USRE47690E1 - Heterocyclic hydroxamic acids as protein deacetylase inhibitors and dual protein deacetylase-protein kinase inhibitors and methods of use thereof - Google Patents

Heterocyclic hydroxamic acids as protein deacetylase inhibitors and dual protein deacetylase-protein kinase inhibitors and methods of use thereof Download PDF

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USRE47690E1
USRE47690E1 US15/968,188 US201515968188A USRE47690E US RE47690 E1 USRE47690 E1 US RE47690E1 US 201515968188 A US201515968188 A US 201515968188A US RE47690 E USRE47690 E US RE47690E
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aryl
heteroaryl
alkyl
cycloalkyl
optionally substituted
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Xuedong Liu
Gan Zhang
Daniel Chuen-Fong Chan
Anthony D. Piscopio
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University of Colorado
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D513/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for in groups C07D463/00, C07D477/00 or C07D499/00 - C07D507/00
    • C07D513/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for in groups C07D463/00, C07D477/00 or C07D499/00 - C07D507/00 in which the condensed system contains two hetero rings
    • C07D513/04—Ortho-condensed systems
    • 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
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A61K31/52—Purines, e.g. adenine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/08—Antiallergic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/04—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D473/00—Heterocyclic compounds containing purine ring systems
    • C07D473/02—Heterocyclic compounds containing purine ring systems with oxygen, sulphur, or nitrogen atoms directly attached in positions 2 and 6
    • C07D473/16—Heterocyclic compounds containing purine ring systems with oxygen, sulphur, or nitrogen atoms directly attached in positions 2 and 6 two nitrogen atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D473/00—Heterocyclic compounds containing purine ring systems
    • C07D473/26—Heterocyclic compounds containing purine ring systems with an oxygen, sulphur, or nitrogen atom directly attached in position 2 or 6, but not in both
    • C07D473/32—Nitrogen atom
    • C07D473/34—Nitrogen atom attached in position 6, e.g. adenine
    • 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

Definitions

  • the present invention relates to novel hydroxamic acids which are specific histone deacetylase (HDAC) inhibitors and/or TTK/Mps1 kinase inhibitors, including pharmaceutically acceptable salts thereof, and which are useful for modulating HDAC and/or TTK/Mps1 kinase activity, therefore altering cellular activities such as signal transduction, cell proliferation, cell survival and cytokine secretion. More specifically, the invention relates to hydroxamate compounds which inhibit, regulate and/or modulate HDAC and or TTK/Mps1 kinase activity, such as HDAC6 and/or TTK/Mps1 kinase activity, and signal transduction pathways relating to cellular activities as mentioned above.
  • HDAC histone deacetylase
  • Histone deacetylases catalyze the removal of acetyl groups from lysine residues in histone amino termini, leading to chromatin condensation and changes in gene expression. Reversible lysine acetylation is an important phenomenon for homeostatic regulation of many cellular processes. The best characterized proteins that are subjected to this mode of regulation are histones (Strahl, B. D et al., Nature 2000, 403, (6765), 41-5).
  • Lysine residues in the N-terminal tail are tightly regulated by acetylation and deacetylation catalyzed by enzymes known as histone acetyltransferase (HAT) or histone deacetylase (HDAC) (Minucci, S. et al., Nat Rev Cancer 2006, 6, (1), 38-51; Yang, X. J. et al., Oncogene 2007, 26, (37), 5310-8).
  • HAT histone acetyltransferase
  • HDAC histone deacetylase
  • Acetylation of histones has also been correlated with other important cellular functions including chromatin assembly, DNA repair, and recombination.
  • HDAC enzymes there are 18 HDAC enzymes in the human genome that are subdivided into four distinct classes (Lane, A. A. et al., J Clin Oncol 2009, 27, (32), 5459-68; Marks, P. et al., Nat Rev Cancer 2001, 1, (3), 194-202).
  • Classes I, II and IV (11 enzymes) contain a zinc (Zn 2+ ) molecule in their active site.
  • Class III contains seven mechanistically diverse NAD+-dependent enzymes known as sirtuins.
  • Class II is subdivided into Class IIa (HDAC4, 5, 7 and 9) and Class IIb (HDAC6 and HDAC10).
  • HDACi histone deacetylase enzymes
  • Class II HDAC enzymes exhibit tissue-specific expression and can shuttle between the nucleus and cytoplasm. There is a growing interest in this class of HDAC enzymes because their substrates are broader and not limited to histones.
  • Class IIb enzyme HDAC6 predominantly resides in cytoplasm and hence its substrates are nonhistone proteins including ⁇ -tubulin, cortactin, peroxiredoxins, chaperone proteins, HSP90, ⁇ -Catenin, hypoxia inducible factor-1 ⁇ (HIF-1 ⁇ ) and other proteins (Li, Y. et al., FEBS J 2013, 280, (3), 775-93; Shankar, S. et al., Adv Exp Med Biol 2008, 615, 261-98).
  • HDAC6 contains two functional homologous catalytic domains and an ubiquitin-binding zinc finger domain at the C-terminal region.
  • HDAC6 is an authentic protein lysine deacetylase and appears to be important for a myriad biological processes and aberrant regulation of HDAC6 is implicated in numerous pathological conditions from cancer to neurodegenerative diseases (Valenzuela-Fernandez, A. et al., Trends Cell Biol 2008, 18, (6), 291-7; Simoes-Pires, C. et al., Mol Neurodegener 2013, 8, (1), 7).
  • HDAC6 stably associates with tubulin and regulate its acetylation states. Since microtubules are at the heart of cellular self-organization, it is not surprising that the deacetylation activity of HDAC6 towards tubulin affects many cellular processes. HDAC6 is known to play important roles in cell migration and cell-cell interaction. Aberrant regulation of HDAC6 is associated with cancer development (Valenzuela-Fernandez, A. et al., Trends Cell Biol 2008, 18, (6), 291-7; Simoes-Pires, C. et al., Mol Neurodegener 2013, 8, (1), 7).
  • HDAC6 overexpression of HDAC6 correlates with invasive metastatic behavior of tumor cells (Aldana-Masangkay, G. I. et al., J Biomed Biotechnol 2011, 875824).
  • HDAC6 directly or indirectly regulates angiogenesis by deacetylating several key factors that control angiogenesis (Li, Y. et al., FEBS J 2013, 280, (3), 775-93; Aldana-Masangkay, G. I. et al., J Biomed Biotechnol 2011, 875824).
  • Recent studies also suggest HDAC6 regulates acetylation of beta-catenin in CD133 signaling pathway which is known to be important for tumor stem cell maintenance (Mak, A. B. et al., Cell Rep 2012, 2, (4), 951-63).
  • HDAC6 has also been linked to cell survival pathways through several different mechanisms. HDAC6 regulates reversible acetylation of Hsp90 chaperon whose client proteins include steroid hormone receptors and a number of protein kinases critical for cell proliferation and apoptosis. Inactivation of HDAC6 perturbs the chaperon activity of Hsp90 and attenuates the activity of growth promoting client proteins (Aldana-Masangkay, G. I. et al., J Biomed Biotechnol 2011, 875824).
  • HDAC6 can bind polyubiquitinated misfolded proteins and deliver them to the dynein motor proteins for transport into aggresomes for degradation by lysosomes (Kawaguchi, Y. et al., Cell 2003, 115, (6), 727-38). HDAC6 also plays a role in the eventual clearance of aggresomes by promoting fusion of autophagosome with lysosomes (Lee, J. Y. et al., EMBO J 2010, 29, (5), 969-80; Iwata, A. et al., J Biol Chem 2005, 280, (48), 40282-92; Pandey, U. B. et al., Nature 2007, 447, (7146), 859-63).
  • HDAC6 selective inhibition of HDAC6 can enhance apoptotic response to DNA damaging agents such as etoposide and doxorubicin (Namdar, M. et al., Proc Natl Acad Sci USA 2010, 107, (46), 20003-8). Conversely there is also evidence supporting a role of inhibition of HDAC6 in protecting normal cells from DNA-damage induced cell death and promote neuron regeneration (Rivieccio, M. A. et al., Proc Natl Acad Sci USA 2009, 106, (46), 19599-604). Thus, inhibition of HDAC6 may dramatically improve therapeutic index of cytotoxic agents.
  • HDAC6 is a target for protection and regeneration following injury in the nervous system. Damage of neurons leads to an increase in HDAC6 expression and inhibition of HDAC6 can promote survival and regeneration of neurons. Importantly, selective inhibition of HDAC6 avoids cell death associated with non-selective HDAC inhibitors (pan-HDAC inhibitors). Therefore HDAC6 may be promising target for the treatment of, for example, stroke, ischemia and spinal cord injury (Rivieccio, M. A. et al., Proc Natl Acad Sci USA 2009, 106, (46), 19599-604).
