WO2014052669A1 - Modulation of ire1 - Google Patents

Modulation of ire1 Download PDF

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Publication number
WO2014052669A1
WO2014052669A1 PCT/US2013/062039 US2013062039W WO2014052669A1 WO 2014052669 A1 WO2014052669 A1 WO 2014052669A1 US 2013062039 W US2013062039 W US 2013062039W WO 2014052669 A1 WO2014052669 A1 WO 2014052669A1
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substituted
unsubstituted
disease
nhc
compound
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PCT/US2013/062039
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French (fr)
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Bradley J. Backes
Dustin J. MALY
Scott A. OAKES
Feroz R. PAPA
Gayani PERERA
Likun WANG
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The Regents Of The University Of California
University Of Washington Through Its Center For Commercialization
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Priority to CA2886240A priority Critical patent/CA2886240A1/en
Priority to AU2013323426A priority patent/AU2013323426A1/en
Priority to CN201380061276.4A priority patent/CN104995192A/en
Priority to MX2015003874A priority patent/MX2015003874A/en
Application filed by The Regents Of The University Of California, University Of Washington Through Its Center For Commercialization filed Critical The Regents Of The University Of California
Priority to RU2015115631A priority patent/RU2015115631A/en
Priority to JP2015534672A priority patent/JP2015532287A/en
Priority to KR1020157010751A priority patent/KR20150061651A/en
Priority to EP13841491.7A priority patent/EP2900673A4/en
Priority to SG11201502331RA priority patent/SG11201502331RA/en
Priority to BR112015006828A priority patent/BR112015006828A8/en
Publication of WO2014052669A1 publication Critical patent/WO2014052669A1/en
Priority to US14/670,088 priority patent/US10131668B2/en
Priority to IL237970A priority patent/IL237970A0/en
Priority to US16/149,606 priority patent/US10822340B2/en
Priority to US17/031,132 priority patent/US11613544B2/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
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Definitions

  • ER stress can result from secretory work overload, expression of folding-defective secretory proteins, deprivation of nutrients or oxygen, changes in luminal calcium concentration, and deviation from resting redox state. Sophisticated cellular surveillance and quality control systems work to maintain ER homeostasis under such perturbations. Under ER stress, secretory proteins accumulate in unfolded forms within the organelle to trigger a set of intracellular signaling pathways called the unfolded protein response (UPR).
  • URR unfolded protein response
  • UPR signaling increases transcription of genes encoding chaperones, oxidoreductases, lipid-biosynthetic enzymes, and ER-associated degradation (ERAD) components (Travers, K. J. et al. Cell 101, 249-258 (2000)).
  • ESD ER-associated degradation
  • Apoptosis of irremediably stressed cells is an extreme, yet definitive, quality control strategy that protects multicellular organisms from exposure to immature and damaged secretory proteins. So at the cost of losing some cells, multicellular organisms may benefit temporarily from Terminal UPR-induced apoptosis.
  • Terminal UPR-induced apoptosis many deadly human diseases occur if too many cells die through this process. Conversely, many human diseases such as diabetes mellitus and retinopathies proceed from unchecked cell degeneration under ER stress (Merksamer, P.I., and Papa, F.R., J Cell Sci 123, 1003-1006 (2010); Papa, F.R.
  • Type 2 diabetes may be a prototype of cell degenerative diseases caused by UPR-mediated apoptosis under irremediable ER stress. These same principles appear to be at play in type 1 diabetes, wherein immune attack on islet ⁇ -cells elevates ER workload and causes ER stress in remaining cells. A deeper fundamental and mechanistic understanding of the etiology and pathogenesis of diabetes mellitus may lead to increasing opportunities for the development of novel and effective therapies. Terminal UPR signaling is central to these conditions as shown through experimental data and uses of proprietary compounds that defeat the consequences of terminal UPR signaling in ER stress- challenged ⁇ -cells to afford significant cytoprotection.
  • IRE la and IRE1 ⁇ are ER-transmembrane proteins that become activated when unfolded proteins accumulate within the organelle.
  • IRE la is the more widely expressed and well-studied family member.
  • the bifunctional kinase/endoribonuclease IRE la controls entry into the terminal UPR.
  • IRE la senses unfolded proteins through an ER lumenal domain that becomes oligomerized during stress (Zhou, J. et al. Proceedings of the National Academy of Sciences of the United States of America 103, 14343-14348 (2006); Credle, J. J. et al. Proc Natl Acad Sci USA 102, 18773-18784 (2005); Aragon, T. et al.
  • XBPls's target genes encode products that enhance ER protein folding and quality control (Lee, A. H. et al, Molecular and cellular biology 23, 7448-7459 (2003)).
  • IRE 1 a promotes adaptation via XBP 1 s .
  • IRElcc Under irremediable ER stress, positive feedback signals emanate from the UPR and become integrated and amplified at key nodes to trigger apoptosis.
  • IRElcc is a key initiator of these pro-apoptotic signals.
  • IRElcc employs auto-phosphorylation as a "timer.”
  • Remediable ER stress causes low-level, transient auto-phosphorylation that confines RNase activity to XBPl mRNA splicing.
  • sustained kinase autophosphorylation causes IREl 's RNase to acquire relaxed specificity, causing it to endonucleolytically degrade thousands of ER-localized mRNAs in close proximity to IRElcc (Han, D. et al.
  • mRNAs encode secretory proteins being co-translationally translocated (e.g., insulin in ⁇ cells).
  • secretory proteins e.g., insulin in ⁇ cells.
  • transcripts encoding ER- resident enzymes also become depleted, thus destabilizing the entire ER protein-folding machinery.
  • IREl 's RNase becomes hyperactive, adaptive signaling through XBP l splicing becomes eclipsed by ER mRNA destruction, which pushes cells into apoptosis.
  • a terminal UPR signature tightly controlled by IREla's hyperactive RNase activity causes (1) widespread mRNA degradation at the ER membrane that leads to mitochondrial apoptosis (Han, D. et al. Cell 138, 562-575, (2009)), (2) induction of the pro-oxidant thioredoxin-interacting protein (TXNIP), which activates the NLRP3 inflammasome to produce maturation and secretion of interleukin- ⁇ ⁇ , and consequent sterile inflammation in pancreatic islets leading to diabetes (Lerner, A. G. et al.
  • Retinitis pigmentosa is a clinically and genetically heterogeneous group of inherited retinal disorders characterized by diffuse progressive dysfunction and loss of rod and cone photoreceptors, and retinal pigment epithelium. There are no approved therapies to offer the over 100,000 Americans who currently suffer from RP. As RP is a leading cause of irreversible vision loss, new therapeutic approaches for this condition would be expected to have significant cost-saving benefits for health care systems.
  • RP Retinitis pigmentosa
  • a great deal of evidence suggests that the accumulation of misfolded proteins within the ER is a central causative mechanism in many forms of RP. When the protein- folding capacity of the ER is overwhelmed, cells experience "ER stress" and actively commit programmed cell death. For example, mutations in rhodopsin are the most common cause of RP in the US and lead to a defective rhodopsin protein that misfolds and accumulates in the ER to cause high levels ER stress.
  • novel ATP-competitive small molecule kinase inhibitors of IRE la that prevent oligomerization and/or allosterically inhibit its RNase activity.
  • ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
  • L 1 is a bond or unsubstituted C1-C5 alkylene;
  • L 2 is a bond, -NR 6a -, -0-, -S-, -C(O)-
  • R 1 is hydrogen, oxo, halogen, -CX 3 , -CN, -S0 2 C1, -SO n R 10 , -SO v NR 7 R 8 ,
  • R 10b , -NR 7b C (0)R 9b , -NR 7b C(0)OR 9b , -NR 7b OR 9b , -OCX b 3 , -OCHX b 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
  • R 4 and R 5 are independently hydrogen or unsubstituted Ci-Ce alkyl;
  • R 7 , R 8 , R 9 , R 10 , R 6a , R 7a , R 8a , R 9a , R 10a , R 6b , R 7b , R 8b , R 9b and R 10b are independently hydrogen, halogen, -CF 3 , -CN
  • composition including a
  • a method of treating a disease in a patient in need of such treatment including administering a therapeutically effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof, to the patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
  • a compound described herein e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim
  • the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
  • a method of modulating the activity of an Irel protein including contacting the Irel protein with an effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof.
  • a compound described herein e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim
  • R , R , R 4d , R 5d , R 6d , R 7d , R 8d , R 9d , and R 10d are each independently C 2 _ 6 alkyl, Ci_ 6 haloalkyl, -C 1-4 alkyl-R 12d , C 2 _6 alkenyl, C 2 _6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R l ld groups; each R l ld is independently Ci-6 alkyl, Ci_ 6 haloalkyl, -C(0)R d , -C(0)OR d , -C(0)NR d 2 , S(0) 2
  • R 2d and R 3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR d , -SR d , -NR d 2 , -C(O) R d , C(0)OR d , -C(0)NR d 2 , -S(0) 2 R d , -OC(O) R d , -OC(0)OR d , OC(0)NR d 2 , N(R d )C(0) R d , - N(R d )C(0)OR d , or -N(R d )C(0)NR
  • each R od is independently hydrogen or Ci_ 6 alkyl,each R d is independently hydrogen, or Ci_6 alkyl.
  • R ld is -OR d , -SR d , -NR d 2 , -C(0)R d , -C(0)OR d , -C(0)NR d 2 , - N(R d )C(0)R d , -N(R d )C(0)OR d , -N(R d )C(0)NR d 2 , phenyl, monocyclic heteroaryl, C 3 - 8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR d , -SR d , -NR d 2 , -C(0)R d , C(0)OR d
  • the present disclosure is directed to compositions and methods for activating IRE la RNase activity using human and murine IRE la.
  • the present disclosure is directed to compositions and methods for inhibiting human and murine IRE la RNase activity using compounds: GPl 17 (KIRA2), GPl 18 (KIRA1), GP 146 (KIRA3), GP146 (NMe), GP 146(Am), Formula B, Formula (A), compounds shown Figs. 7 and 8, and other derivative compounds disclosed herein
  • the present disclosure may also be directed to pharmaceutical compositions comprising any of the compounds disclosed herein.
  • the present disclosure provides a compound having Formula
  • the present disclosure provides those compounds illustrated in Fig. 8, and pharmaceutically acceptable salts thereof.
  • the present disclosure provides methods for treating disorders associated with deregulated UPR signaling comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) any of the compounds disclosed herein, or (ii) a pharmaceutical composition comprising any of the compounds disclosed herein and a pharmaceutically acceptable excipient, carrier, or diluent.
  • the present disclosure provides methods for treating disorders associated with deregulated UPR signaling comprising providing to a patient in need of such treatment a therapeutically effective amount of either a compound of formula (B), the compound illustrated in Fig. 7 and any described derivatives, and those compounds illustrated in Fig. 8 or any of the described or illustrated derivatives thereof, or (ii) a pharmaceutical composition comprising a compound of formula (B) or any of the derivatives thereof described herein and a pharmaceutically acceptable excipient, carrier, or diluent, wherein the compound of formula (B) is
  • Fig. 1 Interaction of ATP-competitive inhibitors with the bifunctional kinase/RNase, IRE la.
  • a Proposed binding modes of type I and type II kinase inhibitors with the ATP-binding pocket of IRE 1 a.
  • Left panel shows the contacts a type I inhibitor, APY29, forms with yeast IRE la (PDB code 3SDJ) 18 (SEQ ID NO:3).
  • the right panel shows the proposed contacts a type II inhibitor, GP l 18, forms with IRE la based on the co-crystal structure of the same inhibitor bound to Src (PDB code 3EL8) (SEQ ID NO:4) (also see Fig. 15).
  • Fig. 2 APY29 and GP146 (KIRA3) divergently modulate the RNase activity and oligomerization state of IREla*.
  • ⁇ -PPase treatment of IREla* produces dephosphorylated IREla* (dP-IREla*); immunoblots using anti- IREla and anti-phospho IREla antibodies are shown,
  • Fig. 3 Characterization of GP146's interaction with the ATP-binding site of IREla.
  • (a) A crystal structure of the kinase domain of human IREla bound to ADP; the native cysteine residues that were monitored using the ICAT footprinting method are labeled and shown as thick rods and the DFG-motif is shown as thin bars; cys715 is part of the hinge region of IREla and its side chain partially occupies the ATP-binding site; cys645 is in the activation loop, two residues away from the DFG-motif; cys572 is located on the top of the N-terminal lobe of the catalytic domain and is distant from the ATP-binding site, (b) Results of the ICAT footprinting experiments with IREla*; alkylation rates were measured in the presence of DMSO (circle), APY29 (square) (20 ⁇ ), or GP 146 (triangle) (20 ⁇ ) (mean ⁇ SD, n
  • Fig. 4. APY29 and GP146 differentially affect oligomerization state of IREla*.
  • Fig. 5 Chemical-genetic modulation of IREla kinase and RNase activity in vivo,
  • (a) Anti-total and anti-phospho IREla immunoblots of T-Rex 293 cells expressing "holed" IREla 1642 A under Doxy eye line (Dox) control; cells were pre-treated for 1 hr with GP146 at indicated concentrations, then induced with Dox (1 ⁇ ) for 8 hrs; plots show normalized phosphorylation levels and ratios of spliced XBP l mRNA under varying [GP146] (mean ⁇ SD, n > 3).
  • APY29 Model of how type I kinase inhibitors (APY29), type II kinase inhibitors (GP146), and RNase inhibtors (STF-083010) modulate the enzymatic activities of WT IREla.
  • APY29 inhibits IREla trans-autophosphorylation but promotes oligomerization and activates the RNase domain;
  • STF-083010 inhibits the RNase activity of IREla but does not affect kinase activity or the overall oligomerization state.
  • GP 146 inhibits both the kinase and RNase domains of IREla and stabilizes the monomeric form; cartoons are not meant to differentiate between the relative orientations of monomer subunits in IREla.
  • Fig. 7 illustrates the compound Formula (A), wherein the R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , and R 10 are each defined herein.
  • Fig. 8 illustrates analogs of GP146 that demonstrate the ability to modulate and/or inhibit IREla RNase activity.
  • Fig. 9 ER stress-induced apoptosis can be replicated by simply overexpressing IREla.
  • A Percentage of INS- 1 cells staining positive for Annexin V after being treated with increasing concentrations of Thapsigargin (Tg) for 24, 48 and 72 h.
  • B Anti-Procaspase-3 and Cleaved Caspase-3 immunoblot of INS- 1 cells treated with indicated concentrations of Tg for 12, 24 and 48h; anti-GAPDH immunoblot serves as loading control.
  • C Model of ER stress mediated activation of IREla leading to ER-localized mRNA endonucleolytic decay, terminal UPR endpoints, and apoptosis.
  • D Anti-Phospho-IREla and anti-Myc immunoblot of INS-1 stable line expressing transgenic wild-type IREla (WT) under increasing doses of Doxycycline (Dox) for 24h; anti-GAPDH immunoblot serves as loading control.
  • E Ethidium-bromide (EtBr)- stained agarose gel of XBP 1 cDNA amplicons after induction by treating INS-1 IRE1 a (WT)- expressing stable cells with increasing concentrations of Dox for 24 hours; the cDNA amplicon of unspliced XBP1 mRNA is cleaved by a Pstl site within a 26 nucleotide intron to give 2U and 3U; IRE la-mediated cleavage of the intron and re-ligation in vivo removes the Pstl site to give the I S (spliced) amplicon; *is a spliced/unspliced XBP1 hybrid amplicon; the ratio of spliced over (spliced + unspliced) amplicons— 1 S/(1S+2U+3U)— is reported as % XBP1 splicing; three independent biological samples were used.
  • FIG. 10 Chemical-genetic manipulation of IREla activity reveals both the necessity and the sufficiency of the IREla RNase domain for triggering apoptosis.
  • A Model of IREla (I642G) "holed"-kinase mutant and its activation by the "bumped” kinase inhibitor, 1NMPP1.
  • E Percent of INS-1 IRE1(I642G) and INS-1 IRE1(I642G/N906A) cells staining positive for Annexin V after treatment for 72h with 1NM-PP1, Dox and Tg as indicated.
  • F Anti-Pro and Cleaved Caspase-3 immunoblots of INS-1 IREl (I642G) and INS-1
  • Fig. 1 Direct inhibition of IREla RNase prevents IREl dependent ER-localized mRNA degradation and ER stress-induced apoptosis.
  • A Model of inhibition of IREla RNase activity by STF-083010 (STF).
  • B Percent XBPl splicing in INS-1 IREl WT stable cells treated with 5ng/mL Dox and 50 ⁇ STF for indicated times as shown (upper panel). EtBr-stained agarose gel of XBP l cDNA amplicons is shown for the same samples above (lower panel).
  • C Q-PCR for Insulin 1 mRNA (normalized to GAPDH) in INS-1 IREl WT stable cells treated Dox and STF for 12, 24, 48 and 72h.
  • D Anti-Phospho-IREla and Anti-Total IREl a immunoblots of INS-1 IREl WT stable cells treated for 48h with 5ng/mL Dox and 50 ⁇ STF.
  • E Anti- Phospho and Total ⁇ immunoblots of same samples.
  • F Anti-Pro Caspase and Cleaved
  • Fig. 12. a) Percent of INS-1 cells staining positive for Annexin-V 72 hrs after treatment of 500 ng/ml Tm +/- GP165. (b) EtBr-stained agarose gel of XBPl cDNA amplicons from INS-1 cells 8 hrs after treatment of 200 ng/ml Tm +/- GP 165.
  • XBP1U unspliced XBP l
  • XBP1 S spliced XBPl
  • the lower panel shows the ratios of spliced XBPl (XBP1 S) over (spliced + unspliced (XBP1U)).
  • Fig. 13 Coomassie blue-stained PAGE of purified IREla*; M, protein marker.
  • Fig. 14 Structures of several type II kinase inhibitors screened against IREla * in the XBPl RNA minisubstrate assay; the relative endpoint fluorescence intensities for the IREla*- catalyzed cleavage reaction of XBP l minisubstrate in the presence of varying concentrations of inhibitors are shown.
  • Fig. 15 Crystal structure of Src bound to the type II kinase inhibitor, GP 118 (PDB code 3EL8); hydrogen bond interactions between Src and GP l 18 are denoted as dotted lines; only the backbone atoms are shown for residues in the hinge region except for Thr338 (gatekeeper residue); the proposed model of GP l 18 bound to IREla shown in Fig. la is based on the Src- GP 118 complex structure.
  • Fig. 16 GP146 and APY29 modulation of IREla *-mediated cleavage of an in vitro- transcribed 352 nucleotide, internally a 32P-labeled XBPl RNA.
  • Fig. 17 The EC50 of GP146 for IREla * RNase inhibition increases in the presence of a fixed concentration of APY29; the line marked with circles shows IREla* RNase inhibition by GP 146 in the absence of a competitor (APY29); the line marked with squares shows IREla * RNase inhibition by GPl 46 in the presence of APY29 (2 ⁇ ).
  • Fig. 18 Sunitinib inhibits IREla * autophosphorylation but activates the RNase domain, (a) Autoradiograms of IREla * autophosphorylation levels under serial two-fold dilutions of sunitinib (from 80 ⁇ to 0.0098 ⁇ ). (b) Urea PAGE analysis of XBPl
  • Fig. 19 A molecular model of APY29's interaction with the DFG-in conformation of human IREla.
  • IREla is in the DFG-in active conformation; the pyrimidine ring of APY29 occupies the adenine pocket and the 3-aminopyraozole makes several hydrogen bonds with the kinase hinge; no favorable poses for APY29 bound to the DFG-out conformation of IREla could be determined.
  • Fig. 20 GP146 inhibits autophosphorylation and XBP 1 mRNA splicing by WT IREla in T-REx 293 cells, (a) Anti-total and anti-phospho IREla immunoblots, and EtBr-stained agarose gel of XBP 1 cDNA amplicons from T-REx 293 cells expressing WT IREla under Doxy eye line (Dox) control; cells were pre-treated for 1 hr with GP146 at indicated
  • Fig. 21 Molecular model of GP 146 bound to the ATP-binding site of human IREla I642A ; IREla is in the DFG-out inactive conformation; the imidazopyrazine ring of GP146 occupies the adenine pocket and the 3-trifluoromethylurea occupies the DFG-out pocket; the naphthyl ring of GP146 rotates 180 degrees and is able to access the enlarged hydrophobic pocket next to the gatekeeper residue; no favorable poses for GP146 bound to the DFG-in conformation of IREla I642A could be determined.
  • Fig. 23 Death of pancreatic islet ⁇ -cells due to unchecked ER stress and terminal UPR signaling is central to development of types 1 and 2 diabetes.
  • Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR.
  • FIG. 24 (A) Immunoblots of IREla* after treatment with the crosslinker DSS;
  • Fig. 25 Synthetic strategy for generating KIRAs.
  • Fig. 26 Representative KIRAs synthesized and tested.
  • Fig. 27 (A) General structure of irreversible KIRAs that target a cysteine residue located in the activation loop of IRE 1 ; representative electrophiles are shown. (B) A close-up of the ATP -binding site of IRE la.
  • Fig. 28 Increasing magnitude and duration of exposure of cells to myriad ER stressors causes increasing activation of IRE la (autophosphorylation, XBP l mRNA splicing, ER localized decay of Insl mRNA), and switch-like entry of the stressed into dysfunctional states culminating in apoptosis (see text for details);
  • IRE la autophosphorylation, XBP l mRNA splicing, ER localized decay of Insl mRNA
  • switch-like entry of the stressed into dysfunctional states culminating in apoptosis (see text for details);
  • A Percent Annexin-V staining INS-1 cells treated in a time course of increasing concentrations of Tg.
  • B Pro- and cleaved Caspase-3 immunoblot of Tg-treated INS-1 cells.
  • C Time of exposure to the agent are directly linked to the percentage of cells entering apoptosis, as can be defined for other ER stress inducers such as the glycosylation inhibitor, tunicamycin (Tm)
  • D Increasing ER stress causes progressive increases in endogenous IRE la phosphorylation.
  • E Increasing ER stress causes progressive increases in endogenous XBPl mRNA splicing.
  • F Increasing ER stress causes progressive depletion through endonucleolytic decay of the ER-localized mRNA, Insl, which encodes proinsulin.
  • G Increasing ER stress causes progressive induction of the pro-apoptotic transcription factor, CHOP.
  • H Diagram of effects due to increasing exposure to ER stress inducers and increasing severity of ER stress.
  • Fig. 29 Conditional overexpression (using Dox) of IRE la in stable INS-1 cells mimics a Terminal UPR by forcing IRE la autophosphorylation, XBPl mRNA splicing, ER localized decay of Ins 1 mRNA, decay of miR- 17, induction of CHOP, accumulation and cleavage of upstream (Caspase 2) and downstream (Caspase 3) caspases of the mitochondrial apoptotic pathway, as well as inflammatory (Caspase 1) caspase mediating pyroptosis, and switch-like entry of cells into programmed cell death.
  • A Anti-Phospho-IREla and anti-Myc-IREla immunoblot of INS-1 IREla (WT) cells treated with increasing concentrations of Dox for 24h.
  • B Agarose gel of Pstl-digested XBPl cDNA amplicons from INS-1 IREla (WT) cells treated with increasing [Dox] for 24h.
  • % XBPl splicing represents the ratio of spliced over (spliced + unspliced) amplicons— 1 S/(1 S+2U+3U).
  • C Model of how severe ER stress causes IREla to switche from homeostatic to apoptotic outputs.
  • D Q-PCR for miR-17 in INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h.
  • E Q-PCR for Insulinl (Insl) and CHOP mRNA in INS-1 IRE la (WT) cells treated with increasing [Dox] for 24 h; anti-Proinsulin immunoblot of INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h.
  • Fig. 30 KIRA6 inhibits IRE la autophosphorylation, breaks oligomers, reduces RNase activity, and protects cells from entry into apoptosis.
  • A Structure of KIRA6.
  • C Inhibition of IRE la* kinase activity in vitro by KIRA6; IC 50 values were determined by fitting percent phosphorylation.
  • KIRA6 inhibits endogenous IRE la auto-phosphorylation in a dose-dependent manner; in contrast the aldehyde-based IRE la RNase-inhibitor, STF, does not inhibit IRE la auto-phosphorylation, nor does a control compound KIRA6(in).
  • FIG. 31 KIRA6 inhibits IRE la* RNAse endonucleolytically cleaves pre-miR-17 at sites distinct from those cleaved by DICER but related to XBPl scission sites (A), KIRA6 prevents cleavage of pre-miR-17 by IRE la* in vitro (B) cleavage sites (C) pre-miR-17 (D), rescues mature miR-17 levels in vivo (E), reduces caspase 2 accumulation and cleavage (F), and prevents TXNIP protein accumulation in C57BL/6 islets exposed to ER stress inducers (G). Sequence legend (FIG. 3 IB): SEQ ID NOs: 11-15 (in order top to bottom); (FIG. 17C): SEQ ID NO: 16.
  • Fig. 32 Bumped type I kinase inhibitor, 1NM-PP1, increases oligomeric state of holed IREla* (I642G) mutant to promote RNAse activity and cell death under ER stress.
  • A Quantitation of the ratios of oligomeric to monomeric IRE la* from immunoblots of increasing concentrations of recombinant IREla*(WT), IREla*(I642G) or IREla*(I642G) incubated with 1NM-PP1, before treatment with the crosslinker disuccinimidyl suberate (DSS) (250 Mm) and quantitation of time course of cleavage reactions of a 32 P-labeled XBP l RNA or Insulin2 (Ins2) RNA by recombinant IREla*(WT), IRE la* (1642 G), and IREla*(I642G) incubated with 1NM- PP 1 (10 ⁇ ) from urea PAGE.
  • DSS cross
  • Compounds, pharmaceutical compositions, and methods described herein may modulate the terminal UPR.
  • Fig. 34 Death of pancreatic islet ⁇ -cells due to unchecked ER stress and terminal UPR signaling is central to development of types 1 and 2 diabetes.
  • Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR.
  • Fig. 35 Fibrotic remodeling due to unchecked ER stress is central to development of fibrotic disease such as idiopathic pulmonary fibrosis (IPF).
  • IPF idiopathic pulmonary fibrosis
  • Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR.
  • Fig. 36 Inhibiting the Terminal UPR by attenuating IRE la's RNAse with kinase inhibitors (KIRAs).
  • KIRAs kinase inhibitors
  • Fig. 37 KIRA6 shuts down all critical terminal UPR events in pancreatic islet beta cells experiencing ER stress; inhibition of pro-inflammatory signaling through TXNIP and Interleukin 1-beta.
  • Fig. 38 Testing cascade to improve potency, selectivity, and efficacy of IRE la KIRAs.
  • Fig. 39 KIRA6 protects viability and preserves function of retinal photoreceptors during tunicamycin- and mutant rhodopsin-induced stress.
  • A Fundus and OCT images of Sprague-Dawley rats injected intravitreally with tunicamycin +/- 10 ⁇ KIRA6.
  • B Fundus and OCT images of P23H-1 rats at P40 injected intravitreally with DMSO or 10 ⁇ KIRA6.
  • C Histological sections of retinas from P23H-1 rats at P30 after intravitreal injection of DMSO or 10 ⁇ KIRA6.
  • (D) Quantification of outer nuclear layer (ONL) thickness (n 2) of P23H-1 rats at P30; higher thickness line is KIRA6 and lower line is DMSO.
  • Fig. 40 Survival curves of murine embryonic stem cell (ESC)-derived motor neurons.
  • A Wild-type (WT) Hb9:GFP ESCs were differentiated into GFP+ motor neurons (MNs) and subsequently treated with brefeldin A (BFA) with or without KIRA6 at the indicated
  • Activation of IREla's RNase is normally dependent on kinase autophosphorylation (Tirasophon, W. et al. Genes Dev 12, 1812-1824 (1998)), but an allosteric relationship between these two domains exists, which allows nucleotides (ADP and ATP) and small molecule inhibitors that stabilize an active ATP-binding site conformation to directly activate the RNase without autophosphorylation (Papa, F. R. et al. Science 302, 1533-1537 (2003); Han, D. et al. Biochemical and biophysical research communications 365, 777-783, (2008); Korennykh, A. V. et al. BMC biology 9, 48, (2011)).
  • kinase inhibitors (called type II) stabilize an inactive ATP-binding site conformation of IRE la and are able to potently inhibit its RNase activity by breaking high-order oligomerization state (Figs. 1A and 36) (Wang, L. et al. Nature chemical biology 8, 982-989, (2012)). These compounds are herein labeled—
  • KIRAs for kinase-inhibiting R ase-attenuators.
  • kinase inhibitors that have been described to selectively stabilize the inactive conformation of the ATP-binding site (type II inhibitors) for a variety of kinases; examples include the clinically-approved drugs imatinib and sorafenib (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006); Wan, P. T. et al. Cell 116, 855-867 (2004); Schindler, T. et al. Science 289, 1938-1942 (2000)), provides support for this approach.
  • imatinib and sorafenib Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006); Wan, P. T. et al. Cell 116, 855-867 (2004); Schindler, T. et al. Science 289, 1938-1942 (2000)
  • the inactive ATP- binding site conformation stabilized by type II inhibitors is characterized by outward movement of the catalytically-important Asp-Phe-Gly (DFG) motif, and is therefore called the DFG-out conformation (Fig. la) (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006); Ranjitkar, P. et al. Chem. Biol. 17, 195-206 (2010)).
  • the kinase domain adopts the DFG-in conformation (Korennykh, A. V. et al. Nature 457, 687-693 (2009); Ali, M. M. et al. EMBO J. 30, 894-905 (201 1); Lee, K. P. et al. Cell 132, 89-100 (2008)).
  • KIRAs Kinase inhibiting RNase Attenuators
  • KIRA6 inhibits all IRE la outputs, and preserves cell viability and function under ER stress.
  • intravitreal KIRA6 prevents photoreceptor loss.
  • saturated means the referenced chemical structure does not contain any multiple carbon carbon bonds.
  • a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.
  • alkyl by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e., unbranched) or branched carbon chain (or carbon), or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e., Ci-Cio means one to ten carbons).
  • saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec -butyl, (cyclohexyl)methyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like.
  • An unsaturated alkyl group is one having one or more double bonds or triple bonds.
  • unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(l,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers.
  • An alkoxy is an alkyl attached to the remainder of the molecule via an oxygen linker (-0-).
  • an alkyl is a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified.
  • an alkyl is an alkenyl, wherein the term "alkenyl” is used in accordance with its plain ordinary meaning.
  • an alkenyl is a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon carbon double bond.
  • alkenyl include, but are not limited to, ethenyl, 2 propenyl, 2 methyl 2 propenyl, 3 butenyl, 4 pentenyl, 5 hexenyl, 2 heptenyl, 2 methyl 1 heptenyl, 3 decenyl, and 3,7 dimethylocta 2,6 dienyl.
  • an alkyl is an alkynyl, wherein the term "alkynyl" is used in accordance with its plain ordinary meaning.
  • an alkynyl is a straight or branched chain hydrocarbon group containing from 2 to 10 carbon atoms and containing at least one carbon carbon triple bond. Examples of alkynyl include, but are not limited, to acetylenyl, 1 propynyl, 2 propynyl, 3 butynyl, 2 pentynyl, and 1 butynyl.
  • alkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkyl, as exemplified, but not limited
  • alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being preferred in the present invention.
  • a “lower alkyl” or “lower alkylene” is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.
  • alkenylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene.
  • heteroalkyl by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom selected from the group consisting of O, N, P, Si, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized.
  • the heteroatom(s) O, N, P, S, and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Examples include, but are not limited
  • heteroalkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from heteroalkyl, as exemplified, but not limited by, -CH 2 -CH 2 -S-CH 2 -CH 2 - and -CH 2 -S-CH 2 -CH 2 -NH-CH 2 -.
  • heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy,
  • heteroalkyl groups include those groups that are attached to the remainder of the molecule through a heteroatom, such as -C(0)R, -C(0)NR, -NR'R", -OR', -SR, and/or -S0 2 R'.
  • heteroalkyl is recited, followed by recitations of specific heteroalkyl groups, such as -NR'R" or the like, it will be understood that the terms heteroalkyl and -NR'R" are not redundant or mutually exclusive.
  • heteroalkyl should not be interpreted herein as excluding specific heteroalkyl groups, such as -NR'R" or the like.
  • cycloalkyl and heterocycloalkyl by themselves or in combination with other terms, mean, unless otherwise stated, cyclic versions of “alkyl” and “heteroalkyl,” respectively, wherein the carbons making up the ring or rings do not necessarily need to be bonded to a hydrogen due to all carbon valencies participating in bonds with non-hydrogen atoms. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 1 -cyclohexenyl,
  • heterocycloalkyl examples include, but are not limited to, l-(l,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl,
  • a "cycloalkylene” and a “heterocycloalkylene,” alone or as part of another substituent, means a divalent radical derived from a cycloalkyl and heterocycloalkyl, respectively.
  • cycloalkyl means a monocyclic, bicyclic, or a multicyclic cycloalkyl ring system.
  • monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups can be saturated or unsaturated, but not aromatic.
  • cycloalkyl groups are fully saturated. Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl.
  • Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings.
  • bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form (CH 2 ) W , where w is 1, 2, or 3).
  • bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane.
  • fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the bridged or fused bicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkyl ring.
  • cycloalkyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia.
  • multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • Examples of multicyclic cycloalkyl groups include, but are not limited to tetradecahydrophenanthrenyl,
  • a cycloalkyl is a cycloalkenyl.
  • the term "cycloalkenyl" is used in accordance with its plain ordinary meaning.
  • a cycloalkenyl is a monocyclic, bicyclic, or a multicyclic cycloalkenyl ring system.
  • monocyclic cycloalkenyl ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon carbon double bond), but not aromatic.
  • Examples of monocyclic cycloalkenyl ring systems include cyclopentenyl and cyclohexenyl.
  • bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings.
  • bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form (CH 2 ) w , where w is 1, 2, or 3).
  • bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct 2 enyl.
  • fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the bridged or fused bicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkenyl ring.
  • cycloalkenyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • a heterocycloalkyl is a heterocyclyl.
  • heterocyclyl as used herein, means a monocyclic, bicyclic, or multicyclic heterocycle.
  • the heterocyclyl monocyclic heterocycle is a 3, 4, 5, 6 or 7 membered ring containing at least one heteroatom independently selected from the group consisting of O, N, and S where the ring is saturated or unsaturated, but not aromatic.
  • the 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of O, N and S.
  • the 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of O, N and S.
  • the 6 or 7 membered ring contains zero, one or two double bonds and one, two or three heteroatoms selected from the group consisting of O, N and S.
  • the heterocyclyl monocyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heterocyclyl monocyclic heterocycle.
  • heterocyclyl monocyclic heterocycles include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3 dioxanyl, 1,3 dioxolanyl, 1,3 dithiolanyl, 1,3 dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl
  • the heterocyclyl bicyclic heterocycle is a monocyclic heterocycle fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocycle, or a monocyclic heteroaryl.
  • the heterocyclyl bicyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle portion of the bicyclic ring system.
  • bicyclic heterocyclyls include, but are not limited to, 2,3
  • heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the bicyclic heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring fused to a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia.
  • Multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic heterocyclyl is attached to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring.
  • multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • multicyclic heterocyclyl groups include, but are not limited to lOH-phenothiazin-10-yl, 9, 10-dihydroacridin-9-yl, 9, 10- dihydroacridin-10-yl, lOH-phenoxazin-10-yl, 10,1 l-dihydro-5H-dibenzo[b,fJazepin-5-yl, l,2,3,4-tetrahydropyrido[4,3-g]isoquinolin-2-yl, 12H-benzo[b]phenoxazin-12-yl, and dodecahydro- lH-carbazol-9-yl.
  • halo or halogen
  • haloalkyl by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom.
  • terms such as “haloalkyl” are meant to include monohaloalkyl and polyhaloalkyl.
  • halo(Ci-C4)alkyl includes, but is not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.
  • acyl means, unless otherwise stated, -C(0)R where R is a substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • aryl means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (preferably from 1 to 3 rings) that are fused together (i.e., a fused ring aryl) or linked covalently.
  • a fused ring aryl refers to multiple rings fused together wherein at least one of the fused rings is an aryl ring.
  • heteroaryl refers to aryl groups (or rings) that contain at least one heteroatom such as N, O, or S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized.
  • heteroaryl includes fused ring heteroaryl groups (i.e., multiple rings fused together wherein at least one of the fused rings is a heteroaromatic ring).
  • a 5,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 5 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
  • a 6,6- fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
  • a 6,5-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 5 members, and wherein at least one ring is a heteroaryl ring.
  • a heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom.
  • Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1- pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2- thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4- pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1- is
  • arylene and heteroarylene independently or as part of another substituent, mean a divalent radical derived from an aryl and heteroaryl, respectively, such as for example a divalent radical of indoline.
  • heteroaryl groups include pyridinyl, pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl, benzothiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, furylthienyl, pyridyl, pyrimidyl, benzo
  • an aryl is a phenyl (i.e., monocyclic aryl), a bicyclic ring system containing at least one phenyl ring or an aromatic bicyclic ring containing only carbon atoms in the aromatic bicyclic ring system or a multicyclic aryl ring system, provided that the bicyclic or multicyclic aryl ring system does not contain a heteroaryl ring when fully aromatic.
  • the bicyclic aryl can be azulenyl, naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocyclyl.
  • the bicyclic aryl may be attached to the parent molecular moiety through any carbon atom contained within the phenyl portion of the bicyclic system, or any carbon atom with the napthyl or azulenyl ring.
  • the fused monocyclic cycloalkyl or monocyclic heterocyclyl portions of the bicyclic aryl are optionally substituted with one or two oxo and/or thia groups.
  • bicyclic aryls include, but are not limited to, azulenyl, naphthyl, dihydroinden 1 yl, dihydroinden 2 yl, dihydroinden 3 yl, dihydroinden 4 yl, 2,3 dihydroindol 4 yl, 2,3 dihydroindol 5 yl, 2,3 dihydroindol 6 yl, 2,3 dihydroindol 7 yl, inden 1 yl, inden 2 yl, inden 3 yl, inden 4 yl, dihydronaphthalen 2 yl, dihydronaphthalen 3 yl, dihydronaphthalen 4 yl, dihydronaphthalen 1 yl, 5,6,7,8 tetrahydronaphthalen 1 yl, 5,6,7,8 tetrahydronaphthalen 2 yl, 2,3 dihydrobenzofuran 4 yl, 2,3
  • the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl,
  • multicyclic aryl may be attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the bicyclic cycloalky
  • the term "heteroaryl,” as used herein, means a monocyclic, bicyclic, or a multicyclic heteroaryl ring system.
  • the monocyclic heteroaryl can be a 5 or 6 membered ring.
  • the 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom.
  • the 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms.
  • the 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl.
  • monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl.
  • the bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia.
  • bicyclic heteroaryl when the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system.
  • the bicyclic heteroaryl when the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system.
  • Representative examples of bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl,
  • the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the multicyclic heteroaryl group is a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic heterocyclyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic cycloalkyl.
  • multicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring.
  • multicyclic heteroaryl groups are a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic heterocyclyl, a monocyclic cycloalkenyl, and a monocyclic cycloalkyl.
  • multicyclic heteroaryls include, but are not limited to 5H-[l,2,4]triazino[5,6-b]indol-5-yl, 2,3,4,9-tetrahydro-lH-carbazol-9-yl, 9H-pyrido[3,4-b]indol-9-yl, 9H-carbazol-9-yl, acridin-9-yl, [0086]
  • a fused ring heterocyloalkyl-aryl is an aryl fused to a heterocycloalkyl.
  • a fused ring heterocycloalkyl-heteroaryl is a heteroaryl fused to a heterocycloalkyl.
  • a fused ring ring heterocycloalkyl-heteroaryl is a heteroaryl fused to a heterocycloalkyl.
  • a fused ring ring heterocycloalkyl-heteroaryl is a heteroaryl fused to a hetero
  • heterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a cycloalkyl.
  • heterocycloalkyl-heterocycloalkyl is a heterocycloalkyl fused to another heterocycloalkyl.
  • Fused ring heterocycloalkyl-aryl, fused ring heterocycloalkyl-heteroaryl, fused ring heterocycloalkyl- cycloalkyl, or fused ring heterocycloalkyl-heterocycloalkyl may each independently be unsubstituted or substituted with one or more of the substitutents described herein.
  • oxo means an oxygen that is double bonded to a carbon atom.
  • alkylsulfonyl means a moiety having the formula -S(0)2- ', where R' is a substituted or unsubstituted alkyl group as defined above. R' may have a specified number of carbons (e.g., "C1-C4 alkylsulfonyl”).
  • arylalkyl and alkylaryl as used herein, means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • arylalkyl include, but are not limited to, benzyl, 2 phenylethyl, 3 phenylpropyl, and 2 naphth 2 ylethyl.
  • heteroarylalkyl and " alkylheteroaryl” as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • heteroarylalkyl include, but are not limited to, fur 3 ylmethyl, 1H imidazol 2 ylmethyl, 1H imidazol 4 ylmethyl, 1 (pyridin 4 yl)ethyl, pyridin 3 ylmethyl, pyridin 4 ylmethyl, pyrimidin 5 ylmethyl, 2 (pyrimidin 2 yl)propyl, thien 2 ylmethyl, and thien 3 ylmethyl.
  • -NRC (0)NR"NR"'R"", -CN, -N0 2 , in a number ranging from zero to (2m'+l), where m' is the total number of carbon atoms in such radical.
  • R, R, R", R", and R"" each preferably
  • each of the R groups is independently selected as are each R, R", R'", and R"" group when more than one of these groups is present.
  • R' and R" When R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7-membered ring.
  • -NR'R includes, but is not limited to, 1-pyrrolidinyl and 4-morpholinyl.
  • alkyl is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., -CF 3 and -CH 2 CF 3 ) and acyl (e.g., -C(0)CH 3 , -C(0)CF 3 , -C(0)CH 2 OCH 3 , and the like).
  • R, R", R'", and R" are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
  • R groups are independently selected as are each R, R", R", and R"” groups when more than one of these groups
  • Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups.
  • Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure.
  • the ring-forming substituents are attached to adjacent members of the base structure.
  • two ring- forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure.
  • the ring- forming substituents are attached to a single member of the base structure.
  • two ring- forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure.
  • the ring- forming substituents are attached to non-adjacent members of the base structure.
  • Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -T-C(0)-(CRR') q -U-, wherein T and U are
  • q is an integer of from 0 to 3.
  • two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH 2 ) r -B-, wherein A and B are independently -CRR'-, -0-, -NR-, -S-, -S(O) -, -S(0) 2 -, -S(0) 2 NR'-, or a single bond, and r is an integer of from 1 to 4.
  • One of the single bonds of the new ring so formed may optionally be replaced with a double bond.
  • two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the
  • R, R', R", and R" are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
  • heteroatom or "ring heteroatom” are meant to include, oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si).
  • a "substituent group,” as used herein, means a group selected from the following moieties:
  • a "size-limited substituent” or " size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a "substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C 2 o alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C1 0 aryl, and each substituted or unsubstituted heteroary
  • a "lower substituent” or " lower substituent group,” as used herein, means a group selected from all of the substituents described above for a "substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-Cs alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C1 0 aryl, and each substituted or unsubstituted heteroaryl is a substituted or un
  • each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group.
  • each substituted or unsubstituted alkyl may be a substituted or unsubstituted C1-C2 0 alkyl
  • each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl
  • each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl
  • each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl
  • each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C1 0 aryl
  • each substituted or unsubstituted heteroaryl is a substituted or unsubstituted or unsubstituted
  • each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C2 0 alkylene
  • each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered heteroalkylene
  • each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C8 cycloalkylene
  • each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene
  • each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene
  • each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered heteroarylene.
  • each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-Cs alkyl
  • each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl
  • each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl
  • each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl
  • each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C1 0 aryl
  • each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl.
  • each substituted or unsubstituted alkylene is a substituted or unsubstituted Ci-Cs alkylene
  • each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene
  • each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C7 cycloalkylene
  • each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene
  • each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C1 0 arylene
  • each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene.
  • the compound is a chemical species set forth in the Examples section below.
  • salts are meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein.
  • base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
  • acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,
  • Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.
  • Other pharmaceutically acceptable carriers known to those of skill in the art are suitable for the present invention. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms.
  • the preparation may be a lyophilized powder in 1 mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
  • the compounds of the present invention may exist as salts, such as with
  • the present invention includes such salts.
  • salts include hydrochlorides, hydrobromides, sulfates, methanesulfonates, nitrates, maleates, acetates, citrates, fumarates, tartrates (e.g., (+)-tartrates, (-)-tartrates, or mixtures thereof including racemic mixtures), succinates, benzoates, and salts with amino acids such as glutamic acid.
  • These salts may be prepared by methods known to those skilled in the art.
  • the neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner.
  • the parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents.
  • the present invention provides compounds, which are in a prodrug form.
  • Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention.
  • prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
  • Certain compounds of the present invention can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present invention. Certain compounds of the present invention may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present invention and are intended to be within the scope of the present invention.
  • salt refers to acid or base salts of the compounds used in the methods of the present invention.
  • acceptable salts are mineral acid (hydrochloric acid, hydrobromic acid, phosphoric acid, and the like) salts, organic acid (acetic acid, propionic acid, glutamic acid, citric acid and the like) salts, quaternary ammonium (methyl iodide, ethyl iodide, and the like) salts.
  • Certain compounds of the present invention possess asymmetric carbon atoms (optical or chiral centers) or double bonds; the enantiomers, racemates, diastereomers, tautomers, geometric isomers, stereoisometric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids, and individual isomers are encompassed within the scope of the present invention.
  • the compounds of the present invention do not include those which are known in art to be too unstable to synthesize and/or isolate.
  • the present invention is meant to include compounds in racemic and optically pure forms.
  • Optically active (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques.
  • the compounds described herein contain olefinic bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers.
  • the term “isomers” refers to compounds having the same number and kind of atoms, and hence the same molecular weight, but differing in respect to the structural arrangement or configuration of the atoms.
  • tautomer refers to one of two or more structural isomers which exist in equilibrium and which are readily converted from one isomeric form to another.
  • structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the invention.
  • structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13 C- or 14 C-enriched carbon are within the scope of this invention.
  • the compounds of the present invention may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds.
  • the compounds may be radiolabeled with radioactive isotopes, such as for example tritium ( 3 H), iodine-125 ( 125 I), or carbon-14 ( 14 C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are encompassed within the scope of the present invention.
  • the symbol /w denotes the point of attachment of a chemical moiety to the remainder of a molecule or chemical formula.
  • a or “an,” as used in herein means one or more.
  • substituted with a[n] means the specified group may be substituted with one or more of any or all of the named substituents.
  • a group such as an alkyl or heteroaryl group
  • the group may contain one or more unsubstituted C1-C2 0 alkyls, and/or one or more unsubstituted 2 to 20 membered heteroalkyls.
  • R-substituted where a moiety is substituted with an R substituent, the group may be referred to as "R-substituted.” Where a moiety is R-substituted, the moiety is substituted with at least one R substituent and each R substituent is optionally different.
  • Descriptions of compounds of the present invention are limited by principles of chemical bonding known to those skilled in the art. Accordingly, where a group may be substituted by one or more of a number of substituents, such substitutions are selected so as to comply with principles of chemical bonding and to give compounds which are not inherently unstable and/or would be known to one of ordinary skill in the art as likely to be unstable under ambient conditions, such as aqueous, neutral, and several known physiological conditions.
  • a heterocycloalkyl or heteroaryl is attached to the remainder of the molecule via a ring heteroatom in compliance with principles of chemical bonding known to those skilled in the art thereby avoiding inherently unstable compounds.
  • the terms "treating" or “treatment” refers to any indicia of success in the treatment or amelioration of an injury, disease, pathology or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology or condition more tolerable to the patient; slowing in the rate of degeneration or decline; making the final point of degeneration less debilitating; improving a patient's physical or mental well-being.
  • the treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of a physical examination, neuropsychiatric exams, and/or a psychiatric evaluation.
  • certain methods herein treat cancer (e.g. multiple myeloma, cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes (type I or type II).
  • certain methods herein treat cancer by decreasing or reducing or preventing the occurrence, growth, metastasis, or progression of cancer; treat neurodegeneration by improving mental wellbeing, increasing mental function, slowing the decrease of mental function, decreasing dementia, delaying the onset of dementia, improving cognitive skills, decreasing the loss of cognitive skills, improving memory, decreasing the degradation of memory, or extending survival; treat demyelinating diseases by reducing a symptom of demyelinating diseases or reducing the loss of myelin or increasing the amount of myelin or increasing the level of myelin; treat diabetes by decreasing a symptom of diabetes or decreasing loss of insulin producing cells or decreasing loss of pancreatic cells or reducing insulin insensitivity; treat cancer by decreasing a symptom of cancer, or treat neurodegeneration by treating a symptom of neurodegeneration.
  • Symptoms of cancer e.g. multiple myeloma, cancers of secretory cells
  • neurodegenerative diseases demyelinating diseases, eye diseases, fibrotic diseases, or diabetes
  • the term “treating” and conjugations thereof include prevention of an injury, pathology, condition, or disease (e.g. preventing the development of one or more symptoms of cancer, neurodegenerative diseases, demyelinating diseases, and/or diabetes).
  • an "effective amount” is an amount sufficient to accomplish a stated purpose (e.g.
  • an "effective amount” is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a
  • a “reduction” of a symptom or symptoms means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s).
  • a “prophylactically effective amount” of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset (or reoccurrence) of an injury, disease, pathology or condition, or reducing the likelihood of the onset (or reoccurrence) of an injury, disease, pathology, or condition, or their symptoms.
