WO2023018236A1 - Novel plk1 degradation inducing compound - Google Patents

Novel plk1 degradation inducing compound Download PDF

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Publication number
WO2023018236A1
WO2023018236A1 PCT/KR2022/011961 KR2022011961W WO2023018236A1 WO 2023018236 A1 WO2023018236 A1 WO 2023018236A1 KR 2022011961 W KR2022011961 W KR 2022011961W WO 2023018236 A1 WO2023018236 A1 WO 2023018236A1
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Prior art keywords
methyl
mmol
amino
cancer
mixture
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PCT/KR2022/011961
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English (en)
French (fr)
Inventor
Soo Hee RYU
Im Suk MIN
Han Kyu Lee
Seong Hoon Kim
Hye Guk Ryu
Keum Young KANG
Sang Youn Kim
So Hyun Chung
Jun Kyu Lee
Gibbeum Lee
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Uppthera Inc
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Uppthera Inc
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Priority to KR1020227036557A priority Critical patent/KR102604801B1/ko
Priority to US18/019,034 priority patent/US11939334B2/en
Priority to MX2024001774A priority patent/MX2024001774A/es
Priority to PE2024000208A priority patent/PE20240894A1/es
Priority to IL310678A priority patent/IL310678A/en
Priority to CA3228601A priority patent/CA3228601A1/en
Priority to AU2022327025A priority patent/AU2022327025A1/en
Priority to CR20240120A priority patent/CR20240120A/es
Application filed by Uppthera Inc filed Critical Uppthera Inc
Priority to JP2023514149A priority patent/JP7555155B2/ja
Priority to EP22808931.4A priority patent/EP4157850A4/en
Priority to CN202280006544.1A priority patent/CN116261458B/zh
Publication of WO2023018236A1 publication Critical patent/WO2023018236A1/en
Priority to CONC2024/0001256A priority patent/CO2024001256A2/es
Anticipated expiration legal-status Critical
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    • 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
    • A61K31/55—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole
    • 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
    • A61K31/55—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole
    • A61K31/551—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole having two nitrogen atoms, e.g. dilazep
    • 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
    • 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
    • A61K47/55—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 the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • 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
    • C07D487/10—Spiro-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

  • the present disclosure relates to a novel PLK1 degradation inducing compound, a method for preparing the same, and the use thereof. It can specifically act on abnormal cells, etc. and can be usefully used in the treatment of various diseases through efficient degradation of PLK1.
  • Polo-like kinase 1 is a serine/threonine kinase involved in the conversion of G2/M phase during cell growth and division. PLK1 is expressed and activated in a pulse form from the S phase to the G2/M phase, and rapidly degrades as mitosis ends.
  • PLK1 is overexpressed in various carcinomas such as colon cancer, lung cancer, bladder cancer, and melanoma, etc., and cancer cells overexpressing PLK1 tend to show resistance to various types of anticancer drugs.
  • PLK1 inhibitor compounds such as volasertib (also known as BI6727), etc.
  • the conventional PLK1 inhibitors do not sufficiently inhibit PLK1 activity at concentrations that are clinically safe.
  • the conventional PLK1 inhibitors do not sufficiently inhibit PLK1 activity at concentrations that are clinically safe.
  • many pharmaceutical companies such as Boehringer Ingelheim, GlaxoSmithKline, etc., have attempted to develop small-molecular compound-based PLK1 inhibitors, but most of them have failed or stopped in the clinical trial stage, and thus there are no commercially available PLK1 inhibitors to date.
  • PROTAC proteolysis targeting chimera
  • the PROTAC is a bifunctional compound in which a ligand molecule that binds to disease-related target protein and an E3 ubiquitin ligase binding moiety are linked by a chemical linker.
  • the PROTAC compound is capable of inducing degradation of the target protein by placing the disease-related target protein near the E3 ubiquitin ligase. Based on this new mechanism different from the existing inhibitors, a lot of PROTAC compounds have been developed as therapeutic agents for cancer and inflammatory diseases, etc., and being studied with various extensibility (e.g.
  • the PROTAC compound described in the above-described document is characterized by a compound that simultaneously degrades PLK1 and BRD4, and degrade various proteins such as other PLK family proteins and BRD4, etc.), which may cause side effects due to off-target toxicities at the time of drug development.