  • TTK/Mps1 a dual specificity protein kinase
  • TTK/Mps1 a dual specificity protein kinase
  • elevated level of TTK/Mps1 is found in a variety of human cancer cell lines and primary tumor tissues.
  • Mps1 transcription is deregulated in a variety of human tumors.
  • Elevated Mps1 mRNA levels are found in several human cancers, including thyroid papillary carcinoma, breast cancer, gastric cancer tissue, bronchogenic carcinoma, and lung cancers (Mills, 1992 #187; Salvatore, 2007 #209; Yuan, 2006 #216; Kilpinen, 2010 #197; Daniel, 2010 #49; Landi, 2008 #217).
  • Mps1 correlates with high histological grade in breast cancers (Daniel, 2010 #49). Conversely, Mps1 mRNA is markedly reduced or absent in resting cells and in tissues with a low proliferative index (Hogg, 1994 #190). Thus, there is a correlation between elevated Mps1 levels and cell proliferation as well as tumor aggressiveness. Consistent with the notion that oncogenic signaling promotes Mps1 expression, the levels and activity of Mps1 are increased by 3 and 10 fold respectively in human melanoma cell lines containing B-Raf (V600E) mutant (Cui, 2008 #153). Inhibition of B-Raf or MEK1 reduces Mps1 expression (Borysova, 2008 #147; Cui, 2008 #153).
  • checkpoint protein expression such as Mps1
  • overexpression of these proteins may promote either cancer initiation or survival of aneuploid cancer cells (Sotillo, 2007 #219; Daniel, 2010 #49). Accordingly, reductions in key checkpoint proteins should severely decrease human cancer cell viability. This prediction is confirmed for several checkpoint proteins, including Mps1 (Fisk, 2003 #118; Daniel, 2010 #49), BubRI (Janssen, 2009 #173) and Mad2 (Kops, 2004 #220; Michel, 2004 #221).
  • Mps1 inhibitors as singular agent can be effective in cancer therapeutics.
  • the therapeutic index of Mps1 inhibitor is rather narrow which is consistent with the essential function of Mps1 in both normal and cancer cell proliferation.
  • animal xenograft studies clearly indicates that Mps1 inhibition exhibited significant neutropenia and animal toxicity (body weight loss and death) (Brandi Williams, Molecular Cancer Therapeutics Paper 2011, Mol Cancer Ther. 2011 December; 10(12):2267-75. doi: 10.1158/1535-7163.MCT-11-0453. Epub 2011 Oct. 6).
  • the current studies clearly revealed that using Mps1 inhibitor as singular agent clearly has its limitation in cancer therapeutics. New concepts, methodology and target agents are sorely needed to overcome these barriers to successful cancer therapeutics.
  • HDACi histone deacetylase inhibitors
  • HDAC6 Inhibition of HDAC6 exacerbates the effects of Mps1 inhibitor.
  • Mps1 inhibitor Inhibition of HDAC6 exacerbates the effects of Mps1 inhibitor.
  • combination of an HDAC inhibitor with a Mps1 inhibitor results in robust tumor inhibition and minimal cytotoxicity.
  • dual inhibitors that combine HDAC inhibitory activity with Mps1 inhibitory active is highly effective in tumor growth inhibition in vivo.
  • the present invention describes new selective inhibitors of HDAC6 and/or TTK/Mps1 Kinase.
  • the present invention provides novel hydroxamic acids, which are specific histone deacetylase (HDAC) inhibitors, including pharmaceutically acceptable salts, which are useful for modulating HDAC activity for modulating cellular activities such as signal transduction, cell proliferation, cell survival and cytokine secretion. More specifically, the invention relates to hydroxamate compounds which inhibit, regulate and/or modulate HDAC activity, in particular HDAC6 activity, and signal transduction pathways relating to cellular activities as mentioned above. The present invention also provides novel compounds which are TTK/Mps1 Kinase inhibitors, including pharmaceutically acceptable salts, which are useful for modulating TTK/Mps1 Kinase activity for modulating cellular activities such as signal transduction, cell proliferation, cell survival and cytokine secretion.
  • HDAC histone deacetylase
  • the present invention also provides compounds which are capable of inhibiting both HDAC6 activity and TTK/Mps1 Kinase activity, either simultaneously or in a mutually exclusive manner, and are useful as therapeutics.
  • An aspect of the invention is a compound of formula (I):
  • Z is NH or CH 2 ;
  • X is O, S, SO, SO 2 , CO, CR 2 R 3 , NR 4 , SO 2 NR 4 , NR 4 SO 2 , CONR 4 , NR 4 CO, NR 4 CO 2 , NR 4 (CO)NR 5 or a bond;
  • M is CR 6 or N;
  • Q 1 and Q 2 are independently N or CH;
  • Q 3 is CR 7 or Q 3 is NR 8 when R 1 is not present;
  • n is 0-6;
  • Y is H, CN, Cl, Br, I, F, C 1 -C 6 alkyl, haloalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, (CH 2 ) n -aryl, (CH 2 ) n -heteroaryl, OR 9 , SR 9 , COR 9 , COOR 9 , SOR 9 , SO 2 R 9 , SO 2 NR
  • An exemplary embodiment of the invention is a compound of formula (I) wherein Y is NR 10 R 11 ; R 10 is alkyl, aryl, heteroaryl, aryl-alkyl or heteroaryl-alkyl; and R 11 is alkyl or H, and where R 3 and R 4 taken together may form a 4-7 membered ring which is optionally substituted.
  • An exemplary embodiment of the invention is a compound of formula (I) wherein X is O, S, SO 2 , SO 2 NR 4 or CONR 4 .
  • An exemplary embodiment of the invention is a compound of formula (I) wherein n is 2, 3, 4 or 5.
  • An exemplary embodiment of the invention is a compound of formula (I) wherein R 1 is H or C 1 -C 6 alkyl; Q 3 is NR 8 where R 8 is absent; and M is CR 6 where R 6 is H.
  • An exemplary embodiment of the invention is a compound of formula (I) wherein R 1 is H or C 1 -C 6 alkyl; Q 3 is CR 7 where R 7 is H; and M is N.
  • An exemplary embodiment of the invention is a compound of formula (I) wherein Y is aryl, heteroaryl or NR 10 R 11 .
  • Another aspect of the invention is a compound of formula (II):
  • Ring A is an optionally substituted aryl or optionally substituted heteroaryl
  • Ring B is an optionally substituted aryl or optionally substituted heteroaryl
  • Ring C is an optionally substituted heteroaryl, optionally substituted cycloalkyl or optionally substituted heterocycloalkyl
  • Z is N, CR 2 , O, S, C ⁇ O, SO or SO 2
  • R 1 is H, absent, C 1 -C 6 alkyl, haloalkyl, hydroxyalkyl, carboxyalkyl, aryl, aryl-alkyl, heteroaryl, heterocyclic or carbocyclic, each of which may be optionally substituted
  • Z is CR 2 , R 1 and R 2 taken together may form a 3-7 membered ring which may be optionally substituted
  • X is O, S, SO, SO 2 , CO, CR 2 R 3 , NR 4 , SO 2 NR
  • An exemplary embodiment of the invention is a compound of formula (II) or a pharmaceutically acceptable salt thereof, wherein ring A is phenyl, pyridinyl, pyrimidinyl or pyrazinyl.
  • An exemplary embodiment of the invention is compound of formula (II) or a pharmaceutically acceptable salt thereof, wherein ring B is phenyl, pyridinyl, pyrimidinyl or pyrazinyl.
  • An exemplary embodiment of the invention is compound of formula (II) or a pharmaceutically acceptable salt thereof, wherein ring C is independently selected from a 5-membered heteroaryl or a 5-membered heterocycloalkyl.
  • An exemplary embodiment of the invention is compound according to formula (II) or a pharmaceutically acceptable salt thereof, wherein Y is aryl, heteroaryl, (CH 2 ) n -aryl, (CH 2 ) n -heteroaryl, NH 2 , NH(alkyl), N(alkyl)(alkyl), N(aryl)(alkyl), NH(cycloalkyl), N(alkyl)(cycloalkyl), NH(heteroaryl), NH(heterocycle), N(alkyl)(heteroaryl), N(alkyl)(heterocycle), NH(alkylheteroaryl), NH(alkylheterocycle), N(alkyl)(alkyl heteroaryl) or N(alkyl)(alkylheterocycle).
