WO2023097007A1 - Compounds and methods for modulating splicing - Google Patents

Compounds and methods for modulating splicing Download PDF

Info

Publication number
WO2023097007A1
WO2023097007A1 PCT/US2022/050914 US2022050914W WO2023097007A1 WO 2023097007 A1 WO2023097007 A1 WO 2023097007A1 US 2022050914 W US2022050914 W US 2022050914W WO 2023097007 A1 WO2023097007 A1 WO 2023097007A1
Authority
WO
WIPO (PCT)
Prior art keywords
seq
compound
heteroaryl
formula
alkyl
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2022/050914
Other languages
English (en)
French (fr)
Inventor
Dominic Reynolds
Michael W. SEILER
Anant A. AGRAWAL
Frederic VAILLANCOURT
Peter Smith
Sudeep PRAJAPATI
Allen T. Hopper
Stepan Vyskocil
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Remix Therapeutics Inc
Original Assignee
Remix Therapeutics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Remix Therapeutics Inc filed Critical Remix Therapeutics Inc
Priority to EP22830059.6A priority Critical patent/EP4436961A1/en
Priority to JP2024531070A priority patent/JP2024541481A/ja
Priority to CA3239110A priority patent/CA3239110A1/en
Priority to KR1020247020813A priority patent/KR20240149387A/ko
Priority to CN202280085944.6A priority patent/CN118804912A/zh
Priority to US18/713,561 priority patent/US20250082633A1/en
Priority to AU2022398247A priority patent/AU2022398247A1/en
Publication of WO2023097007A1 publication Critical patent/WO2023097007A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • A61K31/50—Pyridazines; Hydrogenated pyridazines
    • A61K31/5025—Pyridazines; Hydrogenated pyridazines 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/4353—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/437—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a five-membered ring having nitrogen as a ring hetero atom, e.g. indolizine, beta-carboline
    • 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
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/438—The ring being spiro-condensed with carbocyclic or 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/454—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
    • 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
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/4545—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a six-membered ring with nitrogen as a ring hetero atom, e.g. pipamperone, anabasine
    • 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
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/472—Non-condensed isoquinolines, e.g. papaverine
    • A61K31/4725—Non-condensed isoquinolines, e.g. papaverine 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
    • A61K31/495—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
    • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene or sparfloxacin
    • 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
    • A61K31/4985—Pyrazines or piperazines 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
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/545—Heterocyclic compounds
    • 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
    • A61P25/14—Drugs for disorders of the nervous system for treating abnormal movements, e.g. chorea, dyskinesia
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P9/00—Drugs for disorders of the cardiovascular system
    • 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
    • C07D403/04—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
    • 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
    • C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
    • C07D413/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • 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
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/14—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing 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
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D519/00—Heterocyclic compounds containing more than one system of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring system not provided for in groups C07D453/00 or C07D455/00

