Synthesis of bromodomain inhibitors

Abstract

Provided herein are methods useful for preparing small molecule bromodomain inhibitors.

Description

Related applications

[0001] This application claims priority to U.S. Provisional Application No. 63 / 612,455, filed December 20, 2023, the entire contents of which are incorporated herein by reference. Background Technology

[0002] The bromodomain (BRD) protein family is involved in multiple functions and regulates gene expression through histone acetylation, histone recognition, chromatin remodeling, and transcriptional machinery. BRD-containing proteins are frequently dysregulated in cancer, and small-molecule inhibitors targeting the bromodomain and extraterminal (BET) domains of the BRD family are currently in clinical trials. Recently, the BET protein family, along with the JAK / STAT pathway, has been shown to be associated with the occurrence and progression of myelofibrosis. Both pathways can increase the levels of pro-inflammatory cytokines and stimulate the production of abnormal blood cell precursors called megakaryocytes. The BET protein family is gradually becoming a promising therapeutic target; its regulation may alter the underlying pathogenesis of myelofibrosis and may synergize with JAK inhibition.

[0003] Compounds designed to inhibit the BET protein have been previously described (see, for example, PCT / US2011 / 063046 and PCT / US2015 / 036347), and are believed to have potential applications in treating various cancers (such as myelofibrosis), as well as certain inflammatory conditions and viral infections. Further synthetic methods are needed to facilitate the development of new compounds and to enrich current methods for producing BET inhibitors. Summary of the Invention

[0004] This article provides methods for preparing intermediates for the preparation of BET inhibitors. In one aspect, such methods include methods for preparing compounds having Formula I: (I). In another aspect, such methods include methods for preparing compounds having formula II: (II). In another aspect, such methods include methods for preparing compounds having Formula III: (III).

[0005] This article also describes other compounds and methods for their preparation. Detailed Implementation

[0006] In this embodiment, a method for preparing a compound having Formula I is provided: (I), The method includes reacting a compound having formula A in the presence of ethyl acetate: (A) reacts with a strong base and then undergoes ester hydrolysis to form a compound having formula I.

[0007] In an embodiment, for the method of preparing a compound having Formula I, the strong base is a metal-containing base. In an embodiment, for the method of preparing a compound having Formula I, the strong base is a sterically hindered metal base. In an embodiment, for the method of preparing a compound having Formula I, the strong base is selected from lithium bis(trimethylsilyl)amino (LiHMDS), sodium bis(trimethylsilyl)amino (NaHMDS), potassium bis(trimethylsilyl)amino (KHMDS), etc. In an embodiment, for the method of preparing a compound having Formula I, the strong base is potassium bis(trimethylsilyl)amino.

[0008] In an embodiment, for a method of preparing a compound having formula I, the method further includes reacting the compound having formula A with a strong base in the presence of ethyl acetate and at least one organic solvent. In an embodiment, for a method of preparing a compound having formula I, the method further includes reacting the compound having formula A with a strong base in the presence of ethyl acetate and tetrahydrofuran (THF).

[0009] In one embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out under alkaline conditions. In another embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out using an inorganic hydroxide base. In another embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out using an inorganic hydroxide base selected from: lithium hydroxide, sodium hydroxide, potassium hydroxide, etc. In another embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out using lithium hydroxide. In another embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out under aqueous conditions. In another embodiment, for the method of preparing a compound having Formula I, the ester hydrolysis is carried out using lithium hydroxide, water, and ethanol.

[0010] In this embodiment, a method for preparing a compound having formula II is provided: (II), The method includes reacting a compound of formula I in the presence of a palladium source and a base: (I) With compounds having formula B: (B) Reaction.

[0011] In embodiments, for the method of preparing compounds having formula II, the palladium source is selected from Pd(Ph3P)4, Pd(OAc)2, Pd2(dba)3, Pd(Ph3)2Cl2, Pd(dppf)Cl2, etc. In embodiments, for the method of preparing compounds having formula II, the palladium source may be combined with one or more suitable phosphine ligands. Such ligands include, for example, Ph3P, (t-Bu)3P, XPhos, SPhos, DPPE, DPPF, BINAP, DPPB, etc. In embodiments, for the method of preparing compounds having formula II, the palladium source is Pd(dppf)Cl2.