  • Another aspect of the invention is a compound of formula (III):
  • Z is N or CR 2 ;
  • R 1 is H, C 1 -C 6 alkyl, haloalkyl, hydroxyalkyl, carboxyalkyl, aryl, aryl-alkyl, heteroaryl, heterocyclic or carbocyclic, each of which may be optionally substituted, wherein, when Z is CR 2 , R 1 and R 2 taken together may form a 3-7 membered ring which may be optionally substituted;
  • Ring A is an optionally substituted phenyl, pyridinyl, pyrimidinyl, or pyrazinyl;
  • M 1 and M 2 are independently N or CR 3 ;
  • Q 1 is CR 4 , NR 5 , O or S;
  • Q 2 is CR 4 , NR 5 , O or S;
  • J is N or CR 6 ;
  • X is O, S, SO, SO 2 , CO, CR 7 R 8 , NR 9 , SO 2 NR 9
  • An exemplary embodiment of the invention is a compound according to formula (III), wherein Z is nitrogen and R 1 is H.
  • An exemplary embodiment of the invention is a compound according to formula (III), wherein X and Z are oriented para to each other.
  • An exemplary embodiment of the invention is a compound according to formula (III) or a pharmaceutically acceptable salt thereof, wherein Y is aryl, heteroaryl, alkyl-aryl, alkyl-heteroaryl, NH 2 , NH(alkyl), N(alkyl)(alkyl), N(aryl)(alkyl), NH(cycloalkyl), N(alkyl)(cycloalkyl), NH(heteroaryl), NH(heterocycle), N(alkyl)(heteroaryl), N(alkyl)(heterocycle), NH(alkylheteroaryl), NH(alkylheterocycle), N(alkyl)(alkylheteroaryl) or N(alkyl)(alkylheterocycle).
  • An exemplary embodiment of the invention is a compound according to formula (III), wherein M 1 , and M 2 are independently N or CR 3 , where R 3 is H.
  • An exemplary embodiment of the invention is a compound according to formula (III), wherein Q 1 is NR 5 ; Q 2 is NR 7 ; and J is CR 6 , where R 5 is absent and R 7 is H or alkyl.
  • An exemplary embodiment of the invention is a compound according to formula (III), wherein Q 1 is NR 5 ; Q 2 is NR 7 ; and J is CR 6 , where R 5 is alkyl and R 7 is absent.
  • Another aspect of the invention is a compound of formula (IV):
  • Z is N or CR 3 ;
  • R 1 is H, C 1 -C 6 alkyl, haloalkyl, hydroxyalkyl, carboxyalkyl, aryl, aryl-alkyl, heteroaryl, heterocyclic or carbocyclic, each of which may be optionally substituted, wherein, when Z is CR 3 , R 1 and R 3 taken together may form a 3-7 membered ring which may be optionally substituted;
  • R 2 is H, C 1 -C 6 alkyl, aryl, (CH 2 ) q -aryl, heteroaryl, (CH 2 ) q -heteroaryl, cycloalkyl or heterocyclic, any of which is substituted or unsubstituted;
  • R 3 is H, C 1 -C 6 alkyl, hydroxy, alkoxy, aryl, (CH 2 ) q -aryl, heteroaryl, (CH 2 ) q -heter
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein rings B and C taken together form a purine, pyrazolopyrimidine, pyrazolopyridine, pyrrolopyrimidine, thiazolopyrimidine, purinone, indole, pyrrolopyrimidinone or dihydropyrrolopyrimidine.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein Q 1 and Q 3 are N; and Q 2 and Q 4 are CR 4 where R 4 is H.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein Q 1 and Q 3 are CR 4 where R 4 is H; and Q 2 and Q 4 are N.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein Q 1 , Q 2 , Q 3 and Q 4 are CR 4 where R 4 is H.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein Z is N; and R 1 is H.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein X is O, (CO)NR 8 or S(O) 2 NR 8 ; and R 8 is H, alkyl, aryl, heteroaryl, cycloalkyl or heterocyclic, any of which is substituted or unsubstituted.
  • An exemplary embodiment of the invention is a compound of formula (IV), wherein n is 3; m is 1; and R 2 is H or alkyl.
  • Another aspect of the invention is a compound of formula (V):
  • Z is N or CR 2 ;
  • R 1 is H, C 1 -C 6 alkyl, haloalkyl, hydroxyalkyl, carboxyalkyl, aryl, aryl-alkyl, heteroaryl, heterocyclic or carbocyclic, each of which may be optionally substituted;
  • each of Q 1 , Q 2 , Q 3 , and Q 4 is independently N or CR 3 ;
  • Ring B is an optionally substituted phenyl, pyridinyl, pyrimidinyl or pyrazinyl;
  • Ring C is an optionally substituted heteroaryl, optionally substituted cycloalkyl or optionallysubstituted heterocycloalkyl;
  • R 2 is H, C 1 -C 6 alkyl, hydroxy, alkoxy, aryl, (CH 2 ) n -aryl, heteroaryl, (CH 2 ) n -heteroaryl, cycloalkyl or heterocyclic,
  • An exemplary embodiment of the invention is a compound of formula (V), wherein rings B and C taken together form a purine, pyrazolopyrimidine, pyrazolopyridine, pyrrolopyrimidine, thiazolopyrimidine, purinone, indole, pyrrolopyrimidinone or dihydropyrrolopyrimidine.
  • An exemplary embodiment of the invention is a compound of formula (V), wherein Z is N, and R 1 is H.
  • An exemplary embodiment of the invention is a compound of formula (V), wherein Q 1 , Q 2 , Q 3 and Q 4 are CR 3 where R 3 is H.
  • An exemplary embodiment of the invention is a compound of formula (V), wherein X is CR 4 R 5 , SO 2 , CO, NR 4 CO or absent.
  • An exemplary embodiment of the invention is a compound of formula (V), wherein Y is aryl, heteroaryl, (CH 2 ) n -aryl, (CH 2 ) n -heteroaryl or NR 7 R 8 .
  • Another aspect of the invention is a compound of formula (VI):
  • Ring A is an optionally substituted aryl or optionally substituted heteroaryl
  • Z is N or CR 3
  • R 1 is H, C 1 -C 6 alkyl, haloalkyl, hydroxyalkyl, carboxyalkyl, aryl, aryl-alkyl, heteroaryl, heterocyclic or carbocyclic, each of which may be optionally substituted
  • R 2 is an optionally substituted C 1 -C 6 alkyl, acyl, aryl or heteroaryl
  • Q 1 and Q 2 are independently N or CR 4
  • M is NR 5 , CR 6 R 7 , O or S
  • J is O, S or absent
  • X is O, S, SO, SO 2 , CO, CR 8 R 9 , NR 10 , SO 2 NR 10 , NR 10 SO 2 , CONR 10 , NR 9 CO, NR 10 CO 2 , NR 10 (CO)NR 11 or absent
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein Z is N; and R 1 is H.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein Q 1 and Q 2 are independently N or CR 4 where R 4 is H.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein M is CR 6 R 7 where R 6 and R 7 are alkyl, or taken together form a 3, 4, or 5 membered ring.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein Ring A is phenyl.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein X and Z are oriented para to each other.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein X is O, CR 8 R 9 or CONR 10 .
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein J is O or absent.
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein Y is aryl, heteroaryl, (CH 2 ) n -aryl, (CH 2 ) n -heteroaryl or NR 7 R 8 .
  • An exemplary embodiment of the invention is a compound of formula (VI), wherein L is C 3 -C 8 alkylene.
  • the invention provides compounds, such as those selected from formulae (I) through (VI), that are HDAC inhibitors which inhibit at least one HDAC isoform selected from the group consisting of HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9 and a combination thereof.
  • the invention provides HDAC inhibitors, such as those selected from formulae (I) through (VI), that are selective to the HDAC6 isoform.
  • the invention provides TTK/Mps1 kinase inhibitors, such as those selected from formulae (I) through (VI).
  • the invention provides compounds, such as those selected from formulae (I) through (VI), that are inhibitors of both HDAC6 and TTK/Mps1 kinase.
  • the invention provides the use of HDAC6 inhibitors and/or TTK/Mps1 kinase inhibitors, such as those selected from formulae (I) through (VI) in a method for treating or preventing an immunological, proliferative, inflammatory, autoimmune or allergic disorder or disease, or a transplant rejection, or a graft-versus host disease, or a neurodegenerative disease or neuron injury in a mammal, such as a human, by administering a therapeutically effective amount of the compound, either alone or co-administered with a known therapeutic agent.
  • HDAC6 inhibitors and/or TTK/Mps1 kinase inhibitors such as those selected from formulae (I) through (VI) in a method for treating or preventing an immunological, proliferative, inflammatory, autoimmune or allergic disorder or disease, or a transplant rejection, or a graft-versus host disease, or a neurodegenerative disease or neuron injury in a mammal, such as a human, by administering
  • the invention provides pharmaceutical compositions of a compound such as those selected from formulae (I) through (VI), and/or the pharmaceutically acceptable salts of such compounds as described herein and including a pharmaceutically acceptable carrier or excipient.