  • the full prophylactic effect does not necessarily occur by administration of one dose, and may occur only after administration of a series of doses.
  • a prophylactically effective amount may be administered in one or more administrations.
  • An “activity decreasing amount,” as used herein, refers to an amount of antagonist (inhibitor) required to decrease the activity of an enzyme or protein relative to the absence of the antagonist.
  • An “activity increasing amount,” as used herein, refers to an amount of agonist (activator) required to increase the activity of an enzyme or protein relative to the absence of the agonist.
  • a “function disrupting amount,” as used herein, refers to the amount of antagonist (inhibitor) required to disrupt the function of an enzyme or protein relative to the absence of the antagonist.
  • a “function increasing amount,” as used herein, refers to the amount of agonist (activator) required to increase the function of an enzyme or protein relative to the absence of the agonist.
  • a symptom of a disease or condition associated with an increase in Irel e.g. Irela
  • a symptom of a disease or condition associated with an increase in Irel e.g. Irela
  • Irela a symptom that results (entirely or partially) from an increase in Irel
  • Irela activity e.g increase in Irel (e.g. Irela) phosphorylation or activity of phosphorylated Irel (e.g. Irela) or activity of Irel (e.g. Irela) or increase in activity of an Irel (e.g. Irela) signal transduction or signalling pathway, Irel (e.g. Irela) RNase activity).
  • Irel e.g. Irela
  • a disease associated with increased Irel (e.g. Irela) activity or Irel (e.g. Irela) pathway activity e.g.
  • phosphorylated Irel (e.g. Irela) activity or pathway)
  • an agent e.g. compound as described herein
  • a disease associated with phosphorylated Irel may be treated with an agent (e.g. compound as described herein) effective for decreasing the level of activity of Irel (e.g. Irela) activity or Irel (e.g. Irela) pathway or phosphorylated Irel (e.g. Irela) activity or pathway.
  • a disease associated with phosphorylated Irel (e.g. Irela)
  • an agent e.g. compound as described herein) effective for decreasing the level of activity of
  • phosphorylated Irel e.g. Irela
  • a disease associated with Irel e.g. Irela
  • an agent e.g. compound as described herein
  • Control or "control experiment” is used in accordance with its plain ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects.
  • Contacting is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g. chemical compounds including
  • the term "contacting" may include allowing two species to react, interact, or physically touch, wherein the two species may be a compound as described herein and a protein or enzyme (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Ire la) or component of Irel (e.g. Ire la) pathway or component of phosphorylated Irel (e.g. Irela) pathway).
  • Irel e.g. Irela
  • phosphorylated Irel e.g. Ire la
  • component of Irel e.g. Ire la
  • component of phosphorylated Irel e.g. Irela
  • contacting includes allowing a compound described herein to interact with a protein or enzyme that is involved in a signaling pathway (e.g. Irel (e.g. Irela) protein or Irel (e.g. Irela) pathway).
  • a protein or enzyme that is involved in a signaling pathway (e.g. Irel (e.g. Irela) protein or Irel (e.g. Irela) pathway).
  • Irel e.g. Irela
  • Irel Irel
  • Irela Irel
  • Irel Irel
  • Irela Irela
  • the term “inhibition”, “inhibit”, “inhibiting” and the like in reference to a protein-inhibitor (e.g. antagonist) interaction means negatively affecting (e.g. decreasing) the activity or function of the protein relative to the activity or function of the protein in the absence of the inhibitor.
  • inhibition refers to reduction of a disease or symptoms of disease.
  • inhibition refers to a
  • inhibition includes, at least in part, partially or totally blocking stimulation, decreasing, preventing, or delaying activation, or inactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein.
  • inhibition refers to a decrease in the activity of a signal transduction pathway or signaling pathway (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) or Irel (e.g. Irela) pathway or phosphorylated Irel (e.g. Irela) pathway or pathway activated by Irel (e.g. Irela) phosphorylation).
  • a signal transduction pathway or signaling pathway e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) or Irel (e.g. Irela) pathway or pathway activated by Irel (e.g. Irela) phosphorylation).
  • inhibition may include, at least in part, partially or totally decreasing stimulation, decreasing or reducing activation, or inactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein increased in a disease (e.g. level of Irel (e.g. Irela) activity or protein or level or activity of a component of an Irel (e.g. Irela) pathway or level of phosphorylated Irel (e.g. Irela) activity or protein or level or activity of a component of a phosphorylated Irel (e.g. Irela) pathway, wherein each is associated with cancer (e.g.
  • Inhibition may include, at least in part, partially or totally decreasing stimulation, decreasing or reducing activation, or deactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein (e.g. Irel (e.g. Irela),
  • phosphorylated Irel e.g. Irela
  • protein downstream in a pathway from Irel e.g. Irela
  • protein downstream in a pathway activated by phosphorylated Irel e.g. Irela
  • phosphorylated Irel e.g. Irela
  • activation means positively affecting (e.g.
  • activation refers to an increase in the activity of a signal transduction pathway or signaling pathway (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway).
  • a signal transduction pathway or signaling pathway e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway.
  • activation may include, at least in part, partially or totally increasing stimulation, increasing or enabling activation, or activating, sensitizing, or up-regulating signal transduction or enzymatic activity or the amount of a protein decreased in a disease (e.g. level of Irel (e.g. Irela) activity or level of protein or activity decreased by phosphorylation of Irel (e.g. Irela) or protein associated with cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes).
  • a disease e.g. level of Irel (e.g. Irela) activity or level of protein or activity decreased by phosphorylation of Irel (e.g. Irela) or protein associated with cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes).
  • Activation may include, at least in part, partially or totally increasing stimulation, increasing or enabling activation, or activating, sensitizing, or up- regulating signal transduction or enzymatic activity or the amount of a protein (e.g. Irel (e.g. Irela), protein downstream of Irel (e.g. Irela), protein activated or upregulated by Irel (e.g. Irela), protein activated or upregulated by phosphorylation of Irel (e.g. Irela)) that may modulate the level of another protein or increase cell survival (e.g. increase in Irel (e.g. Irela) activity may increase cell survival in cells that may or may not have a reduction in Irel (e.g. Irela) activity relative to a non-disease control).
  • a protein e.g. Irel (e.g. Irela), protein downstream of Irel (e.g. Irela), protein activated or upregulated by Irel (e.g.
  • modulator refers to a composition that increases or decreases the level of a target molecule or the function of a target molecule.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway or phosphorylation of Irel (e.g. Irela) or pathway activated by phorphorylation of Irel (e.g. Irela) is a compound that reduces the severity of one or more symptoms of a disease associated with Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. disease associated with an increase in the level of Irel (e.g.
  • Irela activity or protein or Irel (e.g. Irela) pathway activity or protein or Irel (e.g. Irela) phorphorylation or pathway activated by Irel (e.g. Irela) phosphorylation for example cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demylelinating diseases, eye diseases, fibrotic diseases, or diabetes) or a disease that is not caused by Irel (e.g. Irela) or Irel (e.g. Irela) pathway but may benefit from modulation of Irel (e.g. Irela) or Irel (e.g. Irela) pathway activity (e.g.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway is an anti-cancer agent.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e..g phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway is e..g phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway
  • Irel (e.g. Irela) or Irel (e.g. Irela) pathway is an anti- demyelinating agent.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway is a memory enhancing agent.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e.g. phosphorylated Irel (e.g.
  • Irela or phosphorylated Irel (e.g. Irela) pathway is an anti-diabetic agent.
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway
  • a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g.
  • Irela pathway is an anti-fibrosis agent.
  • "Patient” or “subject in need thereof refers to a living organism suffering from or prone to a disease or condition that can be treated by administration of a compound or pharmaceutical composition, as provided herein. Non-limiting examples include humans, other mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals.
  • a patient is human.
  • a patient is an ape.
  • a patient is a monkey.
  • a patient is a mouse.
  • a patient is an experimental animal.
  • a patient is a rat.
  • a patient is a test animal. In some embodiments, a patient is a newborn animal. In some embodiments, a patient is a newborn human. In some embodiments, a patient is a juvenile animal. In some embodiments, a patient is a juvenile human. In some embodiments, a patient is a newborn mammal. In some embodiments, a patient is an elderly animal. In some embodiments, a patient is an elderly human. In some embodiments, a patient is an elderly mammal. In some embodiments, a patient is a geriatric patient.
  • Disease or “condition” refer to a state of being or health status of a patient or subject capable of being treated with a compound, pharmaceutical composition, or method provided herein.
  • the disease is a disease related to (e.g. caused by) an increase in the level of Irel (e.g. Irela), Irel (e.g. Irela) phosphorylation, Irel (e.g. Irela) RNase activity, or Irel (e.g. Irela) pathway activity, or pathway activated by phosphorylation of Irel (e.g.
  • the disease is a disease related to (e.g. caused by) neurodegeneration. In some embodiments, the disease is a disease related to (e.g. caused by) neural cell death. In some embodiments, the disease is a disease related to (e.g. caused by) cell death. In some embodiments, the disease is a disease related to (e.g. caused by) pancreatic cell death. In some embodiments, the disease is a disease related to (e.g. caused by) insulin- producing cell death. In some embodiments, the disease is a disease related to (e.g. caused by) loss of myelin. In some embodiments, the disease is a disease related to (e.g. caused by) reduction in myelin.
  • the disease is a disease related to (e.g. caused by) an increase in the level of Irel (e.g. Irela) activity (e.g. R ase activity), Irel (e.g. Irela) phosphorylation, Irel (e.g. Irela) pathway activity, or phosphorylated Irel (e.g. Irela) pathway activity.
  • the disease is cancer (e.g. multiple myeloma or cancers of secretory cells).
  • the disease is a neurodegenerative disease.
  • the disease is a demyelinating disease.
  • the disease is diabetes.
  • the disease is an interstitial lung disease (ILD).
  • the disease is idiopathic pulmonary fibrosis (IPF).
  • the disease is a fibrotic disease.
  • the disease is an eye disease (e.g., disease causing vision impairment).
  • diseases, disorders, or conditions include, but are not limited to, cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, and diabetes.
  • cancer e.g. multiple myeloma or cancers of secretory cells
  • neurodegenerative diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e.g. multiple myeloma or cancers of secretory cells
  • eye diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e
  • cancer refers to human cancers and carcinomas, sarcomas, adenocarcinomas, lymphomas, leukemias, melanomas, etc., including solid and lymphoid cancers, kidney, breast, lung, bladder, colon, ovarian, prostate, pancreas, stomach, brain, head and neck, skin, uterine, testicular, glioma, esophagus, liver cancer, including hepatocarcinoma, lymphoma, including B-acute lymphoblastic lymphoma, non- Hodgkin's lymphomas (e.g., Burkitt's, Small Cell, and Large Cell lymphomas), Hodgkin's lymphoma, leukemia (including AML, ALL, and CML), and/or multiple myeloma.
  • cancer refers to human cancers and carcinomas, sarcomas, adenocarcinomas, lymphomas, leukemias, melanomas, etc., including solid and
  • cancer refers to all types of cancer, neoplasm or malignant tumors found in mammals, including leukemia, lymphoma, carcinomas and sarcomas.
  • Exemplary cancers that may be treated with a compound, pharmaceutical composition, or method provided herein include multiple myeloma, blood cancers, lymphoma, sarcoma, bladder cancer, bone cancer, brain tumor, cervical cancer, colon cancer, esophageal cancer, gastric cancer, head and neck cancer, kidney cancer, myeloma, thyroid cancer, leukemia, prostate cancer, breast cancer (e.g. ER positive, ER negative, chemotherapy resistant, herceptin resistant, HER2 positive, doxorubicin resistant, tamoxifen resistant, ductal carcinoma, lobular carcinoma, primary, metastatic), ovarian cancer, pancreatic cancer, liver cancer (e.g.hepatocellular carcinoma) , lung cancer (e.g.
  • non-small cell lung carcinoma squamous cell lung carcinoma, adenocarcinoma, large cell lung carcinoma, small cell lung carcinoma, carcinoid, sarcoma), glioblastoma multiforme, glioma, or melanoma.
  • Additional examples include, cancer of the thyroid, endocrine system, brain, breast, cervix, colon, head & neck, liver, kidney, lung, non- small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus or Medulloblastoma, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, primary brain tumors, cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer
  • Phyllodes Tumors Lobular Carcinoma, Ductal Carcinoma, cancer of the pancreatic stellate cells, cancer of the hepatic stellate cells, or prostate cancer.
  • leukemia refers broadly to progressive, malignant diseases of the blood- forming organs and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemia is generally clinically classified on the basis of (1) the duration and character of the disease-acute or chronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid (lymphogenous), or monocytic; and (3) the increase or non-increase in the number abnormal cells in the blood-leukemic or aleukemic (subleukemic).
  • Exemplary leukemias that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy- cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous
  • sarcoma generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar or homogeneous substance.
  • Sarcomas that may be treated with a compound, pharmaceutical composition, or method provided herein include a chondrosarcoma,
  • fibrosarcoma lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma, immuno
  • melanoma is taken to mean a tumor arising from the melanocytic system of the skin and other organs.
  • Melanomas that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungal melanoma, or superficial spreading melanoma.
  • carcinoma refers to a malignant new growth made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases.
  • exemplary carcinomas that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, ductal carcinoma, carcinoma durum,
  • neurodegenerative disease refers to a disease or condition in which the function of a subject's nervous system becomes impaired (e.g. relative to a control subject who does not have the neurodegenerative disease).
  • Examples of neurodegenerative diseases that may be treated with a compound, pharmaceutical composition, or method described herein include Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease (also known as Spielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiform encephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt- Jakob disease, frontotemporal dementia, Gerstmann- Straussler-Scheinker syndrome, Huntington's disease, HlV-associated dementia, Kennedy's disease, Krabbe's disease, kuru, Lewy body dementia, Machado-Jos
  • Parkinson's Disease Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru.
  • demyelinating disease refers to a disease or condition is which the myelin sheath of a subject's neurons is or becomes impaired (e.g. relative to a control subject who does not have the demyelinating disease).
  • demyelinating disease examples include Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot- Marie-Tooth Disease, and Multiple Sclerosis.
  • diabetes refers to a disease or condition is which a subject has high blood sugar.
  • diabetes examples include type I diabetes (type I diabetes mellitus), which is characterized by the subject's failure to produce insulin or failure to produce sufficient insulin for the subject's metabolic needs; type II diabetes (type II diabetes mellitus), which is characterized by insulin resistance (i.e. the failure of the subject (e.g. subject's cells) to use insulin properly; and gestational diabetes, which is high blood sugar during pregnancy.
  • type I diabetes type I diabetes mellitus
  • type II diabetes mellitus which is characterized by insulin resistance (i.e. the failure of the subject (e.g. subject's cells) to use insulin properly
  • gestational diabetes which is high blood sugar during pregnancy.
  • diabetes is type I diabetes.
  • diabetes is type II diabetes.
  • diabetes is gestational diabetes.
  • diabetes is a disease or condition in which a subject has high blood sugar as determined by an AIC test (e.g. 6.5% or greater), fasting plasma glucose test (e.g. 126 mg/dL or greater), or oral glucose tolerance test (e.g. 200 mg/dL or greater).
  • the diabetes is associated with Wolfram Syndrome.
  • eye disease or “disease causing vision impairment” refers to a disease or condition is which the function of a subject's eye or eyes is impaired (e.g. relative to a subject without the disease). Examples of eye diseases that may be treated with a compound, pharmaceutical composition, or method described herein include retinitis pigmentosa, retinal degeneration, macular degeneration, and Wolfram Syndrome.
  • fibrosis refers to the formation of excess fibrous connective tissue.
  • fibrotic disease refers to a disease or condition caused by aberrant fibrosis or a disease or condition in which a symptom is aberrant fibrosis (e.g. relative to a control subject without the disease).
  • fibrotic diseases examples include idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), and hepatic fibrosis.
  • IPF idiopathic pulmonary fibrosis
  • Myocardial infarction myocardial infarction
  • cardiac hypertrophy heart failure
  • cirrhosis acetominophen (Tylenol) liver toxicity
  • hepatitis C liver disease hepatosteatosis (fatty liver disease)
  • hepatic fibrosis examples include hepatic fibrosis.
  • signaling pathway refers to a series of interactions between cellular and optionally extra-cellular components (e.g. proteins, nucleic acids, small molecules, ions, lipids) that conveys a change in one component to one or more other components, which in turn may convey a change to additional components, which is optionally propagated to other signaling pathway components.
  • extra-cellular components e.g. proteins, nucleic acids, small molecules, ions, lipids
  • “Pharmaceutically acceptable excipient” and “pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient.
  • Non-limiting examples of pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer's, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer's solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, mannitol, gum acacia, calcium phosphate, alginates, tragacanth, calcium silicate, microcrystalline cellulose, cellulose, syrup, and methyl cellulose, colors, and the like.
  • the formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl and propylhydroxy benzoates; sweetening agents; and flavoring agents.
  • lubricating agents such as talc, magnesium stearate, and mineral oil
  • wetting agents such as talc, magnesium stearate, and mineral oil
  • emulsifying and suspending agents preserving agents such as methyl and propylhydroxy benzoates
  • sweetening agents and flavoring agents.
  • the compositions described herein can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art. Such preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic
  • preparation is intended to include the formulation of the active compound with encapsulating material as a carrier providing a capsule in which the active component with or without other carriers, is surrounded by a carrier, which is thus in association with it.
  • cachets and lozenges are included. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration.
  • administering means administration by any route, including systemic, local, oral administration, administration as a suppository, topical contact, intravenous, parenteral, intraperitoneal, intramuscular, intralesional, intrathecal, intracranial, intranasal or subcutaneous administration, topical (including ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal), ocular, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to a subject.
  • Parenteral administration includes, e.g.,
  • Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump.
  • Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders.
  • Methods for ocular delivery can include topical administration (eye drops), subconjunctival, periocular or intravitreal injection or introduction by balloon catheter or ophthalmic inserts surgically placed in the conjunctival sac.
  • Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc.
  • compositions described herein are administered at the same time, just prior to, or just after the administration of one or more additional therapies (e.g. anti-cancer agent, chemotherapeutic, treatment for an eye disease, treatment for fibrosis, treatment for a demyelinating disease, diabetes treatment, or treatment for a neurodegenerative disease).
  • additional therapies e.g. anti-cancer agent, chemotherapeutic, treatment for an eye disease, treatment for fibrosis, treatment for a demyelinating disease, diabetes treatment, or treatment for a neurodegenerative disease.
  • the compound of the invention can be administered alone or can be coadministered to the patient.
  • the compositions (e.g. compounds) described herein can also be formulated in combination with one or more additional active ingredients which can include any pharmaceutical agent such as anti viral agents, vaccines, antibodies, immune enhancers, immune suppressants, anti inflammatory agents and the like.
  • Coadministration is meant to include simultaneous or sequential administration of the compound individually or in combination (more than one compound or agent).
  • the preparations can also be combined, when desired, with other active substances (e.g. to reduce metabolic degradation).
  • the compositions of the present invention can be delivered by trans dermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.
  • Oral preparations include tablets, pills, powder, dragees, capsules, liquids, lozenges, cachets, gels, syrups, slurries, suspensions, etc., suitable for ingestion by the patient.
  • Solid form preparations include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules.
  • Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions.
  • the compositions of the present invention may additionally include components to provide sustained release and/or comfort. Such components include high molecular weight, anionic mucomimetic polymers, gelling polysaccharides and finely-divided drug carrier substrates. These components are discussed in greater detail in U.S. Pat. Nos. 4,91 1,920; 5,403,841 ; 5,212,162; and 4,861,760. The entire contents of these patents are incorporated herein by reference in their entirety for all purposes.
  • compositions of the present invention can also be delivered as microspheres for slow release in the body.
  • microspheres can be administered via intradermal injection of drug-containing microspheres, which slowly release subcutaneously (see Rao, J. Biomater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gel formulations
  • the formulations of the compositions of the present invention can be delivered by the use of liposomes which fuse with the cellular membrane or are endocytosed, i.e., by employing receptor ligands attached to the liposome, that bind to surface membrane protein receptors of the cell resulting in endocytosis.
  • compositions of the present invention can focus the delivery of the compositions of the present invention into the target cells in vivo.
  • the compositions of the present invention can also be delivered as nanoparticles.
  • compositions provided by the present invention include compositions wherein the active ingredient (e.g. compounds described herein, including embodiments or examples) is contained in a therapeutically effective amount, i.e., in an amount effective to achieve its intended purpose.
  • the actual amount effective for a particular application will depend, inter alia, on the condition being treated.
  • such compositions When administered in methods to treat a disease, such compositions will contain an amount of active ingredient effective to achieve the desired result, e.g., modulating the activity of a target molecule (e.g. Irel (e.g. Irel a) or component of Irel (e.g. Irel a) signal transduction pathway or component of phosphorylated Irel (e.g.
  • a target molecule e.g. Irel (e.g. Irel a) or component of Irel (e.g. Irel a) signal transduction pathway or component of phosphorylated Irel (e.g.
  • Irel a) pathway reducing, eliminating, or slowing the progression of disease symptoms (e.g. symptoms of cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes).
  • disease symptoms e.g. symptoms of cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes.
  • Determination of a therapeutically effective amount of a compound of the invention is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure herein.
  • the dosage and frequency (single or multiple doses) administered to a mammal can vary depending upon a variety of factors, for example, whether the mammal suffers from another disease, and its route of administration; size, age, sex, health, body weight, body mass index, and diet of the recipient; nature and extent of symptoms of the disease being treated (e.g. symptoms of cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes), kind of concurrent treatment, complications from the disease being treated or other health-related problems.
  • Other therapeutic regimens or agents can be used in conjunction with the methods and compounds of Applicants' invention. Adjustment and manipulation of established dosages (e.g., frequency and duration) are well within the ability of those skilled in the art.
  • the therapeutically effective amount can be initially determined from cell culture assays.
  • Target concentrations will be those concentrations of active compound(s) that are capable of achieving the methods described herein, as measured using the methods described herein or known in the art.
  • therapeutically effective amounts for use in humans can also be determined from animal models.
  • a dose for humans can be formulated to achieve a concentration that has been found to be effective in animals.
  • the dosage in humans can be adjusted by monitoring compounds effectiveness and adjusting the dosage upwards or downwards, as described above. Adjusting the dose to achieve maximal efficacy in humans based on the methods described above and other methods is well within the capabilities of the ordinarily skilled artisan.
  • Dosages may be varied depending upon the requirements of the patient and the compound being employed.
  • the dose administered to a patient, in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the patient over time.
  • the size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects. Determination of the proper dosage for a particular situation is within the skill of the practitioner. Generally, treatment is initiated with smaller dosages which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached.
  • Dosage amounts and intervals can be adjusted individually to provide levels of the administered compound effective for the particular clinical indication being treated. This will provide a therapeutic regimen that is commensurate with the severity of the individual's disease state.
  • an effective prophylactic or therapeutic treatment regimen can be planned that does not cause substantial toxicity and yet is effective to treat the clinical symptoms demonstrated by the particular patient. This planning should involve the careful choice of active compound by considering factors such as compound potency, relative bioavailability, patient body weight, presence and severity of adverse side effects, preferred mode of administration and the toxicity profile of the selected agent.
  • the compounds described herein can be used in combination with one another, with other active agents known to be useful in treating cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes, or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent.
  • cancer e.g. multiple myeloma or cancers of secretory cells
  • neurodegenerative diseases e.g. multiple myeloma or cancers of secretory cells
  • demyelinating diseases e.g. multiple myeloma or cancers of secretory cells
  • eye diseases e.g. multiple myeloma or cancers of secretory cells
  • fibrotic diseases e.g., fibrotic diseases, or diabetes
  • co-administration includes administering one active agent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a second active agent.
  • Co-administration includes administering two active agents simultaneously, approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other), or sequentially in any order.
  • co-administration can be accomplished by co-formulation, i.e., preparing a single pharmaceutical composition including both active agents.
  • the active agents can be formulated separately.
  • the active and/or adjunctive agents may be linked or conjugated to one another.
  • the compounds described herein may be combined with treatments for cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, or diabetes, such as surgery.
  • Irel or “Ire la” or “ERN1” refers to the protein "Serine/threonine-protein kinase/endoribonuclease IRET'a.k.a. "Endoplasmic reticulum to nucleus signaling 1".
  • Irel or “Irela” or “ERN1” refers to the human protein. Included in the term “Irel” or “Irela” or “ERN1” are the wildtype and mutant forms of the protein.
  • “Irel” or “Irela” or “ERN1” refers to the protein associated with Entrez Gene 2081, OMIM
  • the reference numbers immediately above refer to the protein, and associated nucleic acids, known as of the date of filing of this application.
  • “Irel” or “Irela” or “ERN1” refers to the wildtype human protein.
  • “Irel” or “Irela” or “ER 1” refers to the wildtype human nucleic acid.
  • Anti-cancer agent is used in accordance with its plain ordinary meaning and refers to a composition (e.g. compound, drug, antagonist, inhibitor, modulator) having antineoplastic properties or the ability to inhibit the growth or proliferation of cells.
  • an anti-cancer agent is a chemotherapeutic.
  • an anti-cancer agent is an agent identified herein having utility in methods of treating cancer.
  • an anticancer agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating cancer.
  • anti-cancer agents include, but are not limited to, MEK inhibitors , alkylating agents, anti-metabolites, plant alkaloids, topoisomerase inhibitors, antitumor antibiotics, platinum-based compounds, adrenocortical suppressants,
  • epipodophyllotoxins antibiotics, enzymes, inhibitors of mitogen-activated protein kinase signaling, antibodies, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec.RTM.), agents that arrest cells in the G2-M phases and/or modulate the formation or stability of microtubules (e.g. Taxol.TM (i.e.
  • “Chemotherapeutic” or “chemotherapeutic agent” is used in accordance with its plain ordinary meaning and refers to a chemical composition or compound having antineoplastic properties or the ability to inhibit the growth or proliferation of cells.
  • the compounds described herein can be co-administered with conventional immunotherapeutic agents including, but not limited to, immunostimulants (e.g., Bacillus Calmette-Guerin (BCG), levamisole, interleukin-2, alpha- interferon, etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti-VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33 monoclonal antibody-calicheamicin conjugate, anti- CD22 monoclonal antibody -pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy (e.g., anti-CD20 monoclonal antibody conjugated to m In, 90 Y, or 131 I, etc.).
  • immunostimulants e.g., Bacillus Calmette-Guerin (BCG), levamisole, interleukin-2, alpha- interferon,
  • the compounds described herein can be co-administered with conventional radiotherapeutic agents including, but not limited to, radionuclides such as 47 Sc, 64 Cu, 67 Cu, 89 Sr, 86 Y, 87 Y, 90 Y, 105 Rh, m Ag, m In, 117m Sn, 149 Pm, 153 Sm, 166 Ho, 177 Lu, 186 Re,
  • radionuclides such as 47 Sc, 64 Cu, 67 Cu, 89 Sr, 86 Y, 87 Y, 90 Y, 105 Rh, m Ag, m In, 117m Sn, 149 Pm, 153 Sm, 166 Ho, 177 Lu, 186 Re,
  • Anti-diabetic agent or “antidiabetic agent” is used in accordance with its plain ordinary meaning and refers to a composition (e.g. compound, drug, antagonist, inhibitor, modulator) having the ability to lower blood glucose levels in a subject.
  • an anti-diabetic agent is an agent identified herein having utility in methods of treating diabetes.
  • an anti-diabetic agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating diabetes.
  • Examples of antidiabetic agents include, but are not limited to, insulin, insulin sensitizers (e.g. biguanides (e.g.
  • metformin, phenformin, or buformin metformin, phenformin, or buformin
  • thiazolidinediones e.g. rosiglitazone, pioglitazone, troglitazone
  • secretagogues e.g. sulfonylureas (e.g. tolbutamide, acetohexamide, tolazamide, chlorpropamide, glipizide, glyburide, glibenclamide, glimepiride, gliclazide, glycopyramide, gliquidone), meglitinides (e.g. repaglinide, nateglinide)), alpha-glucosidase inhibitors (e.g.
  • miglitol miglitol, acarbose, voglibose
  • peptide analog antidiabetic agents e.g. incretins (glucagon-like peptide- 1, gastric inhibitory peptide), glucagon-like peptide agonists (e.g. exenatide, liraglutide, taspoglutide), gastric inhibitoty peptide analogs, or dipeptidyl peptidase-4 inhibitors (e.g.
  • ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
  • L 1 is a bond or unsubstituted C1-C5 alkylene;
  • L 2 is a bond, -NR 6a -, -0-, -S-, -C(O)-
  • R 3 is independently hydrogen, oxo,
  • R 10b , -NR 7b C (0)R 9b , -NR 7b C(0)OR 9b , -NR 7b OR 9b , -OCX b 3 , -OCHX b 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R 4 and R 5 are independently hydrogen or unsubstituted Ci-Ce alkyl; R 7 , R 8b , -N(0) m2 , -NR 7b R 8b , -C(0)R 9b , -C(0)-OR 9b , -C(0)NR 7b R 8b , -OR 10b , - NR 7b SO
  • R 10b , -NR 7b C (0)
  • R substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4; each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2; the symbol z is an integer from 0 to 2; the symbol z2 is an integer from 1 to 4; and each occurrence of the symbols X, X a , and X b is independently a halogen.
  • ring A is substituted or unsubstituted monocyclic cycloalkylene, substituted or unsubstituted monocyclic heterocycloalkylene, substituted or unsubstituted monocyclic arylene, or substituted or unsubstituted monocyclic heteroarylene.
  • ring A is substituted monocyclic cycloalkylene, substituted monocyclic heterocycloalkylene, substituted monocyclic arylene, or substituted monocyclic heteroarylene.
  • ring A is unsubstituted monocyclic cycloalkylene, unsubstituted monocyclic heterocycloalkylene, unsubstituted monocyclic arylene, or unsubstituted monocyclic heteroarylene.
  • ring A is substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C1 0 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
  • ring A is substituted C3-C8 cycloalkylene, substituted 3 to 8 membered heterocycloalkylene, substituted C6-C1 0 arylene, or substituted 5 to 10 membered heteroarylene.
  • ring A is unsubstituted C3-C8 cycloalkylene, unsubstituted 3 to 8 membered heterocycloalkylene, unsubstituted C6-C10 arylene, or unsubstituted 5 to 10 membered heteroarylene.
  • ring A is substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.
  • ring A is substituted C3-C6 cycloalkylene, substituted 3 to 6 membered heterocycloalkylene, substituted C6-C10 arylene, or substituted 5 to 9 membered heteroarylene.
  • ring A is unsubstituted C3-C6 cycloalkylene, unsubstituted 3 to 6 membered heterocycloalkylene, unsubstituted C6-C10 arylene, or unsubstituted 5 to 9 membered heteroarylene.
  • ring A is substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene.
  • ring A is substituted or unsubstituted C6-C10 arylene.
  • ring A is unsubstituted naphthalenyl (i.e. divalent naphthalene moiety).
  • ring A is substituted naphthalenyl. In embodiments, ring A is unsubstituted phenylene (divalent benzene moiety or benzene-di-yl). In embodiments, ring A is substituted phenylene (divalent benzene moiety or benzene-di-yl).
  • ring A is R 41 -substituted or unsubstituted cycloalkylene, R 41 - substituted or unsubstituted heterocycloalkylene, R 41 -substituted or unsubstituted arylene, or R 41 - substituted or unsubstituted heteroarylene.
  • ring A is substituted with 1 to 6 optionally different R 41 substituents.
  • ring A is substituted with 1 R 41 substituent.
  • ring A is substituted with 2 optionally different R 41 substituents.
  • ring A is substituted with 3 optionally different R 41 substituents.
  • ring A is substituted with 4 optionally different R 41 substituents. In embodiments, ring A is substituted with 5 optionally different R 41 substituents. In embodiments, ring A is substituted with 6 optionally different R 41 substituents. [0164] R 41 is independently oxo,
  • R 1 is hydrogen, oxo,
  • R 1 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 1 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 1 is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R 1 is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, R 1 is hydrogen. In embodiments, R 1 is hydrogen and L 2 is -NHC(O)-.
  • R 1 is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C 3 -Cs cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- Cio aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • R 1 is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C 3 -C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
  • R 1 is substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R 1 is substituted or unsubstituted aryl or substituted or
  • R 1 is substituted phenyl. In embodiments, R 1 is unsubstituted phenyl. In embodiments, R 1 is phenyl substituted with -CF 3 or halogen. In embodiments, R 1 is phenyl meta-substituted with -CF 3 . In embodiments, R 1 is phenyl meta- substituted with -F. In embodiments, R 1 is phenyl meta-substituted with -CI. In embodiments, R 1 is phenyl meta-substituted with -Br. In embodiments, R 1 is phenyl meta-substituted with -I. In embodiments, R 1 is phenyl meta-substituted with -CH 3 . In embodiments, R 1
  • R 1 is -OPh, -CH 2 Ph, -OCH 2 Ph, -NHC(0)H, or -CHO.
  • R 1 is phenyl meta- substituted with -CC1 3 .
  • R 1 is phenyl para-substituted with -CF 3 , - CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is phenyl meta- substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is phenyl ortho-substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is aryl meta-substituted with -CF 3 , - CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is aryl ortho- substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is aryl para-substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is aryl substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is heteroaryl substituted with -CF 3 , -
  • R 1 is phenyl substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is 5 to 6 membered heteroaryl substituted with -CF 3 , -CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 1 is unsubstituted cyclohexyl. In embodiments, R 1 is substituted cyclohexyl. In embodiments, R 1 is unsubstituted cyclopenyl. In embodiments, R 1 is substituted cyclopenyl. In embodiments, R 1 is unsubstituted cyclobutyl. In embodiments, R 1 is substituted cyclobutyl. In embodiments, R 1 is unsubstituted cyclopropyl. In embodiments, R 1 is substituted cyclopropyl.
  • R 1 is a substituted or unsubstituted heteroaryl selected from the group consisting of pyridinyl, pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl, benzothiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, fu
  • R 1 is substituted with 1 to 6 optionally different R 11 substituents. In embodiments, R 1 is substituted with 1 R 11 substituent. In embodiments, R 1 is substituted with 2 optionally different R 11 substituents. In embodiments, R 1 is substituted with 3 optionally different R 11 substituents. In embodiments, R 1 is substituted with 4 optionally different R 11 substituents. In embodiments, R 1 is substituted with 5 optionally different R 11 substituents. In embodiments, R 1 is substituted with 6 optionally different R 11 substituents. In embodiments, R 1 is substituted with 7 optionally different R 11 substituents. In embodiments, R 1 is phenyl substituted with 1 to 5 optionally different R 11 substituents.
  • R 1 is phenyl substituted with 1 R 11 substituent. In embodiments, R 1 is phenyl substituted with 2 optionally different R 11 substituents. In embodiments, R 1 is phenyl substituted with 3 optionally different R 11 substituents. In embodiments, R 1 is phenyl substituted with 4 optionally different R 11 substituents. In embodiments, R 1 is phenyl substituted with 5 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 1 to 6 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 1 R 11 substituent. In embodiments, R 1 is aryl substituted with 2 optionally different R 11 substituents.
  • R 1 is aryl substituted with 3 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 4 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 5 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 6 optionally different R 11 substituents. In embodiments, R 1 is aryl substituted with 7 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 1 to 6 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 1 R 11 substituent. In
  • R 1 is heteroaryl substituted with 2 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 3 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 4 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 5 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 6 optionally different R 11 substituents. In embodiments, R 1 is heteroaryl substituted with 7 optionally different R 11 substituents.
  • R 11 is independently oxo
  • R 11 is -CCI 3 , -CF 3 , - CI, -OCF 3 , -CH 3 , -F, -OCH 3 , -OPh, -CH 2 Ph, or -CHO.
  • R 12 is independently oxo
  • R 2 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 2 is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl.
  • R 2 is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.
  • R 2 is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C 3 -C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • R 2 is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C 3 -C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C1 0 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
  • R 2 is substituted or unsubstituted alkyl.
  • R 2 is substituted or unsubstituted Ci-Ce alkyl.
  • R 2 is unsubstituted Ci-Ce alkyl. In embodiments, R 2 is unsubstituted methyl. In embodiments, R 2 is unsubstituted isopropyl. In embodiments, R 2 is unsubstituted ethyl. In embodiments, R 2 is unsubstituted propyl (e.g. n- propyl or isopropyl). In embodiments, R 2 is unsubstituted isopropyl. In embodiments, R 2 is unsubstituted butyl (e.g. n-butyl, sec -butyl, isobutyl, or tert-butyl).
  • butyl e.g. n-butyl, sec -butyl, isobutyl, or tert-butyl.
  • R 2 is unsubstituted tert-butyl. In embodiments, R 2 is unsubstituted iso-butyl. In embodiments, R 2 is unsubstituted pentyl (e.g. n-pentyl, tert-pentyl, neopentyl, isopentyl, sec-pentyl, or 3-pentyl). In embodiments, R 2 is unsubstituted cyclopropyl. In embodiments, R 2 is unsubstituted cyclobutyl. In embodiments, R 2 is unsubstituted cyclopentyl. In embodiments, R 2 is unsubstituted cyclohexyl.
  • R 2 is independently hydrogen
  • R 14 is independently oxo
  • R 15 is independently oxo
  • R 3 is independently hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 3 is independently hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl.
  • R 3 is independently hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.
  • R 3 is independently hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3- Cs cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C6-C1 0 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • R 3 is independently hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted Ce- C1 0 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
  • R 3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
  • R 3 is independently hydrogen. In embodiments, R 3 is independently halogen.
  • R 3 is independently hydrogen
  • R 17 is independently oxo
  • R 4 and R 5 are independently hydrogen. In embodiments, R 4 and R 5 are independently unsubstituted C1-C6 alkyl. In embodiments, R 4 and R 5 are independently unsubstituted C1-C5 alkyl. In embodiments, R 4 and R 5 are independently unsubstituted C1-C4 alkyl. In embodiments, R 4 and R 5 are independently unsubstituted C1-C 3 alkyl. In embodiments, R 4 and R 5 are independently unsubstituted Ci-C 2 alkyl. In embodiments, R 4 and R 5 are independently unsubstituted methyl.
  • L 1 is a bond. In embodiments, L 1 is unsubstituted C1-C5 alkylene. In embodiments, L 1 is unsubstituted C1-C4 alkylene. In embodiments, L 1 is unsubstituted C1-C 3 alkylene. In embodiments, L 1 is unsubstituted Ci-C 2 alkylene. In embodiments, L 1 is unsubstituted methylene.
  • L 2 is a bond. In embodiments, L 2 is -NR 6a -. In embodiments, L 2 is -0-. In embodiments, L 2 is -S-. In embodiments, L 2 is -C(O)-. In embodiments, L 2 is -S(O)-. In embodiments, L 2 is -S(0) 2 -. In embodiments, L 2 is -C(0)(CH 2 ) z2 -. In embodiments, L 2 is -NR 6a C(0)-. In embodiments, L 2 is -C ⁇ NR*-. In embodiments, L 2 is -NR 6a C(0)0-. In embodiments, L 2 is -NR 6a C(0)NR 6b -.
  • L 2 is -NH-. In embodiments, L 2 is -NHC(O)-. In embodiments, L 2 is -C(0)NH-. In embodiments, L 2 is -NHC(0)NH-. In embodiments, L 2 is -NHC(0)OCH 2 -. In embodiments, L 2 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. In embodiments, L 2 is -C(0)(CH 2 )-. In
  • L 2 is -C(0)(CH 2 )2-. In embodiments, L 2 is -C(0)(CH 2 )3-. In embodiments, L 2 is -C(0)(CH 2 ) 4 -.
  • L 2 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
  • L 2 is substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, or substituted heteroarylene.
  • L 2 is unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, or unsubstituted heteroarylene.
  • L 2 is substituted or unsubstituted Ci-C 8 alkylene, substituted or unsubstituted 2 to 8 membered heteroalkylene, substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C1 0 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
  • L 2 is substituted or unsubstituted C1-C6 alkylene, substituted or unsubstituted 2 to 6 membered heteroalkylene, substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C1 0 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.
  • L 2 is independently R 44 -substituted or unsubstituted alkylene, R 44 -substituted or unsubstituted heteroalkylene, R 44 -substituted or unsubstituted cycloalkylene, R 44 -substituted or unsubstituted heterocycloalkylene, R ⁇ -substituted or unsubstituted arylene, or R 44 -substituted or unsubstituted heteroarylene.
  • R 44 is independently oxo
  • R 45 is independently oxo
  • R 6a is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 6a is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl.
  • R 6a is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, R 6a is hydrogen. In embodiments, R 6a is unsubstituted methyl. In embodiments, R 6a is unsubstituted ethyl. In embodiments, R 6a is unsubstituted propyl.
  • R 6a is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C1 0 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • R 6a is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C1 0 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
  • R 26a is independently oxo
  • R 6b is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 6b is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl.
  • R 6b is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.
  • R 6b is hydrogen.
  • R* is unsubstituted methyl.
  • R 6b is unsubstituted ethyl.
  • R 6b is unsubstituted propyl.
  • R 6b is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C 3 -C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C1 0 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • R 6b is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C 3 -C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C1 0 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
  • R 27b is independently oxo
  • each R 7 , R 8 , R 9 , R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
  • each R 7 , R 8 , R 9 , R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl.
  • R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.
  • each R 7 , R 8 , R 9 , R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen.
  • each R 7 , R 8 , R 9 , R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C6-C1 0 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
  • each R 7 , R 8 , R 9 , R 10 , R 7a , R 8a , R 9a , R 10a , R 7b , R 8b , R 9b and R 10b is independently hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or
  • R 7 is independently hydrogen
  • R 7 and R 8 substituents bonded to the same nitrogen atom may be joined to form an R 29 -substituted or unsubstituted heterocycloalkyl or R 29 - substituted or unsubstituted heteroaryl.
  • R 29 is independently oxo
  • R 30 is independently oxo
  • R 7a is independently hydrogen
  • R 7a and R 8a substituents bonded to the same nitrogen atom may be joined to form an R 29a -substituted or unsubstituted heterocycloalkyl or R 29a - substituted or unsubstituted heteroaryl.
  • R 29a is independently oxo
  • R 7b is independently hydrogen
  • R and R substituents bonded to the same nitrogen atom may be joined to form an R 29b -substituted or unsubstituted heterocycloalkyl or R 29b - substituted or unsubstituted heteroaryl.
  • R 29b is independently 0X0
  • R 30b is independently oxo
  • R 8 is independently hydrogen
  • R 7 and R 8 substituents bonded to the same nitrogen atom may be joined to form an R 32 -substituted or unsubstituted heterocycloalkyl or R 32 - substituted or unsubstituted heteroaryl.
  • R 32 is independently oxo
  • R 33 is independently oxo
  • R 7a and R 8a substituents bonded to the same nitrogen atom may be joined to form an R 32a -substituted or unsubstituted heterocycloalkyl or R 32a - substituted or unsubstituted heteroaryl.
  • R 32a is independently oxo
  • R 33a is independently oxo
  • R 7b and R 8b substituents bonded to the same nitrogen atom may be joined to form an R 32b -substituted or unsubstituted heterocycloalkyl or R 32b - substituted or unsubstituted heteroaryl.
  • R 32b is independently oxo
  • R 33b is independently oxo
  • R 9 is independently hydrogen
  • R 35 is independently oxo
  • R 36 is independently oxo
  • R 9a is independently hydrogen
  • R 36a is independently oxo
  • R 9b is independently hydrogen
  • R 36b is independently oxo
  • R 10 is independently hydrogen
  • R is independently oxo,
  • R 39 is independently oxo
  • R 38a is independently oxo
  • R 39a is independently oxo
  • R 10b is independently hydrogen,
  • R 38b is independently oxo
  • R 39b is independently oxo
  • halogen -CF 3 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -N0 2 , -SH, -S0 2 C1, -S0 3 H, -S0 4 H, -
  • v is 1. In embodiments, v is 2. In embodiments, vl is 1. In embodiments, vl is 2. In embodiments, v2 is 1. In embodiments, v2 is 2. In embodiments, m is
  • n is 2. In embodiments, ml is 1. In embodiments, ml is 2. In embodiments,
  • m2 is 1. In embodiments, m2 is 2. In embodiments, n is independently 0. In embodiments, n is independently 1. In embodiments, n is independently 2. In embodiments, n is independently 3. In embodiments, n is independently 4. In embodiments, nl is independently 0.
  • nl is independently 1. In embodiments, nl is independently 2. In embodiments, nl is independently 3. In embodiments, nl is independently 4. In embodiments, n2 is independently 0. In embodiments, n2 is independently 1. In embodiments, n2 is independently 2. In embodiments, n2 is independently 3. In embodiments, n2 is independently 4. In embodiments, X is -CI. In embodiments, X is -Br. In embodiments, X is -I. In embodiments, X is -F. In embodiments, X a is -CI. In embodiments, X a is -Br. In embodiments, X a is -I. In embodiments, X a is -F.
  • X b is -CI. In embodiments, X b is -Br. In embodiments, X b is -I. In embodiments, X b is -F. In embodiments, z is 0. In embodiments, z is 1. In embodiments, z is 2. In embodiments, z2 is 1. In embodiments, z2 is 2. In embodiments, z2 is 3. In embodiments, z2 is 4. [0243] In embodiments, the compound has the formula:
  • L 3 is a bond, -0-, -NR*-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
  • L 3 is a bond.
  • L 3 is -NR 6b -, wherein R 6b is as defined herein including embodiments thereof.
  • L 3 is -NH-.
  • L 3 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
  • L 3 is -0-. .
  • L 3 is -OCH 2 -.
  • L 3 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
  • L 3 is substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, or substituted heteroarylene.
  • L 3 is unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, or unsubstituted heteroarylene.
  • L 3 is substituted or unsubstituted Ci-C 8 alkylene, substituted or unsubstituted 2 to 8 membered heteroalkylene, substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C1 0 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
  • L 3 is substituted or unsubstituted Ci-Ce alkylene, substituted or unsubstituted 2 to 6 membered heteroalkylene, substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C1 0 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.
  • L 3 is independently R 47 -substituted or unsubstituted alkylene, R 47 -substituted or unsubstituted heteroalkylene, R 47 -substituted or unsubstituted cycloalkylene, R 47 -substituted or unsubstituted heterocycloalkylene, R 47 -substituted or unsubstituted arylene, or R 47 -substituted or unsubstituted heteroarylene.
  • R 47 is independently oxo
  • R 48 is independently oxo
  • Each R 13 , R 16 , R 19 , R 28a , R 28b , R 31 , R 31a , R 31b , R 34 , R 34a , R 34b , R 37 , R 37a , R 37b , R 40 , R 40a , R 40b , R 43 , R 46 , and R 49 is independently a hydrogen, oxo,
  • each R 13 , R 16 , R 19 , R 28a , R 28b , R 31 , R 31a , R 31b , R 34 , R 34a , R 34b , R 37 , R 37a , R 37b , R 40 , R 40a , R 40b , R 43 , R 46 , and R 49 is independently hydrogen, unsubstituted Ci-C 8 alkyl, unsubstituted 2 to 8 membered heteroalkyl, unsubstituted C3-C8 cycloalkyl, unsubstituted 3 to 8 membered heterocycloalkyl, unsubstituted C6-C1 0 aryl, or unsubstituted 5 to 10 membered heteroaryl.
  • each R 13 , R 16 , R 19 , R 28a , R 28b , R 31 , R 31a , R 31b , R 34 , R 34a , R 34b , R 37 , R 37a , R 37b , R 40 , R 40a , R 40b , R 43 , R 46 , and R 49 is independently hydrogen, unsubstituted Ci-C 6 alkyl, unsubstituted 2 to 6 membered heteroalkyl, unsubstituted C3-C6 cycloalkyl, unsubstituted 3 to 6 membered heterocycloalkyl, unsubstituted C6-C1 0 aryl, or unsubstituted 5 to 9 membered heteroaryl.
  • each R 13 , R 16 , R 19 , R 28a , R 28b , R 31 , R 31a , R 31b , R 34 , R 34a , R 34b , R 37 , R 37a , R 37b , R 40 , R 40a , R 40b , R 43 , R 46 , and R 49 is hydrogen, oxo,
  • the compound has the formula:
  • the compound is an inhibitor of Irel . In embodiments, the compound is an inhibitor of Ire la. In embodiments, the compound is an inhibitor of Ire la kinase activity. In embodiments, the compound is an inhibitor of Ire la RNase activity. In embodiments, the compound binds the ATP binding site of Ire la. In embodiments, the compound binds Ire la in the DFG-out conformation. In embodiments, the compound induces the DFG-out conformation of Irel a. In embodiments, the compound is an inhibitor of Ire la oligomerization. In embodiments, the compound is an inhibitor of Ire la dimerization. In embodiments, the compound is an inhibitor of Irela phosphorylation.
  • the compound is an inhibitor of Irela autophosphorylation. In embodiments, the compound is an inhibitor of apoptosis. In embodiments, the compound is an inhibitor of Irela induced apoptosis. In embodiments, the compound is an inhibitor of cell death. In embodiments, the compound is an inhibitor of Irela induced cell death. In embodiments, the compound is an inhibitor of a pathway induced by Irela phosphorylation. In embodiments, the compound is an inhibitor of a pathway induced by Irela kinase activity. In embodiments, the compound is an inhibitor of a pathway induced by Irela RNase activity. In embodiments, the compound is an inhibitor of neuronal cell death. In embodiments, the compound is a cytotoxic agent. In embodiments, the compound is an anti-cancer agent. In embodiments, the compound is an inhibitor of
  • the compound is an inhibitor of diabetes. In embodiments, the compound is an anti-diabetic agent. In embodiments, the compound is a neuroprotective agent. In embodiments, the compound is an inhibitor of fibrosis. In embodiments, the compound decreases apoptosis in cells under ER stress. In embodiments, the compound decreases apoptosis in cells under ER stress but not cells under the same conditions except that they are not under ER stress. In embodiments, the compound decreases apoptosis in cells under ER stress more than in cells under the same conditions except that they are not under ER stress. In embodiments, the compound decreases cleavage of miR-17.
