Methods and intermediates for preparing JAK inhibitors

Abstract

Improved processes and intermediates for preparing ruxolitinib, deuterated analogs of ruxolitinib, and other JAK inhibitors are disclosed.

Description

[0001] Cross-references to related applications

[0002] This application claims the benefit of U.S. Provisional Patent Application No. 63 / 045,627, filed June 29, 2020. The entire instruction of the above application is incorporated herein by reference. Background Technology

[0003] Ruxotinib phosphate is a heteroaryl-substituted pyrrolo[2,3-d]pyrimidine, also known as 3(R)-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propionitrile phosphate and (R)-3-(4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl)-3-cyclopentylpropionitrile phosphate, which inhibits Janus-associated kinases (JAK) JAK1 and JAK2. These kinases mediate the signaling of many cytokines and growth factors important for hematopoietic and immune functions. JAK signaling involves the recruitment of STATs (signal transducers and activators of transcription) to cytokine receptors, activation, and subsequent localization of STATs to the nucleus, leading to the regulation of gene expression.

[0004] Ruxotinib phosphate has been approved in the United States and Europe for the treatment of myelofibrosis and polycythemia vera. Ruxotinib is currently in clinical trials for the treatment of graft-versus-host disease and other conditions.

[0005] A deuterated analogue of ruxotinib phosphate (referred to in this article as CTP-543 or compound (I)) is currently in clinical trials for the treatment of alopecia areata.

[0006] Due to the beneficial activity of ruxolitinib and its deuterated analogues, there is a continued need for improved methods for synthesizing ruxolitinib and its deuterated forms. Summary of the Invention

[0007] This invention provides improved compounds and methods for synthesizing intermediates that can be used to prepare ruxotinib, deuterated forms of ruxotinib, and other JAK inhibitors. In one aspect, this invention provides a method for preparing compounds having Formula 5:

[0008]

[0009] The method includes making a compound having Formula 1:

[0010]

[0011] With compound 4

[0012]

[0013] The step of reacting with a base (e.g., a base selected from lithium hexamethyldisilamide (LiHMDS) and sodium hexamethyldisilamide (NaHMDS)); wherein R 1 Selected from H or protecting group (PG), wherein R 2 It is a C1-C4 alkyl group.

[0014] In another aspect, the present invention provides a method for preparing compounds having Formula 7:

[0015]

[0016] The method includes making a compound having Formula 5:

[0017]

[0018] The steps involved in the reaction with formamidine or its salts;

[0019] Where R 1 Selected from H or protecting group (PG).

[0020] In another aspect, the present invention provides a method for preparing a compound having formula 7, the method comprising reacting a compound having formula 5 with formamidin or a salt thereof; or reacting it with an ammonium source and a trialkyl orthoformate; wherein R 1 Selected from H or protecting group (PG).

[0021] In another aspect, the present invention provides a method for preparing compounds having formula 6a:

[0022]

[0023] The method includes making a compound having Formula 5:

[0024]

[0025] The steps involved in the reaction with ammonium salts;

[0026] Where R 1 Selected from H or protecting group (PG).

[0027] In another aspect, the present invention provides a method for preparing a compound having formula 6a, the method comprising the step of reacting a compound having formula 5 with an ammonium source (such as an ammonium salt or ammonia);

[0028] Where R 1 Selected from H or protecting group (PG). In some embodiments, the ammonium source is an ammonium salt. In some embodiments, the ammonium salt is ammonium formate, ammonium chloride, or ammonium acetate.

[0029] In another aspect, the present invention provides a method for preparing compounds having Formula 7:

[0030]

[0031] The method includes making a compound having formula 6a:

[0032]

[0033] The steps involved in the reaction with formamidine or its salts;

[0034] Where R 1 Selected from H or protecting group (PG).

[0035] Other aspects and embodiments of the invention will become apparent from the detailed description and claims herein. Detailed Implementation

[0036] definition

[0037] The term "alkyl" refers to a monovalent saturated hydrocarbon group. C1-C6 alkyl groups are alkyl groups having 1 to 6 carbon atoms; C1-C4 alkyl groups are alkyl groups having 1 to 4 carbon atoms. In some embodiments, the alkyl group may be straight-chain or branched. In some embodiments, the alkyl group may be primary, secondary, or tertiary alkyl. Non-limiting examples of alkyl groups include methyl; ethyl; propyl, including n-propyl and isopropyl; butyl, including n-butyl, isobutyl, sec-butyl, and tertiary butyl; pentyl, including, for example, n-pentyl, isopentyl, and neopentyl; and hexyl, including, for example, n-hexyl and 2-methylpentyl. Non-limiting examples of primary alkyl groups include methyl, ethyl, n-propyl, n-butyl, n-pentyl, and n-hexyl. Non-limiting examples of secondary alkyl groups include isopropyl, sec-butyl, and 2-methylpentyl. Non-limiting examples of tertiary alkyl groups include tertiary butyl.

[0038] The term "alkenyl" refers to a monovalent unsaturated hydrocarbon group, where the degree of unsaturation is represented by a double bond. C2-C6 alkenyl groups are alkenyl groups having 2 to 6 carbon atoms. Alkenyl groups can be straight-chain or branched. Examples of alkenyl groups include CH2=CH- (vinyl), CH2=C(CH3)-, CH2=CH-CH2- (allyl), CH3-CH=CH-CH2- (crotonyl), CH3-CH=C(CH3)-, and CH3-CH=CH-CH(CH3)-CH2-. In cases where double bond stereoisomers are possible, the stereochemistry of the alkenyl group can be (E), (Z), or a mixture thereof.

[0039] "Aryl" itself, or as part of another substituent, refers to a monocyclic or polycyclic monovalent aromatic hydrocarbon group having the stated number of carbon atoms (i.e., C5-C1). 14This refers to groups with 5 to 14 carbon atoms. Typical aryl groups include, but are not limited to, those derived from the following groups: acepanthene, acenaphthene, phenanthrene, anthracene, azulene, benzene, chrysoprase, fluoranthene, phenanthrene, hexane, hexene, as-indacene, s-indacene, indene, indene, naphthalene, octaphenyl, octane, oleene, pentyl-2,4-diene, pentane, pentane, pentane, perylene, phenaene, phenanthrene, heptane, pyrene, pyranthrene, rubigin, benzo[a]phenanthrene, ternaphthalene, etc. In specific embodiments, the aryl group is cyclopentadienyl, phenyl, or naphthyl. In more specific embodiments, the aryl group is phenyl or naphthyl.