[0012] In an embodiment, for the method of preparing a compound having formula II, the base is an inorganic base. In an embodiment, for the method of preparing a compound having formula II, the base is selected from Na₂CO₃, K₂CO₃, Cs₂CO₃, t-BuOK, NaOEt, K₃PO₄, etc. In an embodiment, for the method of preparing a compound having formula II, the base is K₃PO₄.

[0013] In an embodiment, for a method of preparing a compound having formula II, the reaction of the compound having formula I with the compound having formula B further includes the addition of at least one organic solvent. In an embodiment, for a method of preparing a compound having formula II, the reaction of the compound having formula I with the compound having formula B further includes the addition of at least one aprotic organic solvent selected from THF, 2MeTHF, MTBE, 1,4-dioxane, DME, etc. In an embodiment, for a method of preparing a compound having formula II, the reaction of the compound having formula I with the compound having formula B further includes the addition of 2MeTHF.

[0014] In an embodiment, for a method of preparing a compound having formula III, the reaction of the compound having formula I with the compound having formula B further comprises reacting the compound having formula II with an acid and reacting the resulting intermediate with a base to form a compound having formula III: (III).

[0015] In an embodiment, for the method of preparing a compound having formula III, the acid is an aqueous acid. In an embodiment, for the method of preparing a compound having formula III, the acid is selected from HCl, HBr, HI, H3PO4, and H2SO4. In an embodiment, for the method of preparing a compound having formula III, the acid is HCl. In an embodiment, for the method of preparing a compound having formula III, the base is an aqueous base. In an embodiment, for the method of preparing a compound having formula III, the base is selected from Na2CO3, K2CO3, and K3PO4. In an embodiment, for the method of preparing a compound having formula III, the base is K3PO4.

[0016] In an embodiment, this document also provides a compound having Formula I: (I) or its salt.

[0017] In an embodiment, a compound having formula II is also provided herein: (II) or its salts.

[0018] In an embodiment, this document also provides a compound having Formula III: (III) or its salts.

[0019] Salts are well known in the field of chemistry and include those derived from suitable inorganic and organic acids and bases. The term "pharmaceutically acceptable salt" means that, within reasonable medical judgment, it is suitable for use in contact with human and lower animal tissues without excessive toxicity, irritation, allergic reactions, etc., and in proportion to a reasonable benefit / risk ratio. Pharmaceutically acceptable salts of the compounds (including those in the examples) are included as part of this invention.

[0020] Example Abbreviations APhos (4-(N,N-dimethylamino)phenyl)di-tert-butylphosphine, A-taPhos, [4-(dimethylamino)phenyl]bis(tert-butylphosphine) aq water-based Boc2O di-tert-butyl dicarbonate CuSO4 Copper(II) sulfate EtOAc (ethyl acetate) EtOH (ethanol) HCl hydrochloric acid KHMDS bis(trimethylsilyl)aminopotassium K3PO4.3H2O Potassium phosphate trihydrate LiOH (Lithium hydroxide) MeTHF 2-methyltetrahydrofuran (NH4)2CO3 Ammonium carbonate PinBH Pinarol Borane Pd2(dba)3 tris(dibenzylacetone)dipalladium(0) Pd(dppf)Cl2-DCM [1,1'-bis(diphenylphosphino)ferrocene]palladium(II) dichloromethane complex THF hydrochloric acid The following provides procedures for synthesizing intermediates and bromine domain inhibitors.

[0021] Preparation of (4-chlorophenyl)(2-(4,4,5,5-tetramethyl-1,3,2-dioxaborone-2-yl)phenyl)methyl ketone (B) (4-Chlorophenyl)(2-iodophenyl) methyl ketone was dissolved in toluene. Triethylamine, pinacol borane, bis(di-tert-butyl)-4-dimethylaminophenylphosphine (APhos), and tris(dibenzylacetone)dipalladium (Pd2(dba)3) were added sequentially to the solution. The resulting mixture was inertized with N2 and heated to 45–65 °C until the reaction was complete as determined by HPLC. The mixture was cooled, quenched with ethanol, and filtered. The filter cake was washed with toluene. The combined filtrates were displaced into isopropanol. The product was crystallized from isopropanol / n-heptane (approximately 3:1 v / v) at -10 to 10 °C. The solid was filtered, washed with isopropanol / n-heptane (approximately 3:1 v / v), and dried under vacuum at 40–60 °C to yield the separated product B. Typical yields range from 84–91 mol%.

