Classifications

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  • 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
  • A61K31/506—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
• • 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
  • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
  • A61K31/5375—1,4-Oxazines, e.g. morpholine
  • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
• • 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
  • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
  • A61K31/5375—1,4-Oxazines, e.g. morpholine
  • A61K31/5383—1,4-Oxazines, e.g. morpholine ortho- or peri-condensed with heterocyclic ring 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
  • A61K31/66—Phosphorus compounds
  • A61K31/675—Phosphorus compounds having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
• • 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
  • A61P25/00—Drugs for disorders of the nervous system
  • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• • 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
  • 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
  • C07D401/14—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 three or more hetero rings
• • 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
  • C07D403/10—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 linked by a carbon chain containing aromatic rings
• • 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
  • C07D403/14—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 three or more hetero rings
• • 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
  • C07D413/14—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing three or more hetero rings
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
  • C07D471/04—Ortho-condensed systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
  • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
  • C07D491/04—Ortho-condensed systems
  • C07D491/044—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
  • C07D491/052—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring the oxygen-containing ring being six-membered
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
  • C07D491/12—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains three hetero rings
  • C07D491/14—Ortho-condensed systems
  • C07D491/147—Ortho-condensed systems the condensed system containing one ring with oxygen as ring hetero atom and two rings with nitrogen as ring hetero atom
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
  • C07D498/12—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains three hetero rings
  • C07D498/14—Ortho-condensed systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
  • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
  • C07F9/02—Phosphorus compounds
  • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
  • C07F9/6558—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system
  • C07F9/65583—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system each of the hetero rings containing nitrogen as ring hetero atom

Definitions

• the invention relates to heteroarenes and their use for therapeutic treatment of neurological disorders in patients, such as human patients.
• TDP-43 is a nuclear DNA/RNA binding protein involved in RNA splicing. Under pathological cell stress, TDP-43 translocates to the cytoplasm and aggregates into stress granules and related protein inclusions. These phenotypes are hallmarks of degenerating motor neurons and are found in 97% of all ALS cases. The highly penetrant nature of this pathology indicates that TDP-43 is broadly involved in both familial and sporadic ALS. Additionally, TDP-43 mutations that promote aggregation are linked to higher risk of developing ALS, suggesting protein misfolding and aggregation act as drivers of toxicity. TDP-43 toxicity can be recapitulated in yeast models, where the protein induces a viability deficit and localizes to stress granules.
• the disclosure provides a compound of Formula I:
• V is -NH-, -NR 5 -, -CH2NH-, -CH2NR 5 -, -O-, -CO-, or -CHOH-;
• R 1 is optionally substituted morpholin-4-yl, pyridin-4-yl, pyridin-3-yl, optionally substituted 2-oxo- pyrrolidin-1 -yl, optionally substituted piperidin-1-yl, or optionally substituted pyridiazin-4-yl;
• R 2 is halogen, -(CH2)nOH, optionally substituted C1-6 alkoxy, optionally substituted C2-C9 heteroaryl, optionally substituted 2-oxo-pyrrolidin-1-yl, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(0)kR 7e ; and R 3 is optionally substituted pyridin-2-yl, optionally substituted pyridin-3-yl, optionally substituted pyridin-4-yl, optionally substituted pyrazol-1-yl, optionally substituted pyrazol-3-yl, optionally substituted pyridazin-3-yl, optionally substituted pyrimidin-4-yl, or optionally substituted Ce-C aryl; or R 2 and R 3 , together with the ring to which they are attached, combine to form optionally substituted C4-C12 heteroaryl; n is 1 , 2, 3, 4, 5, or 6; k is 0,
• R 4 is optionally substituted pyridin-4-yl, optionally substituted 1 -methylpyridin-1-ium-4-yl, optionally substituted pyridin-3-yl, optionally substituted 1 -methylpiperidin-3-yl, optionally substituted pyridazine-3-yl, or -NHR 8 ;
• R 5 is optionally substituted Ci-Ce alkyl
• R 6 is H or optionally substituted Ci-Ce alkyl
• each of R 7a and R 7b is, independently, H or optionally substituted Ci-Ce alkyl; or R 7a and R 7b , together with the nitrogen atom to which they are attached, combine to form optionally substituted C2-C9 heterocyclyl
• each of R 7c , R 7d , and R 7e is independently optionally substituted C1-6 alkyl, optionally substituted C1-6 alkoxy, or hydroxyl;
• R 8 is optionally substituted phenyl or optionally substituted C3-C6 cycloalkyl.
• R 1 is optionally substituted morpholin-4-yl. In some embodiments, R 1 is optionally substituted pyridin-4-yl. In some embodiments, R 1 is optionally substituted pyridin-3-yl.
• R 1 is . , or . In some embodiments, R 1 is morpholin-4-yl. In some embodiments, R 1 is optionally substituted piperidin-1-yl. In some embodiments,
• V is -NH-. In some embodiments, V is -CH2NH-. In some embodiments, V is -O-. In some embodiments, V is -CO-. In some embodiments, V is -CHOH-. In some embodiments, V is -NR 5 -. In some embodiments, V is -CH2NR 5 -.
• R 4 is optionally substituted pyridin-4-yl, optionally substituted 1 - methylpyridin-1-ium-4-yl, optionally substituted pyridin-3-yl, optionally substituted 1 -methylpiperidin-3-yl, optionally substituted pyridazine-3-yl. In some embodiments, R 4 is optionally substituted pyridin-4-yl, optionally substituted pyridin-3-yl, optionally substituted 1 -methylpiperidin-3-yl, optionally substituted pyridazine-3-yl. In some embodiments, R 4 is optionally substituted pyridin-4-yl or optionally substituted pyridin-3-yl. In some embodiments, R 4 is pyridin-4-yl or pyridin-3-yl.
• R 2 and R 3 together with the ring to which they are attached, combine to form optionally substituted C4-C12 heteroaryl. In some embodiments, R 2 and R 3 , together with the ring to which they are attached, combine to form optionally substituted C4-C9 heteroaryl. In some embodiments, the compound is of the following structure: pharmaceutically acceptable salt thereof.
• R 2 is halogen, -(CH2)nOH, optionally substituted Ci-e alkoxy, optionally substituted C2-C9 heteroaryl, optionally substituted 2-oxo-pyrrolidin-1-yl, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(O)kR 7e .
• R 2 is optionally substituted C1-6 alkoxy, optionally substituted C2-C9 heteroaryl, optionally substituted 2-oxo-pyrrolidin-1-yl, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(0)kR 7e .
• R 2 is optionally substituted C1-6 alkoxy. In some embodiments, R 2 is -OCH3.
• R 2 is -(CO)NR 7a R 7b .
• each of R 7a and R 7b is, independently, optionally substituted Ci-Ce alkyl.
• each of R 7a and R 7b is methyl.
• R 7a and R 7b together with the nitrogen atom to which they are attached, combine to form optionally substituted C2-C9 heterocyclyl.
• -(CO)NR 7a R 7b is
• R 2 is -P(O)R 7c R 7d , or -S(0)kR 7e . In some embodiments, R 2 is ⁇ "CH 3
• R 2 is optionally substituted C2-C9 heteroaryl. In some embodiments, R 2 is
• R 2 is halogen. In some embodiments, R 2 is Cl. In some embodiments, R 2 is -(CH2)nOH. In some embodiments, n is 1 , 2, or 3. In some embodiments, n is 1 .
• R 3 is optionally substituted pyridin-2-yl, optionally substituted pyridin-3-yl, optionally substituted pyridin-4-yl, optionally substituted pyrazol-1-yl, optionally substituted pyrazol-3-yl, optionally substituted pyridazin-3-yl, optionally substituted pyrimidin-4-yl, or optionally substituted Ce-C aryl.
• R 3 is optionally substituted pyridin-3-yl, optionally substituted pyridin-4-yl, or optionally substituted Ce-Cw aryl.
• R 3 is optionally substituted Ce aryl. In some embodiments, R 3 is
• R 3 is optionally substituted pyridin-3-yl or optionally substituted pyridin-4-
• R 3 is optionally substituted pyridin-2-yl, optionally substituted pyrazol-1-yl, optionally substituted pyrazol-3-yl, optionally substituted pyridazin-3-yl, or optionally substituted pyrimidin-
• the disclosure provides a compound of Formula II:
• R 9 is optionally substituted morpholin-4-yl, optionally substituted morpholin-3-ylalkoxy, optionally substituted 2-(pyridin-2-yl)alkoxy, optionally substituted 1 -methylpiperazin-2-yl, or optionally substituted Ce-Cw aryl;
• R 10 is optionally substituted Ci-e alkoxy, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(0)kR 7e ; each of R 7a and R 7b is, independently, H or optionally substituted Ci-Ce alkyl; or R 7a and R 7b , together with the nitrogen atom to which they are attached, combine to form optionally substituted C2-C9 heterocyclyl; each of R 7c , R 7d , and R 7e is independently optionally substituted Ci-e alkyl, optionally substituted C1-6 alkoxy, or hydroxyl; k is 0, 1 , or 2;
• R 11 is optionally substituted morpholin-4-yl, optionally substituted pyridin-4-yl, optionally substituted pyrazol-4-yl, optionally substituted 1 H-imidazol-2-yl, optionally substituted quinoline-6-yl, or optionally substituted Ce-Cw aryl;
• R 12 is optionally substituted 1-methylpiperazin-2-onyl, optionally substituted 2-(pyridin-2-yl)alkoxy, optionally substituted N-(pyridin-3-ylmethyl)amine, optionally substituted N-(pyridin-4-yl)amine, or optionally substituted Ce-Cw aryl.
• R 9 is morpholin-4-yl.
• R 9 is optionally substituted morpholin-3-ylalkoxy. In some embodiments, R 9 is optionally substituted 2-(pyridin-2-yl)alkoxy. In some embodiments,
• R 9 is optionally substituted 1-methylpiperazin-2-yl. In some embodiments, R 9 is optionally substituted Ce-C aryl. In some embodiments,
• R 10 is optionally substituted C1-6 alkoxy. In some embodiments, R 10 is methoxy.
• R 11 is optionally substituted morpholin-4-yl. In some embodiments, R 11 is morpholin-4-yl. In some embodiments, R 11 is optionally substituted pyridin-4-yl. In some embodiments, R 11 is pyridin-4-yl.
• R 11 is optionally substituted pyrazol-4-yl. In some embodiments, R 11 is diments, R 11 is optionally substituted 1 H-imidazol-2-yl. In some embodiments, R 11 diments, R 11 is optionally substituted quinolin-6-yl. In some embodiments, R 11 is
• R 11 is optionally substituted Ce-Cw aryl.
• R 12 is optionally substituted 1-methylpiperazin-2-only. In some embodiments,
• R 12 is optionally substituted 2-(pyridin-2-yl)alkoxy. In some embodiments,
• R 12 is optionally substituted N-(pyridin-3-ylmethyl)amine. In some embodiments,
• R 12 is optionally substituted N-(pyridin-4-yl)amine. In some embodiments,
• R 12 is optionally substituted Ce-C aryl. In some embodiments, R 12 is
• the compound has the structure of any one of compounds 1-78 in Table 1 , or a pharmaceutically acceptable salt thereof. In some embodiments, the compound has the structure of any one of compounds 1-3, 6-29, 31-36, 38-41 , 43-51 , 53-57, 59, 62, and 64-78 in Table 1 , or a pharmaceutically acceptable salt thereof. In some embodiments, the compound has the structure of any one of compounds 4, 5, 30, 37, 42, 52, 58, 60, 61 , and 63 in Table 1 , or a pharmaceutically acceptable salt thereof.
• the compound has the structure of any one of compounds 1-78 in Table 1 , or a pharmaceutically acceptable salt thereof.
• the compound has the structure of any one of compounds 1-3, 6-29, 31-36, 38-41 , 43-51 , 53-57, 59, 62, and 64-78 in Table 1 , or a pharmaceutically acceptable salt thereof.
• the compound has the structure of any one of compounds 4, 5, 30, 37, 42, 52, 58, 60, 61 , and 63 in Table 1 , or a pharmaceutically acceptable salt thereof.
• the compound has the structure of any one of compounds 66 and 34 in Table 1 , or a pharmaceutically acceptable salt thereof.
• Table 1 Compounds of the Invention
• the invention provides an intermediate in the synthesis of some compounds of the invention.
• the intermediates include compounds i-1 to i-4 in Table 2.
• the invention features a pharmaceutical composition comprising any of the foregoing compounds and a pharmaceutically acceptable excipient.
• the invention features a method of treating a neurological disorder (e.g., frontotemporal dementia (FTLD-TDP), chronic traumatic encephalopathy, ALS, Alzheimer’s disease, limbic-predominant age-related TDP-43 encephalopathy (LATE), or frontotemporal lobar degeneration) in a subject in need thereof.
• a neurological disorder e.g., frontotemporal dementia (FTLD-TDP), chronic traumatic encephalopathy, ALS, Alzheimer’s disease, limbic-predominant age-related TDP-43 encephalopathy (LATE), or frontotemporal lobar degeneration
• This method includes administering an effective amount of any of the foregoing compounds or pharmaceutical compositions.
• the invention features a method of inhibiting toxicity in a cell (e.g., mammalian neural cell) related to a protein (e.g., TDP-43 or C9orf72).
• a cell e.g., mammalian neural cell
• a protein e.g., TDP-43 or C9orf72.
• the invention features a method of treating a TDP-43-associated disorder or C9orf72-associated disorder (e.g., FTLD-TDP, chronic traumatic encephalopathy, ALS, Alzheimer’s disease, LATE, or frontotemporal lobar degeneration) in a subject in need thereof.
• This method includes administering to the subject an effective amount of a compounds described herein or a pharmaceutical composition containing one or more compounds described herein.
• the method includes administering to the subject in need thereof an effective amount of the compound of Formula I or a pharmaceutically acceptable salt thereof (e.g., a compound having the structure of any one of compounds 1-3, 6-29, 31-36, 38-41 , 43-51 , 53-57, 59, 62, and 64-78 in Table 1 or a pharmaceutically acceptable salt thereof).