[0040] The term "heterocyclic" refers to a monocyclic or bicyclic monovalent saturated or non-aromatic unsaturated ring system, wherein one to four ring atoms are heteroatoms independently selected from the group consisting of O, N, and S. The term "3- to 10-membered heterocyclic alkyl" refers to a heterocyclic alkyl system in which the number of ring atoms ranges from 3 to 10. Examples of 3- to 10-membered heterocyclic alkyls include 3- to 6-membered heterocyclic alkyls. Bicyclic systems include fused, bridged, and spirocyclic ring systems. More specific examples of heterocyclic alkyls include aziridine, aziridine, aziridinyl, imidazolyl, morpholinyl, oxazolyl, oxazolyl, piperazinyl, piperidinyl, pyrazolyl, pyrrolidinyl, quininecycloyl, and thiomorpholinyl.

[0041] In the aforementioned heterocyclic substituents, nitrogen, phosphorus, carbon, or sulfur atoms can optionally be oxidized to various oxidation states. In a specific example, the group -S(O)... 0-2 - refers to -S- (sulfide), -S(O)- (sulfoxide), and -SO2- (sulfone), respectively. For convenience, nitrogen, particularly but not exclusively, is intended to include their corresponding N-oxide forms, although not explicitly defined in certain instances. Thus, for compounds of the invention having, for example, a pyridyl ring; the corresponding pyridyl-N-oxide is intended to be included as another compound of the invention. Furthermore, the cyclic nitrogen atom may optionally be quaternized; and the cyclic substituents may be partially or fully saturated or aromatic.

[0042] “CTP-543” is a deuterated analogue of ruxotinib, known chemically as (R)-3-(4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl)-3-(cyclopentyl-2,2,3,3,4,4,5,5-d8)propionitrile. Compound (I) may also be referred to herein as D8-ruxotinib. Compound (I) is represented by the following structural formula:

[0043]

[0044]

[0045] As used herein, the terms “contact” and “reaction” are as known in the art and generally refer to a way in which chemical reagents are brought together in a manner that allows them to interact at the molecular level to achieve a chemical or physical transformation. In some embodiments, a contact or reaction involves two (or more) reagents, wherein one or more equivalents of a second reagent are used relative to a first reagent. The reaction steps described herein can be carried out at times and under conditions suitable for the preparation of the identified product.

[0046] The preparation of compounds can involve the protection and deprotection of various chemical groups. The need for protection and deprotection, and the selection of appropriate protecting groups, can be readily determined by those skilled in the art. The chemistry of protecting groups can be found, for example, in Greene et al., Protective Groups in Organic Synthesis, 4th ed., Wiley & Sons, 2007, which is incorporated herein by reference in its entirety. Thus, for example, a nitrogen atom can be protected to a carbamate by a protecting group such as tert-butoxycarbonyl (Boc); to a sulfonamide by a protecting group such as trifluoromethanesulfonyl (Tf, SO2-CF3); to an amide by a protecting group such as acetyl, benzoyl, or trifluoroacetyl (F3-Ac); to an amine by a protecting group such as benzyl or triphenylmethyl (Tr, -CPh3); or to a silylamine (e.g., with a protecting group such as SiPh2Bu). t The protecting groups described herein, as well as the methods for their formation and cleavage, can be adjusted as needed based on various substituents.

[0047] The reactions described herein can be carried out in suitable solvents that can be readily selected by those skilled in the art of organic synthesis. At the temperature at which the reaction takes place, for example in the range from the freezing point to the boiling point of the solvent, a suitable solvent can be substantially non-reactive with the starting materials (reactants), intermediates, or products. A given reaction can be carried out in one solvent or a mixture of more than one solvent. Depending on the specific reaction step, a suitable solvent can be selected for that specific reaction step. In some embodiments, the reaction can be carried out in the absence of a solvent, for example when at least one reagent is a liquid or gas.

[0048] Suitable solvents may include halogenated solvents such as carbon tetrachloride, bromodichloromethane, dibromochloromethane, bromoform, chloroform, bromochloromethane, dibromomethane, butyl chloride, dichloromethane (DCM), tetrachloroethylene, trichloroethylene, 1,1,1-trichloroethane, 1,1,2-trichloroethane, 1,1-dichloroethane, 2-chloropropane, α,α,α-trifluorotoluene, 1,2-dichloroethane, 1,2-dibromoethane, hexafluorobenzene, 1,2,4-trichlorobenzene, 1,2-dichlorobenzene, chlorobenzene, fluorobenzene, trifluorotoluene (TFT), and mixtures thereof.

[0049] Suitable ether solvents include: dimethoxymethane, tetrahydrofuran (THF), 1,3-dioxane, 1,4-dioxane, furan, diethyl ether, ethylene glycol dimethyl ether, ethylene glycol diethyl ether, diethylene glycol dimethyl ether, diethylene glycol diethyl ether, triethylene glycol dimethyl ether, anisole, tert-butyl methyl ether, and mixtures thereof. Other ether solvents include 2-methyltetrahydrofuran and cyclopentylmethyl ether (and mixtures thereof, including mixtures with other ether solvents described herein).

[0050] Suitable proton solvents may include, for example, but not limited to, water, methanol (MeOH), ethanol (EtOH), isopropanol (iPrOH), 2-nitroethanol, 2-fluoroethanol, 2,2,2-trifluoroethanol (TFE), ethylene glycol, 1-propanol, 2-propanol, 2-methoxyethanol, 1-butanol, 2-butanol, isobutanol, tert-butanol, 2-ethoxyethanol, diethylene glycol, 1-, 2- or 3-pentanol, neopentanol, tert-pentanol, diethylene glycol monomethyl ether, diethylene glycol monoethyl ether, cyclohexanol, benzyl alcohol, phenol, glycerol, hexafluoroisopropanol (HFIP), acetic acid (AcOH), and mixtures thereof.