[0022] Preparation of (S,E)-N-((4-iodo-3-methylisoxazol-5-methyl)methylene)-2-methylpropane-2-sulfonamide (A) 4-Iodo-3-methylisoxazole-5-carboxaldehyde was dissolved in toluene. Anhydrous copper(II) sulfate was added to the solution, followed by (S)-tert-butylsulfinamide and acetic acid. The resulting mixture was heated to 43–58 °C until the reaction was complete as determined by HPLC. The mixture was cooled and filtered. The filter cake was washed with MTBE. The combined filtrates were adjusted to pH 3.5–5.5 with NaHCO3, washed with water, and partitioned. The organic layer was concentrated and crystallized from toluene / MTBE / n-heptane at -10 to 7 °C. The solid was filtered and washed with cold toluene / MTBE / n-heptane. The batch was dried under vacuum at 30–55 °C to produce the product. Typical yields ranged from 75–84 mol%.

[0023] Preparation of (S)-3-(((S)-tert-butylsulfinyl)amino)-3-(4-iodo-3-methylisoxazol-5-yl)propionic acid (I) Compound A was dissolved in THF at -15 to 15°C to form feed solution A. KHMDS (1M in THF) was diluted with THF at -15 to 15°C to form feed solution B. EtOAc was mixed with THF at ambient temperature to form feed solution C. AcOH was mixed with H2O at ambient temperature to form quench solution D. After cooling the flow reactor to -60 to -80°C, the KHMDS solution (B) and EtOAc solution (C) were charged into the first flow reactor to form the ester enol intermediate. Feed solution (A) was then added into the second flow reactor to form the ethyl ester. The reaction mixture was quenched with AcOH / H2O (solution D) in a continuous stirred tank reactor (CSTR) at 5 to 30°C. After reaching steady state, the reaction completion of the enriched product solution was checked. The quenched reaction mixture was collected in multiple containers and combined if it passed quality control. After phase separation, the organic solvent is exchanged into EtOH.

[0024] LiOH solution was added to the EtOH solution of ethyl acetate described above at -5 to 15°C. The reaction mixture was stirred at this temperature until hydrolysis was confirmed to be complete by HPLC analysis. The reaction mixture was quenched with an aqueous HCOOH solution to pH 2.0–5.0 to precipitate the product. The slurry was filtered, and the filter cake was washed with water. The solids were re-slurryed in MTBE and water at 30–60°C for at least 0.5 h, and then cooled to 0–20°C. After stirring for at least another 0.5 h, the product was filtered and washed with cold water and MTBE. The product was dried under vacuum below 65°C. Typical yields range from 78–84 mol%.

[0025] Preparation of (S)-3-(((S)-tert-butylsulfinyl)amino)-3-(4-(2-(4-chlorobenzoyl)phenyl)-3-methylisoxazol-5-yl)propionic acid (II) Compound I, 2-MeTHF, and compound B were charged into an aqueous solution of K3PO4·3H2O. After bubbling with N2, Pd(dppf)Cl2·DCM was added. The reaction mixture was purged with N2 and then stirred at 50–70 °C until the reaction was complete as indicated by HPLC analysis. Note: For the addition of compound B, the validated acceptable range is 0.97 to 1.02 eq, and careful control is required. Excessive addition of compound B results in the formation of acid dimer impurities as shown below.

[0026] Cool the batch to room temperature and partition it. Discard the bottom aqueous layer and extract the top organic layer of the enriched product with water. Wash the resulting aqueous layer of the enriched product with 2-MeTHF and MTBE, then treat with an aqueous solution of L-cysteine ​​and 1M NaHSO3. Adjust the pH to 5.7–6.2 to precipitate the product. Add 2-MeTHF to extract the product and separate the phase. Wash the organic solution of the enriched product with a diluted aqueous solution of NaCl. Heat the organic solution to 30–50 °C and treat with activated carbon. Concentrate under vacuum to approximately 3.5–5.5 volumes below 50 °C. Heat the batch to 30–50 °C and purge with toluene and n-heptane, then cool to approximately 10–30 °C to allow the product to crystallize. Filter the resulting slurry and wash the filter cake with n-heptane. Dry the wet cake under vacuum to obtain the product. Typical yields range from 74–81 mol percent.