Definitions

  • RNA expression involves oligonucleotide targeting and gene therapy; however, each of these modalities exhibit unique challenges as currently presented. As such, there is a need for new technologies to modulate RNA expression, including the development of small molecule compounds that target splicing.
  • S UMMARY The present disclosure features compounds and related compositions that, inter alia, modulate nucleic acid splicing, e.g., splicing of a pre-mRNA, as well as methods of use thereof.
  • the compounds described herein are compounds of Formula (I) (e.g., a compound of Formulas (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) and pharmaceutically acceptable salts, solvates, hydrates, tautomers, or stereoisomers thereof.
  • Formula (I) e.g., a compound of Formulas (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-
  • the present disclosure additionally provides methods of using the compounds of the invention (e.g., compounds of Formulas (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers thereof), and compositions thereof, e.g., to target, and in embodiments bind or form a complex with, a nucleic acid (e.g., a pre-mRNA or nucleic acid component of a small nuclear ribonucleoprotein (snRNP) or spliceosome), a protein (e.g., a protein component of an
  • the compounds described herein may be used to alter the composition or structure of a nucleic acid (e.g., a pre-mRNA or mRNA (e.g., a pre-mRNA and the mRNA which arises from the pre-mRNA), e.g., by increasing or decreasing splicing at a splice site. In some embodiments, increasing or decreasing splicing results in modulating the level of a gene product (e.g., an RNA or protein) produced.
  • the compounds described herein may be used for the prevention and/or treatment of a disease, disorder, or condition, e.g., a disease, disorder or condition associated with splicing, e.g., alternative splicing.
  • a proliferative disease, disorder, or condition e.g., a disease, disorder,
  • the compounds described herein e.g., compounds of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers thereof) and compositions thereof are used for the prevention and/or treatment of a non-proliferative disease, disorder, or condition.
  • the present disclosure provides compounds of Formula (I): ( ), or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; L is absent, C1-C6-alkylene, C1-C6-heteroalkylene, C(O), or -C(O)N(R B )-, wherein each alkylene and heteroalkylene is optionally substituted with one or more R 8 ; W, X, Z 1 , and Z 2 are each independently C(R 3 ) or N, wherein at least one of W and X is N; each R 1 is independently hydrogen, C1-C6-alkyl, C2-C6-alkenyl, C2-C6-alkynyl, C1-C6-heteroalkyl, C1-C6-hal
  • the present invention provides pharmaceutical compositions comprising a compound of Formula (I) (e.g., a compound of Formulas (I-a), (I-b), (I-c), (I-d), (I- e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)), or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, and optionally a pharmaceutically acceptable excipient.
  • a compound of Formula (I) e.g., a compound of Formulas (I-a), (I-b), (I-c), (I-d), (I- e), (I-f), (I-g), (I-h), (I-i), (I-j),
  • the pharmaceutical compositions described herein include an effective amount (e.g., a therapeutically effective amount) of a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)), or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I
  • the present disclosure provides methods for modulating splicing, e.g., splicing of a nucleic acid (e.g., a DNA or RNA, e.g., a pre-mRNA) with a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I- k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b
  • compositions for use in modulating splicing e.g., splicing of a nucleic acid (e.g., a DNA or RNA, e.g., a pre-mRNA) with a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I- o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (
  • Modulation of splicing may comprise impacting any step involved in splicing and may include an event upstream or downstream of a splicing event.
  • the compound of Formula (I) binds to a target, e.g., a target nucleic acid (e.g., DNA or RNA, e.g., a precursor RNA, e.g., a pre-mRNA), a target protein, or combination thereof (e.g., an snRNP and a pre-mRNA).
  • a target may include a splice site in a pre-mRNA or a component of the splicing machinery, such as the U1 snRNP.
  • the compound of Formula (I) alters a target nucleic acid (e.g., DNA or RNA, e.g., a precursor RNA, e.g., a pre-mRNA), target protein, or combination thereof.
  • a target nucleic acid e.g., DNA or RNA, e.g., a precursor RNA, e.g., a pre-mRNA
  • target protein e.g., a pre-mRNA
  • the compound of Formula (I) increases or decreases splicing at a splice site on a target nucleic acid (e.g., an RNA, e.g., a precursor RNA, e.g., a pre-mRNA) by about 0.5% or more (e.g., about 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 75%, 90%, 95%, or more), relative to a reference (e.g., the absence of a compound of Formula (I), e.g., in a healthy or diseased cell or tissue).
  • a target nucleic acid e.g., an RNA, e.g., a precursor RNA, e.g., a pre-mRNA
  • a reference e.g., the absence of a compound of Formula (I), e.g., in a healthy or diseased cell or tissue.
  • the presence of a compound of Formula (I) results an increase or decrease of transcription of a target nucleic acid (e.g., an RNA) by about 0.5% or more (e.g., about 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 75%, 90%, 95%, or more), relative to a reference (e.g., the absence of a compound of Formula (I), e.g., in a healthy or diseased cell or tissue).
  • a target nucleic acid e.g., an RNA
  • a reference e.g., the absence of a compound of Formula (I), e.g., in a healthy or diseased cell or tissue.
  • the present disclosure provides methods for preventing and/or treating a disease, disorder, or condition in a subject by administering a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, or related compositions.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g),
  • the disease or disorder entails unwanted or aberrant splicing.
  • the disease or disorder is a proliferative disease, disorder, or condition.
  • Exemplary proliferative diseases include cancer, a benign neoplasm, or angiogenesis.
  • the present disclosure provides methods for treating and/or preventing a non- proliferative disease, disorder, or condition.
  • the present disclosure provides methods for treating and/or preventing a neurological disease or disorder, autoimmune disease or disorder, immunodeficiency disease or disorder, lysosomal storage disease or disorder, cardiovascular disease or disorder, metabolic disease or disorder, respiratory disease or disorder, renal disease or disorder, or infectious disease.
  • the present disclosure provides methods of down-regulating the expression of (e.g., the level of or the rate of production of) a target protein with a compound of Formula (I) (e.g., a compound of Formulas (I), ((I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I- i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), ((I-a), (I-b), (I-c), (I-d), (I-e
  • the present disclosure provides methods of up-regulating the expression of (e.g., the level of or the rate of production of) a target protein with a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I- v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (
  • the present disclosure provides methods of altering the isoform of a target protein with a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I- o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (
  • Another aspect of the disclosure relates to methods of inhibiting the activity of a target protein in a biological sample or subject.
  • administration of a compound of Formula (I) to a biological sample, a cell, or a subject comprises inhibition of cell growth or induction of cell death.
  • compositions for use in preventing and/or treating a disease, disorder, or condition in a subject by administering a compound of Formula (I) (e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I- i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, or related compositions.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g),
  • the disease or disorder entails unwanted or aberrant splicing.
  • the disease or disorder is a proliferative disease, disorder, or condition.
  • Exemplary proliferative diseases include cancer, a benign neoplasm, or angiogenesis.
  • the present disclosure provides methods for treating and/or preventing a non-proliferative disease, disorder, or condition.
  • the present disclosure provides methods for treating and/or preventing a neurological disease or disorder, autoimmune disease or disorder, immunodeficiency disease or disorder, lysosomal storage disease or disorder, cardiovascular disease or disorder, metabolic disease or disorder, respiratory disease or disorder, renal disease or disorder, or infectious disease.
  • compositions for use in down-regulating the expression of (e.g., the level of or the rate of production of) a target protein with a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I- v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I
  • compositions for use in up-regulating the expression of (e.g., the level of or the rate of production of) a target protein with a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I- d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I- u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I- d), (I-e),
  • compositions for use in altering the isoform of a target protein with a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof in a biological sample or subject.
  • a compound of Formula (I) e.g., a compound of Formulas (I), (I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-
  • compositions for use in inhibiting the activity of a target protein in a biological sample or subject comprises inhibition of cell growth or induction of cell death.
  • kits comprising a container with a compound of Formula (I) (e.g., a compound of Formulas (I), ((I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I-k), (I-l), (I-m), (I-n), (I-o), (I-p), (I-q), (I-r), (I-s), (I-t), (I-u), or (I-v)) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer thereof, or a pharmaceutical composition thereof.
  • a compound of Formula (I) e.g., a compound of Formulas (I), ((I-a), (I-b), (I-c), (I-d), (I-e), (I-f), (I-g), (I-h), (I-i), (I-j), (I
  • kits described herein further include instructions for administering the compound of Formula (I) or the pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer thereof, or the pharmaceutical composition thereof.
  • the details of one or more embodiments of the invention are set forth herein. Other features, objects, and advantages of the invention will be apparent from the Detailed Description, the Examples, and the Claims.
  • DETAILED DESCRIPTION Selected Chemical Definitions Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75 th Ed., inside cover, and specific functional groups are generally defined as described therein.
  • C1-C6 alkyl is intended to encompass, C1, C2, C3, C4, C5, C6, C 1 -C 6 , C 1 -C 5 , C 1 -C 4 , C 1 -C 3 , C 1 -C 2 , C 2 -C 6 , C 2 -C 5 , C 2 -C 4 , C 2 -C 3 , C 3 -C 6 , C 3 -C 5 , C 3 -C 4 , C 4 -C 6 , C 4 - C 5 , and C 5 -C 6 alkyl.
  • alkyl refers to a radical of a straight–chain or branched saturated hydrocarbon group having from 1 to 24 carbon atoms (“C1-C24 alkyl”). In some embodiments, an alkyl group has 1 to 12 carbon atoms (“C 1 -C 12 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1-C8 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C1-C6 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2-C6 alkyl”).
  • an alkyl group has 1 carbon atom (“C 1 alkyl”).
  • C 1 - C 6 alkyl groups include methyl (C 1 ), ethyl (C 2 ), n–propyl (C 3 ), isopropyl (C 3 ), n–butyl (C 4 ), tert– butyl (C4), sec–butyl (C4), iso–butyl (C4), n–pentyl (C5), 3–pentanyl (C5), amyl (C5), neopentyl (C5), 3–methyl–2–butanyl (C5), tertiary amyl (C5), and n–hexyl (C6).
  • alkyl groups include n–heptyl (C 7 ), n–octyl (C 8 ) and the like.
  • Each instance of an alkyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents; e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent.
  • the alkyl group is unsubstituted C1–C10 alkyl (e.g., –CH3).
  • the alkyl group is substituted C1–C6 alkyl.
  • alkenyl refers to a radical of a straight–chain or branched hydrocarbon group having from 2 to 24 carbon atoms, one or more carbon–carbon double bonds, and no triple bonds (“C2-C24 alkenyl”).
  • an alkenyl group has 2 to 10 carbon atoms (“C 2 -C 10 alkenyl”).
  • an alkenyl group has 2 to 8 carbon atoms (“C 2 -C 8 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C 2 -C 6 alkenyl”).
  • an alkenyl group has 2 carbon atoms (“C2 alkenyl”).
  • the one or more carbon–carbon double bonds can be internal (such as in 2–butenyl) or terminal (such as in 1– butenyl).
  • Examples of C 2 -C 4 alkenyl groups include ethenyl (C 2 ), 1–propenyl (C 3 ), 2–propenyl (C3), 1–butenyl (C4), 2–butenyl (C4), butadienyl (C4), and the like.
  • Examples of C2-C6 alkenyl groups include the aforementioned C2–4 alkenyl groups as well as pentenyl (C5), pentadienyl (C 5 ), hexenyl (C 6 ), and the like.
  • alkenyl examples include heptenyl (C 7 ), octenyl (C 8 ), octatrienyl (C 8 ), and the like.
  • Each instance of an alkenyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent.
  • the alkenyl group is unsubstituted C1– C10 alkenyl.
  • the alkenyl group is substituted C2–C6 alkenyl.
  • alkynyl refers to a radical of a straight–chain or branched hydrocarbon group having from 2 to 24 carbon atoms, one or more carbon–carbon triple bonds (“C2-C24 alkenyl”).
  • an alkynyl group has 2 to 10 carbon atoms (“C2-C10 alkynyl”).
  • an alkynyl group has 2 to 8 carbon atoms (“C 2 -C 8 alkynyl”).
  • an alkynyl group has 2 to 6 carbon atoms (“C 2 -C 6 alkynyl”).
  • an alkynyl group has 2 carbon atoms (“C2 alkynyl”).
  • the one or more carbon– carbon triple bonds can be internal (such as in 2–butynyl) or terminal (such as in 1–butynyl).
  • Examples of C 2 -C 4 alkynyl groups include ethynyl (C 2 ), 1–propynyl (C 3 ), 2–propynyl (C 3 ), 1– butynyl (C4), 2–butynyl (C4), and the like.
  • Each instance of an alkynyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent.
  • the alkynyl group is unsubstituted C2–10 alkynyl.
  • the alkynyl group is substituted C2–6 alkynyl.
  • haloalkyl refers to a non-cyclic stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one halogen selected from the group consisting of F, Cl, Br, and I.
  • the halogen(s) F, Cl, Br, and I may be placed at any position of the haloalkyl group.
  • haloalkyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted haloalkyl”) or substituted (a “substituted haloalkyl”) with one or more substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent
  • substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent
  • heteroalkyl refers to a non-cyclic stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom selected from the group consisting of O, N, P, Si, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized.
  • heteroalkyl Up to two or three heteroatoms may be consecutive, such as, for example, -CH2-NH-OCH3 and -CH2-O-Si(CH3)3.
  • heteroalkyl is recited, followed by recitations of specific heteroalkyl groups, such as –CH 2 O, –NR C R D , or the like, it will be understood that the terms heteroalkyl and –CH 2 O or –NR C R D are not redundant or mutually exclusive. Rather, the specific heteroalkyl groups are recited to add clarity. Thus, the term “heteroalkyl” should not be interpreted herein as excluding specific heteroalkyl groups, such as –CH2O, –NR C R D , or the like.
  • Each instance of a heteroalkyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted heteroalkyl”) or substituted (a “substituted heteroalkyl”) with one or more substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent
  • aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having 6–14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C 6 -C 14 aryl”).
  • an aryl group has six ring carbon atoms (“C 6 aryl”; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms (“C10 aryl”; e.g., naphthyl such as 1–naphthyl and 2–naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms (“C 14 aryl”; e.g., anthracyl).
  • An aryl group may be described as, e.g., a C6-C10-membered aryl, wherein the term “membered” refers to the non-hydrogen ring atoms within the moiety.
  • Aryl groups include phenyl, naphthyl, indenyl, and tetrahydronaphthyl. Each instance of an aryl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is unsubstituted C6-C14 aryl.
  • the aryl group is substituted C 6 -C 14 aryl.
  • heteroaryl refers to a radical of a 5–10 membered monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 ⁇ electrons shared in a cyclic array) having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5–10 membered heteroaryl”).
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system.
  • Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom e.g., indolyl, quinolinyl, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2–indolyl) or the ring that does not contain a heteroatom (e.g., 5–indolyl).
  • a heteroaryl group may be described as, e.g., a 6-10-membered heteroaryl, wherein the term “membered” refers to the non-hydrogen ring atoms within the moiety.
  • Each instance of a heteroaryl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”) with one or more substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent
  • substituents e.g., for instance from 1 to 5 substituents, 1 to 3 substituents, or 1 substituent
  • Exemplary 5–membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl.
  • Exemplary 5–membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl.
  • Exemplary 5–membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
  • Exemplary 5–membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6–membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl.
  • Exemplary 6–membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • Exemplary 6– membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively.
  • Exemplary 7–membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl.
  • Exemplary 5,6– bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
  • Exemplary 6,6–bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Other exemplary heteroaryl groups include heme and heme derivatives.
  • cycloalkyl refers to a radical of a non–aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C 3 -C 10 cycloalkyl”) and zero heteroatoms in the non–aromatic ring system.
  • a cycloalkyl group has 3 to 8 ring carbon atoms (“C3-C8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C3-C6 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C 3 -C 6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C5-C10 cycloalkyl”).
  • a cycloalkyl group may be described as, e.g., a C4-C7-membered cycloalkyl, wherein the term “membered” refers to the non-hydrogen ring atoms within the moiety.
  • Exemplary C 3 -C 6 cycloalkyl groups include, without limitation, cyclopropyl (C 3 ), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like.
  • Exemplary C3-C8 cycloalkyl groups include, without limitation, the aforementioned C 3 -C 6 cycloalkyl groups as well as cycloheptyl (C 7 ), cycloheptenyl (C 7 ), cycloheptadienyl (C 7 ), cycloheptatrienyl (C 7 ), cyclooctyl (C8), cyclooctenyl (C8), cubanyl (C8), bicyclo[1.1.1]pentanyl (C5), bicyclo[2.2.2]octanyl (C 8 ), bicyclo[2.1.1]hexanyl (C 6 ), bicyclo[3.1.1]heptanyl (C 7 ), and the like.
  • Exemplary C 3 -C 10 cycloalkyl groups include, without limitation, the aforementioned C 3 -C 8 cycloalkyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro–1H–indenyl (C9), decahydronaphthalenyl (C10), spiro[4.5]decanyl (C10), and the like.
  • the cycloalkyl group is either monocyclic (“monocyclic cycloalkyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic cycloalkyl”) and can be saturated or can be partially unsaturated.
  • “Cycloalkyl” also includes ring systems wherein the cycloalkyl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is on the cycloalkyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the cycloalkyl ring system.
  • Each instance of a cycloalkyl group may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents.
  • the cycloalkyl group is unsubstituted C3-C10 cycloalkyl.
  • the cycloalkyl group is a substituted C 3 -C 10 cycloalkyl.
  • Heterocyclyl refers to a radical of a 3– to 16–membered non–aromatic ring system having ring carbon atoms and 1 to 8 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3–16 membered heterocyclyl”).
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated.
  • Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heterocyclyl also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more cycloalkyl groups wherein the point of attachment is either on the cycloalkyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system.
  • a heterocyclyl group may be described as, e.g., a 3-7-membered heterocyclyl, wherein the term “membered” refers to the non- hydrogen ring atoms, i.e., carbon, nitrogen, oxygen, sulfur, boron, phosphorus, and silicon, within the moiety.
  • Each instance of heterocyclyl may be independently optionally substituted, i.e., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents.
  • the heterocyclyl group is unsubstituted 3–16 membered heterocyclyl.
  • the heterocyclyl group is substituted 3– 16 membered heterocyclyl.
  • Exemplary 3–membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl.
  • Exemplary 4–membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl.
  • Exemplary 5–membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl–2,5–dione.
  • Exemplary 5–membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin–2–one.
  • Exemplary 5–membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplary 6–membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl (e.g., 2,2,6,6-tetramethylpiperidinyl), tetrahydropyranyl, dihydropyridinyl, pyridinonyl (e.g., 1-methylpyridin2-onyl), and thianyl.
  • Exemplary 6–membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, pyridazinonyl (2-methylpyridazin-3-onyl), pyrimidinonyl (e.g., 1-methylpyrimidin-2-onyl, 3- methylpyrimidin-4-onyl), dithianyl, dioxanyl.
  • Exemplary 6–membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl.
  • Exemplary 7–membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl.
  • Exemplary 8–membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
  • Exemplary 5–membered heterocyclyl groups fused to a C6 aryl ring include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like.
  • Exemplary 5–membered heterocyclyl groups fused to a heterocyclyl ring include, without limitation, octahydropyrrolopyrrolyl (e.g., octahydropyrrolo[3,4-c]pyrrolyl), and the like.
  • Exemplary 6-membered heterocyclyl groups fused to a heterocyclyl ring include, without limitation, diazaspirononanyl (e.g., 2,7- diazaspiro[3.5]nonanyl).
  • Exemplary 6–membered heterocyclyl groups fused to an aryl ring include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.
  • Exemplary 6–membered heterocyclyl groups fused to a cycloalkyl ring include, without limitation, azabicyclooctanyl (e.g., (1,5)-8-azabicyclo[3.2.1]octanyl).
  • Exemplary 6–membered heterocyclyl groups fused to a cycloalkyl ring include, without limitation, azabicyclononanyl (e.g., 9- azabicyclo[3.3.1]nonanyl).
  • alkylene alkenylene, alkynylene, haloalkylene,” “heteroalkylene,” “cycloalkylene,” or “heterocyclylene,” alone or as part of another substituent, mean, unless otherwise stated, a divalent radical derived from an alkyl, alkenyl, alkynyl, haloalkylene, heteroalkylene, cycloalkyl, or heterocyclyl respectively.
  • alkenylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene.
  • alkylene, alkenylene, alkynylene, haloalkylene, heteroalkylene, cycloalkylene, or heterocyclylene group may be described as, e.g., a C1-C6-membered alkylene, C 2 -C 6 -membered alkenylene, C 2 -C 6 -membered alkynylene, C 1 -C 6 -membered haloalkylene, C 1 - C 6 -membered heteroalkylene, C 3 -C 8 -membered cycloalkylene, or C 3 -C 8 -membered heterocyclylene, wherein the term “membered” refers to the non-hydrogen atoms within the moiety.
  • heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, no orientation of the linking group is implied by the direction in which the formula of the linking group is written.
  • the formula - C(O) 2 R’- may represent both -C(O) 2 R’- and –R’C(O) 2 -.
  • the terms “cyano” or “–CN” refer to a substituent having a carbon atom joined to a nitrogen atom by a triple bond, e.g., C ⁇ N.
  • halogen or “halo” refer to fluorine, chlorine, bromine or iodine.
  • hydroxy refers to –OH.
  • nitro refers to a substitutent having two oxygen atoms bound to a nitrogen atom, e.g., -NO2.
  • nucleoside the basic building blocks of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
  • the primary, or naturally occurring, nucleobases are cytosine (DNA and RNA), guanine (DNA and RNA), adenine (DNA and RNA), thymine (DNA) and uracil (RNA), abbreviated as C, G, A, T, and U, respectively. Because A, G, C, and T appear in the DNA, these molecules are called DNA-bases; A, G, C, and U are called RNA-bases.
  • Adenine and guanine belong to the double-ringed class of molecules called purines (abbreviated as R). Cytosine, thymine, and uracil are all pyrimidines.
  • nucleobases that do not function as normal parts of the genetic code, are termed non-naturally occurring.
  • a nucleobase may be chemically modified, for example, with an alkyl (e.g., methyl), halo, -O-alkyl, or other modification.
  • nucleic acid refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double-stranded form.
  • the term “nucleic acid” includes a gene, cDNA, pre-mRNA, or an mRNA.
  • the nucleic acid molecule is synthetic (e.g., chemically synthesized) or recombinant.
  • nucleic acids containing analogues or derivatives of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides.
  • a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementarity sequences as well as the sequence explicitly indicated.
  • oxo refers to a carbonyl, i.e., -C(O)-.
  • substituted means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, such as any of the substituents described herein that result in the formation of a stable compound.
  • the present disclosure contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocyclyl groups. Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure.
  • the ring-forming substituents are attached to adjacent members of the base structure.
  • two ring- forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure.
  • the ring-forming substituents are attached to a single member of the base structure.
  • two ring-forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure.
  • the ring- forming substituents are attached to non-adjacent members of the base structure.
  • the compounds provided herein may exist in one or more particular geometric, optical, enantiomeric, diasteriomeric, epimeric, stereoisomeric, tautomeric, conformational, or anomeric forms, including but not limited to: cis- and trans-forms; E- and Z-forms; endo- and exo-forms; R-, S-, and meso-forms; D- and L-forms; d- and l-forms; (+) and (-) forms; keto-, enol-, and enolate-forms; syn- and anti-forms; synclinal- and anticlinal-forms; ⁇ - and ⁇ -forms; axial and equatorial forms; boat-, chair-, twist-, envelope-, and half chair-forms; and combinations thereof, hereinafter collectively referred to as "isomers” (or "isomeric forms").
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • the stereochemistry depicted in a compound is relative rather than absolute.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high-pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistry of Carbon Compounds (McGraw–Hill, NY, 1962); and Wilen, Tables of Resolving Agents and Optical Resolutions p.268 (E.L. Eliel, Ed., Univ.
  • enantiomerically pure or “pure enantiomer” denotes that the compound comprises more than 75% by weight, more than 80% by weight, more than 85% by weight, more than 90% by weight, more than 91% by weight, more than 92% by weight, more than 93% by weight, more than 94% by weight, more than 95% by weight, more than 96% by weight, more than 97% by weight, more than 98% by weight, more than 99% by weight, more than 99.5% by weight, or more than 99.9% by weight, of the enantiomer.
  • the weights are based upon total weight of all enantiomers or stereoisomers of the compound.
  • an enantiomerically pure compound can be present with other active or inactive ingredients.
  • a pharmaceutical composition comprising an enantiomerically pure R–compound can comprise, for example, about 90% excipient and about 10% enantiomerically pure R–compound.
  • the enantiomerically pure R–compound in such compositions can, for example, comprise, at least about 95% by weight R–compound and at most about 5% by weight S–compound, by total weight of the compound.
  • a pharmaceutical composition comprising an enantiomerically pure S– compound can comprise, for example, about 90% excipient and about 10% enantiomerically pure S–compound.
  • the enantiomerically pure S–compound in such compositions can, for example, comprise, at least about 95% by weight S–compound and at most about 5% by weight R–compound, by total weight of the compound.
  • a diastereomerically pure compound can be present with other active or inactive ingredients.
  • a pharmaceutical composition comprising a diastereometerically pure exo compound can comprise, for example, about 90% excipient and about 10% diastereometerically pure exo compound.
  • the diastereometerically pure exo compound in such compositions can, for example, comprise, at least about 95% by weight exo compound and at most about 5% by weight endo compound, by total weight of the compound.
  • a pharmaceutical composition comprising a diastereometerically pure endo compound can comprise, for example, about 90% excipient and about 10% diastereometerically pure endo compound.
  • the diastereometerically pure endo compound in such compositions can, for example, comprise, at least about 95% by weight endo compound and at most about 5% by weight exo compound, by total weight of the compound.
  • an isomerically pure compound can be present with other active or inactive ingredients.
  • a pharmaceutical composition comprising a isomerically pure exo compound can comprise, for example, about 90% excipient and about 10% isomerically pure exo compound.
  • the isomerically pure exo compound in such compositions can, for example, comprise, at least about 95% by weight exo compound and at most about 5% by weight endo compound, by total weight of the compound.
  • a pharmaceutical composition comprising an isomerically pure endo compound can comprise, for example, about 90% excipient and about 10% isomerically pure endo compound.
  • the isomerically pure endo compound in such compositions can, for example, comprise, at least about 95% by weight endo compound and at most about 5% by weight exo compound, by total weight of the compound.
  • the active ingredient can be formulated with little or no excipient or carrier.
  • Compound described herein may also comprise one or more isotopic substitutions.
  • pharmaceutically acceptable salt is meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein.
  • base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
  • acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent.
  • Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like.
  • inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like,
  • salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, e.g., Berge et al, Journal of Pharmaceutical Science 66: 1-19 (1977)).
  • Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. These salts may be prepared by methods known to those skilled in the art.
  • Other pharmaceutically acceptable carriers known to those of skill in the art are suitable for the present invention.
  • the present disclosure provides compounds in a prodrug form. Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention.
  • prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment.
  • prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
  • solvate refers to forms of the compound that are associated with a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding.
  • Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like.
  • the compounds of Formula (I) may be prepared, e.g., in crystalline form, and may be solvated.
