Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
  • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
  • C07D403/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/517—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D217/00—Heterocyclic compounds containing isoquinoline or hydrogenated isoquinoline ring systems
  • C07D217/22—Heterocyclic compounds containing isoquinoline or hydrogenated isoquinoline ring systems with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to carbon atoms of the nitrogen-containing ring
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
  • C07D239/70—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings condensed with carbocyclic rings or ring systems
  • C07D239/72—Quinazolines; Hydrogenated quinazolines
  • C07D239/78—Quinazolines; Hydrogenated quinazolines with hetero atoms directly attached in position 2
  • C07D239/84—Nitrogen atoms
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
  • C07D401/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
  • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
  • C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
  • C07D413/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring-member bond
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
  • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
  • C07D417/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond

Definitions

• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci- C 4 alkyl, -X-optionally substituted Ci-C 4 heteroalkyl, -X-optionally substituted Ci- C 4 fluoroalkyl, optionally substituted C 3 -C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; or two R 6 are taken together with the N atom to which they are attached to form an
• each R 7 is independently optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fiuoroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• each R 8 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, , optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• each R 9 is independently optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• a 2 is N or CR A ;
• R A , R A1 , R A2 , and R A3 are each independently H, halogen, optionally substituted Ci-
• R 10 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• ring A is a monocyclic carbocycle or a monocyclic heterocycle
• each R 3 is independently H, halogen, -CN, -OR 11 , -SR 11 , -N(R U ) 2 , optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted C 3 -C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; each R 11 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• n 0, 1, 2, 3, or 4;
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2 , optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 -C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; and
• R 12 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Cioheterocycloalkyl, optionally substituted ar l or o tionall substituted heteroar l.
• q 0, 1, 2, or 3.
• q 0, 1, 2, or 3.
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X-optionally substituted Ci-
• each R 6 is independently H.
• each R 2 is independently H, optionally substituted Ci-
• C 4 alkyl optionally substituted Ci-C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 6 is H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X-optionally substituted Ci- C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl; q is 0 or 1; and R 2 is H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, or optionally substituted Ci- C 4 fluoroalkyl.
• R 6 is H. In some embodiments, A 2 is N. In some embodiments, A 2 is CR A . In some embodiments, R A is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R A is H. In some embodiments, R A1 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R A1 is H. In some embodiments, R ⁇ is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R is H. In some embodiments,
• R is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl,
• R AJ is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, or -OR . In some embodiments,
• R is optionally substituted Ci-C 4 alkyl
• R AJ is methyl, ethyl, propyl or butyl .
• R A3 is -OR 10 and R 10 is methyl, ethyl, propyl or butyl .
• ring A is phenylene or a monocyclic C3-C 8 cycloalkylene that is selected from cyclopropylene, cyclobutylene, cyclopentylene, cyclohexylene, cycloheptylene, and
• ring A is phenylene.
• ring A is a monocyclic Ci-Csheteroarylene containing 1-4 N atoms, and 0 or 1 O or S atom, or a monocyclic Ci-Csheteroarylene containing 0-4 N atoms, and 1 O or S atom.
• ring A is a monocyclic 6-membered heteroarylene selected from pyridinylene, pyrimidinylene, pyrazinylene, and pyridazinylene.
• ring A is pyridinylene.
• ring A is a monocyclic 5-membered heteroarylene selected from furanylene, thienylene, pyrrolylene, oxazolylene, thiazolylene, imidazolylene, pyrazolylene, triazolylene, tetrazolylene, isoxazolylene, isothiazolylene, oxadiazolylene, and thiadiazolylene.
• ring A is oxazolylene, thiazolylene, imidazolylene, pyrazolylene, or oxadiazolylene.
• ring A is pyrazolylene.
• ring A is a ring A is a monocyclic Ci-Csheterocycloalkyle containing at least 1 N atom in the ring that is selected from aziridinylene, azetidinylene, pyrrolidinylene, pipendinylene, piperazinylene, and azepanylene.
• each R 3 is independently H, halogen, -CN, -OR 11 , -SR 11 , optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fiuoroalkyl; and n is 1, 2, or 3.
• R 3 is optionally substituted Ci-C 4 alkyl.
• R 3 is methyl, ethyl, propyl, or butyl. In some embodiments, R 3 is - OR 11 . In some embodiments, R 11 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R 11 is methyl, ethyl, propyl, or butyl. In some embodiments, R 11 is -CF 3 or -CH 2 CF 3.
• R 4 is H, halogen, -CN, - OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted d-C 4 alkyl, or optionally substituted d- C 4 fluoroalkyl.
• R 4 is H.
• R 4 is halogen.
• R 4 is -CI, -Br, -F, or -I.
• R 4 is -OR 12 . In some
• R 12 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci- C 4 fluoroalkyl.
• R 4 is optionally substituted Ci-C 4 alkyl.
• R 4 is methyl, ethyl, propyl, or butyl.
• R 4 is optionally substituted Ci-C 4 fluoroalkyl.
• R 4 is -CF 3 or -CH 2 CF 3 .
• R 5 is H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 5 is H.
• R 5 is halogen.
• R 5 is -CI, -Br, -F, or -I.
• R 5 is - OR 12 .
• R 12 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 5 is optionally substituted Ci-C 4 alkyl.
• R 5 is methyl, ethyl, propyl, or butyl. In some embodiments, R 5 is optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R 5 is -CF 3 or -CH 2 CF 3 .
• the compound has the structure of formula (la)
• the compound has the structure of formula (lb)
• the compound has the structure of formula (Ic)
• q 0 or 1.
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X-optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted
• each R 6 is independently H.
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-
• a 2 is N. In some embodiments, A 2 is CR A . In some embodiments, R A is H, optionally substituted Ci-C 4 fluoroalkyl.
• R A is H.
• R A1 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-
• R A1 is H.
• R A2 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R ⁇ is
• R A3 is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted aryl, or -OR 10 . In some embodiments, R A3 is
• Ci-C 4 alkyl optionally substituted Ci-C 4 fluoroalkyl, or -OR 10 .
• R A3 is optionally substituted Ci-C 4 alkyl .
• R A3 is methyl, ethyl, propyl, or butyl .
• R A3 is ethyl
• ring A is phenylene.
• ring A is a monocyclic 6-membered heteroarylene selected from pyridinylene, pyrimidinylene, pyrazinylene, and pyridazinylene.
• ring A is pyridinylene.
• ring A is a monocyclic 5-membered heteroarylene selected from furanylene, thienylene, pyrrolylene, oxazolylene, thiazolylene, imidazolylene, pyrazolylene, triazolylene, tetrazolylene, isoxazolylene, isothiazolylene, oxadiazolylene, and thiadiazolylene.
• ring A is pyrazolylene.
• each R 3 is independently H, -OR 11 , optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-
• R 11 is H, optionally substituted Ci- C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted d-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• the compound has the structure of formula (Id)
• R is optionally substituted Ci-C 4 alkyl
• the compound has the structure of formula (Ie)
• ring A is phenylene, pyridinylene, pyrazolylene, thiazolylene, imidazolylene, oxazolylene, or oxadiazolylene.
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted d-C 4 alkyl, or optionally substituted Ci-C 4 fiuoroalkyl.
• a compound, or a pharmaceutically acceptable salt, or solvate thereof selected from:
• the compound or pharmaceutically acceptable salt, or solvate thereof selectively binds to IRE la at one or more binding sites.
• the IREla comprises an RNase domain, a kinase domain, or any combination thereof.
• the kinase domain is an auto-transphosphorylation kinase domain.
• the kinase domain comprises an ATP -binding pocket.
• the kinase domain comprises an activation loop.
• at least one binding site is within the RNase domain. In some embodiments, at least one binding site is within the kinase domain.
• the at least one binding site is within the ATP -binding pocket of the kinase domain. In some embodiments, the at least one binding site is within the activation loop of the kinase domain. In some embodiments, binding occurs at a first binding site. In some embodiments, the first binding site is located within the RNase domain, kinase domain, ATP -binding pocket, or activation loop. In some embodiments, the first binding site comprises at least one amino acid residue of within amino acid residues 465-977 of SEQ ID NO: 1. In some embodiments, the first binding site comprises at least one amino acid residue within amino acid residues 568-833 of SEQ ID NO: 1.