  • a compound that simultaneously degrades PLK1 and BRD4 and degrade various proteins such as other PLK family proteins and BRD4, etc.
  • BRD4 activity inevitably accompanies on-target toxicity such as blood toxicity and gastrointestinal toxicity along with pharmacological effects. Therefore, the PROTAC compound described in the above document would expect to face greater clinical side effects as more BRD4 protein gets degraded (see Bolden et al. Cell Reports, 2014).
  • the PROTAC compound which simultaneously degrades PLK1 and BRD4, has much stronger BRD4 degradation ability than PLK1 degradation ability at the cellular level, and the cell cycle thereof almost stops in the G1 phase, etc., that is, the PROTAC compound actually acts only as a BRD4 inhibitor regardless of the way that the conventional PLK1 inhibitors exert pharmacological effects.
  • An object of the present disclosure is to provide novel PLK1 degradation inducing compounds.
  • Another object of the present disclosure is to provide a method for preparing the compounds.
  • Still another object of the present disclosure is to provide a use of the compounds.
  • novel PROTAC compounds of the present invention specifically act on abnormal cells overexpressing PLK1 through appropriate structural combination and optimization of E3 Ligase binder, Target binding moiety, and Linker to induce effective PLK1 degradation and minimize side effects, and completed the present invention.
  • the present disclosure provides novel compounds that induce effective polo-like kinase 1 (PLK1) degradation.
  • PLK1 polo-like kinase 1
  • the present disclosure provides a bifunctional compound in which a PLK1 binding moiety and an E3 ubiquitin ligase-binding moiety are linked by a chemical linker.
  • ULM is a moiety represented by the following Formula 1;
  • PTM is a moiety represented by the following Formula 2;
  • Linker is a group that chemically links ULM and PTM;
  • X 1 and X 2 are each independently CH 2 , CH, or N;
  • ring U is phenyl or 5- to 6-membered heteroaryl linked to the X 1 or X 2 ⁇ wherein at least one H of the phenyl or 5- to 6-membered heteroaryl ring may be substituted with R U ⁇ ;
  • R U is -C 1-4 alkyl, -C 1-4 hydroxyalkyl, -C 1-4 aminoalkyl, -C 1-4 haloalkyl, -C 1-4 alkoxy or -halo;
  • Y is CR 7 or N
  • R 1 is -C 1-4 alkyl
  • R 2 is -H or -C 1-4 alkyl, or is linked with R 1 to form 5- to 6-membered ring together with N atom;
  • R 3 and R 4 are each independently -H, -C 1-4 alkyl or -halo, or R 3 and R 4 are linked each other to form 3- to 6-membered ring;
  • R 5 is -C 1-4 alkyl
  • R 6 is -C 1-4 alkyl, -C 1-4 hydroxyalkyl, -C 1-4 aminoalkyl, -C 1-4 haloalkyl, -C 1-4 alkoxy or -halo;
  • R 7 is -H or -halo.
  • ULM is a moiety represented by following Formula 1;
  • X 1 and X 2 are each independently CH 2 , CH or N;
  • ring U is phenyl, pyridinyl, pyrimidinyl or pyrazolyl linked to the X 1 or X 2 ⁇ wherein at least one H of the phenyl, pyridinyl, pyrimidinyl or pyrazolyl ring may be substituted with R U ⁇ ; and
  • R U is -C 1-4 alkyl, -C 1-4 haloalkyl, -C 1-4 alkoxy or -halo.
  • R U1 and R U2 are each independently -C 1-4 alkyl, -C 1-4 haloalkyl, -C 1-4 alkoxy or -halo.
  • ULM is , , , , , , or ;
  • R U1 and R U2 are each independently -C 1-4 alkyl, -C 1-4 haloalkyl, -C 1-4 alkoxy or -halo.
  • PTM is , , or ;
  • Y is CH, CF or N
  • R 6 is -C 1-4 alkyl, -C 1-4 alkoxy or -halo.