• the method includes administering to the subject in need thereof an effective amount of the compound of Formula II or a pharmaceutically acceptable salt thereof (e.g., a compound having the structure of any one of compounds 4, 5, 30, 37, 42, 52, 58, 60, 61 , and 63 in Table 1 or a pharmaceutically acceptable salt thereof).
• the method includes administering to the subject in need thereof an effective amount of the compound having the structure of any one of compounds 1-78 in Table 1 or a pharmaceutically acceptable salt thereof.
• the invention features a method of inhibiting PlKfyve.
• This method includes contacting a cell with an effective amount of any of the foregoing compounds or pharmaceutical compositions.
• the method includes administering to the subject in need thereof an effective amount of the compound of Formula I or a pharmaceutically acceptable salt thereof (e.g., a compound having the structure of any one of compounds 1-3, 6-29, 31-36, 38-41 , 43-51 , 53-57, 59, 62, and 64-78 in Table 1 or a pharmaceutically acceptable salt thereof).
• a pharmaceutically acceptable salt thereof e.g., a compound having the structure of any one of compounds 1-3, 6-29, 31-36, 38-41 , 43-51 , 53-57, 59, 62, and 64-78 in Table 1 or a pharmaceutically acceptable salt thereof.
• the method includes administering to the subject in need thereof an effective amount of the compound of Formula II or a pharmaceutically acceptable salt thereof (e.g., a compound having the structure of any one of compounds 4, 5, 30, 37, 42, 52, 58, 60, 61 , and 63 in Table 1 or a pharmaceutically acceptable salt thereof). In some embodiments, the method includes administering to the subject in need thereof an effective amount of the compound having the structure of any one of compounds 1-78 in Table 1 or a pharmaceutically acceptable salt thereof.
• the compound of Formula II or a pharmaceutically acceptable salt thereof e.g., a compound having the structure of any one of compounds 4, 5, 30, 37, 42, 52, 58, 60, 61 , and 63 in Table 1 or a pharmaceutically acceptable salt thereof.
• the invention features a method of treating a neurological disorder in a patient, such as a human patient, identified as likely to benefit from treatment with a compound of the invention on the basis of TDP-43 toxicity.
• the method may include (i) determining that the patient exhibits, or is prone to develop, TDP-43 toxicity, and (ii) providing to the patient a therapeutically effective amount of a compound of the invention.
• the patient has previously been determined to exhibit, or to be prone to developing, TDP-43 toxicity, and the method includes providing to the patient a therapeutically effective amount of a compound of the invention.
• the susceptibility of the patient to developing TDP-43 aggregation may be determined, e.g., by determining whether the patient expresses a mutant isoform of TDP-43 containing a mutation that is associated with TDP-43 aggregation and toxicity, such as a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D. This may be performed, for example, by determining the amino acid sequence of a TDP-43 isoform isolated from a sample obtained from the patient or by determining the nucleic acid sequence of a TDP-43 gene isolated from a sample obtained from the patient. In some embodiments, the method includes the step of obtaining the sample from the patient.
• the invention features a method of treating a neurological disorder in a patient, such as a human patient, identified as likely to benefit from treatment with a compound of the invention on the basis of TDP-43 expression.
• the method includes (i) determining that the patient expresses a mutant form of TDP-43 having a mutation associated with TDP-43 aggregation (e.g., a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D), and (ii) providing to the patient a therapeutically effective amount of a compound of the invention.
• a mutant form of TDP-43 having a mutation associated with TDP-43 aggregation e.g., a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D
• the patient has previously been determined to express a mutant form of TDP-43 having a mutation associated with TDP-43 aggregation, such as a Q331 K, M337V, Q343R, N345K, R361S, or N390D mutation, and the method includes providing to the patient a therapeutically effective amount of a compound of the invention.
• a mutation associated with TDP-43 aggregation such as a Q331 K, M337V, Q343R, N345K, R361S, or N390D mutation
• the invention features a method of determining whether a patient (e.g., a human patient) having a neurological disorder is likely to benefit from treatment with a compound of the invention by (i) determining whether the patient exhibits, or is prone to develop, TDP-43 aggregation and (ii) identifying the patient as likely to benefit from treatment with a compound of the invention if the patient exhibits, or is prone to develop, TDP-43 aggregation.
• the method further includes the step of (iii) informing the patient whether he or she is likely to benefit from treatment with a compound of the invention.
• the susceptibility of the patient to developing TDP-43 aggregation may be determined, e.g., by determining whether the patient expresses a mutant isoform of TDP-43 containing a mutation that is associated with TDP-43 aggregation and toxicity, such as a mutation selected from Q331 K, M337V, Q343R, N345K, R361 S, and N390D. This may be performed, for example, by determining the amino acid sequence of a TDP-43 isoform isolated from a sample obtained from the patient or by determining the nucleic acid sequence of a TDP-43 gene isolated from a sample obtained from the patient. In some embodiments, the method includes the step of obtaining the sample from the patient.
• the invention features a method of determining whether a patient (e.g., a human patient) having a neurological disorder is likely to benefit from treatment with a compound of the invention by (i) determining whether the patient expresses a TDP-43 mutant having a mutation associated with TDP-43 aggregation (e.g., a mutation selected from Q331 K, M337V, Q343R, N345K, R361 S, and N390D) and (ii) identifying the patient as likely to benefit from treatment with a compound of the invention if the patient expresses a TDP-43 mutant.
• a mutation associated with TDP-43 aggregation e.g., a mutation selected from Q331 K, M337V, Q343R, N345K, R361 S, and N390D
• the method further includes the step of (iii) informing the patient whether he or she is likely to benefit from treatment with a compound of the invention.
• the TDP-43 isoform expressed by the patient may be assessed, for example, by isolated TDP- 43 protein from a sample obtained from the patient and sequencing the protein using molecular biology techniques described herein or known in the art.
• the TDP-43 isoform expressed by the patient is determined by analyzing the patient’s genotype at the TDP-43 locus, for example, by sequencing the TDP-43 gene in a sample obtained from the patient.
• the method includes the step of obtaining the sample from the patient.
• the compound of the invention is provided to the patient by administration of the compound of the invention to the patient. In some embodiments, the compound of the invention is provided to the patient by administration of a prodrug that is converted in vivo to the compound of the invention.
• the neurological disorder is a neuromuscular disorder, such as a neuromuscular disorder selected from amyotrophic lateral sclerosis, congenital myasthenic syndrome, congenital myopathy, cramp fasciculation syndrome, Duchenne muscular dystrophy, glycogen storage disease type II, hereditary spastic paraplegia, inclusion body myositis, Isaac's Syndrome, Kearns-Sayre syndrome, Lambert-Eaton myasthenic syndrome, mitochondrial myopathy, muscular dystrophy, myasthenia gravis, myotonic dystrophy, peripheral neuropathy, spinal and bulbar muscular atrophy, spinal muscular atrophy, Stiff person syndrome, Troyer syndrome, and Guillain- Barre syndrome.
• the neurological disorder is amyotrophic lateral sclerosis.
• the neurological disorder is selected from frontotemporal degeneration (also referred to as frontotemporal lobar degeneration and frontotemporal dementia), Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD), sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy.
• frontotemporal degeneration also referred to as frontotemporal lobar degeneration and frontotemporal dementia
• Alzheimer’s disease Parkinson’s disease
• dementia with Lewy Bodies corticobasal degeneration
• progressive supranuclear palsy dementia parkinsonism ALS complex of Guam
• Huntington’s disease Inclusion body myopathy with early-onset Paget disease and
• the neurological disorder is amyotrophic lateral sclerosis
• the neurological disorder is amyotrophic lateral sclerosis
• following administration of the compound of the invention to the patient the patient exhibits one or more, or all, of the following responses:
• an increase in slow vital capacity such as an increase in the patient’s slow vital capacity within one or more days, weeks, or months following administration of the compound of the invention (e.g., an increase in the patient’s slow vital capacity within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks,
• a reduction in decremental responses exhibited by the patient upon repetitive nerve stimulation such as a reduction that is observed within one or more days, weeks, or months following administration of the compound of the invention (e.g., a reduction that is observed within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35
• an improvement in muscle strength as assessed, for example, by way of the Medical Research Council muscle testing scale (as described, e.g., in Jagtap et al., Ann. Indian. Acad. Neurol. 17:336-339 (2014), the disclosure of which is incorporated herein by reference as it pertains to measuring patient response to neurological disease treatment), such as an improvement that is observed within one or more days, weeks, or months following administration of the compound of the invention (e.g., an improvement that is observed within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14
• an improvement in quality of life as assessed, for example, using the amyotrophic lateral sclerosis-specific quality of life (ALS-specific QOL) questionnaire, such as an improvement in the patient’s quality of life that is observed within one or more days, weeks, or months following administration of the compound of the invention (e.g., an improvement in the subject’s quality of life that is observed within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24
• a decrease in the frequency and/or severity of muscle cramps such as a decrease in cramp frequency and/or severity within one or more days, weeks, or months following administration of the compound of the invention (e.g., a decrease in cramp frequency and/or severity within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34
• a decrease in TDP-43 aggregation such as a decrease in TDP-43 aggregation within one or more days, weeks, or months following administration of the compound of the invention (e.g., a decrease in TDP-43 aggregation within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks,
• one or more compounds depicted herein may exist in different tautomeric forms.
• references to such compounds encompass all such tautomeric forms.
• tautomeric forms result from the swapping of a single bond with an adjacent double bond and the concomitant migration of a proton.
• a tautomeric form may be a prototropic tautomer, which is an isomeric protonation states having the same empirical formula and total charge as a reference form.
• moieties with prototropic tautomeric forms are ketone - enol pairs, amide - imidic acid pairs, lactam - lactim pairs, amide - imidic acid pairs, enamine - imine pairs, and annular forms where a proton can occupy two or more positions of a heterocyclic system, such as, 1 H- and 3H-imidazole, 1 H-, 2H- and 4H- 1 ,2,4-triazole, 1 H- and 2H- isoindole, and 1 H- and 2H-pyrazole.
• tautomeric forms can be in equilibrium or sterically locked into one form by appropriate substitution.
• tautomeric forms result from acetal interconversion, e.g., the interconversion illustrated in the scheme below:
• isotopes of compounds described herein may be prepared and/or utilized in accordance with the present invention.
• “Isotopes” refers to atoms having the same atomic number but different mass numbers resulting from a different number of neutrons in the nuclei.
• isotopes of hydrogen include tritium and deuterium.
• an isotopic substitution e.g., substitution of hydrogen with deuterium
• many chemical entities in particular, many organic molecules and/or many small molecules
• can adopt a variety of different solid forms such as, for example, amorphous forms and/or crystalline forms (e.g., polymorphs, hydrates, solvates, etc).
• such entities may be utilized in any form, including in any solid form.
• such entities are utilized in a particular form, for example in a particular solid form.
• compounds described and/or depicted herein may be provided and/or utilized in salt form.
• compounds described and/or depicted herein may be provided and/or utilized in hydrate or solvate form.
• substituents of compounds of the present disclosure are disclosed in groups or in ranges. It is specifically intended that the present disclosure include each and every individual subcombination of the members of such groups and ranges.
• the term “Ci-Ce alkyl” is specifically intended to individually disclose methyl, ethyl, C3 alkyl, C4 alkyl, C5 alkyl, and Ce alkyl.
• the present disclosure is intended to cover individual compounds and groups of compounds (e.g., genera and subgenera) containing each and every individual subcombination of members at each position.
• optionally substituted X e.g., optionally substituted alkyl
• X optionally substituted
• alkyl wherein said alkyl is optionally substituted
• acyl represents a hydrogen or an alkyl group, as defined herein that is attached to a parent molecular group through a carbonyl group, as defined herein, and is exemplified by formyl (i.e., a carboxyaldehyde group), acetyl, trifluoroacetyl, propionyl, and butanoyl.
• exemplary unsubstituted acyl groups include from 1 to 6, from 1 to 11 , or from 1 to 21 carbons.
• alkyl refers to a branched or straight-chain monovalent saturated aliphatic hydrocarbon radical of 1 to 20 carbon atoms (e.g., 1 to 16 carbon atoms, 1 to 10 carbon atoms, or 1 to 6 carbon atoms).
• An alkylene is a divalent alkyl group.
• alkenyl refers to a straight-chain or branched hydrocarbon residue having a carbon-carbon double bond and having 2 to 20 carbon atoms (e.g., 2 to 16 carbon atoms, 2 to 10 carbon atoms, 2 to 6, or 2 carbon atoms).
• alkynyl refers to a straight-chain or branched hydrocarbon residue having a carbon-carbon triple bond and having 2 to 20 carbon atoms (e.g., 2 to 16 carbon atoms, 2 to 10 carbon atoms, 2 to 6, or 2 carbon atoms).
• amino represents -N(R N1 )2, wherein each R N1 is, independently, H, OH, NO2, N(R N2 ) 2 , SO2OR N2 , SO2R N2 , SOR N2 , an A/-protecting group, alkyl, alkoxy, aryl, arylalkyl, cycloalkyl, acyl (e.g., acetyl, trifluoroacetyl, or others described herein), wherein each of these recited R N1 groups can be optionally substituted; or two R N1 combine to form an alkylene or heteroalkylene, and wherein each R N2 is, independently, H, alkyl, or aryl.
• the amino groups of the invention can be an unsubstituted amino (i.e., -NH2) or a substituted amino (i.e., -N(R N1 )2).
• aryl refers to an aromatic mono- or polycarbocyclic radical of 6 to 12 carbon atoms having at least one aromatic ring.
• groups include, but are not limited to, phenyl, naphthyl, 1 ,2,3,4-tetrahydronaphthyl, 1 ,2-dihydronaphthyl, indanyl, and 7/7-indenyl.
• arylalkyl represents an alkyl group substituted with an aryl group.
• exemplary unsubstituted arylalkyl groups are from 7 to 30 carbons (e.g., from 7 to 16 or from 7 to 20 carbons, such as Ci-Ce alkyl Ce-w aryl, C1-C10 alkyl Ce-w aryl, or C1-C20 alkyl Ce- aryl), such as, benzyl and phenethyl.