• the first binding site comprises at least one amino acid residue within amino acid residues 577-586, 597, 599, 626, 642-643, 645, 648, 688, 692-693, 695, or 711 of SEQ ID NO: 1. In some embodiments, the first binding site comprises at least one amino acid residue within amino acid residues 710-725 or 729-736 of SEQ ID NO: 1. In some embodiments, the first binding site comprises at least one amino acid residue within amino acid residues 835-963 of SEQ ID NO: 1. In some
• binding further occurs at a second binding site.
• the second binding site is located within the RNase domain, the kinase domain, the ATP -binding pocket, or the activation loop.
• the second binding site comprises at least one amino acid residue of within amino acid residues 465-977 of SEQ ID NO: 1.
• the second binding site comprises at least one amino acid residue within amino acid residues 568- 833 of SEQ ID NO: 1.
• the second binding site comprises at least one amino acid residue within amino acid residues 577-586, 597, 599, 626, 642-643, 645, 648, 688, 692-693, 695, or 711 of SEQ ID NO: 1.
• the second binding site comprises at least one amino acid residue within amino acid residues 710-725 or 729-736 of SEQ ID NO: 1. In some embodiments, the second binding site comprises at least one amino acid residue within amino acid residues 835-963 of SEQ ID NO: 1. In some embodiments, binding occurs when the IREla is in a homo-dimerized conformation. In some embodiments, binding occurs when the IREla is in an oligomerized conformation. In some embodiments, binding occurs when the IREla is in a non-oligomerized or non-dimerized conformation. In some embodiments, binding occurs when the IREla is in an ATP -bound state.
• binding occurs when the IREla is in a non-ATP -bound state.
• the compound selectively binds to a first IREla.
• selectively binding to the first IREla blocks dimerization of the first IREla to a second IREla.
• selectively binding to the first IREla blocks auto-transphosphorylation of the first IREla.
• selectively binding to the first IREla blocks auto-transphosphorylation of a second IREla to which the first IREla is dimerized.
• selectively binding to the first IREla blocks activation of the first IREla.
• selectively binding to the first IREla blocks activation a second IREla to which the first IREla is dimerized. In some embodiments, selectively binding to the first IREla blocks kinase activity of the first IREla. In some embodiments, selectively binding to the first IREla blocks kinase activity of a second IREla to which the first IREla is dimerized. In some embodiments, selectively binding to the first IREla blocks RNase activity of the first IREla. In some embodiments, selectively binding to the first IREla blocks RNase activity of a second IREla to which the first IREla is dimerized.
• a compound that selectively binds a first IREla at two or more sites wherein when the compound is bound to the first IREla protein, the compound binds to an ATP -binding pocket of the first IREla and blocks the binding of ATP to the first IREla.
• the ATP binding pocket is comprised within a kinase domain.
• the ATP binding pocket is comprised within amino acid residues 465-977 of SEQ ID NO: 1.
• the ATP binding pocket is comprised within amino acid residues 568-833 of SEQ ID NO: 1.
• the ATP binding pocket comprises one or more of amino acid resides 577-586, 597, 599, 626, 642-643, 645, 648, 688, 692-693, 695, or 711 of SEQ ID NO: 1.
• a pharmaceutical composition comprising any one of the compounds described herein, or a pharmaceutically acceptable salt or solvate thereof.
• the pharmaceutical composition further comprises one or more
• a method for treating or ameliorating the effects of a disease associated with altered IREl signaling comprising administering to a subject in need thereof a pharmaceutical composition, wherein the pharmaceutical composition comprises the compound of any one of the compounds described herein.
• the disease is cancer.
• the cancer is a solid cancer or a hematologic cancer.
• the cancer is ovarian cancer, breast cancer, or triple negative breast cancer (TNBC).
• a method for treating or ameliorating a cell proliferative disorder comprising administering a pharmaceutical composition comprising a compound, or a pharmaceutically acceptable salt, or solvate thereof, that selectively binds to at least one amino acid residue of a IRE1 family protein comprising an RNase domain and kinase domain.
• the IRE1 family protein is IREla.
• the compound binds to an ATP -binding site of IREla.
• the cell proliferative disorder is cancer.
• the cancer is a solid cancer or a hematologic cancer, lung cancer, or bladder cancer.
• Figure 1 shows an example diagram of the domain structure of IREla. A signal peptide (P) and transmembrane (TM) region are indicated.
• Figure 2 shows an example alignment of the C-terminal half IREl orthologues from yeast (Sclrel) (SEQ ID NO: 4), human (Hslrel) (SEQ ID NO: 5), mouse (Mmlrel) (SEQ ID NO: 6), and rat (RnlREl) (SEQ ID NO: 7).
• Stars indicate kinase domain dimer interface residues.
• Circles indicate Kinase extension nuclease (KEN) domain dimer interface residues.
• Triangles indicate putative nuclease active site residues. Yellow highlighted residues are highly conserved in Irel orthologues. Green highlighted residues are invariant in all analyzed Irel orthologues. Blue highlighted residues are invariant in analyzed RNaseL and Irel orthologues.
• Figure 3 depicts the bioavailability of Compound 3 and Compound 37 in vivo. Mice were dosed with Compound 3 or Compound 37 intravenously, orally, and intraperitoneally.
• Figure 4 shows suppression of IRE la-dependent splicing of X-box binding protein 1 (XBP1).
• the bottom left panel shows the unspliced (XBPlu) and spliced XBPl(s) protein with varying combinations of Compound 3 and TM, where mpk is mg/kg.
• Figure 5 shows that Compound 3 can inhibit IRE la-dependent signaling in various cell types in the tumor microenvironment.
• Amino refers to the - H 2 radical.
• Cyano refers to the -CN radical.
• Niro refers to the -N0 2 radical.
• Oxa refers to the -O- radical.
• Ci-C x includes C 1 -C 2 , C 1 -C3 . . . Ci-C x .
• a group designated as "C 1 -C4" indicates that there are one to four carbon atoms in the moiety, i.e. groups containing 1 carbon atom, 2 carbon atoms, 3 carbon atoms or 4 carbon atoms.
• C 1 -C 4 alkyl indicates that there are one to four carbon atoms in the alkyl group, i.e., the alkyl group is selected from among methyl, ethyl, propyl, z ' so-propyl, /7-butyl, z ' so-butyl, sec-butyl, and /-butyl.
• alkyl refers to an aliphatic hydrocarbon group.
• the alkyl group is branched or straight chain.
• the "alkyl” group has 1 to 10 carbon atoms, i.e. a Ci- Cioalkyl.
• a numerical range such as “1 to 10” refers to each integer in the given range; e.g., " 1 to 10 carbon atoms” means that the alkyl group consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, 4 carbon atoms, 5 carbon atoms,6 carbon atoms, etc., up to and including 10 carbon atoms, although the present definition also covers the occurrence of the term "alkyl” where no numerical range is designated.
• an alkyl is a Ci- C 6 alkyl.
• the alkyl is methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, or t-butyl.
• Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tertiary butyl, pentyl, neopentyl, or hexyl.
• an "alkylene” group refers refers to a divalent alkyl radical. Any of the above mentioned monovalent alkyl groups may be an alkylene by abstraction of a second hydrogen atom from the alkyl.
• an alkelene is a Ci-C 6 alkylene.
• an alkylene is a Ci-C 4 alkylene.
• an alkylene comprises one to four carbon atoms ⁇ e.g., C 1 -C 4 alkylene).
• an alkylene comprises one to three carbon atoms ⁇ e.g., C 1 -C3 alkylene).
• an alkylene comprises one to two carbon atoms ⁇ e.g., C 1 -C 2 alkylene). In other embodiments, an alkylene comprises one carbon atom ⁇ e.g., alkylene). In other embodiments, an alkylene comprises two carbon atoms ⁇ e.g., C 2 alkylene). In other embodiments, an alkylene comprises two to four carbon atoms ⁇ e.g., C 2 -C 4 alkylene).
• Typical alkylene groups include, but are not limited to, -CH 2 -, -CH(CH 3 )-, -C(CH 3 ) 2 -, -CH 2 CH 2 -, -CH 2 CH(CH 3 )-, -CH 2 C(CH 3 ) 2 -, -CH 2 CH 2 CH 2 -, -CH 2 CH 2 CH 2 CH 2 -, and the like.
• alkenyl refers to a type of alkyl group in which at least one carbon-carbon double bond is present.