  • Linker is -L U -L 1 -L 2 -L 3 -L P -;
  • L 3 is cycloalkyl, heterocycloalkyl or nothing (null) ⁇ wherein, when the L 3 is nothing (null), L 2 and L p are directly linked, the heterocycloalkyl contains at least one N atom in the ring, and at least one H of the cycloalkyl or heterocycloalkyl ring may be substituted with -C 1-4 alkyl, -C 1-4 haloalkyl or -halo ⁇ ; and
  • L 3 is 4- to 6-membered cycloalkyl, 4- to 12-membered heterocycloalkyl or nothing (null) ⁇ wherein, when the L 3 is nothing (null), L 2 and L p are directly linked, the 4- to 12-membered heterocycloalkyl is single ring, bridged bicyclic ring or spiro ring, the 4- to 12-membered heterocycloalkyl contains at least one N atom in the ring, and at least one H of the 4- to 6-membered cycloalkyl or 4- to 12-membered heterocycloalkyl ring may be substituted with -halo ⁇ ; and
  • the compound represented by Formula I is a compound that is selected from the group consisting of Compound 1 to 59.
  • a pharmaceutically acceptable salt refers to any organic or inorganic acid addition salt with a concentration that is relatively non-toxic, is harmless, and has effective action to patients, wherein side effects caused by this salt does not deteriorate beneficial efficacy of the compound represented by Formula I.
  • the pharmaceutically acceptable salt may be an inorganic acid such as hydrochloric acid, phosphoric acid, sulfuric acid, nitric acid, or the like, or an organic acid such as methanesulfonic acid, p-toluenesulfonic acid, acetic acid, trifluoroacetic acid, maleic acid, succinic acid, oxalic acid, benzoic acid, tartaric acid, fumaric acid, manderic acid, propionic acid, citric acid, lactic acid, glycolic acid, gluconic acid, galacturonic acid, glutamic acid, glutaric acid, glucuronic acid, aspartic acid, ascorbic acid, carbonic acid, vanillic acid or hydroiodic acid, but is not limited thereto.
  • an inorganic acid such as hydrochloric acid, phosphoric acid, sulfuric acid, nitric acid, or the like
  • an organic acid such as methanesulfonic acid, p-toluenesulf
  • An embodiment of the present disclosure is a composition for inducing PLK1 degradation including a compound represented by Formula I or a pharmaceutically acceptable salt thereof.
  • the Formula I is the same as defined above.
  • the PLK1 degradation-inducing PROTAC compound of the present disclosure is capable of fundamentally degrading the target protein, PLK1 in view of the mechanism of action, thereby achieving an excellent PLK1 inhibitory effect as compared to the conventional PLK1 small molecule inhibitor that inhibits the simple activity of PLK1.
  • composition including the compound represented by Formula I of the present disclosure or a pharmaceutically acceptable salt thereof may be effectively employed for selective degradation of PLK1.
  • An embodiment of the present disclosure is a composition for preventing or treating PLK1-related diseases including the compound represented by Formula I or the pharmaceutically acceptable salt thereof.
  • An another embodiment of the present disclosure is a method for the preventon or treatment of PLK-related diseases comprising administering the composition to a subject in need thereof.
  • the Formula I is the same as defined above.
  • the PLK1-related disease refers to any disease or condition capable of being treated, alleviated, delayed, inhibited or prevented from induction of degradation or inhibition of activity of PLK1.
  • the PLK1-related disease may be a cancer (malignant tumor), a benign tumor, a neurological disease, or other genetic or non-genetic diseases caused by excessive cell division.
  • the cancer includes all cancers capable of exhibiting prophylactic or therapeutic efficacy due to inhibition of PLK1 activity, and may be solid cancer or blood cancer.
  • the cancer may be one or more selected from the group consisting of squamous cell carcinoma, small cell lung cancer, non-small cell lung cancer, lung adenocarcinoma, lung squamous cell carcinoma, peritoneal cancer, skin cancer, skin or intraocular melanoma, rectal cancer, anal muscle cancer, esophageal cancer, small intestine cancer, endocrine cancer, parathyroid cancer, adrenal cancer, soft tissue sarcoma, urethral cancer, chronic or acute leukemia, lymphocytic lymphoma, hepatocellular carcinoma, gastrointestinal cancer, gastric cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, liver tumor, breast cancer, colon cancer, colorectal cancer, endometrial or uterine cancer, salivary gland cancer, kidney cancer,
  • the benign tumors include all benign tumors capable of exhibiting prophylactic or therapeutic efficacy due to the inhibition of PLK1 activity, such as benign tumors in pre-cancer stages, and may be solid tumors or blood tumors.