  • the compound decreases Irela associated cleavage of miR-17. In embodiments, the compound decreases cleavage of miR-34a. In embodiments, the compound decreases Irela associated cleavage of miR-34a. In embodiments, the compound decreases cleavage of miR-96. In embodiments, the compound decreases Irela associated cleavage of miR-96. In embodiments, the compound decreases cleavage of miR-125b. In embodiments, the compound decreases Irela associated cleavage of miR- 125b. In embodiments, the compound decreases XBP 1 mRNA splicing. In embodiments, the compound decreases Irela associated XBP1 mRNA splicing. In
  • the compound decreases the UPR. In embodiments, the compound decreases Irela associated UPR. In embodiments, the compound decreases the terminal UPR. In embodiments, the compound decreases Irela associated terminal UPR. [0255] In embodiments, the compound is a compound described herein, including in an aspect, embodiment, example, figure, table, or claim. In embodiments, the compound is a compound in Fig. 8.
  • the compounds set forth herein are provided as pharmaceutical compositions including the compound, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In embodiments, the compounds set forth herein are not provided as pharmaceutical compositions. In embodiments, the compound is included in a pharmaceutically acceptable salt. In embodiments, the compound is not included in a pharmaceutically acceptable salt.
  • IRElcc Described herein, inter alia, is a new strategy to: (1) inhibit IREl 's hyperactive RNase by pharmacologically targeting its neighboring kinase domain with small molecules, and (2) test physiological benefits of shutting down IRElcc in cells (e.g. ⁇ -cells) of living mammals (e.g. mice). This work validates IRElcc as a drug target to manipulate ER stress signaling to control cell fate.
  • R , R , R 4d , R 5d , R 6d , R 7d , R 8d , R 9d , and R 10d are each independently C 2 _ 6 alkyl, Ci_ 6 haloalkyl, -C 1-4 alkyl-R 12d , C 2 _6 alkenyl, C 2 _6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R l ld groups; each R l ld is independently Ci_6 alkyl, Ci_ 6 haloalkyl, -C(0)R d , -C(0)OR d , -C(0)NR d 2 , S(0)
  • R , R , R 4d , R 5d , R 6d , R 7d , R 8d , R 9d , and R 10d are each independently C 2 _ 6 alkyl, Ci_ 6 haloalkyl, -Ci_ 4 alkyl-R 12d , C 2 _6 alkenyl, C 2 _6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R l ld groups; each R l ld is independently Ci_6 alkyl, Ci_ 6 haloalkyl, -C(0)R d , -C(0)OR d , -C(0)NR d 2 , S
  • R 2d and R 3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci_ 6 haloalkyl, -OR d , -SR d , -NR d 2 , -C(O) R d , C(0)OR d , -C(0)NR d 2 , -S(0) 2 R d , -OC(O) R d , -OC(0)OR d , OC(0)NR d 2 , N(R d )C(0) R d , - N(R d )C(0)OR d , or -N(R d )C(0)NR
  • R 2d and R 3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci-6 haloalkyl, -OR d , -SR d , -NR d 2, -C(O) R d , C(0)OR d , -C(0)NR d 2 , -S(0) 2 R d , -OC(O) R d , -OC(0)OR d , OC(0)NR d 2 , N(R d )C(0) R d , - N(R d )C(0)OR d , or -N(R d )C(0)NR d 2
  • R ld is -OR d , -SR d , -NR d 2 , -C(0)R d , -C(0)OR d , -C(0)NR d 2 , - N(R d )C(0)R d , -N(R d )C(0)OR d , -N(R d )C(0)NR d 2 , phenyl, monocyclic heteroaryl, C 3 - 8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR d , -SR d , -NR d 2 , -C(0)R d , C(0)OR d
  • composition including a
  • the pharmaceutical composition includes a second agent (e.g. therapeutic agent).
  • the pharmaceutical composition includes a second agent (e.g. therapeutic agent) in a therapeutically effective amount.
  • the second agent is an agent for treating cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes.
  • the second agent is an anti-cancer agent.
  • the second agent is a chemotherapeutic.
  • the second agent is an agent for improving memory.
  • the second agent is an agent for treating a neurodegenerative disease.
  • the second agent is an agent for treating a demyelinating disease.
  • the second agent is an agent for treating an eye disease. In embodiments, the second agent is an agent for treating a fibrotic disease. In embodiments, the second agent is an agent for treating multiple sclerosis. In embodiments, the second agent is an agent for treating Alzheimer's disease. In embodiments, the second agent is an agent for treating Parkinson's disease. In embodiments, the second agent is an agent for treating Huntington's disease. In embodiments, the second agent is an agent for treating a prion disease. In embodiments, the second agent is an agent for treating amyotrophic lateral sclerosis. In embodiments, the second agent is an agent for treating diabetes. In embodiments, the second agent is an agent for treating retinal degeneration.
  • the second agent is an agent for treating retinitis pigmentosa. In embodiments, the second agent is an agent for treating macular degeneration. In embodiments, the second agent is an agent for treating type I diabetes. In embodiments, the second agent is an agent for treating type II diabetes. In embodiments, the second agent is an agent for treating multiple myeloma. In embodiments, the second agent is an agent for treating a cancer of a secretory cell. In embodiments, the second agent is an agent for reducing Irel (e.g.
  • the second agent is an agent for reducing Irel (e.g.
  • the second agent is an agent for inhibiting a pathway activated by Irel (e.g. Irela) phosphorylation. In embodiments, the second agent is an agent for inhibiting a pathway activated by Irel (e.g. Irela) RNase activity. In embodiments, the second agent is an agent for inhibiting Irel (e.g. Irela) oligomerization. In embodiments, the second agent is an agent for inhibiting apoptosis.
  • a method of treating a disease in a patient in need of such treatment including administering a therapeutically effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof, to the patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
  • a compound described herein e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim
  • the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
  • the disease is a neurodegenerative disease, demyelinating disease, cancer, or diabetes. In embodiments, the disease is a neurodegenerative disease.
  • the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease, or Kuru.
  • the disease is amyotrophic lateral sclerosis.
  • the disease is retinal degeneration.
  • the disease is retinitis pigmentosa.
  • the disease is a demyelinating disease.
  • the demyelinating disease is Wolfram Syndrome, Pelizaeus- Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis.
  • the disease is Multiple Sclerosis.
  • the disease is cancer.
  • the cancer is multiple myeloma.
  • the disease is diabetes.
  • the diabetes is type I diabetes.
  • the diabetes is type II diabetes.
  • the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes described herein.
  • the disease is an eye disease.
  • the eye disease is retinitis pigmentosa.
  • the eye disease is retinal degeneration.
  • the eye disease is macular degeneration.
  • the eye disease is Wolfram Syndrome.
  • the disease is idiopathic pulmonary fibrosis (IPF).
  • the disease is a fibrotic disease.
  • the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
  • the disease is interstitial lung disease (ILD).
  • the disease is myocardial infarction.
  • the disease is cardiac hypertrophy.
  • the disease is heart failure.
  • the disease is cirrhosis.
  • the disease is acetominophen
  • (Tylenol) liver toxicity In embodiments, the disease is hepatitis C liver disease. In
  • the disease is hepatosteatosis (fatty liver disease). In embodiments, the disease is hepatic fibrosis.
  • a method of modulating the activity of an Irel (e.g. Ire la) protein including contacting the Irel (e.g. Ire la) protein with an effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof.
  • the modulating is inhibiting.
  • the activity is kinase activity.
  • the kinase activity is autophosphorylation activity.
  • the kinase activity is trans-autophosphorylation activity.
  • the activity is oligomerization activity.
  • the oligomerization activity is dimerization activity.
  • the activity is RNase activity.
  • the activity is miR-17 cleavage.
  • the activity is miR-34a cleavage.
  • the activity is miR-96 cleavage.
  • the activity is miR-125b cleavage.
  • the activity is XBP 1 mRNA splicing.
  • the activity is UPR activation.
  • the activity is terminal UPR activation.
  • a cell includes the Irel (e.g. Ire la) protein.
  • the activity of the Irel e.g.
  • Ire la) protein is increasing apoptosis of the cell.
  • an organ includes the cell.
  • an organism includes the cell.
  • an organism has a disease associated with the Irel (e.g. Irela) protein activity.
  • the disease is a neurodegenerative disease, a demyelinating disease, cancer, an eye disease, a fibrotic disease, or diabetes.
  • the disease is a neurodegenerative disease.
  • the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease, or Kuru.
  • the disease is amyotrophic lateral sclerosis. In embodiments, the disease is retinal degeneration. In embodiments, the disease is retinitis pigmentosa. In embodiments, the disease is a demyelinating disease. In embodiments, the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple
  • the disease is Multiple Sclerosis.
  • the disease is cancer.
  • the cancer is multiple myeloma.
  • the disease is diabetes.
  • the diabetes is type I diabetes.
  • the diabetes is type II diabetes.
  • the disease is an eye disease.
  • the eye disease is retinitis pigmentosa.
  • the eye disease is retinal degeneration.
  • the eye disease is macular degeneration.
  • the eye disease is Wolfram Syndrome.
  • the disease is idiopathic pulmonary fibrosis (IPF).
  • the disease is a fibrotic disease.
  • the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
  • the disease is interstitial lung disease (ILD).
  • the disease is myocardial infarction.
  • the disease is cardiac hypertrophy.
  • the disease is heart failure.
  • the disease is cirrhosis.
  • the disease is acetominophen (Tylenol) liver toxicity.
  • the disease is hepatitis C liver disease. In embodiments, the disease is hepatosteatosis (fatty liver disease). In embodiments, the disease is hepatic fibrosis.
  • the Irel protein is an Irela protein. In embodiments, the Irel (e.g. Irela) protein is a human protein. In embodiments, the Irel protein is a human Irela protein.
  • the present disclosure has identified two classes of kinase inhibitors—called types I and II, which stabilize alternate kinase active site conformations in numerous protein kinase targets (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006)).
  • types I and II stabilize alternate kinase active site conformations in numerous protein kinase targets (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006)).
  • the present disclosure shows that a type I kinase inhibitor and a novel type II kinase inhibitor both modify IRE la by shutting down IRE la trans-autophosphorylation, but have divergent effects on its RNase to activate or inactivate catalytic activity, respectively.
  • IRE la RNase activity can be either up or downregulated through selective targeting of its kinase domain to control UPR signaling, and predict that it may be possible to pharmacologically modulate other kinase-coupled enzymes in a similar way.
  • the present disclosure illustrates that IRE la's kinase-controlled RNase can be regulated in two distinct modes with kinase inhibitors: one class of ligands occupy IRE la's kinase ATP -binding site to activate RNase- mediated XBP1 mRNA splicing even without upstream ER stress, while a second class can inhibit the RNase through the same ATP- binding site, even under ER stress.
  • alternative kinase conformations stabilized by distinct classes of ATP-competitive inhibitors can cause allosteric switching of IREla's RNase— either on or off.
  • dysregulation of the UPR has been implicated in a variety of cell degenerative and neoplastic disorders, small molecule control over IRE la should advance efforts to understand the
  • ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
  • L 1 is a bond or unsubstituted C1-C5 alkylene;
  • L 2 is a bond, -NR 6a -, -0-, -S-, -C(O)-
  • R 10b , -NR 7b C (0)R 9b , -NR 7b C(0)OR 9b , -NR 7b OR 9b , -OCX b 3 , -OCHX b 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R 4 and R 5 are independently hydrogen or unsubstituted Ci-Ce alkyl; R 7 , R 8b , -N(0) m2 , -NR 7b R 8b , -C(0)R 9b , -C(0)-OR 9b , -C(0)NR 7b R 8b , -OR 10b , - NR 7b SO
  • R 10b , -NR 7b C (0)
  • R substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4; each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2; the symbol z is an integer from 0 to 2; the symbol z2 is an integer from 1 to 4; and each occurrence of the symbols X, X a , and X b is independently a halogen. [0273] 2.
  • R 3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • a pharmaceutical composition comprising a pharmaceutically acceptable excipient and a compound of any one of embodiments 1 to 25.
  • 27 A method of treating a disease in a patient in need of such treatment, said method comprising administering a therapeutically effective amount of a compound of any one of embodiments 1 to 25 to said patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
  • neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru.
  • the disease is a demyelinating disease.
  • fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
  • IPF idiopathic pulmonary fibrosis
  • Tylenol acetominophen
  • liver hepatitis C liver disease hepatosteatosis (fatty liver disease), or hepatic fibrosis.
  • 41 A method of modulating the activity of an Irel protein, said method comprising contacting said Irel protein with an effective amount of a compound of any one of embodiments 1 to 25.
  • neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru. [0327] 56. The method of embodiment 53, wherein the disease is cancer.
  • demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot- Marie-Tooth Disease, or Multiple Sclerosis.
  • demyelinating disease is Multiple Sclerosis.
  • 66 The method of embodiment 53, wherein the disease is a fibrotic disease.
  • 67 The method of any one of embodiments 53 and 66, wherein the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
  • IPF idiopathic pulmonary fibrosis
  • Tylenol acetominophen
  • R , R , R , R , R , R , R , R , R , and R are each independently C 2 - 6 alkyl, C 1-6 haloalkyl, -C 1-4 alkyl-R 12d , C2-6 alkenyl, C2-6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R l ld groups; each R l ld is independently Ci_6 alkyl, Ci_ 6 haloalkyl, -C(0)R d , -C(0)OR d , -C(0)NR d 2 , S(0) 2 NR d 2 , or -S(0) 2 R d ; and R 12d is - OR d , -SR d ,
  • R ld is -OR d
  • N(R d )C(0)NR d 2 phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C e alkyl, Ci_ 6 haloalkyl, -OR d , -SR d , -NR d 2 , -C(0)R d , C(0)OR d , -C(0)NR d 2 , -S(0) 2 R d , -OC(0)R d , -OC(0)OR d , OC(0)NR d 2 , N(R d )C(0) R d , -N(R d )C(0)OR d , or -N(R d )C(0)NR d 2 ; and R 2
  • each R od is independently hydrogen or Ci_6 alkyl,each R d is independently hydrogen, or Ci_6 alkyl.
  • composition comprising any of the formulas of embodiments 68 and 69 or a pharmaceutically acceptable salt thereof.
  • a pharmaceutical composition for inhibiting IRE la RNase activity comprising: Formula (A), Formula (B), any derivatives of Formula (A) and Formula (B) disclosed herein, GP17, GP21, GP29, DSA7, DSA8, GP1 17, GP 118, GP 146, GP146 (NMe), GP146(Am), compounds shown Figs. 7 and 8, any of the formulas from embodiments 68 and 69, and combinations thereof.
  • a pharmaceutical composition for activating IRE la RNase activity the composition comprising murine IRE la.
  • 73. A method for inhibiting IRE1 a RNase activity, the method comprising providing a subject in need of such inhibition an effective amount of either: a. a compound of embodiment 68, Formula (A), Formula (B), GP17, GP21, GP29, DSA7, DSA8, GP1 17, GP1 18, GP146, GP 146 (NMe), GP146(Am), a compound shown Figs. 7 or 8, any of the formulas of
  • compositions comprising a compound from 73(a) and a pharmaceutically acceptable excipient, carrier, or diluent.
  • a method for activating IRE la RNase activity comprising providing a subject in need of such inhibition an effective amount of either: a. murine IRE la; or b. a pharmaceutical compsotion comprising murine IRE la and a pharmaceutically acceptable excipient, carrier, or diluent.
  • the orthogonal ATP-competitive inhibitor 1NM-PP1 is able to rescue the RNase activity of IREla mutants that lack kinase activity (Han, D. et al. Biochemical and biophysical research communications 365, 777-783, (2008)).
  • Other ligands that interact with the ATP -binding site of wild-type IREla, including the endogenous co-factors ADP and ATP, are also able to activate RNase activity directly (Lee, K. P. et al. Cell 132, 89-100, (2008); Ali, M. M. et al. The EMBO journal 30, 894-905, (201 1)).
  • the ATP-competitive inhibitors APY29 and sunitinib directly activate the RNase of yeast and murine IREla (Han, D. et al. Cell 138, 562-575, (2009);
  • a crystal structure of APY29 bound to yeast IRE1 shows that the kinase catalytic domain is in an active conformation (Korennykh, A. V. et al. Nature 457, 687-693, (2009)), which is a conformation adopted by protein kinases capable of catalyzing phosphate transfer.
  • an active conformation of IRE la's ATP- binding site certain co-factors and ATP-competitive inhibitors act as ligands that allosterically activate its adjacent RNase domain.
  • Fig. 1A Two classes of ATP-competitive kinase inhibitors—called types I and II— have been identified (Fig. 1A), which stabilize alternate kinase active site conformations in numerous protein kinase targets 51 ' 52 .
  • the inactive ATP-binding site conformation stabilized by type II inhibitors is characterized by outward movement of the catalytically-important Asp-Phe-Gly (DFG) motif, and is therefore called the DFG-out conformation (Fig. 1A) 51 ' 52 .
  • DFG-out conformation Fig. 1A
  • IREla* Since IREla* is basally autophosphorylated, its RNase is active, and can be assayed using a FRET-quenched XBP1 RNA mini-substrate. While all the type II inhibitors tested with this assay contain the core binding elements predicted to stabilize the DFG-out conformation, only one ligand, demonstrated measurable inhibition of IRE la*' s RNase activity at a concentration of 60 ⁇ (Fig. 1C and ID). Because these type II kinase inhibitors also attenuate the RNase activity of IREla*, they were designated KIRAs— for kinase-inhibiting RNase attenuators.
  • KIRAl is a pyrazolopyrimidine-based inhibitor that has been shown to stabilize the DFG-out conformation of the non-receptor tyrosine kinases Src and Abl (Dar, A. C. et al. Chemistry & Biology 15, 1015-1022 (2008)). Based on the co-crystal structure of KIRAl bound to Src (PDB: 3EL8) and molecular modeling, proposed contacts with IREla are shown in Fig. 1A. [0352] Despite its modest potency, KIRAl served as a suitable starting point for developing higher affinity allosteric RNase inhibitors. A number of similar analogs were generated and tested for RNase inhibition.
  • KIRA3 inhibits XBPl RNA cleavage to a similar degree as STF-083010, an imine-based small molecule that directly inhibits the IRE la RNase through covalent modification.
  • KIRA3 and APY29 are both IRE la* kinase inhibitors, they demonstrate opposing effects on its RNase activity, with APY29 acting as an activator.
  • a version of IRE la* was generated with low basal RNase activity by using ⁇ -phosphatase to remove activating phosphates.
  • dP-IREla* dephosphorylated variant of IREla*
  • dP-IREla* has significantly lower basal RNase activity than IREla*; incubating dP -IREla* with increasing APY29 progressively restores its ability to cleave the XBPl mini-substrate, plateauing at -60% of the levels of IREla* (Fig. 2C).
  • KIRA3 suppresses residual RNase activity of dP- IRE la*.
  • Competition experiments were performed to further explore the opposing effects of APY29 and KIRA3. Increasing concentrations of APY29 progressively reverse IREla* RNase inhibition caused by a fixed concentration of KIRA3 (Fig. 2E).
  • the type I inhibitor sunitinib also opposes the RNase inhibitory effect of KIRA3.
  • increasing concentrations of KIRA3 restore RNase inhibition under a fixed concentration of APY29, with an expected increase in the IC5 0 .
  • APY29 cannot rescue direct inhibition caused by the covalent RNase modifier STF-083010.
  • the drug sunitinib is a promiscuous type I inhibitor that has been shown to inhibit the kinase activity of yeast and human IRElal6,19.
  • GP 146 KIRA3
  • sunitinib is a dose-dependent inhibitor of the autophosphorylation activity of IREla* (Fig. 18a).
  • sunitinib activates the RNase activity of dP-IREla*, which is consistent with its type I pharmacophore (Fig. 18b).
  • both APY29 and sunitinib stabilize an ATP-binding site conformation that activates the RNase domain of IRE la.
  • increasing amounts of sunitinib are able to rescue the RNase activity of IREla* in the presence of a fixed concentration of GP 146 (Fig. 18c).
  • GP 146 opposes the stereotypic RNase activation demonstrated by various type I ATP-competitive inhibitors of IREla.
  • KIRA3 prevents dimerization and oligomerization of IREla.
  • Self-association of kinase/RNase monomers has been reported to increase RNase activity as dimers and/or higher- order oligomers form in yeast and mammalian IRE1 proteins, furthermore, the degree of order may correlate directly with activity.
  • APY29 and KIRA3 were used to test the prediction that they would divergently affect the oligomerization state of human IREl as a basis for their opposing effects on its RNase activity. Specifically, RNase activators should drive monomers into higher-order species from baseline.
  • IREla* shows a concentration-dependent increase in the oligomer/monomer ratio.
  • APY29 further enhances— whereas KIRA3 decreases— this concentration-dependent increase in the IREla* oligomer/monomer ratio.
  • STF-083010, Sunitinib, nilotinib, and GP21 were obtained from commercial suppliers. All compounds were verified to be >95% pure by analytical HPLC. APY29 and GP118 was prepared according to a previously reported procedures.
  • N-(4-(8-amino-3 -isopropylimidazo[ 1 ,5-a]pyrazin- 1 -yl)naphthalen- 1 -yl)-3 - (trifluoromethyl)benzamide (GP146(Am)).
  • a mixture of compound 1 (9.5 mg, 0.031 mmol), compound 4 (16.6 mg, 0.038 mmol), Tetrakis(triphenylphosphine)palladium (1.1 mg, 0.94 ⁇ ) and sodium carbonate (7.3 mg, 0.069 mmol) was dissolved in a 3: 1 mixture of DME/water (120 ⁇ ). The mixture was heated overnight at 85 °C. The crude mixture was cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase
  • KIRA3 type II ATP-competitive inhibitor
  • IRE la on-targets
  • Src off-targets
  • KIRA analog synthesis The synthetic strategy for generating inhibitors of general structure Z is shown Fig. 25.
  • Acylation of commercially available amine Zl with carboxylic acids (R1-CO2H) that have been activated with 1 , l'-carbonyldiimidazole (CDI) (or activated with EDCI, DMAP), followed by cyclization with POCI 3 generates imidazopyrimidines (Z2) that are substituted at the 1-position (Ri) (Mulvihill, M. J. et al. Bioorg. Med. Chem. 16, 1359-1375 (2008); Mulvihill, M. J. et al. Bioorganic & Medicinal Chemistry Letters 17, 1091-1097 (2007)).
  • Urea substituents are introduced at the C-3 position by iodinating the scaffold with NIS, nucleophilic substitution with ammonia in isoproponal (in a sealed reaction vessel) and palladium-mediated Suzuki couplings to urea-containing boronic esters (prepared as shown in the box) (Jin, M. et al. Bioorganic & Medicinal Chemistry Letters 21, 1176-1180 (201 1); Wang, J.-X. et al. Org. Lett. 10, 2923-2926 (2008); Board, J. et al. Org. Lett. 11, 5118-5121 (2009)).
  • An alternate synthetic route that introduces substituents at the C-3 position (R2 substituents) without using a metal-mediated cross-coupling can also be used (Mulvihill, M. J. et al.
  • Cys715 is rapidly alkylated with haloacetamide-containing ICAT reagents, and the rate is increased under KIRA3 (Zhang, J. et al. Nature reviews. Cancer 9, 28-39, (2009)). Modeling suggests that Cys715 is in close proximity to the R3 substituent of the KIRA scaffold when the DFG motif is in the "out" conformation (the conformation the IREl ATP-binding site adopts when bound to KIRAs). Of the 518 kinases in the human kinome, 42 have a cysteine residue at an equivalent or adjacent position (Leproult, E. et al. J. Med. Chem. 54, 1347-1355 (2011)).
  • Cys645, which is located in the kinase hinge region, is highly shielded from alkylating agents in the presence of either inhibitor (Fig. 3b).
  • these inhibitors exert opposing effects on the accessibility of Cys715, with APY29 slowing the rate of alkylation and GP146 increasing it.
  • Cys715 is located in the activation loop of IREla (two residues C-terminal to the DFG-motif) and the divergent influence of APY29 and GP146 on this residue is concordant with these ligands stabilizing different conformations of the activation loop (Fig. 3b).
  • no detectable difference in the accessibility of Cys572, which is distal to the kinase active site of IREla is observed in the presence of either inhibitor.
  • the pyrazole ring of APY29 forms hydrogen bonds with the kinase hinge region and the pyrimidine moiety occupies the adenine pocket. Attempts to obtain a favorable pose of APY29 bound to the DFG-out conformation of IREla were unsuccessful, which is consistent with the ability of this ligand to exclusively stabilize the active conformation of the ATP-binding site.
  • GP146 bound to the DFG-out conformation of IREla is shown in Fig. 3c.
  • the pyrazolopyrimidine ring of this ligand forms two hydrogen bonds with the hinge region and occupies the adenine pocket.
  • the bulky naphthyl ring of GP 146 adopts an almost orthogonal conformation relative to the core scaffold and stacks against the He gatekeeper residue.
  • the trifluoromethylphenyl moiety of GP146 occupies the hydrophobic pocket created by movement of the Phe sidechain in the DFG-motif.
  • IREla* shows a concentration-dependent increase in the oligomer/monomer ratio.
  • APY29 further enhances— whereas GP 146 decreases— this concentration- dependent increase in the IREla* oligomer/monomer ratio.
  • the transgenic WT-IREla or IREla I642A spontaneously cluster in the ER, trans-autophosphorylate and splice XBP1 mRNA, without requiring upstream ER stress (Fig. 5a and Fig. 20).
  • GP146 inhibits autophosphorylation and XBP1 mRNA splicing in the WT cell lines (Fig. 20a and 20b). Consistent with these inhibitory effects occurring through a direct interaction with IREla, control compound GP146(NMe) does not affect either of these parameters, even at the highest concentration tested (Fig. 20c).
  • the data illustrates a model for IREla I642A , which can be activated merely through overexpression to basally splice -50% of cellular XBP1 mRNA, that 1NM-PP 1 further increases— while GP146 reduces— the activity of the RNase (Fig. 5d).
  • GP146 blocks both the autophosphorylation and RNase activities of endogenous IREla in vivo
  • IREla modulators affect the kinase and RNase activities of endogenous IREla under ER stress
  • INS-1 rat insulinoma cell lines which are derived from insulin-producing pancreatic ⁇ -cell tumors and contain large well-developed ERs. These cells were treated with the ER SERCA ATPase pump inhibitor, thapsigargin (Tg), to induce ER stress and IREla activation at levels causing -50% splicing of cellular XBP l mRNA (Fig. 6a).
  • GP 146 and APY29 demonstrate opposing dose-dependent effects on ER stress-induced activation of the RNase of endogenous IREla (Fig. 6a). Furthermore, GP 146 abrogates IREla autophosphorylation at a similar concentration as it blocks RNase activity (Figs. 6b and 6c). Control compound
  • GP 146(NMe) does not block the splicing of XBP l mRNA (Figs. 6d). Consistent with its in vitro activity, the type I inhibitor sunitinib is able to partially inhibit the kinase activity of IREla, but has no effect on the RNase activity of this enzyme (Figs. 6b and 6c) at the concentrations tested.
  • the RNase inhibitor STF-083010 was also tested in INS-1 cells that had been treated with Tg. As expected, this compound inhibits XBPl splicing in a dose-dependent manner, but does not prevent IREla auto-phosphorylation (Figs. 6b and 6c). Therefore, GP 146 is the only compound identified to date that has the ability to block both enzymatic activities of IREla, both in vitro and in vivo (Fig. 6e).
  • a construct containing the cytosolic kinase and RNase domains of human IREla was expressed in SF9 insect cells by using Bac-to-Bac baculovirus expression system (Invitrogen) with a 6-His-tag at the N-terminus, and purified with a Ni-NTA (Qiagen) column.
  • IREla* basal phosphorylation sites were removed by incubating IREla* with ⁇ -PPase (NEB) at a molar ratio of 5: 1 (IREa *: ⁇ -PPase) in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM MnC12, 2 mM DTT, 0.01% Brij 35 for 40 min at RT. Dephosphorylation was verified by immunoblotting with an anti-phosphoIREla antibody. 8. In vitro characterization of compounds (IRE la*)
  • KIRAs are tested for ability to inhibit IRElcc* kinase and RNase activities in vitro.
  • the XBP1 minisubstrate assay shown in Fig. IB-ID is amenable to 96- or 384-well format, and is used to determine RNase IC5 0 S.
  • kinase IC5 0 S for all KIRAs are determined in a 96- well dot blot assay with 32 ⁇ - ⁇ and STK peptide substrate 2 as substrates. Time-dependence of inhibition is determined for all electrophile-containing KIRAs.
  • RNase and kinase assays have been used to profile the KIRAs in Fig. 26, showing a strong correlation between kinase and RNase IC5 0 S. The most potent KIRAs are tested in an IRE la* autophosphorylation assay.
  • KIRA3 and KIRA6 have been tested against 12 kinases in this panel and the only off-target inhibition observed is for the tyrosine kinases Src and Abl.
  • the structure- based design strategy uses these two kinases as counter targets (described below).
  • CUGAGUCCGCAGCACUCAG-3 'BHQ was purchased from Dharmacon.
  • 0.2 ⁇ IRE la* or dP-IREla* were incubated with inhibitors or DMSO for 20 min in cleavage buffer, followed by incubation with 3 ⁇ RNA substrate for 5 min.
  • the reaction was quenched by adding urea to a final concentration of 4 M, and the fluorescence was detected on a SpectraMax M5 microplate reader (Molecular Devices) with excitation and emission wavelengths of 494 nm and 525 nm, respectively.
  • the fluorescence intensities were normalized by setting the signal for the reaction with IREla* and DMSO to 1 and the reaction without IREla* to 0.
  • the cleavage products were also resolved by urea PAGE after phenol/chloroform extraction and ethanol precipitation.
  • mouse XBP 1 RNA was also used as a substrate, as described (Han, D. et al. Cell 138, 562-575, (2009)).
  • the DFG-in structure of IREla was generated from a co-crystal structure of human IREla bound to ADP (PDB code 3P23, chain A) (Ali, M. M. et al. EMBO J. 30, 894-905 (201 1)).
  • the structure was prepared using the protein preparation workflow in Maestro
  • the IFD protocol includes a constraint receptor minimization step followed by initial flexible Glide docking of the ligand using a softened potential to generate an ensemble of poses. For each pose, the nearby receptor structure was then refined using Prime. Each ligand was then re-docked (using Glide) into its corresponding optimized low-energy receptor structure and ranked by Glide score. The best pose with highest IFD score obtained for each ligand was again subjected to MD simulation (8-10 ns production runs) for further optimization of the protein ligand complex.
  • the MD protocol includes a multi- step procedure for minimizations and short MD runs followed by the production MD simulation. Ligand poses were observed to be stable during the production MD runs.
  • KIRA6 like KIRA3, stabilizes the monomeric state of IREl .
  • AUC Analytical ultra-centrifugation
  • Crystal structures of the most promising KIRAs bound to IREla and the off-target kinase Src are being obtained. These structures are used to refine the docking protocols for IREla, which aid computational design of inhibitors with increased potency. Structures of KIRA-Src complexes are used to identify interactions that are unique to IREla and inform the design of KIRAs that possess increased selectivity.
  • On-target/off-target structural strategy has been used to develop highly potent and selective inhibitors of Toxoplasma gondii and Cryptosporidium parvum CDPK1 (Murphy, R. C. et al. ACS Med. Chem. Lett. 1, 331-335 (2010); Larson, E. T. et al. J. Med. Chem. 55, 2803-2810 (2012); Johnson, S. M. et al. J. Med. Chem. 55, 2416-2426 (2012); Ojo, K. K. et al. J. Clin. Invest. 122, 2301-2305 (2012)). Diffraction-quality crystals of Src bound to KIRA3 have been obatined.
  • IREla-KIRA3 and IREla- KIRA6 complexes A structure of human IRE la bound to ADP has been reported 48 .
  • This protein is currently being used by to screen for diffraction quality crystals of IREla-KIRA3 and IREla- KIRA6 complexes, and initial screening results are very promising.
  • Increasing concentrations of IREla* (0.49-30 ⁇ ) were incubated with DMSO, GP146 (200 ⁇ ), or APY29 (200 ⁇ ) for 20 min, then cross-linked by adding 250 ⁇ disuccinimidyl suberate (DSS) (Pierce) for 1 hr at RT in cleavage buffer.
  • DSS disuccinimidyl suberate
  • the reaction was quenched by addition of 50 mM Tris-HCl (pH 7.5).
  • the samples were then boiled, resolved on SDS-PAGE, and immunoblotted for IREla with an anti-IREla antibody, (visualization and quantification with a LI-COR Odyssey scanner).
  • TNS-1 cells were grown in RPMI, 10% fetal calf serum, 1 mM sodium pyruvate, 10 mM HEPES, Pen/strep, 2 mM glutamine and 50 mM ⁇ - mercaptoethanol.
  • T-REx 293 IREla or IREla I642A were grown in DME H-21 with 10% fetal calf serum and Pen/strep. After 1 hr incubation with compounds, I S-l cells were treated with 6 nM thapsigargin for 4 hrs, and T-Rex 293 IRE la-expressing cells were treated with 1 ⁇ Dox for 8 hrs.
  • XBP1 splicing was performed as previously described 7 .
  • AAACAGAGTAGCAGCACAGACTGC-3" (SEQ ID NO:7) and antisense primer rXBP 1.2AS (5'- GGATCTCTAAGACTAGAGGCTTGGTG-3 ') (SEQ ID NO:8) for INS-1 cell line, while sense primer mXBP1.3S (5'-AAACAGAGTAGCAGCGCAGACTGC-3 ') (SEQ ID NO:9) and antisense primer mXBP 1.2AS (5 ' -GGATCTCTAAAACTAGAGGCTTGGTG-3 ' ) (SEQ ID NO: 10) for T-Rex 293 cell line.
  • PCR products were resolved on 2.5% agarose gels, stained with EtBr, and quantified by ImageJ.
  • INS-1 cells were incubated with compounds or DMSO for 1 hr, followed by 1 ⁇ Tg for 2 hrs.
  • T-Rex 293 IREla -expressing cells were incubated with compounds or DMSO for 1 hr and then treated with 1 ⁇ Dox for 8 hrs.
  • Cells were lysed in RIPA buffer (20 mM Tris-HCl, pH 7.5, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate, 150 mM NaCl, 1 mM EDTA, 1% NP-40, complete EDTA-free protease inhibitor (Roche) and phosphatase inhibitor cocktail (Sigma)), and cleared lysates were subjected to SDS-PAGE and transferred to nitrocellulose. Blocking, antibody incubation, and washing were done in PBS or TBS with 0.05% Tween-20 (v/v) and 5% (w/v) non-fat dry milk or BSA, or blocking buffer (Odyssey).
  • RIPA buffer 20 mM Tris-HCl, pH 7.5, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate, 150 mM NaCl, 1 mM EDTA, 1% NP-40, complete EDTA-free protease
  • IREla means a recombinant human (rh) IREla.
  • rh IREla has the human IREla (469-977) sequence: SEQ ID NO: 1 (w/ his tag); and SEQ ID NO:2 (w/o his tag).
  • IREla's RNase activity using KIRAs shuts down endonucleolytic decay of mRNAs localizing to the ER membrane.
  • ER-localized mRNA decay has been directly linked to the terminal UPR.
  • IREl RNase targets select microRNA (miR) precursors to terminate their biogenesis.
  • Increasing ER stress causes progressive increases in endogenous IRE la phosphorylation, increases in XBP 1 mRNA splicing (Fig. 28, E), depletion through endonucleolytic decay of the ER-localized mRNA, Ins l, which encodes proinsulin (Fig. 28, F), and induction of the pro-apoptotic transcription factor, CHOP (Fig. 28, G).
  • Fig. 28, E XBP 1 mRNA splicing
  • Ins l which encodes proinsulin
  • CHOP pro-apoptotic transcription factor
  • the transgenic IREla proteins Induced with doxycycline (dox) the transgenic IREla proteins oligomerize, spontaneously trans- autophosphorylate and trigger XBP1 mRNA splicing (Fig. 29, A and B).
  • the transgenic systems are finely tuneable, with increasing [Dox] causing progressively greater IREla induction (the transgenic IREla protein is Myc-tagged).
  • Phospho/Myc IREla ratios are finely controllable (and measureable) with increasing [Dox], as is XBP1 mRNA splicing.
  • UPR (Fig. 29, C). These include reduction of miR-17 (Fig. 29, D) and Insl mRNA, induction of CHOP mRNA (Fig. 29, E), induction and proteolytic cleavage of caspases 1,2, and 3 (Fig. 29, F), and apoptosis as measured by Annexin-V staining (Fig. 29, G).
  • KIRAs break high-order oligomerization of IRE1 a kinase domains, attenuate RNAse activity, and reduce entry of cells into the Terminal UPR.
  • all these terminal UPR endpoints are curtailed by pre-treating cells with KIRA6, before exposing them to ER stress inducers, in vitro, KIRA6 inhibits IRE la* RNase and kinase activities with similar IC5 0 S (Fig. 30, B and C). in vivo, KIRA6 inhibits endogenous IRE la auto-phosphorylation in a dose-dependent manner (Fig.
  • KIRA6 reduces concentration- dependent oligomerization of IREla* (Fig. 30, E).
  • KIRA6 inhibits endogenous IREla - mediated XBP 1 mRNA splicing provoked by Tm (Fig. 30, F).
  • KIRA6 inhibits ER-localized endonucleolytic decay of Ins 1 mRNA at lower doses of the drug than needed to inhibit XBP1 mRNA splicing (Fig.
  • KIRA6 cytoprotective effects are dependent on IREla because they are absent in Irela ⁇ ' ⁇ mouse embryonic fibroblasts (MEFs), but still demonstrable in WT and Xbpl ⁇ ' ⁇ MEFs (Fig. 30, J).
  • a model of KIRA6- mediated cytoprotection is shown (Fig. 30, J); it posits that the type II kinase inhibitor, KIRA6, reduces kinase/RNAse homo-oligomerization on the cytosolic face of IREla, which
  • ⁇ -cells from mouse and human islets exposed to irremediably high ER stress will show activation of many of the terminal UPR endpoints described herein.
  • ER-localized mRNAs and select micro RNAs so far identified as IREla substrates
  • other miRs and small non- coding RNAs remain to be discovered and related changes will constitute a Terminal UPR signature that can be followed as therapeutic endpoints for amelioration by KIRAs.
  • Described herein is the characterization of four select miRs that decay in vivo upon IREla hyperactivation. These are miR-17, miR-34a, miR-96, and miR-125b.
  • WT-IREla* directly cleaved pre-miR-17 in vitro at sites distinct from those cleaved by DICER, as mapped by primer extension.
  • the scission sites of pre-miR-17 are identical to those of XBP 1 mRNA— (G/C)— and diverge at the flanking regions.
  • IREla antagonizes DICER action to reduce cellular levels of the corresponding mature miRs.
  • IRE la* (I642G), which can be activated by 1NM-PP1 to cleave XBP1 mRNA in vitro, can also cleave pre-miR-17 under INM-PPl .
  • An RNAse mutant, IRE la* (N906A) is compromised for cleavage of pre-miR-17 (Fig. 31, A-C). This provokes the hypothesis that
  • IRE la is capable of exhibiting extra-XBPl mRNA endonucleolytic activity in a graded fashion. As IRE la homo-oligomerizes in the ER membrane in proportion to the concentration of unfolded proteins in the ER lumen, it progressively iraws-autophosphorylates. Furthermore, salt bridges between phospho-amino acid groups and other residues reinforce higher-order homo- oligomerization of kinase/RNAse domains, as was shown using yeast IREl . Thus, as IRE la protein clusters into higher-order oligomers, it acquires increasing activity towards its RNA substrates. The most efficient substrate is XBP1 mRNA, followed by select pre-miRs (e.g. 17, 34a, 96, and 125b), then followed by the ER-localized mRNA substrate, Insl .
  • pre-miRs e.g. 17, 34a, 96, and 125b
  • IREla KIRAs should reduce oligomerization by reinforcing the DFG-out, inactive ATP -binding site conformation, and consequently reduce RNase activity to decrease ER stress-induced cell death.
  • type I kinase inhibitors such as INM-PPl
  • INM-PPl should increase oligomerization by reinforcing the DFG-in, active ATP-binding site conformation, and consequently increase RNase activity to increase ER stress-induced cell death.
  • Type I kinase inhibitors antagonize the effects of type II kinase inhibitors (KIRAs) to promote cell death under ER stress.
  • Fig. 32 shows data consistent with this notion.
  • KIRAs should ameliorate terminal UPR endpoints promoted by INM-PPl in the context of the IREla (1642 G) cellular chemical genetic systems under ER stress: Ins l and 2 mRNA decay, miR-17, 34a, 96, and 125b decay, Caspase 1, 2, and 3 cleavage, TXNIP mRNA stabilization and translation, and consequent IL- 1 ⁇ maturation and secretion.
  • Cytotoxicity testing Any KIRAs that show sub-micromolar potency in the cellular models described above are subjected to cytotoxicity assays against seven mammalian cell lines. These assays are helpful in predicting any general or tissue specific toxicity that may occur when KIRAs are administered to animals. KIRAs are tested against the following seven cell lines: L1210 (mouse lymphoblasts), W1-L2 (human lymphoblasts), HT-1080 (human fibrosarcoma), SF-539 (human glioblastoma), NCI-H460 (human large cell lung carcinoma), HCC-2998 (human colon carcinoma), and HL-60 (human promyelocytes).
  • L1210 mouse lymphoblasts
  • W1-L2 human lymphoblasts
  • HT-1080 human fibrosarcoma
  • SF-539 human glioblastoma
  • NCI-H460 human large cell lung carcinoma
  • HCC-2998 human colon carcinoma
  • HL-60 human promyelocytes
  • This panel provides sufficient diversity to predict cellular toxicity in a wide variety of tissues.
  • the fold difference between efficacy in models and mammalian cell cytotoxicity provides a rough therapeutic index (TI).
  • TI rough therapeutic index
  • mice [0398] In vivo PK/ADMET studies: KIRAs that are sufficiently potent in the cellular assays are subjected to pharmacokinetic and toxicity studies in mice. First, compounds are tested in a dose escalation study for any observed toxicity. Mice are sequentially injected with single IV doses of 1 mg kg, 10 mg/kg, and 100 mg/kg of compound. During these single dose studies, the mice are observed for signs of acute toxicity, such as respiratory or neurological abnormalities.
  • PK/ADME testing Compounds that are not toxic at 10 mg/kg are subjected to PK/ADME testing. This involves administration of a single dose (10 mg/kg by IV) followed by blood sampling at intervals of 30, 60, 120, 180, 240, and 300 minutes. These experiments are performed with groups of 3 mice per KIRA. Plasma is separated and extracted with acetonitrile for compound concentration measurements by combined liquid chromatography/electrospray-ionization mass spectrometry (LCMS). The results provide the maximum concentration (C max ), time of maximum
  • T max concentration
  • AUC area under the curve
  • T1/2 estimation of half-life
  • KIRAs inhibit IRE la in cultured cells at concentrations of less than ⁇ and strikingly protect cell viability and function under conditions of ER stress. Moreover, the leading compound in this class has shown efficacy in a rodent model of RP caused by mutation in rhodopsin. Described herein is the optimization of potency and efficacy in the KIRA class of compounds against retinal degeneration to develop a clinical candidate for treatment of RP.
  • KIRA6 a more potent version of earlier KIRAs, whose structure is shown in Fig. 30A has been developed. This compound dose-dependently reduces kinase autophosphorylation and XBP1 splicing activity of IREla* (WT) (Fig. 30B-C). In addition, KIRA6 dose-dependently inhibits IREla* (WT) cleavage of pre-miR-17 (Fig. 3 ID).
  • Tm (20 ⁇ g/ ⁇ L final concentration) plus/minus KIRA6 (10 ⁇ final concentration) was injected into SD rats at P21 with an equivalent amount of DMSO as a vehicle control.
  • Retinas were collected at 48 and 72 hrs after injections in Trizol (Invitrogen) for qPCR analysis. Eyes were examined by optical coherence tomography (OCT) 7 days post injection and subsequently collected for morphological analysis.
  • OCT optical coherence tomography
  • OCT Image guided optical coherence tomography
  • mice were anaesthetized with 1.5-3% isoflurane, eyes were dilated with 2.5% phenylephrine hydrochloride and 1% tropicamide, and corneas were kept moist with regular application of 2.5% methylcellulose. Eyes were examined using a Micron III retinal imaging system (Phoenix Research Labs). Spectral domain OCT images were acquired with a Micron Image Guided OCT System (Phoenix Research Labs) by averaging 10 to 50 scans.

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Abstract

Described herein, inter alia, are compositions and methods of using the same for modulating the activity of Ire1.

Description

MODULATION OF IRE1
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Patent Application Nos.
61/706,037, filed September 26, 2012; 61/783,965, filed March 14, 2013; and 61/831,088, filed June 04, 2013, which are all incorporated herein by reference in their entirety and for all purposes.
STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT
[0002] This invention was made with government support under grant nos. OD001925, DK080955, GM086858, OD001926, awarded by the National Institutes of Health. The government has certain rights in the invention.
REFERENCE TO A "SEQUENCE LISTING," A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII FILE
[0003] The Sequence Listing written in file 84850_884770_ST25.TXT, created on September 24, 2013, 24,576 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference.
BACKGROUND
[0004] Cells often experience conditions during which the workload on the endoplasmic reticulum ("ER") protein folding machinery exceeds its capability. Such cells are said to be experiencing "ER stress." ER stress can result from secretory work overload, expression of folding-defective secretory proteins, deprivation of nutrients or oxygen, changes in luminal calcium concentration, and deviation from resting redox state. Sophisticated cellular surveillance and quality control systems work to maintain ER homeostasis under such perturbations. Under ER stress, secretory proteins accumulate in unfolded forms within the organelle to trigger a set of intracellular signaling pathways called the unfolded protein response (UPR). UPR signaling increases transcription of genes encoding chaperones, oxidoreductases, lipid-biosynthetic enzymes, and ER-associated degradation (ERAD) components (Travers, K. J. et al. Cell 101, 249-258 (2000)). [0005] In some instances, the ER stressed state remains too great, and cannot be remedied through the UPR's homeostatic outputs. In these situations, the UPR switches strategies and actively triggers apoptosis (Zhang, K. & Kaufman, R. J. Neurology 66, S102-109 (2006)); we have named this destructive signaling state the Terminal UPR (signature events of the Terminal UPR are described herein). Apoptosis of irremediably stressed cells is an extreme, yet definitive, quality control strategy that protects multicellular organisms from exposure to immature and damaged secretory proteins. So at the cost of losing some cells, multicellular organisms may benefit temporarily from Terminal UPR-induced apoptosis. However, many deadly human diseases occur if too many cells die through this process. Conversely, many human diseases such as diabetes mellitus and retinopathies proceed from unchecked cell degeneration under ER stress (Merksamer, P.I., and Papa, F.R., J Cell Sci 123, 1003-1006 (2010); Papa, F.R. Cold Spring Harbor perspectives in medicine 2, a007666 (2012); Shore, G.C., Papa, F.R., and Oakes, S.A., Curr Opin Cell Biol 23, 143-149 (201 1)). Type 2 diabetes may be a prototype of cell degenerative diseases caused by UPR-mediated apoptosis under irremediable ER stress. These same principles appear to be at play in type 1 diabetes, wherein immune attack on islet β-cells elevates ER workload and causes ER stress in remaining cells. A deeper fundamental and mechanistic understanding of the etiology and pathogenesis of diabetes mellitus may lead to increasing opportunities for the development of novel and effective therapies. Terminal UPR signaling is central to these conditions as shown through experimental data and uses of proprietary compounds that defeat the consequences of terminal UPR signaling in ER stress- challenged β-cells to afford significant cytoprotection.
[0006] IRE la and IRE1 β are ER-transmembrane proteins that become activated when unfolded proteins accumulate within the organelle. IRE la is the more widely expressed and well-studied family member. The bifunctional kinase/endoribonuclease IRE la controls entry into the terminal UPR. IRE la senses unfolded proteins through an ER lumenal domain that becomes oligomerized during stress (Zhou, J. et al. Proceedings of the National Academy of Sciences of the United States of America 103, 14343-14348 (2006); Credle, J. J. et al. Proc Natl Acad Sci USA 102, 18773-18784 (2005); Aragon, T. et al. Nature (2008); Aragon, T. et al. Nature 457, 736-740 (2009)). On its cytosolic face, IRE1 a possesses bifunctional kinase/RNase activities. Oligomerization juxtaposes IREla's kinase domains, which consequently trans- autophosphorylate. Kinase autophosphorylation activates the RNase activity, which cleaves XBP1 mRNA at specific sites to excise an intron. Religation of IRE la-cleaved XBP 1 mRNA shifts the open reading frame; translation of spliced XBPl mRNA produces a transcription factor called XBPls (s=spliced) (Calfon, M. et al. Nature 415, 92-96, (2002); Yoshida, H. Cell 107, 881-891 (2001)). XBPls's target genes encode products that enhance ER protein folding and quality control (Lee, A. H. et al, Molecular and cellular biology 23, 7448-7459 (2003)). Thus, IRE 1 a promotes adaptation via XBP 1 s .