• R is H or an alkyl.
• an alkenyl is selected from ethenyl ⁇ i.e., vinyl), propenyl ⁇ i.e., allyl), butenyl, pentenyl, pentadienyl, and the like.
• alkynyl refers to a type of alkyl group in which at least one carbon-carbon triple bond is present.
• an alkenyl group has the formula -C ⁇ C-R, wherein R refers to the remaining portions of the alkynyl group.
• R is H or an alkyl.
• an alkynyl is selected from ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like.
• Non-limiting examples of an alkynyl group include -C ⁇ CH, -C ⁇ CCH 3 - C ⁇ CCH 2 CH 3 , -CH 2 C ⁇ CH.
• alkoxy refers to a (alkyl)O- group, where alkyl is as defined herein.
• alkylamine refers to the -N(alkyl) x H y group, where x is 0 and y is 2, or where x is 1 and y is 1, or where x is 2 and y is 0.
• aromatic refers to a planar ring having a delocalized ⁇ -electron system containing 4n+2 ⁇ electrons, where n is an integer.
• aromatic includes both carbocyclic aryl ("aryl”, e.g., phenyl) and heterocyclic aryl (or “heteroaryl” or “heteroaromatic”) groups (e.g., pyridine).
• aryl e.g., phenyl
• heterocyclic aryl or “heteroaryl” or “heteroaromatic” groups
• pyridine e.g., pyridine
• the term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of carbon atoms) groups.
• Carbocyclic refers to a ring or ring system where the atoms forming the backbone of the ring are all carbon atoms. The term thus distinguishes carbocyclic from “heterocyclic” rings or “heterocycles” in which the ring backbone contains at least one atom which is different from carbon. In some embodiments, at least one of the two rings of a bicyclic carbocycle is aromatic. In some embodiments, both rings of a bicyclic carbocycle are aromatic. Carbocycle includes cycloalkyl and aryl.
• aryl refers to an aromatic ring wherein each of the atoms forming the ring is a carbon atom.
• aryl is phenyl or a naphthyl.
• an aryl is a phenyl.
• an aryl is a C 6 -Cioaryl.
• an aryl group is a monoradical or a diradical (i.e., an arylene group).
• cycloalkyl refers to a monocyclic or polycyclic aliphatic, non-aromatic radical, wherein each of the atoms forming the ring (i.e. skeletal atoms) is a carbon atom.
• cycloalkyls are spirocyclic or bridged compounds.
• cycloalkyls are optionally fused with an aromatic ring, and the point of attachment is at a carbon that is not an aromatic ring carbon atom.
• cycloalkyl groups include groups having from 3 to 10 ring atoms.
• cycloalkyl groups include groups having from 3 to 6 ring atoms.
• cycloalkyl groups are selected from among cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, cyclooctyl, spiro[2.2]pentyl, norbornyl and bicycle[ 1.1.1 ]pentyl.
• a cycloalkyl is a C 3 -C 6 cycloalkyl.
• a cycloalkyl is a monocyclic cycloalkyl.
• Monocyclic cycloalkyls include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
• Polycyclic cycloalkyls include, for example, adamantyl, norbornyl (i.e., bicyclo[2.2.1]heptanyl), norbornenyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like.
• cycloalkylene refers to a monocyclic or polycyclic aliphatic, non-aromatic divalent radical, wherein each of the atoms forming the ring (i.e. skeletal atoms) is a carbon atom.
• cycloalkylene are spirocyclic or bridged compounds.
• cycloalkylenes are optionally fused with an aromatic ring, and the point of attachment is at a carbon that is not an aromatic ring carbon atom.
• cycloalkylene groups include groups having from 3 to 10 ring atoms.
• cycloalkylene groups include groups having from 3 to 6 ring atoms.
• halo or, alternatively, "halogen” or “halide” means fluoro, chloro, bromo or iodo. In some embodiments, halo is fluoro, chloro, or bromo.
• haloalkyl refers to an alkyl in which one or more hydrogen atoms are replaced by a halogen atom.
• a fluoralkyl is a Ci-Cefluoroalkyl.
• fluoroalkyl refers to an alkyl in which one or more hydrogen atoms are replaced by a fluorine atom.
• a fluoralkyl is a Ci-C 6 fluoroalkyl.
• a fluoroalkyl is selected from trifluoromethyl, difluoromethyl, fluoromethyl, 2,2,2-trifluoroethyl, 1 -fluoromethyl -2 -fluoroethyl, and the like.
• heteroalkyl refers to an alkyl group in which one or more skeletal atoms of the alkyl are selected from an atom other than carbon, e.g., oxygen, nitrogen (e.g. - H-, - N(alkyl)-, sulfur, or combinations thereof.
• a heteroalkyl is attached to the rest of the molecule at a carbon atom of the heteroalkyl.
• a heteroalkyl is a Ci-C 6 heteroalkyl.
• heteroalkylene refers to an alkylene group in which one or more skeletal atoms of the alkylene are selected from an atom other than carbon, e.g., oxygen, nitrogen (e.g. - H-, -N(alkyl)-, sulfur, or combinations thereof.
• a heteroalkylene is attached to the rest of the molecule at a carbon atom of the heteroalkylene.
• a heteroalkylene is a Ci-C 6 heteroalkylene.
• heteroatom refers to an atom of any element other than carbon or hydrogen.
• the heteroatom is nitrogen, oxygen, or sulfur.
• the heteroatom is nitrogen or oxygen.
• the heteroatom is nitrogen.
• heterocycle refers to heteroaromatic rings (also known as heteroaryls) and heterocycloalkyl rings (also known as heteroalicyclic groups) containing one to four heteroatoms in the ring(s), where each heteroatom in the ring(s) is selected from O, S and N, wherein each heterocyclic group has from 3 to 10 atoms in its ring system, and with the proviso that any ring does not contain two adjacent O or S atoms.
• heterocycles are monocyclic, bicyclic, polycyclic, spirocyclic or bridged compounds.
• Non-aromatic heterocyclic groups include rings having 3 to 10 atoms in its ring system and aromatic heterocyclic groups include rings having 5 to 10 atoms in its ring system.
• the heterocyclic groups include benzo-fused ring systems.
• non-aromatic heterocyclic groups are pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, oxazolidinonyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, piperidinyl, morpholinyl, thiomorpholinyl, thioxanyl, piperazinyl, aziridinyl, azetidinyl, oxetanyl, thietanyl, homopiperidinyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, 1,2,3,6- tetrahydropyridinyl, pyrrolin-2-yl, pyrrolin-3-yl, indolinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl
• aromatic heterocyclic groups are pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl, quinox
• the foregoing groups are either C-attached (or C-linked) or TV-attached where such is possible.
• a group derived from pyrrole includes both pyrrol-l-yl (TV-attached) or pyrrol-3-yl (C-attached).
• a group derived from imidazole includes imidazol-l-yl or imidazol-3-yl (both TV- attached) or imidazol-2-yl, imidazol-4-yl or imidazol-5-yl (all C-attached).
• the heterocyclic groups include benzo-fused ring systems.
• at least one of the two rings of a bicyclic heterocycle is aromatic.
• both rings of a bicyclic heterocycle are aromatic.
• heteroaryl or, alternatively, “heteroaromatic” refers to an aryl group that includes one or more ring heteroatoms selected from nitrogen, oxygen and sulfur.
• heteroaryl groups include monocyclic heteroaryls and bicyclcic heteroaryls.
• Monocyclic heteroaryls include pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, pyridazinyl, triazinyl, oxadiazolyl, thiadiazolyl, and furazanyl.
• Bicyclic heteroaryls include indolizine, indole, benzofuran, benzothiophene, indazole, benzimidazole, purine, quinolizine, quinoline, isoquinoline, cinnoline, phthalazine, quinazoline, quinoxaline, 1,8-naphthyridine, and pteridine.
• a heteroaryl contains 0-4 N atoms in the ring.
• a heteroaryl contains 1-4 N atoms in the ring.
• a heteroaryl contains 0-4 N atoms, 0-1 O atoms, and 0-1 S atoms in the ring.
• a heteroaryl contains 1-4 N atoms, 0-1 O atoms, and 0-1 S atoms in the ring.
• heteroaryl is a Ci-Cgheteroaryl.
• monocyclic heteroaryl is a Ci-C 5 heteroaryl.