  • the tumor may be one or more selected from the group consisting of Barrett's esophagus, colon adenoma and polyp, breast fibroadenoma and cyst, monoclonal gammopathy of undetermined significance (MGUS), monoclonal lymphocytosis, and the like, but is not limited thereto.
  • the neurological diseases include all neurological diseases capable of exhibiting prophylactic or therapeutic efficacy due to the inhibition of PLK1 activity, and specifically, may be one or more selected from the group consisting of central nervous system disease, neurodegenerative disease, Alzheimer's disease, Parkinson's disease, multiple sclerosis, Huntington's disease, senile dementia, epilepsy, Lou Gehrig, stroke, and nerve damage and axonal degeneration-related disorders following brain or spinal cord injury, but is not limited thereto.
  • composition of the present disclosure may further include one or more active ingredients exhibiting the same or similar medicinal effects in addition to the compound represented by Formula I above, or the pharmaceutically acceptable salt thereof.
  • An embodiment of the present disclosure is a method of degrading PLK1 by administering a compound represented by Formula I or a pharmaceutically acceptable salt thereof to mammals including humans.
  • Another embodiment of the present disclosure is a method of degrading PLK1 by administering the compound represented by Formula I or the pharmaceutically acceptable salt thereof to a sample in vitro.
  • the sample may be a cell, a cell culture, a body fluid or tissue of a mammal including a human, but is not limited thereto.
  • the compounds of the present disclosure exhibit an effect of inducing PLK1 degradation. Therefore, the compounds of the present disclosure may be effectively utilized for preventing or treating PLK1-related diseases.
  • Figure 1 shows the luciferase assay results by treating Compound 1 to Compound 25 of the present invention.
  • Figure 2 shows the luciferase assay results by treating Compound 26 to Compound 59 of the present invention.
  • the present disclosure provides synthetic methods for Compound 1 to 59 shown in the table below.
  • the compounds of the present invention were purified according to the following method and the structure was analyzed.
  • LCMS Shimadzu LCMS-2020, Agilent 1200/G6110A, Agilent 1200/G1956A
  • LCMS data were recorded with Shimadzu LCMS-2020 or Agilent 1200/G6110A or Agilent 1200/G1956A equipped with an ESI (Electron Spray Ionization) device.
  • 0.0375% TFA in water (solvent A) and 0.01875% TFA in ACN (solvent B) or 0.025% NH 3 ⁇ H 2 O in water (solvent A) and ACN (solvent B) were used as mobile phases.
  • Kinetex EVO C18 2.1 x 30 mm, 5 ⁇ m
  • HALO C18 3.0 x 30 mm, 2.7 ⁇ m
  • Chiralpak AD-3 50 x 4.6 mm, 3 ⁇ m
  • Chiralpak AS-3 50 x 4.6 mm, 3 ⁇ m
  • Chiralpak OJ-3 50 x 4.6 mm, 3 ⁇ m
  • Chiralpak IA-3 50 x 4.6 mm, 3 ⁇ m
  • Chiralpak OD 50 x 4.6 mm, 3 ⁇ m
  • Chiralpak IC-3 50 x 4.6 mm, 3 ⁇ m
  • S,S Whelk-O1
  • the resulting mixture was degassed and purged with N 2 for three times, then heated to 100 °C and stirred at 100 °C for 14 hrs.
  • LCMS showed a main peak with desired mass.
  • the reaction mixture was diluted with EtOAc (200 mL), dried over Na 2 SO 4 and filtered. The filtrate was concentrated.
  • Step 7 Synthesis of N-(1-(3-(4-(3-(2,6-dioxopiperidin-3-yl)phenyl)piperazin-1-yl)propanoyl) piperidin-4-yl)-4-((9'-isopropyl-5'-methyl-6'-oxo-5',6',8',9'-tetrahydrospiro[cyclopropane-1,7'-pyrimido[4,5-b][1,4]diazepin]-2'-yl)amino)-3-methoxybenzamide ( Compound 5 )
  • reaction mixture was diluted with H 2 O (60 mL) and extracted with EtOAc (60 mL x 5). The organic layer was dried over Na 2 SO 4 , filtered and concentrated to afford product A. The aqueous phase was concentrated in vacuum to afford product B.
  • product A was purified by prep-HPLC (column: Phenomenex luna C18 150 x 40 mm x 15 ⁇ m; mobile phase: [water (FA)-ACN]; B%: 5%-35%, 10 min) and lyophilization to afford product E (620 mg) and product F (420 mg).