[0007] Under irremediable ER stress, positive feedback signals emanate from the UPR and become integrated and amplified at key nodes to trigger apoptosis. IRElcc is a key initiator of these pro-apoptotic signals. IRElcc employs auto-phosphorylation as a "timer." Remediable ER stress causes low-level, transient auto-phosphorylation that confines RNase activity to XBPl mRNA splicing. However, sustained kinase autophosphorylation causes IREl 's RNase to acquire relaxed specificity, causing it to endonucleolytically degrade thousands of ER-localized mRNAs in close proximity to IRElcc (Han, D. et al. Cell 138, 562-575, (2009); Hollien, J. et al. Journal of Cell Biology. These mRNAs encode secretory proteins being co-translationally translocated (e.g., insulin in β cells). As mRNA degradation continues, transcripts encoding ER- resident enzymes also become depleted, thus destabilizing the entire ER protein-folding machinery. Once IREl 's RNase becomes hyperactive, adaptive signaling through XBP l splicing becomes eclipsed by ER mRNA destruction, which pushes cells into apoptosis.
[0008] A terminal UPR signature tightly controlled by IREla's hyperactive RNase activity causes (1) widespread mRNA degradation at the ER membrane that leads to mitochondrial apoptosis (Han, D. et al. Cell 138, 562-575, (2009)), (2) induction of the pro-oxidant thioredoxin-interacting protein (TXNIP), which activates the NLRP3 inflammasome to produce maturation and secretion of interleukin-ΐ β, and consequent sterile inflammation in pancreatic islets leading to diabetes (Lerner, A. G. et al. Cell metabolism 16, 250-264, (2012)), and (3) degradation of pre-miRNA 17, leading to translational upregulation and cleavage of pre- mitochondrial caspase 2 (Upton, J. P. et al. Science 338, 818-822, (2012)) and stabilization of the mRNA encoding TXNIP (Lerner, A. G. et al. Cell metabolism 16, 250-264, (2012)).
[0009] Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of inherited retinal disorders characterized by diffuse progressive dysfunction and loss of rod and cone photoreceptors, and retinal pigment epithelium. There are no approved therapies to offer the over 100,000 Americans who currently suffer from RP. As RP is a leading cause of irreversible vision loss, new therapeutic approaches for this condition would be expected to have significant cost-saving benefits for health care systems. [0010] A great deal of evidence suggests that the accumulation of misfolded proteins within the ER is a central causative mechanism in many forms of RP. When the protein- folding capacity of the ER is overwhelmed, cells experience "ER stress" and actively commit programmed cell death. For example, mutations in rhodopsin are the most common cause of RP in the US and lead to a defective rhodopsin protein that misfolds and accumulates in the ER to cause high levels ER stress.
[0011] Disclosed herein, inter alia, are solutions to these and other problems in the art.
BRIEF SUMMARY
[0012] Provided herein, inter alia, are novel ATP-competitive small molecule kinase inhibitors of IRE la that prevent oligomerization and/or allosterically inhibit its RNase activity.
[0013] In an aspect is provided a compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000006_0001
(I) wherein, ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; L1 is a bond or unsubstituted C1-C5 alkylene; L2 is a bond, -NR6a-, -0-, -S-, -C(O)-
, -S(O)-, -S(0)2-, -NR6aC(0)-, -C(0)(CH2)z2-, -C(0)NR6b-, -NR6aC(0)0-,
-NR6aC(0)NR6b-, substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R1 is hydrogen, oxo, halogen, -CX3, -CN, -S02C1, -SOnR10, -SOvNR7R8,
-NHNH2, -ONR7R8, -NHC=(0)NHNH2,
-NHC=(0)NR7R8, -N(0)m, -NR7R8, -C(0)R9, -C(0)-OR9,
-C(0)NR7R8, -OR10, -NR7SO„R10, -NR7C=(0)R9, -NR7C(0)OR9, -NR7OR9,
-OCX3, -OCHX2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R2 is hydrogen, oxo, halogen, -CXa 3, -CN, -S02C1, -SO„iR10a, -SOviNR7aR8a, -NHNH2, -ONR7aR8a, -NHC=(0)NHNH2,
-NHC=(0)NR7aR8a, -N(0)ml, -NR7aR8a, -C(0)R9a, -C(0)OR9a, -C(0)NR7aR8a, -OR10a, - NR7aSO„iR10a, -NR7aC=(0)R9a, -NR7aC(0)OR9a, -NR7aOR9a, -OCXa 3, -OCHXa 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R3 is independently hydrogen, oxo,
halogen, -CXb 3, -CN, -S02C1, -SO„2R10b, -SOv2NR7bR8b, -NHNH2, -ONR7bR8b,
-NHC=(0)NHNH2,
-NHC=(0)NR7bR8b, -N(0)m2, -NR7bR8b, -C(0)R9b, -C(0)-OR9b, -C(0)NR7bR8b, -OR10b, -
NR7bSO„2R10b, -NR7bC=(0)R9b, -NR7bC(0)OR9b, -NR7bOR9b, -OCXb 3, -OCHXb 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 and R5 are independently hydrogen or unsubstituted Ci-Ce alkyl; R7, R8, R9, R10, R6a, R7a, R8a, R9a, R10a, R6b, R7b, R8b, R9b and R10b are independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - S04H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0)NH2, -NHS02H, - NHC=(0)H, -NHC(0)OH, -NHOH, -OCF3, -OCHF2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R7 and R8 substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7a and R8a substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7b and R8b substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4; each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2; the symbol z is an integer from 0 to 2; the symbol z2 is an integer from 1 to 4; and each occurrence of the symbols X, Xa, and Xb is independently a halogen.
[0014] In another aspect is provided a pharmaceutical composition including a
pharmaceutically acceptable excipient and a compound, or pharmaceutically acceptable salt thereof, as described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim).
[0015] In an aspect is provided a method of treating a disease in a patient in need of such treatment, the method including administering a therapeutically effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof, to the patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
[0016] In an aspect is provided a method of modulating the activity of an Irel protein, the method including contacting the Irel protein with an effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof.
[0017] In another aspect, the present disclosure provides compounds having the formula (A):
d
Figure imgf000008_0001
(also illustrated in Fig. 7) and pharmaceutically acceptable salts thereof, wherein R , R , R , R4d, R5d, R6d, R7d, R8d, R9d, and R10d, are each independently C2_6 alkyl, Ci_6 haloalkyl, -C1-4 alkyl-R12d, C2_6 alkenyl, C2_6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two Rl ld groups; each Rl ld is independently Ci-6 alkyl, Ci_6 haloalkyl, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, S(0)2NRd 2, or -S(0)2Rd; and R12d is - ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, OC(0)ORd, OC(0)NRd 2, -N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl,
C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; and each Rd is independently hydrogen, Ci_6 alkyl, C2-6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl,each Rd is independently hydrogen, or Ci_6 alkyl. [0018] In another aspect, R2d and R3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(O) Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0) Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; wherein each Rd is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, -
N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl,each Rd is independently hydrogen, or Ci_6 alkyl.
[0019] In yet another aspect, Rld is -ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, - N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(0)Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2.
[0020] In one aspect, the present disclosure is directed to compositions and methods for activating IRE la RNase activity using human and murine IRE la. [0021] In another aspect, the present disclosure is directed to compositions and methods for inhibiting human and murine IRE la RNase activity using compounds: GPl 17 (KIRA2), GPl 18 (KIRA1), GP 146 (KIRA3), GP146 (NMe), GP 146(Am), Formula B, Formula (A), compounds shown Figs. 7 and 8, and other derivative compounds disclosed herein [0022] The present disclosure may also be directed to pharmaceutical compositions comprising any of the compounds disclosed herein.
[0023] In an additional aspect, the present disclosure provides a compound having Formula
(B),
Figure imgf000010_0001
Formula (B) and pharmaceutically acceptable salts thereof.
[0024] In still another aspect, the present disclosure provides those compounds illustrated in Fig. 8, and pharmaceutically acceptable salts thereof.
[0025] In another aspect, the present disclosure provides methods for treating disorders associated with deregulated UPR signaling comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) any of the compounds disclosed herein, or (ii) a pharmaceutical composition comprising any of the compounds disclosed herein and a pharmaceutically acceptable excipient, carrier, or diluent.
[0026] In another aspect, the present disclosure provides methods for treating disorders associated with deregulated UPR signaling comprising providing to a patient in need of such treatment a therapeutically effective amount of either a compound of formula (B), the compound illustrated in Fig. 7 and any described derivatives, and those compounds illustrated in Fig. 8 or any of the described or illustrated derivatives thereof, or (ii) a pharmaceutical composition comprising a compound of formula (B) or any of the derivatives thereof described herein and a pharmaceutically acceptable excipient, carrier, or diluent, wherein the compound of formula (B) is
Figure imgf000011_0001
Formula (B)
BRIEF DESCRIPTION OF THE DRAWINGS
[0027] Fig. 1. Interaction of ATP-competitive inhibitors with the bifunctional kinase/RNase, IRE la. (a) Proposed binding modes of type I and type II kinase inhibitors with the ATP-binding pocket of IRE 1 a. Left panel shows the contacts a type I inhibitor, APY29, forms with yeast IRE la (PDB code 3SDJ)18 (SEQ ID NO:3). The right panel shows the proposed contacts a type II inhibitor, GP l 18, forms with IRE la based on the co-crystal structure of the same inhibitor bound to Src (PDB code 3EL8) (SEQ ID NO:4) (also see Fig. 15). (b) XBPl RNA minisubstrate assay used for screening IREla modulators; the recombinant human IREla— IREla*— used in the assay spans residues 469-977, which includes the cytosolic kinase and RNase domains; cleavage of the 5 ' FAM-3 ' BHQ-labeled XBPl minisubstrate by IREla* results in FRET- dequenching. (c) Endpoint fluorescence of IREla* catalyzed cleavage reaction of XBPl minisubstrate in the presence of varying concentrations of inhibitors, or DMSO; STF-083010 is an imine-based compound that covalently inhibits the RNase domain; relative fluorescence intensity is scaled to the signal observed with IREla* (1.0), or without IREla* (0). (mean ± SD, n = 3). (d) Structures of type II kinase inhibitors that inhibit the RNase activity of IREla* (GPl 18/KIRAl, GPl 17/KIRA2, GP146/KIRA3). Numbering of amino acid residues from Irela in figures uses amino acid numbering of human Irela (e.g. including numbering used for human IREla (469-977) sequence in SEQ ID NO:2 as numbered in the Examples section herein).
[0028] Fig. 2. APY29 and GP146 (KIRA3) divergently modulate the RNase activity and oligomerization state of IREla*. (a) Inhibition of IREla* autophosphorylation in vitro by APY29 and GPl 46; top panels show autoradiograms of autophosphorylation levels under serial two-fold dilutions of the respective inhibitors (from 80 μΜ to 0.0098 μΜ); the lower panel shows normalized autophosphorylation levels and IC50 values for both compounds, (b) λ-PPase treatment of IREla* produces dephosphorylated IREla* (dP-IREla*); immunoblots using anti- IREla and anti-phospho IREla antibodies are shown, (c) RNase activities of IREla* and dP- IREla* under varying [APY29] or [GP 146] (KIRA3) per the assay of Fig. lb; EC50 values were determined by fitting normalized fluorescence intensities (mean ± SD, n = 3). (d) Urea PAGE of XBP1 mini-substrate cleavage by IREla* and dP-IREla* with and without GP146 (KIRA3) or APY29. (e) RNase competition assays between APY29 and GP146 (KIRA3); the line marked with circles shows IREla* RNAse activity under fixed GP146 (KIRA3) and varying [APY29]; the line marked with squares shows IREla* RNAse activity under fixed APY29 and varying [GP146] (KIRA3); the line marked with triangles shows IREla* RNAse activity under fixed STF -083010 and varying [APY29] (mean ± SD, n = 3).
[0029] Fig. 3. Characterization of GP146's interaction with the ATP-binding site of IREla. (a) A crystal structure of the kinase domain of human IREla bound to ADP; the native cysteine residues that were monitored using the ICAT footprinting method are labeled and shown as thick rods and the DFG-motif is shown as thin bars; cys715 is part of the hinge region of IREla and its side chain partially occupies the ATP-binding site; cys645 is in the activation loop, two residues away from the DFG-motif; cys572 is located on the top of the N-terminal lobe of the catalytic domain and is distant from the ATP-binding site, (b) Results of the ICAT footprinting experiments with IREla*; alkylation rates were measured in the presence of DMSO (circle), APY29 (square) (20 μΜ), or GP 146 (triangle) (20 μΜ) (mean ± SD, n = 3). (c) A molecular model of GP146's interaction with the ATP-binding site of IREla; IREla is in the DFG-out inactive conformation; the imidazopyrazine ring of GP 146 occupies the adenine pocket and the 3-trifluoromethylurea occupies the DFG-out pocket; no favorable poses for GP146 bound to the DFG-in conformation of IREla could be determined, (d) Control compounds that were generated to test the docked structure of GP146 bound to the DFG-out conformation of IREla; GP 146(NMe) contains a methyl group that is predicted to disrupt a critical hydrogen bond to the hinge region of IREla GP146(Am) contains an amide rather than a urea group linker between the naphthyl ring and the trifluormethylpheny group; the amide linker is predicted to lead to a less favorable interaction with the DFG-out pocket; the IC50S for each compound against IREla* is listed below their structure.
[0030] Fig. 4. APY29 and GP146 differentially affect oligomerization state of IREla*. (a) Left panels shows immunoblots of IREla* after treatment with the crosslinker DSS (250 μΜ);
increasing concentrations of IREla* were incubated with DMSO, APY29 (200 μΜ), or GP 146 (200 μΜ); the right panel shows quantitation of the ratios of oligomeric to monomeric IRE la * (b) Model of how type I and type II kinase inhibitors affect the RNase activities and oligomeric states of IRE la * and dP- IRE la *.
[0031] Fig. 5. Chemical-genetic modulation of IREla kinase and RNase activity in vivo, (a) Anti-total and anti-phospho IREla immunoblots of T-Rex 293 cells expressing "holed" IREla 1642 A under Doxy eye line (Dox) control; cells were pre-treated for 1 hr with GP146 at indicated concentrations, then induced with Dox (1 μΜ) for 8 hrs; plots show normalized phosphorylation levels and ratios of spliced XBP l mRNA under varying [GP146] (mean ± SD, n >= 3). (b) EtBr- stained agarose gel of XBP l cDNA amplicons from the cells described in (a), (c) Competition between the "bumped" kinase inhibitor 1NM-PP1 and GP146 against IREla I642A; T-Rex 293 cells expressing IREla I642A were pre-treated for 1 hr with GP146 (1 μΜ) ± varying [1NM- PP 1] before Dox induction (ΙμΜ) for 8 hrs; histograms show ratios of spliced XBPl mRNA as a function of [GP146] and [1NM-PP 1]. (d) Model of divergent allosteric modulation of IREla RNase by type I and II kinase inhibitors; when overproduced, IREla I642A oligomerizes and trans-autophosphorylates, activating XBPl mRNA splicing by the RNase; type I inhibitor 1NM- PP 1 increases— whereas type II inhibitor GP146 decreases— RNase activity; cartoons are not meant to differentiate between the relative orientations of monomer subunits in IREla.
[0032] Fig. 6. Divergent modulation of endogenous IREla RNase activity under ER stress with types I and II kinase inhibitors, (a) EtBr-stained agarose gel of XBPl complementary DNA (cDNA) amplicons from INS-1 cells pre-treated for 1 hr with GP146 or APY29 at indicated concentrations, followed by thapsigargin (Tg) (6 nM) for 4 hrs; ratios of spliced XBPl (XBP1S) over (spliced + unspliced (XBP1U)) are plotted (mean ± SD, n = 3). (b) Anti-total and anti- phospho IREla immunoblots using extracts from INS-1 cells pre-treated for 1 hr with GP146, sunitinib, or STF-083010 at indicated concentrations, followed by Tg (6 nM) for 2 hrs. (c) EtBr- stained agarose gel of XBP l complementary DNA (cDNA) amplicons from the INS-1 cells described in (b). (d) EtBr-stained agarose gel of XBPl complementary DNA (cDNA) amplicons from INS-1 cells pre-treated for 1 hr with GP146(NMe) at indicated concentrations, followed by thapsigargin (Tg) (6 nM) for 4 hrs. (e) Model of how type I kinase inhibitors (APY29), type II kinase inhibitors (GP146), and RNase inhibtors (STF-083010) modulate the enzymatic activities of WT IREla. APY29 inhibits IREla trans-autophosphorylation but promotes oligomerization and activates the RNase domain; STF-083010 inhibits the RNase activity of IREla but does not affect kinase activity or the overall oligomerization state. GP 146 inhibits both the kinase and RNase domains of IREla and stabilizes the monomeric form; cartoons are not meant to differentiate between the relative orientations of monomer subunits in IREla.
[0033] Fig. 7 illustrates the compound Formula (A), wherein the R1, R2, R3, R4, R5, R6, R7, R8, R9, and R10 are each defined herein. [0034] Fig. 8 illustrates analogs of GP146 that demonstrate the ability to modulate and/or inhibit IREla RNase activity.
[0035] Fig. 9: ER stress-induced apoptosis can be replicated by simply overexpressing IREla.
(A) Percentage of INS- 1 cells staining positive for Annexin V after being treated with increasing concentrations of Thapsigargin (Tg) for 24, 48 and 72 h. (B) Anti-Procaspase-3 and Cleaved Caspase-3 immunoblot of INS- 1 cells treated with indicated concentrations of Tg for 12, 24 and 48h; anti-GAPDH immunoblot serves as loading control. (C) Model of ER stress mediated activation of IREla leading to ER-localized mRNA endonucleolytic decay, terminal UPR endpoints, and apoptosis. (D) Anti-Phospho-IREla and anti-Myc immunoblot of INS-1 stable line expressing transgenic wild-type IREla (WT) under increasing doses of Doxycycline (Dox) for 24h; anti-GAPDH immunoblot serves as loading control. (E) Ethidium-bromide (EtBr)- stained agarose gel of XBP 1 cDNA amplicons after induction by treating INS-1 IRE1 a (WT)- expressing stable cells with increasing concentrations of Dox for 24 hours; the cDNA amplicon of unspliced XBP1 mRNA is cleaved by a Pstl site within a 26 nucleotide intron to give 2U and 3U; IRE la-mediated cleavage of the intron and re-ligation in vivo removes the Pstl site to give the I S (spliced) amplicon; *is a spliced/unspliced XBP1 hybrid amplicon; the ratio of spliced over (spliced + unspliced) amplicons— 1 S/(1S+2U+3U)— is reported as % XBP1 splicing; three independent biological samples were used. (F) Q-PCR for Insulin 1 mRNA (normalized to GAPDH) in INS-1 IREl a (WT)-expressing stable cells treated with indicated doses of Dox for 24h. (G) Percent of INS-1 IREl a (WT)-expressing stable cells staining positive for Annexin V after treatment with increasing doses of Dox for 72h.
[0036] Fig. 10. Chemical-genetic manipulation of IREla activity reveals both the necessity and the sufficiency of the IREla RNase domain for triggering apoptosis. (A) Model of IREla (I642G) "holed"-kinase mutant and its activation by the "bumped" kinase inhibitor, 1NMPP1.
(B) Percent XBP1 splicing in INS-1 IRE1(I642G) stable transgenic cells treated for 24h with Ι μΜ 1NM-PP1, ^g/mL Dox and 6nM Tg as indicated. (C) Percent of INS-1 IRE1(I642G) cells staining positive for Annexin V after treatment for 72h with Ι μΜ 1NM-PP 1, ^g/mL Dox and 6nM Tg as indicated. (D) Percent XBP1 splicing in INS-1 IRE1(I642G) and TNS-1 IREl (I642G/N906A) stable transgenic mutant cells treated for 24h with 1NM-PP1, Dox and Tg as indicated. (E) Percent of INS-1 IRE1(I642G) and INS-1 IRE1(I642G/N906A) cells staining positive for Annexin V after treatment for 72h with 1NM-PP1, Dox and Tg as indicated. (F) Anti-Pro and Cleaved Caspase-3 immunoblots of INS-1 IREl (I642G) and INS-1
IREl (I642G/N906A) mutant stable cells treated for 72h with 1NM-PP 1 , Dox and Tg as indicated.
[0037] Fig. 1 1. Direct inhibition of IREla RNase prevents IREl dependent ER-localized mRNA degradation and ER stress-induced apoptosis. (A) Model of inhibition of IREla RNase activity by STF-083010 (STF). (B) Percent XBPl splicing in INS-1 IREl WT stable cells treated with 5ng/mL Dox and 50μΜ STF for indicated times as shown (upper panel). EtBr-stained agarose gel of XBP l cDNA amplicons is shown for the same samples above (lower panel). (C) Q-PCR for Insulin 1 mRNA (normalized to GAPDH) in INS-1 IREl WT stable cells treated Dox and STF for 12, 24, 48 and 72h. (D) Anti-Phospho-IREla and Anti-Total IREl a immunoblots of INS-1 IREl WT stable cells treated for 48h with 5ng/mL Dox and 50μΜ STF. (E) Anti- Phospho and Total ΓΝΚ immunoblots of same samples. (F) Anti-Pro Caspase and Cleaved
Caspase-3 immunoblots of same samples. (G) Percent of INS-1 IREl WT stable cells staining positive for Annexin V after treatment for 72h with Dox and STF as indicated. (H) Percent of INS-1 cells staining positive for Annexin V after treatment for 72h with increasing doses of Tunicamycin (Tm) and 50μΜ STF as indicated. (I) Immunofluorescence staining on islets from 10 week old C57BL6 mice treated with O^g/mL Tm and 50μΜ STF for 16h as indicated; co- stained for DAPI (left column), insulin (second column from left), and TUNEL (third column from left); merged image is also shown. (J) Quantification of TUNEL positive β-cells normalized to DAPI-positive cells in (I).
[0038] Fig. 12. a) Percent of INS-1 cells staining positive for Annexin-V 72 hrs after treatment of 500 ng/ml Tm +/- GP165. (b) EtBr-stained agarose gel of XBPl cDNA amplicons from INS-1 cells 8 hrs after treatment of 200 ng/ml Tm +/- GP 165. XBP1U, unspliced XBP l; XBP1 S, spliced XBPl ; the lower panel shows the ratios of spliced XBPl (XBP1 S) over (spliced + unspliced (XBP1U)). (c) Immunoblots for CASP3 cleavage in INS-1 cells 72 hrs after treatment of 500 ng/ml Tm +/- GP165 or 50 μΜ STF-083010 as positive control, (d) qPCR of insulin mRNA in INS-1 cells 8 hrs after treatment of 500 ng/ml Tm +/- GP165. (e) A schematic model of how GP165 blocks terminal UPR by inhibiting IREla activation under ER stress; as a type II kinase inhibitor, GP165 binds to the adenosine binding pocket and inhibits both the kinase and RNase domains of IREla and stabilizes the monomeric form; similar results are obtained using GP 146. GPl 65 is KIRA6.
[0039] Fig. 13. Coomassie blue-stained PAGE of purified IREla*; M, protein marker.
[0040] Fig. 14. Structures of several type II kinase inhibitors screened against IREla * in the XBPl RNA minisubstrate assay; the relative endpoint fluorescence intensities for the IREla*- catalyzed cleavage reaction of XBP l minisubstrate in the presence of varying concentrations of inhibitors are shown.
[0041] Fig. 15. Crystal structure of Src bound to the type II kinase inhibitor, GP 118 (PDB code 3EL8); hydrogen bond interactions between Src and GP l 18 are denoted as dotted lines; only the backbone atoms are shown for residues in the hinge region except for Thr338 (gatekeeper residue); the proposed model of GP l 18 bound to IREla shown in Fig. la is based on the Src- GP 118 complex structure.
[0042] Fig. 16. GP146 and APY29 modulation of IREla *-mediated cleavage of an in vitro- transcribed 352 nucleotide, internally a 32P-labeled XBPl RNA. (a) Urea PAGE analysis of 5 minute cleavage reactions of a 32P-labeled XBP l RNA by IREla * in the presence of varying concentrations of GP146. (b) Urea PAGE analysis of 5 minute cleavage reactions of a 32P- labeled XBPl RNA by dP- IREla * in the presence of varying concentrations of APY29.
[0043] Fig. 17. The EC50 of GP146 for IREla * RNase inhibition increases in the presence of a fixed concentration of APY29; the line marked with circles shows IREla* RNase inhibition by GP 146 in the absence of a competitor (APY29); the line marked with squares shows IREla * RNase inhibition by GPl 46 in the presence of APY29 (2 μΜ).
[0044] Fig. 18. Sunitinib inhibits IREla * autophosphorylation but activates the RNase domain, (a) Autoradiograms of IREla * autophosphorylation levels under serial two-fold dilutions of sunitinib (from 80 μΜ to 0.0098 μΜ). (b) Urea PAGE analysis of XBPl
minisubstrate cleavage by IREla * and dP- IREla * with and without sunitinib. (c) Urea PAGE analysis of XBPl minisubstrate cleavage by IREla * with fixed GPl 46 (10 μΜ) and varying sunitinib concentrations.
[0045] Fig. 19. A molecular model of APY29's interaction with the DFG-in conformation of human IREla. IREla is in the DFG-in active conformation; the pyrimidine ring of APY29 occupies the adenine pocket and the 3-aminopyraozole makes several hydrogen bonds with the kinase hinge; no favorable poses for APY29 bound to the DFG-out conformation of IREla could be determined.
[0046] Fig. 20. GP146 inhibits autophosphorylation and XBP 1 mRNA splicing by WT IREla in T-REx 293 cells, (a) Anti-total and anti-phospho IREla immunoblots, and EtBr-stained agarose gel of XBP 1 cDNA amplicons from T-REx 293 cells expressing WT IREla under Doxy eye line (Dox) control; cells were pre-treated for 1 hr with GP146 at indicated
concentrations, then induced with Dox (1 μΜ) for 8 hrs. (b) The plot shows normalized phosphorylation levels under varying [GP146] (mean ± SD, n >= 3). (c) GP146( Me) does not inhibit XBP 1 splicing in T-REx 293 cells expressing WT IREla EtBr-stained agarose gel of XBP1 cDNA amplicons from T-REx 293 cells expressing WT IREla are shown; cells were pre- treated for 1 hr with GP 146(NMe) at indicated concentrations, then induced with Dox (1 μΜ) for 8 hrs.
[0047] Fig. 21. Molecular model of GP 146 bound to the ATP-binding site of human IREla I642A; IREla is in the DFG-out inactive conformation; the imidazopyrazine ring of GP146 occupies the adenine pocket and the 3-trifluoromethylurea occupies the DFG-out pocket; the naphthyl ring of GP146 rotates 180 degrees and is able to access the enlarged hydrophobic pocket next to the gatekeeper residue; no favorable poses for GP146 bound to the DFG-in conformation of IREla I642A could be determined.
[0048] Fig. 22. Forced XBP1 mRNA splicing through conditional overproduction of IREla isogenic T-REx 293 stable cell lines; quantitation of EtBr-stained agarose gels of XBP1 cDNA amplicons from T-REx 293 cells stably expressing either WT -IREla or the "holed" IREla (1642A) mutant under Doxycycline (Dox) control; cells were induced with Dox (Ι μΜ) for 8 hrs, followed by provision of 1NM-PP1 (5 μΜ)— or DMSO— for 4 more hours; the ratio of spliced XBP1 (XBP1 S) over (XBP1S + unspliced amplicons (XBP1U)) at the endpoint is plotted in the histograms (mean ± SD, n >= 3).
[0049] Fig. 23. Death of pancreatic islet β-cells due to unchecked ER stress and terminal UPR signaling is central to development of types 1 and 2 diabetes. Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR.
Fig. 24. (A) Immunoblots of IREla* after treatment with the crosslinker DSS;
g concentrations of IREl * were incubated with DMSO, APY29, or KIRA3. (B) Model of how type kinase inhibitors can affect the RNase activities and oligomeric states of IRElcc and dP-IREla*.
[0051] Fig. 25. Synthetic strategy for generating KIRAs.
[0052] Fig. 26. Representative KIRAs synthesized and tested. [0053] Fig. 27. (A) General structure of irreversible KIRAs that target a cysteine residue located in the activation loop of IRE 1 ; representative electrophiles are shown. (B) A close-up of the ATP -binding site of IRE la.
[0054] Fig. 28. Increasing magnitude and duration of exposure of cells to myriad ER stressors causes increasing activation of IRE la (autophosphorylation, XBP l mRNA splicing, ER localized decay of Insl mRNA), and switch-like entry of the stressed into dysfunctional states culminating in apoptosis (see text for details); (A) Percent Annexin-V staining INS-1 cells treated in a time course of increasing concentrations of Tg. (B) Pro- and cleaved Caspase-3 immunoblot of Tg-treated INS-1 cells. (C) Time of exposure to the agent are directly linked to the percentage of cells entering apoptosis, as can be defined for other ER stress inducers such as the glycosylation inhibitor, tunicamycin (Tm) (D) Increasing ER stress causes progressive increases in endogenous IRE la phosphorylation. (E) Increasing ER stress causes progressive increases in endogenous XBPl mRNA splicing. (F) Increasing ER stress causes progressive depletion through endonucleolytic decay of the ER-localized mRNA, Insl, which encodes proinsulin. (G) Increasing ER stress causes progressive induction of the pro-apoptotic transcription factor, CHOP. (H) Diagram of effects due to increasing exposure to ER stress inducers and increasing severity of ER stress.
[0055] Fig. 29. Conditional overexpression (using Dox) of IRE la in stable INS-1 cells mimics a Terminal UPR by forcing IRE la autophosphorylation, XBPl mRNA splicing, ER localized decay of Ins 1 mRNA, decay of miR- 17, induction of CHOP, accumulation and cleavage of upstream (Caspase 2) and downstream (Caspase 3) caspases of the mitochondrial apoptotic pathway, as well as inflammatory (Caspase 1) caspase mediating pyroptosis, and switch-like entry of cells into programmed cell death. (A) Anti-Phospho-IREla and anti-Myc-IREla immunoblot of INS-1 IREla (WT) cells treated with increasing concentrations of Dox for 24h. (B) Agarose gel of Pstl-digested XBPl cDNA amplicons from INS-1 IREla (WT) cells treated with increasing [Dox] for 24h. % XBPl splicing represents the ratio of spliced over (spliced + unspliced) amplicons— 1 S/(1 S+2U+3U). (C) Model of how severe ER stress causes IREla to switche from homeostatic to apoptotic outputs. (D) Q-PCR for miR-17 in INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h. (E) Q-PCR for Insulinl (Insl) and CHOP mRNA in INS-1 IRE la (WT) cells treated with increasing [Dox] for 24 h; anti-Proinsulin immunoblot of INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h. (F) Immunoblot of Pro- and cleaved Caspase-1, Pro- and cleaved Caspase-2 from INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h and immunoblot of Pro-Caspase-3 and cleaved Caspase-3 from INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h. (G) Percent Annexin-V staining of INS-1 IRE la (WT) cells treated with increasing [Dox] for 72 h; three independent biological samples were used for XBPl splicing, Q-PCR and Annexin V staining experiments; each data point represents the mean value ± SD; P-values: *<0.05 and ** <0.01, ns=not significant.
[0056] Fig. 30. KIRA6 inhibits IRE la autophosphorylation, breaks oligomers, reduces RNase activity, and protects cells from entry into apoptosis. (A) Structure of KIRA6. (B) RNase activities of IRE la* under varying [KIRA6]; half-maximum effective concentration (EC50) values were determined by fitting normalized fluorescence intensities (mean ± s.d., n = 3). (C) Inhibition of IRE la* kinase activity in vitro by KIRA6; IC50 values were determined by fitting percent phosphorylation. (Ό) Ιη vivo, KIRA6 inhibits endogenous IRE la auto-phosphorylation in a dose-dependent manner; in contrast the aldehyde-based IRE la RNase-inhibitor, STF, does not inhibit IRE la auto-phosphorylation, nor does a control compound KIRA6(in). (E)
Immunoblots of IRE la* (WT) incubated with DMSO or KIRA6 (200 μΜ) followed by treatment with the crosslinker DSS (250 μΜ); quantification is on the right. (F) Agarose gel of XBPl cDNA amplicons from INS-1 cells pre-treated with indicated concentrations of KIRA6 for lh, followed by 0.5 μg/ml Tm for 8 h. (G) KIRA6 inhibits ER-localized endonucleolytic decay of Ins 1 mRNA at lower doses of the drug than needed to inhibit XBP 1 mRNA splicing. (H) KIRAs reduce entry of INSl-1 cells into apoptosis. (I) Immunofluorescence of islets from 10 wk old C57BL/6 mice treated with 0.5 μg/mL Tm plus/minus 0.5 μΜ KIRA6 for 16hr. Co-stained for DAPI, insulin, and TUNEL; Quantification of TUNEL positive β-cells (white arrows) normalized to DAPI-positive cells is shown. (J) KIRA6 cytoprotective effects are dependent on IRE1 a because they are absent in Irela ~'~ mouse embryonic fibroblasts (MEFs), but still demonstrable in WT and Xbpl ~'~ MEFs. (K) Model of how KIRA6 prevents the terminal UPR by inhibiting IRE la.
[0057] Fig. 31. KIRA6 inhibits IRE la* RNAse endonucleolytically cleaves pre-miR-17 at sites distinct from those cleaved by DICER but related to XBPl scission sites (A), KIRA6 prevents cleavage of pre-miR-17 by IRE la* in vitro (B) cleavage sites (C) pre-miR-17 (D), rescues mature miR-17 levels in vivo (E), reduces caspase 2 accumulation and cleavage (F), and prevents TXNIP protein accumulation in C57BL/6 islets exposed to ER stress inducers (G). Sequence legend (FIG. 3 IB): SEQ ID NOs: 11-15 (in order top to bottom); (FIG. 17C): SEQ ID NO: 16.
[0058] Fig. 32. Bumped type I kinase inhibitor, 1NM-PP1, increases oligomeric state of holed IREla* (I642G) mutant to promote RNAse activity and cell death under ER stress. (A) Quantitation of the ratios of oligomeric to monomeric IRE la* from immunoblots of increasing concentrations of recombinant IREla*(WT), IREla*(I642G) or IREla*(I642G) incubated with 1NM-PP1, before treatment with the crosslinker disuccinimidyl suberate (DSS) (250 Mm) and quantitation of time course of cleavage reactions of a32P-labeled XBP l RNA or Insulin2 (Ins2) RNA by recombinant IREla*(WT), IRE la* (1642 G), and IREla*(I642G) incubated with 1NM- PP 1 (10 μΜ) from urea PAGE. (B) Percent XBP l splicing (24hr), relative Insulinl (Insl) mRNA levels by Q-PCR (24hr) and percent Annexin V staining (72hr) in ^g/mL Dox treated INS-1 IRE la (1642 G) cells plus/minus ΙμΜ 1NM-PP1 and plus/minus 6 nM Tg; three independent biological samples were used for each experiment and plotted as mean value ± SD; P-values: ** <0.01. (C) Model for how IREla (I642G) is partially activated by 1NMPP1 to splice XBPl mRNA in the absence of ER stress; when driven into an oligomeric state by irremediable ER stress, 1NM-PP 1 -bound IREla (1642 G) induces ER-localized mRNA decay and Terminal UPR. [0059] Fig. 33. IREla RNAse hyperactivation pushes cells into the Terminal UPR.
Compounds, pharmaceutical compositions, and methods described herein may modulate the terminal UPR.
[0060] Fig. 34. Death of pancreatic islet β-cells due to unchecked ER stress and terminal UPR signaling is central to development of types 1 and 2 diabetes. Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR.
[0061] Fig. 35. Fibrotic remodeling due to unchecked ER stress is central to development of fibrotic disease such as idiopathic pulmonary fibrosis (IPF). Compounds, pharmaceutical compositions, and methods described herein may modulate the UPR and treat diseases associated with ER stress and the UPR. [0062] Fig. 36. Inhibiting the Terminal UPR by attenuating IRE la's RNAse with kinase inhibitors (KIRAs).
[0063] Fig. 37. KIRA6 shuts down all critical terminal UPR events in pancreatic islet beta cells experiencing ER stress; inhibition of pro-inflammatory signaling through TXNIP and Interleukin 1-beta.
[0064] Fig. 38. Testing cascade to improve potency, selectivity, and efficacy of IRE la KIRAs.
[0065] Fig. 39: KIRA6 protects viability and preserves function of retinal photoreceptors during tunicamycin- and mutant rhodopsin-induced stress. (A) Fundus and OCT images of Sprague-Dawley rats injected intravitreally with tunicamycin +/- 10 μΜ KIRA6. (B) Fundus and OCT images of P23H-1 rats at P40 injected intravitreally with DMSO or 10 μΜ KIRA6. (C) Histological sections of retinas from P23H-1 rats at P30 after intravitreal injection of DMSO or 10 μΜ KIRA6. (D) Quantification of outer nuclear layer (ONL) thickness (n=2) of P23H-1 rats at P30; higher thickness line is KIRA6 and lower line is DMSO. (E) Fundus and OCT images of P23H-1 rats at P40 after intravitreal injection of DMSO or 10 μΜ KIRA6. (F) Scotopic series of ERG measurements with indicated light intensities (top) and a photopic single flash ERG measurement (+20 dB) (bottom).
[0066] Fig. 40. Survival curves of murine embryonic stem cell (ESC)-derived motor neurons. A. Wild-type (WT) Hb9:GFP ESCs were differentiated into GFP+ motor neurons (MNs) and subsequently treated with brefeldin A (BFA) with or without KIRA6 at the indicated
concentrations. B. G93A-SODl/Hb9:GFP ESCs were differentiated into GFP+ MNs and treated with KIRA6 at the indicated concentrations; MNs derived from WT Hb9:GFP ESCs served as a control, p-values: * < 0.05. MutSODl leads to a form of familial amyotrophic lateral sclerosis.
DETAILED DESCRIPTION
[0067] Activation of IREla's RNase is normally dependent on kinase autophosphorylation (Tirasophon, W. et al. Genes Dev 12, 1812-1824 (1998)), but an allosteric relationship between these two domains exists, which allows nucleotides (ADP and ATP) and small molecule inhibitors that stabilize an active ATP-binding site conformation to directly activate the RNase without autophosphorylation (Papa, F. R. et al. Science 302, 1533-1537 (2003); Han, D. et al. Biochemical and biophysical research communications 365, 777-783, (2008); Korennykh, A. V. et al. BMC biology 9, 48, (2011)). Furthermore, a particular class of kinase inhibitors (called type II) stabilize an inactive ATP-binding site conformation of IRE la and are able to potently inhibit its RNase activity by breaking high-order oligomerization state (Figs. 1A and 36) (Wang, L. et al. Nature chemical biology 8, 982-989, (2012)). These compounds are herein labeled—
KIRAs— for kinase-inhibiting R ase-attenuators.
[0068] Distinct classes of ATP-competitive kinase inhibitors divergently modulate the RNase activity of IREla. A co-crystal structure of yeast IREl bound with APY29— a predicted type I kinase inhibitor— shows that the kinase catalytic domain is in an active conformation, which is a conformation typically adopted by protein kinases when bound to ATP and other type I inhibitors (Fig. la) (Korennykh, A. V. et al. Nature 457, 687-693 (2009); Korennykh, A. V. et al. BMC Biol. 9, 48 (2011)). Moreover, two additional co-crystal structures of yeast IREl and human IREla bound with ADP show that the kinase domain is similarly in an active conformation (Ali, M. M. et al. EMBO J. 30, 894-905 (2011); Lee, K. P. et al. Cell 132, 89-100 (2008)). By stabilizing IRE la's kinase in the active conformation, these type I inhibitors act as ligands that allosterically activate its adjacent RNase domain. It might be possible to stabilize IREla's kinase domain in an alternative conformation, and in so doing disable its RNase activity. Use of a class of small molecule kinase inhibitors that have been described to selectively stabilize the inactive conformation of the ATP-binding site (type II inhibitors) for a variety of kinases; examples include the clinically-approved drugs imatinib and sorafenib (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006); Wan, P. T. et al. Cell 116, 855-867 (2004); Schindler, T. et al. Science 289, 1938-1942 (2000)), provides support for this approach. The inactive ATP- binding site conformation stabilized by type II inhibitors is characterized by outward movement of the catalytically-important Asp-Phe-Gly (DFG) motif, and is therefore called the DFG-out conformation (Fig. la) (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006); Ranjitkar, P. et al. Chem. Biol. 17, 195-206 (2010)). In contrast, in all three co-crystal structures of IREl in an active conformation mentioned previously, the kinase domain adopts the DFG-in conformation (Korennykh, A. V. et al. Nature 457, 687-693 (2009); Ali, M. M. et al. EMBO J. 30, 894-905 (201 1); Lee, K. P. et al. Cell 132, 89-100 (2008)).
[0069] Under high endoplasmic reticulum (ER) stress, hyperactivation of intracellular signaling pathways termed the unfolded protein response (UPR) triggers cell death. Signature events of this "Terminal UPR" are controlled by IREl , an ER bifunctional
kinase/endoribonuclease (RNase), which, when oligomerized, endonucleolytically degrades ER- localized mRNAs and repressive micro-RNA precursors to trigger apoptosis. Irel somatic mutations found in human cancers disable oligomerization and apoptotic function of its RNase. Using these instructive results from human biology, ATP-competitive kinase inhibitors were developed— termed KIRAs (Kinase inhibiting RNase Attenuators)— that allosterically reduce IRE la oligomerization and RNase activity. One such kinase inhibitor, KIRA6, inhibits all IRE la outputs, and preserves cell viability and function under ER stress. In rat models of retinal degeneration caused by ER stress, intravitreal KIRA6 prevents photoreceptor loss.
A. DEFINITIONS
[0070] The abbreviations used herein have their conventional meaning within the chemical and biological arts. The chemical structures and formulae set forth herein are constructed according to the standard rules of chemical valency known in the chemical arts. [0071] Where substituent groups are specified by their conventional chemical formulae, written from left to right, they equally encompass the chemically identical substituents that would result from writing the structure from right to left, e.g., -CH20- is equivalent to -OCH2-. Terms used herein may be preceded and/or followed by a single dash, " ", or a double dash, "=", to indicate the bond order of the bond between the named substituent and its parent moiety; a single dash indicates a single bond and a double dash indicates a double bond. In the absence of a single or double dash it is understood that a single bond is formed between the substituent and its parent moiety; further, substituents having a superscript "d" (e.g. Rd) are intended to be read "left to right" unless a dash indicates otherwise. For example, Ci C6alkoxycarbonyloxy and OC(0)Ci C6alkyl indicate the same functionality; similarly arylalkyl and -alkylaryl indicate the same functionality.
[0072] The term "saturated" as used herein means the referenced chemical structure does not contain any multiple carbon carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.
[0073] The term "alkyl," by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e., unbranched) or branched carbon chain (or carbon), or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e., Ci-Cio means one to ten carbons). Examples of saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec -butyl, (cyclohexyl)methyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl group is one having one or more double bonds or triple bonds. Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(l,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers. An alkoxy is an alkyl attached to the remainder of the molecule via an oxygen linker (-0-). In embodiments, an alkyl is a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified. In embodiments, an alkyl is an alkenyl, wherein the term "alkenyl" is used in accordance with its plain ordinary meaning. In embodiments, an alkenyl is a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon carbon double bond. Examples of alkenyl include, but are not limited to, ethenyl, 2 propenyl, 2 methyl 2 propenyl, 3 butenyl, 4 pentenyl, 5 hexenyl, 2 heptenyl, 2 methyl 1 heptenyl, 3 decenyl, and 3,7 dimethylocta 2,6 dienyl. In embodiments, an alkyl is an alkynyl, wherein the term "alkynyl" is used in accordance with its plain ordinary meaning. In embodiments, an alkynyl is a straight or branched chain hydrocarbon group containing from 2 to 10 carbon atoms and containing at least one carbon carbon triple bond. Examples of alkynyl include, but are not limited, to acetylenyl, 1 propynyl, 2 propynyl, 3 butynyl, 2 pentynyl, and 1 butynyl.
[0074] The term "alkylene," by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkyl, as exemplified, but not limited
by, -CH2CH2CH2CH2-. Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being preferred in the present invention. A "lower alkyl" or "lower alkylene" is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms. The term "alkenylene," by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene.
[0075] The term "heteroalkyl," by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom selected from the group consisting of O, N, P, Si, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized. The heteroatom(s) O, N, P, S, and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Examples include, but are not limited
to: -CH2-CH2-O-CH3, -CH2-CH2-NH-CH3, -CH2-CH2-N(CH3)-CH3, -CH2-S-CH2-CH3, -CH2-CH 2-S(0)-CH3, -CH2-CH2-S(0)2-CH3, -CH=CH-0-CH3, -Si(CH3)3, -CH2-CH=N-OCH3, -CH=CH- N(CH3)-CH3, -0-CH3, -0-CH2-CH3, and -CN. Up to two or three heteroatoms may be consecutive, such as, for example, -CH2-NH-OCH3 and -CH2-0-Si(CH3)3. [0076] Similarly, the term "heteroalkylene," by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from heteroalkyl, as exemplified, but not limited by, -CH2-CH2-S-CH2-CH2- and -CH2-S-CH2-CH2-NH-CH2-. For heteroalkylene groups, heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy,
alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula -C(0)2R'- represents both -C(0)2R'- and -R'C(0)2-. As described above, heteroalkyl groups, as used herein, include those groups that are attached to the remainder of the molecule through a heteroatom, such as -C(0)R, -C(0)NR, -NR'R", -OR', -SR, and/or -S02R'. Where "heteroalkyl" is recited, followed by recitations of specific heteroalkyl groups, such as -NR'R" or the like, it will be understood that the terms heteroalkyl and -NR'R" are not redundant or mutually exclusive.
Rather, the specific heteroalkyl groups are recited to add clarity. Thus, the term "heteroalkyl" should not be interpreted herein as excluding specific heteroalkyl groups, such as -NR'R" or the like.
[0077] The terms "cycloalkyl" and "heterocycloalkyl," by themselves or in combination with other terms, mean, unless otherwise stated, cyclic versions of "alkyl" and "heteroalkyl," respectively, wherein the carbons making up the ring or rings do not necessarily need to be bonded to a hydrogen due to all carbon valencies participating in bonds with non-hydrogen atoms. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 1 -cyclohexenyl,
3-cyclohexenyl, cycloheptyl, and the like. Examples of heterocycloalkyl include, but are not limited to, l-(l,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl,
4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl, 1-piperazinyl, 2-piperazinyl, and the like. A "cycloalkylene" and a "heterocycloalkylene," alone or as part of another substituent, means a divalent radical derived from a cycloalkyl and heterocycloalkyl, respectively.
[0078] In embodiments, the term "cycloalkyl" means a monocyclic, bicyclic, or a multicyclic cycloalkyl ring system. In embodiments, monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups can be saturated or unsaturated, but not aromatic. In embodiments, cycloalkyl groups are fully saturated. Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl. Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings. In embodiments, bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form (CH2)W , where w is 1, 2, or 3). Representative examples of bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane. In embodiments, fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. In embodiments, the bridged or fused bicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkyl ring. In embodiments, cycloalkyl groups are optionally substituted with one or two groups which are independently oxo or thia. In embodiments, the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia. In embodiments, multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. In embodiments, the multicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the base ring. In embodiments, multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl. Examples of multicyclic cycloalkyl groups include, but are not limited to tetradecahydrophenanthrenyl,
perhydrophenothiazin-l-yl, and perhydrophenoxazin-l-yl. [0079] In embodiments, a cycloalkyl is a cycloalkenyl. The term "cycloalkenyl" is used in accordance with its plain ordinary meaning. In embodiments, a cycloalkenyl is a monocyclic, bicyclic, or a multicyclic cycloalkenyl ring system. In embodiments, monocyclic cycloalkenyl ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon carbon double bond), but not aromatic. Examples of monocyclic cycloalkenyl ring systems include cyclopentenyl and cyclohexenyl. In embodiments, bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings. In embodiments, bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form (CH2)w, where w is 1, 2, or 3). Representative examples of bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct 2 enyl. In embodiments, fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. In embodiments, the bridged or fused bicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkenyl ring. In embodiments, cycloalkenyl groups are optionally substituted with one or two groups which are independently oxo or thia. In embodiments, multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. In embodiments, the multicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the base ring. In embodiments, multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
[0080] In embodiments, a heterocycloalkyl is a heterocyclyl. The term "heterocyclyl" as used herein, means a monocyclic, bicyclic, or multicyclic heterocycle. The heterocyclyl monocyclic heterocycle is a 3, 4, 5, 6 or 7 membered ring containing at least one heteroatom independently selected from the group consisting of O, N, and S where the ring is saturated or unsaturated, but not aromatic. The 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of O, N and S. The 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of O, N and S. The 6 or 7 membered ring contains zero, one or two double bonds and one, two or three heteroatoms selected from the group consisting of O, N and S. The heterocyclyl monocyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heterocyclyl monocyclic heterocycle. Representative examples of heterocyclyl monocyclic heterocycles include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3 dioxanyl, 1,3 dioxolanyl, 1,3 dithiolanyl, 1,3 dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl, thiomorpholinyl, 1 , 1 dioxidothiomorpholinyl (thiomorpholine sulfone), thiopyranyl, and trithianyl. The heterocyclyl bicyclic heterocycle is a monocyclic heterocycle fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocycle, or a monocyclic heteroaryl. The heterocyclyl bicyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle portion of the bicyclic ring system.