• the akyl and the aryl each can be further substituted with 1 , 2, 3, or 4 substituent groups as defined herein for the respective groups.
• cyano represents a CN group.
• Carbocyclyl refer to a non-aromatic C3-C12 monocyclic, bicyclic, or tricyclic structure in which the rings are formed by carbon atoms.
• Carbocyclyl structures include cycloalkyl groups and unsaturated carbocyclyl radicals.
• cycloalkyl refers to a saturated, non-aromatic, monovalent mono- or polycarbocyclic radical of three to ten, preferably three to six carbon atoms. This term is further exemplified by radicals such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, norbornyl, and adamantyl.
• halo means a fluorine (fluoro), chlorine (chloro), bromine (bromo), or iodine (iodo) radical.
• heteroalkyl refers to an alkyl group, as defined herein, in which one or more of the constituent carbon atoms have been replaced by nitrogen, oxygen, or sulfur.
• the heteroalkyl group can be further substituted with 1 , 2, 3, or 4 substituent groups as described herein for alkyl groups.
• Examples of heteroalkyl groups are an “alkoxy” which, as used herein, refers alkyl-O- (e.g., methoxy and ethoxy).
• a heteroalkylene is a divalent heteroalkyl group.
• heteroalkenyl refers to an alkenyl group, as defined herein, in which one or more of the constituent carbon atoms have been replaced by nitrogen, oxygen, or sulfur.
• the heteroalkenyl group can be further substituted with 1 , 2, 3, or 4 substituent groups as described herein for alkenyl groups.
• Examples of heteroalkenyl groups are an “alkenoxy” which, as used herein, refers alkenyl-O-.
• a heteroalkenylene is a divalent heteroalkenyl group.
• heteroalkynyl refers to an alkynyl group, as defined herein, in which one or more of the constituent carbon atoms have been replaced by nitrogen, oxygen, or sulfur.
• the heteroalkynyl group can be further substituted with 1 , 2, 3, or 4 substituent groups as described herein for alkynyl groups.
• Examples of heteroalkynyl groups are an “alkynoxy” which, as used herein, refers alkynyl-O-.
• a heteroalkynylene is a divalent heteroalkynyl group.
• heteroaryl refers to a mono- or polycyclic radical of 5 to 12 atoms having at least one aromatic ring and containing one, two, three, or four ring heteroatoms selected from N, O, and S, with the remaining ring atoms being C.
• One or two ring carbon atoms of the heteroaryl group may be replaced with a carbonyl group.
• heteroaryl groups are pyridyl (e.g., pyridin-2- yl, pyridin-3-yl, and pyridin-4-yl), pyrazolyl (e.g., pyrazol-1-yl and pyrazol-3-yl), pyrimidinyl (e.g., pyrimidin- 4-yl), pyridazinyl (e.g., pyridazin-3-yl), benzooxazolyl, benzoimidazolyl, benzothiazolyl, imidazolyl, oxazolyl, and thiazolyl.
• pyridyl e.g., pyridin-2- yl, pyridin-3-yl, and pyridin-4-yl
• pyrazolyl e.g., pyrazol-1-yl and pyrazol-3-yl
• pyrimidinyl e.g., pyrimidin
• heteroarylalkyl represents an alkyl group substituted with a heteroaryl group.
• exemplary unsubstituted heteroarylalkyl groups are from 7 to 30 carbons (e.g., from 7 to 16 or from 7 to 20 carbons, such as Ci-Ce alkyl C2-C9 heteroaryl, C1-C10 alkyl C2-C9 heteroaryl, or C1-C20 alkyl C2-C9 heteroaryl).
• the akyl and the heteroaryl each can be further substituted with 1 , 2, 3, or 4 substituent groups as defined herein for the respective groups.
• heterocyclyl denotes a mono- or polycyclic radical having 3 to 12 atoms having at least one ring containing one, two, three, or four ring heteroatoms selected from N, O or S and no aromatic ring.
• heterocyclyl groups include, but are not limited to, morpholinyl (e.g., morpholin-4-yl), thiomorpholinyl, furyl, piperazinyl, piperidinyl (e.g., piperidin-1-yl), pyranyl, pyrrolidinyl (e.g., pyrrolidin-1 -yl), tetrahydropyranyl, tetrahydrofuranyl, and 1 ,3-dioxanyl.
• a heterocyclyl group may be aromatic or non-aromatic. An aromatic heterocyclyl is also referred to as heteroaryl.
• heterocyclylalkyl represents an alkyl group substituted with a heterocyclyl group.
• exemplary unsubstituted heterocyclylalkyl groups are from 7 to 30 carbons (e.g., from 7 to 16 or from 7 to 20 carbons, such as Ci-Ce alkyl C2-C9 heterocyclyl, C1-C10 alkyl C2-C9 heterocyclyl, or C1-C20 alkyl C2-C9 heterocyclyl).
• the akyl and the heterocyclyl each can be further substituted with 1 , 2, 3, or 4 substituent groups as defined herein for the respective groups.
• hydroxyl represents an -OH group.
• A/-protecting group represents those groups intended to protect an amino group against undesirable reactions during synthetic procedures. Commonly used A/-protecting groups are disclosed in Greene, “Protective Groups in Organic Synthesis,” 3 rd Edition (John Wiley & Sons, New York, 1999).
• A/-protecting groups include acyl, aryloyl, or carbamyl groups such as formyl, acetyl, propionyl, pivaloyl, t-butylacetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl, a-chlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl, 4-nitrobenzoyl, and chiral auxiliaries such as protected or unprotected D, L or D, L-amino acids such as alanine, leucine, and phenylalanine; sulfonyl-containing groups such as benzenesulfonyl, and p-toluenesulfonyl; carbamate forming groups such as benzyloxycarbonyl, p
• Preferred A/-protecting groups are alloc, formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, alanyl, phenylsulfonyl, benzyl, t-butyloxycarbonyl (Boc), and benzyloxycarbonyl (Cbz).
• nitro represents an NO2 group.
• heteroaryl represents a heteroaryl group having at least one endocyclic oxygen atom.
• oxygen atom represents a heterocyclyl group having at least one endocyclic oxygen atom.
• thiol represents an -SH group.
• alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl (e.g., cycloalkyl), aryl, heteroaryl, and heterocyclyl groups may be substituted or unsubstituted. When substituted, there will generally be 1 to 4 substituents present, unless otherwise specified.
• Substituents include, for example: aryl (e.g., substituted and unsubstituted phenyl), carbocyclyl (e.g., substituted and unsubstituted cycloalkyl), halo (e.g., fluoro), hydroxyl, oxo, heteroalkyl (e.g., substituted and unsubstituted methoxy, ethoxy, or thioalkoxy), heteroaryl, heterocyclyl, amino (e.g., NH2 or mono- or dialkyl amino), azido, cyano, nitro, or thiol.
• aryl e.g., substituted and unsubstituted phenyl
• carbocyclyl e.g., substituted and unsubstituted cycloalkyl
• halo e.g., fluoro
• hydroxyl oxo
• heteroalkyl e.g., substituted and
• Aryl, carbocyclyl (e.g., cycloalkyl), heteroaryl, and heterocyclyl groups may also be substituted with alkyl (unsubstituted and substituted such as arylalkyl (e.g., substituted and unsubstituted benzyl)).
• Compounds of the invention can have one or more asymmetric carbon atoms and can exist in the form of optically pure enantiomers, mixtures of enantiomers such as, for example, racemates, optically pure diastereoisomers, mixtures of diastereoisomers, diastereoisomeric racemates or mixtures of diastereoisomeric racemates.
• the optically active forms can be obtained for example by resolution of the racemates, by asymmetric synthesis or asymmetric chromatography (chromatography with a chiral adsorbent or eluant). That is, certain of the disclosed compounds may exist in various stereoisomeric forms.
• Stereoisomers are compounds that differ only in their spatial arrangement.
• Enantiomers are pairs of stereoisomers whose mirror images are not superimposable, most commonly because they contain an asymmetrically substituted carbon atom that acts as a chiral center. "Enantiomer” means one of a pair of molecules that are mirror images of each other and are not superimposable. Diastereomers are stereoisomers that are not related as mirror images, most commonly because they contain two or more asymmetrically substituted carbon atoms and represent the configuration of substituents around one or more chiral carbon atoms. Enantiomers of a compound can be prepared, for example, by separating an enantiomer from a racemate using one or more well-known techniques and methods, such as, for example, chiral chromatography and separation methods based thereon.
• Racemate or “racemic mixture” means a compound containing two enantiomers, wherein such mixtures exhibit no optical activity; i.e., they do not rotate the plane of polarized light.
• Geometric isomer means isomers that differ in the orientation of substituent atoms in relationship to a carbon-carbon double bond, to a cycloalkyl ring, or to a bridged bicyclic system.
• Atoms (other than H) on each side of a carbon- carbon double bond may be in an E (substituents are on opposite sides of the carbon- carbon double bond) or Z (substituents are oriented on the same side) configuration.
• "R,” “S,” “S*,” “R*,” “E,” “Z,” “cis,” and “trans,” indicate configurations relative to the core molecule.
• Certain of the disclosed compounds may exist in atropisomeric forms.
• Atropisomers are stereoisomers resulting from hindered rotation about single bonds where the steric strain barrier to rotation is high enough to allow for the isolation of the conformers.
• the compounds of the invention may be prepared as individual isomers by either isomer-specific synthesis or resolved from an isomeric mixture.
• Conventional resolution techniques include forming the salt of a free base of each isomer of an isomeric pair using an optically active acid (followed by fractional crystallization and regeneration of the free base), forming the salt of the acid form of each isomer of an isomeric pair using an optically active amine (followed by fractional crystallization and regeneration of the free acid), forming an ester or amide of each of the isomers of an isomeric pair using an optically pure acid, amine or alcohol (followed by chromatographic separation and removal of the chiral auxiliary), or resolving an isomeric mixture of either a starting material or a final product using various well known chromatographic methods.
• the stereochemistry of a disclosed compound is named or depicted by structure
• the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99% or 99.9%) by weight relative to the other stereoisomers.
• the depicted or named enantiomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight optically pure.
• the depicted or named diastereomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight pure.
• Percent optical purity is the ratio of the weight of the enantiomer or over the weight of the enantiomer plus the weight of its optical isomer. Diastereomeric purity by weight is the ratio of the weight of one diastereomer or over the weight of all the diastereomers.
• the stereochemistry of a disclosed compound is named or depicted by structure, the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by mole fraction pure relative to the other stereoisomers.
• the depicted or named enantiomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by mole fraction pure.
• diastereomer When a single diastereomer is named or depicted by structure, the depicted or named diastereomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by mole fraction pure. Percent purity by mole fraction is the ratio of the moles of the enantiomer or over the moles of the enantiomer plus the moles of its optical isomer. Similarly, percent purity by moles fraction is the ratio of the moles of the diastereomer or over the moles of the diastereomer plus the moles of its isomer.
• the term “a” may be understood to mean “at least one”; (ii) the term “or” may be understood to mean “and/or”; (iii) the terms “comprising” and “including” may be understood to encompass itemized components or steps whether presented by themselves or together with one or more additional components or steps; and (iv) the terms “about” and “approximately” may be understood to permit standard variation as would be understood by those of ordinary skill in the art; and (v) where ranges are provided, endpoints are included.
• the term “administration” refers to the administration of a composition (e.g., a compound, a complex or a preparation that includes a compound or complex as described herein) to a subject or system.
• Administration to an animal subject may be by any appropriate route.
• administration may be bronchial (including by bronchial instillation), buccal, enteral, interdermal, intra-arterial, intradermal, intragastric, intramedullary, intramuscular, intranasal, intraperitoneal, intrathecal, intravenous, intraventricular, mucosal, nasal, oral, rectal, subcutaneous, sublingual, topical, tracheal (including by intratracheal instillation), transdermal, vaginal and vitreal.
• bronchial including by bronchial instillation
• the term “animal” refers to any member of the animal kingdom. In some embodiments, “animal” refers to humans, at any stage of development. In some embodiments, “animal” refers to non-human animals, at any stage of development. In some embodiments, the non-human animal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a primate, and/or a pig). In some embodiments, animals include, but are not limited to, mammals, birds, reptiles, amphibians, fish, and/or worms. In some embodiments, an animal may be a transgenic animal, genetically-engineered animal, and/or a clone.
• the terms “approximately” and “about” are each intended to encompass normal statistical variation as would be understood by those of ordinary skill in the art as appropriate to the relevant context.
• the terms “approximately” or “about” each refer to a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11 %, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of a stated value, unless otherwise stated or otherwise evident from the context (e.g., where such number would exceed 100% of a possible value).
• Two events or entities are “associated” with one another, as that term is used herein, if the presence, level and/or form of one is correlated with that of the other.
• a particular entity e.g., polypeptide
• a particular disease, disorder, or condition if its presence, level and/or form correlates with incidence of and/or susceptibility of the disease, disorder, or condition (e.g., across a relevant population).
• a subject such as a human subject undergoing therapy for the treatment of a neurological disorder, for example, amyotrophic lateral sclerosis, frontotemporal degeneration (also referred to as frontotemporal lobar degeneration and frontotemporal dementia), Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD), sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy.
• a neurological disorder for example, amyotrophic lateral sclerosis, frontotemporal degeneration (also referred to as frontotemporal lobar degeneration and frontotemporal dementia), Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, cor
• exemplary benefits in the context of a subject undergoing treatment for a neurological disorder using the compositions and methods described herein include the slowing and halting of disease progression, as well as suppression of one or more symptoms associated with the disease.
• a neurological disorder described herein such as amyotrophic lateral sclerosis, with a FYVE-type zinc finger containing phosphoinositide kinase (PlKfyve) inhibitor described herein, such as an inhibitory small molecule, antibody, antigen-binding fragment thereof, or interfering RNA molecule
• PlKfyve phosphoinositide kinase
• examples of clinical “benefits” and “responses” are (i) an improvement in the subject’s condition as assessed using the amyotrophic lateral sclerosis functional rating scale (ALSFRS) or the revised ALSFRS (ALSFRS-R) following administration of the compound of the invention, such as an improvement in the subject’s ALSFRS or ALSFRS-R score within one or more days, weeks, or months following administration of the compound of the invention (e.g., an improvement in the subject’s ALSFRS or ALSFRS-R score within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the compound of the invention to the subject, such as within 1 day,
• the term “dosage form” refers to a physically discrete unit of an active compound (e.g., a therapeutic or diagnostic agent) for administration to a subject.