  • the invention provides pharmaceutical compositions of one or more compounds or pharmaceutically acceptable salts of one or more compounds described herein for use in a therapy to treat or prevent a disorder or disease such as the particular ones described herein.
  • the invention provides pharmaceutical compositions of one or more compounds or pharmaceutically acceptable salts of one or more compounds described herein for use in treatment, prevention, or delay of cancer progression.
  • the invention provides pharmaceutical compositions of compounds or pharmaceutically acceptable salts of one or more compounds described herein for use in the treatment, prevention, or delay of progression of a neurodegenerative disorder.
  • the invention provides pharmaceutical compositions of compounds or pharmaceutically acceptable salts of one or more compounds described herein for use in the treatment, prevention, or delay of the progression of inflammation.
  • the invention provides methods of treating diseases mediated by HDAC enzymes, comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the compounds described herein, such as the compounds of formulae (I) through (VI).
  • Other methods involve co-therapies by administering one or more compounds of the invention with other agents known to treat or prevent cancers, neurodegenerative disorders and inflammation.
  • the invention provides methods for the treatment, prevention or delay of the progression of cancer, neurodegenerative disorder or inflammation in a subject, which comprise administering a therapeutically effective amount of a compound of the invention such as the compounds of formulae (I) through (VI) or a pharmaceutically acceptable salt thereof, or pharmaceutical compositions, further comprising combination therapies with other agents known to treat or prevent cancers, neurodegenerative disorders and inflammation.
  • a compound of the invention such as the compounds of formulae (I) through (VI) or a pharmaceutically acceptable salt thereof, or pharmaceutical compositions, further comprising combination therapies with other agents known to treat or prevent cancers, neurodegenerative disorders and inflammation.
  • FIG. 1 illustrates the results of Tubulin acylation when treated with the compounds of Examples 2-4.
  • FIG. 2 illustrates the results of Tubulin acylation when treated with the compounds of Example 8.
  • FIG. 3 illustrates the results of tumour growth inhibition on a mouse Xenograft model when treated with the compound of Example 2.
  • the term “activity” refers to the activation, production, expression, synthesis, intercellular effect, and/or pathological or aberrant effect of the referenced molecule, either inside and/or outside of a cell.
  • the terms “comprises”, “comprising”, “includes”, “including”, “contains”, “containing” and any variations thereof, are intended to cover a non-exclusive inclusion, such that a process, method, product-by-process, or composition of matter that comprises, includes, or contains an element or list of elements does not include only those elements but may include other elements not expressly listed or inherent to such process, method, product-by-process, or composition of matter.
  • histone deacetylase or “HDAC” refers to any member of the classes of enzymes capable of cleaving an acetyl group (—C( ⁇ O)CH 3 ) from proteins, which includes, but are not limited to, histones and microtubules.
  • a histone deacetylase may be zinc-dependent.
  • HDACs include, but are not limited to, HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, HDAC10 and HDAC11.
  • pharmaceutically acceptable refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human.
  • pharmaceutically acceptable carrier includes any and all solvents, or a dispersion medium including, but not limited to, water, ethanol, a polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils, coatings, isotonic and absorption delaying agents, liposomes, commercially available cleansers, and the like. Supplementary bioactive ingredients also can be incorporated into such carriers.
  • substituted means that at least one hydrogen atom of a molecular arrangement is replaced with a non-hydrogen substituent.
  • a non-hydrogen substituent For example, in the case of an oxo substituent (“ ⁇ O”), two hydrogen atoms are replaced.
  • Substituents may include, but are not limited to, halogen, hydroxy, oxo, cyano, nitro, amino, alkylamino, dialkylamino, alkyl, alkoxy, alkylthio, haloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycle, and heterocyclealkyl, as well as —NRaRb, —NRaC( ⁇ O)Rb, —NRaC( ⁇ O)NRaNRb, —NRaC( ⁇ O)ORb, —NRaSO 2 Rb, —C( ⁇ O)Ra, —C( ⁇ O)ORa, —C( ⁇ O)NRaRb, —OC( ⁇ O)NRaRb, —OR, —SR, —SORa, —S( ⁇ O)aR, —OS( ⁇ O) 2
  • the above substituents may be further substituted with one or more of the above substituents, such that the substituent comprises a substituted alkyl, substituted aryl, substituted arylalkyl, substituted heterocyclyl or substituted heterocycloalkyl.
  • Ra and Rb in this context may be the same or different and typically include, but are not limited to, hydrogen, alkyl, haloalkyl, substituted alkyl, aryl, substituted aryl, arylalkyl, substituted arylalkyl, heterocyclyl, substituted heterocyclyl, heterocycloalkyl or substituted heterocycloalkyl.
  • unsubstituted refers to any compound that does not contain extra substituents attached to the compound.
  • An unsubstituted compound refers to the chemical makeup of the compound without extra substituents, e.g., the compound does not contain protecting group(s).
  • alkyl means any straight chain or branched, non-cyclic or cyclic, unsaturated or saturated aliphatic hydrocarbon containing from 1 to 10 carbon atoms, while the term “lower alkyl” has the same meaning as alkyl but contains from 1 to 6 carbon atoms.
  • the term “higher alkyl” has the same meaning as alkyl but contains from 2 to 10 carbon atoms, such as 6-10 carbon atoms.
  • saturated straight chain alkyls include, but are not limited to, methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, n-heptyl, n-octyl, n-nonyl, and the like; while saturated branched alkyls include, but are not limited to, isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, and the like. Cyclic alkyls may be obtained by joining two alkyl groups bound to the same atom or by joining two alkyl groups each bound to adjoining atoms.
  • saturated cyclic alkyls include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like; while unsaturated cyclic alkyls include, but are not limited to, cyclopentenyl and cyclohexenyl, and the like.
  • Cyclic alkyls are also referred to herein as “cycloalkyls”, “homocycles” or “homocyclic rings.”
  • Unsaturated alkyls contain at least one double or triple bond between adjacent carbon atoms (referred to as an “alkenyl” or “alkynyl”, respectively).
  • Representative straight chain and branched alkenyls include, but are not limited to, ethylenyl, propylenyl, 1-butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl, 3-methyl-1-butenyl, 2-methyl-2-butenyl, 2,3-dimethyl-2-butenyl, and the like; while representative straight chain and branched alkynyls include, but are not limited to, acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, 3-methyl-1-butynyl, and the like.
  • aryl refers to any aromatic carbocyclic moiety such as, but not limited to, phenyl or naphthyl.
  • arylalkyl refers to any alkyl having at least one alkyl hydrogen atom replaced with an aryl moiety, such as benzyl, but not limited to, —(CH 2 ) 2 phenyl, —(CH 2 ) 3 phenyl, —CH(phenyl) 2 , and the like.
  • halogen refers to any fluoro, chloro, bromo, or iodo moiety.
  • haloalkyl refers to any alkyl having at least one hydrogen atom replaced with halogen, such as trifluoromethyl, and the like.
  • heteroaryl refers to any aromatic heterocycle ring of 5 to 10 members and having at least one heteroatom selected from nitrogen, oxygen and sulfur, and containing at least one carbon atom, including, but not limited to, both mono- and bicyclic ring systems.
  • heteroaryls include, but are not limited to, furyl, benzofuranyl, thiophenyl, benzothiophenyl, pyrrolyl, indolyl, isoindolyl, azaindolyl, pyridyl, quinolinyl, isoquinolinyl, oxazolyl, isooxazolyl, benzoxazolyl, pyrazolyl, imidazolyl, benzimidazolyl, thiazolyl, benzothiazolyl, isothiazolyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, cinnolinyl, phthalazinyl, or quinazolinyl.
  • heteroarylalkyl refers to any alkyl having at least one alkyl hydrogen atom replaced with a heteroaryl moiety, such as —CHpyridinyl, —CH 2 pyrimidinyl, and the like.
  • heterocycle refers to any 4- to 7-membered monocyclic or any 7- to 10-membered bicyclic heterocyclic ring which is either saturated, unsaturated, or aromatic, and which contains from 1 to 4 heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen heteroatom may be optionally quaternized, including bicyclic rings in which any of the above heterocycles are fused to a benzene ring.
  • the heterocycle may be attached via any heteroatom or carbon atom.
  • Heterocycles may include heteroaryls exemplified by those defined above.
  • heterocycles may also include, but are not limited to, morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, and the like.
  • heterocycloalkyl refers to any alkyl having at least one alkyl hydrogen atom replaced with a heterocycle, such as —CH 2 morpholinyl, and the like.