[0027] Preparation of (S)-2-(6-(4-chlorophenyl)-1-methyl-4H-benzo[c]isoxazol[4,5-e]aza-4-yl)acetic acid(III) Deprotection / cyclization Compound II was dissolved in 1,4-dioxane and water. Concentrated HCl was added to the solution, and the resulting mixture was stirred at 15–35 °C until deprotection was complete as indicated by HPLC analysis. Toluene was added, followed by a charge with an aqueous solution of K3PO4 to adjust the pH to 1–2.5. The reaction mixture was stirred for at least another 0.5 h. A second charge with an aqueous solution of K3PO4 was added to adjust the pH to 5–6.8. The batch was stirred at 15–35 °C until cyclization was complete. The phases were separated, and the aqueous phase was extracted with toluene. The combined toluene phases were extracted with an aqueous solution of K2CO3. The alkaline aqueous solution enriched with the product was treated with activated carbon at ambient temperature to remove dppf oxide and residual palladium. The resulting aqueous solution was washed with a toluene / 2-MeTHF mixed solvent, followed by washing with heptane. The batch was acidified with an aqueous solution of acetic acid at room temperature to precipitate the product. The resulting suspension was stirred at room temperature to produce a free acid product as a solid. The solid was filtered and washed with water and n-heptane, respectively.

[0028] Optional rework procedures: Dissolve the wet cake in 2-MeTHF at 15–35 °C. Add toluene and concentrate the resulting mixture under vacuum to 2–3.5 times its volume below 55 °C. Add additional toluene and repeat the solvent exchange method until the residual 2-MeTHF meets the quality standards (spec.). Heat the resulting mixture at 50–70 °C for at least 0.5 h and cool to 10–30 °C to complete crystallization. Filter the solid and wash with toluene.

[0029] dry The wet cake is dried under vacuum at below 60°C to produce the product. Typical yields range from 82 to 91 mol percent (without rework). The rework method yields approximately 80 mol percent.

[0030] Preparation of (S)-2-(6-(4-chlorophenyl)-1-methyl-4H-benzo[c]isoxazo[4,5-e]aza-4-yl)acetamide (crystal form B) amidation reaction: Di-tert-butyl pyrocarbonate (Boc anhydride, Boc₂O) was added to a mixture of the above product, ammonium carbonate, and pyridine in 2-MeTHF. The batch was stirred at 10–30 °C until the reaction was complete. The mixture was washed with a diluted aqueous NaCl solution, and the phases were separated. The enriched organic layer was treated with activated carbon at 50–65 °C. The organic solution of the enriched product was concentrated below 65 °C. Additional 2-MeTHF was added, and the concentration was again below 65 °C. This process was repeated until KF analysis showed that the batch was dry. The dried 2-MeTHF solution was heated to 55–65 °C and n-heptane was added. After adding seed crystals, additional n-heptane was added, and the batch was gradually cooled to room temperature. The resulting slurry was stirred at room temperature until crystallization was complete. The product was filtered, washed with n-heptane, and dried below 45 °C to give amorphous form B. Typical yields ranged from 88–94 mol%.

[0031] (S)-2-(6-(4-chlorophenyl)-1-methyl-4H-benzo[c]isoxazo[4,5-e]aza-4-ylacetamide monohydrate (crystal form A) The anhydrous product was dissolved in a solution of ethanol and water (approximately 4:1, v / v) at room temperature. The resulting clear solution was polished and filtered. Water was added to the filtrate, followed by the addition of seed crystals and cooling to -10 to 10°C to allow the product to crystallize in the desired crystal form A. The resulting solid was filtered and washed with purified water. The wet cake was dried under controlled humidity to obtain the monohydrate product in crystal form A. See, for example, U.S. Patent No. 9,969,747. The product was micronized by jet milling with a nitrogen stream.

[0032] While many embodiments have been described, it will be apparent that our basic embodiments can be modified to provide other embodiments utilizing the compounds and methods of this disclosure. Therefore, it should be understood that the scope of this disclosure is defined by the appended claims, and not by the specific embodiments presented by way of example.

[0033] All references cited throughout this application (including bibliographic references, granted patents, published patent applications, and pending patent families) are expressly incorporated herein by reference in their entirety. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

Claims

1. A method for preparing a compound having formula I: (I)， The method includes reacting a compound having formula A in the presence of ethyl acetate: (A) reacts with a strong base and then undergoes ester hydrolysis to form a compound having formula I.