• Each unit contains a predetermined quantity of active agent.
• such quantity is a unit dosage amount (or a whole fraction thereof) appropriate for administration in accordance with a dosing regimen that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population (i.e., with a therapeutic dosing regimen).
• a dosage amount or a whole fraction thereof
• a dosing regimen refers to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time.
• a given therapeutic compound has a recommended dosing regimen, which may involve one or more doses.
• a dosing regimen comprises a plurality of doses each of which are separated from one another by a time period of the same length; in some embodiments, a dosing regimen comprises a plurality of doses and at least two different time periods separating individual doses.
• all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts.
• a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount In some embodiments, a dosing regimen is correlated with a desired or beneficial outcome when administered across a relevant population (i.e., is a therapeutic dosing regimen).
• an “effective amount” of any one of the compounds of the invention or a combination of any of the compounds of the invention or a pharmaceutically acceptable salt thereof is administered via any of the usual and acceptable methods known in the art, either singly or in combination.
• composition represents a composition containing a compound described herein formulated with a pharmaceutically acceptable excipient, and manufactured or sold with the approval of a governmental regulatory agency as part of a therapeutic regimen for the treatment of disease in a mammal.
• Pharmaceutical compositions can be formulated, for example, for oral administration in unit dosage form (e.g., a tablet, capsule, caplet, gelcap, or syrup); for topical administration (e.g., as a cream, gel, lotion, or ointment); for intravenous administration (e.g., as a sterile solution free of particulate emboli and in a solvent system suitable for intravenous use); or in any other pharmaceutically acceptable formulation.
• a “pharmaceutically acceptable excipient,” as used herein, refers any ingredient other than the compounds described herein (for example, a vehicle capable of suspending or dissolving the active compound) and having the properties of being substantially nontoxic and non-inflammatory in a patient.
• Excipients may include, for example: antiadherents, antioxidants, binders, coatings, compression aids, disintegrants, dyes (colors), emollients, emulsifiers, fillers (diluents), film formers or coatings, flavors, fragrances, glidants (flow enhancers), lubricants, preservatives, printing inks, sorbents, suspensing or dispersing agents, sweeteners, and waters of hydration.
• excipients include, but are not limited to: butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, crosslinked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine, methylcellulose, methyl paraben, microcrystalline cellulose, polyethylene glycol, polyvinyl pyrrolidone, povidone, pregelatinized starch, propyl paraben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethyl cellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C,
• the term “pharmaceutically acceptable salt” means any pharmaceutically acceptable salt of the compound of formula (I).
• pharmaceutically acceptable salts of any of the compounds described herein include those that are within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals without undue toxicity, irritation, allergic response and are commensurate with a reasonable benefit/risk ratio.
• Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Berge et al., J. Pharmaceutical Sciences 66:1-19, 1977 and in Pharmaceutical Salts: Properties, Selection, and Use, (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008.
• the salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting a free base group with a suitable organic acid.
• the compounds of the invention may have ionizable groups so as to be capable of preparation as pharmaceutically acceptable salts.
• These salts may be acid addition salts involving inorganic or organic acids or the salts may, in the case of acidic forms of the compounds of the invention be prepared from inorganic or organic bases.
• the compounds are prepared or used as pharmaceutically acceptable salts prepared as addition products of pharmaceutically acceptable acids or bases.
• Suitable pharmaceutically acceptable acids and bases and methods for preparation of the appropriate salts are well-known in the art. Salts may be prepared from pharmaceutically acceptable non-toxic acids and bases including inorganic and organic acids and bases.
• PlKfyve and FYVE-type zinc finger containing phosphoinositide kinase are used interchangeably herein and refer to the enzyme that catalyzes phosphorylation of phosphatidylinositol 3- phosphate to produce phosphatidylinositol 3,5-bisphosphate, for example, in human subjects.
• PlKfyve and FYVE-type zinc finger containing phosphoinositide kinase refer not only to wild-type forms of PlKfyve, but also to variants of wild-type PlKfyve proteins and nucleic acids encoding the same. The gene encoding PlKfyve can be accessed under NCBI Reference Sequence No.
• NG_021188.1 Exemplary transcript sequences of wild-type form of human PlKfyve can be accessed under NCBI Reference Sequence Nos. NM_015040.4, NM_152671.3, and NM_001178000.1 . Exemplary protein sequences of wild-type form of human PlKfyve can be accessed under NCBI Reference Sequence Nos. NP_055855.2, NP_689884.1 , and NP_001171471.1.
• PlKfyve inhibitor refers to substances, such as compounds of Formula I.
• Inhibitors of this type may, for example, competitively inhibit PlKfyve activity by specifically binding the PlKfyve enzyme (e.g., by virtue of the affinity of the inhibitor for the PlKfyve active site), thereby precluding, hindering, or halting the entry of one or more endogenous substrates of PlKfyve into the enzyme’s active site.
• the term “PlKfyve inhibitor” refers to substances that reduce the concentration and/or stability of PlKfyve mRNA transcripts in vivo, as well as those that suppress the translation of functional PlKfyve enzyme.
• pure means substantially pure or free of unwanted components (e.g., other compounds and/or other components of a cell lysate), material defilement, admixture or imperfection.
• Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pe
• alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, and magnesium, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, and ethylamine.
• a variety of clinical indicators can be used to identify a patient as “at risk” of developing a particular neurological disease.
• patients e.g., human patients
• that are “at risk” of developing a neurological disease such as amyotrophic lateral sclerosis, frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD), sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy, include (i) subjects exhibiting or prone to exhibit aggregation of TAR-DNA binding protein (TDP)-43, and (ii) subjects expressing a mutant form of TDP-43 containing a mutation associated with TDP-
• TAR-DNA binding protein-43 and “TDP-43” are used interchangeably and refer to the transcription repressor protein involved in modulating HIV-1 transcription and alternative splicing of the cystic fibrosis transmembrane conductance regulator (CFTR) pre-mRNA transcript, for example, in human subjects.
• the terms “TAR-DNA binding protein-43” and “TDP-43” refer not only to wild-type forms of TDP-43, but also to variants of wild-type TDP-43 proteins and nucleic acids encoding the same.
• the amino acid sequence and corresponding mRNA sequence of a wild-type form of human TDP-43 are provided under NCBI Reference Sequence Nos. NM_007375.3 and NP_031401.1 , respectively.
• TAR-DNA binding protein-43 and “TDP-43” as used herein include, for example, forms of the human TDP-43 protein that have an amino acid sequence that is at least 85% identical to the amino acid sequence of NCBI Reference Sequence No. NP_031401.1 (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% identical to the amino acid sequence of NCBI Reference Sequence No.
• NP_031401.1 and/or forms of the human TDP-43 protein that contain one or more substitutions, insertions, and/or deletions (e.g., one or more conservative and/or nonconservative amino acid substitutions, such as up to 5, 10, 15, 20, 25, or more, conservative or nonconservative amino acid substitutions) relative to a wild-type TDP-43 protein.
• substitutions, insertions, and/or deletions e.g., one or more conservative and/or nonconservative amino acid substitutions, such as up to 5, 10, 15, 20, 25, or more, conservative or nonconservative amino acid substitutions
• patients that may be treated for a neurological disorder as described herein include amyotrophic lateral sclerosis, frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD), sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy, include human patients that express a form of TDP-43 having a mutation associated with elevated TDP-43 aggregation and toxicity, such as a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D.
• a neurological disorder as described herein such as amyotrophic lateral sclerosis, fronto
• TAR-DNA binding protein-43 and “TDP-43” as used herein include, for example, forms of the human TDP-43 gene that encode an mRNA transcript having a nucleic acid sequence that is at least 85% identical to the nucleic acid sequence of NCBI Reference Sequence No. NM_007375.3 (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% identical to the amino acid sequence of NCBI Reference Sequence No. NM_007375.3).
• the term “subject” refers to any organism to which a composition in accordance with the invention may be administered, e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical subjects include any animal (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans). A subject may seek or be in need of treatment, require treatment, be receiving treatment, be receiving treatment in the future, or be a human or animal who is under care by a trained professional for a particular disease or condition.
• animal e.g., mammals such as mice, rats, rabbits, non-human primates, and humans.
• a subject may seek or be in need of treatment, require treatment, be receiving treatment, be receiving treatment in the future, or be a human or animal who is under care by a trained professional for a particular disease or condition.
• a “therapeutic regimen” refers to a dosing regimen whose administration across a relevant population is correlated with a desired or beneficial therapeutic outcome.
• terapéuticaally effective amount means an amount that is sufficient, when administered to a population suffering from or susceptible to a disease, disorder, and/or condition in accordance with a therapeutic dosing regimen, to treat the disease, disorder, and/or condition.
• a therapeutically effective amount is one that reduces the incidence and/or severity of, and/or delays onset of, one or more symptoms of the disease, disorder, and/or condition.
• therapeutically effective amount does not in fact require successful treatment be achieved in a particular individual. Rather, a therapeutically effective amount may be that amount that provides a particular desired pharmacological response in a significant number of subjects when administered to patients in need of such treatment.
• a refractory subject may have a low bioavailability such that clinical efficacy is not obtainable.
• reference to a therapeutically effective amount may be a reference to an amount as measured in one or more specific tissues (e.g., a tissue affected by the disease, disorder or condition) or fluids (e.g., blood, saliva, serum, sweat, tears, urine, etc).
• tissue e.g., a tissue affected by the disease, disorder or condition
• fluids e.g., blood, saliva, serum, sweat, tears, urine, etc.
• a therapeutically effective amount may be formulated and/or administered in a single dose.
• a therapeutically effective amount may be formulated and/or administered in a plurality of doses, for example, as part of a dosing regimen.
• FIG. 1 is a scheme showing an approach to generation of a control TDP-43 yeast model (FAB1 TDP-43).
• a control yeast TDP-43 model was generated by integrating the human TDP-43 gene and the GAL1 promoter into the yeast genome.
• the yeast ortholog of human PIKFYVE is FAB1.
• FIG. 2 is a scheme showing an approach to generation of a humanized PIKFYVE TDP-43 yeast model (PIKFYVE TDP-43).
• FAB1 gene through homologous recombination with a G418 resistance cassette fabl.-.G ⁇ S ⁇ (FIG. 2).
• PIKFYVE was cloned downstream of the GPD promoter harbored on a (JRA3-containing plasmid and introduced into the fab1::G418R ura3 strain.
• the pGAL7-TDP-43 construct was then introduced into the “humanized” yeast strain and assessed for cytotoxicity.
• FIG. 3 is a histogram generated from the flow cytometry-based viability assay of FAB1 TDP-43.
• FIG. 4 is a histogram generated from the flow cytometry-based viability assay of PIKFYVE TDP- 43. Upon induction of TDP-43, there was a marked increase in inviable cells (rightmost population), with a more pronounced effect in PIKFYVE TDP-43 than in FAB1 TDP-43 strain (see FIG. 3).
• FIG. 5 is an overlay of histograms generated from the flow cytometry-based viability assay of FAB1 TDP-43 in the presence of APY0201.
• FIG. 6 is an overlay of histograms generated from the flow cytometry-based viability assay of PIKFYVE TDP-43 in the presence of APY0201 .
• FIG. 7 is a scatter plot comparing cytoprotection efficacy in PIKFYVE TDP-43 to PlKfyve inhibitory activity of test compounds.
• the present invention features compositions and methods for treating neurological disorders, such as amyotrophic lateral sclerosis and other neuromuscular disorders, as well as frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD), sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy among others.
• neurological disorders such as amyotrophic lateral sclerosis and other neuromuscular disorders, as well as frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’
• the invention provides inhibitors of FYVE-type zinc finger containing phosphoinositide kinase (PlKfyve), that may be administered to a patient (e.g., a human patient) so as to treat or prevent a neurological disorder, such as one or more of the foregoing conditions.
• a patient e.g., a human patient
• the PlKfyve inhibitor may be administered to the patient to alleviate one or more symptoms of the disorder and/or to remedy an underlying molecular pathology associated with the disease, such as to suppress or prevent aggregation of TAR-DNA binding protein (TDP)-43.
• TDP TAR-DNA binding protein
• the disclosure herein is based, in part, on the discovery that PlKfyve inhibition modulates TDP- 43 aggregation in cells. Suppression of TDP-43 aggregation exerts beneficial effects in patients suffering from a neurological disorder. Many pathological conditions have been correlated with TDP-43-promoted aggregation and toxicity, such as amyotrophic lateral sclerosis, frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, IBMPFD, sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy.
• TDP-43-promoted aggregation and toxicity such as amyotrophic lateral sclerosis, frontotemporal degeneration, Alzheimer’s disease,
• patients suffering from diseases associated with TDP-43 aggregation and toxicity may be treated, for example, due to the suppression of TDP-43 aggregation induced by the PlKfyve inhibitor.
• Patients that are likely to respond to PlKfyve inhibition as described herein include those that have or are at risk of developing TDP-43 aggregation, such as those that express a mutant form of TDP- 43 associated with TDP-43 aggregation and toxicity in vivo.
• Examples of such mutations in TDP-43 that have been correlated with elevated TDP-43 aggregation and toxicity include Q331 K, M337V, Q343R, N345K, R361 S, and N390D, among others.
• the compositions and methods described herein thus provide the additional clinical benefit of enabling the identification of patients that are likely to respond to PlKfyve inhibitor therapy, as well as processes for treating these patients accordingly.
• the sections that follow provide a description of exemplary PlKfyve inhibitors that may be used in conjunction with the compositions and methods disclosed herein.
• the sections below additionally provide a description of various exemplary routes of administration and pharmaceutical compositions that may be used for delivery of these substances for the treatment of a neurological disorder.