[0051] Suitable aprotic solvents may include, for example, but not limited to, tetrahydrofuran (THF), N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMA), 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU), 1,3-dimethyl-2-imidazolinone (DMI), N-methylpyrrolidone (NMP), formamide, N-methylacetamide, N-methylformamide, acetonitrile, dimethyl sulfoxide (DMSO), propionitrile, ethyl formate, methyl acetate, hexachloroacetone, acetone, ethyl methyl ketone, ethyl acetate (EtOAc), sulfolane, N,N-dimethylpropionamide, tetramethylurea, nitromethane, nitrobenzene, hexamethylphosphoramide, and mixtures thereof.

[0052] Suitable hydrocarbon solvents include benzene, cyclohexane, pentane, hexane, toluene, cycloheptane, methylcyclohexane, heptane, ethylbenzene, meta-, or o- or p-xylene, octane, indane, nonane, naphthalene, and mixtures thereof.

[0053] The reactions described herein can be carried out at a suitable temperature that can be readily determined by a person skilled in the art. The reaction temperature will depend on, for example, the melting and boiling points of the reagents and solvents (if present); the thermodynamics of the reaction (e.g., a violently exothermic reaction may require a lower temperature); and the kinetics of the reaction (e.g., a high activation barrier may require an elevated temperature). “Elevated temperature” refers to a temperature above room temperature (approximately 22°C).

[0054] The reactions described herein can be carried out in air or under an inert atmosphere. Typically, reactions involving reagents or products that react substantially with air can be carried out using air-sensitive synthesis techniques well known to those skilled in the art.

[0055] Examples of acids can be inorganic or organic. Non-limiting examples of inorganic acids include hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, and nitric acid. Non-limiting examples of organic acids include formic acid, acetic acid, propionic acid, butyric acid, benzoic acid, 4-nitrobenzoic acid, methanesulfonic acid, p-toluenesulfonic acid, benzenesulfonic acid, tartaric acid, trifluoroacetic acid, propynic acid, butyric acid, 2-butynic acid, vinylacetic acid, valeric acid, hexanoic acid, heptanoic acid, octanoic acid, nonanoic acid, and decanoic acid.

[0056] Non-limiting examples of bases include lithium hydroxide, sodium hydroxide, potassium hydroxide, lithium carbonate, sodium carbonate, and potassium carbonate. Some exemplary strong bases include, but are not limited to, hydroxides, alkoxides, amino metals, metal hydrides, dialkylamino metals, and silylamino metals (including, for example, lithium hexamethyldisilamide (LiHMDS) and sodium hexamethyldisilamide (NaHMDS)) and arylamines, wherein; alkoxides include lithium, sodium, and potassium salts of methyl, ethyl, and tert-butyl oxides; amino metals include sodium amide, potassium amide, and lithium amide; metal hydrides include sodium hydride, potassium hydride, and lithium hydride; and dialkylamino metals include lithium, sodium, and potassium salts of methyl, ethyl, n-propyl, isopropyl, n-butyl, tert-butyl, trimethylsilyl, and cyclohexyl-substituted amino compounds.

[0057] When preparing compounds according to the methods described herein, common separation and purification operations (such as concentration, filtration, extraction, solid-phase extraction, recrystallization, chromatography, etc.) can be used to separate the desired product.

[0058] In some embodiments, the compounds of the present invention and their salts are substantially isolated. "Substantially isolated" means that the compounds are at least partially or substantially isolated from the environment in which they are formed or detected. Partial isolation may include, for example, compositions rich in the compounds of the present invention. Substantially isolated may include compositions containing at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% by weight of the compounds of the present invention or their salts. Methods for separating the compounds and their salts are conventional in the art.

[0059] This invention also includes salt forms of the compounds described herein. Salts of the compounds of this invention are formed between an acid and a basic group (such as an amino functional group) of the compound, or between a base and an acidic group (such as a carboxyl functional group) of the compound. According to one embodiment, the compound is a pharmaceutically acceptable acid addition salt. In one embodiment, the acid addition salt may be a deuterated acid addition salt.

[0060] As used herein, the term "pharmaceutically acceptable" means a component that, to a reasonable extent medically permissible, is suitable for use in contact with the tissues of humans and other mammals without excessive toxicity, irritation, allergic reactions, etc., and is proportionate to a reasonable benefit / risk ratio. "Pharmaceutically acceptable salt" means any non-toxic salt that, when administered to a recipient, can directly or indirectly provide the compounds of the present invention. "Pharmaceutically acceptable counterion" is the ionic portion of a salt that is non-toxic when released from the salt upon administration to a recipient.

[0061] Acids commonly used to form pharmaceutically acceptable salts include inorganic acids such as hydrochloric acid, hydrobromic acid, hydroiodic acid, sulfuric acid, and phosphoric acid; and organic acids such as p-toluenesulfonic acid, salicylic acid, tartaric acid, hydrotartaric acid, ascorbic acid, maleic acid, besylic acid, fumaric acid, gluconic acid, glucuronic acid, formic acid, glutamic acid, methanesulfonic acid, ethanesulfonic acid, benzenesulfonic acid, lactic acid, oxalic acid, p-bromobenzenesulfonic acid, carbonic acid, succinic acid, citric acid, benzoic acid, and acetic acid, as well as related inorganic and organic acids. Therefore, pharmaceutically acceptable salts of this class include sulfates, pyrosulfates, bisulfates, sulfites, phosphates, monohydrogen phosphates, dihydrogen phosphates, metaphosphates, pyrophosphates, chlorides, bromides, iodides, acetates, propionates, decanoates, caprylates, acrylates, formates, isobutyrates, decanoates, heptanoates, propynylates, oxalates, malonates, succinates, caprylates, sebacic acid, fumarates, maleates, and butyn-1,4-diacids. Hexyne-1,6-diacidate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, hydroxybenzoate, methoxybenzoate, phthalate, terephthalate, sulfonate, xylenesulfonate, phenylacetate, phenylpropionate, phenylbutyrate, citrate, lactate, β-hydroxybutyrate, glycolate, maleate, tartrate, methanesulfonate, propanesulfonate, naphthalene-1-sulfonate, naphthalene-2-sulfonate, mandelate, and other salts. In one embodiment, pharmaceutically acceptable acid addition salts include those formed with inorganic acids (such as hydrochloric acid and hydrobromic acid), and especially those formed with organic acids (such as maleic acid). In one embodiment, acids commonly used to form pharmaceutically acceptable salts include the inorganic acids listed above, wherein at least one hydrogen atom is replaced by deuterium.