2. The method according to claim 1, wherein the strong alkali is a metal-containing alkali.

3. The method according to claim 1 or claim 2, wherein the strong base is a sterically hindered metal-containing base.

4. The method according to any one of claims 1 to 3, wherein the strong base is selected from lithium bis(trimethylsilyl)amino (LiHMDS), sodium bis(trimethylsilyl)amino (NaHMDS), and potassium bis(trimethylsilyl)amino (KHMDS).

5. The method according to any one of claims 1 to 4, wherein the strong base is potassium bis(trimethylsilyl)amino (KHMDS).

6. The method according to any one of claims 1 to 5, further comprising reacting the compound having formula A with a strong base in the presence of ethyl acetate and at least one organic solvent.

7. The method according to claim 6, wherein the at least one additional solvent is tetrahydrofuran (THF).

8. The method according to any one of claims 1 to 7, wherein the ester hydrolysis is carried out under alkaline conditions.

9. The method according to any one of claims 1 to 8, wherein the ester hydrolysis is carried out using an inorganic hydroxide base.

10. The method according to any one of claims 1 to 9, wherein the ester hydrolysis is carried out using an inorganic hydroxide base selected from lithium hydroxide, sodium hydroxide, and potassium hydroxide.

11. The method according to any one of claims 1 to 10, wherein the ester hydrolysis is carried out using lithium hydroxide.

12. The method according to any one of claims 1 to 11, wherein the ester hydrolysis is carried out under aqueous conditions.

13. The method according to any one of claims 1 to 12, wherein the ester hydrolysis is carried out using lithium hydroxide, water and ethanol.

14. A method for preparing a compound having formula II: (II), The method includes reacting a compound of formula I in the presence of a palladium source and a base: (I) With compounds having formula B: (B) Reaction.

15. The method according to claim 14, wherein the palladium source is selected from Pd(Ph3P)4, Pd(OAc)2, Pd2(dba)3, Pd(Ph3)2Cl2, and Pd(dppf)Cl2.

16. The method according to claim 14 or claim 15, wherein the palladium source is Pd(dppf)Cl2.

17. The method according to any one of claims 14 to 16, wherein the base is an inorganic base.

18. The method according to any one of claims 14 to 17, wherein the alkali is selected from Na2CO3, K2CO3, Cs2CO3, t-BuOK, NaOEt and K3PO4.

19. The method according to any one of claims 14 to 18, wherein the base is K3PO4.

20. The method according to any one of claims 14 to 19, wherein the reaction of the compound having formula I with the compound having formula B further comprises adding at least one organic solvent.

21. The method according to any one of claims 14 to 20, wherein the reaction of the compound having formula I with the compound having formula B further comprises adding at least one aprotic organic solvent.

22. The method according to any one of claims 14 to 21, wherein the reaction of the compound having formula I with the compound having formula B further comprises the addition of THF, 2MeTHF, MTBE, 1,4-dioxane or DME.

23. The method according to any one of claims 14 to 22, wherein the reaction of the compound having formula I with the compound having formula B further comprises the addition of 2MeTHF.

24. The method according to any one of claims 14 to 23, further comprising reacting the compound having formula II with an acid and reacting the resulting intermediate with a base to form a compound having formula III: (III)。 25. The method of claim 24, wherein the acid is an aqueous acid.

26. The method according to claim 24 or claim 25, wherein the acid is selected from HCl, HBr, HI, H3PO4 and H2SO4.

27. The method according to any one of claims 24 to 26, wherein the acid is HCl.

28. The method according to any one of claims 24 to 27, wherein the alkali is an aqueous alkali.

29. The method according to any one of claims 24 to 28, wherein the alkali is selected from Na2CO3, K2CO3 and K3PO4.

30. The method according to any one of claims 24 to 29, wherein the base is K3PO4.

31. The method according to any one of claims 14 to 30, wherein the compound having formula I is prepared by the method according to any one of claims 1 to 13.

32. Compounds Or its salt.

33. A compound selected from: , and ; or any of the aforementioned salts.

34. The compound according to claim 33, wherein the compound is Or its salt.

35. The compound according to claim 33, wherein the compound is Or its salt.

36. The compound of claim 33, wherein the compound is , or its salt.

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