• Exemplary PlKfyve inhibitors described herein include compounds of Formula I:
• V is -NH-, -NR 5 -, -CH2NH-, -CH2NR 5 -, -O-, -CO-, or -CHOH-;
• R 1 is optionally substituted morpholin-4-yl, pyridin-4-yl, pyridin-3-yl, optionally substituted 2-oxo- pyrrolidin-1 -yl, optionally substituted piperidin-1-yl, or optionally substituted pyridiazin-4-yl;
• R 2 is halogen, -(CH2)nOH, optionally substituted C1-6 alkoxy, optionally substituted C2-C9 heteroaryl, optionally substituted 2-oxo-pyrrolidin-1-yl, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(0)kR 7e ; and R 3 is optionally substituted pyridin-2-yl, optionally substituted pyridin-3-yl, optionally substituted pyridin-4-yl, optionally substituted pyrazol-1-yl, optionally substituted pyrazol-3-yl, optionally substituted pyridazin-3-yl, optionally substituted pyrimidin-4-yl, or optionally substituted Ce-C aryl; or R 2 and R 3 , together with the ring to which they are attached, combine to form optionally substituted C4-C12 heteroaryl; n is 1 , 2, 3, 4, 5, or 6; k is 0,
• R 4 is optionally substituted pyridin-4-yl, optionally substituted 1 -methylpyridin-1-ium-4-yl, optionally substituted pyridin-3-yl, optionally substituted 1 -methylpiperidin-3-yl, optionally substituted pyridazine-3-yl, or -NHR 8 ;
• R 5 is optionally substituted C1-C6 alkyl
• R 6 is H or optionally substituted Ci-Ce alkyl
• each of R 7a and R 7b is, independently, H or optionally substituted Ci-Ce alkyl
• R 7a and R 7b together with the nitrogen atom to which they are attached, combine to form optionally substituted C2-C9 heterocyclyl
• each of R 7c , R 7d , and R 7e is independently optionally substituted C1-6 alkyl, optionally substituted C1-6 alkoxy, or hydroxyl
• R 8 is optionally substituted phenyl or optionally substituted C3-C6 cycloalkyl.
• Exemplary PlKfyve inhibitors described herein also include compounds of Formula II:
• R 9 is optionally substituted morpholin-4-yl, optionally substituted morpholin-3-ylalkoxy, optionally substituted 2-(pyridin-2-yl)alkoxy, optionally substituted 1 -methylpiperazin-2-yl, or optionally substituted Ce-Cw aryl;
• R 10 is optionally substituted Ci-e alkoxy, -(CO)NR 7a R 7b , -P(O)R 7c R 7d , or -S(0)kR 7e ; each of R 7a and R 7b is, independently, H or optionally substituted Ci-Ce alkyl; or R 7a and R 7b , together with the nitrogen atom to which they are attached, combine to form optionally substituted C2-C9 heterocyclyl; each of R 7c , R 7d , and R 7e is independently optionally substituted Ci-e alkyl, optionally substituted C1-6 alkoxy, or hydroxyl; k is 0, 1 , or 2;
• R 11 is optionally substituted morpholin-4-yl, optionally substituted pyridin-4-yl, optionally substituted pyrazol-4-yl, optionally substituted 1 H-imidazol-2-yl, optionally substituted quinoline-6-yl, or optionally substituted Ce-Cw aryl;
• R 12 is optionally substituted 1-methylpiperazin-2-onyl, optionally substituted 2-(pyridin-2-yl)alkoxy, optionally substituted N-(pyridin-3-ylmethyl)amine, optionally substituted N-(pyridin-4-yl)amine, or optionally substituted Ce-Cw aryl.
• a patient suffering from a neurological disorder may be administered a PlKfyve inhibitor, such as a small molecule described herein, so as to treat the disorder and/or to suppress one or more symptoms associated with the disorder.
• exemplary neurological disorders that may be treated using the compositions and methods described herein are, without limitation, amyotrophic lateral sclerosis, frontotemporal degeneration, Alzheimer’s disease, Parkinson’s disease, dementia with Lewy Bodies, corticobasal degeneration, progressive supranuclear palsy, dementia parkinsonism ALS complex of Guam, Huntington’s disease, IBMPFD, sporadic inclusion body myositis, myofibrillar myopathy, dementia pugilistica, chronic traumatic encephalopathy, Alexander disease, and hereditary inclusion body myopathy, as well as neuromuscular diseases such as congenital myasthenic syndrome, congenital myopathy, cramp fasciculation syndrome, Duchenne muscular dystrophy, glycogen storage disease type II,
• the present disclosure is based, in part, on the discovery that PlKfyve inhibitors, such as the agents described herein, are capable of attenuating TDP-43 toxicity.
• TDP-43-promoted toxicity has been associated with various neurological diseases.
• the discovery that PlKfyve inhibitors modulate TDP-43 aggregation provides an important therapeutic benefit.
• a PlKfyve inhibitor such as a PlKfyve inhibitor described herein
• a patient suffering from a neurological disorder or at risk of developing such a condition may be treated in a manner that remedies an underlying molecular etiology of the disease.
• the compositions and methods described herein can be used to treat or prevent such neurological conditions, for example, by suppressing the TDP-43 aggregation that promotes pathology.
• compositions and methods described herein provide the beneficial feature of enabling the identification and treatment of patients that are likely to respond to PlKfyve inhibitor therapy.
• a patient e.g., a human patient suffering from or at risk of developing a neurological disease described herein, such as amyotrophic lateral sclerosis
• PlKfyve inhibitor if the patient is identified as likely to respond to this form of treatment.
• Patients may be identified as such on the basis, for example, of susceptibility to TDP-43 aggregation.
• the patient is identified is likely to respond to PlKfyve inhibitor treatment based on the isoform of TDP-43 expressed by the patient.
• TDP-43 isoforms having a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D, among others are more likely to develop TDP-43-promoted aggregation and toxicity relative to patients that do not express such isoforms of TDP-43.
• a patient may be identified as likely to respond to PlKfyve inhibitor therapy on the basis of expressing such an isoform of TDP-43, and may subsequently be administered a PlKfyve inhibitor so as to treat or prevent one or more neurological disorders, such as one or more of the neurological disorders described herein.
• a patient having a neurological disorder e.g., a patient at risk of developing TDP-43 aggregation, such as a patient expressing a mutant form of TDP-43 having a mutation associated with elevated TDP-43 aggregation and toxicity, for example, a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D
• PlKfyve inhibition e.g., a patient at risk of developing TDP-43 aggregation, such as a patient expressing a mutant form of TDP-43 having a mutation associated with elevated TDP-43 aggregation and toxicity, for example, a mutation selected from Q331 K, M337V, Q343R, N345K, R361S, and N390D
• successful treatment of a patient having a neurological disease with a PlKfyve inhibitor described herein may be signaled by: (i) an improvement in condition as assessed using the amyotrophic lateral sclerosis functional rating scale (ALSFRS) or the revised ALSFRS (ALSFRS-R), such as an improvement in the patient’s ALSFRS or ALSFRS-R score within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., an improvement in the patient’s ALSFRS or ALSFRS-R score within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks,
• an increase in slow vital capacity such as an increase in the patient’s slow vital capacity within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., an increase in the patient’s slow vital capacity within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35,
• a reduction in decremental responses exhibited by the patient upon repetitive nerve stimulation such as a reduction that is observed within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., a reduction that is observed within from about 1 day to about
• 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, or more, following the initial administration of the PlKfyve inhibitor to the patient);
• an improvement in muscle strength as assessed, for example, by way of the Medical Research Council muscle testing scale (as described, e.g., in Jagtap et al., Ann. Indian. Acad. Neurol. 17:336-339 (2014), the disclosure of which is incorporated herein by reference as it pertains to measuring patient response to neurological disease treatment), such as an improvement that is observed within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., an improvement that is observed within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks,
• an improvement in quality of life as assessed, for example, using the amyotrophic lateral sclerosis-specific quality of life (ALS-specific QOL) questionnaire, such as an improvement in the patient’s quality of life that is observed within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., an improvement in the subject’s quality of life that is observed within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks,
• a decrease in the frequency and/or severity of muscle cramps such as a decrease in cramp frequency and/or severity within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., a decrease in cramp frequency and/or severity within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks,
• a decrease in TDP-43 aggregation such as a decrease in TDP-43 aggregation within one or more days, weeks, or months following administration of the PlKfyve inhibitor (e.g., a decrease in TDP-43 aggregation within from about 1 day to about 48 weeks (e.g., within from about 2 days to about 36 weeks, from about 4 weeks to about 24 weeks, from about 8 weeks to about 20 weeks, or from about 12 weeks to about 16 weeks), or more, following the initial administration of the PlKfyve inhibitor to the patient, such as within 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32
• the compounds of the invention can be combined with one or more therapeutic agents.
• the therapeutic agent can be one that treats or prophylactically treats any neurological disorder described herein.
• a compound of the invention can be used alone or in combination with other agents that treat neurological disorders or symptoms associated therewith, or in combination with other types of treatment to treat, prevent, and/or reduce the risk of any neurological disorders.
• the dosages of one or more of the therapeutic compounds may be reduced from standard dosages when administered alone. For example, doses may be determined empirically from drug combinations and permutations or may be deduced by isobolographic analysis (e.g., Black et al., Neurology 65:S3-S6, 2005). In this case, dosages of the compounds when combined should provide a therapeutic effect.
• the compounds of the invention are preferably formulated into pharmaceutical compositions for administration to human subjects in a biologically compatible form suitable for administration in vivo. Accordingly, in another aspect, the present invention provides a pharmaceutical composition comprising a compound of the invention in admixture with a suitable diluent, carrier, or excipient.
• the compounds of the invention may be used in the form of the free base, in the form of salts, solvates, and as prodrugs. All forms are within the scope of the invention.
• the described compounds or salts, solvates, or prodrugs thereof may be administered to a patient in a variety of forms depending on the selected route of administration, as will be understood by those skilled in the art.
• the compounds of the invention may be administered, for example, by oral, parenteral, buccal, sublingual, nasal, rectal, patch, pump, or transdermal administration and the pharmaceutical compositions formulated accordingly.
• Parenteral administration includes intravenous, intraperitoneal, subcutaneous, intramuscular, transepithelial, nasal, intrapulmonary, intrathecal, rectal, and topical modes of administration. Parenteral administration may be by continuous infusion over a selected period of time.
• a compound of the invention may be orally administered, for example, with an inert diluent or with an assimilable edible carrier, or it may be enclosed in hard or soft shell gelatin capsules, or it may be compressed into tablets, or it may be incorporated directly with the food of the diet.
• a compound of the invention may be incorporated with an excipient and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, and wafers.
• a compound of the invention may also be administered parenterally.
• Solutions of a compound of the invention can be prepared in water suitably mixed with a surfactant.
• Dispersions can also be prepared in glycerol, liquid polyethylene glycols, DMSO and mixtures thereof with or without alcohol, and in oils. Under ordinary conditions of storage and use, these preparations may contain a preservative to prevent the growth of microorganisms.
• Conventional procedures and ingredients for the selection and preparation of suitable formulations are described, for example, in Remington’s Pharmaceutical Sciences (2003, 20 th ed.) and in The United States Pharmacopeia: The National Formulary (USP 24 NF19), published in 1999.
• the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that may be easily administered via syringe.
• compositions for nasal administration may conveniently be formulated as aerosols, drops, gels, and powders.
• Aerosol formulations typically include a solution or fine suspension of the active substance in a physiologically acceptable aqueous or non-aqueous solvent and are usually presented in single or multidose quantities in sterile form in a sealed container, which can take the form of a cartridge or refill for use with an atomizing device.
• the sealed container may be a unitary dispensing device, such as a single dose nasal inhaler or an aerosol dispenser fitted with a metering valve which is intended for disposal after use.
• the dosage form comprises an aerosol dispenser
• a propellant which can be a compressed gas, such as compressed air or an organic propellant, such as fluorochlorohydrocarbon.
• the aerosol dosage forms can also take the form of a pump-atomizer.
• Compositions suitable for buccal or sublingual administration include tablets, lozenges, and pastilles, where the active ingredient is formulated with a carrier, such as sugar, acacia, tragacanth, gelatin, and glycerine.
• Compositions for rectal administration are conveniently in the form of suppositories containing a conventional suppository base, such as cocoa butter.
• the compounds of the invention may be administered to an animal, e.g., a human, alone or in combination with pharmaceutically acceptable carriers, as noted herein, the proportion of which is determined by the solubility and chemical nature of the compound, chosen route of administration, and standard pharmaceutical practice.
• the dosage of the compounds of the invention, and/or compositions comprising a compound of the invention can vary depending on many factors, such as the pharmacodynamic properties of the compound; the mode of administration; the age, health, and weight of the recipient; the nature and extent of the symptoms; the frequency of the treatment, and the type of concurrent treatment, if any; and the clearance rate of the compound in the animal to be treated.
• One of skill in the art can determine the appropriate dosage based on the above factors.
• the compounds of the invention may be administered initially in a suitable dosage that may be adjusted as required, depending on the clinical response. In general, satisfactory results may be obtained when the compounds of the invention are administered to a human at a daily dosage of, for example, between 0.05 mg and 3000 mg (measured as the solid form). Dose ranges include, for example, between 10-1000 mg.
• the dosage amount can be calculated using the body weight of the patient.
• the dose of a compound, or pharmaceutical composition thereof, administered to a patient may range from 0.1-50 mg/kg.
• Step 1 Synthesis of 5-methoxy-2-morpholinopyrimidine-4,6-diol.
• Step 2 Synthesis of 4-(4,6-dichloro-5-methoxypyrimidin-2-yl)morpholine.
• Step 3 Synthesis of 5-methoxy-2-morpholino-6-(1-phenyl-1 H-pyrazol-3-yl)pyrimidin-4-ol.
• Step 4 Synthesis of 4-(4-chloro-5-methoxy-6-(1 -phenyl-1 H-pyrazol-3-yl)pyrimidin-2-yl)morpholine.
• Step 5 Synthesis of methyl 5-methoxy-2-morpholino-6-(1 -phenyl-1 H-pyrazol-3-yl)pyrimidine-4- carboxylate.