[0062] As used herein, the term "stable compound" means a compound that has sufficient stability to allow the manufacture of the compound and maintains the integrity of the compound for the purposes detailed herein (e.g., formulation into a therapeutic product, an intermediate for the production of a therapeutic compound, an isolable or storable intermediate compound, or a compound for treating a disease or condition in response to a therapeutic agent).

[0063] Both “D” and “d” refer to deuterium. “Steroisomer” refers to both the enantiomer and the diastereomer. “Tert” and “t-” each refer to tertiary. “Sec” or “s-” each refer to secondary. “n-” refers to normal. “i-” refers to isomeric. “US” refers to the United States. Throughout this specification, variables can be generic (e.g., “each R”) or specific (e.g., R…). 1 R 2 R 3(etc.). Unless otherwise indicated, when a variable is used generically, it means that all specific embodiments of that particular variable are included.

[0064] method

[0065] In one aspect, the present invention provides a method for preparing compounds having formula A:

[0066]

[0067] The method includes making a compound having Formula 1:

[0068]

[0069] With compounds having formula D:

[0070]

[0071] The step of reacting with a base (e.g., a base selected from lithium hexamethyldisilamide (LiHMDS) and sodium hexamethyldisilamide (NaHMDS)); wherein R 1 Selected from H and protecting group (PG), wherein R 2 Selected from C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, and heterocyclic groups, wherein each R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl (-CH2-phenyl). In some embodiments, R 2 It is a methyl group. In some embodiments, R 2 It is ethyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3It is an ethyl group. In some embodiments, the reaction steps are carried out in an aprotic solvent (such as tetrahydrofuran (THF)). In some embodiments, the reaction steps are carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction steps are carried out at temperatures between -20°C and 20°C, for example between -20°C and 10°C, between -15°C and 0°C, or between -10°C and 0°C.

[0072] In another aspect, the present invention provides a method for preparing compounds having formula E:

[0073]

[0074] The method involves making a compound having formula A:

[0075]

[0076] The steps involved in the reaction with formamidine or its salts;

[0077] Where R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is methyl. In some embodiments, each R 3 It is ethyl, and R 1 It is a protective base. In some embodiments, if each R 3 If it is ethyl, then R 1Not H. In some embodiments, the reaction step is carried out in a nonprotic solvent (such as bis(2-methoxyethyl) ether (diethylene glycol dimethyl ether)). In some embodiments, the reaction step is carried out in a protic solvent (such as methanol). In some embodiments, the reaction step is carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction step is carried out at a temperature between 20°C and 180°C, for example between 50°C and 165°C. In some embodiments, formamidine is formamidine acetate. In another aspect, the present invention provides a method for preparing a compound having formula E, the method comprising reacting a compound having formula A with formamidine or a salt thereof; or reacting with an ammonium source and a trialkyl orthoformate; or reacting with an ammonium source and a dimethylformamide dimethyl acetal; wherein R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3 It is ethyl. In some embodiments, R 3 It is ethyl, and R 1 It is a protective base. In some embodiments, if R 3 If it is ethyl, then R 1Not H. In some embodiments, the reaction step is carried out in an aprotic solvent (such as bis(2-methoxyethyl) ether (diethylene glycol dimethyl ether)). In some embodiments, the reaction step is carried out in a protic solvent (such as methanol). In some embodiments, the reaction step is carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction step is carried out at a temperature between 20°C and 180°C, for example, between 50°C and 165°C. In some embodiments, the method includes the step of reacting a compound having formula A with an ammonium source and a trialkyl orthoformate. In some embodiments, the trialkyl orthoformate is trimethyl orthoformate. In some embodiments, the ammonium source is ammonia. In some embodiments, the ammonium source is an ammonium salt. In some embodiments, the ammonium salt is ammonium acetate. In some embodiments, the trialkyl orthoformate is selected from trimethyl orthoformate and triethyl orthoformate. In some embodiments, the method includes the step of reacting a compound having formula A with ammonium acetate and trimethyl orthoformate.

[0078] In another aspect, the present invention provides a method for preparing compounds having formula B:

[0079] Compounds having formula C:

[0080] A method for using a compound or a mixture thereof, the method comprising making a compound having formula A:

[0081] The steps of reacting with ammonium salts; where R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3It is an ethyl group. In some embodiments, the reaction steps are carried out in a protic solvent (such as ethanol, e.g., anhydrous ethanol) or a non-protic solvent (such as bis(2-methoxyethyl) ether (diethylene glycol dimethyl ether)). In some embodiments, the reaction steps are carried out in a protic solvent (such as methanol, ethanol, or n-butanol, e.g., anhydrous methanol, ethanol, or n-butanol). In some embodiments, the reaction steps are carried out under an inert atmosphere (e.g., a nitrogen atmosphere). In some embodiments, the reaction steps are carried out at a temperature between 20°C and 120°C, for example, between 20°C and 100°C. In some embodiments, the ammonium salt is ammonium formate. In some embodiments, the method produces a compound having formula B. In some embodiments, the method produces a compound having formula C. In some embodiments, the method produces a mixture of a compound having formula B and a compound having formula C.

[0082] In another aspect, the present invention provides a method for preparing a compound having formula B, a compound having formula C, or a mixture thereof, the method comprising the step of reacting a compound having formula A with an ammonia source (such as ammonia or an ammonium salt); wherein R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3It is an ethyl group. In some embodiments, the reaction steps are carried out in a protic solvent (such as methanol, ethanol, n-butanol, for example, anhydrous methanol, ethanol, or n-butanol) or an aprotic solvent (such as bis(2-methoxyethyl) ether (diethylene glycol dimethyl ether)). In some embodiments, the reaction steps are carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction steps are carried out at a temperature between 20°C and 120°C, for example, between 20°C and 100°C. In some embodiments, the method includes the step of reacting a compound having formula A with ammonium formate. In some embodiments, the method includes the step of reacting a compound having formula A with ammonium acetate. In some embodiments, the method includes the step of reacting a compound having formula A with ammonia. In some embodiments, the method produces a compound having formula B. In some embodiments, the method produces a compound having formula C. In some embodiments, the method produces a mixture of a compound having formula B and a compound having formula C.