Representative examples of bicyclic heterocyclyls include, but are not limited to, 2,3
dihydrobenzofuran 2 yl, 2,3 dihydrobenzofuran 3 yl, indolin 1 yl, indolin 2 yl, indolin 3 yl, 2,3 dihydrobenzothien 2 yl, decahydroquinolinyl, decahydroisoquinolinyl, octahydro 1H indolyl, and octahydrobenzofuranyl. In embodiments, heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the bicyclic heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring fused to a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia. Multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. The multicyclic heterocyclyl is attached to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring. In embodiments, multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl. Examples of multicyclic heterocyclyl groups include, but are not limited to lOH-phenothiazin-10-yl, 9, 10-dihydroacridin-9-yl, 9, 10- dihydroacridin-10-yl, lOH-phenoxazin-10-yl, 10,1 l-dihydro-5H-dibenzo[b,fJazepin-5-yl, l,2,3,4-tetrahydropyrido[4,3-g]isoquinolin-2-yl, 12H-benzo[b]phenoxazin-12-yl, and dodecahydro- lH-carbazol-9-yl.
[0081] The terms "halo" or "halogen," by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom. Additionally, terms such as "haloalkyl" are meant to include monohaloalkyl and polyhaloalkyl. For example, the term "halo(Ci-C4)alkyl" includes, but is not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.
[0082] The term "acyl" means, unless otherwise stated, -C(0)R where R is a substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0083] The term "aryl" means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (preferably from 1 to 3 rings) that are fused together (i.e., a fused ring aryl) or linked covalently. A fused ring aryl refers to multiple rings fused together wherein at least one of the fused rings is an aryl ring. The term "heteroaryl" refers to aryl groups (or rings) that contain at least one heteroatom such as N, O, or S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized. Thus, the term "heteroaryl" includes fused ring heteroaryl groups (i.e., multiple rings fused together wherein at least one of the fused rings is a heteroaromatic ring). A 5,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 5 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring. Likewise, a 6,6- fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring. And a 6,5-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 5 members, and wherein at least one ring is a heteroaryl ring. A heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom. Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1- pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2- thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4- pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1- isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl.
Substituents for each of the above noted aryl and heteroaryl ring systems are selected from the group of acceptable substituents described below. An "arylene" and a "heteroarylene," alone or as part of another substituent, mean a divalent radical derived from an aryl and heteroaryl, respectively, such as for example a divalent radical of indoline. Non-limiting examples of heteroaryl groups include pyridinyl, pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl, benzothiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, furylthienyl, pyridyl, pyrimidyl, benzothiazolyl, purinyl, benzimidazolyl, isoquinolyl, thiadiazolyl, oxadiazolyl, pyrrolyl, diazolyl, triazolyl, tetrazolyl, benzothiadiazolyl, isothiazolyl, pyrazolopyrimidinyl,
pyrrolopyrimidinyl, benzotriazolyl, benzoxazolyl, or quinolyl. The examples above may be substituted or unsubstituted and divalent radicals of each heteroaryl example above are non- limiting examples of heteroarylene. [0084] In embodiments, an aryl is a phenyl (i.e., monocyclic aryl), a bicyclic ring system containing at least one phenyl ring or an aromatic bicyclic ring containing only carbon atoms in the aromatic bicyclic ring system or a multicyclic aryl ring system, provided that the bicyclic or multicyclic aryl ring system does not contain a heteroaryl ring when fully aromatic. In embodiments, the bicyclic aryl can be azulenyl, naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocyclyl. In embodiments, the bicyclic aryl may be attached to the parent molecular moiety through any carbon atom contained within the phenyl portion of the bicyclic system, or any carbon atom with the napthyl or azulenyl ring. In embodiments, the fused monocyclic cycloalkyl or monocyclic heterocyclyl portions of the bicyclic aryl are optionally substituted with one or two oxo and/or thia groups.
Representative examples of the bicyclic aryls include, but are not limited to, azulenyl, naphthyl, dihydroinden 1 yl, dihydroinden 2 yl, dihydroinden 3 yl, dihydroinden 4 yl, 2,3 dihydroindol 4 yl, 2,3 dihydroindol 5 yl, 2,3 dihydroindol 6 yl, 2,3 dihydroindol 7 yl, inden 1 yl, inden 2 yl, inden 3 yl, inden 4 yl, dihydronaphthalen 2 yl, dihydronaphthalen 3 yl, dihydronaphthalen 4 yl, dihydronaphthalen 1 yl, 5,6,7,8 tetrahydronaphthalen 1 yl, 5,6,7,8 tetrahydronaphthalen 2 yl, 2,3 dihydrobenzofuran 4 yl, 2,3 dihydrobenzofuran 5 yl, 2,3 dihydrobenzofuran 6 yl, 2,3
dihydrobenzofuran 7 yl, benzo[d][l,3]dioxol 4 yl, benzo[d][l,3]dioxol 5 yl, 2H chromen 2 on 5 yl, 2H chromen 2 on 6 yl, 2H chromen 2 on 7 yl, 2H chromen 2 on 8 yl, isoindoline 1,3 dion 4 yl, isoindoline 1,3 dion 5 yl, inden 1 on 4 yl, inden 1 on 5 yl, inden 1 on 6 yl, inden 1 on 7 yl, 2,3 dihydrobenzo[b][l,4]dioxan 5 yl, 2,3 dihydrobenzo[b][l,4]dioxan 6 yl, 2H
benzo[b][l,4]oxazin3(4H) on 5 yl, 2H benzo[b][l,4]oxazin3(4H) on 6 yl, 2H
benzo[b][l,4]oxazin3(4H) on 7 yl, 2H benzo[b][l,4]oxazin3(4H) on 8 yl, benzo[d]oxazin 2(3H) on 5 yl, benzo[d]oxazin 2(3H) on 6 yl, benzo[d]oxazin 2(3H) on 7 yl, benzo[d]oxazin 2(3H) on 8 yl, quinazolin 4(3H) on 5 yl, quinazolin 4(3H) on 6 yl, quinazolin 4(3H) on 7 yl, quinazolin 4(3H) on 8 yl, quinoxalin 2(1H) on 5 yl, quinoxalin 2(1H) on 6 yl, quinoxalin 2(1H) on 7 yl, quinoxalin 2(1H) on 8 yl, benzo[d]thiazol 2(3H) on 4 yl, benzo[d]thiazol 2(3H) on 5 yl, benzo[d]thiazol 2(3H) on 6 yl, and, benzo[d]thiazol 2(3H) on 7 yl. In embodiments, the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In embodiments, multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic
heterocyclyl. In embodiments, the multicyclic aryl may be attached to the parent molecular moiety through any carbon atom contained within the base ring. In certain embodiments, multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl. Examples of multicyclic aryl groups include but are not limited to anthracen-9-yl and phenanthren-9-yl.
[0085] In embodiments, the term "heteroaryl," as used herein, means a monocyclic, bicyclic, or a multicyclic heteroaryl ring system. In embodiments, the monocyclic heteroaryl can be a 5 or 6 membered ring. In embodiments, the 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom. In embodiments, the 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms. In embodiments, the 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl. Representative examples of monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl. In embodiments, the bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. In embodiments, the fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia. In embodiments, when the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system. In embodiments, when the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system. Representative examples of bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl,
benzothiazolyl, cinnolinyl, 5,6 dihydroquinolin 2 yl, 5,6 dihydroisoquinolin 1 yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8 tetrahydroquinolin 2 yl, 5,6,7,8 tetrahydroquinolin 3 yl, 5,6,7,8 tetrahydroquinolin 4 yl, 5,6,7,8 tetrahydroisoquinolin 1 yl, thienopyridinyl, 4,5,6,7 tetrahydrobenzo[c][l,2,5]oxadiazolyl, and 6,7
dihydrobenzo[c][l,2,5]oxadiazol 4(5H) onyl. In embodiments, the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In embodiments, the multicyclic heteroaryl group is a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic heterocyclyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic cycloalkyl. In embodiments, the multicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring. In embodiments, multicyclic heteroaryl groups are a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic heterocyclyl, a monocyclic cycloalkenyl, and a monocyclic cycloalkyl. Examples of multicyclic heteroaryls include, but are not limited to 5H-[l,2,4]triazino[5,6-b]indol-5-yl, 2,3,4,9-tetrahydro-lH-carbazol-9-yl, 9H-pyrido[3,4-b]indol-9-yl, 9H-carbazol-9-yl, acridin-9-yl, [0086] A fused ring heterocyloalkyl-aryl is an aryl fused to a heterocycloalkyl. A fused ring heterocycloalkyl-heteroaryl is a heteroaryl fused to a heterocycloalkyl. A fused ring
heterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a cycloalkyl. A fused ring
heterocycloalkyl-heterocycloalkyl is a heterocycloalkyl fused to another heterocycloalkyl. Fused ring heterocycloalkyl-aryl, fused ring heterocycloalkyl-heteroaryl, fused ring heterocycloalkyl- cycloalkyl, or fused ring heterocycloalkyl-heterocycloalkyl may each independently be unsubstituted or substituted with one or more of the substitutents described herein.
[0087] The term "oxo," as used herein, means an oxygen that is double bonded to a carbon atom. The term "thia" as used herein means a =S group.
[0088] The term "alkylsulfonyl," as used herein, means a moiety having the formula -S(0)2- ', where R' is a substituted or unsubstituted alkyl group as defined above. R' may have a specified number of carbons (e.g., "C1-C4 alkylsulfonyl"). [0089] The term "arylalkyl" and " alkylaryl" as used herein, means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of arylalkyl include, but are not limited to, benzyl, 2 phenylethyl, 3 phenylpropyl, and 2 naphth 2 ylethyl. [0090] The term "heteroarylalkyl" and " alkylheteroaryl" as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of heteroarylalkyl include, but are not limited to, fur 3 ylmethyl, 1H imidazol 2 ylmethyl, 1H imidazol 4 ylmethyl, 1 (pyridin 4 yl)ethyl, pyridin 3 ylmethyl, pyridin 4 ylmethyl, pyrimidin 5 ylmethyl, 2 (pyrimidin 2 yl)propyl, thien 2 ylmethyl, and thien 3 ylmethyl.
[0091] Each of the above terms (e.g., "alkyl," "heteroalkyl," "aryl," and "heteroaryl") includes both substituted and unsubstituted forms of the indicated radical. Preferred substituents for each type of radical are provided below.
[0092] Substituents for the alkyl and heteroalkyl radicals (including those groups often referred to as alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one or more of a variety of groups selected from, but not limited to, -OR, =0, =NR,
=N-OR, -NR'R", -SR, -halogen, -SiRR"R", -OC(0)R, -C(0)R', -C02R, -CONR'R", -OC(0)N R'R", -NR"C(0)R, -NR'-C(0)NR"R", -NR"C(0)2R, -NR-C(NRR"R")=NR"", -NR-C(NRR")= NR'", -S(0)R, -S(0)2R', -S(0)2NR'R", -NRS02R, -NRTSfR'R", -ONRR",
-NRC=(0)NR"NR"'R"", -CN, -N02, in a number ranging from zero to (2m'+l), where m' is the total number of carbon atoms in such radical. R, R, R", R", and R"" each preferably
independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), substituted or unsubstituted heteroaryl, substituted or unsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R, R", R'", and R"" group when more than one of these groups is present. When R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7-membered ring. For example, -NR'R" includes, but is not limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term "alkyl" is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., -CF3 and -CH2CF3) and acyl (e.g., -C(0)CH3, -C(0)CF3, -C(0)CH2OCH3, and the like).
[0093] Similar to the substituents described for the alkyl radical, substituents for the aryl and heteroaryl groups are varied and are selected from, for
example: -OR', -NR'R", -SR', -halogen, -SiR'R'R'", -OC(0)R, -C(0)R', -C02R, -CONR'R", -OC (O)NR'R", -NR"C(0)R, -NR'-C(0)NR"R", -NR"C(0)2R', -NR-C(NR'R"R"')=NR"", -NR-C(NR R")=NR"', -S(0)R', -S(0)2R, -S(0)2NR'R", -NRS02R, -NR'NR"R"', -ONR'R",
-NR'C=(0)NR"NR"'R"", -CN, -N02, -R, -N3, -CH(Ph)2, fluoro(Ci-C4)alkoxy, and fluoro(Ci- C4)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R, R", R'", and R"" are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R, R", R", and R"" groups when more than one of these groups is present.
[0094] Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure. In one embodiment, the ring-forming substituents are attached to adjacent members of the base structure. For example, two ring- forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure. In another embodiment, the ring- forming substituents are attached to a single member of the base structure. For example, two ring- forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure. In yet another embodiment, the ring- forming substituents are attached to non-adjacent members of the base structure. [0095] Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -T-C(0)-(CRR')q-U-, wherein T and U are
independently -NR-, -0-, -CRR'-, or a single bond, and q is an integer of from 0 to 3.
Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH2)r-B-, wherein A and B are independently -CRR'-, -0-, -NR-, -S-, -S(O) -, -S(0)2-, -S(0)2NR'-, or a single bond, and r is an integer of from 1 to 4. One of the single bonds of the new ring so formed may optionally be replaced with a double bond. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the
formula -(CRR')S-X'- (C"R"R"')d-, where s and d are independently integers of from 0 to 3, and X' is -0-, -NR'-, -S-, -S(O)-, -S(0)2-, or -S(0)2NR'-. The substituents R, R', R", and R" are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
[0096] As used herein, the terms "heteroatom" or "ring heteroatom" are meant to include, oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si).
[0097] A "substituent group," as used herein, means a group selected from the following moieties:
(A) oxo, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - S04H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, - NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, -NHS02CH3, -N3, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
(B) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, substituted with at least one substituent selected from:
(i) oxo, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, - NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, -NHS02CH3, -N3, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
(ii) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, substituted with at least one substituent selected from:
(a) oxo, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, - S03H, -SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, - NHS02H, -NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, -NHS02CH3, -N3, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, , and
(b) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, substituted with at least one substituent selected from: oxo, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - S04H, -S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, - NHS02H, -NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, -NHS02CH3, -N3, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl.
[0098] A "size-limited substituent" or " size-limited substituent group," as used herein, means a group selected from all of the substituents described above for a "substituent group," wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C2o alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. [0099] A "lower substituent" or " lower substituent group," as used herein, means a group selected from all of the substituents described above for a "substituent group," wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-Cs alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl.
[0100] In some embodiments, each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In other embodiments, at least one or all of these groups are substituted with at least one lower substituent group. [0101] In other embodiments of the compounds herein, each substituted or unsubstituted alkyl may be a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. In some embodiments of the compounds herein, each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C20 alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered heteroalkylene, each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C8 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered heteroarylene.
[0102] In some embodiments, each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-Cs alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl. In some embodiments, each substituted or unsubstituted alkylene is a substituted or unsubstituted Ci-Cs alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene, each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C7 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene. In some embodiments, the compound is a chemical species set forth in the Examples section below.
[0103] The term "pharmaceutically acceptable salts" is meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein. When compounds of the present invention contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present invention contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,
monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, e.g., Berge et al, Journal of
Pharmaceutical Science 66: 1-19 (1977)). Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. Other pharmaceutically acceptable carriers known to those of skill in the art are suitable for the present invention. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms. In other cases, the preparation may be a lyophilized powder in 1 mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
[0104] Thus, the compounds of the present invention may exist as salts, such as with
pharmaceutically acceptable acids. The present invention includes such salts. Examples of such salts include hydrochlorides, hydrobromides, sulfates, methanesulfonates, nitrates, maleates, acetates, citrates, fumarates, tartrates (e.g., (+)-tartrates, (-)-tartrates, or mixtures thereof including racemic mixtures), succinates, benzoates, and salts with amino acids such as glutamic acid. These salts may be prepared by methods known to those skilled in the art.
[0105] The neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner. The parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents. [0106] In addition to salt forms, the present invention provides compounds, which are in a prodrug form. Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention. Additionally, prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
[0107] Certain compounds of the present invention can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present invention. Certain compounds of the present invention may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present invention and are intended to be within the scope of the present invention.
[0108] As used herein, the term "salt" refers to acid or base salts of the compounds used in the methods of the present invention. Illustrative examples of acceptable salts are mineral acid (hydrochloric acid, hydrobromic acid, phosphoric acid, and the like) salts, organic acid (acetic acid, propionic acid, glutamic acid, citric acid and the like) salts, quaternary ammonium (methyl iodide, ethyl iodide, and the like) salts.
[0109] Certain compounds of the present invention possess asymmetric carbon atoms (optical or chiral centers) or double bonds; the enantiomers, racemates, diastereomers, tautomers, geometric isomers, stereoisometric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids, and individual isomers are encompassed within the scope of the present invention. The compounds of the present invention do not include those which are known in art to be too unstable to synthesize and/or isolate. The present invention is meant to include compounds in racemic and optically pure forms. Optically active (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques. When the compounds described herein contain olefinic bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. [0110] As used herein, the term "isomers" refers to compounds having the same number and kind of atoms, and hence the same molecular weight, but differing in respect to the structural arrangement or configuration of the atoms. [0111] The term "tautomer," as used herein, refers to one of two or more structural isomers which exist in equilibrium and which are readily converted from one isomeric form to another.
[0112] It will be apparent to one skilled in the art that certain compounds of this invention may exist in tautomeric forms, all such tautomeric forms of the compounds being within the scope of the invention.
[0113] Unless otherwise stated, structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the invention. [0114] Unless otherwise stated, structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13C- or 14C-enriched carbon are within the scope of this invention. [0115] The compounds of the present invention may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds. For example, the compounds may be radiolabeled with radioactive isotopes, such as for example tritium (3H), iodine-125 (125I), or carbon-14 (14C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are encompassed within the scope of the present invention. [0116] The symbol /w " denotes the point of attachment of a chemical moiety to the remainder of a molecule or chemical formula.
[0117] The terms "a" or "an," as used in herein means one or more. In addition, the phrase "substituted with a[n]," as used herein, means the specified group may be substituted with one or more of any or all of the named substituents. For example, where a group, such as an alkyl or heteroaryl group, is "substituted with an unsubstituted C1-C20 alkyl, or unsubstituted 2 to 20 membered heteroalkyl," the group may contain one or more unsubstituted C1-C20 alkyls, and/or one or more unsubstituted 2 to 20 membered heteroalkyls. Moreover, where a moiety is substituted with an R substituent, the group may be referred to as "R-substituted." Where a moiety is R-substituted, the moiety is substituted with at least one R substituent and each R substituent is optionally different. [0118] Descriptions of compounds of the present invention are limited by principles of chemical bonding known to those skilled in the art. Accordingly, where a group may be substituted by one or more of a number of substituents, such substitutions are selected so as to comply with principles of chemical bonding and to give compounds which are not inherently unstable and/or would be known to one of ordinary skill in the art as likely to be unstable under ambient conditions, such as aqueous, neutral, and several known physiological conditions. For example, a heterocycloalkyl or heteroaryl is attached to the remainder of the molecule via a ring heteroatom in compliance with principles of chemical bonding known to those skilled in the art thereby avoiding inherently unstable compounds. [0119] The terms "treating" or "treatment" refers to any indicia of success in the treatment or amelioration of an injury, disease, pathology or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology or condition more tolerable to the patient; slowing in the rate of degeneration or decline; making the final point of degeneration less debilitating; improving a patient's physical or mental well-being. The treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of a physical examination, neuropsychiatric exams, and/or a psychiatric evaluation. For example, certain methods herein treat cancer (e.g. multiple myeloma, cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes (type I or type II). For example certain methods herein treat cancer by decreasing or reducing or preventing the occurrence, growth, metastasis, or progression of cancer; treat neurodegeneration by improving mental wellbeing, increasing mental function, slowing the decrease of mental function, decreasing dementia, delaying the onset of dementia, improving cognitive skills, decreasing the loss of cognitive skills, improving memory, decreasing the degradation of memory, or extending survival; treat demyelinating diseases by reducing a symptom of demyelinating diseases or reducing the loss of myelin or increasing the amount of myelin or increasing the level of myelin; treat diabetes by decreasing a symptom of diabetes or decreasing loss of insulin producing cells or decreasing loss of pancreatic cells or reducing insulin insensitivity; treat cancer by decreasing a symptom of cancer, or treat neurodegeneration by treating a symptom of neurodegeneration. Symptoms of cancer (e.g. multiple myeloma, cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes would be known or may be determined by a person of ordinary skill in the art. The term "treating" and conjugations thereof, include prevention of an injury, pathology, condition, or disease (e.g. preventing the development of one or more symptoms of cancer, neurodegenerative diseases, demyelinating diseases, and/or diabetes).
[0120] An "effective amount" is an amount sufficient to accomplish a stated purpose (e.g.
achieve the effect for which it is administered, treat a disease, reduce enzyme activity, increase enzyme activity, reduce one or more symptoms of a disease or condition). An example of an "effective amount" is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a
"therapeutically effective amount." A "reduction" of a symptom or symptoms (and grammatical equivalents of this phrase) means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s). A "prophylactically effective amount" of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset (or reoccurrence) of an injury, disease, pathology or condition, or reducing the likelihood of the onset (or reoccurrence) of an injury, disease, pathology, or condition, or their symptoms. The full prophylactic effect does not necessarily occur by administration of one dose, and may occur only after administration of a series of doses. Thus, a prophylactically effective amount may be administered in one or more administrations. An "activity decreasing amount," as used herein, refers to an amount of antagonist (inhibitor) required to decrease the activity of an enzyme or protein relative to the absence of the antagonist. An "activity increasing amount," as used herein, refers to an amount of agonist (activator) required to increase the activity of an enzyme or protein relative to the absence of the agonist. A "function disrupting amount," as used herein, refers to the amount of antagonist (inhibitor) required to disrupt the function of an enzyme or protein relative to the absence of the antagonist. A "function increasing amount," as used herein, refers to the amount of agonist (activator) required to increase the function of an enzyme or protein relative to the absence of the agonist. The exact amounts will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); and Remington: The Science and Practice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott, Williams & Wilkins). [0121] The term "associated" or "associated with" in the context of a substance or substance activity or function associated with a disease (e.g cancer (e.g. multiple myeloma, cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes) means that the disease (e.g cancer (e.g. multiple myeloma, cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes) is caused by (in whole or in part), or a symptom of the disease is caused by (in whole or in part) the substance or substance activity or function. For example, a symptom of a disease or condition associated with an increase in Irel (e.g. Irela) activity may be a symptom that results (entirely or partially) from an increase in Irel (e.g. Irela) activity (e.g increase in Irel (e.g. Irela) phosphorylation or activity of phosphorylated Irel (e.g. Irela) or activity of Irel (e.g. Irela) or increase in activity of an Irel (e.g. Irela) signal transduction or signalling pathway, Irel (e.g. Irela) RNase activity). As used herein, what is described as being associated with a disease, if a causative agent, could be a target for treatment of the disease. For example, a disease associated with increased Irel (e.g. Irela) activity or Irel (e.g. Irela) pathway activity (e.g. phosphorylated Irel (e.g. Irela) activity or pathway), may be treated with an agent (e.g. compound as described herein) effective for decreasing the level of activity of Irel (e.g. Irela) activity or Irel (e.g. Irela) pathway or phosphorylated Irel (e.g. Irela) activity or pathway. For example, a disease associated with phosphorylated Irel (e.g. Irela), may be treated with an agent (e.g. compound as described herein) effective for decreasing the level of activity of
phosphorylated Irel (e.g. Irela) or a downstream component or effector of phosphorylated Irel (e.g. Irela). For example, a disease associated with Irel (e.g. Irela), may be treated with an agent (e.g. compound as described herein) effective for decreasing the level of activity of Irel (e.g. Irela) or a downstream component or effector of Irel (e.g. Irela). [0122] "Control" or "control experiment" is used in accordance with its plain ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects. [0123] "Contacting" is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g. chemical compounds including
biomolecules, or cells) to become sufficiently proximal to react, interact or physically touch. It should be appreciated, however, that the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture. The term "contacting" may include allowing two species to react, interact, or physically touch, wherein the two species may be a compound as described herein and a protein or enzyme (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Ire la) or component of Irel (e.g. Ire la) pathway or component of phosphorylated Irel (e.g. Irela) pathway). In some embodiments contacting includes allowing a compound described herein to interact with a protein or enzyme that is involved in a signaling pathway (e.g. Irel (e.g. Irela) protein or Irel (e.g. Irela) pathway). [0124] As defined herein, the term "inhibition", "inhibit", "inhibiting" and the like in reference to a protein-inhibitor (e.g. antagonist) interaction means negatively affecting (e.g. decreasing) the activity or function of the protein relative to the activity or function of the protein in the absence of the inhibitor. In some embodiments inhibition refers to reduction of a disease or symptoms of disease. In some embodiments, inhibition refers to a reduction in the activity of a signal transduction pathway or signaling pathway. Thus, inhibition includes, at least in part, partially or totally blocking stimulation, decreasing, preventing, or delaying activation, or inactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein. In some embodiments, inhibition refers to a decrease in the activity of a signal transduction pathway or signaling pathway (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) or Irel (e.g. Irela) pathway or phosphorylated Irel (e.g. Irela) pathway or pathway activated by Irel (e.g. Irela) phosphorylation). Thus, inhibition may include, at least in part, partially or totally decreasing stimulation, decreasing or reducing activation, or inactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein increased in a disease (e.g. level of Irel (e.g. Irela) activity or protein or level or activity of a component of an Irel (e.g. Irela) pathway or level of phosphorylated Irel (e.g. Irela) activity or protein or level or activity of a component of a phosphorylated Irel (e.g. Irela) pathway, wherein each is associated with cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes). Inhibition may include, at least in part, partially or totally decreasing stimulation, decreasing or reducing activation, or deactivating, desensitizing, or down-regulating signal transduction or enzymatic activity or the amount of a protein (e.g. Irel (e.g. Irela),
phosphorylated Irel (e.g. Irela), protein downstream in a pathway from Irel (e.g. Irela), protein downstream in a pathway activated by phosphorylated Irel (e.g. Irela)) that may modulate the level of another protein or increase cell survival (e.g. decrease in phosphorylated Irel (e.g. Irela) pathway activity may increase cell survival in cells that may or may not have an increase in phosphorylated Irel (e.g. Irela) pathway activity relative to a non-disease control or decrease in Irel (e.g. Irela) pathway activity may increase cell survival in cells that may or may not have a increase in Irel (e.g. Irela) pathway activity relative to a non-disease control). [0125] As defined herein, the term "activation", "activate", "activating" and the like in reference to a protein-activator (e.g. agonist) interaction means positively affecting (e.g.
increasing) the activity or function of the protein (e.g. Irel (e.g. Irela), phosphorylated Irel (e.g. Irela), component of pathway including Irel (e.g. Irela), or component of pathway including phosphorylated Irel (e.g. Irela)) relative to the activity or function of the protein in the absence of the activator (e.g. compound described herein). In some embodiments, activation refers to an increase in the activity of a signal transduction pathway or signaling pathway (e.g. Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway). Thus, activation may include, at least in part, partially or totally increasing stimulation, increasing or enabling activation, or activating, sensitizing, or up-regulating signal transduction or enzymatic activity or the amount of a protein decreased in a disease (e.g. level of Irel (e.g. Irela) activity or level of protein or activity decreased by phosphorylation of Irel (e.g. Irela) or protein associated with cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes). Activation may include, at least in part, partially or totally increasing stimulation, increasing or enabling activation, or activating, sensitizing, or up- regulating signal transduction or enzymatic activity or the amount of a protein (e.g. Irel (e.g. Irela), protein downstream of Irel (e.g. Irela), protein activated or upregulated by Irel (e.g. Irela), protein activated or upregulated by phosphorylation of Irel (e.g. Irela)) that may modulate the level of another protein or increase cell survival (e.g. increase in Irel (e.g. Irela) activity may increase cell survival in cells that may or may not have a reduction in Irel (e.g. Irela) activity relative to a non-disease control).
[0126] The term "modulator" refers to a composition that increases or decreases the level of a target molecule or the function of a target molecule. In some embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway or phosphorylation of Irel (e.g. Irela) or pathway activated by phorphorylation of Irel (e.g. Irela) is a compound that reduces the severity of one or more symptoms of a disease associated with Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. disease associated with an increase in the level of Irel (e.g. Irela) activity or protein or Irel (e.g. Irela) pathway activity or protein or Irel (e.g. Irela) phorphorylation or pathway activated by Irel (e.g. Irela) phosphorylation, for example cancer (e.g. multiple myeloma, or cancers of secretory cells), neurodegenerative diseases, demylelinating diseases, eye diseases, fibrotic diseases, or diabetes) or a disease that is not caused by Irel (e.g. Irela) or Irel (e.g. Irela) pathway but may benefit from modulation of Irel (e.g. Irela) or Irel (e.g. Irela) pathway activity (e.g. decreasing in level or level of activity of Irel (e.g. Irela) or Irel (e.g. Irela) pathway). In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is an anti-cancer agent. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e..g phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is a
neuroprotectant. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is an anti- demyelinating agent. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway is a memory enhancing agent. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is an anti-diabetic agent. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is an anti-eye disease agent. In embodiments, a modulator of Irel (e.g. Irela) or Irel (e.g. Irela) pathway (e.g. phosphorylated Irel (e.g. Irela) or phosphorylated Irel (e.g. Irela) pathway) is an anti-fibrosis agent. [0127] "Patient" or "subject in need thereof refers to a living organism suffering from or prone to a disease or condition that can be treated by administration of a compound or pharmaceutical composition, as provided herein. Non-limiting examples include humans, other mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals. In some embodiments, a patient is human. In some embodiments, a patient is an ape. In some embodiments, a patient is a monkey. In some embodiments, a patient is a mouse. In some embodiments, a patient is an experimental animal. In some embodiments, a patient is a rat. In some embodiments, a patient is a test animal. In some embodiments, a patient is a newborn animal. In some embodiments, a patient is a newborn human. In some embodiments, a patient is a juvenile animal. In some embodiments, a patient is a juvenile human. In some embodiments, a patient is a newborn mammal. In some embodiments, a patient is an elderly animal. In some embodiments, a patient is an elderly human. In some embodiments, a patient is an elderly mammal. In some embodiments, a patient is a geriatric patient.
[0128] "Disease" or "condition" refer to a state of being or health status of a patient or subject capable of being treated with a compound, pharmaceutical composition, or method provided herein. In some embodiments, the disease is a disease related to (e.g. caused by) an increase in the level of Irel (e.g. Irela), Irel (e.g. Irela) phosphorylation, Irel (e.g. Irela) RNase activity, or Irel (e.g. Irela) pathway activity, or pathway activated by phosphorylation of Irel (e.g.
Irela). In some embodiments, the disease is a disease related to (e.g. caused by) neurodegeneration. In some embodiments, the disease is a disease related to (e.g. caused by) neural cell death. In some embodiments, the disease is a disease related to (e.g. caused by) cell death. In some embodiments, the disease is a disease related to (e.g. caused by) pancreatic cell death. In some embodiments, the disease is a disease related to (e.g. caused by) insulin- producing cell death. In some embodiments, the disease is a disease related to (e.g. caused by) loss of myelin. In some embodiments, the disease is a disease related to (e.g. caused by) reduction in myelin. In some embodiments, the disease is a disease related to (e.g. caused by) an increase in the level of Irel (e.g. Irela) activity (e.g. R ase activity), Irel (e.g. Irela) phosphorylation, Irel (e.g. Irela) pathway activity, or phosphorylated Irel (e.g. Irela) pathway activity. In some embodiments, the disease is cancer (e.g. multiple myeloma or cancers of secretory cells). In some embodiments, the disease is a neurodegenerative disease. In some embodiments, the disease is a demyelinating disease. In some embodiments, the disease is diabetes. In some embodiments, the disease is an interstitial lung disease (ILD). In some embodiments, the disease is idiopathic pulmonary fibrosis (IPF). In some embodiments, the disease is a fibrotic disease. In some embodiments, the disease is an eye disease (e.g., disease causing vision impairment).
[0129] Examples of diseases, disorders, or conditions include, but are not limited to, cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, and diabetes. In some instances, "disease" or
"condition" refers to cancer. In some further instances, "cancer" refers to human cancers and carcinomas, sarcomas, adenocarcinomas, lymphomas, leukemias, melanomas, etc., including solid and lymphoid cancers, kidney, breast, lung, bladder, colon, ovarian, prostate, pancreas, stomach, brain, head and neck, skin, uterine, testicular, glioma, esophagus, liver cancer, including hepatocarcinoma, lymphoma, including B-acute lymphoblastic lymphoma, non- Hodgkin's lymphomas (e.g., Burkitt's, Small Cell, and Large Cell lymphomas), Hodgkin's lymphoma, leukemia (including AML, ALL, and CML), and/or multiple myeloma.
[0130] As used herein, the term "cancer" refers to all types of cancer, neoplasm or malignant tumors found in mammals, including leukemia, lymphoma, carcinomas and sarcomas.
Exemplary cancers that may be treated with a compound, pharmaceutical composition, or method provided herein include multiple myeloma, blood cancers, lymphoma, sarcoma, bladder cancer, bone cancer, brain tumor, cervical cancer, colon cancer, esophageal cancer, gastric cancer, head and neck cancer, kidney cancer, myeloma, thyroid cancer, leukemia, prostate cancer, breast cancer (e.g. ER positive, ER negative, chemotherapy resistant, herceptin resistant, HER2 positive, doxorubicin resistant, tamoxifen resistant, ductal carcinoma, lobular carcinoma, primary, metastatic), ovarian cancer, pancreatic cancer, liver cancer (e.g.hepatocellular carcinoma) , lung cancer (e.g. non-small cell lung carcinoma, squamous cell lung carcinoma, adenocarcinoma, large cell lung carcinoma, small cell lung carcinoma, carcinoid, sarcoma), glioblastoma multiforme, glioma, or melanoma. Additional examples include, cancer of the thyroid, endocrine system, brain, breast, cervix, colon, head & neck, liver, kidney, lung, non- small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus or Medulloblastoma, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, primary brain tumors, cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms of the endocrine or exocrine pancreas, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, Paget' s Disease of the Nipple,
Phyllodes Tumors, Lobular Carcinoma, Ductal Carcinoma, cancer of the pancreatic stellate cells, cancer of the hepatic stellate cells, or prostate cancer.
[0131] The term "leukemia" refers broadly to progressive, malignant diseases of the blood- forming organs and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemia is generally clinically classified on the basis of (1) the duration and character of the disease-acute or chronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid (lymphogenous), or monocytic; and (3) the increase or non-increase in the number abnormal cells in the blood-leukemic or aleukemic (subleukemic). Exemplary leukemias that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy- cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocyte leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblasts leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cell leukemia, multiple myeloma, plasmacytic leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia, or undifferentiated cell leukemia. [0132] The term "sarcoma" generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar or homogeneous substance. Sarcomas that may be treated with a compound, pharmaceutical composition, or method provided herein include a chondrosarcoma,
fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, or telangiectaltic sarcoma.
[0133] The term "melanoma" is taken to mean a tumor arising from the melanocytic system of the skin and other organs. Melanomas that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungal melanoma, or superficial spreading melanoma.
[0134] The term "carcinoma" refers to a malignant new growth made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases. Exemplary carcinomas that may be treated with a compound, pharmaceutical composition, or method provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, ductal carcinoma, carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiermoid carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma, gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare, glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroid carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma, lobular carcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullary carcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma, carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma, renal cell carcinoma of kidney, reserve cell carcinoma, carcinoma sarcomatodes, schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti, signet- ring cell carcinoma, carcinoma simplex, small-cell carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma, string carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, carcinoma tuberosum, tubular carcinoma, tuberous carcinoma, verrucous carcinoma, or carcinoma villosum.
[0135] As used herein, the term "neurodegenerative disease" refers to a disease or condition in which the function of a subject's nervous system becomes impaired (e.g. relative to a control subject who does not have the neurodegenerative disease). Examples of neurodegenerative diseases that may be treated with a compound, pharmaceutical composition, or method described herein include Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease (also known as Spielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiform encephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt- Jakob disease, frontotemporal dementia, Gerstmann- Straussler-Scheinker syndrome, Huntington's disease, HlV-associated dementia, Kennedy's disease, Krabbe's disease, kuru, Lewy body dementia, Machado-Joseph disease (Spinocerebellar ataxia type 3), Multiple sclerosis, Multiple System Atrophy, Narcolepsy, Neuroborreliosis, Parkinson's disease, Pelizaeus-Merzbacher Disease, Pick's disease, Primary lateral sclerosis, Prion diseases, Refsum's disease, Sandhoff s disease, Schilder's disease, Subacute combined degeneration of spinal cord secondary to Pernicious Anaemia, Schizophrenia, Spinocerebellar ataxia (multiple types with varying characteristics), Spinal muscular atrophy, Steele-Richardson- Olszewski disease, Wolfram Syndrome, transverse myelitis, Charcot-Marie-Tooth (CMT) disease, or Tabes dorsalis. Examples of neurodegenerative diseases that may be treated with a compound, pharmaceutical composition, or method described herein include retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration,
Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru.
[0136] As used herein, the term "demyelinating disease" refers to a disease or condition is which the myelin sheath of a subject's neurons is or becomes impaired (e.g. relative to a control subject who does not have the demyelinating disease). Examples of demyelinating disease that may be treated with a compound, pharmaceutical composition, or method described herein include Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot- Marie-Tooth Disease, and Multiple Sclerosis.
[0137] As used herein, the term "diabetes" or "diabetes mellitus" refers to a disease or condition is which a subject has high blood sugar. Examples of diabetes that may be treated with a compound, pharmaceutical composition, or method described herein include type I diabetes (type I diabetes mellitus), which is characterized by the subject's failure to produce insulin or failure to produce sufficient insulin for the subject's metabolic needs; type II diabetes (type II diabetes mellitus), which is characterized by insulin resistance (i.e. the failure of the subject (e.g. subject's cells) to use insulin properly; and gestational diabetes, which is high blood sugar during pregnancy. In embodiments, diabetes is type I diabetes. In embodiments, diabetes is type II diabetes. In embodiments, diabetes is gestational diabetes. In embodiments, diabetes is a disease or condition in which a subject has high blood sugar as determined by an AIC test (e.g. 6.5% or greater), fasting plasma glucose test (e.g. 126 mg/dL or greater), or oral glucose tolerance test (e.g. 200 mg/dL or greater). In embodiments, the diabetes is associated with Wolfram Syndrome. [0138] As used herein, the term "eye disease" or "disease causing vision impairment" refers to a disease or condition is which the function of a subject's eye or eyes is impaired (e.g. relative to a subject without the disease). Examples of eye diseases that may be treated with a compound, pharmaceutical composition, or method described herein include retinitis pigmentosa, retinal degeneration, macular degeneration, and Wolfram Syndrome.
[0139] As used herein, the term "fibrosis" refers to the formation of excess fibrous connective tissue. The term "fibrotic disease" refers to a disease or condition caused by aberrant fibrosis or a disease or condition in which a symptom is aberrant fibrosis (e.g. relative to a control subject without the disease). Examples of fibrotic diseases that may be treated with a compound, pharmaceutical composition, or method described herein include idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), and hepatic fibrosis.
[0140] The term "signaling pathway" as used herein refers to a series of interactions between cellular and optionally extra-cellular components (e.g. proteins, nucleic acids, small molecules, ions, lipids) that conveys a change in one component to one or more other components, which in turn may convey a change to additional components, which is optionally propagated to other signaling pathway components.
[0141] "Pharmaceutically acceptable excipient" and "pharmaceutically acceptable carrier" refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient. Non-limiting examples of pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer's, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer's solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, mannitol, gum acacia, calcium phosphate, alginates, tragacanth, calcium silicate, microcrystalline cellulose, cellulose, syrup, and methyl cellulose, colors, and the like. The formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl and propylhydroxy benzoates; sweetening agents; and flavoring agents. The compositions described herein can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art. Such preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the invention. One of skill in the art will recognize that other pharmaceutical excipients are useful in the present invention.
[0142] The term "preparation" is intended to include the formulation of the active compound with encapsulating material as a carrier providing a capsule in which the active component with or without other carriers, is surrounded by a carrier, which is thus in association with it.
Similarly, cachets and lozenges are included. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration.
[0143] As used herein, the term "administering" means administration by any route, including systemic, local, oral administration, administration as a suppository, topical contact, intravenous, parenteral, intraperitoneal, intramuscular, intralesional, intrathecal, intracranial, intranasal or subcutaneous administration, topical (including ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal), ocular, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to a subject. Parenteral administration includes, e.g., intravenous, intraarterial, intramuscular, intra-arteriole, intradermal, subcutaneous, intraperitoneal, intrathecal, intraventricular, and intracranial.
Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump. Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Methods for ocular delivery can include topical administration (eye drops), subconjunctival, periocular or intravitreal injection or introduction by balloon catheter or ophthalmic inserts surgically placed in the conjunctival sac. Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc. By "co-administer" it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies (e.g. anti-cancer agent, chemotherapeutic, treatment for an eye disease, treatment for fibrosis, treatment for a demyelinating disease, diabetes treatment, or treatment for a neurodegenerative disease). The compound of the invention can be administered alone or can be coadministered to the patient. The compositions (e.g. compounds) described herein can also be formulated in combination with one or more additional active ingredients which can include any pharmaceutical agent such as anti viral agents, vaccines, antibodies, immune enhancers, immune suppressants, anti inflammatory agents and the like. Coadministration is meant to include simultaneous or sequential administration of the compound individually or in combination (more than one compound or agent). Thus, the preparations can also be combined, when desired, with other active substances (e.g. to reduce metabolic degradation). The compositions of the present invention can be delivered by trans dermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols. Oral preparations include tablets, pills, powder, dragees, capsules, liquids, lozenges, cachets, gels, syrups, slurries, suspensions, etc., suitable for ingestion by the patient. Solid form preparations include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules. Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions. The compositions of the present invention may additionally include components to provide sustained release and/or comfort. Such components include high molecular weight, anionic mucomimetic polymers, gelling polysaccharides and finely-divided drug carrier substrates. These components are discussed in greater detail in U.S. Pat. Nos. 4,91 1,920; 5,403,841 ; 5,212,162; and 4,861,760. The entire contents of these patents are incorporated herein by reference in their entirety for all purposes. The compositions of the present invention can also be delivered as microspheres for slow release in the body. For example, microspheres can be administered via intradermal injection of drug-containing microspheres, which slowly release subcutaneously (see Rao, J. Biomater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gel formulations
(see, e.g., Gao Pharm. Res. 12:857-863, 1995); or, as microspheres for oral administration (see, e.g., Eyles, J. Pharm. Pharmacol. 49:669-674, 1997). In another embodiment, the formulations of the compositions of the present invention can be delivered by the use of liposomes which fuse with the cellular membrane or are endocytosed, i.e., by employing receptor ligands attached to the liposome, that bind to surface membrane protein receptors of the cell resulting in endocytosis. By using liposomes, particularly where the liposome surface carries receptor ligands specific for target cells, or are otherwise preferentially directed to a specific organ, one can focus the delivery of the compositions of the present invention into the target cells in vivo. (See, e.g., Al-Muhammed, J. Microencapsul. 13 :293-306, 1996; Chonn, Curr. Opin. Biotechnol. 6:698-708, 1995; Ostro, Am. J. Hosp. Pharm. 46: 1576-1587, 1989). The compositions of the present invention can also be delivered as nanoparticles.
[0144] Pharmaceutical compositions provided by the present invention include compositions wherein the active ingredient (e.g. compounds described herein, including embodiments or examples) is contained in a therapeutically effective amount, i.e., in an amount effective to achieve its intended purpose. The actual amount effective for a particular application will depend, inter alia, on the condition being treated. When administered in methods to treat a disease, such compositions will contain an amount of active ingredient effective to achieve the desired result, e.g., modulating the activity of a target molecule (e.g. Irel (e.g. Irel a) or component of Irel (e.g. Irel a) signal transduction pathway or component of phosphorylated Irel (e.g. Irel a) pathway), and/or reducing, eliminating, or slowing the progression of disease symptoms (e.g. symptoms of cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes). Determination of a therapeutically effective amount of a compound of the invention is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure herein.
[0145] The dosage and frequency (single or multiple doses) administered to a mammal can vary depending upon a variety of factors, for example, whether the mammal suffers from another disease, and its route of administration; size, age, sex, health, body weight, body mass index, and diet of the recipient; nature and extent of symptoms of the disease being treated (e.g. symptoms of cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes), kind of concurrent treatment, complications from the disease being treated or other health-related problems. Other therapeutic regimens or agents can be used in conjunction with the methods and compounds of Applicants' invention. Adjustment and manipulation of established dosages (e.g., frequency and duration) are well within the ability of those skilled in the art.
[0146] For any compound described herein, the therapeutically effective amount can be initially determined from cell culture assays. Target concentrations will be those concentrations of active compound(s) that are capable of achieving the methods described herein, as measured using the methods described herein or known in the art.
[0147] As is well known in the art, therapeutically effective amounts for use in humans can also be determined from animal models. For example, a dose for humans can be formulated to achieve a concentration that has been found to be effective in animals. The dosage in humans can be adjusted by monitoring compounds effectiveness and adjusting the dosage upwards or downwards, as described above. Adjusting the dose to achieve maximal efficacy in humans based on the methods described above and other methods is well within the capabilities of the ordinarily skilled artisan.
[0148] Dosages may be varied depending upon the requirements of the patient and the compound being employed. The dose administered to a patient, in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the patient over time. The size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects. Determination of the proper dosage for a particular situation is within the skill of the practitioner. Generally, treatment is initiated with smaller dosages which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached.
[0149] Dosage amounts and intervals can be adjusted individually to provide levels of the administered compound effective for the particular clinical indication being treated. This will provide a therapeutic regimen that is commensurate with the severity of the individual's disease state. [0150] Utilizing the teachings provided herein, an effective prophylactic or therapeutic treatment regimen can be planned that does not cause substantial toxicity and yet is effective to treat the clinical symptoms demonstrated by the particular patient. This planning should involve the careful choice of active compound by considering factors such as compound potency, relative bioavailability, patient body weight, presence and severity of adverse side effects, preferred mode of administration and the toxicity profile of the selected agent.
[0151] The compounds described herein can be used in combination with one another, with other active agents known to be useful in treating cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes, or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent.
[0152] In some embodiments, co-administration includes administering one active agent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a second active agent. Co-administration includes administering two active agents simultaneously, approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other), or sequentially in any order. In some embodiments, co-administration can be accomplished by co-formulation, i.e., preparing a single pharmaceutical composition including both active agents. In other embodiments, the active agents can be formulated separately. In another embodiment, the active and/or adjunctive agents may be linked or conjugated to one another. In some embodiments, the compounds described herein may be combined with treatments for cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, or diabetes, such as surgery.
[0153] The term "Irel" or "Ire la" or "ERN1" refers to the protein "Serine/threonine-protein kinase/endoribonuclease IRET'a.k.a. "Endoplasmic reticulum to nucleus signaling 1". In embodiments, "Irel" or "Irela" or "ERN1" refers to the human protein. Included in the term "Irel" or "Irela" or "ERN1" are the wildtype and mutant forms of the protein. In embodiments, "Irel" or "Irela" or "ERN1" refers to the protein associated with Entrez Gene 2081, OMIM
604033, UniProt 075460, and/or RefSeq (protein) NM_001433. In embodiments, the reference numbers immediately above refer to the protein, and associated nucleic acids, known as of the date of filing of this application. In embodiments, "Irel" or "Irela" or "ERN1" refers to the wildtype human protein. In embodiments, "Irel" or "Irela" or "ER 1" refers to the wildtype human nucleic acid.
[0154] "Anti-cancer agent" is used in accordance with its plain ordinary meaning and refers to a composition (e.g. compound, drug, antagonist, inhibitor, modulator) having antineoplastic properties or the ability to inhibit the growth or proliferation of cells. In some embodiments, an anti-cancer agent is a chemotherapeutic. In some embodiments, an anti-cancer agent is an agent identified herein having utility in methods of treating cancer. In some embodiments, an anticancer agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating cancer. Examples of anti-cancer agents include, but are not limited to, MEK inhibitors , alkylating agents, anti-metabolites, plant alkaloids, topoisomerase inhibitors, antitumor antibiotics, platinum-based compounds, adrenocortical suppressants,
epipodophyllotoxins, antibiotics, enzymes, inhibitors of mitogen-activated protein kinase signaling, antibodies, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec.RTM.), agents that arrest cells in the G2-M phases and/or modulate the formation or stability of microtubules (e.g. Taxol.TM (i.e. paclitaxel), steroids, aromatase inhibitors, gonadotropin- releasing hormone agonists (GnRH), adrenocorticosteroids, progestins, estrogens, antiestrogens, androgens, antiandrogens, immunotoxins, radioimmunotherapy, or the like. [0155] "Chemotherapeutic" or "chemotherapeutic agent" is used in accordance with its plain ordinary meaning and refers to a chemical composition or compound having antineoplastic properties or the ability to inhibit the growth or proliferation of cells.
[0156] Additionally, the compounds described herein can be co-administered with conventional immunotherapeutic agents including, but not limited to, immunostimulants (e.g., Bacillus Calmette-Guerin (BCG), levamisole, interleukin-2, alpha- interferon, etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti-VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33 monoclonal antibody-calicheamicin conjugate, anti- CD22 monoclonal antibody -pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy (e.g., anti-CD20 monoclonal antibody conjugated to mIn, 90Y, or 131I, etc.).