• Step 6 Synthesis of 5-methoxy-2-morpholino-6-(1 -phenyl-1 H-pyrazol-3-yl)pyrimidine-4-carboxylic acid.
• Step 7 Synthesis of 5-methoxy-2-morpholino-N-phenyl-6-(1-phenyl-1 H-pyrazol-3-yl)pyrimidine-4- carboxamide.
• Step 1 Synthesis of 4-(4-chloro-5-methoxy-6-(pyridin-3-yloxy)pyrimidin-2-yl)morpholine.
• Step 2 Synthesis of 4-(5-methoxy-4-(4-phenyl-1 H-pyrazol-1-yl)-6-(pyridin-3-yloxy)pyrimidin-2- yl)morpholine.
• Step 1 Preparation of 4-(4-chloro-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)pyrimidin-2- yl)morpholine.
• Step 2 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholino-N-(pyridin-4- yl)pyrimidin-4-amine.
• Step 1 Synthesis of 4-(2,6-dichloro-5-methoxypyrimidin-4-yl)morpholine.
• Step 2 Synthesis of 4-(2-chloro-5-methoxy-6-(2-(pyridin-2-yl)ethoxy)pyrimidin-4-yl)morpholine.
• Example 6 Synthesis of N-cyclopropyl-5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2- morpholino pyrimidine-4-carboxamide (Compound 6): Step 1 : Synthesis of 4-(4-chloro-5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)pyrimidin-2- yl)morpholine.
• Step 2 Synthesis of methyl 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2 - morpholinopyrimidine-4-carboxylate.
• Step 3 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholinopyrimidine-4- carboxylic acid.
• Step 4 Synthesis of N-cyclopropyl-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2- morpholinopyrimidine-4-carboxamide.
• the residue was subjected to prep-HPLC (SunFire C18, 4.6*50mm, 3.5um column Xbridge C18 3.5pm 4.6x50mm column.
• the mobile phase was acetonitrile/0.1 % Ammonium bicarbonate aqueous solution) to obtain the target product as white solid (42.6mg, 32%).
• Step 1 Synthesis of 6-chloro-5-methoxy-2-morpholino-N-(pyridin-4-yl)pyrimidin-4-amine.
• Step 2 Synthesis of 5-methoxy-6-(5-(1-methyl-1H-pyrazol-3-yl)pyridin-3-yl)-2-morpholino-N- (pyridin-4-yl)pyrimidin-4-amine.
• Step 1 Synthesis of 4-bromo-2-(1-methyl-1H-pyrazol-3-yl)pyridine.
• Step 2 Synthesis of 2-(1-methyl-1H-pyrazol-3-yl)-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)pyridine.
• the mobile phase was acetonitrile/0.1 % ammonium bicarbonate) to obtain 5-methoxy-6-(2-(1-methyl-1 H-pyrazol-3-yl)pyridin-4-yl)-2-morpholino-N-(pyridin-4-yl)pyrimidin-4- amine (76.1 mg, 34%) as yellow solid.
• Step 1 Synthesis of 4-(3-bromophenyl)-1-methylpiperazin-2-one.
• Step 2 Synthesis of 1-methyl-4-(3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)piperazin-2- one.
• Step 3 Synthesis of 4-(3-(5-methoxy-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)phenyl)-1- methylpiperazin-2-one.
• the resultant mixture was stirred at 90°C for 2h and poured into ice-water.
• the aqueous medium was extracted with ethyl acetate (15mL*3), the combined organic layer was washed with brine, dried and concentrated.
• the obtained crude product was purified by prep-HPLC (SunFire C18, 4.6*50mm, 3.5um column.
• the elution system used was a gradient of 5%-95% over 1 .5 min at 2ml/min and the solvent was acetonitrile/0.01 % ammonium bicarbonate aqueous solution) to obtain 4-(3-(5-methoxy-2-morpholino-6-(pyridin-4- ylamino)pyrimidin-4-yl)phenyl)-1-methylpiperazin-2-one (51.3mg, 35%) as white solid.
• Step 1 Synthesis of 2-(3-bromophenyl)pyrimidine.
• Step 2 Synthesis of 2-(3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)pyrimidine.
• Step 3 Synthesis of 5-methoxy-2-morpholino-N-(pyridin-4-yl)-6-(3-(pyrimidin-2- yl)phenyl)pyrimidin-4-amine.
• Step 1 Synthesis of 6-chloro-5-methoxy-2-morpholino-N-(p-tolyl)pyrimidin-4-amine.
• Step 2 Synthesis of 5-methoxy-6-(5-(1 -methyl-1 H-pyrazol-3-yl)pyridazin-3-yl)-2-morpholino-N-(p- tolyl)pyrimidin-4-amine.
• Step 1 Synthesis of 6-chloro-5-methoxy-2-morpholino-N-(pyridin-3-yl)pyrimidin-4-amine.
• Step 1 Synthesis of 2-(1-methyl-1H-pyrazol-3-yl)-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)pyridine.
• Step 2 Synthesis of 5-methoxy-6-(2-(1-methyl-1 H-pyrazol-3-yl)pyridin-4-yl)-2-morpholino-N- (pyridin-3-yl)pyrimidin-4-amine.
• step 1 To the mixture from step 1 , were added 6-chloro-5-methoxy-2-morpholino-N-(pyridin-3- yl)pyrimidin-4-amine (96mg, 0.3mmol), tetrakis(triphenylphosphin)palladium (35mg, 0.03mmol), cesium carbonate (293mg, 0.9mmol) and water (1 mL) and the resultant mixture was stirred at 95 °C for 16h under argon atmosphere. It was then concentrated and subjected to prep-HPLC (BOSTON pHlex ODS 10um 21.2x250mm 120A.
• prep-HPLC BOSTON pHlex ODS 10um 21.2x250mm 120A.
• the mobile phase was acetonitrile/0.1 % ammonium bicarbonate) to obtain 5- methoxy-6-(2-(1-methyl-1 H-pyrazol-3-yl)pyridin-4-yl)-2-morpholino-N-(pyridin-3-yl)pyrimidin-4-amine (34.6mg, 19%) as white solid.
• Step 1 Synthesis of 1-(3-bromophenyl)pyrrolidin-3-ol.
• Step 3 Synthesis of 1-(3-(5-methoxy-2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4- yl)phenyl)pyrrolidin-3-ol.
• Example 20 Synthesis of 4-(3-(5-methoxy-2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4- yl)phenyl)-1 -methylpiperazin-2-one (Compound 27): water/dioxane 85 °C,16h Step 1 : Synthesis of 4-(3-bromophenyl)-1-methylpiperazin-2-one.
• Step 2 Synthesis of 1-methyl-4-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)piperazin-2- one.
• Step 3 Synthesis of 4-(3-(5-methoxy-2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4-yl)phenyl)-1- methylpiperazin-2-one.
• Step 1 Synthesis of 4-(3-bromophenyl)morpholin-3-one.
• Step 2 Synthesis of 4-(3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)morpholin-3-one.
• Step 3 Synthesis of 4-(3-(5-methoxy-2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4- yl)phenyl)morpholin-3-one.
• Step 1 Synthesis of 1-(3-bromophenyl)pyrrolidin-2-one.
• Step 2 Synthesis of 1-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)pyrrolidin-2-one.
• Step 3 Synthesis of 1-(3-(5-methoxy-2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4- yl)phenyl)pyrrolidin-2-one.
• Step 1 Synthesis of 4-(4-chloro-5-methoxy-6-(pyridin-4-yl)pyrimidin-2-yl)morpholine.
• Example 25 Synthesis of (5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2- morpholinopyrimidin-4-yl)(pyridin-4-yl)methanol (Compound 32): Step 1 : Synthesis of 4-(4-iodo-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)pyrimidin-2- yl)morpholine.
• Step 2 Synthesis of (5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholinopyrimidin-4- yl)(pyridin-4-yl)methanol.
• the elution system used was a gradient of 5%-95% over 1 .5 min at 2ml/min and the solvent was acetonitrile/0.01 % ammonium bicarbonate aqueous solution) to obtain (5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2- morpholinopyrimidin-4-yl)(pyridin-4-yl)methanol (34.3mg, 36%) as white solid.
• Example 26 Synthesis of N,N-dimethyl-2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(4- Step 1 : Synthesis of ethyl 4,6-dichloro-2-morpholino-pyrimidine-5-carboxylate.
• Step 2 Synthesis of ethyl 4-chloro-2-morpholino-6-(4-pyridylamino)pyrimidine-5-carboxylate.
• Step 3 Synthesis of ethyl 2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(4-pyridylamino)pyrimidine-5- carboxylate.
• Step 4 Synthesis of 2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(4-pyridylamino)pyrimidine-5- carboxylic acid.
• Step 5 Synthesis of N,N-dimethyl-2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(4- pyridylamino)pyrimidine-5-carboxamide.
• the crude product from DMF was isolated by subjecting it to prep-HPLC (Waters Xbridge BEH C18 100*30mm*10um column; 10-50 % acetonitrile in an a 0.05% ammonia solution and an a 10mM ammonium bicarbonate solution in water, 8min gradient) to obtain N,N-dimethyl-2-morpholino-4-(3- pyrazol-1-ylphenyl)-6-(4-pyridylamino)pyrimidine-5-carboxamide (31 mg, 36%) as pale yellow solid.
• prep-HPLC Waters Xbridge BEH C18 100*30mm*10um column; 10-50 % acetonitrile in an a 0.05% ammonia solution and an a 10mM ammonium bicarbonate solution in water, 8min gradient
• Step 1 Synthesis of 5-methoxy-2-(pyridin-4-yl)pyrimidine-4,6-diol.
• Step 3 Synthesis of 4-chloro-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-(pyridin-4- yl)pyrimidine.
• Step 4 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-N-(pyridin-3-yl)-2-(pyridin-4- yl)pyrimidin-4-amine formate.
• Step 1a Synthesis of 1-phenyl-4-((tetrahydro-2H-pyran-2-yl)oxy)but-2-yn-1-one.
• Step 1b Synthesis of 3-phenyl-5-(((tetrahydro-2H-pyran-2-yl)oxy)methyl)-1 H-pyrazole.
• Step 1 Synthesis of 4-(4,5,6-trichloropyrimidin-2-yl)morpholine.
• Step 2 Synthesis of 4-(4,5-dichloro-6-((1-methylpiperidin-3-yl)oxy)pyrimidin-2-yl)morpholine.
• Step 3 Synthesis of 4-(5-chloro-4-((1-methylpiperidin-3-yl)oxy)-6-(3-phenyl-5-(((tetrahydro-2H- pyran-2-yl)oxy)methyl)-1 H-pyrazol-1-yl)pyrimidin-2-yl)morpholine.
• the reaction was cooled down, the mixture was diluted with ethyl acetate/water (20mL/20mL), the organic layer was separated and the aqueous layer was extracted with ethyl acetate (20mL x 2). The combined organic phase was washed with brine (20mL), dried over sodium sulfate, filtered, and concentrated.
• Step 4 Synthesis of (1 -(5-chloro-6-((1-methylpiperidin-3-yl)oxy)-2-morpholinopyrimidin-4-yl)-3- phenyl-1 H-pyrazol-5-yl)methanol.
• Step 5 Synthesis of 4-((1-methylpiperidin-3-yl)oxy)-2-morpholino-8-phenyl-6H-pyrazolo[1 ,5- d]pyrimido[5,4-b][1 ,4]oxazine.
• Example 29 Synthesis of 4-[5-methoxy-6-morpholino-2-(3-pyrazol-1-ylphenyl)pyrimidin-4-yl]-1- methyl-piperazin-2-one (Compound 36) and 4-[5-methoxy-4-morpholino-6-(3-pyrazol-1- ylphenyl)pyrimidin-2-yl]-1 -methyl-piperazin-2-one (Compound 37):
• Step 1 Synthesis of 4-[2-chloro-5-methoxy-6-(3-pyrazol-1-ylphenyl)pyrimidin-4-yl]morpholine and 4-[6-chloro-5-methoxy-2-(3-pyrazol-1-ylphenyl)pyrimidin-4-yl]morpholine.
• Step 2 Synthesis of 4-[5-methoxy-6-morpholino-2-(3-pyrazol-1-ylphenyl)pyrimidin-4-yl]-1 -methyl- piperazin-2-one (Compound 37).
• Step 3 Synthesis of 4-[5-methoxy-4-morpholino-6-(3-pyrazol-1-ylphenyl)pyrimidin-2-yl]-1-methyl- piperazin-2-one (Compound 38):
• Step 1 Synthesis of ethyl 4-chloro-6-(1-methyl-1 H-pyrazol-3-yl)nicotinate.
• Step 2 Synthesis of (5-(ethoxycarbonyl)-2-(1-methyl-1H-pyrazol-3-yl)pyridin-4-yl)boronic acid and ethyl 6-(1 -methyl-1 H-pyrazol-3-yl)-4-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)nicotinate.
• Step 3 Synthesis of ethyl 4-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-6-(1- methyl-1H-pyrazol-3-yl)nicotinate.
• Step 4 Synthesis of (4-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-6-(1 -methyl-1 H- pyrazol-3-yl)pyridin-3-yl)methanol.
• Lithium aluminum hydride (1.0M in THF, 2.56mL, 2.56mmol) was added to a solution of ethyl 4- (5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-6-(1 -methyl-1 H-pyrazol-3-yl)nicotinate (130 mg, 0.25mmol) in anhydrous tetrahydrofuran (5mL) at 0 °C under nitrogen atmosphere. The mixture was then warmed up and stirred for 1 ,5h at 25 °C. The reaction was then quenched by the careful addition of sodium sulfate decahydrate with ice-bath cooling.
• Step 5 Synthesis of 9-(1 -methyl-1 H-pyrazol-3-yl)-2 -morpholino-N-(pyridin-4-yl)-6H- pyrido[4',3':4,5]pyrano[3,2-d]pyrimidin-4-amine.
• Step 1 Synthesis of 6-chloro-5-methoxy-N,2-di(pyridin-4-yl)pyrimidin-4-amine.