[0083] In another aspect, the present invention provides a method for preparing compounds having formula E:

[0084]

[0085] The method involves making a compound having formula B:

[0086] Compounds having formula C:

[0087] or mixtures thereof

[0088] The steps involved in the reaction with formamidine or its salts;

[0089] Where R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3 It is ethyl. In some embodiments, R 3It is ethyl, and R 1 It is a protective base. In some embodiments, R 3 It is ethyl, and R 1 Not H. In some embodiments, the reaction step is carried out in a protic solvent (such as n-butanol). In some embodiments, the reaction step is carried out in a protic solvent (such as methanol, NH3 / methanol, or n-butanol). In some embodiments, the reaction step is carried out in a non-protic solvent (such as toluene). In some embodiments, the reaction step is carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction step is carried out at a temperature between 20°C and 150°C, for example, between 50°C and 140°C. In some embodiments, formamidine is formamidine acetate. In some embodiments, the method includes the step of reacting a compound having formula B with formamidine or a salt thereof. In some embodiments, the method includes the step of reacting a compound having formula C with formamidine or a salt thereof. In some embodiments, the method includes the step of reacting a mixture of a compound having formula B and a compound having formula C with formamidine or a salt thereof.

[0090] In another aspect, the present invention provides a method for preparing a compound having formula E, the method comprising reacting a compound having formula B, or a compound having formula C, with formamidinium or a salt thereof; or reacting with a trialkyl orthoformate (such as trimethyl orthoformate or triethyl orthoformate) and an ammonium source; or reacting with dimethylformamide dimethyl acetal and an ammonium source; wherein R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is H. In some embodiments, R 1 It is a protective base. In some embodiments, R 1 It is a protecting group, which is benzyl. In some embodiments, R 3 It is a methyl group. In some embodiments, R 3 It is ethyl. In some embodiments, R 3 It is ethyl, and R 1 It is a protective base. In some embodiments, R 3 It is ethyl, and R 1Not H. In some embodiments, the reaction step is carried out in a protic solvent (such as methanol, NH3 / methanol, or n-butanol). In some embodiments, the reaction step is carried out in a non-protic solvent (such as toluene). In some embodiments, the reaction step is carried out under an inert atmosphere (e.g., nitrogen atmosphere). In some embodiments, the reaction step is carried out at a temperature between 20°C and 150°C, for example, between 50°C and 140°C. In some embodiments, the method includes the step of reacting a compound having formula B with trimethyl orthoformate. In some embodiments, the method includes the step of reacting a compound having formula C with trimethyl orthoformate. In some embodiments, the method includes the step of reacting a compound having formula B and a compound having formula C with trimethyl orthoformate. In some embodiments, the method includes the step of reacting a compound having formula B with dimethylformamide dimethyl acetal. In some embodiments, the method includes the step of reacting a compound having formula C with dimethylformamide dimethyl acetal. In some embodiments, the method includes the step of reacting a compound having formula B and a compound having formula C with dimethylformamide dimethyl acetal.

[0091] In some embodiments, the ammonium source is ammonia or an ammonium salt. In some embodiments, the ammonium salt is ammonium formate, ammonium chloride, or ammonium acetate.

[0092] In one aspect, the present invention provides a method for preparing a compound having Formula 7, which is an intermediate that can be used to synthesize ruxotinib, CTP-543, and other JAK inhibitors. In some embodiments, these methods include the steps shown in Scheme 1 below:

[0093] Option 1

[0094]

[0095] In some embodiments, a method for preparing a compound having formula 7 includes reacting a compound having formula 6a with formamidin or a salt thereof; or with trimethyl orthoformate; or with dimethylformamide dimethylacetal.

[0096] In other embodiments, these methods include the steps shown in Scheme 2 below:

[0097] Option 2

[0098]

[0099] In some embodiments, a method for preparing a compound having Formula 7 includes reacting a compound having Formula 6b with formamidin or a salt thereof; or with trimethyl orthoformate; or with dimethylformamide dimethylacetal.

[0100] In some embodiments, these methods include the steps shown in scheme 3 below:

[0101] Option 3

[0102]

[0103] In one respect, compound 8 (i.e., where R...) 1 Compounds of formula 7 (which are H) can be used as intermediates in methods for preparing ruxolitinib, for example, as shown in scheme 4 below:

[0104] Option 4

[0105]

[0106] Ruxotinib produced by the above method is treated with phosphoric acid (H3PO4) to produce ruxotinib phosphate.

[0107] In another respect, compound 8 (i.e., where R) 1 (A compound of formula 7, which is H) can be used as an intermediate in the method for preparing CTP-543, as shown in Scheme 5 below:

[0108] Option 5

[0109]

[0110] CTP-543 produced by the above method is treated with phosphoric acid (H3PO4) to produce phosphate of CTP-543.

[0111] intermediate

[0112] In one aspect, the present invention provides compounds and intermediates that can be used to prepare ruxotinib, deuterated analogs of ruxotinib, and other JAK inhibitors. See, for example, PCT Publication WO 2020 / 163653.

[0113] In some embodiments, the present invention provides compounds represented by the following structures:

[0114] or its salt, wherein R 1 It is H or a protecting group, and each R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, if each R 3 If it is ethyl, then R 1 Not H. In some embodiments, R 1 It is benzyl. In some embodiments, R 1 It is H. In some embodiments, each R 3 It is a methyl group.

[0115] In one embodiment, the present invention provides a compound represented by the following structure:

[0116] Or its salt.

[0117] In another embodiment, the present invention provides compounds represented by the following structures:

[0118] Or its salt.

[0119] In some embodiments, the present invention provides compounds represented by the following structures:

[0120] or its salt, wherein R 1 It is H or a protecting group, and each R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is benzyl. In some embodiments, R 1 It is H. In some embodiments, each R 3 It is methyl. In some embodiments, each R 3 It is ethyl. In some embodiments, if each R 3 If it is ethyl, then R 1 Not H.

[0121] In another embodiment, the present invention provides compounds represented by the following structures:

[0122] Or its salt.

[0123] In another embodiment, the present invention provides compounds represented by the following structures:

[0124] Or its salt.

[0125] In some embodiments, the present invention provides compounds represented by the following structures:

[0126] or its salt, wherein R 1 It is H or a protecting group, and each R 3 It is C1-C 10 Alkyl (e.g., methyl or ethyl), C2-C 10 Alkenyl (e.g., allyl), aryl, or both R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted (e.g., 1,3-dioxolane-2-yl ring, or 1,3-dioxane-2-yl ring, or 1,3-benzodioxolane-2-yl ring, each optionally substituted with one or more methyl groups). In some embodiments, R 1 It is benzyl. In some embodiments, R 1 It is H. In some embodiments, each R 3 It is methyl. In some embodiments, each R 3 It is ethyl. In some embodiments, if each R 3 If it is ethyl, then R 1 Not H.