[0157] In a further embodiment, the compounds described herein can be co-administered with conventional radiotherapeutic agents including, but not limited to, radionuclides such as 47Sc, 64Cu, 67Cu, 89Sr, 86Y, 87Y, 90Y, 105Rh, mAg, mIn, 117mSn, 149Pm, 153Sm, 166Ho, 177Lu, 186Re,
188 211 212
Re, At, and Bi, optionally conjugated to antibodies directed against tumor antigens. [0158] "Anti-diabetic agent" or "antidiabetic agent" is used in accordance with its plain ordinary meaning and refers to a composition (e.g. compound, drug, antagonist, inhibitor, modulator) having the ability to lower blood glucose levels in a subject. In some embodiments, an anti-diabetic agent is an agent identified herein having utility in methods of treating diabetes. In some embodiments, an anti-diabetic agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating diabetes. Examples of antidiabetic agents include, but are not limited to, insulin, insulin sensitizers (e.g. biguanides (e.g. metformin, phenformin, or buformin), thiazolidinediones (e.g. rosiglitazone, pioglitazone, troglitazone)), secretagogues (e.g. sulfonylureas (e.g. tolbutamide, acetohexamide, tolazamide, chlorpropamide, glipizide, glyburide, glibenclamide, glimepiride, gliclazide, glycopyramide, gliquidone), meglitinides (e.g. repaglinide, nateglinide)), alpha-glucosidase inhibitors (e.g. miglitol, acarbose, voglibose), peptide analog antidiabetic agents (e.g. incretins (glucagon-like peptide- 1, gastric inhibitory peptide), glucagon-like peptide agonists (e.g. exenatide, liraglutide, taspoglutide), gastric inhibitoty peptide analogs, or dipeptidyl peptidase-4 inhibitors (e.g.
vildagliptin, sitagliptin, saxagliptin, linagliptin, allogliptin, septagliptin), amylin agonist analogues (e.g. pramlintide). B. COMPOSITIONS
[0159] In an aspect is provided a compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000060_0001
(I) wherein, ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; L1 is a bond or unsubstituted C1-C5 alkylene; L2 is a bond, -NR6a-, -0-, -S-, -C(O)-
, -S(O)-, -S(0)2-, -NR6aC(0)-, -C(0)(CH2)z2-, -C(0)NR6b-, -NR6aC(0)0-,
-NR6aC(0)NR6b-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R1 is hydrogen, oxo, halogen, -CX3, -CN, -S02C1, -SOnR10, -SOvNR7R8, -NHNH2, -ONR7R8, -NHC=(0)NHNH2,
-NHC=(0)NR7R8, -N(0)m, -NR7R8, -C(0)R9, -C(0)-OR9, -C(0)NR7R8, -OR10, -NR7SO„R10, - NR7C=(0)R9, -NR7C(0)OR9, -NR7OR9, -OCX3, -OCHX2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R2 is hydrogen, oxo, halogen, -CXa 3, -CN, -S02C1, -SOniR10a, -SOviNR7aR8a, -NHNH2, -ONR7aR8a, -NHC=(0)NHNH2,
-NHC=(0)NR7aR8a, -N(0)ml, -NR7aR8a, -C(0)R9a, -C(0)OR9a, -C(0)NR7aR8a, -OR10a, -
NR7aSO„iR10a, -NR7aC=(0)R9a, -NR7aC(0)OR9a, -NR7aOR9a, -OCXa 3, -OCHXa 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R3 is independently hydrogen, oxo,
halogen, -CXb 3, -CN, -S02C1, -SO„2R10b, -SOv2NR7bR8b, -NHNH2, -ONR7bR8b,
-NHC=(0)NHNH2,
-NHC=(0)NR7bR8b, -N(0)m2, -NR7bR8b, -C(0)R9b, -C(0)-OR9b, -C(0)NR7bR8b, -OR10b, - NR7bSO„2R10b, -NR7bC=(0)R9b, -NR7bC(0)OR9b, -NR7bOR9b, -OCXb 3, -OCHXb 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 and R5 are independently hydrogen or unsubstituted Ci-Ce alkyl; R7, R8, R9, R10, R6a, R7a, R8a, R9a, R10a, R6b, R7b, R8b, R9b and R10b are independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - S04H, -S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0)NH2, -NHS02H, - NHC=(0)H, -NHC(0)OH, -NHOH, -OCF3, -OCHF2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R7 and R8 substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7a and R8a substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7b and
8b
R substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4; each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2; the symbol z is an integer from 0 to 2; the symbol z2 is an integer from 1 to 4; and each occurrence of the symbols X, Xa, and Xb is independently a halogen.
[0160] In embodiments, ring A is substituted or unsubstituted monocyclic cycloalkylene, substituted or unsubstituted monocyclic heterocycloalkylene, substituted or unsubstituted monocyclic arylene, or substituted or unsubstituted monocyclic heteroarylene. In embodiments, ring A is substituted monocyclic cycloalkylene, substituted monocyclic heterocycloalkylene, substituted monocyclic arylene, or substituted monocyclic heteroarylene. In embodiments, ring A is unsubstituted monocyclic cycloalkylene, unsubstituted monocyclic heterocycloalkylene, unsubstituted monocyclic arylene, or unsubstituted monocyclic heteroarylene.
[0161] In embodiments, ring A is substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene. In embodiments, ring A is substituted C3-C8 cycloalkylene, substituted 3 to 8 membered heterocycloalkylene, substituted C6-C10 arylene, or substituted 5 to 10 membered heteroarylene. In embodiments, ring A is unsubstituted C3-C8 cycloalkylene, unsubstituted 3 to 8 membered heterocycloalkylene, unsubstituted C6-C10 arylene, or unsubstituted 5 to 10 membered heteroarylene. In
embodiments, ring A is substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene. In embodiments, ring A is substituted C3-C6 cycloalkylene, substituted 3 to 6 membered heterocycloalkylene, substituted C6-C10 arylene, or substituted 5 to 9 membered heteroarylene. In embodiments, ring A is unsubstituted C3-C6 cycloalkylene, unsubstituted 3 to 6 membered heterocycloalkylene, unsubstituted C6-C10 arylene, or unsubstituted 5 to 9 membered heteroarylene. [0162] In embodiments, ring A is substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene. In embodiments, ring A is substituted or unsubstituted C6-C10 arylene. In embodiments, ring A is unsubstituted naphthalenyl (i.e. divalent naphthalene moiety). In embodiments, ring A is substituted naphthalenyl. In embodiments, ring A is unsubstituted phenylene (divalent benzene moiety or benzene-di-yl). In embodiments, ring A is substituted phenylene (divalent benzene moiety or benzene-di-yl).
[0163] In embodiments, ring A is R41-substituted or unsubstituted cycloalkylene, R41- substituted or unsubstituted heterocycloalkylene, R41 -substituted or unsubstituted arylene, or R41- substituted or unsubstituted heteroarylene. In embodiments, ring A is substituted with 1 to 6 optionally different R41 substituents. In embodiments, ring A is substituted with 1 R41 substituent. In embodiments, ring A is substituted with 2 optionally different R41 substituents. In embodiments, ring A is substituted with 3 optionally different R41 substituents. In
embodiments, ring A is substituted with 4 optionally different R41 substituents. In embodiments, ring A is substituted with 5 optionally different R41 substituents. In embodiments, ring A is substituted with 6 optionally different R41 substituents. [0164] R41 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R42-substituted or unsubstituted alkyl, R42-substituted or unsubstituted heteroalkyl, R42-substituted or unsubstituted cycloalkyl, R42-substituted or unsubstituted heterocycloalkyl, R42-substituted or unsubstituted aryl, or R42-substituted or unsubstituted heteroaryl. In embodiments, R41 is -OCH3. [0165] R is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R43-substituted or unsubstituted alkyl, R43-substituted or unsubstituted heteroalkyl, R43-substituted or unsubstituted cycloalkyl, R43-substituted or unsubstituted heterocycloalkyl, R43-substituted or unsubstituted aryl, or R43-substituted or unsubstituted heteroaryl.
[0166] In embodiments, R1 is hydrogen, oxo,
halogen, -CX3, -CN, -S02C1, -SOnR10, -SOvNR7R8, -NHNH2, -ONR7R8, -NHC=(0)NHNH2, -NHC=(0)NR7R8, -N(0)m, -NR7R8, -C(0)R9, -C(0)-OR9, -C(0)NR7R8, -OR10, -NR7SO„R10, - NR7C=(0)R9, -NR7C(0)OR9, -NR7OR9, -OCX3, or -OCHX2.
[0167] In embodiments, R1 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R1 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R1 is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R1 is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, R1 is hydrogen. In embodiments, R1 is hydrogen and L2 is -NHC(O)-.
[0168] In embodiments, R1 is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-Cs cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- Cio aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, R1 is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
[0169] In embodiments, R1 is substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R1 is substituted or unsubstituted aryl or substituted or
unsubstituted heteroaryl. In embodiments, R1 is substituted phenyl. In embodiments, R1 is unsubstituted phenyl. In embodiments, R1 is phenyl substituted with -CF3 or halogen. In embodiments, R1 is phenyl meta-substituted with -CF3. In embodiments, R1 is phenyl meta- substituted with -F. In embodiments, R1 is phenyl meta-substituted with -CI. In embodiments, R1 is phenyl meta-substituted with -Br. In embodiments, R1 is phenyl meta-substituted with -I. In embodiments, R1 is phenyl meta-substituted with -CH3. In embodiments, R1
is -OPh, -CH2Ph, -OCH2Ph, -NHC(0)H, or -CHO. In embodiments, R1 is phenyl meta- substituted with -CC13. In embodiments, R1 is phenyl para-substituted with -CF3, - CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is phenyl meta- substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is phenyl ortho-substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is aryl meta-substituted with -CF3, - CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is aryl ortho- substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is aryl para-substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is aryl substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is heteroaryl substituted with -CF3, -
CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is phenyl substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is 5 to 6 membered heteroaryl substituted with -CF3, -CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO. In embodiments, R1 is unsubstituted cyclohexyl. In embodiments, R1 is substituted cyclohexyl. In embodiments, R1 is unsubstituted cyclopenyl. In embodiments, R1 is substituted cyclopenyl. In embodiments, R1 is unsubstituted cyclobutyl. In embodiments, R1 is substituted cyclobutyl. In embodiments, R1 is unsubstituted cyclopropyl. In embodiments, R1 is substituted cyclopropyl.
[0170] In embodiments, R1 is a substituted or unsubstituted heteroaryl selected from the group consisting of pyridinyl, pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl, benzothiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, furylthienyl, pyridyl, pyrimidyl, benzothiazolyl, purinyl, benzimidazolyl, isoquinolyl, thiadiazolyl, oxadiazolyl, pyrrolyl, diazolyl, triazolyl, tetrazolyl, benzothiadiazolyl, isothiazolyl, pyrazolopyrimidinyl, pyrrolopyrimidinyl, benzotriazolyl, benzoxazolyl, and quinolyl.
[0171] In some embodiments of the compounds provided herein, R1 is independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, - SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R11 -substituted or unsubstituted alkyl, R11- substituted or unsubstituted heteroalkyl, R11 -substituted or unsubstituted cycloalkyl, R11- substituted or unsubstituted heterocycloalkyl, R11 -substituted or unsubstituted aryl, or R11- substituted or unsubstituted heteroaryl. In embodiments, R1 is substituted with 1 to 6 optionally different R11 substituents. In embodiments, R1 is substituted with 1 R11 substituent. In embodiments, R1 is substituted with 2 optionally different R11 substituents. In embodiments, R1 is substituted with 3 optionally different R11 substituents. In embodiments, R1 is substituted with 4 optionally different R11 substituents. In embodiments, R1 is substituted with 5 optionally different R11 substituents. In embodiments, R1 is substituted with 6 optionally different R11 substituents. In embodiments, R1 is substituted with 7 optionally different R11 substituents. In embodiments, R1 is phenyl substituted with 1 to 5 optionally different R11 substituents. In embodiments, R1 is phenyl substituted with 1 R11 substituent. In embodiments, R1 is phenyl substituted with 2 optionally different R11 substituents. In embodiments, R1 is phenyl substituted with 3 optionally different R11 substituents. In embodiments, R1 is phenyl substituted with 4 optionally different R11 substituents. In embodiments, R1 is phenyl substituted with 5 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 1 to 6 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 1 R11 substituent. In embodiments, R1 is aryl substituted with 2 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 3 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 4 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 5 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 6 optionally different R11 substituents. In embodiments, R1 is aryl substituted with 7 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 1 to 6 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 1 R11 substituent. In
embodiments, R1 is heteroaryl substituted with 2 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 3 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 4 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 5 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 6 optionally different R11 substituents. In embodiments, R1 is heteroaryl substituted with 7 optionally different R11 substituents.
[0172] R11 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R12-substituted or unsubstituted alkyl, R12-substituted or unsubstituted heteroalkyl, R12-substituted or unsubstituted cycloalkyl, R12-substituted or unsubstituted heterocycloalkyl, R12-substituted or unsubstituted aryl, or R12-substituted or unsubstituted heteroaryl. In embodiments, R11 is -CCI3, -CF3, - CI, -OCF3, -CH3, -F, -OCH3, -OPh, -CH2Ph, or -CHO.
[0173] R12 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R13-substituted or unsubstituted alkyl, R13-substituted or unsubstituted heteroalkyl, R13-substituted or unsubstituted cycloalkyl, R13-substituted or unsubstituted heterocycloalkyl, R13-substituted or unsubstituted aryl, or R13-substituted or unsubstituted heteroaryl.
[0174] In embodiments, R2 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R2 is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R2 is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. [0175] In embodiments, R2 is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, R2 is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl. [0176] In embodiments, R2 is substituted or unsubstituted alkyl. In embodiments, R2 is substituted or unsubstituted Ci-Ce alkyl. In embodiments, R2 is unsubstituted Ci-Ce alkyl. In embodiments, R2 is unsubstituted methyl. In embodiments, R2 is unsubstituted isopropyl. In embodiments, R2 is unsubstituted ethyl. In embodiments, R2 is unsubstituted propyl (e.g. n- propyl or isopropyl). In embodiments, R2 is unsubstituted isopropyl. In embodiments, R2 is unsubstituted butyl (e.g. n-butyl, sec -butyl, isobutyl, or tert-butyl). In embodiments, R2 is unsubstituted tert-butyl. In embodiments, R2 is unsubstituted iso-butyl. In embodiments, R2 is unsubstituted pentyl (e.g. n-pentyl, tert-pentyl, neopentyl, isopentyl, sec-pentyl, or 3-pentyl). In embodiments, R2 is unsubstituted cyclopropyl. In embodiments, R2 is unsubstituted cyclobutyl. In embodiments, R2 is unsubstituted cyclopentyl. In embodiments, R2 is unsubstituted cyclohexyl.
[0177] In some embodiments, R2 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R14-substituted or unsubstituted alkyl, R14-substituted or unsubstituted heteroalkyl, R14-substituted or unsubstituted cycloalkyl, R14-substituted or unsubstituted heterocycloalkyl, R14-substituted or unsubstituted aryl, or R14-substituted or unsubstituted heteroaryl.
[0178] R14 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R15-substituted or unsubstituted alkyl, R15-substituted or unsubstituted heteroalkyl, R15-substituted or unsubstituted cycloalkyl, R15-substituted or unsubstituted heterocycloalkyl, R15-substituted or unsubstituted aryl, or R15-substituted or unsubstituted heteroaryl.
[0179] R15 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R16-substituted or unsubstituted alkyl, R16-substituted or unsubstituted heteroalkyl, R16-substituted or unsubstituted cycloalkyl, R16-substituted or unsubstituted heterocycloalkyl, R16-substituted or unsubstituted aryl, or R16-substituted or unsubstituted heteroaryl. [0180] In embodiments, R3 is independently hydrogen, oxo,
halogen, -CXb 3, -CN, -S02C1, -SO„2R10b, -SOv2NR7bR8b, -NHNH2, -ONR7bR8b,
-NHC=(0)NHNH2,
-NHC=(0)NR7bR8b, -N(0)m2, -NR7bR8b, -C(0)R9b, -C(0)-OR9b, -C(0)NR7bR8b, -OR10b, - NR7bSO„2R10b, -NR7bC=(0)R9b, -NR7bC(0)OR9b, -NR7bOR9b, -OCXb 3, or -OCHXb 2. In embodiments, R3 is independently hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R3 is independently hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R3 is independently hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.
[0181] In embodiments, R3 is independently hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3- Cs cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, R3 is independently hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted Ce- C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
[0182] In embodiments, R3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl. In embodiments, R3 is independently hydrogen. In embodiments, R3 is independently halogen.
[0183] In some embodiments, R3 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R17-substituted or unsubstituted alkyl, R17-substituted or unsubstituted heteroalkyl, R17-substituted or unsubstituted cycloalkyl, R17-substituted or unsubstituted heterocycloalkyl, R -substituted or unsubstituted aryl, or R -substituted or unsubstituted heteroaryl.
[0184] R17 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R18-substituted or unsubstituted alkyl, R18-substituted or unsubstituted heteroalkyl, R18-substituted or unsubstituted cycloalkyl, R18-substituted or unsubstituted heterocycloalkyl, R18-substituted or unsubstituted aryl, or R18-substituted or unsubstituted heteroaryl. [0185] R18 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R19-substituted or unsubstituted alkyl, R19-substituted or unsubstituted heteroalkyl, R19-substituted or unsubstituted cycloalkyl, R19-substituted or unsubstituted heterocycloalkyl, R19-substituted or unsubstituted aryl, or R19-substituted or unsubstituted heteroaryl.
[0186] In embodiments, R4 and R5 are independently hydrogen. In embodiments, R4 and R5 are independently unsubstituted C1-C6 alkyl. In embodiments, R4 and R5 are independently unsubstituted C1-C5 alkyl. In embodiments, R4 and R5 are independently unsubstituted C1-C4 alkyl. In embodiments, R4 and R5 are independently unsubstituted C1-C3 alkyl. In embodiments, R4 and R5 are independently unsubstituted Ci-C2 alkyl. In embodiments, R4 and R5 are independently unsubstituted methyl.
[0187] In embodiments, L1 is a bond. In embodiments, L1 is unsubstituted C1-C5 alkylene. In embodiments, L1 is unsubstituted C1-C4 alkylene. In embodiments, L1 is unsubstituted C1-C3 alkylene. In embodiments, L1 is unsubstituted Ci-C2 alkylene. In embodiments, L1 is unsubstituted methylene.
[0188] In embodiments, L2 is a bond. In embodiments, L2 is -NR6a-. In embodiments, L2 is -0-. In embodiments, L2 is -S-. In embodiments, L2 is -C(O)-. In embodiments, L2 is -S(O)-. In embodiments, L2 is -S(0)2-. In embodiments, L2 is -C(0)(CH2)z2-. In embodiments, L2 is -NR6aC(0)-. In embodiments, L2 is -C^NR*-. In embodiments, L2 is -NR6aC(0)0-. In embodiments, L2 is -NR6aC(0)NR6b-. In embodiments, L2 is -NH-. In embodiments, L2 is -NHC(O)-. In embodiments, L2 is -C(0)NH-. In embodiments, L2 is -NHC(0)NH-. In embodiments, L2 is -NHC(0)OCH2-. In embodiments, L2 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. In embodiments, L2 is -C(0)(CH2)-. In
embodiments, L2 is -C(0)(CH2)2-. In embodiments, L2 is -C(0)(CH2)3-. In embodiments, L2 is -C(0)(CH2)4-.
[0189] In embodiments, L2 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. In embodiments, L2 is substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, or substituted heteroarylene. In embodiments, L2 is unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, or unsubstituted heteroarylene.
[0190] In embodiments, L2 is substituted or unsubstituted Ci-C8 alkylene, substituted or unsubstituted 2 to 8 membered heteroalkylene, substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene. In
embodiments, L2 is substituted or unsubstituted C1-C6 alkylene, substituted or unsubstituted 2 to 6 membered heteroalkylene, substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.
[0191] In some embodiments, L2 is independently R44-substituted or unsubstituted alkylene, R44-substituted or unsubstituted heteroalkylene, R44-substituted or unsubstituted cycloalkylene, R44-substituted or unsubstituted heterocycloalkylene, R^-substituted or unsubstituted arylene, or R44-substituted or unsubstituted heteroarylene.
[0192] R44 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R45-substituted or unsubstituted alkyl, R45-substituted or unsubstituted heteroalkyl, R45-substituted or unsubstituted cycloalkyl, R45-substituted or unsubstituted heterocycloalkyl, R -substituted or unsubstituted aryl, or R -substituted or unsubstituted heteroaryl.
[0193] R45 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R46-substituted or unsubstituted alkyl, R46-substituted or unsubstituted heteroalkyl, R46-substituted or unsubstituted cycloalkyl, R46-substituted or unsubstituted heterocycloalkyl, R46-substituted or unsubstituted aryl, or R46-substituted or unsubstituted heteroaryl. [0194] In embodiments, R6a is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R6a is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R6a is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, R6a is hydrogen. In embodiments, R6a is unsubstituted methyl. In embodiments, R6a is unsubstituted ethyl. In embodiments, R6a is unsubstituted propyl.
[0195] In embodiments, R6a is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, R6a is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
[0196] In some embodiments of the compounds provided herein, R6a is independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, - SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R26a-substituted or unsubstituted alkyl, R26a- substituted or unsubstituted heteroalkyl, R26a-substituted or unsubstituted cycloalkyl, R26a- substituted or unsubstituted heterocycloalkyl, R a-substituted or unsubstituted aryl, or R a- substituted or unsubstituted heteroaryl.
[0197] R26a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R27a-substituted or unsubstituted alkyl, R27a-substituted or unsubstituted heteroalkyl, R27a-substituted or unsubstituted cycloalkyl, R27a-substituted or unsubstituted heterocycloalkyl, R27a-substituted or unsubstituted aryl, or R27a-substituted or unsubstituted heteroaryl. [0198] R27a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R28a-substituted or unsubstituted alkyl, R28a-substituted or unsubstituted heteroalkyl, R28a-substituted or unsubstituted cycloalkyl, R28a-substituted or unsubstituted heterocycloalkyl, R28a-substituted or unsubstituted aryl, or R28a-substituted or unsubstituted heteroaryl.
[0199] In embodiments, R6b is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, R6b is hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, R6b is hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, R6b is hydrogen. In embodiments, R* is unsubstituted methyl. In embodiments, R6b is unsubstituted ethyl. In embodiments, R6b is unsubstituted propyl.
[0200] In embodiments, R6b is hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted Ce- C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, R6b is hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
[0201] In some embodiments of the compounds provided herein, R* is independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -SO2CI, -SO3H, - SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, -NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R26b-substituted or unsubstituted alkyl, R26b- substituted or unsubstituted heteroalkyl, R26b-substituted or unsubstituted cycloalkyl, R26b- substituted or unsubstituted heterocycloalkyl, R26b-substituted or unsubstituted aryl, or R26b- substituted or unsubstituted heteroaryl. [0202] R26b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R27b-substituted or unsubstituted alkyl, R27b-substituted or unsubstituted heteroalkyl, R27b-substituted or unsubstituted cycloalkyl, R27b-substituted or unsubstituted heterocycloalkyl, R27b-substituted or unsubstituted aryl, or R27b-substituted or unsubstituted heteroaryl.
[0203] R27b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R28b-substituted or unsubstituted alkyl, R28b-substituted or unsubstituted heteroalkyl, R28b-substituted or unsubstituted cycloalkyl, R28b-substituted or
28b 28b
unsubstituted heterocycloalkyl, R -substituted or unsubstituted aryl, or R -substituted or unsubstituted heteroaryl.
[0204] In embodiments, each R7, R8, R9, R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, each R7, R8, R9, R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen, substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl. In embodiments, each R7, R8, R9,
R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, each R7, R8, R9, R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen.
[0205] In embodiments, each R7, R8, R9, R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen, substituted or unsubstituted Ci-Cs alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, each R7, R8, R9, R10, R7a, R8a, R9a, R10a, R7b, R8b, R9b and R10b is independently hydrogen, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or
unsubstituted C3-C6 cycloalkyl, substituted or unsubstituted 3 to 6 membered heterocycloalkyl, substituted or unsubstituted C6-C10 aryl, or substituted or unsubstituted 5 to 9 membered heteroaryl.
[0206] In some embodiments, R7 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R29-substituted or unsubstituted alkyl, R29-substituted or unsubstituted heteroalkyl, R29-substituted or unsubstituted cycloalkyl, R29-substituted or unsubstituted heterocycloalkyl, R29-substituted or unsubstituted aryl, or R29-substituted or unsubstituted heteroaryl. In embodiments, R7 and R8 substituents bonded to the same nitrogen atom may be joined to form an R29-substituted or unsubstituted heterocycloalkyl or R29- substituted or unsubstituted heteroaryl.
[0207] R29 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R30-substituted or unsubstituted alkyl, R30-substituted or unsubstituted heteroalkyl, R30-substituted or unsubstituted cycloalkyl, R30-substituted or unsubstituted heterocycloalkyl, R30-substituted or unsubstituted aryl, or R30-substituted or unsubstituted heteroaryl.
[0208] R30 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R31-substituted or unsubstituted alkyl, R31-substituted or unsubstituted heteroalkyl, R31 -substituted or unsubstituted cycloalkyl, R31-substituted or unsubstituted heterocycloalkyl, R31-substituted or unsubstituted aryl, or R31-substituted or unsubstituted heteroaryl.
[0209] In some embodiments, R7a is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R29a-substituted or unsubstituted alkyl, R29a-substituted or unsubstituted heteroalkyl, R29a-substituted or unsubstituted cycloalkyl, R29a-substituted or unsubstituted heterocycloalkyl, R29a-substituted or unsubstituted aryl, or R29a-substituted or unsubstituted heteroaryl. In embodiments, R7a and R8a substituents bonded to the same nitrogen atom may be joined to form an R29a-substituted or unsubstituted heterocycloalkyl or R29a- substituted or unsubstituted heteroaryl.
[0210] R29a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R30a-substituted or unsubstituted alkyl, R30a-substituted or unsubstituted heteroalkyl, R30a-substituted or unsubstituted cycloalkyl, R30a-substituted or unsubstituted heterocycloalkyl, R30a-substituted or unsubstituted aryl, or R30a-substituted or unsubstituted heteroaryl. [0211] R30a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R31a-substituted or unsubstituted alkyl, R31a-substituted or unsubstituted heteroalkyl, R31a-substituted or unsubstituted cycloalkyl, R31a-substituted or unsubstituted heterocycloalkyl, R31a-substituted or unsubstituted aryl, or R31a-substituted or unsubstituted heteroaryl.
[0212] In some embodiments, R7b is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R29b-substituted or unsubstituted alkyl, R29b-substituted or unsubstituted heteroalkyl, R29b-substituted or unsubstituted cycloalkyl, R29b-substituted or unsubstituted heterocycloalkyl, R29b-substituted or unsubstituted aryl, or R29b-substituted or unsubstituted heteroaryl. In embodiments, R and R substituents bonded to the same nitrogen atom may be joined to form an R29b-substituted or unsubstituted heterocycloalkyl or R29b- substituted or unsubstituted heteroaryl.
[0213] R29b is independently 0X0,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R30b-substituted or unsubstituted alkyl, R30b-substituted or unsubstituted heteroalkyl, R30b-substituted or unsubstituted cycloalkyl, R30b-substituted or unsubstituted heterocycloalkyl, R30b-substituted or unsubstituted aryl, or R30b-substituted or unsubstituted heteroaryl.
[0214] R30b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R31b-substituted or unsubstituted alkyl, R31b-substituted or unsubstituted heteroalkyl, R31b-substituted or unsubstituted cycloalkyl, R31b-substituted or unsubstituted heterocycloalkyl, R31b-substituted or unsubstituted aryl, or R31b-substituted or unsubstituted heteroaryl.
[0215] In some embodiments, R8 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R32-substituted or unsubstituted alkyl, R32-substituted or unsubstituted heteroalkyl, R32-substituted or unsubstituted cycloalkyl, R32-substituted or unsubstituted heterocycloalkyl, R32-substituted or unsubstituted aryl, or R32-substituted or unsubstituted heteroaryl. In embodiments, R7 and R8 substituents bonded to the same nitrogen atom may be joined to form an R32-substituted or unsubstituted heterocycloalkyl or R32- substituted or unsubstituted heteroaryl.
[0216] R32 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R33-substituted or unsubstituted alkyl, R33-substituted or unsubstituted heteroalkyl, R33-substituted or unsubstituted cycloalkyl, R33-substituted or unsubstituted heterocycloalkyl, R -substituted or unsubstituted aryl, or R -substituted or unsubstituted heteroaryl.
[0217] R33 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R34-substituted or unsubstituted alkyl, R34-substituted or unsubstituted heteroalkyl, R34-substituted or unsubstituted cycloalkyl, R34-substituted or unsubstituted heterocycloalkyl, R34-substituted or unsubstituted aryl, or R34-substituted or unsubstituted heteroaryl. [0218] In some embodiments, R8a is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R32a-substituted or unsubstituted alkyl, R32a-substituted or unsubstituted heteroalkyl, R32a-substituted or unsubstituted cycloalkyl, R32a-substituted or unsubstituted heterocycloalkyl, R32a-substituted or unsubstituted aryl, or R32a-substituted or unsubstituted heteroaryl. In embodiments, R7a and R8a substituents bonded to the same nitrogen atom may be joined to form an R32a-substituted or unsubstituted heterocycloalkyl or R32a- substituted or unsubstituted heteroaryl.
[0219] R32a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R33a-substituted or unsubstituted alkyl, R33a-substituted or unsubstituted heteroalkyl, R33a-substituted or unsubstituted cycloalkyl, R33a-substituted or unsubstituted heterocycloalkyl, R33a-substituted or unsubstituted aryl, or R33a-substituted or unsubstituted heteroaryl.
[0220] R33a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R34a-substituted or unsubstituted alkyl, R34a-substituted or unsubstituted heteroalkyl, R34a-substituted or unsubstituted cycloalkyl, R34a-substituted or unsubstituted heterocycloalkyl, R34a-substituted or unsubstituted aryl, or R34a-substituted or unsubstituted heteroaryl. [0221] In some embodiments, R is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R32b-substituted or unsubstituted alkyl, R32b-substituted or unsubstituted heteroalkyl, R32b-substituted or unsubstituted cycloalkyl, R32b-substituted or unsubstituted heterocycloalkyl, R32b-substituted or unsubstituted aryl, or R32b-substituted or unsubstituted heteroaryl. In embodiments, R7b and R8b substituents bonded to the same nitrogen atom may be joined to form an R32b-substituted or unsubstituted heterocycloalkyl or R32b- substituted or unsubstituted heteroaryl. [0222] R32b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R33b-substituted or unsubstituted alkyl, R33b-substituted or unsubstituted heteroalkyl, R33b-substituted or unsubstituted cycloalkyl, R33b-substituted or unsubstituted heterocycloalkyl, R33b-substituted or unsubstituted aryl, or R33b-substituted or unsubstituted heteroaryl.
[0223] R33b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R34b-substituted or unsubstituted alkyl, R34b-substituted or unsubstituted heteroalkyl, R34b-substituted or unsubstituted cycloalkyl, R34b-substituted or unsubstituted heterocycloalkyl, R34b-substituted or unsubstituted aryl, or R34b-substituted or unsubstituted heteroaryl.
[0224] In some embodiments, R9 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R35-substituted or unsubstituted alkyl, R35-substituted or unsubstituted heteroalkyl, R35-substituted or unsubstituted cycloalkyl, R35-substituted or unsubstituted heterocycloalkyl, R35-substituted or unsubstituted aryl, or R35-substituted or unsubstituted heteroaryl.
[0225] R35 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R36-substituted or unsubstituted alkyl, R36-substituted or unsubstituted heteroalkyl, R36-substituted or unsubstituted cycloalkyl, R36-substituted or unsubstituted heterocycloalkyl, R36-substituted or unsubstituted aryl, or R36-substituted or unsubstituted heteroaryl.
[0226] R36 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R37-substituted or unsubstituted alkyl, R37-substituted or unsubstituted heteroalkyl, R37-substituted or unsubstituted cycloalkyl, R37-substituted or unsubstituted heterocycloalkyl, R37-substituted or unsubstituted aryl, or R37-substituted or unsubstituted heteroaryl.
[0227] In some embodiments, R9a is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R35a-substituted or unsubstituted alkyl, R35a-substituted or unsubstituted heteroalkyl, R35a-substituted or unsubstituted cycloalkyl, R35a-substituted or unsubstituted heterocycloalkyl, R35a-substituted or unsubstituted aryl, or R35a-substituted or unsubstituted heteroaryl. [0228] R35a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R36a-substituted or unsubstituted alkyl, R36a-substituted or unsubstituted heteroalkyl, R36a-substituted or unsubstituted cycloalkyl, R36a-substituted or unsubstituted heterocycloalkyl, R36a-substituted or unsubstituted aryl, or R36a-substituted or unsubstituted heteroaryl.
[0229] R36a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R37a-substituted or unsubstituted alkyl, R37a-substituted or unsubstituted heteroalkyl, R37a-substituted or unsubstituted cycloalkyl, R37a-substituted or unsubstituted heterocycloalkyl, R a-substituted or unsubstituted aryl, or R a-substituted or unsubstituted heteroaryl.
[0230] In some embodiments, R9b is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R35b-substituted or unsubstituted alkyl, R35b-substituted or unsubstituted heteroalkyl, R35b-substituted or unsubstituted cycloalkyl, R35b-substituted or unsubstituted heterocycloalkyl, R35b-substituted or unsubstituted aryl, or R35b-substituted or unsubstituted heteroaryl. [0231] R35b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R36b-substituted or unsubstituted alkyl, R36b-substituted or unsubstituted heteroalkyl, R36b-substituted or unsubstituted cycloalkyl, R36b-substituted or unsubstituted heterocycloalkyl, R36b-substituted or unsubstituted aryl, or R36b-substituted or unsubstituted heteroaryl.
[0232] R36b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R37b-substituted or unsubstituted alkyl, R37b-substituted or unsubstituted heteroalkyl, R37b-substituted or unsubstituted cycloalkyl, R37b-substituted or unsubstituted heterocycloalkyl, R37b-substituted or unsubstituted aryl, or R37b-substituted or unsubstituted heteroaryl.
[0233] In some embodiments, R10 is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R38-substituted or unsubstituted alkyl, R38-substituted or unsubstituted heteroalkyl, R38-substituted or unsubstituted cycloalkyl, R38-substituted or unsubstituted heterocycloalkyl, R38-substituted or unsubstituted aryl, or R38-substituted or unsubstituted heteroaryl. [0234] R is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R39-substituted or unsubstituted alkyl, R39-substituted or unsubstituted heteroalkyl, R39-substituted or unsubstituted cycloalkyl, R39-substituted or unsubstituted heterocycloalkyl, R39-substituted or unsubstituted aryl, or R39-substituted or unsubstituted heteroaryl.
[0235] R39 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R40-substituted or unsubstituted alkyl, R40-substituted or unsubstituted heteroalkyl, R40-substituted or unsubstituted cycloalkyl, R40-substituted or unsubstituted heterocycloalkyl, R40-substituted or unsubstituted aryl, or R40-substituted or unsubstituted heteroaryl. [0236] In some embodiments, R10a is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R38a-substituted or unsubstituted alkyl, R38a-substituted or unsubstituted heteroalkyl, R38a-substituted or unsubstituted cycloalkyl, R38a-substituted or unsubstituted heterocycloalkyl, R38a-substituted or unsubstituted aryl, or R38a-substituted or unsubstituted heteroaryl.
[0237] R38a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R39a-substituted or unsubstituted alkyl, R39a-substituted or unsubstituted heteroalkyl, R39a-substituted or unsubstituted cycloalkyl, R39a-substituted or unsubstituted heterocycloalkyl, R39a-substituted or unsubstituted aryl, or R39a-substituted or unsubstituted heteroaryl.
[0238] R39a is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R4Ua-substituted or unsubstituted alkyl, R4Ua-substituted or unsubstituted heteroalkyl, R40a-substituted or unsubstituted cycloalkyl, R40a-substituted or unsubstituted heterocycloalkyl, R40a-substituted or unsubstituted aryl, or R40a-substituted or unsubstituted heteroaryl. [0239] In some embodiments, R10b is independently hydrogen,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R38b-substituted or unsubstituted alkyl, R38b-substituted or unsubstituted heteroalkyl, R38b-substituted or unsubstituted cycloalkyl, R38b-substituted or
38b 38b
unsubstituted heterocycloalkyl, R -substituted or unsubstituted aryl, or R -substituted or unsubstituted heteroaryl.
[0240] R38b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R39b-substituted or unsubstituted alkyl, R39b-substituted or unsubstituted heteroalkyl, R39b-substituted or unsubstituted cycloalkyl, R39b-substituted or unsubstituted heterocycloalkyl, R39b-substituted or unsubstituted aryl, or R39b-substituted or unsubstituted heteroaryl.
[0241] R39b is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R40b-substituted or unsubstituted alkyl, R40b-substituted or unsubstituted heteroalkyl, R40b-substituted or unsubstituted cycloalkyl, R40b-substituted or unsubstituted heterocycloalkyl, R40b-substituted or unsubstituted aryl, or R40b-substituted or unsubstituted heteroaryl.
[0242] In embodiments, v is 1. In embodiments, v is 2. In embodiments, vl is 1. In embodiments, vl is 2. In embodiments, v2 is 1. In embodiments, v2 is 2. In embodiments, m is
1. In embodiments, m is 2. In embodiments, ml is 1. In embodiments, ml is 2. In
embodiments, m2 is 1. In embodiments, m2 is 2. In embodiments, n is independently 0. In embodiments, n is independently 1. In embodiments, n is independently 2. In embodiments, n is independently 3. In embodiments, n is independently 4. In embodiments, nl is independently 0.
In embodiments, nl is independently 1. In embodiments, nl is independently 2. In embodiments, nl is independently 3. In embodiments, nl is independently 4. In embodiments, n2 is independently 0. In embodiments, n2 is independently 1. In embodiments, n2 is independently 2. In embodiments, n2 is independently 3. In embodiments, n2 is independently 4. In embodiments, X is -CI. In embodiments, X is -Br. In embodiments, X is -I. In embodiments, X is -F. In embodiments, Xa is -CI. In embodiments, Xa is -Br. In embodiments, Xa is -I. In embodiments, Xa is -F. In embodiments, Xb is -CI. In embodiments, Xb is -Br. In embodiments, Xb is -I. In embodiments, Xb is -F. In embodiments, z is 0. In embodiments, z is 1. In embodiments, z is 2. In embodiments, z2 is 1. In embodiments, z2 is 2. In embodiments, z2 is 3. In embodiments, z2 is 4. [0243] In embodiments, the compound has the formula:
Figure imgf000083_0001
are as described herein (e.g. compounds of formula I, including embodiments).
[0244] L3 is a bond, -0-, -NR*-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
[0245] In embodiments, L3 is a bond. In embodiments, L3 is -NR6b-, wherein R6b is as defined herein including embodiments thereof. In embodiments, L3 is -NH-. In embodiments, L3 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. In embodiments, L3 is -0-. . In embodiments, L3 is -OCH2-.
[0246] In embodiments, L3 is substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. In embodiments, L3 is substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, or substituted heteroarylene. In embodiments, L3 is unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, or unsubstituted heteroarylene. [0247] In embodiments, L3 is substituted or unsubstituted Ci-C8 alkylene, substituted or unsubstituted 2 to 8 membered heteroalkylene, substituted or unsubstituted C3-C8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene. In
embodiments, L3 is substituted or unsubstituted Ci-Ce alkylene, substituted or unsubstituted 2 to 6 membered heteroalkylene, substituted or unsubstituted C3-C6 cycloalkylene, substituted or unsubstituted 3 to 6 membered heterocycloalkylene, substituted or unsubstituted C6-C10 arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.
[0248] In some embodiments, L3 is independently R47-substituted or unsubstituted alkylene, R47-substituted or unsubstituted heteroalkylene, R47-substituted or unsubstituted cycloalkylene, R47-substituted or unsubstituted heterocycloalkylene, R47-substituted or unsubstituted arylene, or R47-substituted or unsubstituted heteroarylene.
[0249] R47 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, _NHC=(0) NH2, -NHS02H, -NHC= (0)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R48-substituted or unsubstituted alkyl, R48-substituted or unsubstituted heteroalkyl, R48-substituted or unsubstituted cycloalkyl, R48-substituted or unsubstituted heterocycloalkyl, R48-substituted or unsubstituted aryl, or R48-substituted or unsubstituted heteroaryl.
[0250] R48 is independently oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, -
S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, R49-substituted or unsubstituted alkyl, R49-substituted or unsubstituted heteroalkyl, R49-substituted or unsubstituted cycloalkyl, R49-substituted or unsubstituted heterocycloalkyl, R49-substituted or unsubstituted aryl, or R49-substituted or unsubstituted heteroaryl. [0251] Each R13, R16, R19, R28a, R28b, R31, R31a, R31b, R34, R34a, R34b, R37, R37a, R37b, R40, R40a, R40b, R43, R46, and R49 is independently a hydrogen, oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NH H2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, -OCHF2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In embodiments, each R13, R16, R19, R28a, R28b, R31, R31a, R31b, R34, R34a, R34b, R37, R37a, R37b, R40, R40a, R40b, R43, R46, and R49 is independently hydrogen, unsubstituted Ci-C8 alkyl, unsubstituted 2 to 8 membered heteroalkyl, unsubstituted C3-C8 cycloalkyl, unsubstituted 3 to 8 membered heterocycloalkyl, unsubstituted C6-C10 aryl, or unsubstituted 5 to 10 membered heteroaryl. In embodiments, each R13, R16, R19, R28a, R28b, R31, R31a, R31b, R34, R34a, R34b, R37, R37a, R37b, R40, R40a, R40b, R43, R46, and R49 is independently hydrogen, unsubstituted Ci-C6 alkyl, unsubstituted 2 to 6 membered heteroalkyl, unsubstituted C3-C6 cycloalkyl, unsubstituted 3 to 6 membered heterocycloalkyl, unsubstituted C6-C10 aryl, or unsubstituted 5 to 9 membered heteroaryl. In embodiments, each R13, R16, R19, R28a, R28b, R31, R31a, R31b, R34, R34a, R34b, R37, R37a, R37b, R40, R40a, R40b, R43, R46, and R49 is hydrogen, oxo,
halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -S04H, - S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0) NH2, -NHS02H, -NHC= (O)H, - NHC(0)-OH, -NHOH, -OCF3, or -OCHF2. [0252] In embodiments, the compound has the formula:
Figure imgf000085_0001
(III) wherein, R1, R2, R3, R6a, L3, and ring A are as described herein (e.g. compounds of formula I or II, including embodiments).
Figure imgf000086_0001
[0254] In embodiments, the compound is an inhibitor of Irel . In embodiments, the compound is an inhibitor of Ire la. In embodiments, the compound is an inhibitor of Ire la kinase activity. In embodiments, the compound is an inhibitor of Ire la RNase activity. In embodiments, the compound binds the ATP binding site of Ire la. In embodiments, the compound binds Ire la in the DFG-out conformation. In embodiments, the compound induces the DFG-out conformation of Irel a. In embodiments, the compound is an inhibitor of Ire la oligomerization. In embodiments, the compound is an inhibitor of Ire la dimerization. In embodiments, the compound is an inhibitor of Irela phosphorylation. In embodiments, the compound is an inhibitor of Irela autophosphorylation. In embodiments, the compound is an inhibitor of apoptosis. In embodiments, the compound is an inhibitor of Irela induced apoptosis. In embodiments, the compound is an inhibitor of cell death. In embodiments, the compound is an inhibitor of Irela induced cell death. In embodiments, the compound is an inhibitor of a pathway induced by Irela phosphorylation. In embodiments, the compound is an inhibitor of a pathway induced by Irela kinase activity. In embodiments, the compound is an inhibitor of a pathway induced by Irela RNase activity. In embodiments, the compound is an inhibitor of neuronal cell death. In embodiments, the compound is a cytotoxic agent. In embodiments, the compound is an anti-cancer agent. In embodiments, the compound is an inhibitor of
demyelination. In embodiments, the compound is an inhibitor of diabetes. In embodiments, the compound is an anti-diabetic agent. In embodiments, the compound is a neuroprotective agent. In embodiments, the compound is an inhibitor of fibrosis. In embodiments, the compound decreases apoptosis in cells under ER stress. In embodiments, the compound decreases apoptosis in cells under ER stress but not cells under the same conditions except that they are not under ER stress. In embodiments, the compound decreases apoptosis in cells under ER stress more than in cells under the same conditions except that they are not under ER stress. In embodiments, the compound decreases cleavage of miR-17. In embodiments, the compound decreases Irela associated cleavage of miR-17. In embodiments, the compound decreases cleavage of miR-34a. In embodiments, the compound decreases Irela associated cleavage of miR-34a. In embodiments, the compound decreases cleavage of miR-96. In embodiments, the compound decreases Irela associated cleavage of miR-96. In embodiments, the compound decreases cleavage of miR-125b. In embodiments, the compound decreases Irela associated cleavage of miR- 125b. In embodiments, the compound decreases XBP 1 mRNA splicing. In embodiments, the compound decreases Irela associated XBP1 mRNA splicing. In
embodiments, the compound decreases the UPR. In embodiments, the compound decreases Irela associated UPR. In embodiments, the compound decreases the terminal UPR. In embodiments, the compound decreases Irela associated terminal UPR. [0255] In embodiments, the compound is a compound described herein, including in an aspect, embodiment, example, figure, table, or claim. In embodiments, the compound is a compound in Fig. 8.
[0256] In embodiments, the compounds set forth herein are provided as pharmaceutical compositions including the compound, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In embodiments, the compounds set forth herein are not provided as pharmaceutical compositions. In embodiments, the compound is included in a pharmaceutically acceptable salt. In embodiments, the compound is not included in a pharmaceutically acceptable salt.
[0257] Described herein, inter alia, is a new strategy to: (1) inhibit IREl 's hyperactive RNase by pharmacologically targeting its neighboring kinase domain with small molecules, and (2) test physiological benefits of shutting down IRElcc in cells (e.g. β-cells) of living mammals (e.g. mice). This work validates IRElcc as a drug target to manipulate ER stress signaling to control cell fate.
[0258] In another aspect, provided herein are compounds having the formula (A):
d
Figure imgf000088_0001
(also illustrated in Fig. 7) and pharmaceutically acceptable salts thereof, wherein R , R , R , R4d, R5d, R6d, R7d, R8d, R9d, and R10d, are each independently C2_6 alkyl, Ci_6 haloalkyl, -C1-4 alkyl-R12d, C2_6 alkenyl, C2_6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two Rl ld groups; each Rl ld is independently Ci_6 alkyl, Ci_6 haloalkyl, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, S(0)2NRd 2, or -S(0)2Rd; and R12d is - ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, OC(0)ORd, OC(0)NRd 2, -N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; and each Rd is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci-6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl,each Rd is independently hydrogen, or Ci_6 alkyl.
[0259] In another aspect, provided herein are compounds having the formula (A) Formula (A)
Figure imgf000089_0001
(also illustrated in Fig. 7) and pharmaceutically acceptable salts thereof, wherein R , R , R , R4d, R5d, R6d, R7d, R8d, R9d, and R10d, are each independently C2_6 alkyl, Ci_6 haloalkyl, -Ci_4 alkyl-R12d, C2_6 alkenyl, C2_6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two Rl ld groups; each Rl ld is independently Ci_6 alkyl, Ci_6 haloalkyl, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, S(0)2NRd 2, or -S(0)2Rd; and R12d is - ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, OC(0)ORd, OC(0)NRd 2, -N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; and each Rd is independently hydrogen, C1-6 alkyl, C2.6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl. In embodiments, each Rd is independently hydrogen or Ci-6 alkyl.
[0260] In another aspect, R2d and R3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(O) Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0) Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; wherein each Rd is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or C1-6 alkyl,each Rd is inpendently hydrogen, or Ci_6 alkyl.
[0261] In another aspect, R2d and R3d are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci-6 haloalkyl, -ORd, -SRd, -NRd2, -C(O) Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(O) Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0) Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; wherein each Rd is independently hydrogen, Ci_6 alkyl, C2-6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl. In embodiments, each Rd is independently hydrogen or Ci_6 alkyl.
[0262] In yet another aspect, Rld is -ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, - N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(0)Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2.
C. PHARMACEUTICAL COMPOSITIONS [0263] In another aspect is provided a pharmaceutical composition including a
pharmaceutically acceptable excipient and a compound, or pharmaceutically acceptable salt thereof, as described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim).
[0264] In embodiments of the pharmaceutical compositions, the compound, or
pharmaceutically acceptable salt thereof, as described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim) is included in a therapeutically effective amount.
[0265] In embodiments of the pharmaceutical compositions, the pharmaceutical composition includes a second agent (e.g. therapeutic agent). In embodiments of the pharmaceutical compositions, the pharmaceutical composition includes a second agent (e.g. therapeutic agent) in a therapeutically effective amount. In embodiments of the pharmaceutical compositions, the second agent is an agent for treating cancer (e.g. multiple myeloma or cancers of secretory cells), neurodegenerative diseases, demyelinating diseases, eye diseases, fibrotic diseases, or diabetes. In embodiments, the second agent is an anti-cancer agent. In embodiments, the second agent is a chemotherapeutic. In embodiments, the second agent is an agent for improving memory. In embodiments, the second agent is an agent for treating a neurodegenerative disease. In embodiments, the second agent is an agent for treating a demyelinating disease. In
embodiments, the second agent is an agent for treating an eye disease. In embodiments, the second agent is an agent for treating a fibrotic disease. In embodiments, the second agent is an agent for treating multiple sclerosis. In embodiments, the second agent is an agent for treating Alzheimer's disease. In embodiments, the second agent is an agent for treating Parkinson's disease. In embodiments, the second agent is an agent for treating Huntington's disease. In embodiments, the second agent is an agent for treating a prion disease. In embodiments, the second agent is an agent for treating amyotrophic lateral sclerosis. In embodiments, the second agent is an agent for treating diabetes. In embodiments, the second agent is an agent for treating retinal degeneration. In embodiments, the second agent is an agent for treating retinitis pigmentosa. In embodiments, the second agent is an agent for treating macular degeneration. In embodiments, the second agent is an agent for treating type I diabetes. In embodiments, the second agent is an agent for treating type II diabetes. In embodiments, the second agent is an agent for treating multiple myeloma. In embodiments, the second agent is an agent for treating a cancer of a secretory cell. In embodiments, the second agent is an agent for reducing Irel (e.g.