• Step 3 Synthesis of 5-methoxy-6-(2-(1-methyl-1 H-pyrazol-3-yl)pyridin-4-yl)-N,2-di(pyridin-4- yl)pyrimidin-4-amine.
• step-2 To the mixture from step-2 was added 5mL of 1 ,4-dioxane/water (4mL/1 mL) followed by 6-chloro- 5-methoxy-N,2-di(pyridin-4-yl)pyrimidin-4-amine (0.08g, 0.25mmol), cesium carbonate (0.16g, 0.5mmol) and tetrakis(triphenylphosphine)palladium (0.03g, 0.025mmol). The resultant reaction mixture was stirred at 90 °C for 16h under argon atmosphere and concentrated.
• Step 1 Synthesis of ethyl 5-bromo-3-chloropicolinate.
• Step 3 Synthesis of ethyl 5-(1-methyl-1H-pyrazol-3-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)picolinate.
• Step 4 Synthesis of ethyl 3-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-5-(1- methyl-1H-pyrazol-3-yl)picolinate.
• Step 5 Synthesis of (3-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-5-(1-methyl-1H- pyrazol-3-yl)pyridin-2-yl)methanol.
• Step 6 Synthesis of 9-(1-methyl-1H-pyrazol-3-yl)-2-morpholino-N-(pyridin-4-yl)-6H- pyrido[3',2':4,5]pyrano[3,2-d]pyrimidin-4-amine.
• Step 1 Synthesis of 3-bromo-1,4-dimethyl-1H-pyrazole.
• Step 2 Synthesis of 3-(3-bromophenyl)-1 ,4-dimethyl-1 H-pyrazole.
• Step 3 Synthesis of 1 ,4-dimethyl-3-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)-1 H- pyrazole.
• Step 4 Synthesis of 6-(3-(1 ,4-dimethyl-1 H-pyrazol-3-yl)phenyl)-5-methoxy-2-morpholino-N- (pyridin-4-yl)pyrimidin-4-amine.
• reaction mixture was filtered, and the filtrate was subjected to prep-HPLC [Welch Xtimate C18 21.2x250mm,10um, with mobile phase acetonitrile /water(10mM NH4HCO3 and NH3 H2O)] to obtain 6-(3-(1 ,4-dimethyl-1 H-pyrazol-3-yl)phenyl)-5-methoxy-2- morpholino-N-(pyridin-4-yl)pyrimidin-4-amine ( 20.0mg, 14%) as yellow solid.
• the mobile phase was acetonitrile/0.1 % ammonium bicarbonate) to afford (R)-5-methoxy-6-(3-(1- methyl-1 H-pyrazol-3-yl)phenyl)-2-(morpholin-3-ylmethoxy)-N-(pyridin-4-yl)pyrimidin-4-amine (17.2 mg, 0.036 mmol, yield: 26 % ) as white solid.
• Step 1 Synthesis of 4-chloro-5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2- (methylthio)pyrimidine.
• Step 2 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-(methylthio)-N-(pyridin-4- yl)pyrimidin-4-amine.
• Step 3 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2 -(methylsulfonyl)-N- (pyridin-4-yl)pyrimidin-4-amine.
• Step 4 Synthesis of (R)-(4-(5-methoxy-4-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-6-(pyridin-4- ylamino)pyrimidin-2-yl)morpholin-3-yl)methanol.
• the mobile phase was acetonitrile/0.1 % ammonium bicarbonate) to obtain (R)-(4-(5-methoxy-4-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-6-(pyridin-4- ylamino)pyrimidin-2-yl)morpholin-3-yl)methanol (4mg, 7.7 % ) as white solid.
• Step 1 Synthesis of 5-methoxy-4-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)-6-(pyridin-4- ylamino)pyrimidin-2-ol.
• Step 2 Synthesis of 2-chloro-5-methoxy-6-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)-N-(pyridin-4- yl)pyrimidin-4-amine.
• Step 3 Synthesis of 1-(5-methoxy-4-(3-(1-methyl-1 H-pyrazol-S-yljphenylj-e-fpyridin ⁇ - ylaminojpyrimidin ⁇ -yljpyrrolidin ⁇ -one.
• Step 1 Synthesis of 5-bromo-6-iodo-2-morpholino-N-(pyridin-3-yl)pyrimidin-4-amine.
• Step 2 Synthesis of 5-bromo-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholino-N-(pyridin-3- yl)pyrimidin-4-amine.
• Step 3 Synthesis of dimethyl(4-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholino-6-(pyridin-3- ylamino)pyrimidin-5-yl)phosphine oxide.
• Step 1 Synthesis of 6-hydroxy-5-methoxy-2-thioxo-2,5-dihydropyrimidin-4(3H)-one.
• Step 2 Synthesis of 5-methoxy-2-(methylthio)pyrimidine-4, 6(1 H, 5H)-dione.
• Step 3 Synthesis of 4,6-dichloro-5-methoxy-2-(methylthio)pyrimidine.
• Step 4 Synthesis of 6-chloro-5-methoxy-2-(methylthio)-N-(pyridin-4-yl)pyrimidin-4-amine.
• Step 5 Synthesis of 6-chloro-5-methoxy-2-(methylsulfonyl)-N-(pyridin-4-yl)pyrimidin-4-amine.
• Step 6 Synthesis of 5-methoxy-6-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)-2-(methylsulfonyl)-N- (pyridin-4-yl)pyrimidin-4-amine.
• Step 7 Synthesis of 1-(5-methoxy-4-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-6-(pyridin-4- ylamino)pyrimidin-2-yl)piperidin-4-ol.
• Step 1 Synthesis of 3-iodo-4-methoxy-1 H-pyrazole.
• Step 2 Synthesis of 3-iodo-4-methoxy-1-methyl-1 H-pyrazole.
• Step 3 Synthesis of 3-(3-bromophenyl)-4-methoxy-1-methyl-1 H-pyrazole.
• Step 4 Synthesis of 4-methoxy-1 -methyl-3-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)- 1 H-pyrazole.
• Step 5 Synthesis of 5-methoxy-6-(3-(4-methoxy-1-methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholino-N- (pyridin-4-yl)pyrimidin-4-amine.
• reaction mixture was filtered, the filtrate was subjected to prep-HPLC [Welch Xtimate C18 21 .2x250mm,10um, with mobile phase acetonitrile /water(10mM NH4HCO3 and NH3 H2O)] to obtain 5-methoxy-6-(3-(4-methoxy-1-methyl-1 H-pyrazol-3- yl)phenyl)-2-morpholino-N-(pyridin-4-yl)pyrimidin-4-amine ( 58.8mg, 40%) as yellow solid.
• Step 1 Synthesis of 1-(3-bromophenyl)piperidin-4-ol.
• Step 2 Synthesis of 1-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)piperidin-4-ol.
• Step 3 Synthesis of 1 -(3-(5-methoxy-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4- yl)phenyl)piperidin-4-ol.
• Step 1 Synthesis of ethyl 2-bromo-4-iodobenzoate.
• Step 2 Synthesis of ethyl 2-bromo-4-(1 -methyl-1 H-pyrazol-3-yl)benzoate.
• Step 4 Synthesis of ethyl 2-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-4-(1- methyl-1H-pyrazol-3-yl)benzoate.
• Step 5 Synthesis of (2-(5-chloro-2-morpholino-6-(pyridin-4-ylamino)pyrimidin-4-yl)-4-(1-methyl-1H- pyrazol-3-yl)phenyl)methanol.
• Step 6 Synthesis of 9-(1-methyl-1H-pyrazol-3-yl)-2-morpholino-N-(pyridin-4-yl)-6H- isochromeno[4,3-d]pyrimidin-4-amine.
• Step 1 Synthesis of 4-(4,6-diiodopyrimidin-2-yl)morpholine.
• Step 2 Synthesis of 4-(5-chloro-4,6-diiodopyrimidin-2-yl)morpholine.
• Step 3 Synthesis of 5-chloro-6-iodo-2-morpholino-N-(pyridin-4-yl)pyrimidin-4-amine.
• Step 4 Synthesis of 6-(3-(1H-pyrazol-1-yl)phenyl)-5-chloro-2-morpholino-N-(pyridin-4-yl)pyrimidin- 4-amine.
• Step 1 Synthesis of 2-bromo-6-iodo-3-methoxypyridine.
• Step 2 Synthesis of 6-iodo-2,3-dimethoxypyridine.
• Step 3 Synthesis of 3-dimethoxy-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine.
• Step 4 Synthesis of 6-(5,6-dimethoxypyridin-2-yl)-5-methoxy-2-morpholino-N-(pyridin-4- yl)pyrimidin-4-amine.
• the mobile phase was acetonitrile/0.1% ammonium bicarbonate) to obtain 6-(5,6-dimethoxypyridin-2-yl)-5-methoxy-2-morpholino-N-(pyridin-4-yl)pyrimidin-4-amine (20.6mg, 31 .2%) as yellow solid.
• Step 1 Synthesis of 4-(4-chloro-5-methoxy-6-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)pyrimidin-2- yl)morpholine.
• Step 2 Synthesis of 4-(5-methoxy-4-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-6-(1-methyl-1 H-pyrazol-4- yl)pyrimidin-2-yl)morpholine.
• reaction mixture was concentrated, and the residue was subjected to prep-HPLC (BOSTON pHlex ODS 10um 21.2x250mm 120A, with mobile phase acetonitrile/0.1 % ammonium bicarbonate) to obtain 5-methoxy-6- (3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-N,2-di(pyridin-4-yl)pyrimidin-4-amine as yellow solid (8.8mg, 10%).
• prep-HPLC BOSTON pHlex ODS 10um 21.2x250mm 120A, with mobile phase acetonitrile/0.1 % ammonium bicarbonate
• Stepl Synthesis of 2-(3-bromophenyl)oxazole.
• Step 2 Synthesis of 2-(3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl) oxazole.
• Step 3 Synthesis of 5-methoxy-2-morpholino-6-(3-(oxazol-2-yl)phenyl)-N-(pyridin-4-yl)pyrimidin-4- amine.
• Step 1 Synthesis of 1-(3-bromophenyl)piperidin-4-ol.
• Step 2 Synthesis of 1-(3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl)piperidin-4-ol.
• Step 1 Synthesis of 4-methoxy-2-(1-methyl-1H-pyrazol-3-yl)pyrimidine.
• Step 3 Synthesis of 4-chloro-2-(1-methyl-1H-pyrazol-3-yl)pyrimidine.
• Step 4 Synthesis of 5-methoxy-2'-(1-methyl-1H-pyrazol-3-yl)-2-morpholino-N-(pyridin-4-yl)-4,4'- bipyrimidin-6-amine.
• Step 1 Synthesis of 4-(4-chloro-5-methoxy-6-(quinolin-6-yl)pyrimidin-2-yl)morpholine.
• Step 2 Synthesis of 4-(5-methoxy-4-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-6-(quinolin-6-yl)pyrimidin- 2-yl)morpholine.
• Step 1 Synthesis of 4-(4,6-dichloro-5-(methylthio)pyrimidin-2-yl)morpholine.
• Step 2 Synthesis of 4-(4,6-dichloro-5-(methylsulfinyl)pyrimidin-2-yl)morpholine.
• Step 4 Synthesis of 6-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)-5-(methylsulfinyl)-2-morpholino-N- (pyridin-3-yl)pyrimidin-4-amine.
• Step 1 Synthesis of 4-(4-chloro-5-methoxy-6-(3-(1-methyl-1H-pyrazol-3-yl)phenyl)pyrimidin-2- yl)morpholine.
• Step 2 Synthesis of 4-(5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholinopyrimidin-4- yl)-1 -methylpiperazin-2-one.
• reaction mixture was filtered to remove solids, the filtrate was concentrated, and the residue was subjected to prep-HPLC [Welch Xtimate C18 21 .2x250mm,10um, with mobile phase acetonitrile Zwater(1 OmM NH4HCO3 and NH3 H2O)] to obtain 4-(5-methoxy-6-(3-(1- methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholinopyrimidin-4-yl)-1-methylpiperazin-2-one ( 64mg, 34.5%) as white solid.
• Step 1 Synthesis of methyl 6-(3-(1 H-pyrazol-1-yl)phenyl)-5-methoxy-2-morpholinopyrimidine-4- carboxylate.
• Step 2 Synthesis of 6-(3-(1H-pyrazol-1-yl)phenyl)-5-methoxy-2-morpholinopyrimidine-4-carboxylic acid.
• Step 3 Synthesis of 6-(3-(1 H-pyrazol-1 -yl)phenyl)-5-methoxy-2-morpholino-N-(2-oxo-2- phenylethyl)pyrimidine-4-carboxamide.
• Step 4 Synthesis of 4-(4-(3-(1 H-pyrazol-1 -yl)phenyl)-5-methoxy-6-(4-phenyl-1 H-imidazol-2- yl)pyrimidin-2-yl)morpholine.
• Step 1 Synthesis of 2,6-dichloro-5-methoxy-N-(pyridin-3-ylmethyl)pyrimidin-4-amine.
• Step 2 Synthesis of 2 -chloro-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-N-(pyridin-3- ylmethyl)pyrimidin-4-amine and 6-chloro-5-methoxy-2-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-N- (pyridin-3-ylmethyl)pyrimidin-4-amine.
• Step 3 Synthesis of 5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-N-(pyridin-3-ylmethyl)-2- (pyridin-4-yl)pyrimidin-4-amine.
• Step 1 Synthesis of 1-(3-bromo-4-nitro-phenyl)pyrazole.
• Step 2 Synthesis of 1-[4-nitro-3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl]pyrazole.
• Step 3 Synthesis of ethyl 2-morpholino-4-(2-nitro-5-pyrazol-1-yl-phenyl)-6-(4- pyridylamino)pyrimidine-5-carboxylate.
• Step 4 Synthesis of 2-morpholino-9-pyrazol-1-yl-4-(4-pyridylamino)-6H-pyrimido[5,4-c]quinolin-5- one.
• Step 5 Synthesis of 6-methyl-2-morpholino-9-pyrazol-1-yl-4-(4-pyridylamino)pyrimido[5,4- c]quinolin-5-one.
• Step 1 Synthesis of ethyl 4,6-dichloro-2-morpholino-pyrimidine-5-carboxylate.
