported methods are limited to the screening of plasma cells or virus-infected cells, however, and are therefore unsuitable for identifying compounds useful in the treatment or prevention of disorders in more general cell types and tissues. The methods also fail to account for the effects of tumor microenvironment, such as, for example, hypoxia, on the activity of potential therapeutic compounds. The methods also lack steps to counterscreen for compounds causing non-specific effects on the detectable marker and for compounds that are toxic to cells even in the absence of ER stress. The methods would therefore falsely identify compounds that have nothing to do with the UPR and that would be unsuitable for therapeutic use. Furthermore, the methods have not been shown to be suitable for use in high throughput screening assays. [0023] Due to the importance of the unfolded protein response in cellular metabolism, and, in particular, in pathological processes, there is great interest in developing inhibitors with defined specificities against this process. Such inhibitors can help to identify target enzymes in cells, particularly where the cells are associated with particular indications, and can provide new drug candidates. There is thus a need for inhibitors of the unfolded protein response and novel methods of inhibiting this pathway, as well as methods of treating or preventing disorders of the unfolded protein response and methods of identifying novel inhibitors of the pathway.