• monocyclic heteroaryl is a 5-membered or 6-membered heteroaryl.
• bicyclic heteroaryl is a C 6 -C 9 heteroaryl.
• a “heterocycloalkyl” or “heteroalicyclic” group refers to a cycloalkyl group that includes at least one heteroatom selected from nitrogen, oxygen and sulfur.
• a heterocycloalkyl is a spirocyclic or bridged compound.
• a heterocycloalkyl is a spirocyclic or bridged compound.
• heterocycloalkyl is fused with an aryl or heteroaryl.
• the heterocycloalkyl is oxazolidinonyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, tetrahydrothiopyranyl, piperidinyl, morpholinyl, thiomorpholinyl, piperazinyl, piperidin-2-onyl, pyrrolidine-2,5-dithionyl, pyrrolidine-2,5-dionyl, pyrrolidinonyl, imidazolidinyl, imidazolidin-2- onyl, or thiazolidin-2-onyl.
• heteroalicyclic also includes all ring forms of the carbohydrates, including but not limited to the monosaccharides, the disaccharides and the oligosaccharides.
• a heterocycloalkyl is a C2-Cioheterocycloalkyl.
• a heterocycloalkyl is a C 4 -Ci 0 heterocycloalkyl.
• a heterocycloalkyl contains 0-2 N atoms in the ring.
• a heterocycloalkyl contains 0-2 N atoms, 0-2 O atoms and 0-1 S atoms in the ring.
• bond refers to a chemical bond between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure.
• bond when a group described herein is a bond, the referenced group is absent thereby allowing a bond to be formed between the remaining identified groups.
• moiety refers to a specific segment or functional group of a molecule.
• Chemical moieties are often recognized chemical entities embedded in or appended to a molecule.
• optional substituents are independently selected from D, halogen, -CN, - H 2 , -OH, - H(CH 3 ), -N(CH 3 ) 2 , -CH 3 , -CH 2 CH 3 , -CH 2 H 2 , - CF 3 , -OCH 3 , and -OCF 3 .
• substituted groups are substituted with one or two of the preceding groups.
• a "tautomer” refers to a molecule wherein a proton shift from one atom of a molecule to another atom of the same molecule is possible.
• the compounds presented herein may, in certain embodiments, exist as tautomers. In circumstances where tautomerization is possible, a chemical equilibrium of the tautomers will exist. The exact ratio of the tautomers depends on several factors, including physical state, temperature, solvent, and pH.
• Optional or “optionally” means that a subsequently described event or circumstance may or may not occur and that the description includes instances when the event or circumstance occurs and instances in which it does not.
• optionally substituted aryl means that the aryl radical may or may not be substituted and that the description includes both substituted aryl radicals and aryl radicals having no substitution.
• “Pharmaceutically acceptable salt” includes both acid and base addition salts.
• a pharmaceutically acceptable salt of any one of the pyrazole compounds described herein is intended to encompass any and all pharmaceutically suitable salt forms.
• pharmaceutically acceptable salts of the compounds described herein are pharmaceutically acceptable acid addition salts and pharmaceutically acceptable base addition salts.
• “Pharmaceutically acceptable acid addition salt” refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise undesirable, and which are formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, hydroiodic acid, hydrofluoric acid, phosphorous acid, and the like.
• salts that are formed with organic acids such as aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and. aromatic sulfonic acids, etc.
• acetic acid trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like.
• Exemplary salts thus include sulfates, pyrosulfates, bisulfates, sulfites, bisulfites, nitrates, phosphates, monohydrogenphosphates, dihydrogenphosphates, metaphosphates, pyrophosphates, chlorides, bromides, iodides, acetates, trifluoroacetates, propionates, caprylates, isobutyrates, oxalates, malonates, succinate suberates, sebacates, fumarates, maleates, mandelates, benzoates, chlorobenzoates, methylbenzoates, dinitrobenzoates, phthalates, benzenesulfonates,
• toluenesulfonates phenylacetates, citrates, lactates, malates, tartrates, methanesulfonates, and the like.
• salts of amino acids such as arginates, gluconates, and galacturonates (see, for example, Berge S.M. et al., "Pharmaceutical Salts," Journal of Pharmaceutical Science, 66: 1-19 (1997)).
• Acid addition salts of basic compounds may be prepared by contacting the free base forms with a sufficient amount of the desired acid to produce the salt according to methods and techniques with which a skilled artisan is familiar.
• “Pharmaceutically acceptable base addition salt” refers to those salts that retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise undesirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Pharmaceutically acceptable base addition salts may be formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like.
• Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, for example, isopropylamine, trimethylamine, diethylamine, triethylamine,
• tripropylamine ethanolamine, diethanolamine, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, N,N-dibenzylethylenediamine, chloroprocaine, hydrabamine, choline, betaine, ethylenediamine, ethylenedianiline, N- methylglucamine, glucosamine, methylglucamine, theobromine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like. See Berge et al., supra.
• Prodrug is meant to indicate a compound that may be converted under physiological conditions or by solvolysis to a biologically active compound described herein.
• prodrug refers to a precursor of a biologically active compound that is pharmaceutically acceptable.
• a prodrug may be inactive when administered to a subject, but is converted in vivo to an active compound, for example, by hydrolysis.
• the prodrug compound often offers advantages of solubility, tissue compatibility or delayed release in a mammalian organism ⁇ see, e.g., Bundgard, H., Design of Prodrugs (1985), pp. 7-9, 21-24 (Elsevier, Amsterdam).
• prodrugs are provided in Higuchi, T., et al., "Pro-drugs as Novel Delivery Systems," A.C.S. Symposium Series, Vol. 14, and in Bioreversible Carriers in Drug Design, ed. Edward B. Roche, American Pharmaceutical Association and Pergamon Press, 1987.
• prodrug is also meant to include any covalently bonded carriers, which release the active compound in vivo when such prodrug is administered to a mammalian subject.
• Prodrugs of an active compound, as described herein may be prepared by modifying functional groups present in the active compound in such a way that the modifications are cleaved, either in routine manipulation or in vivo, to the parent active compound.
• Prodrugs include compounds wherein a hydroxy, amino or mercapto group is bonded to any group that, when the prodrug of the active compound is administered to a mammalian subject, cleaves to form a free hydroxy, free amino or free mercapto group, respectively.
• Examples of prodrugs include, but are not limited to, acetate, formate and benzoate derivatives of alcohol or amine functional groups in the active compounds and the like.
• module means to interact with a target either directly or indirectly so as to alter the activity of the target, including, by way of example only, to enhance the activity of the target, to inhibit the activity of the target, to limit the activity of the target, or to extend the activity of the target.
• modulator refers to a molecule that interacts with a target either directly or indirectly.
• the interactions include, but are not limited to, the interactions of an agonist, partial agonist, an inverse agonist, antagonist, degrader, or combinations thereof.
• a modulator is an agonist.
• administer refers to the methods that may be used to enable delivery of compounds or compositions to the desired site of biological action. These methods include, but are not limited to oral routes, intraduodenal routes, parenteral injection (including intravenous, subcutaneous, intraperitoneal, intramuscular, intravascular or infusion), topical and rectal administration. Those of skill in the art are familiar with administration techniques that can be employed with the compounds and methods described herein. In some embodiments, the compounds and compositions described herein are administered orally.
• co-administration are meant to encompass administration of the selected therapeutic agents to a single patient, and are intended to include treatment regimens in which the agents are administered by the same or different route of administration or at the same or different time.
• an “effective amount” or “therapeutically effective amount,” as used herein, refer to a sufficient amount of an agent or a compound being administered, which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result includes reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system.
• an “effective amount” for therapeutic uses is the amount of the composition comprising a compound as disclosed herein required to provide a clinically significant decrease in disease symptoms.
• An appropriate “effective” amount in any individual case is optionally determined using techniques, such as a dose escalation study.
• the terms “enhance” or “enhancing,” as used herein, means to increase or prolong either in potency or duration a desired effect.
• the term “enhancing” refers to the ability to increase or prolong, either in potency or duration, the effect of other therapeutic agents on a system.
• An “enhancing-effective amount,” as used herein, refers to an amount adequate to enhance the effect of another therapeutic agent in a desired system.
• pharmaceutical combination means a product that results from the mixing or combining of more than one active ingredient and includes both fixed and non- fixed combinations of the active ingredients.