  • Suitable solvates include pharmaceutically acceptable solvates and further include both stoichiometric solvates and non-stoichiometric solvates. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. “Solvate” encompasses both solution-phase and isolable solvates. Representative solvates include hydrates, ethanolates, and methanolates. The term “hydrate” refers to a compound which is associated with water. Typically, the number of the water molecules contained in a hydrate of a compound is in a definite ratio to the number of the compound molecules in the hydrate.
  • a hydrate of a compound may be represented, for example, by the general formula R ⁇ x H2O, wherein R is the compound and wherein x is a number greater than 0.
  • a given compound may form more than one type of hydrates, including, e.g., monohydrates (x is 1), lower hydrates (x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R ⁇ 0.5 H 2 O)), and polyhydrates (x is a number greater than 1, e.g., dihydrates (R ⁇ 2 H 2 O) and hexahydrates (R ⁇ 6 H 2 O)).
  • tautomer refers to compounds that are interchangeable forms of a particular compound structure, and that vary in the displacement of hydrogen atoms and electrons. Thus, two structures may be in equilibrium through the movement of ⁇ electrons and an atom (usually H). For example, enols and ketones are tautomers because they are rapidly interconverted by treatment with either acid or base. Another example of tautomerism is the aci- and nitro- forms of phenylnitromethane that are likewise formed by treatment with acid or base. Tautomeric forms may be relevant to the attainment of the optimal chemical reactivity and biological activity of a compound of interest. Other Definitions The following definitions are more general terms used throughout the present disclosure.
  • the articles “a” and “an” refer to one or more than one (e.g., to at least one) of the grammatical object of the article.
  • an element means one element or more than one element.
  • the term “and/or” means either “and” or “or” unless indicated otherwise.
  • the term “about” is used herein to mean within the typical ranges of tolerances in the art. For example, “about” can be understood as about 2 standard deviations from the mean. In certain embodiments, about means + 10%. In certain embodiments, about means + 5%. When about is present before a series of numbers or a range, it is understood that “about” can modify each of the numbers in the series or range.
  • “Acquire” or “acquiring” as used herein, refer to obtaining possession of a value, e.g., a numerical value, or image, or a physical entity (e.g., a sample), by “directly acquiring” or “indirectly acquiring” the value or physical entity.
  • “Directly acquiring” means performing a process (e.g., performing an analytical method or protocol) to obtain the value or physical entity.
  • “Indirectly acquiring” refers to receiving the value or physical entity from another party or source (e.g., a third-party laboratory that directly acquired the physical entity or value).
  • Directly acquiring a value or physical entity includes performing a process that includes a physical change in a physical substance or the use of a machine or device.
  • Examples of directly acquiring a value include obtaining a sample from a human subject. Directly acquiring a value includes performing a process that uses a machine or device, e.g., mass spectrometer to acquire mass spectrometry data.
  • the terms “administer,” “administering,” or “administration,” as used herein refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing an inventive compound, or a pharmaceutical composition thereof.
  • the terms “condition,” “disease,” and “disorder” are used interchangeably.
  • An “effective amount” of a compound of Formula (I) refers to an amount sufficient to elicit the desired biological response, i.e., treating the condition.
  • the effective amount of a compound of Formula (I) may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject.
  • An effective amount encompasses therapeutic and prophylactic treatment.
  • an effective amount of an inventive compound may reduce the tumor burden or stop the growth or spread of a tumor.
  • a “therapeutically effective amount” of a compound of Formula (I) is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition.
  • a therapeutically effective amount is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to minimize one or more symptoms associated with the condition.
  • a therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition.
  • the term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the condition, or enhances the therapeutic efficacy of another therapeutic agent.
  • peptide polypeptide
  • protein are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds.
  • a protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprised therein.
  • Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds.
  • the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types.
  • prevention refers to a treatment that comprises administering a therapy, e.g., administering a compound described herein (e.g., a compound of Formula (I)) prior to the onset of a disease, disorder, or condition in order to preclude the physical manifestation of said disease, disorder, or condition.
  • a therapy e.g., administering a compound described herein (e.g., a compound of Formula (I)) prior to the onset of a disease, disorder, or condition in order to preclude the physical manifestation of said disease, disorder, or condition.
  • prevention require that signs or symptoms of the disease, disorder, or condition have not yet developed or have not yet been observed.
  • treatment comprises prevention and in other embodiments it does not.
  • a “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle–aged adult, or senior adult)) and/or other non–human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys).
  • mammals e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (
  • the animal is a mammal.
  • the animal may be a male or female and at any stage of development.
  • a non–human animal may be a transgenic animal.
  • the terms “treatment,” “treat,” and “treating” refer to reversing, alleviating, delaying the onset of, or inhibiting the progress of one or more of a symptom, manifestation, or underlying cause of a disease, disorder, or condition (e.g., as described herein), e.g., by administering a therapy, e.g., administering a compound described herein (e.g., a compound of Formula (I)).
  • treating comprises reducing, reversing, alleviating, delaying the onset of, or inhibiting the progress of a symptom of a disease, disorder, or condition. In an embodiment, treating comprises reducing, reversing, alleviating, delaying the onset of, or inhibiting the progress of a manifestation of a disease, disorder, or condition. In an embodiment, treating comprises reducing, reversing, alleviating, reducing, or delaying the onset of, an underlying cause of a disease, disorder, or condition. In some embodiments, “treatment,” “treat,” and “treating” require that signs or symptoms of the disease, disorder, or condition have developed or have been observed.
  • treatment may be administered in the absence of signs or symptoms of the disease or condition, e.g., in preventive treatment.
  • treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors).
  • Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.
  • Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.
  • treatment comprises prevention and in other embodiments it does not.
  • a “proliferative disease” refers to a disease that occurs due to abnormal extension by the multiplication of cells (Walker, Cambridge Dictionary of Biology; Cambridge University Press: Cambridge, UK, 1990).
  • a proliferative disease may be associated with: 1) the pathological proliferation of normally quiescent cells; 2) the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); 3) the pathological expression of proteolytic enzymes such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); 4) the pathological angiogenesis as in proliferative retinopathy and tumor metastasis; or 5) evasion of host immune surveillance and elimination of neoplastic cells.
  • Exemplary proliferative diseases include cancers (i.e., “malignant neoplasms”), benign neoplasms, and angiogenesis.
  • non-proliferative disease refers to a disease that does not primarily extend through the abnormal multiplication of cells.
  • a non-proliferative disease may be associated with any cell type or tissue type in a subject.
  • Exemplary non-proliferative diseases include neurological diseases or disorders (e.g., a repeat expansion disease); autoimmune disease or disorders; immunodeficiency diseases or disorders; lysosomal storage diseases or disorders; inflammatory diseases or disorders; cardiovascular conditions, diseases, or disorders; metabolic diseases or disorders; respiratory conditions, diseases, or disorders; renal diseases or disorders; and infectious diseases.
  • a and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ;
  • L is absent, C1-C6- alkylene, C 1 -C 6 -heteroalkylene, C(O), or -C(O)N(R B )-, wherein each alkylene and heteroalkylene is optionally substituted with one or more R 8 ;
  • W, X, Z 1 , and Z 2 are each independently C(R 3 ) or N, wherein at least one of W and X is N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 -C 6 -alkenyl, C 2 -C 6 -alkynyl, C 1 -C 6 -heteroalkyl, C 1
  • each of A and B are independently a monocyclic ring, e.g., monocyclic cycloalkyl, monocyclic heterocyclyl, monocyclic aryl, or monocyclic heteroaryl.
  • the monocyclic ring may be saturated, partially unsaturated, or fully unsaturated (e.g., aromatic).
  • a or B are independently a monocyclic ring comprising between 3 and 10 ring atoms (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 ring atoms).
  • A is a 4-membered monocyclic ring.
  • B is a 4-membered monocyclic ring.
  • A is a 5-membered monocyclic ring.
  • B is a 5-membered monocyclic ring.
  • A is a 6-membered monocyclic ring.
  • B is a 6-membered monocyclic ring.
  • A is a 7-membered monocyclic ring.
  • B is a 7-membered monocyclic ring.
  • A is an 8-membered monocyclic ring.
  • B is an 8-membered monocyclic ring.
  • a or B are independently a monocyclic ring optionally substituted with one or more R 1 .
  • a or B are independently a bicyclic ring, e.g., bicyclic cycloalkyl, bicyclic heterocyclyl, bicyclic aryl, or bicyclic heteroaryl.
  • the bicyclic ring may be saturated, partially unsaturated, or fully unsaturated (e.g., aromatic).
  • a or B are independently a bicyclic ring comprising a fused, bridged, or spiro ring system.
  • a or B are independently a bicyclic ring comprising between 4 and 18 ring atoms (e.g., 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 ring atoms).
  • A is a 6-membered bicyclic ring. In some embodiments, B is a 6-membered bicyclic ring. In some embodiments, A is a 7-membered bicyclic ring. In some embodiments, B is a 7-membered bicyclic ring. In some embodiments, A is an 8-membered bicyclic ring. In some embodiments, B is an 8-membered bicyclic ring. In some embodiments, A is a 9-membered bicyclic ring. In some embodiments, B is a 9-membered bicyclic ring. In some embodiments, A is a 10- membered bicyclic ring.
  • B is a 10-membered bicyclic ring. In some embodiments, A is an 11-membered bicyclic ring. In some embodiments, B is an 11-membered bicyclic ring. In some embodiments, A is a 12-membered bicyclic ring. In some embodiments, B is a 12-membered bicyclic ring. In some embodiments, A or B are independently a bicyclic ring optionally substituted with one or more R 1 . In some embodiments, A or B are independently a tricyclic ring, e.g., tricyclic cycloalkyl, tricyclic heterocyclyl, tricyclic aryl, or tricyclic heteroaryl.
  • the tricyclic ring may be saturated, partially unsaturated, or fully unsaturated (e.g., aromatic).
  • a or B are independently a tricyclic ring that comprises a fused, bridged, or spiro ring system, or a combination thereof.
  • a or B are independently a tricyclic ring comprising between 6 and 24 ring atoms (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 ring atoms).
  • A is an 8-membered tricyclic ring.
  • B is an 8-membered tricyclic ring.
  • A is a 9- membered tricyclic ring.
  • B is a 9-membered tricyclic ring. In some embodiments, A is a 10-membered tricyclic ring. In some embodiments, B is a 10-membered tricyclic ring. In some embodiments, A or B are independently a tricyclic ring optionally substituted with one or more R 1 . In some embodiments, A or B are independently monocyclic cycloalkyl, monocyclic heterocyclyl, monocyclic aryl, or monocyclic heteroaryl. In some embodiments, A or B are independently bicyclic cycloalkyl, bicyclic heterocyclyl, bicyclic aryl, or bicyclic heteroaryl.
  • a or B are independently tricyclic cycloalkyl, tricyclic heterocyclyl, tricyclic aryl, or tricyclic heteroaryl.
  • A is monocyclic heterocyclyl.
  • B is monocyclic heterocyclyl.
  • A is bicyclic heterocyclyl.
  • B is bicyclic heterocyclyl.
  • A is monocyclic heteroaryl.
  • B is monocyclic heteroaryl.
  • A is bicyclic heteroaryl.
  • B is bicyclic heteroaryl.
  • B is bicyclic heteroaryl.
  • a or B are independently a nitrogen-containing heterocyclyl, e.g., heterocyclyl comprising one or more nitrogen atom.
  • the one or more nitrogen atom of the nitrogen-containing heterocyclyl may be at any position of the ring.
  • the nitrogen-containing heterocyclyl is monocyclic, bicyclic, or tricyclic.
  • a or B are independently heterocyclyl comprising at least 1, at least 2, at least 3, at least 4, at least 5, or at least 6 nitrogen atoms.
  • A is heterocyclyl comprising 1 nitrogen atom.
  • B is heterocyclyl comprising 1 nitrogen atom.
  • A is heterocyclyl comprising 2 nitrogen atoms.
  • B is heterocyclyl comprising 2 nitrogen atoms. In some embodiments, A is heterocyclyl comprising 3 nitrogen atoms. In some embodiments, B is heterocyclyl comprising 3 nitrogen atoms. In some embodiments, A is heterocyclyl comprising 4 nitrogen atoms. In some embodiments, B is heterocyclyl comprising 4 nitrogen atoms. In some embodiments, A or B are independently a nitrogen-containing heterocyclyl comprising one or more additional heteroatoms, e.g., one or more of oxygen, sulfur, boron, silicon, or phosphorus. In some embodiments, the one or more nitrogen of the nitrogen-containing heterocyclyl is substituted, e.g., with R 1 .
  • a or B are independently a nitrogen-containing heteroaryl, e.g., heteroaryl comprising one or more nitrogen atom.
  • the one or more nitrogen atom of the nitrogen-containing heteroaryl may be at any position of the ring.
  • the nitrogen-containing heteroaryl is monocyclic, bicyclic, or tricyclic.
  • a or B are independently heteroaryl comprising at least 1, at least 2, at least 3, at least 4, at least 5, or at least 6 nitrogen atoms.
  • A is heteroaryl comprising 1 nitrogen atom.
  • B is heteroaryl comprising 1 nitrogen atom.
  • A is heteroaryl comprising 2 nitrogen atoms.
  • B is heteroaryl comprising 2 nitrogen atoms. In some embodiments, A is heteroaryl comprising 3 nitrogen atoms. In some embodiments, B is heteroaryl comprising 3 nitrogen atoms. In some embodiments, A is heteroaryl comprising 4 nitrogen atoms. In some embodiments, B is heteroaryl comprising 4 nitrogen atoms. In some embodiments, A or B are independently a nitrogen-containing heteroaryl comprising one or more additional heteroatoms, e.g., one or more of oxygen, sulfur, boron, silicon, or phosphorus. In some embodiments, the one or more nitrogen of the nitrogen- containing heteroaryl is substituted, e.g., with R 1 .
  • A is a 6-membered nitrogen-containing heterocyclyl, e.g., a 6- membered heterocyclyl comprising one or more nitrogen. In some embodiments, A is a 6- membered heterocyclyl comprising 1 nitrogen atom. In some embodiments, A is a 6-membered heterocyclyl comprising 2 nitrogen atoms. In some embodiments, A is a 6-membered heterocyclyl comprising 3 nitrogen atoms. In some embodiments, A is a 6-membered heterocyclyl comprising 4 nitrogen atoms. The one or more nitrogen atom of the 6-membered nitrogen-containing heterocyclyl may be at any position of the ring.
  • A is a 6-membered nitrogen-containing heterocyclyl optionally substituted with one or more R 1 .
  • the one or more nitrogen of the 6-membered nitrogen-containing heterocyclyl is substituted, e.g., with R 1 .
  • A is a 6-membered nitrogen- containing heterocyclyl comprising one or more additional heteroatoms, e.g., one or more of oxygen, sulfur, boron, silicon, or phosphorus.
  • B is a 5-membered nitrogen-containing heterocyclyl or heteroaryl, e.g., a 5-membered heterocyclyl or heteroaryl comprising one or more nitrogen.
  • B is a 5-membered heterocyclyl comprising 1 nitrogen atom. In some embodiments, B is a 5-membered heteroaryl comprising 1 nitrogen atom. In some embodiments, B is a 5-membered heterocyclyl comprising 2 nitrogen atoms. In some embodiments, B is a 5- membered heteroaryl comprising 2 nitrogen atoms. In some embodiments, B is a 5-membered heterocyclyl comprising 3 nitrogen atoms. In some embodiments, B is a 5-membered heteroaryl comprising 3 nitrogen atoms. The one or more nitrogen atom of the 5-membered nitrogen- containing heterocyclyl or heteroaryl may be at any position of the ring.
  • B is a 5-membered nitrogen-containing heterocyclyl optionally substituted with one or more R 1 . In some embodiments, B is a 5-membered nitrogen-containing heteroaryl optionally substituted with one or more R 1 . In some embodiments, the one or more nitrogen of the 5-membered nitrogen-containing heterocyclyl or heteroaryl is substituted, e.g., with R 1 . In some embodiments, B is a 5-membered nitrogen-containing heterocyclyl or heteroaryl comprising one or more additional heteroatoms, e.g., one or more of oxygen, sulfur, boron, silicon, or phosphorus.
  • B is a nitrogen-containing bicyclic heteroaryl (e.g., a 9-membered nitrogen-containing bicyclic heteroaryl), that is optionally substituted with one or more R 1 .
  • B is a 9-membered bicyclic heteroaryl comprising 1 nitrogen atom.
  • B is a 9-membered bicyclic heteroaryl comprising 2 nitrogen atoms.
  • B is a 9-membered bicyclic heteroaryl comprising 3 nitrogen atoms.
  • B is a 9-membered bicyclic heteroaryl comprising 4 nitrogen atoms.
  • the one or more nitrogen atom of the 9-membered bicyclic heteroaryl may be at any position of the ring.
  • B is a 9-membered bicyclic heteroaryl substituted with one or more R 1 .
  • each of A and B are independently selected from: ,
  • each R 1 is as defined herein.
  • a and B are each independently a saturated, partially saturated, or unsaturated (e.g., aromatic) derivative of one of the rings described above.
  • a and B are each independently a stereoisomer of one of the rings described above.
  • a and B are each independently a saturated, partially saturated, or unsaturated (e.g., aromatic) derivative of one of the rings described above. In an embodiment, A and B are each independently a stereoisomer of one of the rings described above. In some embodiments, one of A and B is independently selected from as described herein. In some embodiments, one of A and B is independently selected from ,, described herein.
  • one of A and B is independently selected from , , , , wherein each R 1 is independently C 1 -C 6 -alkyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 -haloalkyl, halo, cyano, or –OR A , and each alkyl, heteroalkyl, and haloalkyl is optionally substituted with one or more R 4 .
  • one of A and B is independently selected from , independently C1-C6-alkyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, halo, cyano, or –OR A , and each alkyl, heteroalkyl, and haloalkyl is optionally substituted with one or more R 7 .
  • one of A and B is independently , wherein each R 1a is independently C1-C6-alkyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, halo, cyano, or –OR A , and each alkyl, heteroalkyl, and haloalkyl is optionally substituted with one or more R 7 .
  • each R 1a is independently C1-C6-alkyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, halo, cyano, or –OR A , and each alkyl, heteroalkyl, and haloalkyl is optionally substituted with one or more R 7 .
  • one of A and B is independently selected from , , some embodiments, one of A and B is independently . In some embodiments, one of A and B is independently a monocyclic heterocyclyl or bicyclic heterocyclyl, each of which is optionally substituted with one or more R 1 . In some embodiments, one of A and B is independently a nitrogen-containing heterocyclyl optionally substituted with one or more R 1 . In some embodiments, one of A and B is independently a 4-8 membered heterocyclyl optionally substituted with one or more R 1 . In some embodiments, one of A and B is independently selected from , , , and , wherein R 1 is as described herein.
  • one of A and B is independently selected from , wherein R 1 is as described herein. In some embodiments, one , wherein R 1 is as described herein. In some embodiments, A is selected from , , wherein R 1 is as described herein. In some embodiments, B is selected from , , wherein R 1 is as described herein. , embodiments, one of A and B is independently selected from , , is selected one of A and B is independently selected from , , In some embodiments, X is N. In some embodiments, W is N. In some embodiments, both of W and X is independently N. In some embodiments, Z 1 is C(R 3 ) (e.g., CH). In some embodiments, Z 1 is N.
  • X is N and W, Z 1 , and Z 2 are each independently C(R 3 ). In some embodiments, X and Z 1 are each independently N and W and Z 2 are C(R 3 ). In some embodiments, X and W are each independently N and Z 1 is C(R 3 ). In some embodiments, each of W, X, and Z 1 are each independently N, and Z 1 is C(R 3 ). In some embodiments, R 1 is hydrogen. In some embodiments, R 1 is C 1 -C 6 -alkyl. In some embodiments, R 1 is C2-C6-alkenyl. In some embodiments, R 1 is C2-C6-alkynyl.
  • R 1 is C1-C6-heteroalkyl. In some embodiments, R 1 is C1-C6-haloalkyl (e.g., -CF3). In some embodiments, R 1 is C 1 -alkyl (e.g., methyl). In some embodiments, R 1 is unsubstituted C1-C6-alkyl, unsubstituted C2-C6-alkenyl, unsubstituted C2-C6-alkynyl, unsubstituted C1-C6- heteroalkyl, or unsubstituted C1-C6-haloalkyl.
  • R 1 is C1-C6-alkyl substituted with one or more R 5 . In some embodiments, R 1 is C 2 -C 6 -alkenyl substituted with one or more R 5 . In some embodiments, R 1 is C2-C6-alkynyl substituted with one or more R 5 . In some embodiments, R 1 is C1-C6-heteroalkyl substituted with one or more R 5 . In some embodiments, R 1 is C 1 -C 6 -haloalkyl substituted with one or more R 5 . In some embodiments, R 1 is methyl. In some embodiments, R 1 is cycloalkyl (e.g., 3-7 membered cycloalkyl).
  • R 1 is heterocyclyl (e.g., 3-7 membered heterocyclyl). In some embodiments, R 1 is aryl. In some embodiments, R 1 is C 1 -C 6 alkylene-aryl (e.g., benzyl). In some embodiments, R 1 is C1-C6 alkenylene-aryl. In some embodiments, R 1 is C1-C6 alkylene-heteroaryl. In some embodiments, R 1 is heteroaryl.
  • R 1 is unsubstituted cycloalkyl, unsubstituted heterocyclyl, unsubstituted aryl, unsubstituted C 1 -C 6 alkylene-aryl, unsubstituted C1-C6 alkenylene-aryl, unsubstituted C1-C6 alkylene-heteroaryl, or unsubstituted heteroaryl.
  • R 1 is cycloalkyl substituted with one or more R 5 .
  • R 1 is heterocyclyl substituted with one or more R 5 .
  • R 1 is aryl substituted with one or more R 5 .
  • R 1 is C 1 -C 6 alkylene-aryl substituted with one or more R 5 . In some embodiments, R 1 is C1-C6 alkenylene-aryl substituted with one or more R 5 . In some embodiments, R 1 is C 1 -C 6 alkylene-heteroaryl substituted with one or more R 5 . In some embodiments, R 1 is heteroaryl substituted with one or more R 5 . In some embodiments, R 1 is –OR A . In some embodiments, R 1 is –NR B R C (e.g., NH2 or NMe2). In some embodiments, R 1 is –NR B C(O)R D .
  • R 1 is–C(O)NR B R C . In some embodiments, R 1 is –C(O)R D . In some embodiments, R 1 is –C(O)OR D . In some embodiments, R 1 is–SR E . In some embodiments, R 1 is –S(O)xR D . In some embodiments, R 1 is halo, e.g., fluoro, chloro, bromo, or iodo. In some embodiments, R 1 is cyano. In some embodiments, R 1 is nitro (-NO 2 ). In some embodiments, R 1 is oxo.
  • two R 1 groups, together with the atoms to which they are attached form a 3-7-membered cycloalkyl. In some embodiments, two R 1 groups, together with the atoms to which they are attached, form a 3-7-membered heterocyclyl. In some embodiments, two R 1 groups, together with the atoms to which they are attached, form a 5- or 6-membered aryl. In some embodiments, two R 1 groups, together with the atoms to which they are attached, form a 5- or 6-membered heteroaryl.
  • the cycloalkyl, heterocyclyl, aryl, or heteroaryl may be substituted with one or more R 5 .
  • R 3 is hydrogen.
  • R 3 is C1-C6 alkyl. In some embodiments, R 3 is C1-C6 haloalkyl. In some embodiments, R 3 is methyl. In some embodiments, L is absent. In some embodiments, L is C 1 -C 6 -alkylene optionally substituted with one or more R 8 . In some embodiments, L is C 1 -C 6 -heteroalkylene optionally substituted with one or more R 8 . In some embodiments, L is C(O). In some embodiments, L is - C(O)N(R B )-. In some embodiments, R 5 is C 1 -C 6 -alkyl.
  • R 5 is C 2 -C 6 -alkenyl. In some embodiments, R 5 is C2-C6-alkynyl. In some embodiments, R 5 is C1-C6-heteroalkyl. In some embodiments, R 5 is C1-C6-haloalkyl. In some embodiments, R 5 is unsubstituted C1-C6- alkyl, unsubstituted C 2 -C 6 -alkenyl, unsubstituted C 2 -C 6 -alkynyl, unsubstituted C 1 -C 6 -haloalkyl, or unsubstituted C1-C6-heteroalkyl.
  • R 5 is C1-C6-alkyl substituted with one or more R 6 .
  • R 5 is C2-C6-alkenyl substituted with one or more R 6 .
  • R 5 is C 2 -C 6 -alkynyl substituted with one or more R 6 .
  • R 5 is C 1 -C 6 -haloalkyl substituted with one or more R 6 .
  • R 5 is C 1 -C 6 -heteroalkyl substituted with one or more R 6 .
  • R 5 is cycloalkyl.
  • R 5 is heterocyclyl.
  • R 5 is aryl.
  • R 5 is heteroaryl. In some embodiments, R 5 is unsubstituted cycloalkyl, unsubstituted heterocyclyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R 5 is cycloalkyl substituted with one or more R 6 . In some embodiments, R 5 is heterocyclyl substituted with one or more R 6 . In some embodiments, R 5 is aryl substituted with one or more R 6 . In some embodiments, R 5 is heteroaryl substituted with one or more R 6 . In some embodiments, R 5 is halo (e.g., fluoro, chloro, bromo, or iodo).
  • R 5 is halo (e.g., fluoro, chloro, bromo, or iodo).
  • R 5 is cyano. In some embodiments, R 5 is oxo. In some embodiments, R 5 is – OR A . In some embodiments, R 5 is –NR B R C . In some embodiments, R 5 is –NR B C(O)R D . In some embodiments, R 5 is –NO2. In some embodiments, R 5 is –C(O)NR B R C . In some embodiments, R 5 is –C(O)R D . In some embodiments, R 5 is –C(O)OR D . In some embodiments, R 5 is –SR E . In some embodiments, R 5 is –S(O)xR D .
  • R 6 is C1-C6-alkyl. In some embodiments, R 6 is C1-C6-heteroalkyl. In some embodiments, R 6 is C 1 -C 6 -haloalkyl (e.g., –CF 3 or –CHF 2 ). In some embodiments, R 6 is cycloalkyl. In some embodiments, R 6 is heterocyclyl. In some embodiments, R 6 is aryl. In some embodiments, R 6 is heteroaryl. In some embodiments, R 6 is halo. In some embodiments, R 6 is cyano. In some embodiments, R 6 is oxo. In some embodiments, R 6 is –OR A . In some embodiments, R A is hydrogen.
  • R A is C 1 -C 6 alkyl (e.g., methyl). In some embodiments, R A is C1-C6 haloalkyl. In some embodiments, R A is aryl. In some embodiments, R A is heteroaryl. In some embodiments, R A is C 1 -C 6 alkylene-aryl (e.g., benzyl). In some embodiments, R A is C 1 -C 6 alkylene-heteroaryl. In some embodiments, R A is C(O)R D . In some embodiments, R A is –S(O)xR D .
  • R B , R C , or both are independently hydrogen, C1-C6-alkyl, C1-C6- heteroalkyl, cycloalkyl, heterocyclyl, or –OR A .
  • each of R B and R C is independently hydrogen.
  • each of R B and R C is independently C1-C6 alkyl.
  • one of R B and R C is hydrogen, and the other of R B and R C is C1-C6 alkyl.
  • R B and R C together with the atom to which they are attached form a 3-7- membered heterocyclyl ring optionally substituted with one or more of R 7 (e.g., 1, 2, or 3 R 7 ).
  • R D is hydrogen, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, C 1 -C 6 haloalkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl, C 1 -C 6 alkylene-aryl (e.g., benzyl), or C 1 -C 6 alkylene-heteroaryl.
  • R D is hydrogen.
  • R D is C1-C6 alkyl (e.g., methyl).
  • R D is C1-C6 heteroalkyl.
  • R D is C1-C6 haloalkyl. In some embodiments, R D is cycloalkyl. In some embodiments, R D is heterocyclyl. In some embodiments, R D is aryl. In some embodiments, R E is aryl. In some embodiments, R D is heteroaryl. In some embodiments, R D is C1-C6 alkylene-aryl (e.g., benzyl). In some embodiments, R D is C1-C6 alkylene-heteroaryl. In some embodiments, x is an integer between 0 and 2 (e.g., 0, 1, or 2). In some embodiments, x is 0. In some embodiments, x is 1. In some embodiments, x is 2.
  • the compound of Formula (I) is a compound of Formula (I-a): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof,
  • a and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ;
  • W, X, Z 1 , and Z 2 are each independently C(R 3 ) or N, wherein at least one of W and X is N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 -C 6 -alkenyl, C 2 -C 6 -alkynyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 -haloalkyl, cycloalkyl, heterocyclyl, aryl, C 1 -C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C 1 -C 6 heteroalky
  • the compound of Formula (I) is a compound of Formula (I-b): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W, X, Z 1 , and Z 2 are each independently C(R 3 ) or N, wherein at least one of W and X is N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 -C 6 -alkenyl, C 2 -C 6 -alkynyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 - haloalkyl, cycloalkyl, heterocyclyl, aryl, C 1 -C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C 1 -C 6
  • the compound of Formula (I) is a compound of Formula (I-c): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W and Z 1 are each independently C(R 3 ) or N; each R 1 is independently hydrogen, C1-C6-alkyl, C2- C6-alkenyl, C2-C6-alkynyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, cycloalkyl, heterocyclyl, aryl, C1- C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C 1 -C 6 heteroalkylene-aryl, heteroaryl, C 1 -C 6 alkylene- heteroaryl, C1-C6 heteroalkylene
  • the compound of Formula (I) is a compound of Formula (I-d): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W and Z 2 are each independently C(R 3 ) or N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 - C6-alkenyl, C2-C6-alkynyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, cycloalkyl, heterocyclyl, aryl, C1- C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C 1 -C 6 heteroalkylene-aryl, heteroaryl, C 1 -C 6 alkylene- heteroaryl, C 1 -C 6 alkylene
  • the compound of Formula (I) is a compound of Formula (I-e): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W is C(R 3 ) or N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 -C 6 -alkenyl, C 2 -C 6 -alkynyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 -haloalkyl, cycloalkyl, heterocyclyl, aryl, C 1 -C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C1-C6 heteroalkylene-aryl, heteroaryl, C1-C6 alkylene-heteroaryl, C
  • the compound of Formula (I) is a compound of Formula (I-f): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W is C(R 3 ) or N; each R 1 is independently hydrogen, C1-C6-alkyl, C2-C6-alkenyl, C2-C6-alkynyl, C1-C6-heteroalkyl, C1-C6-haloalkyl, cycloalkyl, heterocyclyl, aryl, C1-C6 alkylene-aryl, C2-C6 alkenylene-aryl, C 1 -C 6 heteroalkylene-aryl, heteroaryl, C 1 -C 6 alkylene-heteroaryl, C 1 -C 6 heteroalkylene-hetero;
  • the compound of Formula (I) is a compound of Formula (I-g): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W is C(R 3 ) or N; each R 1 is independently hydrogen, C1-C6-alkyl, C2-C6-alkenyl, C2-C6-alkynyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 -haloalkyl, cycloalkyl, heterocyclyl, aryl, C 1 -C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C1-C6 heteroalkylene-aryl, heteroaryl, C1-C6 alkylene-heteroaryl, C1-C6 heteroalkylene