• Step 2 Synthesis of ethyl 4-chloro-2-morpholino-6-(4-pyridylamino)pyrimidine-5-carboxylate.
• Step 3 Synthesis of ethyl 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylate.
• Step 4 Synthesis of 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylic acid.
• Step 5 Synthesis of N,N-dimethyl-4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxamide.
• Step 1 Synthesis of ethyl 4-(3-cyanophenyl)-2-morpholino-6-(4-pyridylamino)pyrimidine-5- carboxylate.
• Step 2 Synthesis of 4-(3-cyanophenyl)-2-morpholino-6-(4-pyridylamino)pyrimidine-5-carboxylic acid.
• Step 3 Synthesis of 4-(3-cyanophenyl)-N,N-dimethyl-2-morpholino-6-(4-pyridylamino)pyrimidine-5- carboxamide.
• Step 1 Synthesis of ethyl 4-chloro-2-morpholino-6-(4-pyridylamino)pyrimidine-5-carboxylate.
• Step 2 Synthesis of ethyl 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylate.
• Step 3 Synthesis of 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylic acid.
• 150mg of this product was purified by prep-HPLC (Waters Xbridge Prep OBD C18 150*40mm*10um; 5-45% acetonitrile in an a 10mM ammonium bicarbonate solution in water, 8 min gradient) to obtain compound 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylic acid (78mg, 41 %) as white solid.
• prep-HPLC Waters Xbridge Prep OBD C18 150*40mm*10um; 5-45% acetonitrile in an a 10mM ammonium bicarbonate solution in water, 8 min gradient
• Step 4 Synthesis of azetidin-1 -y I (4-(3-( 1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-morpholino-6-(pyridin-4- ylamino)pyrimidin-5-yl)methanone.
• Step 1 Synthesis of ethyl 2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(3-pyridylamino)pyrimidine-5- carboxylate.
• Step 2 Synthesis of 2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(3-pyridylamino)pyrimidine-5- carboxylic acid.
• Step 3 Synthesis of N,N-dimethyl-2-morpholino-4-(3-pyrazol-1-ylphenyl)-6-(3- pyridylamino)pyrimidine-5-carboxamide.
• Step 1 Synthesis of tert-butyl N-(2-bromo-4-iodo-phenyl)carbamate.
• Step 2 Synthesis of tert-butyl N-(2-bromo-4-iodo-phenyl)-N-methylcarbamate.
• Step 3 Synthesis of tert-butyl N-[2-bromo-4-(1-methylpyrazol-3-yl)phenyl]-N-methylcarbamate.
• Step 4 Synthesis of 2-bromo-N-methyl-4-(1-methylpyrazol-3-yl)aniline.
• Step 5 Synthesis of N-methyl-4-(1-methylpyrazol-3-yl)-2-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2- yl)aniline.
• Step 6 Synthesis of 6-methyl-9-(1-methylpyrazol-3-yl)-2-morpholino-4-(4- pyridylamino)pyrimido[5,4-c]quinolin-5-one.
• Step 1 Synthesis of 2-bromo-4-(1-methylpyrazol-3-yl)aniline.
• Step 2 Synthesis of 4-(1 -methylpyrazol-3-yl)-2-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)aniline.
• Step 3 Synthesis of 9-(1-methylpyrazol-3-yl)-2-morpholino-4-(4-pyridylamino)-6H-pyrimido[5,4- c]quinolin-5-one.
• reaction mixture was stirred at 80°C for 4h under argon atmosphere and concentrated.
• residue was subjected to prep-HPLC (Waters Xbridge Prep OBD C18 150*40mm*10um column; 25%-65% acetonitrile in 0.05% ammonium hydroxide and 10mM sodium bicarbonate solution in water, 8min gradient) to obtain 9-(1-methylpyrazol-3-yl)-2-morpholino-4-(4-pyridylamino)-6H-pyrimido[5,4-c]quinolin-5-one (7mg, 3%) as pale-yellow solid.
• prep-HPLC Waters Xbridge Prep OBD C18 150*40mm*10um column; 25%-65% acetonitrile in 0.05% ammonium hydroxide and 10mM sodium bicarbonate solution in water, 8min gradient
• Example 63 Synthesis of 6-[3-(1-methylpyrazol-3-yl)phenyl]-N-(1-methylpyridin-1-ium-4-yl)-2- morpholino-5-oxazol-2-yl-pyrimidin-4-amine (Compound 73) and 6-[3-(1-methylpyrazol-3- yl)phenyl]-2-morpholino-5-oxazol-2-yl-N-(4-pyridyl)pyrimidin-4-amine (Compound 74):
• Step 1 Synthesis of 3-(3-bromophenyl)-1-methyl-pyrazole.
• Step 2 Synthesis 1-methyl-3-[3-(4,4,5,5-tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenyl]pyrazole.
• Step 3 Synthesis of ethyl 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylate.
• Step 4 Synthesis of 4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxylic acid.
• Step 5 Synthesis of N-(2,2-dimethoxyethyl)-4-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino-6-(4- pyridylamino)pyrimidine-5-carboxamide.
• Step 6 Syntheses of 6-[3-(1-methylpyrazol-3-yl)phenyl]-N-(1-methylpyridin-1-ium-4-yl)-2- morpholino-5-oxazol-2-yl-pyrimidin-4-amine and 6-[3-(1-methylpyrazol-3-yl)phenyl]-2-morpholino- 5-oxazol-2-yl-N-(4-pyridyl)pyrimidin-4-amine.
• Example 64 Synthesis of (R)-5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3-yl)phenyl)-2-(2- methylmorpholino)-N-(pyridin-4-yl)pyrimidin-4-amine (Compound 75): Step 1 : Synthesis of 4-chloro-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2- (methylthio)pyrimidine.
• Step 2 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2-(methylthio)-N-(pyridin-4- yl)pyrimidin-4-amine.
• Step 3 Synthesis of 5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2 -(methylsulfonyl)-N- (pyridin-4-yl)pyrimidin-4-amine.
• Step 4 Synthesis of (R)-5-methoxy-6-(3-(1 -methyl-1 H-pyrazol-3-yl)phenyl)-2 -(2-methylmorpholino)- N-(pyridin-4-yl)pyrimidin-4-amine.
• the mobile phase was acetonitrile/0.1 % ammonium bicarbonate) to obtain (R)-5-methoxy-6-(3-(1-methyl-1 H-pyrazol-3- yl)phenyl)-2-(2-methylmorpholino)-N-(pyridin-4-yl)pyrimidin-4-amine (12.7mg, 8.2%) as white solid.
• PlKfyve Biochemical Assay The biochemical PlKFyve inhibition assays were run by Carna Biosciences according to proprietary methodology based on the Promega ADP-GloTM Kinase assay.
• a full-length human PIKFYVE [1-2098(end) amino acids and S696N, L932S, Q995L, T998S, S1033A and Q1183K of the protein having the sequence set forth in NCBI Reference Sequence No. NP_055855.2] was expressed as N-terminal GST-fusion protein (265 kDa) using baculovirus expression system.
• GST- PIKFYVE was purified by using glutathione sepharose chromatography and used in an ADP-GloTM Kinase assay (Promega). Reactions were set up by adding the test compound solution, substrate solution, ATP solution and kinase solution, each at 4x final concentrations. Reactions were prepared with assay buffer (50 mM MOPS, 1 mM DTT, pH7.2), mixed, and incubated in black 384 well polystyrene plates for 1 hour at room temperature. ADP-GloTM reagent was then added for 40 minutes, followed by kinase detection reagent for an additional 40 minutes. The kinase activity was evaluated by detecting relative light units on a luminescence plate reader.
• assay buffer 50 mM MOPS, 1 mM DTT, pH7.2
• PlKfyve EEA1 Assay Genetic or pharmacological disruption of PlKfyve activity results in enlargement of endosomal vesicles. This enlargement was utilized as a surrogate readout of PlKFyve inhibition for routine triage of PlKfyve inhibitors.
• U2OS cells grown in 96-well assay plates were treated with compound diluted in DMEM media containing 10% fetal bovine serum. After 3 hours of treatment, cells were fixed with paraformaldehyde, permeabilized with 0.2% Triton-X in phosphate buffered saline and stained against EEA1 .
• * ++++ stands for ⁇ 10 nM; +++ stands for 10-100 nM; ++ stands for 100-1000 nM; + stands for 1-10 pM;
• Example 66 Viability Assay to Assess TDP-43 Toxicity in FAB1 TDP-43 and PlKfyve TDP-43 Yeast Cells.
• Human PIKFYVE (“entry clone”) was cloned into pAG416GPDccdB (“destination vector”) according to standard Gateway cloning protocols (Invitrogen, Life Technologies). The resulting pAG416GPD-PIKFYVE plasmids were amplified in E. coli and plasmid identity confirmed by restriction digest and Sanger sequencing.
• Lithium acetate/polyethylene glycol-based transformation was used to introduce the above PIKFYVE plasmid into a BY4741 yeast strain auxotrophic for the ura3 gene and deleted for two transcription factors that regulate the xenobiotic efflux pumps, a major efflux pump, and FAB1, the yeast ortholog of PIKFYVE (MATa, snq2::KILeu2; pdr3::Klura3;pdr1 ::NATMX; fab1 ::G418 R , his3;leu2;ura3;met15;LYS2+) (FIG. 2).
• Transformed yeast were plated on solid agar plates with complete synthetic media lacking uracil (CSM- ura) and containing 2% glucose. Individual colonies harboring the control or PIKFYVE TDP-43 plasmids were recovered. A plasmid containing wild-type TDP-43 under the transcriptional control of the GAL1 promoter and containing the hygromycin-resistance gene as a selectable marker was transformed into the fab7::G418 R pAG416GPD-PIKFYVE yeast strain (FIG. 1). Transformed yeast were plated on CSM- ura containing 2% glucose and 200 Dg/mL G418 after overnight recovery in media lacking antibiotic. Multiple independent isolates were further evaluated for cytotoxicity and TDP-43 expression levels.
• Yeast cultures were then diluted to an optical density at 600 nm wavelength (ODeoo) of 0.005 in 3 mL of CSM-ura/2% raffinose and grown overnight at 30°C with aeration to an ODeoo of 0.3-0.8.
• Logphase overnight cultures were diluted to ODeoo of 0.005 in CSM-ura containing either 2% raffinose or galactose and 150 DL dispensed into each well of a flat bottom 96-well plates.
• Compounds formulated in 100% dimethyl sulfoxide (DMSO) were serially diluted in DMSO and 1 .5 DL diluted compound transferred to the 96-well plates using a multichannel pipet.
• DMSO dimethyl sulfoxide
• Wells containing DMSO alone were also evaluated as controls for compound effects. Tested concentrations ranged from 15 DM to 0.11 DM. Cultures were immediately mixed to ensure compound distribution and covered plates incubated at 30°C for 24 hours in a stationary, humified incubator.
• PI propidium iodide
• a working solution of PI was made where, for each plate, 1 DL of 10 mM PI was added to 10 mL of CSM-ura (raffinose or galactose). The final PI solution (50 DL/well) was dispensed into each well of a new round bottom 96-well plate. The overnight 96-well assay plate was then mixed with a multichannel pipet and 50 DL transferred to the Pl-containing plate. This plate was then incubated for 30 minutes at 30°C in the dark.
• CSM-ura raffinose or galactose
• a benchtop flow cytometer (Miltenyi MACSquant) was then used to assess red fluorescence (B2 channel), forward scatter, and side scatter (with following settings: gentle mix, high flow rate, fast measurement, 10,000 events). Intensity histograms were then gated for “Plpositive” or “Pl-negative” using the raffinose and galactose cultures treated with DMSO as controls. The DMSO controls for raffinose or galactose-containing cultures were used to determine the window of increased cell death and this difference set to 100. All compounds were similarly gated and then compared to this maximal window to establish the percent reduction in Pl-positive cells. IC50 values were then calculated for compounds that demonstrated a concentration-dependent enhancement of viability by fitting a logistic regression curve.
• PlKfyve Inhibition Suppresses Toxicity in PlKfyve TDP-43 Model.
• the biochemical PlKFyve inhibition assays were run by Carna Biosciences according to proprietary methodology based on the Promega ADP-GloTM Kinase assay.
• a full-length human PIKFYVE [1-2098(end) amino acids and S696N, L932S, Q995L.T998S, S1033A and Q1183K of accession number NP_055855.2] was expressed as N- terminal GST-fusion protein (265 kDa) using baculovirus expression system.
• GST-PIKFYVE was purified by using glutathione sepharose chromatography and used in an ADP-GloTM Kinase assay (Promega). Reactions were set up by adding the test compound solution, substrate solution, ATP solution and kinase solution, each at 4x final concentrations.
• Reactions were prepared with assay buffer (50 mM MOPS, 1 mM DTT, pH7.2), mixed, and incubated in black 384 well polystyrene plates for 1 hour at room temperature. ADP-GloTM reagent was then added for 40 minutes, followed by kinase detection reagent for an additional 40 minutes. The kinase activity was evaluated by detecting relative light units on a luminescence plate reader. Samples were run in duplicate from 10 uM to 3 nM. Data was analyzed by setting the control wells (+ PlKfyve, no compound) to 0% inhibition and the readout value of background (no PlKfyve) set to 100% inhibition, then the % inhibition of each test solution calculated. IC50 values were calculated from concentration vs % inhibition curves by fitting to a four-parameter logistic curve.
• a panel of compounds was tested in a biochemical PIKFYVE assay (ADP-GloTM with full-length PlKfyve) and IC50’s determined (nM) (see the Table below).
• the same compounds were also tested in both FAB1 and PIKFYVE TDP-43 yeast models. Their activity is reported here as “active” or “inactive.”
• Compounds with low nanomolar potency in the biochemical assay were active in the PIKFYVE TDP-43 yeast model.
• Compounds that were less potent or inactive in the biochemical assay were inactive in the PIKFYVE TDP-43 model.
• Compounds that were inactive in the biochemical or PIKFYVE TDP-43 assays were plotted with the highest concentrations tested in that assay.

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