  • cycloalkyl refers to any saturated or unsaturated (but not aromatic) carbocyclic ring containing from 3-7 carbon atoms, such as, but not limited to, cyclopropane, cyclobutane, cyclopentane, cyclohexane, cycloheptane, cyclohexene, and the like.
  • alkylamino refers to at least one alkyl moiety attached through a nitrogen bridge (i.e., —N-(alkyl)N, such as a dialkylamino) including, but not limited to, methylamino, ethylamino, dimethylamino, diethylamino, and the like.
  • alkyloxy refers to any alkyl moiety attached through an oxygen bridge (i.e., —O-alkyl) such as, but not limited to, methoxy, ethoxy, and the like.
  • alkylthio refers to any alkyl moiety attached through a sulfur bridge (i.e., —S— alkyl) such as, but not limited to, methylthio, ethylthio, and the like.
  • alkenyl refers to an unbranched or branched hydrocarbon chain having one or more double bonds therein.
  • the double bond of an alkenyl group can be unconjugated or conjugated to another unsaturated group.
  • Suitable alkenyl groups include, but are not limited to vinyl, allyl, butenyl, pentenyl, hexenyl, butadienyl, pentadienyl, hexadienyl, 2-ethylhexenyl, 2-propyl-2-butenyl,4-(2-methyl-3-butene)-pentenyl.
  • An alkenyl group can be unsubstituted or substituted with one or two suitable substituents.
  • alkynyl refers to an unbranched or branched hydrocarbon chain having one or more triple bonds therein.
  • the triple bond of an alkynyl group can be unconjugated or conjugated to another unsaturated group.
  • Suitable alkynyl groups include, but are not limited to ethynyl, propynyl, butynyl, pentynyl, hexynyl, methylpropynyl, 4-methyl-1-butynyl, 4-propyl-2-pentynyl- and 4-butyl-2-hexynyl.
  • An alkynyl group can be unsubstituted or substituted with one or two suitable substituents.
  • alkylene alkenylene and alkynylene as used herein refer to a divalent alkane, alkene and alkyne radical, respectively. It is understood that the alkylene, alkenylene and alkynylene may be straight or branched. An alkylene, alkenylene and alkynylene may also be substituted and unsubstituted.
  • salts refers to any salt that complexes with identified compounds described herein.
  • examples of such salts include, but are not limited to, acid addition salts formed with inorganic acids (e.g., hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid, and the like), and salts formed with organic acids such as, but not limited to, acetic acid, oxalic acid, tartaric acid, succinic acid, malic acid, fumaric acid, maleic acid, ascorbic acid, benzoic acid, tannic acid, pamoic acid, alginic acid, polyglutamic, acid, naphthalene sulfonic acid, naphthalene disulfonic acid, and polygalacturonic acid.
  • inorganic acids e.g., hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid, and the like
  • organic acids such as, but not limited to, acetic acid,
  • Salt compounds can also be administered as pharmaceutically acceptable quaternary salts known to a person skilled in the art, which specifically includes the quaternary ammonium salts of the formula —NRR′R′′+Z—, wherein R, R′, R′′ is independently hydrogen, alkyl, or benzyl, and Z is a counter ion, including, but not limited to, chloride, bromide, iodide, alkoxide, toluenesulfonate, methylsulfonate, sulfonate, phosphate, or carboxylate (such as benzoate, succinate, acetate, glycolate, maleate, malate, fumarate, citrate, tartrate, ascorbate, cinnamoate, mandeloate, and diphenylacetate).
  • R, R′, R′′ is independently hydrogen, alkyl, or benzyl
  • Z is a counter ion, including, but not limited to, chloride, bromide, iodide
  • Salt compounds can also be administered as pharmaceutically acceptable pyridine cation salts having a substituted or unsubstituted partial formula: wherein Z is a counter ion, including, but not limited to, chloride, bromide, iodide, alkoxide, toluenesulfonate, methylsulfonate, sulfonate, phosphate, or carboxylate (such as benzoate, succinate, acetate, glycolate, maleate, malate, fumarate, citrate, tartrate, ascorbate, cinnamoate, mandeloate, and diphenylacetate).
  • Z is a counter ion, including, but not limited to, chloride, bromide, iodide, alkoxide, toluenesulfonate, methylsulfonate, sulfonate, phosphate, or carboxylate (such as benzoate, succinate, acetate, glycolate, maleate, malate, fum
  • prodrug refers to a derivative of a compound that can hydrolyze, oxidize, or otherwise react under biological conditions (in vitro or in vivo) to provide a compound of the invention.
  • Prodrugs may only become active upon some reaction under biological conditions, but they may have activity in their unreacted forms.
  • Examples of prodrugs contemplated herein include, without limitation, analogs or derivatives of compounds of the invention, and/or their salts when salt formation is possible, but in particular, derivatives of zinc binding thiol moiety.
  • prodrug moieties include substituted and unsubstituted, branched or unbranched lower alkyl ester moieties, (e.g., a propionic acid ester), lower alkenyl esters, di-lower alkyl-amino lower-alkyl esters (e.g., a dimethylaminoethyl ester), acylamino lower alkyl esters (e.g., an acetyloxymethyl ester), acyloxy lower alkyl esters (e.g., a pivaloyloxymethyl ester), aryl esters (e.g., a phenyl ester), aryl-lower alkyl esters (e.g., a benzyl ester), heteroaryl esters (e.g., a nicotinate ester), substituted (e.g., with methyl, halo, or methoxy substituents) aryl and aryl-lower alky
  • Naturally occurring amino acid esters or their enantiomers, dipeptide esters, phosphate esters, methoxyphosphate esters, disulfides and disulfide dimers may also qualify as prodrugs.
  • Prodrugs and their uses are well known in the art (see, e.g., Berge et al. 1977). Prodrugs can typically be prepared using well-known methods, such as those described in Burger's Medicinal Chemistry and Drug Discovery (Manfred E. Wolff ed. 1995) and (Rautio, 2008).
  • Cancer is a term used for diseases in which abnormal cells divide without control and are able to invade other tissues. There are more than 100 different types of cancer. Most cancers are named for the organ or type of cell in which they start—for example, cancer that begins in the colon is called colon cancer; cancer that begins in basal cells of the skin is called basal cell carcinoma. The main categories of cancer include carcinomas, sarcomas, leukemias, lymphomas and myelomas, and central nervous system cancers.
  • cancers contemplated for treatment herein include colon and breast cancers.
  • Neurodegenerative disease or condition is a term used for a range of conditions which primarily affect the neurons in the human brain. Some common neurodegenerative diseases are Parkinson's disease, Alzheimer's disease and other dementias, motor neuron diseases, prion disease, Huntington's disease, Spinocerebellar ataxia and spinal muscular atrophy.
  • the terms “reduce,” “inhibit,” “diminish,” “suppress,” “decrease,” “prevent” and grammatical equivalents when in reference to the expression of any symptom in an untreated subject relative to a treated subject, mean that the quantity and/or magnitude of the symptoms in the treated subject is lower than in the untreated subject by any amount that is recognized as clinically relevant by any medically trained personnel.
  • the quantity and/or magnitude of the symptoms in the treated subject is at least 10% lower than, at least 25% lower than, at least 50% lower than, at least 75% lower than, and/or at least 90% lower than the quantity and/or magnitude of the symptoms in the untreated subject.
  • inhibitory compound refers to any compound capable of interacting with (i.e., for example, attaching, binding etc.) to a binding partner under conditions such that the binding partner becomes unresponsive to its natural ligands.
  • Inhibitory compounds may include, but are not limited to, small organic molecules, antibodies, and proteins/peptides.
  • Attachment refers to any interaction between a medium (or carrier) and a drug. Attachment may be reversible or irreversible. Such attachment includes, but is not limited to, covalent bonding, ionic bonding, Van der Waals forces or friction, and the like.
  • a drug is attached to a medium (or carrier) if it is impregnated, incorporated, coated, in suspension with, in solution with, mixed with, etc.
  • drug refers to any pharmacologically active substance capable of being administered which achieves a desired effect.
  • Drugs or compounds can be synthetic or naturally occurring, non-peptide, proteins or peptides, oligonucleotides or nucleotides, polysaccharides or sugars.
  • administered refers to any method of providing a composition to a patient such that the composition has its intended effect on the patient.
  • An exemplary method of administering is by a direct mechanism such as, local tissue administration (i.e., for example, extravascular placement), oral ingestion, transdermal patch, topical, inhalation, suppository, etc.
  • patient is an animal, such as, for example, a mammal, such as, for example, a human that need not be hospitalized.
  • a mammal such as, for example, a human that need not be hospitalized.
  • out-patients and persons in nursing homes are “patients.”