  • the compound of Formula (I) is a compound of Formula (I-h): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A and B are each independently cycloalkyl, heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one or more R 1 ; W is C(R 3 ) or N; each R 1 is independently hydrogen, C 1 -C 6 -alkyl, C 2 -C 6 -alkenyl, C 2 -C 6 -alkynyl, C 1 -C 6 -heteroalkyl, C 1 -C 6 -haloalkyl, cycloalkyl, heterocyclyl, aryl, C 1 -C 6 alkylene-aryl, C 2 -C 6 alkenylene-aryl, C1-C6 heteroalkylene-aryl, heteroaryl, C1-C6 alkylene-heteroaryl, C
  • the compound of Formula (I) is a compound of Formula (I-i): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein A, B, W, X, Z 1 , Z 2 , and R 2 are as defined for Formula (I); each R 8a and R 8b is independently C1-C6-alkyl, halo, cyano, oxo, or –OR A1 ; and y is 0, 1, 2, 3, or 4.
  • the compound of Formula (I) is a compound of Formula (I-j): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein each R 1a , R 1b , R 1c , R 8a and R 8b is independently C1-C6-alkyl, halo, cyano, oxo, or –OR A1 ; X 1 is C(R 1 ) or N; X 2 is C(R 1 )2 or N(R 1 ); y is 0, 1, 2, 3, or 4; and W, X, Z 1 , Z 2 , R 1 and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-k): , hydrate, tautomer, or stereoisomer thereof, wherein each of X 1 and X 3 is independently C(R 3 ) or N; X 2 is C or N; and wherein A, Z 1 , R 1 , R 2 , and R 3 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-l): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein each of R 1a , R 1b , and R 1c is independently hydrogen, C1-C6-alkyl, halo, or -OR A ; and wherein A, R A , Z 1 , R 1 , R 2 , and R 3 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-m): , hydrate, tautomer, or stereoisomer thereof, wherein each of X 1 and X 3 is independently C(R 1 ) or N; X 2 is C or N; and wherein A, Z 1 , R 1 and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-n): , tautomer, or stereoisomer thereof, wherein each of R 1a and R 1b is independently hydrogen, C1- C6-alkyl, halo, or -OR A ; and wherein A, R A , Z 1 , R 1 , R 2 , and R 3 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-o): , tautomer, or stereoisomer thereof, wherein each of X 1 and X 2 is independently C(R 1 ) or N; and wherein A, Z 1 , R 1 and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-p): , hydrate, tautomer, or stereoisomer thereof, wherein each of R 1a , R 1b , and R 1c is independently hydrogen, C1-C6-alkyl, halo, or -OR A ; and wherein A, R A , Z 1 , R 1 and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-q): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein X 1 is C(R 1 ); X 2 is C(R 1 ) 2 or N(R 1 ); and wherein B, Z 1 , R 1 , R 2 and R 3 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-r): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein each of R 1c , R 1d and R 1e is independently hydrogen, alkyl, halo, or heteroalkyl; or R 1d and R 1e together with the atoms to which they are attached, form a three or four membered cycloalkyl group; and wherein each of B, Z 1 , Z 2 , R 2 , and R 3 are as defined as for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-s): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein X 1 is C(R 1 ); X 2 is C(R 1 )2 or N(R 1 ); each of R 1a , R 1b , and R 1c is independently hydrogen, C 1 -C 6 -alkyl, halo, or -OR A and wherein R A , Z 1 , R 1 , R 2 , and R 3 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-t): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein X 1 is C(R 1 ); X 2 is C(R 1 )2 or N(R 1 ); each of R 1a , R 1b , and R 1c is independently hydrogen, C 1 -C 6 -alkyl, halo, or -OR A and wherein R A , Z 1 , R 1 , and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-u): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein X 1 is C(R 1 ); X 2 is C(R 1 )2 or N(R 1 ); each of R 1a and R 1b is independently hydrogen, C 1 -C 6 -alkyl, halo, or -OR A and wherein R A , Z 1 , R 1 , and R 2 are as defined for Formula (I).
  • the compound of Formula (I) is a compound of Formula (I-v): pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, wherein each of R 1a , R 1b , R 1c , R 1d , R 1e , and R 1f is independently hydrogen, C1-C6-alkyl, halo, or R A ; and wherein R A , Z 1 , R 1 , and R 2 are as defined in for Formula (I).
  • one of A and B is selected from , 1 is as described herein. In some embodiments, one of A and B is independently selected from described herein. In some embodiments, one of A and B is independently selected from
  • one of A and B is independently selected from , some embodiments, one of A and B is independently selected from , , , , wherein R 1 is as described herein. In some embodiments, one of A and B is independently selected , wherein R 1 is as described herein. In some embodiments, one of A and B is independently selected from ,
  • B is .
  • B is embodiments, . some embodiments, . some embodiments, B .
  • B is .
  • L is absent.
  • L is C 1 -C 6 -alkylene (e.g., C 1 - alkylene, C2-alkylene, C3-alkylene, C4-alkylene, C5-alkylene, or C6-alkylene).
  • L is unsubstituted C 1 -C 6 alkylene.
  • L is substituted C 1 -C 6 - alkylene, e.g., C 1 -C 6 alkylene substituted with one or more R 4 . In some embodiments, L is C 1 - alkylene substituted with one R 4 . In some embodiments, L is -CH2- (or methylene). In some embodiments, L is -C(O)- (or carbonyl). In some embodiments, L is absent, C 1 -C 6 -alkylene, or C 1 -C 6 -heteroalkylene, wherein each alkylene and heteroalkylene is optionally substituted with one or more R 4 .
  • R 2 is selected from hydrogen, halo (e.g., fluoro, chloro), C 1 -C 6 -alkyl (e.g., CH 3 ), or –OR A1 (e.g., -OCH 3 ). In some embodiments, R 2 is hydrogen.
  • R 2 is halo (e.g., fluoro, chloro). In some embodiments, R 2 is C1-C6-alkyl (e.g., CH3). In some embodiments, R 2 is –OR A1 (e.g., -OCH3). In some embodiments, the compound of Formula (I) is selected from a compound in Table 1, or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof. Table 1. Exemplary compounds.
  • compositions comprising a compound of Formula (I), e.g., a compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer, as described herein, and optionally a pharmaceutically acceptable excipient.
  • the pharmaceutical composition described herein comprises a compound of Formula (I) or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.
  • the compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof is provided in an effective amount in the pharmaceutical composition. In certain embodiments, the effective amount is a therapeutically effective amount.
  • the effective amount is a prophylactically effective amount.
  • Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the compound of Formula (I) (the “active ingredient”) into association with a carrier and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
  • Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses.
  • a “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient.
  • the amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
  • Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between 0.1% and 100% (w/w) active ingredient.
  • pharmaceutically acceptable excipient refers to a non-toxic carrier, adjuvant, diluent, or vehicle that does not destroy the pharmacological activity of the compound with which it is formulated.
  • Pharmaceutically acceptable excipients useful in the manufacture of the pharmaceutical compositions of the invention are any of those that are well known in the art of pharmaceutical formulation and include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils.
  • compositions of the invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat.
  • ion exchangers alumina, aluminum stearate, lecithin
  • serum proteins such as human serum albumin
  • buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate,
  • compositions of the present invention may be administered orally, parenterally (including subcutaneous, intramuscular, intravenous and intradermal), by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir.
  • provided compounds or compositions are administrable intravenously and/or orally.
  • parenteral as used herein includes subcutaneous, intravenous, intramuscular, intraocular, intravitreal, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intraperitoneal intralesional and intracranial injection or infusion techniques.
  • the compositions are administered orally, subcutaneously, intraperitoneally, or intravenously.
  • Sterile injectable forms of the compositions of this invention may be aqueous or oleaginous suspension. These suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that may be employed are water, Ringer’s solution and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, aqueous suspensions or solutions.
  • carriers commonly used include lactose and corn starch.
  • Lubricating agents such as magnesium stearate, are also typically added.
  • useful diluents include lactose and dried cornstarch.
  • aqueous suspensions are required for oral use, the active ingredient is combined with emulsifying and suspending agents. If desired, certain sweetening, flavoring or coloring agents may also be added.
  • a provided oral formulation is formulated for immediate release or sustained/delayed release.
  • the composition is suitable for buccal or sublingual administration, including tablets, lozenges and pastilles.
  • a provided compound can also be in micro-encapsulated form.
  • pharmaceutically acceptable compositions of this invention may be administered in the form of suppositories for rectal administration.
  • Pharmaceutically acceptable compositions of this invention may also be administered topically, especially when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin, or the lower intestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.
  • provided pharmaceutically acceptable compositions may be formulated as micronized suspensions or in an ointment such as petrolatum.
  • compositions In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.
  • compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
  • Compounds provided herein are typically formulated in dosage unit form, e.g., single unit dosage form, for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
  • the specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.
  • the exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like.
  • the desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks.
  • the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).
  • an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.
  • the compounds of Formula (I) may be at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect. It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult.
  • the amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult. It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional pharmaceutical agents. The compounds or compositions can be administered in combination with additional pharmaceutical agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects.
  • the compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional pharmaceutical agents, which may be useful as, e.g., combination therapies.
  • Pharmaceutical agents include therapeutically active agents.
  • Pharmaceutical agents also include prophylactically active agents.
  • Each additional pharmaceutical agent may be administered at a dose and/or on a time schedule determined for that pharmaceutical agent.
  • the additional pharmaceutical agents may also be administered together with each other and/or with the compound or composition described herein in a single dose or administered separately in different doses.
  • the particular combination to employ in a regimen will take into account compatibility of the inventive compound with the additional pharmaceutical agents and/or the desired therapeutic and/or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually.
  • exemplary additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-diabetic agents, anti-inflammatory agents, immunosuppressant agents, and a pain-relieving agent.
  • Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved by the U.S.
  • kits e.g., pharmaceutical packs.
  • kits may be useful for preventing and/or treating a proliferative disease or a non-proliferative disease, e.g., as described herein.
  • the kits provided may comprise an inventive pharmaceutical composition or compound and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container).
  • a container e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container.
  • provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or compound.
  • the inventive pharmaceutical composition or compound provided in the container and the second container are combined to form one-unit dosage form.
  • kits including a first container comprising a compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, or a pharmaceutical composition thereof.
  • the kit of the disclosure includes a first container comprising a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof.
  • the kits are useful in preventing and/or treating a disease, disorder, or condition described herein in a subject (e.g., a proliferative disease or a non-proliferative disease).
  • kits further include instructions for administering the compound, or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, or stereoisomer thereof, or a pharmaceutical composition thereof, to a subject to prevent and/or treat a proliferative disease or a non-proliferative disease.
  • Methods of Use Described herein are compounds useful for modulating splicing.
  • a compound of Formula (I) may be used to alter the amount, structure, or composition of a nucleic acid (e.g., a precursor RNA, e.g., a pre-mRNA, or the resulting mRNA) by increasing or decreasing splicing at a splice site.
  • increasing or decreasing splicing results in modulating the level or structure of a gene product (e.g., an RNA or protein) produced.
  • a compound of Formula (I) may modulate a component of the splicing machinery, e.g., by modulating the interaction with a component of the splicing machinery with another entity (e.g., nucleic acid, protein, or a combination thereof).
  • the splicing machinery as referred to herein comprises one or more spliceosome components.
  • Spliceosome components may comprise, for example, one or more of major spliceosome members (U1, U2, U4, U5, U6 snRNPs), or minor spliceosome members (U11, U12, U4atac, U6atac snRNPs) and their accessory splicing factors.
  • a target e.g., a precursor RNA, e.g., a pre-mRNA
  • the method comprises providing a compound of Formula (I).
  • inclusion of a splice site in a target results in addition or deletion of one or more nucleic acids to the target (e.g., a new exon, e.g. a skipped exon).
  • Addition or deletion of one or more nucleic acids to the target may result in an increase in the levels of a gene product (e.g., RNA, e.g., mRNA, or protein).
  • the present disclosure features a method of modifying a target (e.g., a precursor RNA, e.g., a pre-mRNA, or the resulting mRNA) through exclusion of a splice site in the target, wherein the method comprises providing a compound of Formula (I).
  • exclusion of a splice site in a target e.g., a precursor RNA, e.g., a pre-mRNA
  • results in deletion or addition of one or more nucleic acids from the target e.g., a skipped exon, e.g. a new exon).
  • RNA e.g., mRNA, or protein
  • the methods of modifying a target comprise suppression of splicing at a splice site or enhancement of splicing at a splice site (e.g., by more than about 0.5%, e.g., 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or more), e.g., as compared to a reference (e.g., the absence of a compound of Formula (I), or in a healthy or diseased cell or tissue).
  • a reference e.g., the absence of a compound of Formula (I)
  • RNA e.g., DNA or RNA, e.g., pre-mRNA
  • genes encoding a target sequence include, inter alia, ABCA4, ABCA9, ABCB1, ABCB5, ABCC9, ABCD1, ACADL, ACADM, ACADSB, ACSS2, ACTB, ACTG2, ADA, ADAL, ADAM10, ADAM15, ADAM22, ADAM32, ADAMTS12, ADAMTS13, ADAMTS20, ADAMTS6, ADAMTS9, ADAR, ADCY3, ADCY10, ADCY8, ADNP, ADRBK2, AFP, AGL, AGT, AHCTF1, AHR, AKAP10, AKAP3, AKNA, ALAS1, ALS2CL, ALB, ALDH3A2, ALG6, AMBRA
  • Additional exemplary genes encoding a target sequence include genes include A1CF, A4GALT, AAR2, ABAT, ABCA11P, ZNF721, ABCA5, ABHD10, ABHD13, ABHD2, ABHD6, AC000120.3, KRIT1, AC004076.1, ZNF772, AC004076.9, ZNF772, AC004223.3, RAD51D, AC004381.6, AC006486.1, ERF, AC007390.5, AC007780.1, PRKAR1A, AC007998.2, INO80C, AC009070.1, CMC2, AC009879.2, AC009879.3, ADHFE1, AC010487.3, ZNF816-ZNF321P, ZNF816, AC010328.3, AC010522.1, ZNF587B, AC010547.4, ZNF19, AC012313.3, ZNF4
  • the gene encoding a target sequence comprises the HTT gene. In some embodiments, the gene encoding a target sequence comprises the MYB gene. In some embodiments, the gene encoding a target sequence comprises the SMN2 gene. In some embodiments, the gene encoding a target sequence comprises the FOXM1 gene.
  • Exemplary genes that may be modulated by the compounds of Formula (I) described herein may also include, inter alia, AC005258.1, AC005943.1, AC007849.1, AC008770.2, AC010487.3, AC011477.4, AC012651.1, AC012531.3, AC034102.2, AC073896.4, AC104472.3, AL109811.3, AL133342.1, AL137782.1, AL157871.5, AF241726.2, AL355336.1, AL358113.1, AL360181.3, AL445423.2, AL691482.3, AP001267.5, RF01169, and RF02271.
  • the compounds described herein may further be used to modulate a sequence comprising a particular splice site sequence, e.g., an RNA sequence (e.g., a pre-mRNA sequence).
  • a particular splice site sequence e.g., an RNA sequence (e.g., a pre-mRNA sequence).
  • the splice site sequence comprises a 5’ splice site sequence.
  • the splice site sequence comprises a 3’ splice site sequence.
  • Exemplary gene sequences and splice site sequences include AAAgcaaguu (SEQ ID NO: 1), AAAguaaaa (SEQ ID NO: 2), AAAguaaaau (SEQ ID NO: 3), AAAguaaagu (SEQ ID NO: 4), AAAguaaaua (SEQ ID NO: 5), AAAguaaaug (SEQ ID NO: 6), AAAguaaauu (SEQ ID NO: 7), AAAguaacac (SEQ ID NO: 8), AAAguaacca (SEQ ID NO: 9), AAAguaacuu (SEQ ID NO: 10), AAAguaagaa (SEQ ID NO: 11), AAAguaagac (SEQ ID NO: 12), AAAguaagag (SEQ ID NO: 13), AAAguaagau (SEQ ID NO: 14), AAAguaagca (SEQ ID NO: 15), AAAguaagcc (SEQ ID NO: 16), AAAguaaguu (SEQ ID NO: 1), AAAguaaaa
  • Additional exemplary gene sequences and splice site sequences include AAGgcaagau (SEQ ID NO: 96), AUGguaugug (SEQ ID NO: 937), GGGgugaggc (SEQ ID NO: 2281), CAGguaggug (SEQ ID NO: 1222), AAGgucagua (SEQ ID NO: 293), AAGguuagag (SEQ ID NO: 3055), AUGgcacuua (SEQ ID NO: 3056), UAAguaaguc (SEQ ID NO: 2423), UGGgugagcu (SEQ ID NO: 3057), CGAgcugggc (SEQ ID NO: 3058), AAAgcacccc (SEQ ID NO: 3059), UAGguggggg (SEQ ID NO: 3060), AGAguaacgu (SEQ ID NO: 3061), UCGgugaugu (SEQ ID NO: 3062), AAUgucaguu (SEQ ID NO: 96), AUGguaugug (SEQ ID
  • Additional exemplary gene sequences and splice site sequences include UCCguaaguu (SEQ ID NO: 4551), GUGguaaacg (SEQ ID NO: 4552), CGGgugcggu (SEQ ID NO: 4553), CAUguacuuc (SEQ ID NO: 4554), AGAguaaagg (SEQ ID NO: 4555), CGCgugagua (SEQ ID NO: 4556), AGAgugggca (SEQ ID NO: 4557), AGAguaagcc (SEQ ID NO: 4558), AGAguaaaca (SEQ ID NO: 4559), GUGguuauga (SEQ ID NO: 4560), AGGguaauaa (SEQ ID NO: 4561), UGAguaagac (SEQ ID NO: 4562), AGAguuuguu (SEQ ID NO: 4563), CGGgucugca (SEQ ID NO: 4564), CAGgu
  • the splice site sequence (e.g., 5’ splice site sequence) comprises AGA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AAA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AAC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AAU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AAG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises ACA.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises AUA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AUU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AUG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AUC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CAA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CAU.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises CAC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CAG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GAA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GAC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GAU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GAG.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises GGA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GCA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GGG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GGC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GUU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GGU.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises GUC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GUA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GUG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UCU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UCC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UCA.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises UCG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UUU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UUC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UUA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UUG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UGU.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises UAU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises GGA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CUU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CUC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CUA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CUG.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises CCU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CCC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CCA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CCG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises ACU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises ACC.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises ACG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AGC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AGU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises AGG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CGU. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UAC.
  • the splice site sequence (e.g., 5’ splice site sequence) comprises UAA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises UAG. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CGC. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CGA. In some embodiments, the splice site sequence (e.g., 5’ splice site sequence) comprises CGG. In some embodiments, the splice site sequence comprises AGAguaaggg (SEQ ID NO: 667).
  • the splice site sequence comprises UGAguaagca (SEQ ID NO: 2768).
  • a gene sequence or splice site sequence provided herein is related to a proliferative disease, disorder, or condition (e.g., cancer, benign neoplasm, or inflammatory disease).
  • a gene sequence or splice site sequence provided herein is related to a non-proliferative disease, disorder, or condition.
  • a gene sequence or splice site sequence provided herein is related to a neurological disease or disorder; autoimmune disease or disorder; immunodeficiency disease or disorder; lysosomal storage disease or disorder; cardiovascular condition, disease or disorder; metabolic disease or disorder; respiratory condition, disease, or disorder; renal disease or disorder; or infectious disease in a subject.
  • a gene sequence or splice site sequence provided herein is related to a neurological disease or disorder (e.g., Huntington’s disease).
  • a gene sequence or splice site sequence provided herein is related to an immunodeficiency disease or disorder.
  • a gene sequence or splice site sequence provided herein is related to a lysosomal storage disease or disorder.
  • a gene sequence or splice site sequence provided herein is related to a cardiovascular condition, disease or disorder. In an embodiment, a gene sequence or splice site sequence provided herein is related to a metabolic disease or disorder. In an embodiment, a gene sequence or splice site sequence provided herein is related to a respiratory condition, disease, or disorder. In an embodiment, a gene sequence or splice site sequence provided herein is related to a renal disease or disorder. In an embodiment, a gene sequence or splice site sequence provided herein is related to an infectious disease. In an embodiment, a gene sequence or splice site sequence provided herein is related to a mental retardation disorder.
  • a gene sequence or splice site sequence provided herein is related to a mutation in the SETD5 gene. In an embodiment, a gene sequence or splice site sequence provided herein is related to an immunodeficiency disorder. In an embodiment, a gene sequence and splice site sequence provided herein is related to a mutation in the GATA2 gene. In an embodiment, a gene sequence or splice site sequence provided herein is related to a lysosomal storage disease.
  • a compound of Formula (I) described herein interacts with (e.g., binds to) a splicing complex component (e.g., a nucleic acid (e.g., an RNA) or a protein).
  • the splicing complex component is selected from 9G8, Al hnRNP, A2 hnRNP, ASD-1, ASD-2b, ASF, BRR2, B1 hnRNP, C1 hnRNP, C2 hnRNP, CBP20, CBP80, CELF, F hnRNP, FBP11, Fox-1, Fox-2, G hnRNP, H hnRNP, hnRNP 1, hnRNP 3, hnRNP C, hnRNP G, hnRNP K, hnRNP M, hnRNP U, Hu, HUR, I hnRNP, K hnRNP, KH-type splicing regulatory protein (KSRP), L hnRNP, LUC7L, M hnRNP, mBBP, muscle-blind like (MBNL), NF45, NFAR, Nova-1, Nova-2, nPTB, P54/SFRS11, polypyr
  • the splicing complex component comprises RNA (e.g., snRNA).
  • a compound described herein binds to a splicing complex component comprising snRNA.
  • the snRNA may be selected from, e.g., U1 snRNA, U2 snRNA, U4 snRNA, U5 snRNA, U6 snRNA, U11 snRNA, U12 snRNA, U4atac snRNA, and any combination thereof.
  • the splicing complex component comprises a protein, e.g., a protein associated with an snRNA.
  • the protein comprises SC35, SRp55, SRp40, SRm300, SFRS10, TASR-1, TASR-2, SF2/ASF, 9G8, SRp75, SRp30c, SRp20 and P54/SFRS11.
  • the splicing complex component comprises a U2 snRNA auxiliary factor (e.g., U2AF65, U2AF35), Urp/U2AF1-RS2, SF1/BBP, CBP80, CBP 20, SF1 or PTB/hnRNP1.
  • the hnRNP protein comprises A1, A2/B1, L, M, K, U, F, H, G, R, I or C1/C2.
  • Human genes encoding hnRNPs include HNRNPA0, HNRNPA1, HNRNPA1L1, HNRNPA1L2, HNRNPA3, HNRNPA2B1, HNRNPAB, HNRNPB1, HNRNPC, HNRNPCL1, HNRNPD, HNRPDL, HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, HNRNPK, HNRNPL, HNRPLL, HNRNPM, HNRNPR, HNRNPU, HNRNPUL1, HNRNPUL2, HNRNPUL3, and FMR1.
  • the compounds of Formula (I) and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers, and compositions thereof may modulate (e.g., increase or decrease) a splicing event of a target nucleic acid sequence (e.g., DNA, RNA, or a pre-mRNA), for example, a nucleic acid encoding a gene described herein, or a nucleic acid encoding a protein described herein, or a nucleic acid comprising a splice site described herein.
  • the splicing event is an alternative splicing event.
  • the compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer, and compositions thereof increases splicing at splice site on a target nucleic acid (e.g., an RNA, e.g., a pre-mRNA), by about 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more, e.g., as determined by a known method in the art, e.g., qPCR.
  • a target nucleic acid e.g., an RNA, e.g., a pre-mRNA
  • the compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer, and compositions thereof decreases splicing at splice site on a target nucleic acid (e.g., an RNA, e.g., a pre-mRNA), by about 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more, e.g., as determined by a known method in the art, e.g., qPCR.
  • a target nucleic acid e.g., an RNA, e.g., a pre-mRNA
  • the present disclosure features a method of forming a complex comprising a component of a spliceosome (e.g., a major spliceosome component or a minor spliceosome component), a nucleic acid (e.g., a DNA, RNA, e.g., a pre-mRNA), and a compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer, or composition thereof, comprising contacting the nucleic acid (e.g., a DNA, RNA, e.g., a pre-mRNA) with said compound of Formula (I).
  • a spliceosome e.g., a major spliceosome component or a minor spliceosome component
  • a nucleic acid e.g., a DNA, RNA, e.g., a pre-mRNA
  • the component of a spliceosome is selected from the U1, U2, U4, U5, U6, U11, U12, U4atac, U6atac small nuclear ribonucleoproteins (snRNPs), or a related accessory factor.
  • the component of a spliceosome is recruited to the nucleic acid in the presence of the compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer, or composition thereof.
  • the present disclosure features a method of altering the conformation of a nucleic acid (e.g., a DNA, RNA, e.g., a pre-mRNA) comprising contacting the nucleic acid with a compound of Formula (I) or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer, or composition thereof.
  • the altering comprises forming a bulge or kink in the nucleic acid.
  • the altering comprises stabilizing a bulge or a kink in the nucleic acid.
  • the altering comprises reducing a bulge or a kink in the nucleic acid.
  • the nucleic acid comprises a splice site.
  • the compound of Formula (I) interacts with a nucleobase, ribose, or phosphate moiety of a nucleic acid (e.g., a DNA, RNA, e.g., pre-mRNA).
  • a nucleic acid e.g., a DNA, RNA, e.g., pre-mRNA.
  • the present disclosure also provides methods for the treatment or prevention of a disease, disorder, or condition.
  • the disease, disorder or condition is related to (e.g., caused by) a splicing event, such as an unwanted, aberrant, or alternative splicing event.
  • the disease, disorder or condition comprises a proliferative disease (e.g., cancer, benign neoplasm, or inflammatory disease) or non-proliferative disease.
  • the disease, disorder, or condition comprises a neurological disease, autoimmune disorder, immunodeficiency disorder, cardiovascular condition, metabolic disorder, lysosomal storage disease, respiratory condition, renal disease, or infectious disease in a subject.
  • the disease, disorder, or condition comprises a haploinsufficiency disease, an autosomal recessive disease (e.g., with residual function), or a paralogue activation disorder.
  • the disease, disorder, or condition comprises an autosomal dominant disorder (e.g., with residual function).
  • Such methods comprise the step of administering to the subject in need thereof an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt, solvate, hydrate, tautomer, stereoisomer thereof, or a pharmaceutical composition thereof.
  • the methods described herein include administering to a subject an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof.
  • the subject being treated is a mammal.
  • the subject is a human.
  • the subject is a domesticated animal, such as a dog, cat, cow, pig, horse, sheep, or goat.
  • the subject is a companion animal such as a dog or cat.
  • the subject is a livestock animal such as a cow, pig, horse, sheep, or goat. In certain embodiments, the subject is a zoo animal. In another embodiment, the subject is a research animal such as a rodent, dog, or non-human primate. In certain embodiments, the subject is a non-human transgenic animal such as a transgenic mouse or transgenic pig.
  • a proliferative disease may also be associated with inhibition of apoptosis of a cell in a biological sample or subject. All types of biological samples described herein or known in the art are contemplated as being within the scope of the disclosure.
  • the compounds of Formula (I) and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers, and compositions thereof may induce apoptosis, and therefore, be useful in treating and/or preventing proliferative diseases.
  • the proliferative disease to be treated or prevented using the compounds of Formula (I) is cancer.
  • cancer refers to a malignant neoplasm (Stedman’s Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990). All types of cancers disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • Exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocar
  • Wilms tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.
  • HCC hepatocellular cancer
  • lung cancer e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung
  • myelofibrosis MF
  • chronic idiopathic myelofibrosis chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)
  • neuroblastoma e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis
  • neuroendocrine cancer e.g., gastroenteropancreatic neuroendocrine tumor (GEP-NET), carcinoid tumor
  • osteosarcoma e.g., bone cancer
  • ovarian cancer e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma
  • papillary adenocarcinoma pancreatic cancer
  • pancreatic cancer e.g., pancreatic adenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors
  • the cancer is selected from adenoid cystic carcinoma (ACC), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), non-Hodgkin lymphoma (NHL), Burkitt lymphoma, colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma), prostate cancer (e.g., prostate adenocarcinoma), ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma), and myelodysplastic syndrome (MDS).
  • AML acute myelocytic leukemia
  • CML chronic myelocytic leukemia
  • NHL non-Hodgkin lymphoma
  • Burkitt lymphoma e.g.,
  • the proliferative disease is associated with a benign neoplasm.
  • a benign neoplasm may include adenoma, fibroma, hemangioma, tuberous sclerosis, and lipoma. All types of benign neoplasms disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the proliferative disease is associated with angiogenesis. All types of angiogenesis disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a non-proliferative disease.
  • non-proliferative diseases include a neurological disease, autoimmune disorder, immunodeficiency disorder, lysosomal storage disease, cardiovascular condition, metabolic disorder, respiratory condition, inflammatory disease, renal disease, or infectious disease.
  • the non-proliferative disease is a neurological disease.
  • the compound of Formula (I), or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a neurological disease, disorder, or condition.
  • a neurological disease, disorder, or condition may include a neurodegenerative disease, a psychiatric condition, or a musculoskeletal disease.
  • a neurological disease may further include a repeat expansion disease, e.g., which may be characterized by the expansion of a nucleic acid sequence in the genome.
  • a repeat expansion disease includes myotonic dystrophy, amyotrophic lateral sclerosis, Huntington’s disease, a trinucleotide repeat disease, or a polyglutamine disorder (e.g., ataxia, fragile X syndrome).
  • the neurological disease comprises a repeat expansion disease, e.g., Huntington’s disease.
  • Additional neurological diseases, disorders, and conditions include Alzheimer’s disease, Huntington’s chorea, a prion disease (e.g., Creutzfeld- Jacob disease, bovine spongiform encephalopathy, Kuru, or scrapie), a mental retardation disorder (e.g., a disorder caused by a SETD5 gene mutation, e.g., intellectual disability-facial dysmorphism syndrome, autism spectrum disorder), Lewy Body disease, diffuse Lewy body disease (DLBD), dementia, progressive supranuclear palsy (PSP), progressive bulbar palsy (PBP), psuedobulbar palsy, spinal and bulbar muscular atrophy (SBMA), primary lateral sclerosis, Pick’s disease, primary progressive aphasia, corticobasal dementia, Parkinson’s disease, Down’s syndrome, multiple system atrophy, spinal muscular atrophy (SMA), progressive spinobulbar muscular atrophy (e.g., Kennedy disease), post-polio syndrome (PPS), spinocere
  • the neurological disease comprises Friedrich’s ataxia or Sturge Weber syndrome. In some embodiments, the neurological disease comprises Huntington’s disease. In some embodiments, the neurological disease comprises spinal muscular atrophy. All types of neurological diseases disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the non-proliferative disease is an autoimmune disorder or an immunodeficiency disorder.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat an autoimmune disease, disorder, or condition, or an immunodeficiency disease, disorder, or condition.
  • autoimmune and immunodeficiency diseases, disorders, and conditions include arthritis (e.g., rheumatoid arthritis, osteoarthritis, gout), Chagas disease, chronic obstructive pulmonary disease (COPD), dermatomyositis, diabetes mellitus type 1, endometriosis, Goodpasture’s syndrome, Graves’ disease, Guillain-Barr ⁇ syndrome (GBS), Hashiomoto’s disease, Hidradenitis suppurativa, Kawasaki disease, ankylosing spondylitis, IgA nephropathy, idiopathic thrombocytopenic purpura, inflammatory bowel disease, Crohn’s disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischemic colitis, diversion colitis, Behcet’s syndrome, infective colitis, indeterminate colitisinterstitial cystitis, lupus (e.g., systemic lupus erythemato
  • the autoimmune or immunodeficiency disorder comprises chronic mucocutaneous candidiasis. All types of autoimmune disorders and immunodeficiency disorders disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the non-proliferative disease is a cardiovascular condition.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a cardiovascular disease, disorder, or condition.
  • a cardiovascular disease, disorder, or condition may include a condition relating to the heart or vascular system, such as the arteries, veins, or blood.
  • Exemplary cardiovascular diseases, disorders, or conditions include angina, arrhythmias (atrial or ventricular or both), heart failure, arteriosclerosis, atheroma, atherosclerosis, cardiac hypertrophy, cardiac or vascular aneurysm, cardiac myocyte dysfunction, carotid obstructive disease, endothelial damage after PTCA (percutaneous transluminal coronary angioplasty), hypertension including essential hypertension, pulmonary hypertension and secondary hypertension (renovascular hypertension, chronic glomerulonephritis), myocardial infarction, myocardial ischemia, peripheral obstructive arteriopathy of a limb, an organ, or a tissue; peripheral artery occlusive disease (PAOD), reperfusion injury following ischemia of the brain, heart or other organ or tissue, restenosis, stroke, thrombosis, transient ischemic attack (TIA), vascular occlusion, vasculitis, and vasoconstriction.
  • PTCA percutaneous transluminal
  • the non-proliferative disease is a metabolic disorder.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a metabolic disease, disorder, or condition.
  • a metabolic disease, disorder, or condition may include a disorder or condition that is characterized by abnormal metabolism, such as those disorders relating to the consumption of food and water, digestion, nutrient processing, and waste removal.
  • a metabolic disease, disorder, or condition may include an acid- base imbalance, a mitochondrial disease, a wasting syndrome, a malabsorption disorder, an iron metabolism disorder, a calcium metabolism disorder, a DNA repair deficiency disorder, a glucose metabolism disorder, hyperlactatemia, a disorder of the gut microbiota.
  • Exemplary metabolic conditions include obesity, diabetes (Type I or Type II), insulin resistance, glucose intolerance, lactose intolerance, eczema, hypertension, Hunter syndrome, Krabbe disease, sickle cell anemia, maple syrup urine disease, Pompe disease, and metachromatic leukodystrophy. All types of metabolic diseases, disorders, or conditions disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the non-proliferative disease is a respiratory condition.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a respiratory disease, disorder, or condition.
  • a respiratory disease, disorder, or condition can include a disorder or condition relating to any part of the respiratory system, such as the lungs, alveoli, trachea, bronchi, nasal passages, or nose.
  • Exemplary respiratory diseases, disorders, or conditions include asthma, allergies, bronchitis, allergic rhinitis, chronic obstructive pulmonary disease (COPD), lung cancer, oxygen toxicity, emphysema, chronic bronchitis, and acute respiratory distress syndrome.
  • COPD chronic obstructive pulmonary disease
  • the non-proliferative disease is a renal disease.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a renal disease, disorder, or condition.
  • a renal disease, disorder, or condition can include a disease, disorder, or condition relating to any part of the waste production, storage, and removal system, including the kidneys, ureter, bladder, urethra, adrenal gland, and pelvis.
  • Exemplary renal diseases include acute kidney failure, amyloidosis, Alport syndrome, adenovirus nephritis, acute lobar nephronia, tubular necrosis, glomerulonephritis, kidney stones, urinary tract infections, chronic kidney disease, polycystic kidney disease, and focal segmental glomerulosclerosis (FSGS).
  • the renal disease, disorder, or condition comprises HIV-associated nephropathy or hypertensive nephropathy. All types of renal diseases, disorders, or conditions disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the non-proliferative disease is an infectious disease.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat an infectious disease, disorder, or condition.
  • An infectious disease may be caused by a pathogen such as a virus or bacteria.
  • infectious diseases include human immunodeficiency syndrome (HIV), acquired immunodeficiency syndrome (AIDS), meningitis, African sleeping sickness, actinomycosis, pneumonia, botulism, chlamydia, Chagas disease, Colorado tick fever, cholera, typhus, giardiasis, food poisoning, ebola hemorrhagic fever, diphtheria, Dengue fever, gonorrhea, streptococcal infection (e.g., Group A or Group B), hepatitis A, hepatitis B, hepatitis C, herpes simplex, hookworm infection, influenza, Epstein-Barr infection, Kawasaki disease, kuru, leprosy, leishmaniasis, measles, mumps, norovirus, meningococcal disease, malaria, Lyme disease, listeriosis, rabies, rhinovirus, rubella, tetanus, shingles, scarlet fever, scabies, Zika
  • the infectious disease comprises cytomegalovirus. All types of infectious diseases, disorders, or conditions disclosed herein or known in the art are contemplated as being within the scope of the disclosure.
  • the disease, disorder, or condition is a haploinsufficiency disease.
  • the compound of Formula (I) or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a haploinsufficiency disease, disorder, or condition.
  • a haploinsufficiency disease, disorder, or condition may refer to a monogenic disease in which an allele of a gene has a loss-of-function lesion, e.g., a total loss of function lesion.
  • the loss-of-function lesion is present in an autosomal dominant inheritance pattern or is derived from a sporadic event.
  • the reduction of gene product function due to the altered allele drives the disease phenotype despite the remaining functional allele (i.e. said disease is haploinsufficient with regard to the gene in question).
  • a compound of Formula (I) increases expression of the haploinsufficient gene locus.
  • a compound of Formula (I) increases one or both alleles at the haploinsufficient gene locus.
  • haploinsufficiency diseases, disorders, and conditions include Robinow syndrome, cardiomyopathy, cerebellar ataxia, pheochromocytoma, Charcot-Marie-Tooth disease, neuropathy, Takenouchi-Kosaki syndrome, Coffin-Siris syndrome 2, chromosome 1p35 deletion syndrome, spinocerebellar ataxia 47, deafness, seizures, dystonia 9, GLUT1 deficiency syndrome 1, GLUT1 deficiency syndrome 2, stomatin-deficient cryohydrocytosis, basal cell carcinoma, basal cell nevus syndrome, medulloblastoma, somatic, brain malformations, macular degeneration, cone-rod dystrophy, Dejerine-Sottas disease, hypomyelinating neuropathy, Roussy-Levy syndrome, glaucoma, autoimmune lymphoproliferative syndrome, pituitary hormone deficiency, epileptic encephalopathy, early infantile, popliteal pteryg
  • the disease, disorder, or condition is an autosomal recessive disease, e.g., with residual function.
  • the compound of Formula (I), or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat an autosomal recessive disease, disorder, or condition.
  • An autosomal recessive disease with residual function may refer to a monogenic disease with either homozygous recessive or compound heterozygous heritability. These diseases may also be characterized by insufficient gene product activity (e.g., a level of gene product greater than 0%).
  • a compound of Formula (I) may increase the expression of a target (e.g., a gene) related to an autosomal recessive disease with residual function.
  • a target e.g., a gene
  • autosomal recessive diseases with residual function include Friedreich’s ataxia, Stargardt disease, Usher syndrome, chlorioderma, fragile X syndrome, achromatopsia 3, Hurler syndrome, hemophilia B, alpha-1-antitrypsin deficiency, Gaucher disease, X-linked retinoschisis, Wiskott-Aldrich syndrome, mucopolysaccharidosis (Sanfilippo B), DDC deficiency, epidermolysis bullosa dystrophica, Fabry disease, metachromatic leukodystrophy, and odontochondrodysplasia.
  • the disease, disorder, or condition is an autosomal dominant disease.
  • the compound of Formula (I), or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat an autosomal dominant disease, disorder, or condition.
  • An autosomal dominant disease may refer to a monogenic disease in which the mutated gene is a dominant gene. These diseases may also be characterized by insufficient gene product activity (e.g., a level of gene product greater than 0%).
  • a compound of Formula (I) may increase the expression of a target (e.g., a gene) related to an autosomal dominant disease.
  • Exemplary autosomal dominant diseases include Huntington’s disease, achondroplasia, antithrombin III deficiency, Gilbert’s disease, Ehlers-Danlos syndrome, hereditary hemorrhagic telangiectasia, intestinal polyposis, hereditary elliptosis, hereditary spherocytosis, marble bone disease, Marfan’s syndrome, protein C deficiency, Treacher Collins syndrome, Von Willebrand’s disease, tuberous sclerosis, osteogenesis imperfecta, polycystic kidney disease, neurofibromatosis, and idiopathic hypoparathyroidism.
  • the disease, disorder, or condition is a paralogue activation disorder.
  • the compound of Formula (I), or a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof is used to prevent or treat a paralogue activation disease, disorder, or condition.
  • a paralogue activation disorder may comprise a homozygous mutation of genetic locus leading to loss-of-function for the gene product.
  • a compound of Formula (I) activates a gene connected with a paralogue activation disorder (e.g., a paralogue gene).
  • the cell described herein may be an abnormal cell.
  • the cell may be in vitro or in vivo.
  • the cell is a proliferative cell.
  • the cell is a cancer cell.
  • the cell is a non-proliferative cell.
  • the cell is a blood cell.
  • the cell is a lymphocyte.
  • the cell is a benign neoplastic cell.
  • the cell is an endothelial cell.
  • the cell is an immune cell.
  • the cell is a neuronal cell.
  • the cell is a glial cell.
  • the cell is a brain cell.
  • the cell is a fibroblast.
  • the cell is a primary cell, e.g., a cell isolated from a subject (e.g., a human subject).
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has improved cell permeability over a reference compound, e.g., in a standard assay for measuring cell permeability.
  • Cell permeability may be investigated, for example, using a standard assay run in either Madin-Darby Canine Kidney (MDCK) cells expressing Breast Cancer Resistance Protein (BCRP) or subclone MDCKII cells expressing Multidrug Resistance Protein 1 (MDR1); see, e.g., Drug Metabolism and Disposition 36, 268- 275 (2008) and Journal of Pharmaceutical Sciences 1072225-2235 (2016).
  • MDCK Madin-Darby Canine Kidney
  • BCRP Breast Cancer Resistance Protein
  • MDR1 Multidrug Resistance Protein 1
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell permeability measurement (Papp) of ⁇ 2 ⁇ 10 -6 cm s -1 .
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell permeability measurement (Papp) of between 2-6 ⁇ 10 -6 cm s -1 .
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell permeability measurement (Papp) of Papp greater than 6 ⁇ 10 -6 cm s -1 .
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell permeability greater than 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%.85%, 90%, 95%, 99% or more, e.g., compared with a reference compound.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein exhibits decreased cell efflux, e.g., over a reference compound, e.g., in a standard assay for measuring cell efflux.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell efflux ratio of less than 1.5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a cell efflux ratio of between 1.5 and 5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a cell efflux ratio greater than 5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a cell efflux ratio less than 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%.85%, 90%, 95%, 99% or more, e.g., compared with a reference compound.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof modulates the expression of a target protein (e.g., HTT or MYB) in a reference cell or sample.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof increases the expression of a target protein (e.g., HTT or MYB) in a reference cell or sample.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, decreases the expression of a target protein (e.g., HTT or MYB) in a reference cell or sample.
  • the effect of an exemplary compound of Formula (I) on protein abundance may be measured using a standard assay for measuring protein abundance, such as the HiBit-assay system (Promega).
  • a four-parameter logistical regression may be fit to the data and the response may be interpolated at the 50% value to determine a concentration for protein abundance at 50% (IC 50 ) an untreated control.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a protein abundance response less than 100 nM.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a protein abundance response between 100-1000 nM. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, has a protein abundance response greater than 1000 nM. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, has a protein abundance response greater than 10 uM.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof modulates the protein abundance of a target protein by about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%. 85%, 90%, 95%, 99% or more, e.g., compared with a reference compound.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof modulates the viability of a target cell in a subject or sample.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof increases the viability of a target cell in a subject or sample.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof decreases the viability of a target cell in a subject or sample.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof does not impact the viability of a cell (e.g., is non-toxic) in a subject or sample.
  • the effect an exemplary compound of Formula (I) on cell viability may be measured using a standard assay for measuring cell toxicity, such as the Cell Titer Glo 2.0 assay in either K562 (human chronic myelogenous leukemia) or SH- SY5Y (human neuroblastoma) cells.
  • the concentration at which cell viability is measured may be based on the particular assay used.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, is tolerated by a target cell at a concentration of less than 100 nM.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein is tolerated by a target cell at a concentration of between 100-1000 nM. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, is tolerated by a target cell at a concentration of greater than 1000 nM. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, is tolerated by a target cell at a concentration of greater than 10 uM.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has improved brain permeability over a reference compound, e.g., in a standard assay for measuring brain permeability.
  • Brain permeability may be measured, for example, by determining the unbound partition coefficient (Kpuu), brain.
  • the unbound brain partition coefficient (K p,uu,brain ) may be defined as the ratio of unbound brain- free compound concentration to unbound plasma concentration.
  • the f u,brain and f u,plasma may be the unbound fraction of the compound in brain and plasma, respectively.
  • Both fu,brain and fu,plasma may be determined in vitro via equilibrium dialysis.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a Kp value of greater than 5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a Kp value between 1 and 5. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, has a Kp value between 0.2-1. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, has a Kp value of less than 0.2. In an embodiment, a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein, has a Kpuu value of greater than 2.5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a Kpuu value between 0.5-2.5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a Kpuu value between 0.1-0.5.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a Kpuu value of less than 0.1.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a brain permeability greater than 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%.85%, 90%, 95%, 99% or more, e.g., compared with a reference compound.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof exhibits selectivity for one target nucleic acid sequence, e.g., pre-mRNA transcript sequence or bulge, compared to another target nucleic acid sequence, e.g., pre-mRNA transcript sequence or bulge.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof exhibits selectivity for HTT, e.g., an HTT-related nucleic acid sequence.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein exhibits selectivity for SMN2, e.g., an SMN2-related nucleic acid sequence.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein exhibits selectivity for Target C, e.g., a Target C-related nucleic acid sequence.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein exhibits selectivity for MYB, e.g., a MYB-related nucleic acid sequence.
  • Selectivity for one target nucleic acid sequence over another may be measured using any number of methods known in the art.
  • selectivity may be measured by determining the ratio of derived qPCR values (e.g., as described herein) for one target nucleic acid sequence over another.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for one target nucleic acid sequence over another.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for HTT over another target nucleic acid sequence.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for SMN2 over another.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for MYB over another target nucleic acid sequence.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for Target C sequence over another.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for HTT over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for MYB over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for HTT over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for SMN2 over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for SMN2 over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a ratio of greater than 1.1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, or 100 selectivity for MYB over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for HTT over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for MYB over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 10-fold greater selectivity for HTT over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof, e.g., as described herein has a 10-fold greater selectivity for MYB over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for HTT over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for SMN2 over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 10-fold greater selectivity for HTT over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 10-fold greater selectivity for SMN2 over HTT.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for MYB over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a 3-fold greater selectivity for SMN2 over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a 10-fold greater selectivity for MYB over SMN2.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof e.g., as described herein, has a 10-fold greater selectivity for SMN2 over MYB.
  • a compound of Formula (I) or a pharmaceutically acceptable salt thereof has a selectivity for one target nucleic acid sequence that is greater than 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%.85%, 90%, 95%, 99% or more, e.g., compared with a second nucleic acid sequence.
  • the methods described herein comprise the additional step of administering one or more additional pharmaceutical agents in combination with the compound of Formula (I), a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof.
  • Such additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-diabetic agents, anti-inflammatory agents, immunosuppressant agents, and a pain-relieving agent.
  • the additional pharmaceutical agent(s) may synergistically augment the modulation of splicing induced by the inventive compounds or compositions of this disclosure in the biological sample or subject.
  • the combination of the inventive compounds or compositions and the additional pharmaceutical agent(s) may be useful in treating, for example, a cancer or other disease, disorder, or condition resistant to a treatment using the additional pharmaceutical agent(s) without the inventive compounds or compositions.
  • General Synthetic Scheme Compounds of the present disclosure may be prepared using a synthetic protocol illustrated in the exemplary scheme shown below. Scheme A.
  • An exemplary method of preparing a compound described herein, e.g., a compound of Formula (I-I) is provided in Scheme A.
  • B-3 is prepared by incubating B-1 with B-2 in the presence of a base (e.g., Cs2CO3, DIEA, N-methylimidazole, or a suitable alternative). The reaction may be conducted in dimethylformamide or a similar solvent, at a temperature sufficient to provide B-3.
  • B-3 and B-4 are coupled to provide a compound of Formula (I-I) in Step 2.
  • This coupling reaction may be conducted in the presence of a catalyst, such as a ruthenium, palladium, or copper catalyst (e.g., Pd-PEPPSI-IPentCl 2-methylpyridine, Pd(dppf)Cl2, Pd2(dba)3, XPhos- Pd(II)-G2, XPhos-Pd(II)-G3, t BuBrettphos-Pd(II)-G3, RuPhos-Pd(II), RuPhos-Pd(II)-G2, RuPhos-Pd(II)-G3, or CuI, or similar reagent), and a base (e.g., Cs 2 CO 3 , K 2 CO 3 , t BuONa, or a similar reagent).
  • a catalyst such as a ruthenium, palladium, or copper catalyst
  • reaction may be conducted in dimethylformamide or a similar solvent, at 100 °C or a temperature sufficient to provide the compound of Formula (I-I).
  • Each starting material and/or intermediate in Scheme A may be protected and deprotected using standard protecting group methods.
  • purification and characterization of each intermediate as well as the final compound of Formula (I) may be afforded by any accepted procedure.
  • reactions can be purified or analyzed according to any suitable method known in the art.
  • product formation can be monitored by spectroscopic means, such as nuclear magnetic resonance (NMR) spectroscopy (e.g., 1 H or 13 C), infrared (IR) spectroscopy, spectrophotometry (e.g., UV-visible), mass spectrometry (MS), or by chromatographic methods such as high performance liquid chromatography (HPLC) or thin layer chromatography (TLC).
  • NMR nuclear magnetic resonance
  • IR infrared
  • MS mass spectrometry
  • HPLC high performance liquid chromatography
  • TLC thin layer chromatography
  • Mobile phase A Water/5mM NH4HCO3, Mobile phase B: CH3CN.
  • Preparative HPLC purification was performed using one of the following HPLC conditions: Condition 1: Column: Xselect CSH OBD Column 30*150 mm 5um; Mobile Phase A: water (10mmol/L NH4HCO3); Mobile Phase B: acetonitrile; Flow rate:60 mL/min; Gradient 1: 5 B to 45 B in 6 min; Gradient 2: 5 B to 40 B in 8 min; Gradient 3: 10 B to 50 B in 10 min; Gradient 4: 3 B to 33 B in 8 min.
  • Condition 1 Column: Xselect CSH OBD Column 30*150 mm 5um; Mobile Phase A: water (10mmol/L NH4HCO3); Mobile Phase B: acetonitrile; Flow rate:60 mL/min; Gradient 1: 5 B to 45 B in 6 min; Gradient 2: 5 B to 40 B in 8 min; Gradient 3: 10 B to 50 B in 10 min; Gradient 4: 3 B to 33 B in 8 min.
  • Condition 2 Column: X-Bridge Prep OBD C18, 30-150mm 5um; Mobile phase A: water (10 mmol/L NH 4 HCO 3 ); Mobile phase B: acetonitrile; Gradient 1: 5% Phase B up to 55% in 8 min; Gradient 2: 10% B to 43% B in 8 min; Gradient 3: 10% B to 50% B in 8 min; Gradient 4: 20% B to 52% B in 8 min; Gradient 5: 5% B to 45% B in 8 min; Gradient 6: 10% B to 30% B in 10 min; Gradient 7: 30% B to 70% B in 8 min.
  • Condition 3 Column: Waters Xbridge BEH C18250 * 50 mm * 10 um; Mobile Phase A: Water (NH4HCO3) Mobile Phase B: Acetonitrile; Gradient 1: 70% B-90% B in 10 min; Gradient 2: 50% B to 70% B in 8 min.
  • Condition 1 Column: IG 2 cm x 25cm; Mobile Phase A: methyl tert-butyl ether; Mobile Phase B: ethanol; Gradient 1:1; Flow rate: 18 mL/min.
  • Condition 2 Gilson 281 semi-preparative: Column: Phenomenex Luna 80 x 30mm x 3 ⁇ m; Mobile Phase A: Water (4.8 mmol/L HCl), Mobile Phase B: Acetonitrile; Gradient 1:1% B to 30% B in 8 min.
  • Condition 3 Column, Kinetex EVO C18 Column, 30 x 150, 5um; Mobile Phase A: Water(10 mmol/L NH 4 HCO 3 ), Mobile Phase B: Acetonitrile; Gradient 1: 20% B to 55% B in 8 min.
  • Example 1 Synthesis of Compound 100 Synthesis of Intermediate B3 To a stirred solution of 5-bromo-7-fluoro-2H-indazole (B1, 500 mg, 2.32 mmol, 1 equiv) and tert-butyl 4-(methanesulfonyloxy) piperidine-1-carboxylate (B2, 974.36 mg, 3.48 mmol, 1.5 equiv) in DMF (10 mL) was added K2CO3 (964.11 mg, 6.97 mmol, 3 equiv) dropwise at room temperature under nitrogen atmosphere. The resulting mixture was stirred overnight at 100 °C, and the reaction was quenched with water at room temperature.
  • Example 2 Synthesis of Compound 103 Synthesis of Intermediate B7 To a solution of 5-bromo-3-fluoro-benzene-1,2-diamine (B6, 5 g, 24.39 mmol, 1 equiv) in H2O (50 mL) was added a solution of NaNO 2 (1.85 g, 26.83 mmol, 1.1 equiv) in H 2 O (50 mL) at 15°C. The mixture was stirred at 15 °C for 15 min. Then AcOH (18.90 g, 314.73 mmol, 18 mL, 12.91 equiv) was added dropwise at 15 °C. The resulting mixture was stirred at 85 °C for 1 hr.
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was quenched with water (10 mL), and extracted with ethyl acetate (3 ⁇ 10 mL).
  • the organic layer was dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (10/1 to 1/0) to give tert-butyl 4-(5-(2,8-dimethylimidazo [1,2-b]pyridazin-6-yl)-7-fluoro-2H- indazol-2-yl) piperidine-1-carboxylate (B21, 150 mg, 70%) as an oil.
  • the reaction mixture was stirred at 80 °C for 1 hr under N2 protection.
  • the reaction mixture was diluted with water (10 mL) and extracted with ethyl acetate (3 ⁇ 10 mL). The organic layer was dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give an oil.
  • Example 6 Synthesis of Compound 129 Synthesis of Intermediate B25 To a mixture of tert-butyl 4-(7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan- 2-yl)-2H- indazol-2-yl)piperidine-1-carboxylate (B19, 250 mg, 561.38 umol, 1.5 equiv) and 6-bromo-8- fluoro-2-methylimidazo[1,2-a]pyridine (B24, 85.72 mg, 374.25 umol, 1 equiv) in dioxane (2 mL) and H2O (0.5 mL) was added K2CO3 (103.45 mg, 748.50 umol, 2 equiv) and [1,1’- Bis(diphenylphosphino)ferrocene]-dichloropalladium (II) (54.77 mg, 74.85 umol, 0.2 equiv) successively.
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with water (10 mL) and extracted with ethyl acetate (3 ⁇ 10 mL).
  • the organic layer was dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (5/1 to 0/1) to give tert-butyl 4-(7-fluoro-5-(8-fluoro-2-methylimidazo[1,2-a]pyridin-6-yl)-2H-indazol-2- yl)piperidine-1-carboxylate (B25, 110 mg, 49%) as an oil.
  • Example 7 Synthesis of Compound 128 Synthesis of Intermediate B27 To a mixture of tert-butyl 4-(7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)- 2H- indazol-2-yl)piperidine-1-carboxylate (B19, 300 mg, 673.65 umol, 1.5 equiv) and 5-chloro-2- methyl-2H-pyrazolo[4,3-b]pyridine (B26, 75.27 mg, 449.10 umol, 1 equiv) in dioxane (2.4 mL) and H 2 O (0.6 mL) was added K 2 CO 3 (124.14 mg, 898.2 umol, 2 equiv) and [1,1’- Bis(diphenylphosphino)ferrocene]-dichloropalladium (II) (65.72 mg, 89.82 umol, 0.2 equiv
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with water (10 mL) and extracted with ethyl acetate (3 ⁇ 10 mL).
  • the organic layer was dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (5/1 to 0/1) to give tert-butyl 4-(7-fluoro-5-(2-methyl-2H-pyrazolo [4,3-b]pyridin-5-yl)-2H-indazol-2-yl) piperidine-1-carboxylate (B27, 140 mg, 64%) as an oil.