• fixed combination means that the active ingredients, e.g. a compound described herein, or a pharmaceutically acceptable salt thereof, and a co-agent, are both administered to a patient simultaneously in the form of a single entity or dosage.
• non-fixed combination means that the active ingredients, e.g.
• a compound described herein, or a pharmaceutically acceptable salt thereof, and a co-agent are administered to a patient as separate entities either simultaneously, concurrently or sequentially with no specific intervening time limits, wherein such administration provides effective levels of the two compounds in the body of the patient.
• cocktail therapy e.g. the administration of three or more active ingredients.
• the term "subject” or “patient” encompasses mammals.
• mammals include, but are not limited to, any member of the Mammalian class: humans, non-human primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice and guinea pigs, and the like.
• the mammal is a human.
• treatment or “treating” or “palliating” or “ameliorating” are used interchangeably herein. These terms refers to an approach for obtaining beneficial or desired results including but not limited to therapeutic benefit and/or a prophylactic benefit.
• compositions may be administered to a patient at risk of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci- C 4 alkyl, -X-optionally substituted Ci-C 4 heteroalkyl, -X-optionally substituted Ci- C 4 fluoroalkyl, optionally substituted C 3 -C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; or two R 6 are taken together with the N atom to which they are attached to form an
• each R 7 is independently optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fiuoroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• each R 8 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fiuoroalkyl, , optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• each R 9 is independently optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• a 2 is N or CR A ;
• R A , R A1 , R A2 , and R A3 are each independently H, halogen, optionally substituted Ci-
• R 10 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• ring A is a monocyclic carbocycle or a monocyclic heterocycle;
• each R 3 is independently H, halogen, -CN, -OR 11 , -SR 11 , -N(R U ) 2 , optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted C3-C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; each R 11 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl;
• n 0, 1, 2, 3, or 4;
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2 , optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 -C 6 cycloalkyl, optionally substituted C 2 - Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; and
• R 12 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C 3 - C 6 cycloalkyl, optionally substituted C 2 -Ci 0 heterocycloalkyl, optionally substituted ar l or o tionall substituted heteroar l. substituted with
• q 0, 1, 2, or 3.
• q 0, 1, 2, or 3.
• q is 0 or 1.
• each R is
• Ci-C 4 alkyl independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X-optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl.
• each R 6 is independently H.
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 6 is H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X-optionally substituted Ci- C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl; q is 0 or 1 ; and R 2 is H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, or optionally substituted Ci- C 4 fluoroalkyl.
• R 6 is H. In some embodiments, A 2 is N. In some embodiments, A 2 is CR A . In some embodiments, R A is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R A is H. In some embodiments, R A1 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R is H. In some embodiments, R is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R is H. In some embodiments,
• R is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl,
• R AJ is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, or -OR . In some embodiments,
• R is optionally substituted Ci-C 4 alkyl
• R AJ is methyl, ethyl, propyl or butyl .
• R A3 is -OR 10 and R 10 is methyl, ethyl, propyl or butyl .
• ring A is phenylene or a monocyclic C3-C 8 cycloalkylene that is selected from cyclopropylene, cyclobutylene, cyclopentylene, cyclohexylene, cycloheptylene, and
• ring A is phenylene.
• ring A is a monocyclic Ci-Csheteroarylene containing 1-4
• ring A is a monocyclic 6-membered heteroarylene selected from pyridinylene, pyrimidinylene, pyrazinylene, and pyridazinylene. In some embodiments, ring A is pyridinylene.
• ring A is a monocyclic 5-membered heteroarylene selected from furanylene, thienylene, pyrrolylene, oxazolylene, thiazolylene, imidazolylene, pyrazolylene, triazolylene, tetrazolylene, isoxazolylene, isothiazolylene, oxadiazolylene, and thiadiazolylene.
• ring A is oxazolylene, thiazolylene, imidazolylene, pyrazolylene, or oxadiazolylene.
• ring A is pyrazolylene.
• ring A is a ring A is a monocyclic C 2 -
• each R 3 is independently H, halogen, -CN, -OR 11 , -SR 11 , optionally substituted Ci- C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl; and n is 1, 2, or 3. In some embodiments, R 3 is optionally substituted Ci-C 4 alkyl.
• R 3 is methyl, ethyl, propyl, or butyl.
• R 3 is -OR 11 .
• R 11 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 11 is methyl, ethyl, propyl, or butyl.
• R 11 is -CF 3 or -CH 2 CF 3.
• R 4 is H, halogen, - CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted d-C 4 alkyl, or optionally substituted C
• R 4 is H. In some embodiments, R 4 is halogen. In some embodiments, R 4 is -CI, -Br, -F, or -I. In some embodiments, R 4 is -OR 12 . In some
• R 12 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci- C 4 fluoroalkyl.
• R 4 is optionally substituted Ci-C 4 alkyl.
• R 4 is methyl, ethyl, propyl, or butyl.
• R 4 is optionally substituted Ci-C 4 fluoroalkyl.
• R 4 is -CF 3 or -CH 2 CF 3 .
• R 5 is H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 5 is H.
• R 5 is halogen.
• R 5 is -CI, -Br, -F, or -I.
• R 5 is - OR 12 .
• R 12 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 5 is optionally substituted Ci-C 4 alkyl.
• R 5 is methyl, ethyl, propyl, or butyl. In some embodiments, R 5 is optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R 5 is -CF 3 or -CH 2 CF 3 .
• the compound has the structure of formula (la)
• the compound has the structure of formula (lb)
• the compound has the structure of formula (Ic)
• q 0 or 1.
• each R 6 is independently H, optionally substituted Ci-
• each R 6 is independently H.
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• a 2 is N. In some embodiments, A 2 is CR A . In some embodiments, R A is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R A is
• R A1 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted
• R A1 is H.
• R ⁇ is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl. In some embodiments, R ⁇ is
• R A3 is H, halogen, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-C 4 fluoroalkyl, optionally substituted aryl, or -OR 10 . In some embodiments, R A3 is
• Ci-C 4 alkyl optionally substituted Ci-C 4 fluoroalkyl, or -OR 10 .
• R A3 is optionally substituted Ci-C 4 alkyl . In some embodiments, R A3 is methyl, ethyl, propyl, or butyl . In some embodiments, R A3 is ethyl In some embodiments, ring
• ring A is phenylene.
• ring A is a monocyclic 6-membered heteroarylene selected from pyridinylene, pyrimidinylene, pyrazinylene, and pyridazinylene.
• ring A is pyridinylene.
• ring A is a monocyclic 5- membered heteroarylene selected from furanylene, thienylene, pyrrolylene, oxazolylene, thiazolylene, imidazolylene, pyrazolylene, triazolylene, tetrazolylene, isoxazolylene,
• ring A is pyrazolylene.
• each R 3 is independently H, -OR 11 , optionally substituted
• R 11 is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• the compound has the structure of formula (Id)
• R is optionally substituted Ci-C 4 alkyl
• the compound has the structure of formula (Ie)
• ring A is phenylene, pyridinylene, pyrazolylene, thiazolylene, imidazolylene, oxazolylene, or oxadiazolylene.
• R 4 and R 5 are each independently H, halogen, -CN, -OR 12 , -SR 12 , -N(R 12 ) 2; optionally substituted C C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl.