  • the product B was re-purified by prep-HPLC (column: Unisil 3-100 C18 ⁇ Ltra 150 x 50 mm x 3 ⁇ m; mobile phase: [water (FA)-ACN]; B%: 5%-35%, 10 min) and lyophilization to afford product D (158 mg).
  • the product F (420 mg) was re-purified by prep-HPLC (column: Waters Xbridge C18 150 x 50 mm x 10 ⁇ m; mobile phase: [water (NH 4 HCO 3 )-ACN]; B%: 25%-55%, 10 min) and lyophilization to afford N-(1-(3-(4-(3-(2,6-dioxopiperidin-3-yl)phenyl)piperazin-1-yl)propanoyl)piperidin-4-yl)-4-((9'-isopropyl-5'-methyl-6'-oxo-5',6',8',9'-tetrahydrospiro[cyclopropane-1,7'-pyrimido[4,5-b][1,4]diazepin]-2'-yl)amino)-3-methoxybenzamide (136 mg, 162.34 ⁇ mol, 9.54% yield, 98% purity) as a white solid. MS(M+H
  • Step 8 Synthesis of N-(3-((2-(1-(3-(2,6-dioxopiperidin-3-yl)phenyl)piperidin-4-yl)ethyl)(methyl)amino)cyclobutyl)-4-((9'-isopropyl-5'-methyl-6'-oxo-5',6',8',9'-tetrahydrospiro[cyclopropane-1,7'-pyrimido[4,5-b][1,4]diazepin]-2'-yl)amino)-3-methoxybenzamide (Compound 6)
  • the resulting mixture was purged and degassed with N 2 for three times, then the reaction mixture was heated to 90 °C and stirred at 90 °C for 4 hrs.
  • LCMS showed a main peak with desired mass.
  • the mixture was filtered through a pad of celite. The filtrate was concentrated in vacuum.
  • Step 8 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-((1r,4r)-4-(((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperidin-4-yl)methyl)(methyl)amino)cyclohexyl)-3-methoxybenzamide (Compound 7)
  • the resulting mixture was purified by prep-HPLC (column: Waters Xbridge C18 150 * 50 mm * 10 ⁇ m; mobile phase: [water (NH 4 HCO 3 )-ACN]; B%: 45% - 75%, 10 min) and re-purified by prep-HPLC (column: Unisil 3-100 C18 ⁇ Ltra 150 * 50 mm * 3 ⁇ m; mobile phase: [water (FA)-ACN]; B%: 16% - 46%, 7 min) and the eluent was lyophilized to afford 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-((1s,4s)-4-(((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluor
  • LCMS showed a peak (30%) with mass of starting material and a peak (54%) with desired mass.
  • the mixture was stirred at 50 °C under H 2 (15 Psi) for another 14 h.
  • LCMS showed 91% of desired mass.
  • the mixture was diluted with CF 3 CH 2 OH (50 mL) and filtered. The filter cake was washed with THF (30 mL), DMF (100 mL) and CF 3 CH 2 OH (50 mL).
  • Step 1 Synthesis of tert-butyl 2-(4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-3-methoxybenzamido)-7-azaspiro[3.5]nonane-7-carboxylate (10C)
  • the reaction mixture was filtered.
  • the filtrate was diluted with H 2 O (50 mL), and extracted with EtOAc (120 mL x 2).
  • the combined organic layers were washed with brine (60 mL x 3), dried over anhydrous Na 2 SO 4 , filtered and the filtrate was concentrated under reduced pressure.
  • the residue was purified by flash silica gel chromatography (Biotage; 120 g SepaFlash® Silica Flash Column, Eluent of 0 ⁇ 10 % EtOAc:Petroleum ether gradient, 60 mL/min) to afford two batches of product.
  • Step 1 Synthesis of tert-butyl 2-(4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-2-fluoro-5-methoxybenzamido)-7-azaspiro[3.5]nonane-7-carboxylate (3)
  • the reaction mixture was filtered and the filtrate was concentrated under reduced pressure.
  • the residue was purified by prep-HPLC (column: Phenomenex Synergi Polar-RP 100 x 25 mm x 4 um; mobile phase: [water (TFA) -ACN]; B%: 33% - 53%, 7 min; Column Temp: 30 °C) followed by lyophilization to give the crude product.