  • Example 8 Synthesis of Compound 171 Synthesis of Intermediate B29 To a mixture of 6-(7-fluoro-2H-indazol-5-yl)-2,8-dimethyl-imidazo[1,2-b]pyridazine (400 mg, 1.42 mmol, 1.0 eq), tert-butyl 7-(p-tolylsulfonyloxy)-4-azaspiro[2.5] octane -4-carboxylate (596 mg, 1.56 mmol, 1.10 eq) in dimethyl formamide (10.0 mL) was added cesium carbonate (1.39 g, 4.27 mmol, 3.0 eq). The reaction was stirred at 80 °C for 12 hrs under nitrogen.
  • reaction mixture was diluted with water (50.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL), washed with brine (100 mL), dried over Na 2 SO 4 , filtered and the filtrate was concentrated under reduced pressure to give a residue.
  • the residue was purified by prep-HPLC (Condition 3, Gradient 1) to afford tert-butyl7-[5-(2,8-dimethylimidazo[1,2-b]pyridazin-6-yl)-7-fluoro-indazol-2-yl]-4- azaspiro [2.5] oct ane-4-carboxylate (0.150 g, 22%) as a solid.
  • reaction mixture was diluted with water (3.00 mL), extracted with ethyl acetate (3 ⁇ 3.00 mL), washed with brine (3.00 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give a residue.
  • the residue was purified by prep-HPLC (Condition 4, Gradient 2) to afford 6-[2-[4-(cyclopropylmethyl)-4-azaspiro[2.5]octan-7-yl]-7-fluoro-indazol-5-yl]-2,8- dimethyl-imidazo[1,2-b]pyridazine (5.32 mg, 5% ) as a solid.
  • reaction mixture was then stirred at 80 °C for 12 hrs.
  • the reaction mixture was diluted with water (50.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL), washed with brine (30.0 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give residue.
  • the reaction was stirred at 80 °C for 2 hrs.
  • the reaction mixture was quenched with water (10.0 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), washed with brine (10.0 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give residue.
  • Example 18 Synthesis of Compound 104 To a solution of acetaldehyde (3.90 mg, 35.4 umol, 4.97 uL, 40% purity, 1.10 eq) in DCM (1.30 mL) was added dropwise TEA (3.26 mg, 32.1 umol, 4.48 uL, 1 eq) at 15°C over 5 min. The mixture was stirred at this temperature for 5min, and then 7-fluoro-5-(7-fluoro-2- methyl-indazol-5-yl)-2-(4-piperidyl)indazole (EVAL-0123-36, 13.0 mg, 32.1 umol, 1 eq, HCl) was added at 15°C.
  • EVAL-0123-36 7.0 mg, 32.1 umol, 1 eq, HCl
  • Example 19 Synthesis of Compound 105 Synthesis of Intermediate C3
  • the resulting mixture was stirred for 2 hrs at 80°C.
  • the reaction mixture was cooled to 20 °C and quenched with water (30.0 mL), the mixture was extracted with ethyl acetate (5 ⁇ 10.0 mL). The organic layer was dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure.
  • Example 25 Synthesis of Compound 115 Synthesis of Intermediate C32
  • tert-butyl 4-(7-fluoro-2H-indazol-5-yl)-3,6-dihydro-2H-pyridine-1- carboxylate (40.0 mg, 126 umol, 1 eq) in MeOH (4.00 mL) was added Pd/C (29.7 mg, 12.6 umol, 5% purity, 0.1 eq) under N 2 atmosphere.
  • the suspension was degassed and purged with H 2 for 3 times.
  • the mixture was stirred under H 2 (15 Psi) at 25°C for 12 hrs.
  • the reaction mixture was quenched by addition water (10.0 mL) at 25°C, and then extracted with ethyl acetate (3 ⁇ 15.0 mL). The combined organic layers were dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue.
  • the residue was purified by prep-HPLC (column: Phenomenex C1875*30mm*3um;mobile phase: [water( NH4HCO3)-CH3CN];B%: 40%- 70%,8min) to give tert-butyl 4-[2-(2,7-dimethylindazol-5-yl)-7-fluoro-indazol-5-yl]piperazine-1- carboxylate (10.0 mg, 9.83%) as a solid.
  • Example 27 Synthesis of Compound 119 Synthesis of Intermediate C43 A mixture of tert-butyl 4-(7-fluoro-2H-indazol-5-yl)piperazine-1-carboxylate (100 mg, 312 umol, 1.5 eq), 6-bromo-2,4-dimethyl-1,3-benzoxazole (47.0 mg, 208 umol, 1 eq), N,N'- bis(2-furylmethyl)oxamide (5.17 mg, 20.8 umol, 0.1 eq), Cu2O (2.98 mg, 20.8 umol, 2.13 uL, 0.1 eq), K 3 PO 4 (88.3 mg, 416 umol, 2 eq) in DMSO (2.00 mL) was degassed and purged with N 2 for 3 times, and then the mixture was stirred at 120°C for 8 hrs under N 2 atmosphere.
  • reaction mixture was quenched by addition water (10.0 mL) at 25 °C, and then diluted with ethyl acetate (10.0 mL) and extracted with ethyl acetate (3 ⁇ 15.0 mL). The combined organic layers were dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue.
  • the oil was purified by column chromatography on silica gel eluted with petrolum ether/ethyl acetate (1/0 to 5/1 ) to give tert-butyl 4-[7-fluoro-5-(5-methoxy-2,4-dimethyl-1,3-benzoxazol-6- yl)indazol-2-yl]piperidine-1-carboxylate (130 mg, 82.5%) as an oil.
  • the reaction mixture was filtered, the filter cake was purified by prep-HPLC (column: waters Xbridge Prep OBD C18 150 * 40 mm * 10 um; mobile phase: [water ( NH 4 HCO 3 )-acetonitrile]; B%: 35%-55%, 8 min) to give 6-[7-fluoro-2-(4-piperidyl)indazol-5-yl]- 2,4-dimethyl-1,3-benzoxazol-5-ol (EVAL-0122-0016, 25.3 mg, 55%) as a solid.
  • LCMS (ESI, m/z): 381.2 [M+H] +.
  • Example 31 Synthesis of Compound 125 Synthesis of Intermediate C56
  • a solution of 5-bromo-7-fluoro-2H-indazole (5.00 g, 23.2 mmol, 1.0 eq) in N,N- dimethylformamide (50.0 mL) was added tert-butyl 4-bromopiperidine-1-carboxylate (18.4 g, 69.7 mmol, 3.0 eq), KI (11.5 g, 69.7 mmol, 3.0 eq) and Cs2CO3 (37.8 g, 116 mmol, 5.0 eq).
  • the reaction mixture was stirred at 100 °C for 12 hrs.
  • the reaction mixture was diluted with H 2 O (100 mL), extracted with ethyl acetate (3 ⁇ 100 mL), washed with brine (2 ⁇ 100 mL), dried over Na2SO4 filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (50/1 to 5/1) to give yellow oil.
  • the yellow oil was purified by prep-HPLC (column: Xtimate C1810u 250 mm * 80mm; mobile phase: [water (NH 4 HCO 3 )-acetonitrile]; B%: 60%-95%, 25 min) to afford tert- butyl 4-(5-bromo-7-fluoro-indazol-2-yl) piperidine-1-carboxylate (3.00 g, 29%) as a solid.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (1/0 to 5/1 ) to give tert- butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)indazol-2-yl]piperidine-1-car- boxylate (3.00 g, 91.2%) as an oil.
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with H2O (10.0 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give brown solid.
  • the oil was triturated with dichloromethane (5.00 mL) and filtered.
  • the filter cake was dried over in vacuum to give tert-butyl 4-[7-fluoro-5-(6- hydroxy-2,7-dimethyl-indazol-5-yl)indazol-2-yl] piperidine-1-carboxylate (65.0 mg, 27.7%) as a solid.
  • the solid was purified by prep-HPLC (column: Phenomenex Luna 80 * 30 mm * 3 um; mobile phase: [water (HCl)-acetonitrile]; B%: 5%-30%, 8 min) to give 5-[7-fluoro-2-(4- piperidyl)indazol-5-yl]-2,7-dimethyl-indazol-6-ol (30.9 mg, 60.1%) as a solid.
  • Example 33 Synthesis of Compound 133 Synthesis of Intermediate C64 To a solution of 6-bromo-2,8-dimethyl-imidazo[1,2-a]pyrazine (60.9 mg, 269 umol, 1.00 eq) and tert-butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)indazol-2-yl]piperidine-1- carboxylate (BC, 180 mg, 404 umol, 1.50 eq) in dioxane (1.50 mL) was added a solution of K2CO3 (74.4 mg, 538 umol, 2.00 eq) in H2O (0.400 mL) and 1,1-bis (diphenylphosphino)ferrocene]dichloropalladium(II) (39.4 mg, 53.9 umol, 0.200 eq) successively under N 2 protection.
  • BC 180 mg, 404 u
  • the reaction mixture was stirred at 80 o C for 1 hr.
  • the reaction mixture was diluted with H 2 O (10.0 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), dried over Na2SO4 filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petrolum ether/ethyl acetate (1/0 to 5/1) to give tert-butyl 4-[5-(2,8-dimethylimidazo[1,2-a]pyrazin-6-yl)-7-fluoro-indazol-2- yl]piperidine-1-carboxylate (80.0 mg, 55%) as an oil.
  • Example 35 Synthesis of Compound 134 Synthesis of C69 To a mixture of tert-butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)indazol-2- yl]piperidine-1-carboxylate (200 mg, 449 umol, 1.50 eq) and 6-bromo-2-methyl-1,3-benzothiazole (68.3 mg, 299 umol, 1 eq) in dioxane (1.60 mL) was added a solution of K2CO3 (82.8 mg, 599 umol, 2.00 eq) in H 2 O (0.400 mL).
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Phenomenex C1875 * 30 mm * 3 um; mobile phase: [water ( NH 4 HCO 3 ) - acetonitrile]; B%: 20%-55%, 8 mins) to give 6-[7-fluoro-2-(4-piperidyl)indazol-5-yl]-2-methyl-1,3-benzoxazole (10.7 mg, 34.4%) as a solid.
  • LCMS (ESI, m/z): 351.2 [M+H] + .
  • Example 37 Synthesis of Compound 136 Synthesis of Intermediate C72 To a mixture of ert-butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)indazol-2-yl]piperidine-1-carboxylate (135 mg, 303 umol, 1.50 eq) and 6-bromo-4-fluoro-2- methyl-1,3-benzoxazole (46.5 mg, 202 umol, 1.00 eq) in dioxane (1.08 mL) was added a solution of K2CO3 (55.7 mg, 404 umol, 2.00 eq) in H2O (0.270 mL).
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Phenomenex C1875 * 30 mm * 3 um; mobile phase: [water (NH4HCO3)-acetonitrile]; B%: 15%-50%, 8 min) to afford 4-fluoro-6-[7-fluoro-2-(4-piperidyl)indazol-5-yl]-2-methyl-1,3- benzoxazole (15.4 mg, 43.5%) as a solid.
  • LCMS (ES, m/z): 369.2 [M+H] + .
  • Example 38 Synthesis of Compound 145 Synthesis of Intermediate C73
  • a mixture of tert-butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)indazol-2- yl]piperidine-1-carboxylate 150 mg, 337 umol, 1.50 eq
  • dioxane 2.80 mL
  • [1,1- bis(diphenylphosphino)ferrocene]dichloropalladium(II) (16.4 mg, 22.5 umol, 0.100 eq)
  • 5- bromo-2-methyl-indazole 47.4 mg, 225 umol, 1.00 eq
  • K2CO3 62.1mg, 449 umol, 2.00 eq
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with water (5.00 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), washed with brine (15.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give residue.
  • the residue was purified by column chromatography on a silica gel eluted with ethyl acetate/petroleum ether (0/1 to 1/1) to give tert-butyl 4-[7-fluoro-5-(2- methylindazol-5-yl)indazol-2-yl]piperidine-1-carboxy late (50.0 mg, 48%) as a solid.
  • reaction mixture was quenched with water (50.0 mL) and extracted with ethyl acetate (3 ⁇ 50.0 mL). The combined organic layer was dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give crude product which was purified by column chromatography on silica gel (SiO 2 , 30% of ethyl acetate in petroleum ether) to give tert-butyl 4- (5-(2,8-dimethylimidazo[1,2-b]pyridazin-6-yl)-6-methoxy-2H-indazol-2-yl)piperidine-1- carboxylate (600 mg, 52.3%) as a solid.
  • reaction mixture was filtered and the filter cake was washed with 10.0 mL of ethyl acetate, dried in vacuum to give 6-(7-fluoro-2H- indazol-5-yl)-2,8-dimethyl-imidazo[1,2-b]pyridazine (2.50 g, 69.8%) as a solid.
  • reaction mixture was filtered and the filter cake was washed with 10.0 mL of ethyl acetate, dried in vacuum to give tert-butyl 4-[7-fluoro-5-(2-methylquinazolin-6-yl)indazol-2-yl]piperidine-1-carboxylate (200 mg, 96.4%) as a solid.
  • Example 53 Synthesis of Compound 207 Synthesis of Intermediate C89 Into a 50 mL bottles were added 1-tert-butylpiperidin-4-ol (900 mg, 5.723 mmol, 1 equiv) and TEA (868.71 mg, 8.585 mmol, 1.5 equiv) in DCM (9 mL) at room temperature. To the above mixture was added MsCl (786.63 mg, 6.868 mmol, 1.2 equiv) dropwise over 1min at 0 °C. The resulting mixture was stirred for additional 1 h at room temperature. The reaction was quenched with water at room temperature. The reaction was quenched with NaHCO3 at room temperature.
  • 1-tert-butylpiperidin-4-ol 900 mg, 5.723 mmol, 1 equiv
  • TEA 868.71 mg, 8.585 mmol, 1.5 equiv
  • MsCl 786.63 mg, 6.868 mmol, 1.2
  • the crude product was purified by Chiral-Prep-HPLC with the following conditions: Column, Kinetex EVO C18 Column, 30 x 150, 5um; mobile phase, water(10 mmol/L NH 4 HCO 3 ) and ACN (20% ACN up to 55% in 8 min); Detector, UV 220 nm to afford 2-(1-tert- butylpiperidin-4-yl)-5- ⁇ 2,8-dimethylimidazo[1,2-b]pyridazin-6-yl ⁇ -7-fluoroindazole (26.0 mg, 24.09%) as a solid.
  • Example 54 Synthesis of Compound 143 Synthesis of Intermediate C92 To a mixture of tert-butyl 4-[7-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)indazol-2- yl]piperidine-1-carboxylate (0.30 g, 673 umol, 1.50 eq) and 5-chloro-2-methyl-pyrazolo [4,3- b]pyridine (75.2 mg, 449 umol, 1.00 eq) in dioxane (2.40 mL) was added a solution of K2CO3 (124 mg, 898 umol, 2.00 eq) in H 2 O (0.600 mL).
  • 1,1- bis(diphenylphosphino)ferrocene]dichloropalladium(II) (65.7 mg, 89.8 umol, 0.20 eq) was added to the above mixture under N2 protection.
  • the reaction mixture was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with H 2 O (20.0 mL), extracted with ethyl acetate (3 ⁇ 20.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Phenomenex Luna 80 * 30 mm * 3 um; mobile phase: [water (HCl)-acetonitrile]; B%: 1%-50%, 8 min ) to give 2,8-dimethyl-6-[2-(4-piperidyl) pyrazolo[4,3-b]pyridin-5-yl]imidazo[1,2- b]pyridazine (17.0 mg, 43.8%) as a solid.
  • LCMS (EIS, m/z): 348.1 [M+H] + .
  • Example 56 Synthesis of Compound 137
  • a suspension of tert-butyl 4-[5-(2,4-dimethyl-1,3-benzoxazol-6-yl)-7-fluoro-indazol-2- yl]piperi dine -1-carboxylate (115 mg, 247 umol, 1.00 eq) in HCl/dioxane (4.00 M, 4.60 mL, 74.3 eq) was stirred at 25 °C for 1 hr. The mixture was concentrated under reduced pressure to give white solid.
  • the solid was purified by prep-HPLC (column: Waters Xbridge BEH C18100 * 30 mm * 10 um; mobile phase: water (NH 4 HCO 3 )-ACN; B%: 25%-55%, 10 mins) to afford 6- [7-fluoro-2-(4-piperidyl)indazol-5-yl]-2,4-dimethyl-1,3-benzoxazole (20.0 mg, 22.1%) as a solid.
  • Example 57 Synthesis of Compound 130 Synthesis of Intermediate C95
  • 5-bromo-2H-indazole-7-carboxylic acid (2 g, 8.30 mmol, 1.00 eq) in ethyl acetate (40.0 mL) was added trimethyloxonium tetrafluoroborate (3.31 g, 22.4 mmol, 2.70 eq). The mixture was stirred at 25 °C for 12 hrs.
  • the reaction was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with water (10 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), washed with brine (3 ⁇ 10.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • Example 58 Synthesis of Compound 124 Synthesis of Intermediate C100 T o a solution of NaOH (58.7 g, 1.47 mol, 4.00 eq) in H 2 O (1.40 L) was added 1H- pyrazole (25.0 g, 367 mmol, 1.00 eq) at 0 °C. Then, Br 2 (176 g, 1.10 mol, 56.7 mL, 3.00 eq) was added to above mixture dropwise at 0 °C for 2 hrs. The reaction mixture was stirred at 25 °C for 1 hr. The reaction mixture was filtered and the filter cake was concentrated in vacuum to get solid. The solid was washed with H2O (1000 mL) and dried in vacuum to afford a solid.
  • H2O 1000 mL
  • the reaction mixture was stirred at 100 °C for 12 hrs.
  • the reaction mixture was diluted with water (100 mL).
  • the resulting mixture was extracted with ethyl acetate (2 ⁇ 100 mL).
  • the combined organic layers were washed with brine (2 ⁇ 200 mL), dried over anhydrous Na2SO4. After filtration, the filtrate was concentrated under reduced pressure to give residue.
  • the residue was diluted with tetrahydrofuran (24.0 mL) and 1 NH4Cl (65.8 mL).
  • the reaction mixture was stirred at 60 °C for 1 hr.
  • the reaction mixture was diluted with water (20.0 mL), extracted with ethyl acetate (3 ⁇ 20.0 mL), washed with brine (4 ⁇ 50.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by reversed-phase HPLC (column: C18 (250 * 50 mm * 10 um), mobile phase: [water (NH 4 HCO 3 )-acetonitrile]; B%: 40%-80%, 10 min) to yield 2,3-dibromo-4,6-dimethyl-pyrazolo [1,5-a]pyrazine (300 mg, 16.9%) as a solid.
  • the reaction mixture was stirred at 0°C for 0.5 hr.
  • the reaction mixture was quenched by additional of methanol (20.0 mL).
  • the reaction mixture was diluted with water (50.0 mL), extracted with ethyl acetate (3 ⁇ 40.0 mL), washed with brine (2 ⁇ 120 mL), dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (1/0 to 5/1) to give 2-bromo-4,6-dimethyl-pyrazolo[1,5-a]pyrazine (100 mg, 44.2%) as a solid.
  • reaction was stirred at 80 °C for 1 hr.
  • the reaction mixture was diluted with water (10.0 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give oil.
  • the oil was purified by column chromatography on silica gel eluted with ethyl acetate/ethanol (1/0 to 5/1) to give product tert- butyl 4-[5-(4,6-dimethylpyrazolo[1,5-a]pyrazin-2-yl)-7-fluoro-indazol-2-yl]piperidine-1- carboxylate (40.0 mg, 20.9%) as a solid.
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Phenomenex Luna 80 * 30 mm * 3 um; mobile phase: [water (HCl)- acetonitrile]; B%: 1%-45%, 8 min) to give 2-[7-fluoro-2-(4-piperidyl) indazol-5-yl]-4,6-dimethyl -pyrazolo[1,5- a]pyrazine (22.7 mg, 92.7%) as a solid.
  • LCMS (ESI, m/z): 365.1 [M+H] + .
  • Example 59 Synthesis of Compound 149 To a solution of 6-[7-fluoro-2-(4-piperidyl)indazol-5-yl]-2,8-dimethyl-imidazo[1,2- b]pyridazine (100 mg, 274 umol, 1 eq) in DCM (1.00 mL) was added AcOH (24.7 mg, 411 umol, 23.5 uL, 1.5 eq), cyclopropanecarbaldehyde (28.8 mg, 411 umol, 30.7 uL, 1.5 eq) and sodium;triacetoxyboranuide (116 mg, 548 umol, 2 eq) under N2 atmosphere.
  • the reaction mixture was stirred at 100 °C for 2 hrs.
  • the reaction mixture was diluted with water (80.0 mL), extracted with ethyl acetate (3 ⁇ 80.0 mL), washed with brine (4 ⁇ 200 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give oil.
  • the oil was purified by column chromatography on silica gel eluted with petroleum ether/ethyl acetate (1/0 to 5/1) to give tert-butyl 4-(7-bromo-5-chloro-pyrazolo[4,3-b]pyridin-2-yl)piperidine-1- carboxylate (1.51 g, 22.5%) as a solid.
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Phenomenex Luna 80 * 30 mm * 3 um; mobile phase: [water (HCl) - acetonitrile]; B%: 1% - 30%, 8 min) to give 5-[7-methoxy-2-(4-piperidyl)pyrazolo[4,3- b]pyridin-5-yl]-2-methyl-indazol-6-ol (14.0 mg, 37.5%) as a solid.
  • Example 61 Synthesis of Compound 150 To a solution of 6-[7-fluoro-2-(4-piperidyl)indazol-5-yl]-2,8-dimethyl-imidazo[1,2-b]pyridazine (100 mg, 274 umol, 1 eq) in MeOH (1.00 mL) was added formaldehyde (66.8 mg, 823 umol, 61.2 uL, 37 wt%, 3 eq), AcOH (49.4 mg, 823 umol, 47.0 uL, 3 eq) and sodium;triacetoxyboranuide (116 mg, 548 umol, 2 eq) under N2 atmosphere.
  • formaldehyde 66.8 mg, 823 umol, 61.2 uL, 37 wt%, 3 eq
  • AcOH 49.4 mg, 823 umol, 47.0 uL, 3 eq
  • sodium;triacetoxyboranuide 116 mg,
  • Example 63 Synthesis of Compound 152 To a solution of 6-[7-fluoro-2-(4-piperidyl) indazol-5-yl]-2,8-dimethyl-imidazo[1,2- b]pyridazine (100 mg, 274 umol, 1 eq) in MeCN (1.00 mL) was added K 2 CO 3 (113 mg, 823 umol, 3 eq) and 2-fluoroethyl 4-methylbenzenesulfonate (59.8 mg, 274 umol, 1 eq) under N2 atmosphere. The mixture was stirred at 100°C for 2 hrs.
  • Example 64 Synthesis of Compound 153 To a solution of tert-butyl 4-[7-benzyloxy-5-(2,8-dimethylimidazo[1,2-b]pyridazin-6- yl)pyrazolo [3,4-c]pyridin-2-yl]piperidine-1-carboxylate (110 mg, 199 umol, 1.00 eq) in dichloromethane (2.20 mL) was added tert-butyldimethylsilyltrifluoromethanesulfonate (105 mg, 397 umol, 2.00 eq) at 0°C. The reaction mixture was stirred at 25°C for 2 hrs. LCMS showed the reaction was completed.
  • the white solid was purified by prep-HPLC (Column: Waters Xbridge BEH C18100 ⁇ 30 mm ⁇ 10 um; mobile phase: [water (NH 4 HCO 3 ) - acetonitrile]; B%: 35%-65%, 8 min) to give 6-[7-benzyloxy-2-(4- piperidyl)pyrazolo [3,4-c]pyridin-5-yl]-2,8-dimethyl-imidazo[1,2-b]pyridazine (7.14 mg, 7.92%) as a solid.
  • reaction mixture was stirred at 100 °C for 2 hrs.
  • the reaction mixture was diluted with H2O (20.0 mL), extracted with ethyl acetate (3 ⁇ 20.0 mL), washed with brine (3 ⁇ 20.0 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give brown oil.
  • reaction mixture was stirred at 80°C for 5 hrs.
  • the reaction mixture was diluted with H 2 O (5.00 mL), extracted with ethyl acetate (3 ⁇ 5.00 mL), washed with brine (3 ⁇ 5.00 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give an oil.
  • the reaction mixture was filtered and the filter cake was dried over in vacuum to afford a solid.
  • the solid was purified by prep-HPLC (column: Phenomenex Luna 80 * 30 mm * 3 um; mobile phase: [water (HCl)-acetonitrile]; B%: 1%-25%, 8 min) to afford 2-(4-azaspiro[2.5]octan-7-yl)-5-(2,8- dimethylimidazo[1,2-b]pyridazin-6-yl)-7-methyl-pyrazolo[4,3-b]pyridine (9.34 mg, 35.6%) as a solid.
  • reaction mixture was cooled to - 70°C and then NaH (64.7 mg, 1.62 mmol, 60 wt%, 1.00 eq) was added in portions.
  • the mixture was stirred at -70°C for 30 min, then warmed up to -65°C and stirred for 2 hrs.
  • the reaction was quenched by addition of saturated NH 4 Cl (20.0 mL) and extracted with ethyl acetate (20 mL ⁇ 2).
  • reaction mixture was stirred at 100 °C for 3 hrs.
  • the reaction was diluted with ethyl acetate (10.0 mL) and washed with water (5.00 mL ⁇ 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give residue.
  • the reaction mixture was concentrated under reduced pressure to give an oil.
  • the oil was diluted with ethyl acetate (5.00 mL) and washed with saturated NaHCO3 (10.0 mL).
  • the aqueous phase was extracted with ethyl acetate (8.00 mL ⁇ 3).
  • the combined organic layer was dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give crude product.
  • reaction mixture was diluted with ethyl acetate (20.0 mL) and washed with saturated brine (20.0 mL).
  • the aqueous layer was extracted with ethyl acetate (10.0 mL ⁇ 2).
  • the organic layers were combined, dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give residue.
  • the reaction mixture was stirred at 80°C for 12 hrs under N 2 protection.
  • the reaction mixture was quenched with saturated ammonium chloride solution (20.0 mL), extracted with ethyl acetate (3 ⁇ 10.0 mL), washed with brine (10.0 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give the crude product.
  • reaction mixture was stirred at 120°C for 16 hrs under N 2 protection.
  • the reaction mixture was diluted with water (15.0 mL), extracted with ethyl acetate (3 ⁇ 5.00 mL), washed with brine (5.00 mL), dried over Na 2 SO 4 , filtered and the filtrate was concentrated under reduced pressure to give crude product.
  • the reaction mixture was stirred at 100 °C for 5 hrs.
  • the reaction mixture was diluted with water (50.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL), washed with brine (100 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give an oil.
  • the reaction was stirred at 100 °C for 5 hrs.
  • the reaction mixture was purified by prep-HPLC (Column: Waters Xbridge BEH C18100 ⁇ 30 mm ⁇ 10 um; mobile phase: [water (NH4HCO3) - acetonitrile]; B%: 30% - 60%, 8 min) to give tert-butyl 4-[5-[6-(methoxy methoxy)-2-methyl-indazol-5-yl]-7- methyl-pyrazolo[4,3-b]pyridin-2-yl]piperidine-1-carboxylate (17.0 mg, 14.7%) as a solid.
  • LCMS (ESI, m/z): 507.3 [M+H] + .
  • reaction mixture was then stirred at 80 °C for 12 hrs.
  • the reaction mixture was diluted with water (50.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL), washed with brine (30.0 mL), dried over Na2SO4, filtered and the filtrate was concentrated under reduced pressure to give residue.
  • reaction mixture was stirred at 25°C for 10 min. Then, acetic acid (0.010 mL) and sodium cyanoboro- hydride (12.3 mg, 196 umol, 2.50 eq) was added. The reaction mixture was stirred at 25°C for 12 hrs.
  • reaction mixture was filtered and the filter cake was purified by prep-HPLC (column: Waters Xbridge Prep OBD C18150 ⁇ 40 mm ⁇ 10 um; mobile phase: [water (NH4HCO3)- acetonitrile]; B%: 25%-55%,8 min) to give 6-[7-fluoro- 2-[(3S,4S)-3-fluoro-1-methyl-4-piperidyl]indazol-5-yl]-2,8-dimethyl-imidazo[1,2-b] pyridazine (4.10 mg, 13.2%) as a solid.
  • LCMS (ESI, m/z): 397.2 [M+H] + .
  • reaction mixture was stirred at 100 °C for 2 hrs.
  • the reaction mixture was diluted with H2O (100.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL).
  • the organic layer was washed with brine (3 ⁇ 50.0 mL), dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give an oil.
  • the oil was purified by prep-HPLC (column: Waters Xbridge Prep OBD C18150 ⁇ 40 mm ⁇ 10 um; mobile phase: [water (NH4HCO3)-acetonitrile]; B%: 60%-90%, 8 min) to give tert- butyl 7-(5-bromo-7-fluoro-indazol-2-yl)-4-azaspiro[2.5]octane-4-carboxylate (1.10 g, 27.3% ).
  • the reaction was stirred at 80 °C for 2.5 hrs.
  • the reaction mixture was diluted with H2O (50.0 mL), extracted with ethyl acetate (3 ⁇ 50.0 mL).
  • the combined organic layer was dried over Na 2 SO 4 , filtered and concentrated under reduced pressure to give an oil.
  • Example 80 Synthesis of Compound 175 To a solution of 6-[2-[(7S)-4-azaspiro[2.5]octan-7-yl]-7-fluoro-indazol-5-yl]-2,8-dimethyl- imidazo[1,2-b]pyridazine (90.0 mg, 230 umol, 1.00 eq) in methanol (1.00 mL) was added triethylamine (46.6 mg, 461 umol, 64.1 uL, 2.00 eq) at 25 °C. The reaction mixture was stirred at 25°C for 30 min.
  • reaction mixture was stirred at 25°C for 30 min. Then formaldehyde (55.3 mg, 1.84 mmol, 50.8 uL, 8.00 eq) and acetic acid (27.6 mg, 461 umol, 26.3 uL, 2.00 eq) was added. The reaction mixture was stirred at 25°C for 10 min and sodium cyanoborohydride (43.4 mg, 691 umol, 3.00 eq) was added to the mixture at 0°C. The reaction mixture was stirred at 25 °C for 8 hrs. The reaction mixture was poured into saturated aqueous NaHCO3 (5.00 mL) and extracted with ethyl acetate (5.00 mL ⁇ 3).
  • RT- qPCR real time quantitative PCR
  • the A673 or K562 cell line was treated with various compounds described herein (e.g., compounds of Formula (I)).
  • the levels of the HTT, MYB, or SMN2 mRNA targets were determined from each sample of cell lysate by cDNA synthesis followed by qPCR.
  • Cells-to-CT 1-step kit ThermoFisher A25602, Cells-to-CT lysis reagent: ThermoFisher 4391851C, TaqManTM Fast Virus 1-Step Master Mix: ThermoFisher 4444436 GAPDH: VIC-PL, ThermoFisher 4326317E (Assay: Hs99999905_m1) – used for K562/suspension cell lines GUSB: VIC-PL, ThermoFisher 4326320E (Assay: Hs99999908_m1) – used for K562/suspension cell lines PPIA: VIC-PL, ThermoFisher 4326316E (Assay: Hs99999904_m1) – used for A673/adherent cell lines Probe/primer sequences Canonical junction (CJ) HTT Primer 1: TCCTCCTGAGAAAGAGAAGGAC HTT Primer 2: GCCTGGAGATCC
  • Cells were diluted with full growth media and plated in a 96-well plate (15,000 cells in 100ul media per well). The plate was incubated at 37°C with 5% CO2 for 24 hours to allow cells to adhere. An 11-point 3-fold serial dilution of the compounds was made in DMSO then diluted in media in an intermediate plate. Compounds were transferred from the intermediate plate to the cell plate with the top dose at a final concentration of 10uM in the well. Final DMSO concentration was kept at or below 0.25%. The cell plate was returned to the incubator at 37°C with 5% CO 2 for an additional 24 hours. The K562 cell line was cultured in IMDM with 10% FBS.
  • the cells were then gently washed with 50uL – 100uL cold PBS before proceeding to addition of lysis buffer.30uL – 50uL of room temperature lysis buffer with DNAse I (and optionally RNAsin) was added to each well. Cells were shaken/mixed thoroughly at room temperature for 5-10 minutes for lysis to take place and then 3uL – 5uL of room temperature stop solution was added and wells were shaken/mixed again. After 2-5 minutes, the cell lysate plate was transferred to ice for RT-qPCR reaction setup. The lysates could also be frozen at - 80°C for later use. In some cases, a direct lysis buffer was used.
  • 3X lysis buffer (10 mM Tris, 150 mM NaCl, 1.5%-2.5% Igepal and 0.1-1 U/uL RNAsin, pH 7.4) was directly added to either K562 or A673 cells in media and mixed by pipetting 3 times. The plates were then incubated at room temperature with shaking/rocking for 20-50 minutes to allow for lysis to take place. After this time, the cell lysate plate was transferred to ice to set up for the RT-qPCR reactions. The lysates could also be frozen at -80°C for later use. To set up 10 uL RT-qPCR reactions, cell lysates were transferred to 384-well qPCR plates containing the master mix according to the table below.
  • the plates were sealed, gently vortexed, and spun down before the run. The volumes were adjusted accordingly in some instances where the reaction was carried in 20 uL.
  • the table below summarizes the components of the RT-qPCR reactions: The RT-qPCR reaction was performed using a QuantStudio (ThermoFisher) under the following fast cycling conditions. All samples and standards were analyzed at least in duplicate. In some instances, bulk room temperature (RT) step of 5-10 minutes was completed for all plates before proceeding with qPCR. The table below summarizes the PCR cycle:
  • the data analysis was performed by first determining the ⁇ Ct vs the housekeeper gene. This ⁇ Ct was then normalized against the DMSO control ( ⁇ Ct) and converted to RQ (relative quantification) using the 2 ⁇ (- ⁇ Ct) equation.
  • the RQ were then converted to a percentage response by arbitrarily setting an assay window of 3.5 and 4.0 ⁇ Ct for HTT-CJ and MYB-CJ respectively and an assay window of 9 and 3 ⁇ Ct for HTT-AJ and MYB-AJ in 96 well format (50,000 K562 cells/well and 15,000 A673 cells per well) and an assay window of 3 and 4 ⁇ Ct for HTT-CJ and MYB-CJ respectively and an assay window of 5 and 3 ⁇ Ct for HTT-AJ and MYB-AJ respectively in 384 well format (8,000 K562 cells/well example).
  • These assay windows correspond to the maximal modulation observed at high concentration of the most active compounds.
  • RNA Splicing by Exemplary Compounds Additional studies were carried out for a larger panel of genes using the protocol provided above. The junction between flanking upstream and downstream exons was used to design canonical junction qPCR assays. At least one of the forward primer, reverse primer or the CY5-labeled 5′ nuclease probe (with 3’ quencher such as ZEN / Iowa Black FQ) was designed to overlap with the exon junction to capture the CJ mRNA transcript. BLAST was used to confirm the specificity of the probeset and parameters such as melting temperature, GC content, amplicon size, and primer dimer formation are considered during their design.
  • IC50 compound concentration having 50% response in CJ decrease.
  • Table 3 Modulation of RNA Splicing by Exemplary Compounds
  • Example 83 Investigating effect of exemplary compounds on cell viability Compounds described herein were screened for toxicity in K562 (human chronic myelogenous leukemia) and SH-SY5Y (human neuroblastoma) cells using a Cell Titer Glo 2.0 assay.
  • Materials Promega CellTiter-Glo® 2.0 Cell Viability Assay (cat#G9241) Corning 384-well TC-treated microplates (cat#3570) Description: Cells were plated at 500 cells/well (K562 cells) in 45 ⁇ L of IMDM supplemented with 10% FBS in a 384-well opaque plate. Wells containing only medium were used as a blank control.
  • Test compounds e.g., compounds of Formula (I), (II), or (III) were first serially diluted in DMSO then diluted 1:100 with IMDM + 10% FBS. The final concentration of DMSO was 0.1% in each well. The cells were incubated for 72 hours at 37 °C and 5% CO 2 before assaying with Cell Titer Glo 2.0 reagent. A summary of the results for viability is illustrated in Table 4, wherein A represents ⁇ 100 nM; B represents 100-1000 nM; C represents 1000-9999 nM; and D represents greater than 10 ⁇ M in K562 cells. Table 4.
  • Example 84 Evaluating effect of exemplary compounds on protein abundance Compounds described herein were used to screen for effects on quantitative protein abundance using a HiBit assay system (Promega). Quantitative protein abundance was determined by measuring the protein levels of HiBit-tagged protein targets expressed in cell culture via luminescence using the Nano-Glo HiBiT Lytic Detection System, which uses a split complementation assay format to reconstitute NanoBiT enzyme to generate a luminescent signal. A protein abundance assay was developed such that endogenous protein targets could be modified with the HiBiT peptide tag and their abundance could be assessed after compound treatment.
  • K562 cell lines containing a HiBiT-modification were treated with various compounds described herein (e.g., compounds of Formulas (I), (II), or (III)). After treatment for 24 hours, the protein abundance of a specific target was determined by measuring luminescence.
  • Treated cell plates were placed in an incubator at 37°C with 5% CO2 for 24 hours. After 24 hours, 25 ⁇ L of Complete HiBit Lytic reagent was added to each well at room temperature (e.g. one plate requiring 10 mL Lytic Buffer, 100 ⁇ L LgBiT Protein, 200 ⁇ L Lytic Substrate), shaken for 5 minutes at 600 RPM, then left to sit for 10 minutes for signal to stabilize before reading on a Spark Cyto plate reader (Tecan) with a 500 ms measurement time.
  • room temperature e.g. one plate requiring 10 mL Lytic Buffer, 100 ⁇ L LgBiT Protein, 200 ⁇ L Lytic Substrate