  • a patient may comprise any age of a human or non-human animal and therefore includes both adult and juveniles (i.e., children). It is not intended that the term “patient” connote a need for medical treatment, therefore, a patient may voluntarily or involuntarily be part of experimentation whether clinical or in support of basic science studies.
  • subject refers to a vertebrate, preferably a mammal, more preferably a primate, still more preferably a human. Mammals include, without limitation, humans, primates, wild animals, feral animals, farm animals, sports animals and pets.
  • the present invention provides novel hydroxamic acids, which are specific histone deacetylase (HDAC) and/or TTK/Mps1 kinase inhibitors, including pharmaceutically acceptable salts, which are useful for modulating HDAC activity and/or TTK/Mps1 kinase activity, and therefore altering cellular activities such as signal transduction, cell proliferation, cell survival and cytokine secretion.
  • HDAC histone deacetylase
  • TTK/Mps1 kinase inhibitors including pharmaceutically acceptable salts, which are useful for modulating HDAC activity and/or TTK/Mps1 kinase activity, and therefore altering cellular activities such as signal transduction, cell proliferation, cell survival and cytokine secretion.
  • the invention provides compounds selective to HDAC6 inhibition for the treatment and/or prevention of diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • the invention provides compounds selective to TTK/Mps1 kinase inhibition for the treatment and/or prevention of diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • the invention provides compounds capable of inhibiting both HDAC6 and TTK/Mps1 kinase either simultaneously or in a mutually exclusive manner for the treatment and/or prevention of diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • the invention provides a pharmaceutical composition comprising at least one pharmaceutically-acceptable carrier, in addition to one or more compounds described herein.
  • the composition can be present in any suitable form for the desired route of administration.
  • any suitable orally deliverable dosage form can be used, including, without limitation, tablets, capsules (solid or liquid filled), powders, granules, syrups and other liquids, elixirs, inhalants, troches, lozenges and solutions.
  • Injectable compositions or i.v. infusions are also provided in the form of solutions, suspensions, and emulsions.
  • a pharmaceutical composition according to the invention may contain one or more additional therapeutic agents, for example, to increase the efficacy or decrease side effects.
  • a pharmaceutical composition further contains one or more additional therapeutic agents selected from active ingredients useful to treat or inhibit disease mediated directly or indirectly by HDAC6 and/or TTK/Mps1 kinase.
  • active ingredients are, without limitation, agents to treat or inhibit diseases such as immunological, inflammatory, autoimmune, allergic disorders, proliferative diseases such as cancer, neurodegenerative disorders or neurological diseases.
  • an additional therapeutic agent is included with the treatment, such as an anti-cancer agent.
  • an anti-cancer agent include, but are not limited to, alkylating agents such as cyclophosphamide, dacarbazine, and cisplatin; anti-metabolites such as methotrexate, mercaptopurine, thioguanine, fluorouracil, and cytarabine; plant alkaloids such as vinblastine, and paclitaxel; antitumor antibiotics such as doxorubicin, bleomycin, and mitomycin; hormones/antihormones such as prednisone, tamoxifen, and flutamide; other types of anticancer agents such as asparaginase, rituximab, trastuzumab, imatinib, retinoic acid and derivatives, colony stimulating factors, amifostine, camptothecin, topotecan, thalidomide analogs such as
  • the target disease is rheumatoid arthritis, osteoarthritis; rheumatoid spondylitis; psoriasis; post ischemic perfusion injury; inflammatory bowel disease; chronic inflammatory pulmonary disease, eczema, asthma, psoriasis, ischemia/reperfusion injury, ulcerative colitis, acute respiratory distress syndrome, psoriatic arthritis, infectious arthritis, progressive chronic arthritis, deforming arthritis, osteoarthritis, traumatic arthritis, gouty arthritis, Reiter's syndrome, polychondritis, acute synovitis and spondylitis, glomerulonephritis, hemolytic anemia, aplastic anemia, idiopathic thrombocytopenia, neutropenia, ulcerative colitis, Crohn's disease, host versus graft disease, allograft rejection, chronic thyroiditis, Graves' disease, scleroderma, diabetes, active hepatitis, primary bilid arthritis, a
  • the target disease is protein deposition disorders, Wilson's disease, spinocerebellar ataxia, prion disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, spinal muscular atrophy, spinal and bulbar muscular atrophy, amyloidosis, Alzheimer's disease, Alexander's disease, alcoholic liver disease, cystic fibrosis, Pick's disease, and Lewy body dementia.
  • the compounds of the invention are useful for disorders associated with tubulin deacetylation activity.
  • the invention provides a method of inhibiting or treating diseases arising from abnormal cell proliferation and/or differentiation in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of one or more compounds according to the present invention.
  • the method of inhibiting or treating disease comprises administering to a subject in need thereof, a composition comprising an effective amount of one or more compounds of the invention and a pharmaceutically acceptable carrier.
  • the composition to be administered may further contain a therapeutic agent such as anti-cancer agent or an agent to treat neurodegenerative diseases.
  • the compounds of the invention are defined herein by their chemical structures and/or chemical names.
  • the compounds of the invention are generally named according to the IUPAC or CAS nomenclature system. Abbreviations that are well known to one of ordinary skill in the art may be used.
  • a compound is referred to by both a chemical structure and a chemical name, and the chemical structure and chemical name conflict, the chemical structure is determinative of the compound's identity.
  • dihalogenated, bicyclic compounds as depicted by structure 1, are subjected to standard nucleophilic aromatic substitution conditions in cases where a carbon-heteroatom bond formation is desired, or to palladium catalyzed cross-coupling conditions when carbon-carbon bond formation is desired.
  • the initial coupling reaction where a halogen group is replaced by Y (intermediate 2), is often a selective process.
  • the substitution reaction is non-selective, the resulting regioisomers are separated chromatographically and the desired isomer is taken forward.
  • intermediate 5 is then converted to the desired hydroxamic acid via ester hydrolysis, amide formation with an O-protected hydroxylamine derivative, such as O-tertrahydropyranyl hydroxylamine in the presence of a suitable coupling reagent, typically a carbodiimide, followed by deprotection, such as acid promoted hydrolysis of the tetrahydropyranyl group.
  • a suitable coupling reagent typically a carbodiimide
  • deprotection such as acid promoted hydrolysis of the tetrahydropyranyl group.
  • an acid labile group such that both protecting groups are removed concomitantly to give the final products, typically as the corresponding hydrochloride salts.
  • intermediate 5 An alternative synthesis for the preparation of intermediate 5 is shown in Scheme 2.
  • a more linear approach is used to construct the appendage containing Ring A, which is particularly useful when X is a heteroatom.
  • intermediate 3 is coupled with intermediate 7 under basic conditions and if necessary in the presence of a palladium catalyst to give intermediate 8. Removal of the protecting group then unmasks X which is coupled with the electrophilic component 9 under basic conditions to give 5.
  • N-substituted imidazo derivatives For the synthesis of N-substituted imidazo derivatives, it is convenient to directly alkylate intermediates of the general structure 12 of Scheme 6 under basic conditions, or perform an N-arylation using, for example, an aryl boronic acid in the presence of a transition metal catalyst followed by chromatographic separation of regioisomers if necessary.
  • intermediate 32 can be can be prepared through the condensation of the 1,2-diamino derivative 31 with a carboxylic acid.
  • the corresponding pyrrazolo derivatives 38 can be synthesized via acylation of 36 to give 37 followed by condensation with a hydrazine derivative to give the desired products.
  • intermediates such as 39 that contain one nitrogen atom in the 5-membered, heterocyclic ring are conveniently protected using a tosylate group.
  • the tosylate group is removed by treatment with aqueous sodium hydroxide and heating.
  • tosylate hydrolysis proceeds with concomitant hydrolysis of an ester group contained in R 3 which serves as the precursor for the desired hydroxamic acid.
  • Step 3 Preparation of N6-cyclohexyl-9-(tetrahydro-2H-pyran-2-yl)-N2-(4-(triisopropylsilyloxy)phenyl)-9H-purine-2,6-diamine
  • the reaction mixture was degassed using Argon for 10 min after which Pd(dppf)Cl 2 complex with CH 2 Cl 2 (0.16 g, 0.20 mmole) was added, followed by sodium t-butoxide (0.77 g, 8.0 mmole).
  • the reaction flask was put into a preheated oil-bath at 100° C. and stirred overnight. The mixture was cooled to room temperature. To the mixture, water and EtOAc were added. The layers were separated and the aqueous layer was extracted with EtOAc. The combined organic layer was dried over Na 2 SO 4 and concentrated.
  • Step 4 Preparation of 4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenol
  • N6-Cyclohexyl-9-(tetrahydro-2H-pyran-2-yl)-N2-(4-(triisopropylsilyloxy)phenyl)-9H-purine-2,6-diamine (1.7 g, 3.0 mmole) was dissolved in 40 ml tetrahydropyran and 3.0 ml tetrabutylammonium fluoride (1.0M in THF, 3.0 mmole) was added. The mixture was stirred for 45 min.