Irela) kinase activity. In embodiments, the second agent is an agent for reducing Irel (e.g.
Irel a) RNase activity. In embodiments, the second agent is an agent for inhibiting a pathway activated by Irel (e.g. Irela) phosphorylation. In embodiments, the second agent is an agent for inhibiting a pathway activated by Irel (e.g. Irela) RNase activity. In embodiments, the second agent is an agent for inhibiting Irel (e.g. Irela) oligomerization. In embodiments, the second agent is an agent for inhibiting apoptosis.
D. METHODS [0266] In an aspect is provided a method of treating a disease in a patient in need of such treatment, the method including administering a therapeutically effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof, to the patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
[0267] In embodiments, the disease is a neurodegenerative disease, demyelinating disease, cancer, or diabetes. In embodiments, the disease is a neurodegenerative disease. In
embodiments, the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease, or Kuru. In embodiments, the disease is amyotrophic lateral sclerosis. In embodiments, the disease is retinal degeneration. In embodiments, the disease is retinitis pigmentosa. In embodiments, the disease is a demyelinating disease. In embodiments, the demyelinating disease is Wolfram Syndrome, Pelizaeus- Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis. In embodiments, the disease is Multiple Sclerosis. In embodiments, the disease is cancer. In embodiments, the cancer is multiple myeloma. In embodiments, the disease is diabetes. In embodiments, the diabetes is type I diabetes. In embodiments, the diabetes is type II diabetes. In embodiments, the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes described herein. In embodiments, the disease is an eye disease. In embodiments, the eye disease is retinitis pigmentosa. In embodiments, the eye disease is retinal degeneration. In embodiments, the eye disease is macular degeneration. In embodiments, the eye disease is Wolfram Syndrome. In embodiments, the disease is idiopathic pulmonary fibrosis (IPF). In embodiments, the disease is a fibrotic disease. In embodiments, the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis. In embodiments, the disease is interstitial lung disease (ILD). In embodiments, the disease is myocardial infarction. In embodiments, the disease is cardiac hypertrophy. In embodiments, the disease is heart failure. In embodiments, the disease is cirrhosis. In embodiments, the disease is acetominophen
(Tylenol) liver toxicity. In embodiments, the disease is hepatitis C liver disease. In
embodiments, the disease is hepatosteatosis (fatty liver disease). In embodiments, the disease is hepatic fibrosis.
[0268] In an aspect is provided a method of modulating the activity of an Irel (e.g. Ire la) protein, the method including contacting the Irel (e.g. Ire la) protein with an effective amount of a compound described herein (e.g. formula I, formula II, formula III, aspect, embodiment, example, figure, table, or claim), or a pharmaceutically acceptable salt thereof. [0269] In embodiments, the modulating is inhibiting. In embodiments, the activity is kinase activity. In embodiments, the kinase activity is autophosphorylation activity. In embodiments, the kinase activity is trans-autophosphorylation activity. In embodiments, the activity is oligomerization activity. In embodiments, the oligomerization activity is dimerization activity. In embodiments, the activity is RNase activity. In embodiments, the activity is miR-17 cleavage. In embodiments, the activity is miR-34a cleavage. In embodiments, the activity is miR-96 cleavage. In embodiments, the activity is miR-125b cleavage. In embodiments, the activity is XBP 1 mRNA splicing. In embodiments, the activity is UPR activation. In embodiments, the activity is terminal UPR activation. In embodiments, a cell includes the Irel (e.g. Ire la) protein. In embodiments, the activity of the Irel (e.g. Ire la) protein is increasing apoptosis of the cell. In embodiments, an organ includes the cell. In embodiments, an organism includes the cell. In embodiments, an organism has a disease associated with the Irel (e.g. Irela) protein activity. In embodiments, the disease is a neurodegenerative disease, a demyelinating disease, cancer, an eye disease, a fibrotic disease, or diabetes. In embodiments, the disease is a neurodegenerative disease. In embodiments, the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease, or Kuru. In embodiments, the disease is amyotrophic lateral sclerosis. In embodiments, the disease is retinal degeneration. In embodiments, the disease is retinitis pigmentosa. In embodiments, the disease is a demyelinating disease. In embodiments, the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple
Sclerosis. In embodiments, the disease is Multiple Sclerosis. In embodiments, the disease is cancer. In embodiments, the cancer is multiple myeloma. In embodiments, the disease is diabetes. In embodiments, the diabetes is type I diabetes. In embodiments, the diabetes is type II diabetes. In embodiments, the disease is an eye disease. In embodiments, the eye disease is retinitis pigmentosa. In embodiments, the eye disease is retinal degeneration. In embodiments, the eye disease is macular degeneration. In embodiments, the eye disease is Wolfram Syndrome. In embodiments, the disease is idiopathic pulmonary fibrosis (IPF). In embodiments, the disease is a fibrotic disease. In embodiments, the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis. In embodiments, the disease is interstitial lung disease (ILD). In embodiments, the disease is myocardial infarction. In embodiments, the disease is cardiac hypertrophy. In embodiments, the disease is heart failure. In embodiments, the disease is cirrhosis. In embodiments, the disease is acetominophen (Tylenol) liver toxicity. In embodiments, the disease is hepatitis C liver disease. In embodiments, the disease is hepatosteatosis (fatty liver disease). In embodiments, the disease is hepatic fibrosis. In embodiments, the Irel protein is an Irela protein. In embodiments, the Irel (e.g. Irela) protein is a human protein. In embodiments, the Irel protein is a human Irela protein.
[0270] In another aspect, the present disclosure, has identified two classes of kinase inhibitors— called types I and II, which stabilize alternate kinase active site conformations in numerous protein kinase targets (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006)). The present disclosure shows that a type I kinase inhibitor and a novel type II kinase inhibitor both modify IRE la by shutting down IRE la trans-autophosphorylation, but have divergent effects on its RNase to activate or inactivate catalytic activity, respectively. The present disclosure further demonstrates that IRE la RNase activity can be either up or downregulated through selective targeting of its kinase domain to control UPR signaling, and predict that it may be possible to pharmacologically modulate other kinase-coupled enzymes in a similar way. [0271] In an additional aspect, the present disclosure illustrates that IRE la's kinase-controlled RNase can be regulated in two distinct modes with kinase inhibitors: one class of ligands occupy IRE la's kinase ATP -binding site to activate RNase- mediated XBP1 mRNA splicing even without upstream ER stress, while a second class can inhibit the RNase through the same ATP- binding site, even under ER stress. Thus, alternative kinase conformations stabilized by distinct classes of ATP-competitive inhibitors can cause allosteric switching of IREla's RNase— either on or off. As dysregulation of the UPR has been implicated in a variety of cell degenerative and neoplastic disorders, small molecule control over IRE la should advance efforts to understand the
UPR's role in pathophysiology and to develop drugs for ER stress-related diseases. E. ADDITIONAL EMBODIMENTS
[0272] 1. A compound having the formula:
Figure imgf000095_0001
(I) wherein, ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; L1 is a bond or unsubstituted C1-C5 alkylene; L2 is a bond, -NR6a-, -0-, -S-, -C(O)-
, -S(O)-, -S(0)2-, -NR6aC(0)-, -C(0)NR6b-, -C(0)(CH2)z2-, -NR6aC(0)0-,
-NR6aC(0)NR6b-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R1 is hydrogen, oxo, halogen, -CX3, -CN, -S02C1, -SOnR10, -SOvNR7R8, -NHNH2, -ONR7R8, -NHC=(0)NHNH2,
-NHC=(0)NR7R8, -N(0)m, -NR7R8, -C(0)R9, -C(0)-OR9, -C(0)NR7R8, -OR10, -NR7SO„R10, - NR7C=(0)R9, -NR7C(0)OR9, -NR7OR9, -OCX3, -OCHX2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R2 is hydrogen, oxo, halogen, -CXa 3, -CN, -S02C1, -SOniR10a, -SOviNR7aR8a, -NHNH2, -ONR7aR8a, -NHC=(0)NHNH2,
-NHC=(0)NR7aR8a, -N(0)mi, -NR7aR8a, -C(0)R9a, -C(0)OR9a, -C(0)NR7aR8a, -OR10a, - NR7aSOniR10a, -NR7aC=(0)R9a, -NR7aC(0)OR9a, -NR7aOR9a, -OCXa 3, -OCHXa 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R3 is independently hydrogen, oxo,
halogen, -CXb 3, -CN, -S02C1, -SO„2R10b, -SOv2NR7bR8b, -NHNH2, -ONR7bR8b,
-NHC=(0)NHNH2,
-NHC=(0)NR7bR8b, -N(0)m2, -NR7bR8b, -C(0)R9b, -C(0)-OR9b, -C(0)NR7bR8b, -OR10b, - NR7bSO„2R10b, -NR7bC=(0)R9b, -NR7bC(0)OR9b, -NR7bOR9b, -OCXb 3, -OCHXb 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 and R5 are independently hydrogen or unsubstituted Ci-Ce alkyl; R7, R8, R9, R10, R6a, R7a, R8a, R9a, R10a, R6b, R7b, R8b, R9b and R10b are independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -S03H, - S04H, -S02NH2, -NH H2, -ONH2, -NHC=(0)NH H2, -NHC=(0)NH2, -NHS02H, - NHC=(0)H, -NHC(0)OH, -NHOH, -OCF3, -OCHF2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R7 and R8 substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7a and R8a substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7b and
8b
R substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4; each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2; the symbol z is an integer from 0 to 2; the symbol z2 is an integer from 1 to 4; and each occurrence of the symbols X, Xa, and Xb is independently a halogen. [0273] 2. The compound of embodiment 1, wherein R3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0274] 3. The compound of any one of embodiments 1 to 2, wherein R3 is hydrogen. [0275] 4. The compound of any one of embodiments 1 to 3, wherein the symbol z is 1.
[0276] 5. The compound of any one of embodiments 1 to 4, wherein R2 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0277] 6. The compound of any one of embodiments 1 to 5, wherein R2 is substituted or unsubstituted alkyl. [0278] 7. The compound of any one of embodiments 1 to 6, wherein R2 is substituted or unsubstituted Ci-Ce alkyl.
[0279] 8. The compound of any one of embodiments 1 to 7, wherein R2 is unsubstituted Ci- C6 alkyl. [0280] 9. The compound of any one of embodiments 1 to 8, wherein R2 is unsubstituted isopropyl or unsubstituted tert-butyl.
[0281] 10. The compound of any one of embodiments 1 to 9, wherein R4 and R5 are hydrogen.
[0282] 1 1. The compound of any one of embodiments 1 to 10, wherein L1 is a bond. [0283] 12. The compound of any one of embodiments 1 to 10, wherein L1 is unsubstituted methylene.
[0284] 13. The compound of any one of embodiments 1 to 12, wherein L2
is -NR6aC(0)NR6b-.
[0285] 14. The compound of any one of embodiments 1 to 13, wherein R6a and R6b are hydrogen.
[0286] 15. The compound of any one of embodiments 1 to 14, wherein R1 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0287] 16. The compound of any one of embodiments 1 to 15, wherein R1 is substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0288] 17. The compound of any one of embodiments 1 to 16, wherein R1 is substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl. [0289] 18. The compound of any one of embodiments 1 to 17, wherein R1 is substituted phenyl.
[0290] 19. The compound of any one of embodiments 1 to 18, wherein R1 is phenyl substituted with -CF3 or halogen. [0291] 20. The compound of any one of embodiments 1 to 19, wherein ring A is substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene.
[0292] 21. The compound of any one of embodiments 1 to 20, wherein ring A is substituted or unsubstituted C6-C10 arylene. [0293] 22. The compound of any one of embodiments 1 to 21, wherein ring A is unsubstituted naphthalenyl.
[0294] 23. The compound of any one of embodiments 1 to 22 having the formula:
Figure imgf000098_0001
unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
[0295] 24. The compound of any one of embodiments 1 to 23 having the formula:
Figure imgf000098_0002
[0296] 25. The compound of any one of embodiments 1 to 24 selected from the group consisting of:
Figure imgf000099_0001
[0297] 26. A pharmaceutical composition comprising a pharmaceutically acceptable excipient and a compound of any one of embodiments 1 to 25. [0298] 27. A method of treating a disease in a patient in need of such treatment, said method comprising administering a therapeutically effective amount of a compound of any one of embodiments 1 to 25 to said patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
[0299] 28. The method of embodiment 27, wherein the disease is a neurodegenerative disease.
[0300] 29. The method of any one of embodiments 27 and 28, wherein the
neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru. [0301] 30. The method of embodiment 27, wherein the disease is a demyelinating disease. [0302] 31. The method of any one of embodiments 27 and 30, wherein the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot- Marie-Tooth Disease, or Multiple Sclerosis.
[0303] 32. The method of embodiment 27, wherein the disease is cancer. [0304] 33. The method of any one of embodiments 27 and 32, wherein the cancer is multiple myeloma.
[0305] 34. The method of embodiment 27, wherein the disease is diabetes.
[0306] 35. The method of any one of embodiments 27 and 34, wherein the diabetes is type I diabetes. [0307] 36. The method of any one of embodiments 27 and 34, wherein the diabetes is type II diabetes.
[0308] 37. The method of embodiment 27, wherein the disease is an eye disease.
[0309] 38. The method of any one of embodiments 27 and 37, wherein the eye disease is retinitis pigmentosa, retinal degeneration, macular degeneration, or Wolfram Syndrome. [0310] 39. The method of embodiment 27, wherein the disease is a fibrotic disease.
[0311] 40. The method of any one of embodiments 27 and 39, wherein the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis. [0312] 41. A method of modulating the activity of an Irel protein, said method comprising contacting said Irel protein with an effective amount of a compound of any one of embodiments 1 to 25.
[0313] 42. The method of embodiment 41, wherein said modulating is inhibiting.
[0314] 43. The method of any one of embodiments 41 to 42, wherein said activity is kinase activity.
[0315] 44. The method of embodiment 43, wherein said kinase activity is
autophosphorylation activity. [0316] 45. The method of any one of embodiments 41 to 42, wherein said activity is oligomerization activity.
[0317] 46. The method of embodiment 45, wherein said oligomerization activity is dimerization activity. [0318] 47. The method of any one of embodiments 41 to 42, wherein said activity is RNase activity.
[0319] 48. The method of any one of embodiments 41 to 42, wherein a cell comprises said Irel protein.
[0320] 49. The method of embodiment 48, wherein said activity of the Irel protein is increasing apoptosis of said cell.
[0321] 50. The method of any one of embodiments 48 to 49, wherein an organ comprises said cell.
[0322] 51. The method of any one of embodiments 48 to 50, wherein an organism comprises said cell. [0323] 52. The method of embodiment 51, wherein said organism has a disease associated with said Irel protein activity.
[0324] 53. The method of embodiment 52, wherein said disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes.
[0325] 54. The method of embodiment 53, wherein the disease is a neurodegenerative disease.
[0326] 55. The method of any one of embodiments 53 and 54, wherein the
neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration, Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru. [0327] 56. The method of embodiment 53, wherein the disease is cancer.
[0328] 57. The method of any one of embodiments 53 and 56, wherein the cancer is multiple myeloma.
[0329] 58. The method of embodiment 53, wherein the disease is diabetes. [0330] 59. The method of any one of embodiments 53 and 58, wherein the diabetes is type I diabetes.
[0331] 60. The method of any one of embodiments 53 and 58, wherein the diabetes is type II diabetes. [0332] 61. The method of embodiment 53, wherein the disease is a demyelinating disease.
[0333] 62. The method of any one of embodiments 53 and 61, wherein the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot- Marie-Tooth Disease, or Multiple Sclerosis.
[0334] 63. The method of any one of embodiments 53, 61, and 62, wherein the
demyelinating disease is Multiple Sclerosis.
[0335] 64. The method of embodiment 53, wherein the disease is an eye disease.
[0336] 65. The method of any one of embodiments 53 and 64, wherein the eye disease is retinitis pigmentosa, retinal degeneration, macular degeneration, or Wolfram Syndrome.
[0337] 66. The method of embodiment 53, wherein the disease is a fibrotic disease. [0338] 67. The method of any one of embodiments 53 and 66, wherein the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
[0339] 68. A compound of the formula
d
Figure imgf000102_0001
or a pharmaceutically acceptable salt thereof, wherein R , R ,
R , R , R , R , R , R , R , and R , are each independently C2-6 alkyl, C1-6 haloalkyl, -C1-4 alkyl-R12d, C2-6 alkenyl, C2-6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two Rl ld groups; each Rl ld is independently Ci_6 alkyl, Ci_6 haloalkyl, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, S(0)2NRd 2, or -S(0)2Rd; and R12d is - ORd, -SRd, -NRd 2, -C(0)Rd, -C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, OC(0)ORd,
OC(0)NRd 2, -N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -ORd, -SRd, -NRd 2, -C(0)Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(O) Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0)Rd, - N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; and each Rd is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, C e haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, - C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d, OC(O)N(R0d)2, N(R0d)C(O)R0d, - N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl,each Rd is independently hydrogen, or Ci_6 alkyl.
[0340] 69. A compound of the formula
d
Figure imgf000103_0001
or a pharmaceutically acceptable salt thereof, wherein Rld is -ORd,
-SRd, -NRd 2, -C(O) Rd, -C(0)ORd, -C(0)NRd 2, -N(Rd)C(0)Rd, -N(Rd)C(0)ORd, -
N(Rd)C(0)NRd 2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C e alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(0)Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0) Rd, -N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; and R2d and R are together a phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -ORd, -SRd, -NRd 2, -C(0)Rd, C(0)ORd, -C(0)NRd 2, -S(0)2Rd, -OC(0)Rd, -OC(0)ORd, OC(0)NRd 2, N(Rd)C(0) Rd, -N(Rd)C(0)ORd, or -N(Rd)C(0)NRd 2; wherein each Rd is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi_6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -ORod, SRod, NR0d2, C(O)R0d, C(O)OR0d, -C(O)N(R0d)2, S(O)2R0d, -OC(O)R0d, -OC(O)OR0d,
OC(O)N(R0d)2, N(R0d)C(O)R0d, -N(R0d)C(O)OR0d, or N(R0d)C(O)N(R0d)2, wherein each Rod is independently hydrogen or Ci_6 alkyl,each Rd is independently hydrogen, or Ci_6 alkyl.
[0341] 70. A composition comprising any of the formulas of embodiments 68 and 69 or a pharmaceutically acceptable salt thereof.
[0342] 71. A pharmaceutical composition for inhibiting IRE la RNase activity, the composition comprising: Formula (A), Formula (B), any derivatives of Formula (A) and Formula (B) disclosed herein, GP17, GP21, GP29, DSA7, DSA8, GP1 17, GP 118, GP 146, GP146 (NMe), GP146(Am), compounds shown Figs. 7 and 8, any of the formulas from embodiments 68 and 69, and combinations thereof.
[0343] 72. A pharmaceutical composition for activating IRE la RNase activity, the composition comprising murine IRE la. [0344] 73. A method for inhibiting IRE1 a RNase activity, the method comprising providing a subject in need of such inhibition an effective amount of either: a. a compound of embodiment 68, Formula (A), Formula (B), GP17, GP21, GP29, DSA7, DSA8, GP1 17, GP1 18, GP146, GP 146 (NMe), GP146(Am), a compound shown Figs. 7 or 8, any of the formulas of
embodiments 68 and 69, and any combinations thereof, or b. a pharmaceutical composition comprising a compound from 73(a) and a pharmaceutically acceptable excipient, carrier, or diluent.
[0345] 74. A method for activating IRE la RNase activity, the method comprising providing a subject in need of such inhibition an effective amount of either: a. murine IRE la; or b. a pharmaceutical compsotion comprising murine IRE la and a pharmaceutically acceptable excipient, carrier, or diluent.
[0346] 75. The method of any one of embodiments 41 to 67, wherein said Irel is Irela. [0347] 76. The method of any one of embodiments 41 to 67 and 75, wherein said Irel is a human Irel.
F. EXAMPLES
1. Screening and Optimization of IREla Modulators [0348] The particulars shown herein are by way of example and for purposes of illustrative discussion of embodiments of the present invention only and are presented in the cause of providing what is believed to be a readily understood description of the principles and conceptual aspects of various embodiments of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for the fundamental understanding of the invention, the description taken with the drawings and/or examples making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.
[0349] Inhibition of IRE la's RNase activity through the ATP -binding site of its kinase domain using kinase inhibitors. Generation of more potent and selective analogs of IREl kinase inhibitors
[0350] Discovery of ATP-competitive kinase inhibitors that are able to inhibit the RNase domain of IREla from a distance. Previous studies have demonstrated that the RNase activity of IREla is dependent on kinase domain autophosphorylation. Shown herein is an unexpected relationship between the kinase and RNase domains, where ligands that interact with the ATP- binding site of the kinase domain are able to bypass the autophosphorylation requirement and activate the RNase domain (Papa, F. R. et al. Science 302, 1533-1537 (2003)). For instance, the orthogonal ATP-competitive inhibitor 1NM-PP1 is able to rescue the RNase activity of IREla mutants that lack kinase activity (Han, D. et al. Biochemical and biophysical research communications 365, 777-783, (2008)). Other ligands that interact with the ATP -binding site of wild-type IREla, including the endogenous co-factors ADP and ATP, are also able to activate RNase activity directly (Lee, K. P. et al. Cell 132, 89-100, (2008); Ali, M. M. et al. The EMBO journal 30, 894-905, (201 1)). Also, the ATP-competitive inhibitors APY29 and sunitinib directly activate the RNase of yeast and murine IREla (Han, D. et al. Cell 138, 562-575, (2009);
Korennykh, A. V. et al. Nature 457, 687-693, (2009)). A crystal structure of APY29 bound to yeast IRE1 shows that the kinase catalytic domain is in an active conformation (Korennykh, A. V. et al. Nature 457, 687-693, (2009)), which is a conformation adopted by protein kinases capable of catalyzing phosphate transfer. By stabilizing an active conformation of IRE la's ATP- binding site, certain co-factors and ATP-competitive inhibitors act as ligands that allosterically activate its adjacent RNase domain. Given the ability to allosterically activate IREla's RNase through its kinase domain, it should be possible to also inhibit the RNase through the same kinase domain with a different class of kinase inhibitors that stabilize an inactive ATP-binding site conformation. Two classes of ATP-competitive kinase inhibitors— called types I and II— have been identified (Fig. 1A), which stabilize alternate kinase active site conformations in numerous protein kinase targets 51'52. Type I inhibitors-like APY29 and sunitinib-stabilize an active ATP-binding site conformation. In contrast, type II inhibitors-like the clinically-approved drugs imatinib and sorafenib-selectively stabilize an inactive ATP-binding site conformation 53~ 55. The inactive ATP-binding site conformation stabilized by type II inhibitors is characterized by outward movement of the catalytically-important Asp-Phe-Gly (DFG) motif, and is therefore called the DFG-out conformation (Fig. 1A) 51'52. Described herein is the generation of a diverse panel of type II inhibitors and characterization of their interactions with a number of protein kinases (Krishnamurty, R. et al. Nature chemical biology 9, 43-50, (2013); Han, D. et al.
Biochemical and biophysical research communications 365, 777-783, (2008); Brigham, J. L. et al. ACS Chem. Biol. (2013); Hill, Z. B. et al. ACS Chem. Biol. 7, 487^195 (2012)). These pharmacological tools served as a starting point towards the goal of identifying ATP-competitive inhibitors able to allosterically inactivate the IRE la RNase. [0351] The diverse panel of type II inhibitors were screened for their ability to block the RNase activity of a recombinant soluble human IREla mini-protein construct (expressed in baculovirus) containing the kinase/RNase domains— called IREla* (Zhang, J. et al. Nature reviews. Cancer 9, 28-39, (2009)). Since IREla* is basally autophosphorylated, its RNase is active, and can be assayed using a FRET-quenched XBP1 RNA mini-substrate. While all the type II inhibitors tested with this assay contain the core binding elements predicted to stabilize the DFG-out conformation, only one ligand, demonstrated measurable inhibition of IRE la*' s RNase activity at a concentration of 60 μΜ (Fig. 1C and ID). Because these type II kinase inhibitors also attenuate the RNase activity of IREla*, they were designated KIRAs— for kinase-inhibiting RNase attenuators. KIRAl is a pyrazolopyrimidine-based inhibitor that has been shown to stabilize the DFG-out conformation of the non-receptor tyrosine kinases Src and Abl (Dar, A. C. et al. Chemistry & Biology 15, 1015-1022 (2008)). Based on the co-crystal structure of KIRAl bound to Src (PDB: 3EL8) and molecular modeling, proposed contacts with IREla are shown in Fig. 1A. [0352] Despite its modest potency, KIRAl served as a suitable starting point for developing higher affinity allosteric RNase inhibitors. A number of similar analogs were generated and tested for RNase inhibition. While most modifications of KIRAl were deleterious, replacing the pyrazolopyrimidine scaffold with an imidazopyrazine core provided a significant increase in overall potency (KIRA2, Fig. 1C and ID). Furthermore, substituting the 4-anilino group at the C-3 position of KIRA2 with a naphthylamine moiety provided KIRA3. Notably, KIRA3 inhibits XBPl RNA cleavage to a similar degree as STF-083010, an imine-based small molecule that directly inhibits the IRE la RNase through covalent modification.
[0353] Similar to the type I inhibitor APY29 (IC50 (autophosphorylation) = 0.28 μΜ), KIRA3 (IC5o (autophosphorylation) = 3.1 μΜ) demonstrates dose-dependent reduction of IRE la * kinase autophosphorylation in vitro. Thus, although KIRA3 and APY29 are both IRE la* kinase inhibitors, they demonstrate opposing effects on its RNase activity, with APY29 acting as an activator. To further characterize differences between the two kinase inhibitors, a version of IRE la* was generated with low basal RNase activity by using λ-phosphatase to remove activating phosphates. As expected, the dephosphorylated variant of IREla* (dP-IREla*) has significantly lower basal RNase activity than IREla*; incubating dP -IREla* with increasing APY29 progressively restores its ability to cleave the XBPl mini-substrate, plateauing at -60% of the levels of IREla* (Fig. 2C). In contrast, KIRA3 suppresses residual RNase activity of dP- IRE la*. Competition experiments were performed to further explore the opposing effects of APY29 and KIRA3. Increasing concentrations of APY29 progressively reverse IREla* RNase inhibition caused by a fixed concentration of KIRA3 (Fig. 2E). Furthermore, the type I inhibitor sunitinib also opposes the RNase inhibitory effect of KIRA3. On the other hand, increasing concentrations of KIRA3 restore RNase inhibition under a fixed concentration of APY29, with an expected increase in the IC50. As predicted, APY29 cannot rescue direct inhibition caused by the covalent RNase modifier STF-083010. Taken together, these results strongly suggest that APY29 and KIRA3 are exerting their opposing effects on RNase activity through the same binding site.
[0354] The drug sunitinib is a promiscuous type I inhibitor that has been shown to inhibit the kinase activity of yeast and human IRElal6,19. To investigate the differences between GP 146 (KIRA3) and other ATP-competitive inhibitors of IRE1 a, the interaction of sunitinib with the IREla* and dP-IREla* constructs was further characterized. As expected, sunitinib is a dose- dependent inhibitor of the autophosphorylation activity of IREla* (Fig. 18a). In addition, sunitinib activates the RNase activity of dP-IREla*, which is consistent with its type I pharmacophore (Fig. 18b). Therefore, both APY29 and sunitinib stabilize an ATP-binding site conformation that activates the RNase domain of IRE la. Like APY29, increasing amounts of sunitinib are able to rescue the RNase activity of IREla* in the presence of a fixed concentration of GP 146 (Fig. 18c). Together, these results show that GP 146 opposes the stereotypic RNase activation demonstrated by various type I ATP-competitive inhibitors of IREla.
[0355] KIRA3 prevents dimerization and oligomerization of IREla. Self-association of kinase/RNase monomers has been reported to increase RNase activity as dimers and/or higher- order oligomers form in yeast and mammalian IRE1 proteins, furthermore, the degree of order may correlate directly with activity. Thus, APY29 and KIRA3 were used to test the prediction that they would divergently affect the oligomerization state of human IREl as a basis for their opposing effects on its RNase activity. Specifically, RNase activators should drive monomers into higher-order species from baseline. To test this, increasing concentrations of IREla* were incubated with either DMSO, or saturating concentrations of APY29 or KIRA3 and the ratio of oligomeric— defined as all species greater than monomers— to monomeric IREla was determined (Fig. 24). In the absence of ligands, IREla* shows a concentration-dependent increase in the oligomer/monomer ratio. APY29 further enhances— whereas KIRA3 decreases— this concentration-dependent increase in the IREla* oligomer/monomer ratio. Taken together, the in vitro data support a model in which these two classes of kinase inhibitors divergently modulate IREla* RNase activity by exerting opposing effects on the oligomerization state of the enzyme.
2. Synthesis and characterization of compositions
[0356] Unless otherwise noted, all reagents were obtained from commercial suppliers and used without purification. TLC was performed on EMD Millipore silica gel 60 F254 plates. IH-NMR spectra were obtained on a Bruker AV-300 or AV301 instrument at room temperature and 13C- NMR spectra were obtained on a Bruker AV-500 instrument at room temperature. Chemical shifts are reported in ppm, and coupling constants are reported in Hz. 1H and 13C resonances are referenced to residual MeOH. Mass spectrometry was performed on a Bruker Esquire Ion Trap MS instrument. The purity of all final compounds was determined by analytical HPLC with two different solvent systems. Analytical conditions A: [CI 8 (150 x 2.1 mm), CH3CN/H2O-0.1% CF3C02H = 1 :99 to 100:0 over 33 min; 1 mL/min; 220 and 254 nm detection for 33 min]. Analytical conditions B: [C18 (150 x 2.1 mm), CH3OH/H2O-0.1% CF3C02H = 1 :99 to 100:0 over 33 min; 1 mL/min; 220 and 254 nm detection for 33 min].
[0357] STF-083010, Sunitinib, nilotinib, and GP21 were obtained from commercial suppliers. All compounds were verified to be >95% pure by analytical HPLC. APY29 and GP118 was prepared according to a previously reported procedures.
[0358] l-iodo-3-isopropylimidazo[l,5-a]pyrazin-8-amine (compound 1). Compound 1 was synthesized according to a previously described procedure. l-(4-(4,4,5,5-tetramethyl- 1,3,2- dioxaborolan-2-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)urea (compound 2). A mixture of 4- Aminophenylboronic acid pinacol ester (50.0 mg, 0.23 mmol) and 3-(Trifluoromethyl)phenyl isocyanate (46.0 uL, 0.31 mmol) in THF (1.9 mL) was stirred overnight at room temperature. The mixture was concentrated, diluted with dichloromethane and washed with water. The organic layer was dried over Na2S04, concentrated in vacuo and the resultant crude product was purified by flash chromatography (20% ethyl acetate in hexanes) to afford 92.5 mg of compound 2 (98% yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf = 0.4; 1H NMR (300 MHz, MeOD): δ 7.90 (s, 1H), 7.71 - 7.68 (m, 2H), 7.60 (d, J = 6.0 Hz, 1H), 7.48 - 7.42 (m, 3H), 7.29 (d, J = 9.0 Hz, 1H), 1.34 (s, 12H); ESI-MS (m/z): [M]+ calcd. for C20H22BF3N2O3, 406.17; [M+l]+ found, 407.5. l-(4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)naphthalen-l-yl)-3-(3- (trifluoromethyl)phenyl)urea (compound 3). A mixture of 4-Aminonaphthalene-l-boronic acid pinacol ester (31.2 mg, 0.1 1 mmol) and 3-(Trifluoromethyl)phenyl isocyanate (21.0 μΐ^, 0.31 mmol) in THF (0.9 mL) was stirred over night at room temperature. The mixture was concentrated, diluted with dichloromethane and washed with water. The organic layer was dried over Na2S04, concentrated in vacuo and the resultant crude product was purified by flash chromatography (20% ethyl acetate in hexanes) to afford 43.6 mg of compound 3 (86% yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf = 0.4; 1H MR (300 MHz, MeOD): δ 8.87 - 8.82 (m, 1H), 8.11 - 7.91 (m, 4H), 7.67 (d, J = 9.0 Hz, 1H), 7.60 - 7.47 (m, 3H), 7.36 - 7.31 (m, 1H), 1.44 (s, 12H); ESI-MS (m/z): [M]+ calcd. for C24H24BF3N203, 456.18; [M+l]+ found, 457.3. N-(4- (4,4,5, 5-tetramethyl-l,3,2-dioxaborolan-2-yl)naphthalen-l-yl)-3-(trifluoromethyl)benzamide (compound 4). 4-Aminonaphthalene-l-boronic acid pinacol ester (75.0 mg, 0.267 mmol), 3- (Trifluoromethyl)benzoic acid (67.5 mg, 0.348 mmol), HOBt (55.1 mg, 0.348 mmol), EDCI (68.0 mg, 0.348 mmol) and DIPEA (141 μί, 0.803 mmol) were dissolved in DMF (790 μ∑) and stirred overnight at room temperature. The crude mixture was diluted in ethyl acetate and washed with NH4C1 and Na2C03. The organic layer was dried over Na2S04 and concentrated in vacuo.
The crude organic product was purified by column chromatography (20% ethyl acetate in hexanes) to afford 16.6 mg of compound 4 (14% yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf = 0.4; 1H MR (300 MHz, MeOD) δ 8.87-8.84 (m, 1H), 8.41-8.36 (m, 2H), 8.13-8.04 (m, 2H), 8.01-7.96 (m, 1H), 7.85-7.78 (m, 1H), 7.68 (d, J = 6.0 Hz, 1H), 7.58-7.55 (m, 2H), 1.47 (s, 12H); ESI-MS (m/z): [M]+ calcd. for C24H23BF3N03, 441.17; [M+l]+ found, 442.2. 8-chloro-l- iodo-3-isopropylimidazo[l,5-a]pyrazine (compound 5). Compound 5 was synthesized according to previously published procedure. l-iodo-3-isopropyl-N-methylimidazo[l,5-a]pyrazin-8-amine (compound 6). Compound 5 (21.8 mg, 0.068 mmol) was dissolved in a solution of 40% MeNH2 in MeOH (91 μί) and was stirred at 80 oC for 2 h in a microwave. The reaction mixture was concentrated in vacuo to obtain 20.3 mg of compound 6 (94% yield). TLC (hexanes :EtO Ac, 50:50 v/v): Rf = 0.2; 1H MR 1H MR (300 MHz, MeOD) δ 7.51 (d, J = 6.0 Hz, 1H), 7.04 (d, J = 6.0 Hz, 1H), 3.42 - 3.34 (m, 1H), 3.07 (s, 3H), 1.37 (d, J = 6.0 Hz, 6H); ESI-MS (m/z): [M]+ calcd. for C10H13I 4, 316.02; [M+l]+ found, 317.1.
[0359] l-(4-(8-amino-3-isopropylimidazo[l,5-a]pyrazin-l-yl)phenyl)-3-(3- (trifluoromethyl)phenyl)urea (KIRA2). A mixture of compound 1 (22.1 mg, 0.073 mmol), compound 2 (35.5 mg, 0.087 mmol), tetrakis(triphenylphosphine)palladium (2.6 mg, 2.1 μιηοΐ) and sodium carbonate (17.0 mg, 0.161 mmol) was dissolved in a 3 : 1 mixture of DME/water (280 uL). The mixture was heated overnight at 85 °C. The crude mixture was then allowed to cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase chromatography (HPLC) to obtain 1 1.5 mg of KIRA2 (35% yield). TLC (CH2C12:MeOH, 95:5 v/v): Rf = 0.5; 1H NMR (300 MHz, MeOD): δ 7.95 (s, 1H), 7.68-7.64 (m, 1H), 7.65-7.63 (m, 2H), 7.60-7.56 (m, 2H), 7.55-7.48 (m, 2H), 7.34-7.31 (m, 1H), 7.02-7.00 (dd, J = 6.0 Hz, J = 3.0 Hz, 1H), 3.49-3.43 (m, 1H), 1.44 (d, J = 6.0 Hz, 6H); ESI-MS (m/z): [M]+ calcd. for C23H21F3N60, 454.17; [M+l]+ found, 455.5. HPLC Purification Conditions: C18 column (250 x 21 mm), CH3CN/H2O-0.1% CF3C02H = 1 :99 to 100:0 over 78 min; 8 mL/min; 220 nm and 254 nm detection for 78 min. The purity of GP 1 17 was determined to be >98% by analytical HPLC in two different solvent systems.
[0360] 1 -(4-(8-amino-3 -isopropylimidazo[ 1 ,5-a]pyrazin- 1 -yl)naphthalen- 1 -yl)-3-(3- (trifluoromethyl)phenyl)urea (KIRA3). A mixture of compound 1 (12.0 mg, 0.040 mmol), compound 3 (21.9 mg, 0.048 mmol), tetrakis(triphenylphosphine)palladium (1.4 mg, 1.2 μιηοΐ) and sodium carbonate (9.3 mg, 0.088 mmol) was dissolved in a 3: 1 mixture of DME/water (160 uL). The mixture was heated overnight at 85 °C. The crude mixture was cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase
chromatography (HPLC) to obtain 12.3 mg of GP146 (61% yield). TLC (CH2C12:MeOH, 95:5 v/v): Rf = 0.4; 1H NMR (300 MHz, MeOD): δ 8.27-8.22 (m, 1H), 8.02-7.96 (m, 2H), 7.90-7.86 (m, 1H), 7.83-7.79 (m, 1H), 7.72-7.49 (m, 5H), 7.37-7.32 (m, 1H), 7.04-6.99 (m, 1H), 3.66-3.55 (m, 1H), 1.54-1.48 (m, 6H); 13C MR (500 MHz, MeOD): δ 154.9, 151.6, 149.8, 140.2, 135.9, 132.9, 129.4, 128.7, 128.7, 127.1, 126.6, 126.6, 125.8, 125.7, 121.9, 121.9, 121.8, 120.2, 118.7, 1 18.7, 115.1, 114.6, 1 12.9, 108.4, 25.8, 19.6; [M+l]+ found, 505.4. HPLC Purification
Conditions: C18 column (250 x 21 mm), CH3CN/H2O-0.1% CF3C02H = 1 :99 to 100:0 over 78 min; 8 mL/min; 220 nm and 254 nm detection for 78 min. The purity of GP 146 was determined to be >98% by analytical HPLC in two different solvent systems.
[0361] 1 -(4-(3 -isopropyl-8-(methylamino)imidazo[ 1 ,5-a]pyrazin- 1 -yl)naphthalen- 1 -yl)-3-(3- (trifluoromethyl)phenyl)urea (GP 146( Me)). A mixture of compound 6 (11.1 mg, 0.035 mmol), compound 3 (19.3mg, 0.042 mmol), Tetrakis(triphenylphosphine)palladium (1.3 mg, 1.0 umol) and sodium carbonate (8.2 mg, 0.08 mmol) was dissolved in a 3 : 1 mixture of DME/water (130 uL). The mixture was heated overnight at 85 °C. The crude mixture was cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase
chromatography (HPLC) to obtain 5.0 mg of the GP 146( Me) (27% yield). TLC
(CH2C12:MeOH, 95:5 v/v): Rf = 0.6; 1H NMR (300 MHz, MeOD) δ 8.26 (d, J = 9.0 Hz, 1H), 8.03 (s, 1H), 7.96 (d, J = 9.0, 1H), 7.90 (d, J = 6.0 Hz, 1H), 7.84 (d, J = 9.0 Hz, 1H), 7.72 - 7.66 (m, 3H), 7.62 - 7.51 (m, 2H), 7.37-7.34 (m, 1H), 7.04 (d, J = 6.0 Hz, 1H), 3.66 - 3.57 (m, 1H), 2.99 (s, 3H), 1.50 (dd, J = 15.0, 6.0 Hz, 6H); 13C NMR (500 MHz, MeOD): δ 154.99, 151.22, 148.86, 140.19, 135.97, 133.04, 131.68, 129.36, 128.96, 128.80, 128.64, 128.54, 126.97, 126.63, 125.86, 125.80, 121.97, 121.84, 120.45, 118.68, 114.99, 1 14.55, 1 13.05, 108.47, 28.25, 25.75, 19.60; ESI-MS (m/z): [M]+ calcd. for C28H25F3N60, 518.2; [M+l]+ found, 519.5. The purity of GP 146(NMe) was determined to be >98% by analytical HPLC.
[0362] N-(4-(8-amino-3 -isopropylimidazo[ 1 ,5-a]pyrazin- 1 -yl)naphthalen- 1 -yl)-3 - (trifluoromethyl)benzamide (GP146(Am)). A mixture of compound 1 (9.5 mg, 0.031 mmol), compound 4 (16.6 mg, 0.038 mmol), Tetrakis(triphenylphosphine)palladium (1.1 mg, 0.94 μιηοΐ) and sodium carbonate (7.3 mg, 0.069 mmol) was dissolved in a 3: 1 mixture of DME/water (120 μί). The mixture was heated overnight at 85 °C. The crude mixture was cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase
chromatography (HPLC) to obtain 5.3 mg of GP146(Am) (34% yield). TLC (CH2C12:MeOH, 95:5 v/v): Rf = 0.5; 1H NMR (300 MHz, MeOD) δ 8.46 (s, 1H), 8.42 (d, J = 6.0 Hz, 2H), 8.16- 8.13 (m, 1H), 8.01-7.98 (m, 1H), 7.86-7.84 (m, 1H), 7.81-7.77 (m, 2H), 7.72-7.69 (m, 1H), 7.68 - 7.62 (m, 2H), 7.60-7.54 (m, 1H), 7.06 (d, J = 6.0 Hz, 1H), 3.61 - 3.52 (m, 1H), 1.53 - 1.46 (m, 6H); ESI-MS (m/z): [M]+ calcd. for C27H22F3N50, 489.18; [M+l]+ found, 490.4 The purity of GP 146(Am) was determined to be >98% by analytical HPLC.
[0363] 1 -(4-(8-amino-3 -tert-butylimidazo [ 1 ,5-a]pyrazin- 1 -yl)naphthalen- 1 -yl)-3 -(3 - (trifluoromethyl)phenyl)urea (KIRA6). A mixture of l-iodo-3-tertbutylimidazo[l,5-a]pyrazin-8- amine (60.0 mg, 0.120 mmol), 3 (66 mg, 0.15 mmol), tetrakis(triphenylphosphine)palladium (5 mg, 4 μιηοΐ) and sodium carbonate (928 mg, 0.27 mmol) was dissolved in a 3: 1 mixture of DME/water (0.5 mL). The mixture was heated overnight at 85 °C. The crude mixture was cooled to room temperature, diluted in a mixture of acetonitrile/water and purified by reverse phase chromatography (HPLC) to obtain 53 mg of KIRA6. TLC (CH2C12:MeOH, 95:5 v/v): Rf = 0.4; 1H NMR (300 MHz, MeOD): δ 8.26 (m, 1H), 8.08-7.99 (m, 2H), 7.90-7.86 (m, 1H), 7.83-7.79 (m, 1H), 7.69- 7.52 (m, 5H), 7.35 (d, J = 7.4 Hz, 1H), 6.98 (m, 1H), 1.65 (s, 9H); 13C NMR (126 MHz, MeOD): δ 154.8, 140.2, 135.7, 133.0, 132.4, 131.7, 131.6, 131.0, 130.7, 129.4, 128.8, 128.6, 128.5, 127.0, 126.6, 125.9, 125.4, 123.2, 121.9, 120.1, 1 18.7, 115.0, 1 14.4, 1 10.1, 33.6, 27.3; ESI-MS (m/z): [M]+ calcd. for C28H25F3N60 (M+H+): 519.2; found 519.4. [0364] Generate potent and selective reversible type II inhibitors of IRElcc. As described above, a type II ATP-competitive inhibitor (KIRA3) that can inactivate IRE la RNase and kinase activities has been identified, in vitro and in vivo (Zhang, J. et al. Nature reviews. Cancer 9, 28-39, (2009)). Described herein are efforts to increase the potency and selectivity of these type II inhibitors. Using structure-based drug design, KIRA3 was further optimized. Initially, a homology model of the IRE la ATP-binding site in the DFG-out conformation, will be used to guide analog synthesis, including use of structures of KIRAs bound to on-targets (IRE la) and off-targets (Src) to refine the inhibitor docking protocol. Described herein is the development of irreversible inhibitors that target a non-conserved cysteine in IRE la's activation loop. Described herein is the development of KIRA3 analogs that contain an electrophile that targets a cysteine predicted to be accessible when IRE la is in the DFG-out conformation. Details are described below.
[0365] KIRA analog synthesis: The synthetic strategy for generating inhibitors of general structure Z is shown Fig. 25. Acylation of commercially available amine Zl with carboxylic acids (R1-CO2H) that have been activated with 1 , l'-carbonyldiimidazole (CDI) (or activated with EDCI, DMAP), followed by cyclization with POCI3 generates imidazopyrimidines (Z2) that are substituted at the 1-position (Ri) (Mulvihill, M. J. et al. Bioorg. Med. Chem. 16, 1359-1375 (2008); Mulvihill, M. J. et al. Bioorganic & Medicinal Chemistry Letters 17, 1091-1097 (2007)). Urea substituents are introduced at the C-3 position by iodinating the scaffold with NIS, nucleophilic substitution with ammonia in isoproponal (in a sealed reaction vessel) and palladium-mediated Suzuki couplings to urea-containing boronic esters (prepared as shown in the box) (Jin, M. et al. Bioorganic & Medicinal Chemistry Letters 21, 1176-1180 (201 1); Wang, J.-X. et al. Org. Lett. 10, 2923-2926 (2008); Board, J. et al. Org. Lett. 11, 5118-5121 (2009)). An alternate synthetic route that introduces substituents at the C-3 position (R2 substituents) without using a metal-mediated cross-coupling can also be used (Mulvihill, M. J. et al.
Bioorganic & Medicinal Chemistry Letters 17, 1091-1097 (2007)). Over 40 analogs have been generated using this synthetic methodology. Representative inhibitors are shown in Fig. 26. KIRA6 (Ri = V; R3 = B), a more potent (IC50(R ase) = 210 nM; IC50(kinase) = 620 nM) analog of KIRA3, is extensively profiled in Aim 2. KIRA7 (Ri = V; R3 = C) is one of the most potent KIRA (IC50(R ase) = < 30 nM; IC50(kinase) = 35 nM) generated to date.
[0366] Irreversible KIRAs that target Cys715 in the activation loop. The IREl kinase domain possesses a cysteine residue (Cys715) two residues C-terminal to the DFG motif (Fig. 27).
Cys715 is rapidly alkylated with haloacetamide-containing ICAT reagents, and the rate is increased under KIRA3 (Zhang, J. et al. Nature reviews. Cancer 9, 28-39, (2009)). Modeling suggests that Cys715 is in close proximity to the R3 substituent of the KIRA scaffold when the DFG motif is in the "out" conformation (the conformation the IREl ATP-binding site adopts when bound to KIRAs). Of the 518 kinases in the human kinome, 42 have a cysteine residue at an equivalent or adjacent position (Leproult, E. et al. J. Med. Chem. 54, 1347-1355 (2011)).
However, chemical proteomic profiling studies with type II inhibitors suggest that none of these 42 kinases, except IREl , are able to adopt the DFG-out inactive conformation (Krishnamurty, R. et al. Nature chemical biology 9, 43-50, (2013); Brigham, J.L. et al. ACS Chem. Biol.
130123155823009). Therefore, it should be possible to selectively target Cys715 with a properly oriented electrophile displayed from the KIRA scaffold. Representative irreversible KIRAs that are being generated are shown in Fig. 27 (electrophiles will be introduced in the last synthetic step to avoid instability issues during the palladium-mediated cross coupling). A number of highly selective irreversible kinase inhibitors have been developed by targeting non-conserved cysteine residues (Kwarcinski, F. E. et al. ACS Chem. Biol. 7, 1910-1917 (2012); Barouch- Bentov, R. et al. Molecular Cell 33, 43-52 (2009); Zhang, T. et al. Chemistry & Biology 19,
140-154 (2012); Zhou, W. et al. Bioorganic & Medicinal Chemistry Letters 21, 638-643 (2011); Zhou, W. et al. Chemistry & Biology 17, 285-295 (2010); Zhou, W. et al. Nature 462, 1070- 1074 (2009); Serafimova, I. M. et al. Nature Chemical Biology 8, 471^176 (2012); Henise, J. C. & Taunton, J. J. Med. Chem. 54, 4133^1146 (201 1); Cohen, M. S. iet al. Science 308, 1318— 1321 (2005)).