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Animal Behavior & Ethology (AREA)
  • General Health & Medical Sciences (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Medicinal Chemistry (AREA)
  • Epidemiology (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Biomedical Technology (AREA)
  • Neurology (AREA)
  • Neurosurgery (AREA)
  • Hospice & Palliative Care (AREA)
  • Psychiatry (AREA)
  • Psychology (AREA)
  • Cardiology (AREA)
  • Heart & Thoracic Surgery (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Acyclic And Carbocyclic Compounds In Medicinal Compositions (AREA)
PCT/US2022/050914 2021-11-24 2022-11-23 Compounds and methods for modulating splicing Ceased WO2023097007A1 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
EP22830059.6A EP4436961A1 (en) 2021-11-24 2022-11-23 Compounds and methods for modulating splicing
JP2024531070A JP2024541481A (ja) 2021-11-24 2022-11-23 スプライシングを調整するための化合物及び方法
CA3239110A CA3239110A1 (en) 2021-11-24 2022-11-23 Compounds and methods for modulating splicing
KR1020247020813A KR20240149387A (ko) 2021-11-24 2022-11-23 스플라이싱 조절을 위한 화합물 및 방법
CN202280085944.6A CN118804912A (zh) 2021-11-24 2022-11-23 用于调节剪接的化合物和方法
US18/713,561 US20250082633A1 (en) 2021-11-24 2022-11-23 Compounds and methods for modulating splicing
AU2022398247A AU2022398247A1 (en) 2021-11-24 2022-11-23 Compounds and methods for modulating splicing