  • Step 1 Preparation of ethyl 7-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)heptanoate
  • Step 2 Preparation of 7-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)heptanoic acid
  • the aqueous layer was acidified with 1N HCl. The layers were separated and the aqueous layer was extracted with ethyl acetate. The combined organic layer was dried with Na 2 SO 4 and concentrated. The crude product was used without further purifications.
  • Step 3 Preparation of 7-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)-N-(tetrahydro-2H-pyran-2-yloxy)heptanamide
  • Step 2 Preparation of 2 N6-cyclohexyl-9-methyl-N2-(4-(triisopropylsilyloxy)phenyl)-9H-purine-2,6-diamine
  • the reaction mixture was degassed using Argon for 10 min after which Pd(dppf)Cl 2 complex with CH 2 Cl 2 (0.16 g, 0.20 mmole) was added, followed by sodium t-butoxide (0.77 g, 7.98 mmole).
  • the reaction flask was put into a preheated oil-bath at 100° C. and stirred overnight. The mixture was cooled to room temperature. To the mixture, water and EtOAc were added. The layers were separated and the aqueous layer was extracted with EtOAc. The combined organic layer was dried over Na 2 SO 4 and concentrated.
  • N6-Cyclohexyl-9-methyl-N2-(4-(triisopropylsilyloxy)phenyl)-9H-purine-2,6-diamine (1.3 g, 2.63 mmole) was dissolved in 35 ml THF and 2.7 ml TBAF (1.0M in THF, 2.7 mmole) was added. The mixture was stirred for 45 min.
  • Step 1 Preparation of ethyl 7-(4-(6-(cyclohexylamino)-9-methyl-9H-purin-2-ylamino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-(6-(cyclohexylamino)-9-methyl-9H-purin-2-ylamino)phenoxy)-N-(tetrahydro-2H-pyran-2-yloxy)heptanamide
  • Step 4 Preparation of 7-(4-(6-(Cyclohexylamino)-9-methyl-9H-purin-2-ylamino)phenoxy)-N-hydroxyheptanamide hydrochloride salt
  • Diisopropyl alcohol 44 mg, 0.73 mmole was dissolved in 5 ml dry THF.
  • Sodium hydride (60% weight, 29.3 mg, 0.73 mmole) was added to the solution and the mixture was stirred at room temperature for 30 min at which time Dichloropurine (100 mg, 0.37 mmole) were added.
  • the mixture was heated in a sealed tube at 65° C. overnight. Column purification to get the desired product.
  • Step 1 Preparation of 2-(3-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)propyl)isoindoline-1,3-dione
  • Step 3 Preparation of methyl 2-(3-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)propylamino)acetate
  • N2-(4-(3-aminopropoxy)phenyl)-N6-cyclohexyl-9-(tetrahydro-2H-pyran-2-yl)-9H-purine-2,6-diamine (20 mg, 0.043 mmole) was dissolved in 1 ml dimethyl formamide. Triethylamine (6.5 mg, 0.64 mmole) and methyl chloroacetate (7 mg, 0.64 mmole) were added. The mixture was heated at 70° C. for two hours. Water and ethyl acetate were added. The layers were separated and the aqueous layer was extracted with ethyl acetate. The combined organic layer was dried with Na 2 SO 4 and concentrated.
  • Step 4 Preparation of methyl 2-(tert-butoxycarbonyl(3-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)propyl)amino)acetate
  • Step 5 Preparation of 2-(tert-butoxycarbonyl(3-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenoxy)propyl)amino)acetic acid
  • Step 7 Preparation of 2-(3-(4-(6-(cyclohexylamino)-9H-purin-2-ylamino)phenoxy)propylamino)-N-hydroxyacetamide hydrochloride salt
  • Step 1 Preparation of N6-cyclohexyl-N2-(4-(piperazin-1-yl)phenyl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purine-2,6-diamine
  • the reaction mixture was degassed using Argon for 10 min after which Pd(dppf)Cl 2 complex with CH 2 Cl 2 (61 mg, 0.075 mmole) was added, followed by sodium t-butoxide (286 mg, 3.0 mmole).
  • the reaction flask was put into a preheated oil-bath at 100° C. and stirred overnight. The mixture was cooled to room temperature. To the mixture, water and EtOAc were added. The layers were separated and the aqueous layer was extracted with EtOAc. The combined organic layer was dried over Na 2 SO 4 and concentrated.
  • Step 2 Preparation of methyl 2-(4-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenyl)piperazin-1-yl)acetate
  • N6-cyclohexyl-N2-(4-(piperazin-1-yl)phenyl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purine-2,6-diamine 87.5 mg, 0.184 mmole
  • triethylamine 74 mg, 0.74 mmole
  • methyl chloroacetate 22 mg, 0.20 mmole
  • the mixture was heated at 40° C. overnight. Water and ethyl acetate were added. The layers were separated and the aqueous layer was extracted with ethyl acetate. The combined organic layer was dried with Na 2 SO 4 and concentrated.
  • Step 3 Preparation of 2-(4-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenyl)piperazin-1-yl) acetic acid
  • Step 4 Preparation of 2-(4-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenyl)piperazin-1-yl)-N-(tetrahydro-2H-pyran-2-yloxy)acetamide
  • Step 1 Preparation of 4-(4-(6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-ylamino)phenyl)-N-hydroxypiperazine-1-carboxamide
  • Step 1 Preparation of N-(tert-butyl)-2-chloro-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-amine
  • Step 2 Preparation of methyl 7-(4-((6-(tert-butylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((6-(tert-butylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((6-(tert-butylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 3 Preparation of methyl 7-(4-((7-(cyclohexylamino)-3-(tetrahydro-2H-pyran-2-yl)-3H-imidazo[4,5-b]pyridin-5-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of: 7-(4-((7-(cyclohexylamino)-3-(tetrahydro-2H-pyran-2-yl)-3H-imidazo[4,5-b]pyridin-5-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of 7-(4-((7-(cyclohexylamino)-3-(tetrahydro-2H-pyran-2-yl)-3H-imidazo[4,5-b]pyridin-5-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((7-(cyclohexylamino)-3H-imidazo[4,5-b]pyridin-5-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 2 Preparation of methyl 7-((4-((tert-butoxycarbonyl)amino)phenyl)thio)heptanoate
  • Step 1 Preparation of methyl 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)thio)heptanoate
  • Step 2 Preparation of 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)thio)heptanoic acid
  • Step 3 Preparation of: 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)thio)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 4 Preparation of 7-((4-((6-(cyclohexylamino)-9H-purin-2-yl)amino)phenyl)thio)-N-hydroxyheptanamide
  • Step 1 Preparation of methyl 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)sulfonyl)heptanoate
  • Step 2 Preparation of 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)sulfonyl)heptanoic acid
  • Step 3 Preparation of 7-((4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)sulfonyl)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 4 Preparation of 7-((4-((6-(cyclohexylamino)-9H-purin-2-yl)amino)phenyl)sulfonyl)-N-hydroxyheptanamide
  • Step 1 Preparation of methyl 8-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)octanoate
  • Step 2 Preparation of 8-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)octanoic acid
  • Step 3 Preparation of 8-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenyl)-N-((tetrahydro-2H-pyran-2-yl)oxy)octanamide
  • Step 4 Preparation of 8-(4-((6-(cyclohexylamino)-9H-purin-2-yl)amino)phenyl)-N-hydroxyoctanamide
  • Step 2 Preparation of methyl 7-(4-((9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 1 Preparation of 2-chloro-N-cyclohexyl-N-methyl-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-amine
  • Step 2 Preparation of methyl 7-(4-((6-(cyclohexyl(methyl)amino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 5 Preparation of 7-(4-((6-(cyclohexyl(methyl)amino)-9H-purin-2-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 1 Preparation of 2-chloro-N-(1-methylpiperidin-4-yl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-amine
  • Step 2 Preparation of methyl 7-(4-((6-((1-methylpiperidin-4-yl)amino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((6-((1-methylpiperidin-4-yl)amino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((6-((1-methylpiperidin-4-yl)amino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 5 Preparation of N-hydroxy-7-(4-((6-((1-methylpiperidin-4-yl)amino)-9H-purin-2-yl)amino)phenoxy)heptanamide
  • Step 2 Preparation of methyl 7-(4-((6-phenyl-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((6-phenyl-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((6-phenyl-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 1 Preparation of methyl 6-(4-((tert-butoxycarbonyl)amino)benzamido)hexanoate
  • Methyl 6-(4-((tert-butoxycarbonyl)amino)benzamido)hexanoate (0.4 g, 1.1 mmol) was added to a solution of HCl/Dioxane (4M, 5 mL) and was stirred at r.t for 2 hrs. The mixture was then concentrated. To the residue, EtOAc and aq. NaHCO 3 solution were added. The layers were separation and the aqueous layer was extracted with EtOAc. The organic extract was dried and concentrated to give methyl 6-(4-aminobenzamido)hexanoate as brown solid (0.30 g) which was used without further purification.