[0127] In another embodiment, the present invention provides compounds represented by the following structures:

[0128] Or its salt.

[0129] In another embodiment, the present invention provides compounds represented by the following structures:

[0130] Or its salt.

[0131] Example

[0132]

[0133] Example 1: Preparation of methyl 1-benzyl-1H-pyrazole-4-carboxylate (16)

[0134]

[0135] Add methyl 1H-pyrazole-4-carboxylate 15a (10 g, 77.7 mmol, 1.0 equivalent) and K₂CO₃ (21.9 g, 158 mmol, 2.04 equivalent) to a 250 mL jacketed flask equipped with a stir bar, thermocouple, and positive nitrogen flow, followed by dimethylformamide (DMF) (80 mL). Cool the mixture to 0 °C. Add benzyl bromide (11.3 mL, 93.3 mmol, 1.2 equivalent) over 10 minutes. Allow the reaction mixture to reach room temperature and stir for 18 hours. Add water (50 mL) and transfer the mixture to a 500 mL separatory funnel. Extract the mixture twice with ethyl acetate (150 mL). The combined organic extracts were washed with brine (30 ml), dried over Na2SO4, and concentrated under vacuum to give a colorless residue. The residue was allowed to stand and crystallize to give methyl 1-benzyl-1H-pyrazole-4-carboxylate 16a (14.1 g, 85% yield).

[0136] 1 H-NMR (400MHz, CDCl3): δ7.85(s,1H),7.75(s,1H),7.31-7.22(m,3H),7.187.13(m,2H),5.21(s,2H),3.71(s,3H).

[0137] Example 2: Preparation of 2-(1-benzyl-1H-pyrazole-4-carbonyl)-4,4-dimethoxybutyronitrile (17)

[0138]

[0139] Add sodium bis(trimethylsilyl)amino (44 ml, 87.5 mmol, 2.2 equivalents, 2 M in tetrahydrofuran (THF)) and 10 ml of anhydrous THF to a 125 ml jacketed flask equipped with a thermocouple, stir bar, and positive nitrogen flow. Cool the mixture to -14 °C. Over 40 minutes, add a solution of compound 1-benzyl-1H-pyrazole-4-carboxylate 16a (8.6 g, 39.8 mmol, 1.0 equivalent) and 4,4-dimethoxybutyronitrile 4 (6.2 ml, 47.7 mmol, 1.2 equivalents) in 15 ml of THF to the mixture. After addition, stir the mixture at -10 °C for 1 hour, then at 0 °C overnight. Acidify the reaction mixture to pH 2 using hydrochloric acid (0.5 N), then extract twice with ethyl acetate (150 ml). The combined organic extracts were washed with water (20 ml) and brine (20 ml), then dried over Na2SO4 and concentrated under vacuum to give a colorless oily residue. The residue was purified by rapid chromatography (using ethyl acetate / heptane (1:1)) to give the product 2-(1-benzyl-1H-pyrazole-4-carbonyl)-4,4-dimethoxybutyronitrile 17 (10.9 g, 87% yield) as a colorless oil.

[0140] 1 H-NMR (400MHz, CDCl3): δ8.05(s,1H),7.99(s,1H),7.42-7.34(m,3H),7.30-7.25(m,2H),5.37 -5.28(m,2H),4.52(dd,1H),4.05(m,1H),3.39(s,3H),3.30(s,3H),2.30(m,1H),2.18(m,1H).

[0141] Example 3: Preparation of 2-(amino(1-benzyl-1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile (18)

[0142]

[0143] Compound 2-(1-benzyl-1H-pyrazole-4-carbonyl)-4,4-dimethoxybutyronitrile 17 (2.66 g, 8.49 mmol, 1.0 equivalent) and ammonium formate (3.0 g, 42.4 mmol, 5 equivalent) were added to a 125 ml jacketed flask equipped with a stir bar, thermocouple, and positive nitrogen flow. Anhydrous ethanol (25 ml) and 0.6 g of [unspecified ingredient] were then added. Molecular sieves were used. The mixture was heated under reflux for 18 hours. The reaction mixture was filtered through a short silica stopper and then washed with ethanol (5 mL). The resulting filtrate was concentrated under vacuum to give a light brown residue, which was purified by column chromatography (using dichloromethane / methanol (10:1)) to provide 2-(amino(1-benzyl-1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile 18 (1.82 g, 69% yield, E:Z = 9:1) as a yellow oil. The E-geometry of the major enamine isomer was confirmed by NOESY data.

[0144] 1 H-NMR (400MHz, CDCl3): δ7.99(s,1H),7.80(s,1H),7.38-7.30(m,3H),7.277. 22(m,2H),5.31(s,2H),4.83(bs,2H),4.45(t,1H),3.43(s,6H),2.51(d,2H).

[0145] Example 4: Preparation of 6-(1-benzyl-1H-pyrazole-4-yl)-5-(2,2-dimethoxyethyl)pyrimidine-4-amine (19)

[0146]

[0147] Compound (E)-2-(amino(1-benzyl-1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile 18 (0.40 g, 1.28 mmol, 1.0 equivalent) and formamidinium acetate (0.40 g, 3.84 mmol, 3 equivalent) were added to a 25 ml two-necked flask equipped with a condenser, stir bar, thermocouple, and positive nitrogen flow. This was followed by the addition of n-butanol (8 ml) and 100 mg of [unspecified substance]. Molecular sieves were used. The resulting mixture was refluxed for 18 hours. Additional formamidine acetate (0.27 g, 2.0 equivalent) was added and reflux was continued for 36 hours. Additional formamidine acetate (810 mg, 5.0 equivalent) was added over 3 days while maintaining reflux. After a total of 6 days, aliquot analysis of the reaction mixture indicated a conversion of >80% to 6-(1-benzyl-1H-pyrazol-4-yl)-5-(2,2-dimethoxyethyl)pyrimidine-4-amine 19, which was identified by HPLC-MS by comparison with a reference marker.