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X- optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl;
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl;
• a 2 is N;
• R A1 is H
• R ⁇ is H, optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl;
• R A3 is methyl, ethyl, propyl or butyl
• ring A is a monocyclic 6-membered heteroarylene selected from pyridinylene, pyrimidinylene, pyrazinylene, and pyridazinylene.;
• R 3 is independently H, halogen, -CN, -OR 11 , -SR 11 , optionally substituted Ci-C 4 alkyl, or optionally substituted Ci-C 4 fluoroalkyl; and n is 1, 2, or 3;
• R 11 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 fluoroalkyl, optionally substituted Ci-C 4 heteroalkyl, optionally substituted C3-C 6 cycloalkyl, optionally substituted C2-Cioheterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl
• R 4 is -CI, -Br, -F, or -I;
• R 5 is hydrogen
• IS or ( R )2 and q is O, 1, 2, or 3;
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fluoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X- optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl;
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl;
• a 2 is N;
• R A1 is H
• R ⁇ is H
• R A3 is methyl, ethyl, propyl or butyl
• ring A is pyridinylene
• R 3 is methyl, ethyl, propyl, or butyl and n is 1, 2 or 3;
• R 4 is -CI, -Br, -F, or -I:
• each R 6 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fiuoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X- optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl;
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci-
• Ci-C 4 fluoroalkyl or optionally substituted Ci-C 4 fluoroalkyl;
• a 2 is N;
• R A1 is H
• R ⁇ is H
• R A3 is methyl, ethyl, propyl or butyl
• ring A is pyridinylene
• R 3 is -OR 11 and n is 1, 2 or 3;
• R 11 is methyl, ethyl, propyl, or butyl
• R 4 is -CI, -Br, -F, or -I;
• R 5 is hydrogen
• each R 6 is independently H, optionally substituted CrC 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, optionally substituted Ci-C 4 fiuoroalkyl, -X-optionally substituted Ci-C 4 alkyl, -X- optionally substituted Ci-C 4 heteroalkyl, or -X-optionally substituted Ci-C 4 fluoroalkyl;
• each R 2 is independently H, optionally substituted Ci-C 4 alkyl, optionally substituted Ci- C 4 heteroalkyl, or optionally substituted Ci-C 4 fluoroalkyl;
• a 2 is N;
• R A1 is H
• R ⁇ is H
• R A3 is methyl, ethyl, propyl or butyl
• ring A is pyridinylene
• R 3 is -OR 11 and n is 1, 2 or 3;
• R 11 is CF 3 or -CH 2 CF 3
• R 4 is -CI, -Br, -F, or -I;
• R 5 is hydrogen
• a compound described herein is selected from any one of the compounds from Table 1.
• a compound disclosed herein selectively binds to a protein of the serine/threonine-protein kinase/endoribonuclease inositol -requiring enzyme 1 (IREl) family of proteins.
• IREl is encoded by the ERN1 gene.
• Exemplary IREl family proteins include isoforms IREl and IREla.
• Other exemplary IREl family proteins include IREl homologues or orthologues in other organisms. Exemplary organisms include human, non-human primate, mouse, rat, chicken, fruit fly, yeast, and others listed in Table 2.
• the IREl protein is human IREla.
• a compound disclosed herein selectively binds to an IREl family protein comprising a kinase domain and/or an RNase domain.
• the kinase domain is a trans-autophosphorylation kinase domain.
• the IREl family protein is IREla.
• An example arrangement of domains within an IREla protein is depicted in Figure 1.
• An example alignment of IREl family protein orthologues is depicted in Figure 2 [00131]
• a compound disclosed herein selectively binds to a trans- autophosphorylation kinase domain region of IREla.
• a compound disclosed herein selectively binds to a trans-autophosphorylation kinase domain region of IREla, for example within amino acid residues 568-833 of SEQ ID NO: 1, or equivalent amino acid residues thereof.
• a compound disclosed herein selectively binds to an ATP- binding pocket within a trans-autophosphorylation kinase domain region of IREla. In some embodiments, a compound disclosed herein selectively binds to an ATP -binding pocket within a trans-autophosphorylation kinase domain region of IREla, for example, one or more of amino acid resides 577-711, 577-586, 597, 599, 626, 642-643, 645, 648, 688, 692-693, 695, or 711 of SEQ ID NO: 1, or equivalent amino acid residues thereof.
• a compound disclosed herein selectively binds to an activation loop within a trans-autophosphorylation kinase domain region of IREla. In some embodiments, a compound disclosed herein selectively binds to an activation loop within a trans- autophosphorylation kinase domain region of IREla, for example, one or more of amino acid residues 710-736, 710-725, or 729-736 of SEQ ID NO: 1, or equivalent amino acid residues thereof.
• a compound disclosed herein selectively binds to an RNase domain region of IREla. In some embodiments, a compound disclosed herein selectively binds to an RNase domain region of IREla, for example within amino acid residues 835-963 of SEQ ID NO: 1, or equivalent amino acid residues thereof.
• a compound disclosed herein selectively binds to a kinase domain dimer interface amino acid residue. In some embodiments, a compound disclosed herein selectively binds to a kinase domain dimer interface amino acid residue, such as one or more of amino acid residues 569-701, 569, 591, 592, 594, 617, 620 ,627, 628, 631, 674, 678, or 701 of SEQ ID NO: 1.
• a compound disclosed herein selectively binds to a first IREla and blocks dimerization between kinase domain dimer interface amino acid residues of the first IREla and a second IREla. In some embodiments, a compound disclosed herein selectively binds to a first IREla, and inhibit dimerization at one or more of amino acid residues 569-701, 569, 591, 592, 594, 617, 620 ,627, 628, 631, 674, 678, or 701 of SEQ ID NO: 1.
• a compound disclosed herein selectively binds to a kinase- extension nuclease (KEN) domain dimer interface amino acid residue of an IREla.
• KEN kinase- extension nuclease
• a compound disclosed herein selectively binds to a KEN domain dimer interface amino acid residue, such as one or more of amino acid residues 840-925, 840, 844, 851, 908, 912, or 925 of SEQ ID NO: 1.
• a compound disclosed herein selectively binds to amino acid residues of a nuclease active site. In some embodiments, a compound disclosed herein selectively binds to amino acid residues of a nuclease active site, such as one or more of amino acid residues 847-910, 847, 850, 886, 888, 889, 890, 892, 902, 905, 906, or 910 of SEQ ID NO: 1.
• a compound disclosed herein selectively binds to an RNase domain and a trans-autophosphorylation kinase domain region of IREla. In some embodiments, a compound disclosed herein selectively binds to an RNase domain and an ATP -binding pocket within a trans-autophosphorylation kinase domain region of IREla. In some embodiments, a compound disclosed herein selectively binds to an RNase domain and an activation loop within a trans autophosphorylation kinase domain region of IREla.
• a compound disclosed herein selectively binds to IREla at two sites located in an RNase domain, trans-autophosphorylation kinase domain region, ATP- binding pocket, activation loop, or any combination thereof. In some embodiments, a compound disclosed herein selectively binds to IREla at two or more sites. In some embodiments, a compound disclosed herein selectively binds to IREla at two or more sites located in an RNase domain, trans-autophosphorylation kinase domain region, ATP -binding pocket, activation loop, or any combination thereof. In some embodiments, a compound disclosed herein selectively binds to IREla at three sites located in an RNase domain, trans-autophosphorylation kinase domain region, ATP -binding pocket, activation loop, or any combination thereof.
• a compound disclosed herein selectively binds to IREla at a first site located in an RNase domain, trans-autophosphorylation kinase domain region, ATP- binding pocket, or activation loop.
• a first site comprises one or more of any amino acid residue within amino acid residues 465-977 of SEQ ID NO: 1.
• a compound disclosed herein selectively binds to IREla at a second site located in an RNase domain, trans-autophosphorylation kinase domain region, ATP -binding pocket, or activation loop.
• the first site is located within the same domain or region as the second site. In some examples, the first site is located within a different domain or region as the second site.
• a compound disclosed herein selectively binds to first
• IREla thereby blocking dimerization of the first IREla to a second IREla.
• a compound disclosed herein selectively binds to first IREla, thereby blocking auto-transphosphorylation of the first IREla or a second IREla to which the first IREla is dimerized. In some embodiments, a compound disclosed herein selectively binds to a first IREla, thereby blocking activation of the first IREla or a second IREla to which the first IREla is dimerized. In some embodiments, a compound disclosed herein selectively binds to a first IREla, thereby blocking kinase activity of the first IREla or a second IREla to which the first IREla is dimerized. In some embodiments, a compound disclosed herein selectively binds to a first IREla, thereby blocking RNase activity of the first IREla or a second IREla to which the first IREla is dimerized.
• a compound disclosed herein selectively binds to IREla when in a homo-dimerized conformation. In some embodiments, a compound disclosed herein selectively binds to IREla when in an oligomerized conformation. In some embodiments, a compound disclosed herein selectively binds to IREla when in a non-oligomerized or non- dimerized conformation. In some embodiments, a compound disclosed herein selectively binds to IREla when in an ATP -bound state. In some embodiments, a compound disclosed herein selectively binds to a IREl family protein when in a non-ATP -bound state. In some
• the compound is a pharmaceutically acceptable salt, or solvate thereof.