3. Analysis of the GP146- IRE la and APY29- IRE la interactions.
[0367] To further confirm that AYP29 and GP 146 are exerting their opposing effects through the same ATP-binding site, a series of biochemical footprinting experiments were conducted (Tu, B. P. & Wang, J. C. Proc. Natl. Acad. Sci. USA 96, 4862-4867 (1999); Underbakke, E. S. et al. Angew. Chem. Int. Ed. 47, 9677-9680 (2008)). Specifically, the accessibility of three native cysteine residues within human IRE la (Cys572, Cys645, and Cys715) to alkylating agents in the presence or absence of APY29 and GP 146 was determined (Fig. 3a). For these studies, electrophilic isotope-coded affinity tag (ICAT) reagents were used to allow a ratiometric and, therefore, quantitative comparison of alkylation rates (Underbakke, E. S. et al. Angew. Chem. Int. Ed. 47, 9677-9680 (2008)). As Cys645 and Cys715 are located within the ATP-binding cleft of IRE la, the accessibility of these residues would be expected to be affected by ligands that occupy this site, while Cys572 is a solvent-exposed residue located on the top of the N-terminal lobe of the kinase. Consistent with both APY29 and GP146 occupying the ATP-binding site of IRE la, Cys645, which is located in the kinase hinge region, is highly shielded from alkylating agents in the presence of either inhibitor (Fig. 3b). In contrast, these inhibitors exert opposing effects on the accessibility of Cys715, with APY29 slowing the rate of alkylation and GP146 increasing it. Cys715 is located in the activation loop of IREla (two residues C-terminal to the DFG-motif) and the divergent influence of APY29 and GP146 on this residue is concordant with these ligands stabilizing different conformations of the activation loop (Fig. 3b). As expected, no detectable difference in the accessibility of Cys572, which is distal to the kinase active site of IREla, is observed in the presence of either inhibitor.
[0368] Next, molecular docking experiments were performed to obtain a better understanding of how GP146 and APY29 interact with the ATP-binding site of human IREla. A model of the DFG-in ATP-binding site conformation was generated from a co-crystal structure of human IREla bound to ADP (PDB code 3P23, chain A) (Ali, M. M. et al. EMBO J. 30, 894-905 (201 1)). As a structure of IREla in the DFG-out conformation has not yet been described, a homology model of this form was generated by using the activation loop of another kinase, the tyrosine kinase Abl2, as a template. Both the DFG-in and DFG-out models were optimized using multi-step all-atom minimization and explicit water molecular dynamics (MD) simulations (Bowers, K. J. et al. in Proceedings of the ACM/IEEE Conference on Supercomputing (SC06) (Tampa, Florida, USA, 2006)). Predictably, the docked structure of APY29 bound to the DFG-in conformation of human IRE la is similar to that of this ligand bound to the yeast IRE1 enzyme (Fig. 19) (Korennykh, A. V. et al. Nature 457, 687-693 (2009)). The pyrazole ring of APY29 forms hydrogen bonds with the kinase hinge region and the pyrimidine moiety occupies the adenine pocket. Attempts to obtain a favorable pose of APY29 bound to the DFG-out conformation of IREla were unsuccessful, which is consistent with the ability of this ligand to exclusively stabilize the active conformation of the ATP-binding site.
[0369] The most favorable docking pose for GP146 bound to the DFG-out conformation of IREla is shown in Fig. 3c. In this pose, the pyrazolopyrimidine ring of this ligand forms two hydrogen bonds with the hinge region and occupies the adenine pocket. The bulky naphthyl ring of GP 146 adopts an almost orthogonal conformation relative to the core scaffold and stacks against the He gatekeeper residue. Like other type II inhibitors, the trifluoromethylphenyl moiety of GP146 occupies the hydrophobic pocket created by movement of the Phe sidechain in the DFG-motif. While GP146 is well accommodated in the DFG-out conformation of human IREl a, no favorable poses were observed for this inhibitor bound to the DFG-in conformation. Indeed, the docking studies predict that the only way that GP 146 can bind to IREla without movement of the DFG motif in the activation loop is if the inhibitor disrupts canonical interactions with the hinge region of the kinase.
[0370] To further experimentally test the docking model, analogs of GP146 that contain structural elements predicted to lower inhibitor potency were generated (Fig. 3d). GP146( Me) contains an N-methyl group that would be predicted to disrupt its interaction with the hinge region of IREla, and the amide linkage of GP146(Am) should not allow the
trifluoromethylphenyl moiety to form as favorable interactions with the hydrophobic pocket created by movement of the DFG-motif. Consistent with the model, both GP146( Me) and GP(146Am) show a markedly diminished ability to inhibit the R ase activity of IREla compared to GP146 (Fig. 3d).
4. GP146 and APY29 divergently affect the oligomerization state of IREla
[0371] Increasing concentrations of IREla* were incubated with either DMSO, or saturating concentrations of APY29 or GP146 and the ratio of oligomeric— defined as all species greater than monomers (mostly dimers)— to monomeric IREla was determined (Fig. 4a). In the absence of ligands, IREla* shows a concentration-dependent increase in the oligomer/monomer ratio. The presence of APY29 further enhances— whereas GP 146 decreases— this concentration- dependent increase in the IREla* oligomer/monomer ratio. Taken together, the in vitro data support a model in which these two classes of kinase inhibitors divergently modulate IREla* RNase activity by exerting opposing effects on the oligomerization state of the enzyme (Fig. 4b). 5. IREla mutants with an enlarged ATP-binding pocket show increased sensitivity to GP146
[0372] Having used a truncated form of IREla for in vitro studies, cell-based experiments were used to test whether it would be possible to replicate divergent modulation of the full- length IREla transmembrane protein with the two classes of kinase inhibitors. The on-target effects of GP 146 were tested and confirmed using IREla chemical-genetic systems previously developed (Han, D. et al. Cell 138, 562-575, (2009)). Specifically, tetracycline-inducible isogenic T-REx 293 stable cell lines expressing either WT or a "holed" IREla gatekeeper mutantI642A were used to determine whether GP146 is able to block the RNase activity of IREla in vivo. Induced with doxycycline (Dox), the transgenic WT-IREla or IRElaI642A spontaneously cluster in the ER, trans-autophosphorylate and splice XBP1 mRNA, without requiring upstream ER stress (Fig. 5a and Fig. 20). As expected, GP146 inhibits autophosphorylation and XBP1 mRNA splicing in the WT cell lines (Fig. 20a and 20b). Consistent with these inhibitory effects occurring through a direct interaction with IREla, control compound GP146(NMe) does not affect either of these parameters, even at the highest concentration tested (Fig. 20c).
Furthermore, it was hypothesized that the enlarged ATP-binding pocket of IRE 1 aI642A would better accommodate the bulky C-3 substituent of GP 146, leading to enhanced sensitivity. Indeed, the docking studies suggest that the naphthyl ring of GP146 is able to occupy a hydrophobic pocket that is accessible in IRElaI642A and not the wild type protein (Fig. 21). Confirming this notion, low nanomolar concentrations of GP146 are sufficient to completely block
autophosphorylation and XBP 1 splicing through this mutant (Fig. 5a and 5b). Furthermore, increasing concentrations of the type I "bumped" inhibitor 1NM-PP1, which is selective for mutant kinases that contain Ala or Gly gatekeeper residues, is able to rescue the RNase activity of IRElaI642A in the presence of GP146 (Fig. 5c).
[0373] The data illustrates a model for IRElaI642A, which can be activated merely through overexpression to basally splice -50% of cellular XBP1 mRNA, that 1NM-PP 1 further increases— while GP146 reduces— the activity of the RNase (Fig. 5d). These divergent effects proceed from the stabilization of the kinase active site in two distinct modes by these inhibitors, with 1NM-PP1 acting on the "holed" IREla kinase in a similar fashion as APY29 does for WT IREla. In summary, the type II pharmacophore GP146 likely enforces an inactive kinase conformation in IRElaI642A, and as it does with WT IREla.
6. GP146 blocks both the autophosphorylation and RNase activities of endogenous IREla in vivo
[0374] To further explore how IREla modulators affect the kinase and RNase activities of endogenous IREla under ER stress, in vivo studies using INS-1 rat insulinoma cell lines, which are derived from insulin-producing pancreatic β-cell tumors and contain large well-developed ERs, were conducted. These cells were treated with the ER SERCA ATPase pump inhibitor, thapsigargin (Tg), to induce ER stress and IREla activation at levels causing -50% splicing of cellular XBP l mRNA (Fig. 6a). Recapitulating the in vitro results, GP 146 and APY29 demonstrate opposing dose-dependent effects on ER stress-induced activation of the RNase of endogenous IREla (Fig. 6a). Furthermore, GP 146 abrogates IREla autophosphorylation at a similar concentration as it blocks RNase activity (Figs. 6b and 6c). Control compound
GP 146(NMe) does not block the splicing of XBP l mRNA (Figs. 6d). Consistent with its in vitro activity, the type I inhibitor sunitinib is able to partially inhibit the kinase activity of IREla, but has no effect on the RNase activity of this enzyme (Figs. 6b and 6c) at the concentrations tested. The RNase inhibitor STF-083010 was also tested in INS-1 cells that had been treated with Tg. As expected, this compound inhibits XBPl splicing in a dose-dependent manner, but does not prevent IREla auto-phosphorylation (Figs. 6b and 6c). Therefore, GP 146 is the only compound identified to date that has the ability to block both enzymatic activities of IREla, both in vitro and in vivo (Fig. 6e).
7. Expression and purification of IREla* and dP-IREla *.
[0375] A construct containing the cytosolic kinase and RNase domains of human IREla (residues 469-977, IREla *) was expressed in SF9 insect cells by using Bac-to-Bac baculovirus expression system (Invitrogen) with a 6-His-tag at the N-terminus, and purified with a Ni-NTA (Qiagen) column. To generate dP-IREla*, basal phosphorylation sites were removed by incubating IREla* with λ-PPase (NEB) at a molar ratio of 5: 1 (IREa *: λ-PPase) in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM MnC12, 2 mM DTT, 0.01% Brij 35 for 40 min at RT. Dephosphorylation was verified by immunoblotting with an anti-phosphoIREla antibody. 8. In vitro characterization of compounds (IRE la*)
[0376] KIRAs are tested for ability to inhibit IRElcc* kinase and RNase activities in vitro. The XBP1 minisubstrate assay shown in Fig. IB-ID, is amenable to 96- or 384-well format, and is used to determine RNase IC50S. In parallel, kinase IC50S for all KIRAs are determined in a 96- well dot blot assay with 32γ-ΑΤΡ and STK peptide substrate 2 as substrates. Time-dependence of inhibition is determined for all electrophile-containing KIRAs. RNase and kinase assays have been used to profile the KIRAs in Fig. 26, showing a strong correlation between kinase and RNase IC50S. The most potent KIRAs are tested in an IRE la* autophosphorylation assay.
Compounds that exhibit an ICsoCRNase) < 200 nM are counter-screened against a panel of kinases that are likely off-targets (Src, Abl, p38cc), affect cell fate (mTor, ΙΚΚβ), down-regulate protein translation (PKR, PERK, GCN2, HRI), are down-stream targets of IRE 1 signaling (Jnkl/2, MKK4, MKK7), and are representative of the entire kinome (AurA, Erk2, Cdk2, EGFR, FAK, MAP3K5, PKA). The profiling data obtained from these screens are used to design more selective KIRAs. KIRA3 and KIRA6 have been tested against 12 kinases in this panel and the only off-target inhibition observed is for the tyrosine kinases Src and Abl. Thus, the structure- based design strategy uses these two kinases as counter targets (described below).
9. Kinase assays.
[0377] Inhibitors (initial concentration = 80 μΜ, 2-fold serial dilutions) were incubated with IRE la* in cleavage buffer (20 mM Hepes at pH 7.5, 0.05% Triton X100, 50mM KOAC, 1 mM Mg(OAC)2, 1 mM DTT) for 20 min, followed by incubation with 10 μθί [γ-32Ρ]ΑΤΡ (3000 Ci/mmol, Perkin Elmer) at RT for 30 min. Samples were then separated by SDS-PAGE, and autoradiographed. The auto-phosphorylation level were quantified by setting the band intensity of IRE la* without compound treatment as 1 and the background as 0.
10. In vitro RNase assay. [0378] 5 'FAM-3 'BHQ-labeled XBP 1 single stem-loop minisubstrate (5'FAM-
CUGAGUCCGCAGCACUCAG-3 'BHQ) was purchased from Dharmacon. 0.2 μΜ IRE la* or dP-IREla* were incubated with inhibitors or DMSO for 20 min in cleavage buffer, followed by incubation with 3 μΜ RNA substrate for 5 min. The reaction was quenched by adding urea to a final concentration of 4 M, and the fluorescence was detected on a SpectraMax M5 microplate reader (Molecular Devices) with excitation and emission wavelengths of 494 nm and 525 nm, respectively. The fluorescence intensities were normalized by setting the signal for the reaction with IREla* and DMSO to 1 and the reaction without IREla* to 0. The cleavage products were also resolved by urea PAGE after phenol/chloroform extraction and ethanol precipitation.
Internally 32P-labelled mouse XBP 1 RNA was also used as a substrate, as described (Han, D. et al. Cell 138, 562-575, (2009)).
11. ICAT Footprinting.
[0379] Heavy and light iodonated ICAT reagents were made as previously described
(Underbakke, E. S. et al. Angew. Chem. Int. Ed. 47, 9677-9680 (2008)). Purified human Ire la was exchanged into 50 mM Tris (pH 8.0), 50 mM KCl, 5 mM MgC12, and 0.5 mM TCEP. One 3 μΜ stock solution was divided into three solutions, and each was mixed with either DMSO, APY29, or GP146 to yield solutions containing 1% DMSO and 20 μΜ of inhibitor. Heavy labeling reagent was added to the protein solutions, and 25 μΕ aliquots were taken at specified times and quenched with excess DTT. Samples were precipitated with 0.2% sodium
deoxycholate and 10% trichloroacetic acid on ice for 10 min. The mixtures were centrifuged at 4 °C for 15 min, and pellets were washed with cold acetone. The pellets were then resuspended in 30 μϊ^ of 200 mM Tris (pH 8.0), 7 M urea, and 2.4 mM light labeling reagent, and incubated in the dark for 30 min. The solutions were diluted with 210 μϊ^ 200 mM Tris (pH 8.0), 5.7 mM CaCi2, 0.5 μg porcine trypsin (TPCK treated, Sigma), and 125 ng GluC (Roche), and incubated at room temperature overnight. Samples (0.3 pmol) were injected onto a Thermo Scientific Dionex Acclaim PepmaplOO NanoLC capillary column (C18, 150 mm length, I.D. 75 μιη, 3 μιη particle size) connected inline to a Finnigan LCQ mass spectrometer. Peptides of interest were identified by MS/MS data (Sequest), and corresponding XIC peaks were integrated. Alkylation curves were fit using GraphPad Prism software (Binding - Kinetics, Dissociation - One-phase exponential decay). 12. Molecular Modeling.
[0380] Molecular modeling of KIRA interactions with the ATP-binding site of IREl : To gain insight into how KIRA3 and KIRA6 interact with the IREla ATP-binding site, molecular modeling experiments were used. A model of the DFG-in ATP-binding site conformation was generated from a co-crystal structure of human IREla bound to ADP. As a structure of IREla in the DFG-out conformation has not yet been described, a homology model of this form was generated by using the activation loop of another kinase, the tyrosine kinase Abl2, as a template. Both the DFG-in and DFG-out models were optimized using multi-step all-atom minimization and explicit water molecular dynamics (MD) simulations. Consistent with the observed SAR and type II pharmacophores of KIRA3 and KIRA6, these ligands are only accommodated in the ATP-binding site of IREl when the DFG-motif is in the "out" conformation (DFG-out).
Furthermore, the most favorable docking poses for both KIRA3 and KIRA6 involve both of these ligands making all of the canonical contacts of type II inhibitors. Using this model, the predicted docking scores for the KIRAs shown in Fig. 3c are very consistent with in vitro kinase and R ase inhibition results. For example, KIRA7 (Ri = V; R3 = C: IC50(R ase) = < 30 nM; IC50(kinase) = 35 nM) and KIRA6 (Ri = V; R3 = B: IC50(R ase) = 210 nM; IC50(kinase) = 620 nM) have significantly and slightly more favorable Glide_SP and MMGBSA scores than
KIRA3, respectively. Furthermore, this model has been used to design inactive KIRA3 analogs for controls in cellular assays. Currently, the model for the IREla "DFG-out "inactive conformation is used to filter potential analog syntheses based upon their docking scores.
[0381] The DFG-in structure of IREla was generated from a co-crystal structure of human IREla bound to ADP (PDB code 3P23, chain A) (Ali, M. M. et al. EMBO J. 30, 894-905 (201 1)). The structure was prepared using the protein preparation workflow in Maestro
(Schrodinger) to assign hydrogens, optimize hydrogen bonds, and to perform constraint minimization (impref). The homology model of IREla in the DFG-out conformation was built using the activation loop of a DFG-out template kinase (Abl2; PDB code 3GVU) (SEQ ID NO:6) (Salah, E. et al. J. Med. Chem. 54, 2359-2367 (201 1)) in Prime (Schrodinger). The initial DFG-out model was optimized using the protein preparation workflow described above. Both DFG-in and DFG-out models were then optimized using a multi-step all-atom minimization and molecular dynamics (MD) simulation implemented in the software package Desmond (DE Shaw Research) (Bowers, K. J. et al. in Proceedings of the ACM/IEEE Conference on Supercomputing (SC06) (Tampa, Florida, USA, 2006)). Optimizations were run using the OPLS-AA force field, the TIP4P explicit solvent model in an orthorhombic simulation box 10 A distance in all directions and adding counter ions. Simulations were performed at 300 K and 1.01325 bar using the NPT ensemble class. All other settings were default. The production simulation time was 12 ns. Simulations were run on an IBM E-server 1350 cluster (36 nodes of 8 Xeon 2.3 GHZ cores and 12 GB of memory). Several later simulation frames were extracted from the DFG-in and DFG-out simulations based on conformational diversity and low (stable) RMSD. These frames were then used to generate the DFG-in and DFG-out models of IRElaI642A. To avoid side chain clashes, constraint (impref) minimization (in Maestro, Schrodinger) was performed for the WT and I642A structures of IRE la. These structures were then used for further modeling.
[0382] Using the optimized DFG-in and DFG-out structures of WT and IRE1 aI642A described above, initial binding poses for APY29 and GP146 were generated as follows. Ligands were prepared using ligprep (Schrodinger Inc.) to generate ionization states (pH=7) and stereoisomers resulting in two representations for GP 146 and four for APY29. Ligands were initially docked into the DFG-in and DFG-out models of IRE la using the Induced Fit Docking (IFD)
(Schrodinger Inc.) protocol with default settings. The IFD protocol includes a constraint receptor minimization step followed by initial flexible Glide docking of the ligand using a softened potential to generate an ensemble of poses. For each pose, the nearby receptor structure was then refined using Prime. Each ligand was then re-docked (using Glide) into its corresponding optimized low-energy receptor structure and ranked by Glide score. The best pose with highest IFD score obtained for each ligand was again subjected to MD simulation (8-10 ns production runs) for further optimization of the protein ligand complex. The MD protocol includes a multi- step procedure for minimizations and short MD runs followed by the production MD simulation. Ligand poses were observed to be stable during the production MD runs. The final frames of these simulations were then used for ligand docking after constraint (impref) minimization (Maestro, Schrodinger Inc.). The best pose for each ligand was selected based on the Glide score, known interactions and visual inspection. The 3D plots of ligand poses were produced using PyMol.
13. IREla* Cross-linking to determine oligomer to monomer ratio.
[0383] Structural analysis of IRE1-KIRA and off-target kinase-KIRA complexes: For KIRAs that show sufficient potency and selectivity, further biochemical and biophysical characterization are performed. It is determined if new KIRA analogs are able to prevent the
dimerization/oligomerization of IREla using the crosslinking strategy shown in Figs. 4 and 30. KIRA6, like KIRA3, stabilizes the monomeric state of IREl . Analytical ultra-centrifugation (AUC) is used to further confirm that KIRAs stabilize the monomeric form of IRE la 49. Crystal structures of the most promising KIRAs bound to IREla and the off-target kinase Src are being obtained. These structures are used to refine the docking protocols for IREla, which aid computational design of inhibitors with increased potency. Structures of KIRA-Src complexes are used to identify interactions that are unique to IREla and inform the design of KIRAs that possess increased selectivity. On-target/off-target structural strategy has been used to develop highly potent and selective inhibitors of Toxoplasma gondii and Cryptosporidium parvum CDPK1 (Murphy, R. C. et al. ACS Med. Chem. Lett. 1, 331-335 (2010); Larson, E. T. et al. J. Med. Chem. 55, 2803-2810 (2012); Johnson, S. M. et al. J. Med. Chem. 55, 2416-2426 (2012); Ojo, K. K. et al. J. Clin. Invest. 122, 2301-2305 (2012)). Diffraction-quality crystals of Src bound to KIRA3 have been obatined. A structure of human IRE la bound to ADP has been reported 48. Using the same IRE la expression construct, and purification protocol multi- milligram quantities of homogenous unphosphorylated IRE la have been obtained. This protein is currently being used by to screen for diffraction quality crystals of IREla-KIRA3 and IREla- KIRA6 complexes, and initial screening results are very promising. [0384] Increasing concentrations of IREla* (0.49-30 μΜ) were incubated with DMSO, GP146 (200 μΜ), or APY29 (200 μΜ) for 20 min, then cross-linked by adding 250 μΜ disuccinimidyl suberate (DSS) (Pierce) for 1 hr at RT in cleavage buffer. The reaction was quenched by addition of 50 mM Tris-HCl (pH 7.5). The samples were then boiled, resolved on SDS-PAGE, and immunoblotted for IREla with an anti-IREla antibody, (visualization and quantification with a LI-COR Odyssey scanner).
[0385] Cell culture and XBP1 mRNA splicing. TNS-1 cells were grown in RPMI, 10% fetal calf serum, 1 mM sodium pyruvate, 10 mM HEPES, Pen/strep, 2 mM glutamine and 50 mM β- mercaptoethanol. T-REx 293 IREla or IREla I642A were grown in DME H-21 with 10% fetal calf serum and Pen/strep. After 1 hr incubation with compounds, I S-l cells were treated with 6 nM thapsigargin for 4 hrs, and T-Rex 293 IRE la-expressing cells were treated with 1 μΜ Dox for 8 hrs. The RNA was then extracted using RNeasy Mini Kit (Qiagen), and reverse transcribed using the QuantiTect Reverse Transcription Kit (Qiagen). XBP1 splicing was performed as previously described7. Primers used: sense primer rXBP 1.3S (5'-
AAACAGAGTAGCAGCACAGACTGC-3") (SEQ ID NO:7) and antisense primer rXBP 1.2AS (5'- GGATCTCTAAGACTAGAGGCTTGGTG-3 ') (SEQ ID NO:8) for INS-1 cell line, while sense primer mXBP1.3S (5'-AAACAGAGTAGCAGCGCAGACTGC-3 ') (SEQ ID NO:9) and antisense primer mXBP 1.2AS (5 ' -GGATCTCTAAAACTAGAGGCTTGGTG-3 ' ) (SEQ ID NO: 10) for T-Rex 293 cell line. PCR products were resolved on 2.5% agarose gels, stained with EtBr, and quantified by ImageJ. [0386] Immunoblot analysis. INS-1 cells were incubated with compounds or DMSO for 1 hr, followed by 1 μΜ Tg for 2 hrs. T-Rex 293 IREla -expressing cells were incubated with compounds or DMSO for 1 hr and then treated with 1 μΜ Dox for 8 hrs. Cells were lysed in RIPA buffer (20 mM Tris-HCl, pH 7.5, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate, 150 mM NaCl, 1 mM EDTA, 1% NP-40, complete EDTA-free protease inhibitor (Roche) and phosphatase inhibitor cocktail (Sigma)), and cleared lysates were subjected to SDS-PAGE and transferred to nitrocellulose. Blocking, antibody incubation, and washing were done in PBS or TBS with 0.05% Tween-20 (v/v) and 5% (w/v) non-fat dry milk or BSA, or blocking buffer (Odyssey). Primary antibodies were diluted: IREla (1 : 1000) (Santa Cruz Biotechnology), phospho-IREla (1 : 1000) (Novus Biologicals), GAPDH (1 :3000) (Santa Cruz Biotechnology), Myc (1 :4000) (Santa Cruz Biotechnology). The antibody binding was detected by using near- infrared-dye-conjugated secondary antibodies and visualized on the LI-COR Odyssey scanner. [0387] As described herein, IREla* means a recombinant human (rh) IREla. rh IREla has the human IREla (469-977) sequence: SEQ ID NO: 1 (w/ his tag); and SEQ ID NO:2 (w/o his tag).
14. Determine whether blocking the terminal UPR with IREla kinase inhibitors prevents ER stress-induced β-cell degeneration. On-target effects of KIRAs, underlying mechanisms, and amelioration of beta cell death and preservation of function under ER stress by KIRA6
Inhibiting IREla's RNase activity using KIRAs shuts down endonucleolytic decay of mRNAs localizing to the ER membrane. ER-localized mRNA decay has been directly linked to the terminal UPR. One model holds that depletion of key mRNAs encoding factors needed to maintain ER structural and functional integrity (e.g. ER chaperones) may underlie apoptotic effects. IREl RNase targets select microRNA (miR) precursors to terminate their biogenesis. These mature miRs normally exert inhibitory effects on gene expression of key pro-apoptotic targets; e.g., depletion of four select miRs leads to: (i) translational derepression of the apoptosis initiator caspase 2, and (ii) stabilization of the mRNA encoding pro-oxidant thioredoxin- interacting protein (TXNIP). Using engineered chemical-genetic systems is elucidating these mechanistic signature events of IREla RNase-induced cell death, and helping to understand the physiological consequences of inhibiting IREla RNase activity by KIRAs. 15. Duration and magnitude of ER stress determine entry into the
terminal UPR through high-order oligomerization and
hyperactivation of IREla kinase/RNase catalytic domains.
[0388] To rigorously test for cytoprotective effects, thresholds of ER stress were dilenated that when crossed push cells into apoptosis. Using rat insulinoma (INS-1) cells that have a well- developed ER and secrete insulin, the duration and magnitude of ER stress that triggers apoptosis were quantified. Two variables— concentration of ER stress inducer (e.g. Thapsigargin— Tg) and time of exposure to the agent— are directly linked to the percentage of cells entering apoptosis (Fig. 28, A and B). Such regimes can be defined for other ER stress inducers such as the glycosylation inhibitor, tunicamycin (Tm) (Fig. 28, C). Increasing ER stress causes progressive increases in endogenous IRE la phosphorylation, increases in XBP 1 mRNA splicing (Fig. 28, E), depletion through endonucleolytic decay of the ER-localized mRNA, Ins l, which encodes proinsulin (Fig. 28, F), and induction of the pro-apoptotic transcription factor, CHOP (Fig. 28, G). [0389] These aforementioned terminal UPR signaling events can be completely mimicked simply by controlled over-expression of IREla, in the complete absence of upstream ER stress. Tetracycline-inducible isogenic INS-1 stable cell lines expressing WT IREla were generated. Induced with doxycycline (dox) the transgenic IREla proteins oligomerize, spontaneously trans- autophosphorylate and trigger XBP1 mRNA splicing (Fig. 29, A and B). The transgenic systems are finely tuneable, with increasing [Dox] causing progressively greater IREla induction (the transgenic IREla protein is Myc-tagged). Phospho/Myc IREla ratios are finely controllable (and measureable) with increasing [Dox], as is XBP1 mRNA splicing. Mimicking dose- dependency by ER stress agents into a terminal UPR, increasing [Dox] spontaneously triggers entry into a terminal UPR by causing IREla kinase hyper-phosphorylation and RNase hyperactivation past a critical threshold and induction of key signature events of the terminal
UPR (Fig. 29, C). These include reduction of miR-17 (Fig. 29, D) and Insl mRNA, induction of CHOP mRNA (Fig. 29, E), induction and proteolytic cleavage of caspases 1,2, and 3 (Fig. 29, F), and apoptosis as measured by Annexin-V staining (Fig. 29, G).
[0390] KIRAs break high-order oligomerization of IRE1 a kinase domains, attenuate RNAse activity, and reduce entry of cells into the Terminal UPR. In exciting preliminary data, all these terminal UPR endpoints are curtailed by pre-treating cells with KIRA6, before exposing them to ER stress inducers, in vitro, KIRA6 inhibits IRE la* RNase and kinase activities with similar IC50S (Fig. 30, B and C). in vivo, KIRA6 inhibits endogenous IRE la auto-phosphorylation in a dose-dependent manner (Fig. 30, D); in contrast the aldehyde-based IREla RNase-inhibitor, STF, does not inhibit IREla auto-phosphorylation, nor does a control compound KIRA6(in). [0391] Furthermore, in vitro, KIRA6 reduces concentration- dependent oligomerization of IREla* (Fig. 30, E). in vivo, KIRA6 inhibits endogenous IREla - mediated XBP 1 mRNA splicing provoked by Tm (Fig. 30, F). Intriguingly, KIRA6 inhibits ER-localized endonucleolytic decay of Ins 1 mRNA at lower doses of the drug than needed to inhibit XBP1 mRNA splicing (Fig. 30, G); this discriminatory effect may occur because higher-order oligomers are needed to catalyze Ins l mRNA decay, whereas dimers suffice for XBP1 mRNA splicing. Because ER- localized endonucleolytic mRNA decay promotes apoptosis— in contrast to XBP 1 mRNA splicing, which promotes adaptation— this differential effect of KIRAs reveals the existence of a natural "therapeutic window" which reduces entry of INSl-1 cells into apoptosis (Fig. 30, H). These cytoprotective effects of KIRA6 extend to myriad cell types, including freshly harvested pancreatic islets from C57/BL6 mice treated with Tm (Fig. 30, 1). KIRA6 cytoprotective effects are dependent on IREla because they are absent in Irela ~'~ mouse embryonic fibroblasts (MEFs), but still demonstrable in WT and Xbpl ~'~ MEFs (Fig. 30, J). A model of KIRA6- mediated cytoprotection is shown (Fig. 30, J); it posits that the type II kinase inhibitor, KIRA6, reduces kinase/RNAse homo-oligomerization on the cytosolic face of IREla, which
consequently reduces RNase hyperactivity under ER stress, preventing pro-apoptotic ER- localized mRNA decay and granting cells extended reprieve from programmed cell death.
16. UPR and Diabetes
[0392] β-cells from mouse and human islets exposed to irremediably high ER stress will show activation of many of the terminal UPR endpoints described herein. Besides the ER-localized mRNAs and select micro RNAs so far identified as IREla substrates, other miRs and small non- coding RNAs remain to be discovered and related changes will constitute a Terminal UPR signature that can be followed as therapeutic endpoints for amelioration by KIRAs.
[0393] Described herein is the characterization of four select miRs that decay in vivo upon IREla hyperactivation. These are miR-17, miR-34a, miR-96, and miR-125b. WT-IREla* directly cleaved pre-miR-17 in vitro at sites distinct from those cleaved by DICER, as mapped by primer extension. The scission sites of pre-miR-17 are identical to those of XBP 1 mRNA— (G/C)— and diverge at the flanking regions. Thus, by reducing levels of pre-miRs, IREla antagonizes DICER action to reduce cellular levels of the corresponding mature miRs.
Intriguingly, IRE la* (I642G), which can be activated by 1NM-PP1 to cleave XBP1 mRNA in vitro, can also cleave pre-miR-17 under INM-PPl . An RNAse mutant, IRE la* (N906A), is compromised for cleavage of pre-miR-17 (Fig. 31, A-C). This provokes the hypothesis that
IRE la is capable of exhibiting extra-XBPl mRNA endonucleolytic activity in a graded fashion. As IRE la homo-oligomerizes in the ER membrane in proportion to the concentration of unfolded proteins in the ER lumen, it progressively iraws-autophosphorylates. Furthermore, salt bridges between phospho-amino acid groups and other residues reinforce higher-order homo- oligomerization of kinase/RNAse domains, as was shown using yeast IREl . Thus, as IRE la protein clusters into higher-order oligomers, it acquires increasing activity towards its RNA substrates. The most efficient substrate is XBP1 mRNA, followed by select pre-miRs (e.g. 17, 34a, 96, and 125b), then followed by the ER-localized mRNA substrate, Insl .
[0394] By breaking higher-order IRE la oligomers with KIRAs, many miR targets will be preserved at levels found in unstressed cells. As the four miRs found to exert inhibitory effects on post-transcriptional gene regulation of caspase 2 and the NLRP3 inflammasome
activator,TX IP, KIRA6 will reduce levels of these amplifiers of ER stress, even though unfolded proteins still persist in the ER lumen. Preliminary dataare consistent with these predictions. It is an interesting possibility that it is not unfolded proteins in the ER per se that compromise cell function and lead to programmed cell death, but instead active terminal UPR signaling through IREla RNase hyperactivation. Thus, IREla KIRAs should reduce oligomerization by reinforcing the DFG-out, inactive ATP -binding site conformation, and consequently reduce RNase activity to decrease ER stress-induced cell death. As a corollary, type I kinase inhibitors, such as INM-PPl, should increase oligomerization by reinforcing the DFG-in, active ATP-binding site conformation, and consequently increase RNase activity to increase ER stress-induced cell death.
[0395] Type I kinase inhibitors antagonize the effects of type II kinase inhibitors (KIRAs) to promote cell death under ER stress. Fig. 32 shows data consistent with this notion. KIRAs should ameliorate terminal UPR endpoints promoted by INM-PPl in the context of the IREla (1642 G) cellular chemical genetic systems under ER stress: Ins l and 2 mRNA decay, miR-17, 34a, 96, and 125b decay, Caspase 1, 2, and 3 cleavage, TXNIP mRNA stabilization and translation, and consequent IL- 1 β maturation and secretion. Measurement of cell death endpoints (Annexin-V staining) are being made in the engineered cell systems as a function of the competing effects of 1NM-PP1 and KIRAs. As a prelude to testing in in vivo mouse models, is testing of all terminal UPR endpoints, with and without KIRA6, in freshly-harvested murine (C57BL/6) islets subjected to exogenous ER stress agents, as well as islets from two spontaneous models of diabetes: the Ins2(C96Y)— "Akita"— diabetic mouse and overexpression of IREl in islets.
17. Characterization of KIRAs
[0396] Potent and selective IREl inhibitors are being tested for their general toxicity against human cultured cell lines. For compounds that lack toxicity, the ADME, pharmacokinetic and toxicological properties are being determined. Compounds with favorable PK/ADMET properties are tested for efficacy in two mouse diabetic models— the proinsulin folding mutant, Akita, and overexpression of IREla in murine islets.
[0397] Cytotoxicity testing: Any KIRAs that show sub-micromolar potency in the cellular models described above are subjected to cytotoxicity assays against seven mammalian cell lines. These assays are helpful in predicting any general or tissue specific toxicity that may occur when KIRAs are administered to animals. KIRAs are tested against the following seven cell lines: L1210 (mouse lymphoblasts), W1-L2 (human lymphoblasts), HT-1080 (human fibrosarcoma), SF-539 (human glioblastoma), NCI-H460 (human large cell lung carcinoma), HCC-2998 (human colon carcinoma), and HL-60 (human promyelocytes). This panel provides sufficient diversity to predict cellular toxicity in a wide variety of tissues. The fold difference between efficacy in models and mammalian cell cytotoxicity provides a rough therapeutic index (TI). In some embodiments, there is >50-fold TI for KIRAs that are tested in vivo.
[0398] In vivo PK/ADMET studies: KIRAs that are sufficiently potent in the cellular assays are subjected to pharmacokinetic and toxicity studies in mice. First, compounds are tested in a dose escalation study for any observed toxicity. Mice are sequentially injected with single IV doses of 1 mg kg, 10 mg/kg, and 100 mg/kg of compound. During these single dose studies, the mice are observed for signs of acute toxicity, such as respiratory or neurological abnormalities.
Compounds that are not toxic at 10 mg/kg are subjected to PK/ADME testing. This involves administration of a single dose (10 mg/kg by IV) followed by blood sampling at intervals of 30, 60, 120, 180, 240, and 300 minutes. These experiments are performed with groups of 3 mice per KIRA. Plasma is separated and extracted with acetonitrile for compound concentration measurements by combined liquid chromatography/electrospray-ionization mass spectrometry (LCMS). The results provide the maximum concentration (Cmax), time of maximum
concentration (Tmax), area under the curve (AUC), and an estimation of half-life (T1/2).
Compounds that demonstrate sufficient exposure are candidates for the in vivo efficacy studies described herein. 18. Inhibitors of IREla kinase/endoribonuclease to treat Retinitis
Pigmentosa
[0399] KIRAs inhibit IRE la in cultured cells at concentrations of less than ΙΟΟηΜ and strikingly protect cell viability and function under conditions of ER stress. Moreover, the leading compound in this class has shown efficacy in a rodent model of RP caused by mutation in rhodopsin. Described herein is the optimization of potency and efficacy in the KIRA class of compounds against retinal degeneration to develop a clinical candidate for treatment of RP.
19. Allosteric modulation of the IREla RNase with novel kinase inhibitor.
[0400] KIRA6, a more potent version of earlier KIRAs, whose structure is shown in Fig. 30A has been developed. This compound dose-dependently reduces kinase autophosphorylation and XBP1 splicing activity of IREla* (WT) (Fig. 30B-C). In addition, KIRA6 dose-dependently inhibits IREla* (WT) cleavage of pre-miR-17 (Fig. 3 ID).
20. Intravitreal Injections of small molecules
Based on known rat vitreous volumes, 2 μΐ was injected intravitreally into each eye. Tm (20 μg/μL final concentration) plus/minus KIRA6 (10 μΜ final concentration) was injected into SD rats at P21 with an equivalent amount of DMSO as a vehicle control. Retinas were collected at 48 and 72 hrs after injections in Trizol (Invitrogen) for qPCR analysis. Eyes were examined by optical coherence tomography (OCT) 7 days post injection and subsequently collected for morphological analysis. P23H rats were injected with KIRA6 (10 μΜ final concentration) or DMSO vehicle control at P9 and P15, and eyes were examined at P40 by OCT, and
morphological analysis.
21. Image guided optical coherence tomography (OCT)
[0401] Mice were anaesthetized with 1.5-3% isoflurane, eyes were dilated with 2.5% phenylephrine hydrochloride and 1% tropicamide, and corneas were kept moist with regular application of 2.5% methylcellulose. Eyes were examined using a Micron III retinal imaging system (Phoenix Research Labs). Spectral domain OCT images were acquired with a Micron Image Guided OCT System (Phoenix Research Labs) by averaging 10 to 50 scans.
22. Morphological analysis of retinas
[0402] Outer nuclear layers (ONL) were quantified as previously described (Lewin, A.S. et al, Nature medicine 4, 967-971 (1998)). Briefly, rats were euthanized by CO2 inhalation and their eyes were immediately enucleated and immersed in 2% paraformaldehyde and 2.5%
glutaraldehyde in phosphate buffered saline. Subsequently, eyes were bisected on the vertical meridian through the optic nerve head and embedded in Epon-Araldite resin; 1 μιη sections were cut and stained with toluidine blue. ONL thickness was measured at 54 locations around the retina using Bioquant image analysis (Bioquant; R&M Biometrics).
SEQ ID NO: 1
MSYYHHHHHHDYDI PTTENLYFQGAMDPE hq qqqlqhqqfq 480
kelekiqllq qqqqqlpfhp pgdtaqdgel ldtsgpyses sgtsspstsp rasnhslcsg 540 ssaskagssp sleqddgdee tswivgkis fcpkdvlghg aegtivyrgm fdnrdvavkr 600 ilpecfsfad revqllresd ehpnviryfc tekdrqfqyi aielcaatlq eyveqkdfah 660 lglepitllq qttsglahlh slnivhrdlk phnilismpn ahgkikamis dfglckklav 720 grhsf srrsg vpgtegwiap emlsedcken ptytvdif sa gcvfyyvise gshpfgkslq 780 rqanillgac sldclhpekh edviarelie kmiamdpqkr psakhvlkhp ffwslekqlq 840 f fqdvsdrie kesldgpivk qlerggraw kmdwrenitv plqtdlrkfr tykggsvrdl 900 lramrnkkhh yrelpaevre tlgslpddfv cyftsrfphi lahtyramel csherlfqpy 960 yfheppepqp pvtpdal
SEQ ID NO:2
hq qqqiqhqqfq 4 so
kelekiqllq qqqqqlpfhp pgdtaqdgel ldtsgpyses sgtsspstsp rasnhslcsg 540 ssaskagssp sleqddgdee tswivgkis fcpkdvlghg aegtivyrgm fdnrdvavkr 600 ilpecfsfad revqllresd ehpnviryfc tekdrqfqyi aielcaatlq eyveqkdfah 660 lglepitllq qttsglahlh slnivhrdlk phnilismpn ahgkikamis dfglckklav 720 grhsfsrrsg vpgtegwiap emlsedcken ptytvdifsa gcvfyyvise gshpfgkslq 780 rqanillgac sldclhpekh edviarelie kmiamdpqkr psakhvlkhp ffwslekqlq 840 ffqdvsdrie kesldgpivk qlerggraw kmdwrenitv plqtdlrkfr tykggsvrdl 900 lramrnkkhh yrelpaevre tlgslpddfv cyftsrfphl lahtyramel csherlfqpy 960 yfheppepqp pvtpdal
[0403] It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

Claims

WHAT IS CLAIMED IS:
1. A compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000131_0001
wherein,
ring A is substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
L1 is a bond or unsubstituted C1-C5 alkylene;
L2 is a bond, -NR6a-, -0-, -S-, -C(O)-
, -S(O)-, -S(0)2-, -NR6aC(0)-, -C(0)NR6b-, -C(0)(CH2)z2-, -NR6aC(0)0-, -NR6aC(0)NR6b-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
R1 is hydrogen, oxo, halogen, -CX3, -CN, -S02C1, -SOnR10, -SOvNR7R8,
-NHNH2, -ONR7R8, -NHC=(0)NHNH2,
-NHC=(0)NR7R8, -N(0)m, -NR7R8, -C(0)R9, -C(0)-OR9, -C(0)NR7R8, -OR10, -NR7SO„R10, - NR7C=(0)R9, -NR7C(0)OR9, -NR7OR9, -OCX3, -OCHX2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R2 is hydrogen, oxo, halogen, -CXa 3, -CN, -S02C1, -SO„iR10a, -SOviNR7aR8a, -NHNH2, -ONR7aR8a, -NHC=(0)NHNH2,
-NHC=(0)NR7aR8a, -N(0)mi, -NR7aR8a, -C(0)R9a, -C(0)OR9a, -C(0)NR7aR8a, -OR10a, - NR7aSO„iR10a, -NR7aC=(0)R9a, -NR7aC(0)OR9a, -NR7aOR9a, -OCXa 3, -OCHXa 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R3 is independently hydrogen, oxo, halogen, -CXb 3, -CN, -S02C1, -SOn2R10b, - SOv2NR7bR8b, -NHNH2, -ONR7bR8b, -NHC=(0)NHNH2,
-NHC=(0)NR7bR8b, -N(0)m2, -NR7bR8b, -C(0)R9b, -C(0)-OR9b, -C(0)NR7bR8b, -OR10b, - NR7bSO„2R10b, -NR7bC=(0)R9b, -NR7bC(0)OR9b, -NR7bOR9b, -OCXb 3, -OCHXb 2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R4 and R5 are independently hydrogen or unsubstituted C1-C6 alkyl; R7, R8, R9, R10, R6a, R7a, R8a, R9a, R10a, R6b, R7b, R8b, R9b and R10b are independently hydrogen, halogen, -CF3, -CN, -OH, -NH2, -COOH, -CONH2, -N02, -SH, -S02C1, -SO3H, -SO4H, -S02NH2, -NHNH2, -ONH2, -NHC=(0)NHNH2, -NHC=(0)NH2, -NHS02H, - NHC=(0)H, -NHC(0)OH, -NHOH, -OCF3, -OCHF2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R7 and R8 substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7a and R8a substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R7b and
R 8b substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
each occurrence of the symbols n, nl, and n2 is independently an integer from 0 to 4;
each occurrence of the symbols m, ml, m2, v, vl, and v2 is independently an integer from 1 to 2;
the symbol z is an integer from 0 to 2;
the symbol z2 is an integer from 1 to 4;
each occurrence of the symbols X, Xa, and Xb is independently a halogen. 2. The compound of claim 1, wherein R3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. 3. The compound of claim 2, wherein R3 is hydrogen.
4. The compound of claim 3, wherein the symbol z is 1. 5. The compound of claim 1 , wherein R2 is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
6. The compound of claim 5, wherein R2 is substituted or unsubstituted alkyl.
7. The compound of claim 6, wherein R2 is substituted or unsubstituted C l-
C6 alkyl.
8. The compound of claim 7, wherein R2 is unsubstituted Ci-Ce alkyl.
9. The compound of claim 8, wherein R2 is unsubstituted isopropyl.
10. The compound of claim 8, wherein R2 is unsubstituted tert-butyl.
1 1. The compound of claim 1 , wherein R4 and R5 are hydrogen.
12. The compound of claim 1 , wherein L1 is a bond.
13. The compound of claim 1 , wherein L1 is unsubstituted methylene.
14. The compound of claim 1 , wherein L2 is -NR6aC(0)NR6b-.
15. The compound of claim 14, wherein R6a and R* are hydrogen.
16. The compound of claim 1 , wherein R1 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. 17. The compound of claim 16, wherein R1 is substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. 18. The compound of claim 17, wherein R1 is substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl.
19. The compound of claim 18, wherein R1 is substituted phenyl. 20. The compound of claim 19, wherein R1 is phenyl substituted with -CF3 or halogen. 21. The compound of claim 1 , wherein ring A is substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene. 22. The compound of claim 21, wherein ring A is substituted or unsubstituted C6-Cio arylene. 23. The compound of claim 22, wherein ring A is unsubstituted naphthalenyl. 24. The compound of claim 1 having the formula:
Figure imgf000134_0001
wherein,
L3 is a bond, -NR6b-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. 25. The compound of claim 24 having the formula:
Figure imgf000134_0002
The compound of claim 1 selected from the group consisting of:
Figure imgf000135_0001
27. A pharmaceutical composition comprising a pharmaceutically acceptable excipient and a compound, or a pharmaceutically acceptable salt thereof, of any one of claims 1 to 26. 28. A method of treating a disease in a patient in need of such treatment, said method comprising administering a therapeutically effective amount of a compound, or a pharmaceutically acceptable salt thereof, of any one of claims 1 to 26 to said patient, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes. 29. The method of claim 28, wherein the disease is a neurodegenerative disease, demyelinating disease, cancer, or diabetes.
30. The method of claim 28, wherein the disease is a neurodegenerative disease.
31. The method of claim 30, wherein the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration,
Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru. 32. The method of claim 28, wherein the disease is a demyelinating disease. 33. The method of claim 32, wherein the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis. 34. The method of claim 28, wherein the disease is cancer. 35. The method of claim 34, wherein the cancer is multiple myeloma. 36. The method of claim 28, wherein the disease is diabetes. 37. The method of claim 36, wherein the diabetes is type I diabetes. 38. The method of claim 36, wherein the diabetes is type II diabetes. 39. The method of claim 28, wherein the disease is an eye disease. 40. The method of claim 39, wherein the eye disease is retinitis pigmentosa, retinal degeneration, macular degeneration, or Wolfram Syndrome. 41. The method of claim 28, wherein the disease is a fibrotic disease. 42. The method of claim 41, wherein the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis. 43. A method of modulating the activity of an Irel protein, said method comprising contacting said Irel protein with an effective amount of a compound, or a pharmaceutically acceptable salt thereof, of any one of claims 1 to 26. 44. The method of claim 43, wherein said modulating is inhibiting.
45. The method of claim 44, wherein said activity is kinase activity. 46. The method of claim 45, wherein said kinase activity is
autophosphorylation activity. 47. The method of claim 44, wherein said activity is oligomerization activity. 48. The method of claim 47, wherein said oligomerization activity is dimerization activity. 49. The method of claim 44, wherein said activity is RNase activity. 50. The method of claim 44, wherein a cell comprises said Irel protein. 51. The method of claim 50, wherein said activity of the Irel protein is increasing apoptosis of said cell. 52. The method of claim 50, wherein an organ comprises said cell. 53. The method of claim 50, wherein an organism comprises said cell. 54. The method of claim 53, wherein said organism has a disease associated with said Irel protein activity. 55. The method of claim 54, wherein said disease is a neurodegenerative disease, demyelinating disease, cancer, eye disease, fibrotic disease, or diabetes 56. The method of claim 55, wherein the disease is a neurodegenerative disease. 57. The method of claim 56, wherein the neurodegenerative disease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinal degeneration, macular degeneration,
Parkinson's Disease, Alzheimer Disease, Huntington's Disease, Prion Disease, Creutzfeldt- Jakob Disease, or Kuru. 58. The method of claim 55, wherein the disease is a demyelinating disease.
59. The method of claim 58, wherein the demyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis. 60. The method of claim 59, wherein the demyelinating disease is Multiple Sclerosis. 61. The method of claim 55, wherein the disease is cancer. 62. The method of claim 61, wherein the cancer is multiple myeloma. 63. The method of claim 55, wherein the disease is diabetes. 64. The method of claim 63, wherein the diabetes is type I diabetes. 65. The method of claim 63, wherein the diabetes is type II diabetes. 66. The method of claim 55, wherein the disease is an eye disease. 67. The method of claim 66, wherein the eye disease is retinitis pigmentosa, retinal degeneration, macular degeneration, or Wolfram Syndrome. 68. The method of claim 55, wherein the disease is a fibrotic disease. 69. The method of claim 68, wherein the fibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liver disease), or hepatic fibrosis.
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CN104995192A (en) 2015-10-21
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