[0148] UV max: 240 and 290; LCMS (ESI, positive mode): expected value: 340.2 (M+H); found value: 340.1 (M+H).

[0149] Example 5a: Preparation of 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile (20)

[0150]

[0151] Sodium bis(trimethylsilyl)amino (NaHMDS) (67.5 mL, 135 mmol, 3.4 equivalents, 2 M in THF) was added to a 250 mL jacketed flask equipped with a thermocouple, stir bar, and slow nitrogen flow, and cooled to -14 °C. A solution of methyl pyrazole-4-carboxylate 15a (5 g, 39.6 mmol, 1.0 equivalent) and 4,4-dimethoxybutyronitrile 4 (7.3 mL, 55.5 mmol, 1.4 equivalents) in 15 mL THF was added to the solution of sodium bis(trimethylsilyl)amino over 3 hours. The mixture was stirred at -10 °C for 1 hour, then at 0 °C overnight. The reaction mixture was cooled to -10 °C and acidified to pH 2 using hydrochloric acid (0.5 N). The solution was then transferred to a 500 mL separatory funnel and extracted twice with ethyl acetate (100 mL). The combined organic layers were washed with water (20 ml) and brine (20 ml), dried over Na2SO4, and concentrated under vacuum to provide a colorless oil. The residue was purified by rapid chromatography (using ethyl acetate / heptane (8:2)) to provide 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile 20 (6.0 g, 61% yield) as a colorless oil.

[0152] 1H-NMR (400MHz, CDCl3): δ8.24(s,2H),4.55(dd,1H),4.17(dd,1H),3.41(s,3H),3.34(s,3H),2.35(m,1H),2.24(m,1H).

[0153] Example 5b: Preparation of 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile (20)

[0154]

[0155] Add 53.5 mL (1.8 V) of THF to a 2 M solution of NaHMDS in THF (375 mL, 749 mmol, 3.5 equivalences) and cool the solution to -5 °C. Then add a solution of ethyl 4-pyrazolium carboxylate 15b (30.0 g, 214 mmol, 1.0 equivalences) in THF (33 mL, 1.1 V) and wash with another 5.0 mL (0.2 V) of THF. Over a 6-hour period, at a temperature ranging from -5 °C to 0 °C, add a solution of 3-cyanopropanal dimethyl acetal 4 (36.0 g, 278 mmol, 1.3 equivalences) in THF (72 mL, 2.4 V) to the resulting orange suspension. Then maintain the reaction mixture at this temperature for another 15 hours, then add water (180 mL, 6.0 V) while maintaining the temperature ≤5 °C. Stop stirring and remove the upper organic layer. The aqueous phase was adjusted to pH approximately 11 with 6N HCl (92 mL, 3.0 v / v) and then washed with 2-MeTHF (2 × 120 mL, 2 × 4 v / v). The organic phase was discarded, and n-butanol (150 mL, 5 v / v) was added to the remaining aqueous solution. The resulting mixture was adjusted to pH 5 with 85% phosphoric acid (approximately 8 mL), stirring was stopped, and the layers were separated. The organic layer was collected, and the remaining aqueous solution was further extracted with n-butanol (150 mL, 5 v / v). The organic layers were combined, washed with water (100 mL, 3.3 v / v), and then concentrated under vacuum to a target volume of 120 mL (4 v / v) to provide dimethyl acetal 20, a red / orange transparent solution in n-butanol (135.6 g, 28.2% w / w, quantified by QNMR). 1 H-NMR determination: 38.2 g, 20, 80% yield).

[0156] Example 6a: Preparation of 5-(2,2-dimethoxyethyl)-6-(1H-pyrazol-4-yl)pyrimidine-4-amine (8)

[0157] Add 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile 20 (45.9 mg), formamidinium acetate (300 mg, 14 equivalents), and bis(2-methoxyethyl) ether (0.500 mL) to a 4 mL glass vial equipped with a stir bar. Heat the vial in a heater vial holder maintained at 150 °C for 1.5 hours with stirring, then cool to room temperature. Add sodium hydroxide solution (15 wt%, 1.0 mL in water) to the vial. Gently shake the vial for 5 minutes. Add phosphate buffer (3 M phosphate, pH 7, 1 mL), bis(2-methoxyethyl) ether (0.500 mL), and activated carbon (DARCO KB-G) to the vial. Gently shake the vial for 5 minutes, then filter through a polypropylene filter to provide a clear dark red organic layer and a clear pale yellow aqueous layer. The organic layer was purified by column chromatography (0% to 10% methanol in dichloromethane). The fraction containing the product was dried over a stream of nitrogen, and the residue was dissolved in n-butanol (1.0 mL) and washed with tripotassium phosphate solution (1.0 mL, 1 mol). The organic compound was concentrated to provide 5-(2,2-dimethoxyethyl)-6-(1H-pyrazol-4-yl)pyrimidine-4-amine 8 (13.2 mg, 25.7% yield).

[0158] 1 H-NMR(400MHz,DMSO-d6)δ13.10(s,1H),8.24(s,1H),8.07(br s,1H),7.95(br s, 1H), 6.57 (s, 2H), 4.63 (t, J = 5.5Hz, 1H), 3.28 (s, 6H), 2.93 (d, J = 5.5Hz, 2H).

[0159] 13 C-NMR (101MHz, DMSO) δ163.44,156.03,155.75,139.38(br),129.28(br),119.81,107.80,103.49,53.88,31.36.

[0160] LCMS (ESI, positive mode): Expected value: 250.1 (M+H); Found value: 250.1 (M+H).

[0161] Example 6b: Preparation of 5-(2,2-dimethoxyethyl)-6-(1H-pyrazol-4-yl)pyrimidine-4-amine (8)

[0162]

[0163] NH4OAc (6.7 equivalents) in methanol (6 volumes) was added to a flask containing 20 g (5 g) of 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile. The mixture was stirred overnight at 68 °C, and then the methanol was removed by distillation and replaced with trimethyl orthoformate. The mixture was heated to 92 °C and stirred for 4 hours, then cooled to about 0 °C and stirred for 2 hours, followed by filtration to remove solids. The filter cake was washed with acetonitrile (2 × 5 mL), and the resulting filtrate was concentrated under vacuum. Acetonitrile (15 mL) was added, and the resulting mixture was stirred at ambient temperature for 1.5 hours, followed by filtration to remove solids. The filter cake was washed with acetonitrile (5 mL), and the resulting filtrate was concentrated under vacuum to a brown liquid. The crude product was purified by silica gel chromatography (using 0%–70% methanol / CH2Cl2 as eluent) to give an 8-Q NMR (CD3OD) of a light brown solid, indicating a molar yield of 65%.