• a compound disclosed herein selectively binds to an IREl family protein and alters a downstream signaling pathway. In some embodiments, a compound disclosed herein selectively binds to an IREl family protein and alters signaling of
• a compound disclosed herein selectively binds to an IREl family protein and alters a downstream cellular process.
• an IREl family protein is IREl, IREla, or ERN1.
• a compound disclosed herein selectively binds to an IREl family protein and decreases or blocks a downstream signaling pathway. In some embodiments, a compound disclosed herein selectively binds to an IREl family protein and decreases or blocks activity or signaling of TXNTP, Caspase 1, Interleukin 1-beta, INK, Bim, cytochrome C, Caspase 3, Caspase 8, mRNA degradation, miRNA degradation, apoptotosis-inducing proteins, or inflammation-inducing proteins. In some embodiments, a compound disclosed herein selectively binds to an IRE1 family protein and decreases XBP1 mRNA levels. In some embodiments, a compound disclosed herein selectively binds to an IRE1 family protein and decreases
• a compound disclosed herein selectively binds to an IRE1 family protein and decreases spliced XBP1 mRNA levels.
• an IRE1 family protein is IRE1, IREla, or ERN1.
• a compound disclosed herein selectively binds to an IREl family protein and increases, activates, or removes a block of a downstream signaling pathway. In some embodiments, a compound disclosed herein selectively binds to an IREl family protein and increases, activates, or removes a block of activity or signaling of Bcl2, Bel -XL, Mcl-1, Bax, Bak, other anti-apoptotic proteins, or an mRNA translocon proteins. In some embodiments, an IREl family protein is IREl, IREla, or ERN1.
• a compound disclosed herein selectively binds to an IRElfamily protein and disrupts binding with an effector protein.
• the effector protein binds to the IREl family protein when in a dimerized or oligomerized state.
• the effector protein binds to the IREl family protein when in a non-dimerized or non- oligomerized state.
• the effector protein is immunoglobulin heavy-chain binding protein (BIP), protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK), glucose regulate protein 78 (Grp78), tumor necrosis factor receptor-associated factor 2 (TRAF2), JUN N- terminal kinase (JNK), transcriptionally active XBP1 (XBPls), unspliced XBP1 (XBPlu), regulated IREl -dependent decay (RIDD), Heat shock protein 90 kDa alpha (HSP 90-alpha), or misfolded protein.
• an IREl family protein is IREl, IREla, or ERN1.
• a compound disclosed herein selectively binds to an IREl family protein and alters activity of a cellular process or cellular function, such as regulated IREl -dependent decay (RIDD), RNA decay, translation, autophagy, cell survival, ER protein folding, ERAD, reactive oxygen species generation, transport, ER-associated protein degradation (ERAD), protein synthesis, or apoptosis.
• RIDD regulated IREl -dependent decay
• ERAD reactive oxygen species generation
• transport ER-associated protein degradation
• protein synthesis or apoptosis.
• an altered or lack of a cellular process or cellular function is associate with a disease state
• selective binding of a compound disclosed herein results in inhibiting or alleviating the disease state, or inhibiting a deleterious activity associated with the disease state.
• an IREl family protein is IREl, IREla, or ERN1.
• a compound disclosed herein is used to treat or ameliorate a disease associated with altered IREla pathway signaling when administered to a subject in need thereof.
• a compound disclosed herein is used to treat or ameliorate the effects of a disease associated with altered IREla pathway signaling when administered to a subject in need thereof.
• Exemplary disease associated with altered IREla signaling include cancer.
• a compound disclosed herein is used to treat or ameliorate a cancer when administered to a subject in need thereof.
• Exemplary cancers include tumors, solid and hematologic cancers.
• a compound disclosed herein is used to treat or ameliorate a cell proliferative disorder when administered to a subject in need thereof.
• the cell proliferative disorder is a cancer.
• the cancer is ovarian cancer, lung cancer, bladder cancer, breast cancer, or triple negative breast cancer (T BC).
• An IREla pathway can be involved in a variety of pathological conditions, including neurodegenerative diseases, inflammation, metabolic disorders, liver dysfunction, brain ischemia, heart ischemia, autoimmune diseases, and cancer. In some cases, modulation of this pathway provides therapeutic methods useful for treatment of such diseases.
• a compound disclosed herein is used to reinforce anti-tumor mechanisms.
• an anti-tumor mechanism comprises direct inhibition of tumor growth.
• an anti-tumor mechanism comprises induction of anti-tumor immunity.
• anti-tumor mechanisms comprise direct inhibition of tumor growth and simultaneous induction of anti-tumor immunity.
• a compound disclosed herein can prevent lipid accumulation in myeloid cells exposed to ovarian cancer-derived ascites supernatants.
• a compound disclosed herein can block myeloid cell
• a compound disclosed herein can be employed as therapeutic compound that enhances dendritic cell and T cell antitumor activity in mammals.
• the compounds disclosed herein can be used to treat murine and human ovarian cancers.
• the compounds described herein, or a pharmaceutically acceptable salt thereof are used in the preparation of medicaments for the treatment of diseases or conditions in a mammal that would benefit from administration of any one of the compounds disclosed.
• Methods for treating any of the diseases or conditions described herein in a mammal in need of such treatment involves administration of pharmaceutical compositions that include at least one compound described herein or a pharmaceutically acceptable salt, active metabolite, prodrug, or pharmaceutically acceptable solvate thereof, in therapeutically effective amounts to said mammal.
• compositions containing the compound(s) described herein are administered for prophylactic and/or therapeutic treatments.
• the compositions are administered to a patient already suffering from a disease or condition, in an amount sufficient to cure or at least partially arrest at least one of the symptoms of the disease or condition. Amounts effective for this use depend on the severity and course of the disease or condition, previous therapy, the patient's health status, weight, and response to the drugs, and the judgment of the treating physician.
• Therapeutically effective amounts are optionally determined by methods including, but not limited to, a dose escalation and/or dose ranging clinical trial.
• compositions containing the compounds described herein are administered to a patient susceptible to or otherwise at risk of a particular disease, disorder or condition. Such an amount is defined to be a "prophylactically effective amount or dose.”
• prophylactically effective amount or dose the precise amounts also depend on the patient's state of health, weight, and the like. When used in patients, effective amounts for this use will depend on the severity and course of the disease, disorder or condition, previous therapy, the patient's health status and response to the drugs, and the judgment of the treating physician.
• prophylactic treatments include administering to a mammal, who previously experienced at least one symptom of the disease being treated and is currently in remission, a pharmaceutical composition comprising a compound described herein, or a pharmaceutically acceptable salt thereof, in order to prevent a return of the symptoms of the disease or condition.
• the administration of the compounds are administered chronically, that is, for an extended period of time, including throughout the duration of the patient's life in order to ameliorate or otherwise control or limit the symptoms of the patient's disease or condition.
• the dose of drug being administered is temporarily reduced or temporarily suspended for a certain length of time (e.g., a "drug holiday").
• the length of the drug holiday is between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, or more than 28 days.
• the dose reduction during a drug holiday is, by way of example only, by 10%-100%, including by way of example only 10%, 15%, 20%, 25%), 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, and 100%.
• a maintenance dose is administered if necessary. Subsequently, in specific embodiments, the dosage or the frequency of administration, or both, is reduced, as a function of the symptoms, to a level at which the improved disease, disorder or condition is retained. In certain embodiments, however, the patient requires intermittent treatment on a long-term basis upon any recurrence of symptoms.
• the amount of a given agent that corresponds to such an amount varies depending upon factors such as the particular compound, disease condition and its severity, the identity (e.g., weight, sex) of the subject or host in need of treatment, but nevertheless is determined according to the particular circumstances surrounding the case, including, e.g., the specific agent being administered, the route of administration, the condition being treated, and the subject or host being treated.
• doses employed for adult human treatment are typically in the range of 0.01 mg to 5000 mg per day. In one aspect, doses employed for adult human treatment are from about 1 mg to about 1000 mg per day. In one embodiment, the desired dose is conveniently presented in a single dose or in divided doses administered simultaneously or at appropriate intervals, for example as two, three, four or more sub-doses per day.
• the daily dosages appropriate for the compound described herein, or a pharmaceutically acceptable salt thereof are from about 0.01 mg/kg to about 50 mg/kg per body weight.
• the daily dosage or the amount of active in the dosage form are lower or higher than the ranges indicated herein, based on a number of variables in regard to an individual treatment regime.