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202163283127P 2021-11-24 2021-11-24
US63/283,127 2021-11-24

Publications (1)

Publication Number Publication Date
WO2023097007A1 true WO2023097007A1 (en) 2023-06-01

Family

ID=84602127

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2022/050914 Ceased WO2023097007A1 (en) 2021-11-24 2022-11-23 Compounds and methods for modulating splicing

Country Status (8)

Country Link
US (1) US20250082633A1 (https=)
EP (1) EP4436961A1 (https=)
JP (1) JP2024541481A (https=)
KR (1) KR20240149387A (https=)
CN (1) CN118804912A (https=)
AU (1) AU2022398247A1 (https=)
CA (1) CA3239110A1 (https=)
WO (1) WO2023097007A1 (https=)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023225244A1 (en) * 2022-05-20 2023-11-23 Biogen Ma Inc. Heterocyclic compounds for treating huntington's disease
WO2025111409A1 (en) * 2023-11-21 2025-05-30 Biogen Ma Inc. Heterocyclic compounds of formula (i) for use in the treatment of spinal muscular atrophy via modulation of smn2 splicing

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013159064A1 (en) * 2012-04-20 2013-10-24 Gilead Sciences, Inc. Benzothiazol- 6 -yl acetic acid derivatives and their use for treating an hiv infection
WO2015140717A1 (en) * 2014-03-18 2015-09-24 Iteos Therapeutics Novel 3-indol substituted derivatives, pharmaceutical compositions and methods for use
WO2018068017A1 (en) * 2016-10-07 2018-04-12 Araxes Pharma Llc Heterocyclic compounds as inhibitors of ras and methods of use thereof
WO2021207554A1 (en) * 2020-04-08 2021-10-14 Remix Therapeutics Inc. Compounds and methods for modulating splicing
WO2021207530A1 (en) * 2020-04-08 2021-10-14 Remix Therapeutics Inc. Compounds and methods for modulating splicing

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013159064A1 (en) * 2012-04-20 2013-10-24 Gilead Sciences, Inc. Benzothiazol- 6 -yl acetic acid derivatives and their use for treating an hiv infection
WO2015140717A1 (en) * 2014-03-18 2015-09-24 Iteos Therapeutics Novel 3-indol substituted derivatives, pharmaceutical compositions and methods for use
WO2018068017A1 (en) * 2016-10-07 2018-04-12 Araxes Pharma Llc Heterocyclic compounds as inhibitors of ras and methods of use thereof
WO2021207554A1 (en) * 2020-04-08 2021-10-14 Remix Therapeutics Inc. Compounds and methods for modulating splicing
WO2021207530A1 (en) * 2020-04-08 2021-10-14 Remix Therapeutics Inc. Compounds and methods for modulating splicing

Non-Patent Citations (15)

* Cited by examiner, † Cited by third party
Title
BERGE ET AL., JOURNAL OF PHARMACEUTICAL SCIENCE, vol. 66, 1977, pages 1 - 19
CARRUTHERS: "Some Modern Methods of Organic Synthesis", 1987, CAMBRIDGE UNIVERSITY PRESS
DRUG METABOLISM AND DISPOSITION, vol. 36, 2008, pages 268 - 275
ELIEL: "Stereochemistry of Carbon Compounds", 1962, MCGRAW-HILL
EMMANUEL PINARD ET AL: "Discovery of a Novel Class of Survival Motor Neuron 2 Splicing Modifiers for the Treatment of Spinal Muscular Atrophy", JOURNAL OF MEDICINAL CHEMISTRY, vol. 60, no. 10, 4 May 2017 (2017-05-04), US, pages 4444 - 4457, XP055614701, ISSN: 0022-2623, DOI: 10.1021/acs.jmedchem.7b00406 *
FAUSTINOCOOPER, GENES DEV, vol. 17, no. 4, 2003, pages 419 - 37
GREENE ET AL.: "Protecting Groups in Organic Synthesis", 1991, WILEY
JACQUES ET AL.: "Enantiomers, Racemates and Resolutions", 1981, WILEY INTERSCIENCE
JOURNAL OF PHARMACEUTICAL SCIENCES, vol. 107, 2018, pages 2225 - 2235
LAROCK: "Comprehensive Organic Transformations", 1989, VCH PUBLISHERS, INC.
SMITHMARCH: "March's Advanced Organic Chemistry", 2001, JOHN WILEY & SONS, INC.
THOMAS SORRELL: "Handbook of Chemistry and Physics", 1999, UNIVERSITY SCIENCE BOOKS
WALKER: "Cambridge Dictionary of Biology", 1990, CAMBRIDGE UNIVERSITY PRESS
WILEN ET AL., TETRAHEDRON, vol. 33, 1977, pages 2725
WILEN: "Tables of Resolving Agents and Optical Resolutions", 1972, UNIV. OF NOTRE DAME PRESS, pages: 268

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023225244A1 (en) * 2022-05-20 2023-11-23 Biogen Ma Inc. Heterocyclic compounds for treating huntington's disease
WO2025111409A1 (en) * 2023-11-21 2025-05-30 Biogen Ma Inc. Heterocyclic compounds of formula (i) for use in the treatment of spinal muscular atrophy via modulation of smn2 splicing

Also Published As

Publication number Publication date
CA3239110A1 (en) 2023-06-01
US20250082633A1 (en) 2025-03-13
EP4436961A1 (en) 2024-10-02
KR20240149387A (ko) 2024-10-14
JP2024541481A (ja) 2024-11-08
AU2022398247A1 (en) 2024-06-13
CN118804912A (zh) 2024-10-18

Similar Documents

Publication Publication Date Title
IL295954A (en) Compounds and methods for modulating splicing
EP4110464A1 (en) Compounds and methods for modulating splicing
IL297137A (en) Splicing Modulation Compounds and Methods
EP4132935A1 (en) Compounds and methods for modulating splicing
KR20220158237A (ko) 스플라이싱을 조절하기 위한 화합물 및 방법
EP4396177A1 (en) Compounds and methods for modulating splicing
WO2023097007A1 (en) Compounds and methods for modulating splicing
WO2024182747A2 (en) Compounds and methods for modulating splicing
AU2022339925A1 (en) Compounds and methods for modulating splicing
EP4416156A1 (en) Compounds and methods for modulating nucleic acid splicing
US20250154169A1 (en) Compounds and methods for modulating splicing
EP4395889A1 (en) Compounds and methods for modulating splicing
EP4724438A1 (en) Compounds and methods for modulating splicing
WO2024182788A1 (en) Compounds and methods for modulating splicing
WO2024259017A1 (en) Compounds and methods for modulating splicing

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 22830059

Country of ref document: EP

Kind code of ref document: A1

ENP Entry into the national phase

Ref document number: 2024531070

Country of ref document: JP

Kind code of ref document: A

ENP Entry into the national phase

Ref document number: 3239110

Country of ref document: CA

WWE Wipo information: entry into national phase

Ref document number: 2022398247

Country of ref document: AU

Ref document number: AU2022398247

Country of ref document: AU

ENP Entry into the national phase

Ref document number: 2022398247

Country of ref document: AU

Date of ref document: 20221123

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: 202417047976

Country of ref document: IN

WWE Wipo information: entry into national phase

Ref document number: 2022830059

Country of ref document: EP

NENP Non-entry into the national phase

Ref country code: DE

WWE Wipo information: entry into national phase

Ref document number: 202280085944.6

Country of ref document: CN

ENP Entry into the national phase

Ref document number: 2022830059

Country of ref document: EP

Effective date: 20240624

WWP Wipo information: published in national office

Ref document number: 18713561

Country of ref document: US