  • Step 1 Preparation of methyl 6-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)benzamido)hexanoate
  • Step 2 Preparation of 6-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)benzamido)hexanoic acid
  • Step 3 Preparation of 4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)-N-(6-oxo-6-(((tetrahydro-2H-pyran-2-yl)oxy)amino)hexyl)benzamide
  • Step 4 Preparation of 4-((6-(cyclohexylamino)-9H-purin-2-yl)amino)-N-(6-(hydroxyamino)-6-oxohexyl)benzamide
  • Step 1 Preparation of methyl 5-(4-((tert-butoxycarbonyl)amino)benzamido)pentanoate
  • Step 1 Preparation of methyl 5-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)benzamido)pentanoate
  • Step 2 Preparation of 5-(4-((6-(cyclohexylamino)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)benzamido)pentanoic acid
  • Step 4 Preparation of 4-((6-(cyclohexylamino)-9H-purin-2-yl)amino)-N-(5-(hydroxyamino)-5-oxopentyl)benzamide
  • Step 3 Preparation of methyl 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((4-(cyclohexylamino)-1H-imidazo[4,5-c]pyridin-6-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 2 Preparation of methyl 7-(4-((7-(cyclohexylamino)thiazolo[4,5-d]pyrimidin-5-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((7-(cyclohexylamino)thiazolo[4,5-d]pyrimidin-5-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((7-(cyclohexylamino)thiazolo[4,5-d]pyrimidin-5-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 5 Preparation of 7-(4-((7-(cyclohexylamino)thiazolo[4,5-d]pyrimidin-5-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 2 Preparation of methyl 7-(4-((4-(cyclohexylamino)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((4-(cyclohexylamino)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 3 Preparation of methyl 7-(4-((6-benzyl-9-(4-methoxybenzyl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of methyl 7-(4-((6-benzyl-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 6 Preparation of 7-(4-((6-benzyl-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 7 Preparation of: 7- ⁇ 4-[(6-benzyl-9H-purin-2-yl)amino]phenoxy ⁇ -N-hydroxyheptanamide
  • Step 3 Preparation of methyl 7-(4-((4-(cyclohexylamino)-7-(4-methoxybenzyl)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of methyl 7-(4-((4-(cyclohexylamino)-7-(4-methoxybenzyl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoate
  • Step 5 Preparation of methyl 7-(4-((4-(cyclohexylamino)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoate
  • Step 6 Preparation of 7-(4-((4-(cyclohexylamino)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoic acid
  • Step 7 Preparation of 7-(4-((4-(cyclohexylamino)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 8 Preparation of 7-(4-((4-(cyclohexylamino)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 2 Preparation of methyl 7-(4-((4-(cyclohexylamino)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((4-(cyclohexylamino)-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 3 Preparation of methyl 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of: 7-(4-((4-(cyclohexylamino)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((4-(cyclohexylamino)-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino)phenoxy)-N-hydroxyheptanamide
  • Step 3 Preparation of methyl 7-(4-((6-(cyclohexylamino)-7-methyl-7H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 4 Preparation of 7-(4-((6-(cyclohexylamino)-7-methyl-7H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 5 Preparation of 7-(4-((6-(cyclohexylamino)-7-methyl-7H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • Step 6 Preparation of 7-(4-((6-(cyclohexylamino)-7-methyl-7H-purin-2-yl)amino)phenoxy)-N-hydroxyheptanamide
  • 2,6-Dichloro-9-(tetrahydro-2H-pyran-2-yl)-9H-purine (2.0 g, 7.3 mol), piperidine (1.0 g, 12.2 mmol), butanol (4 mL) and TEA (0.8 g, 8 mmol) were combined and heated to 60° C. with stirring for 3 hrs. The mixture was then cooled, poured ito water and extracted with EA. The combined extracts were dried and concentrated, and the residue was purified by column chromatography to give 2-chloro-6-(piperidin-1-yl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purine as a gray solid (1.6 g, 65%).
  • Step 2 Preparation of methyl 7-(4-((6-(piperidin-1-yl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoate
  • Step 3 Preparation of 7-(4-((6-(piperidin-1-yl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)heptanoic acid
  • Step 4 Preparation of 7-(4-((6-(piperidin-1-yl)-9-(tetrahydro-2H-pyran-2-yl)-9H-purin-2-yl)amino)phenoxy)-N-((tetrahydro-2H-pyran-2-yl)oxy)heptanamide
  • HDAC Fluorescent Activity Assay based on the unique Fluor de LysTM Substrate and Developer combination.
  • the Fluor de LysTM system Fluorogenic Histone deAcetylase Lysyl Substrate/Developer
  • the human HDAC enzymes (1-11) were expressed as recombinant proteins using baculoviral expression system. Recombinant HDAC enzymes were purified as either as 6 ⁇ His or GST fusion proteins.
  • class I HDAC enzymes fluorogenic, acetylated peptide substrate based on residues 379-382 of p53 (Arg-His-Lys-Lys(Ac)) were used as the substrate.
  • the enzymes were diluted in HDAC reaction buffer (50 mM Tris-HCl, pH8.0, 137 mM NaCl, 2.7 mM KCl, 1 mM MgCl2. Before use, 1 mg/ml BSA (1% DMSO) was added.
  • HDAC reaction buffer 50 mM Tris-HCl, pH8.0, 137 mM NaCl, 2.7 mM KCl, 1 mM MgCl2.
  • BSA 1% DMSO
  • Class IIb HDAC enzymes fluorogenic, Acetyl-Lys(trifluoroacetyl) were used.
  • the Fluor de LysTM substrate which comprises an acetylated lysine side chain, is incubated with test compounds at 30° C. for 2 hr.
  • the reaction was terminated by adding Fluor de LysTM Developer to produce a fluorophore which can be recorded with PerkinElmer Envision reader (Excite 360 nm/Emission 460 nm) at 15 min over a period of 1.5 hr.
  • PerkinElmer Envision reader Excite 360 nm/Emission 460 nm
  • the data was collected and the IC 50 was determined using GraphPad Prism software by quadratic regression analysis.
  • An example of the potency and selectivity of this class of compounds (as exemplified by Examples 8 and 9) compared with literature standard Trichostatin A is shown in Table 1.
  • total protein extracts were prepared by lysing cells in lysis buffer (50 mM Tris-Cl [pH 8.0], 5 mM EDTA, 150 mM NaCl, 1% NP-40, 0.1% SDS, and 1 mM phenylmethylsulfonyl fluoride). 50 ⁇ g of total soluble proteins were separated by SDS-PAGE. Proteins were transferred to nitrocellulose membrane and the membrane was blocked for 1 hour with 4% nonfat milk, followed by overnight incubation at 4° C.
  • lysis buffer 50 mM Tris-Cl [pH 8.0], 5 mM EDTA, 150 mM NaCl, 1% NP-40, 0.1% SDS, and 1 mM phenylmethylsulfonyl fluoride. 50 ⁇ g of total soluble proteins were separated by SDS-PAGE. Proteins were transferred to nitrocellulose membrane and the membrane was blocked for 1 hour with 4% nonfat milk, followed by overnight incubation at 4° C.
  • GAPDH Glyceraldehyde 3-phosphate dehydrogenase
  • FIGS. 1 and 2 show the results of Tubulin acylation when treated with exemplary compounds of the invention.
  • Example 43 NCI 60 Cell Line Data for Example 3
  • NCI60 tumour cell lines were screened for the activity of the test compounds and the resulting data is displayed in Table 2 below.
  • the response parameters GI50 (50% growth inhibition) are extracted from concentration-response curves by linear interpolation. Table 2
  • the lung non-small cell epithelial cancer cell lines A549 cultured at 37° C. with 5% CO2 and grown in media.
  • NCI (nru) athymic nude mice 6 weeks of age were obtained from the NCI (Bethesda, Md.) and maintained in pathogen-limited conditions.
  • s.c. injections of 2 ⁇ 10 6 A549 NSCLC tumor cells in an equal volume of Matrigel (Collaborative Biomedical Products, Bedford, Mass.) were implanted into the mouse posterior flanks before the administration of drugs. Tumor-bearing mice were randomly divided into five per group.
  • the control group was treated with vehicle (saline solution), and the other groups were treated with 30 mg/kg/3x/wk ip of example 2.

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