• the daily and unit dosages are altered depending on a number of variables including, but not limited to, the activity of the compound used, the disease or condition to be treated, the mode of administration, the requirements of the individual subject, the severity of the disease or condition being treated, and the judgment of the practitioner.
• Toxicity and therapeutic efficacy of such therapeutic regimens are determined by standard pharmaceutical procedures in cell cultures or experimental animals, including, but not limited to, the determination of the LD50 and the ED50.
• the dose ratio between the toxic and therapeutic effects is the therapeutic index and it is expressed as the ratio between LD50 and ED50.
• the data obtained from cell culture assays and animal studies are used in formulating the therapeutically effective daily dosage range and/or the therapeutically effective unit dosage amount for use in mammals, including humans.
• the daily dosage amount of the compounds described herein lies within a range of circulating concentrations that include the ED50 with minimal toxicity.
• the daily dosage range and/or the unit dosage amount varies within this range depending upon the dosage form employed and the route of administration utilized.
• any of the aforementioned aspects are further embodiments in which the effective amount of the compound described herein, or a pharmaceutically acceptable salt thereof, is: (a) systemically administered to the mammal; and/or (b) administered orally to the mammal; and/or (c) intravenously administered to the mammal; and/or (d) administered by injection to the mammal; and/or (e) administered topically to the mammal; and/or (f) administered non-systemically or locally to the mammal.
• any of the aforementioned aspects are further embodiments comprising single administrations of the effective amount of the compound, including further embodiments in which (i) the compound is administered once a day; or (ii) the compound is administered to the mammal multiple times over the span of one day, e.g., two, three, four or more times daily.
• any of the aforementioned aspects are further embodiments comprising multiple administrations of the effective amount of the compound, including further
• the method comprises a drug holiday, wherein the administration of the compound is temporarily suspended or the dose of the compound being administered is temporarily reduced; at the end of the drug holiday, dosing of the compound is resumed.
• the length of the drug holiday varies from 2 days to 1 year.
• the therapeutic effectiveness of one of the compounds described herein is enhanced by administration of an adjuvant ⁇ i.e., by itself the adjuvant has minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced).
• the benefit experienced by a patient is increased by administering one of the compounds described herein with another agent (which also includes a therapeutic regimen) that also has therapeutic benefit.
• the dosage regimen to treat, prevent, or ameliorate the condition(s) for which relief is sought is modified in accordance with a variety of factors (e.g. the disease, disorder or condition from which the subject suffers; the age, weight, sex, diet, and medical condition of the subject).
• factors e.g. the disease, disorder or condition from which the subject suffers; the age, weight, sex, diet, and medical condition of the subject.
• the dosage regimen actually employed varies and, in some embodiments, deviates from the dosage regimens set forth herein.
• dosages of the co-administered compounds vary depending on the type of co-drug employed, on the specific drug employed, on the disease or condition being treated and so forth.
• the compound provided herein when coadministered with one or more other therapeutic agents, is administered either simultaneously with the one or more other therapeutic agents, or sequentially.
• the multiple therapeutic agents are administered in any order or even simultaneously. If administration is simultaneous, the multiple therapeutic agents are, by way of example only, provided in a single, unified form, or in multiple forms (e.g., as a single pill or as two separate pills).
• the compounds described herein, or a pharmaceutically acceptable salt thereof, as well as combination therapies are administered before, during or after the occurrence of a disease or condition, and the timing of administering the composition containing a compound varies.
• the compounds described herein are used as a prophylactic and are administered continuously to subjects with a propensity to develop conditions or diseases in order to prevent the occurrence of the disease or condition.
• the compounds and compositions are administered to a subject during or as soon as possible after the onset of the symptoms.
• a compound described herein is administered as soon as is practicable after the onset of a disease or condition is detected or suspected, and for a length of time necessary for the treatment of the disease.
• the length required for treatment varies, and the treatment length is adjusted to suit the specific needs of each subject.
• a compound described herein or a formulation containing the compound is administered for at least 2 weeks, about 1 month to about 5 years.
• the compounds that modulate IRE1 mediated signaling disclosed herein are synthesized according to the following examples. The examples are intended to illustrate but not limit the disclosed embodiments.
• Example 1A Synthesis of tert-butyl ((lr,4r)-4-((6-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan- 2-yl)quinazolin-2-yl)amino)cyclohexyl)carbamate (1A)
• Step 3 1-tert-butyl ((lr, 4r)-4-((6-bromoquinazolin-2-yl)amino)cyclohexyl)carbamate (1A- 4)
• Step 4 tert-butyl ((lr,4r)-4-((6-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)quinazolin-2- yl)amino)cyclohexyl)carbamate (1A)
• Example 2A Synthesis of tert-butyl ((lr,4r)-4-((8-ethyl-6-(4,4,5,5-tetramethyl-l,3,2- dioxaborolan-2-yl)quinazolin-2-yl)amino)cyclohexyl)carbamate (2A)
• Step 1 l-(5-bromo-2-fluorophenyl)ethan-l-ol (2A-2)
• Step 2 4-bromo-2-ethyl-l-fluorobenzene (2A-3) [00176] To a solution of compound 2A-2 (46.0 g, 210.0 mmol) and triethylsilane (48.8 g,
• Step 6 tert-butyl ((lr,4r)-4-((6-bromo-8-ethylquinazolin-2-yl)amino)cyclohexyl)carbamate (2A-7)
• Step 7 tert-butyl ((lr,4r)-4-((8-ethyl-6-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)quinazolin-2-yl)amino)cyclohexyl)carbamate (2A)
• Step 5 [00186] To a solution of tert-butyl ((lr,4r)-4-(bis(tert- butoxycarbonyl)amino)cyclohexyl)(6-(3-((2-chloro phenyl)sulfonamido)-l -methyl- lH-pyrazol- 5-yl)quinazolin-2-yl)carbamate (80 mg, 98.4 umol) in DCM (2.0 mL) was added TFA (1.0 mL). The mixture was stirred at 25°C for 15 min and concentrated to give a residue.
• step 1 step 2 step 3
• step 1 step 2 step 3
• Example 24 Synthesis of N-(5-(2-(((lr,4r)-4-aminocyclohexyl)amino)-8-(l,l- difluoroethyl)quinazolin-6-yl)-6-methoxypyridin-2-yl)-2-chlorobenzenesulfonamide (123) step 1 step 2 step 3
• Step 6 [00256] To a solution of 2-chloro-N-(5-(8-(l, l-difluoroethyl)-2-fluoroquinazolin-6-yl)-6- methoxypyridin-2-yl)benzenesulfonamide (50 mg, 98.2 umol) in n-BuOH (2.0 mL) was added cyclohexane-l,4-diamine (22. mg, 196.5 umol) and DIEA (38 mg, 294.7 umol, 51.3 uL). The mixture was stirred at 100°C for 12 h. The mixture was concentrated to get crude residue.
• step 1 step 2 step 3
• step 1 step 2
• BuOH (6.0 mL) was basified pH to 8 by DIEA. Then the mixture was added 2-chloro-N-(5-(8- ethyl-2-fluoroquinazolin-6-yl)-6-methoxypyridin-2-yl)benzenesulfonamide (200 mg, 422.9 umol) and DIEA (327 mg, 2.5 mmol, 441.9 uL) and stirred at 100°C for 12 h. The reaction mixture was concentrated under reduced pressure to give a residue.
• step 4 step 5 step 6
• IX complete assay buffer (CAB; 1M DTT, 50 mM sodium citrate pH 7.15, ImM magnesium acetate, 0.02% tween 20) was used to dilute SignalChem IREla protein to a final concentration of 2 nM. Selected compounds were serially diluted with DMSO in a non-binding black 384-well plate for a total of 15 ul in each well.
• RNA probes Two RNA probes were used, XBPl wildtype (SEQ ID NO: 2) which is able to be spliced by active IREla or XBPl mutant (SEQ ID NO: 3) which is unable to be spliced. Each probe contained a 5' 6-FAM modification and a 3' IOWA Black FQ modification.
• a second FRET assay was performed to assess ATP-mediated inhibition.
• compounds and IREla were prepared and combined as discussed above, with the addition of ATP up to 1 mM final concentration. This mixture was incubated at room temperature for 60 minutes and then 5 ul of 400 nM XBPl wildtype or mutant RNA probe was added. Plates were then read over 30 minutes in kinetic mode (485/515 nm).

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