  • reaction solution was stirred at 70 °C for another 13 hrs. LCMS showed the starting material was consumed completely and the desired mass.
  • the reaction mixture was poured into water (15 mL) and extracted with EtOAc (10 mL x 4). The combined organic layers were dried over Na 2 SO 4 , filtered. The filtrate was concentrated in vacuum.
  • Step 8 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(4-((4-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperazin-1-yl)methyl)-4-fluoropiperidin-1-yl)-3-methoxybenzamide (Compound 18)
  • Example 20 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methylbenzamide (Compound 20)
  • Example 21 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-2-fluoro-5-methylbenzamide (Compound 21)
  • tert-butyl 2-amino-7-azaspiro[3.5]nonane-7-carboxylate (108.11 mg, 449.83 ⁇ mol) was added, the resulting mixture was stirred at 20 °C for 2 h.
  • LCMS showed a main peak with desired mass.
  • the reaction mixture was diluted with water (15 mL), extracted with EtOAc (10 mL ⁇ 3). The combined organic layers were washed with brine (20 mL ⁇ 2), dried over Na 2 SO 4 , filtered. The filtrate was concentrated in vacuum to give a residue.
  • Step 7 Synthesis of 5-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-4-methoxypicolinamide (Compound 22)
  • reaction mixture was quenched by addition H 2 O (0.2 mL), NaOH (15% aq, 0.2 mL) and H 2 O (0.6 mL), the mixture was dried over Na 2 SO 4 , filtered. The filtrate was concentrated in vacuum to give a residue.
  • Example 28 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)-2-oxopiperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 28)
  • reaction mixture was quenched by addition NH 4 Cl (10 mL) at 0 °C, extracted with EtOAc (10 mL ⁇ 3). The combined organic layers were washed with brine (20 mL ⁇ 2), dried over Na 2 SO 4 , filtered. The filtrate was concentrated in vacuum to give a residue.
  • Step 4 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-((7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)methyl)-3-methoxybenzamide (Compound 30)
  • reaction mixture was quenched by addition of aq. sat NH 4 Cl (30 mL) at 0 °C, then extracted with EtOAc (50 mL x 2). The combined organic layers were washed with brine (20 mL), dried over Na 2 SO 4 , filtered and concentrated under reduced pressure.
  • Example 32 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)-2-methylpiperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 32)
  • Step 7 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)-2-methylpiperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 32)
  • the crude A (0.2 g, 20% purity) was purified by prep-HPLC (column: Phenomenex C18 75*30 mm * 3 ⁇ m; mobile phase: [water (FA) - ACN]; B%: 10% - 40%, 7 min) and the eluent was lyophilized to afford product C (26 mg, 84% purity, FA).
  • the crude B (0.2 g, crude) was purified by prep-HPLC (column: Phenomenex Synergi Polar-RP 100*25mm*4um; mobile phase: [water (TFA) -ACN]; B%: 24% - 44%, 7 min) and the eluent was lyophilized to afford to afford a product D (28 mg, 82% purity, TFA).
  • Example 33 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)-4-hydroxypiperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 33)
  • Step 7 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-fluorobenzyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 34)
  • Example 36 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-2-methoxyphenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 36)
  • the impure product C was re-purified by prep-HPLC (column: 3_Phenomenex Luna C18 75 * 30 mm * 3 ⁇ m; mobile phase: [water (TFA) - ACN]; B%: 15% - 35%, 9 min) and the eluent was lyophilized to afford product D.
  • Example 37 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(7-((1-(4-(2,6-dioxopiperidin-3-yl)-3-methoxyphenyl)piperidin-4-yl)methyl)-7-azaspiro[3.5]nonan-2-yl)-3-methoxybenzamide (Compound 37)
  • Example 40 Synthesis of 4-((7,7-difluoro-9-isopropyl-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino)-N-(4-(7-(4-(2,6-dioxopiperidin-3-yl)-2-fluorophenyl)-2,7-diazaspiro[3.5]nonan-2-yl)piperidin-1-yl)-3-methoxybenzamide (Compound 40)

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WO2026026773A1 (zh) * 2024-07-29 2026-02-05 杭州胶联生物医药科技有限公司 作为vav1蛋白靶点降解剂的新型取代杂环类化合物
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