[0164] Example 7a: Preparation of (E)-2-(amino(1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile (22)

[0165]

[0166] Add 20 mg (161 mg) of 4,4-dimethoxy-2-(1H-pyrazole-4-carbonyl)butyronitrile, 65 mg (1.2 equivalents), and 2.0 mL of bis(2-methoxyethyl) ether to a 4 mL glass vial. Incubate the mixture at 100 °C for 18 hours, then cool to room temperature and transfer to a 20 mL scintillation vial. Add 3.0 mL of methyl tert-butyl ether and 3.0 mL of tripotassium phosphate solution (0.5 M), and age the mixture for 1 hour. Add 0.40 g of solid potassium phosphate and 0.115 g of activated carbon (DARCO KB-G), and gently shake the vial. Filter the mixture to provide a three-phase mixture. Transfer the top layer to another vial. Extract the remaining two layers twice with 5 mL of methyl tert-butyl ether and combine the three methyl tert-butyl ether layers. The combined methyl tert-butyl ether extracts were dried under a nitrogen stream to provide (E)-2-(amino(1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile 22 as a yellow oil containing 21.7 wt% bis(2-methoxyethyl) ether (0.119 g, 58.5% yield).

[0167] 1 ¹H-NMR (400MHz, chloroform-d) δ 10.88 (s, 1H), 7.87 (s, 2H), 5.12 (s, 2H), 4.40 (t, J = 5.1Hz, 1H), 3.34 (s, 6H), 2.42 (d, J = 5.1Hz, 2H).

[0168] 13C-NMR (101MHz, CDCl3) δ151.55,133.83,124.62,116.99,105.51,70.75,54.74,33.58.

[0169] LCMS (ESI, positive mode): Expected value: 223.1 (M+H); Found value: 223.1 (M+H).

[0170] Example 7b: Preparation of (E)-2-(amino(1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile (22)

[0171]

[0172] Ammonium acetate (66.0 g, 856 mmol, 5.0 equivalence) was added to a stirred solution of 20 (38.2 g, 171 mmol) in n-butanol (191 mL, 5 volumes). The resulting mixture was stirred at 60 °C for 15 hours and then cooled to 20 °C. 0.5 M dipotassium hydrogen phosphate solution (191 mL, 5 volumes) was added, followed by n-butanol (76.4 mL, 2 volumes). Stirring was then stopped and the aqueous layer was removed. The organic layer was then washed with 0.5 M dipotassium hydrogen phosphate solution (3 × 135 mL, 3 × 3.5 volumes) followed by 0.05 M dipotassium hydrogen phosphate solution (153 mL, 3.5 volumes). Carbon (Darco KB-G, 1.91 g) was added to the remaining organic solution, and the resulting suspension was stirred at 20 °C for 1 hour, then filtered through diatomaceous earth and washed with n-butanol (76.4 mL, 2 volumes). The combined filtrates were concentrated to approximately 2 volumes to the target volume, and the resulting brown suspension was heated to 60°C. Heptane (131 mL, 3.4 volumes) was added over a 2-hour period at 60°C, and the resulting slurry was then held at this temperature for another hour. After cooling to 20°C, the slurry was filtered under vacuum and washed with 25% n-butanol / heptane (67 mL, 1.75 volumes). The filter cake was dried under vacuum at 50°C to provide 22 (32.1 g, 84% yield) as a brown powder.

[0173] Example 7c: ( E Preparation of 2-(amino(1H-pyrazol-4-yl)methylene)-4,4-dimethoxybutyronitrile (22)

[0174]

[0175] Ammonium acetate (64.3 g, 5.0 equivalent) and methanol (186 mL, 5 volumes) were added to a stirred solution of 20 (37.2 g, 167 mmol, 1.0 equivalent) in MeTHF (45.7% w / w solution). The resulting mixture was stirred at 60 °C for 22 h, then cooled to 20 °C. Carbon (Darco KB-G, 1.86 g) was added to the mixture, and the resulting suspension was stirred at 20 °C for 1 h, then filtered through diatomaceous earth and washed with methanol (112 mL, 3 volumes). The combined filtrates were concentrated to dryness to give a clear, amber-colored oil, which was cooled to 20 °C–25 °C with stirring to give a slurry. Water (223 mL, 6 volumes) was added, and the batch was stirred at 20 °C–25 °C for 5 min. After cooling to 0 °C–5 °C, the mixture was stirred at this temperature for 2 h. The filtrate was filtered under vacuum, and the filter cake was washed with water (112 mL, 3 volumes). The filter cake was dried under vacuum at 50-60 °C to provide 22 (37.9 g, 100% yield - 98.6% w / w, QNMR) as a beige solid.

[0176] Example 8: Preparation of 6-(1-benzyl-1H-pyrazole-4-yl)-5-(2,2-dimethoxyethyl)pyrimidine-4-amine (8)

[0177]

[0178] Example 8a:

[0179]

[0180] Methylamidine acetate (11.8 g, 5.2 equivalents) was added to a solution of 22 (5.0 g, 1.0 equivalent) in dimethylacetamide (DMAc) (20 mL), and the resulting suspension was heated to 115 °C. After stirring at 115 °C for 36 hours, the reaction mixture was cooled to 90 °C and water (10 mL) was added. After stirring at 90 °C for one hour, the reaction mixture was cooled to 20 °C and additional DMAc (10 mL) was added. The resulting dark solution was filtered through a diatomaceous earth mat and then washed with 3:1 DMAc / water (15 mL). The filtrates were combined, diluted with water (28 mL), and carbon (1.5 g) was added. The resulting suspension was stirred at 20 °C for one hour, then filtered and washed with 1:1 DMAc / water (7.5 mL). Add 25% w / w NaCl (4 mL) in water to the combined filtrate, and extract the resulting mixture with 17% n-butanol / CH2Cl2 (4 × 24 mL). Combine the organic layers, wash with 15% w / w K3PO4 in water (15 mL), and then concentrate to approximately 10 mL under vacuum. Add DMAc (4 mL) to bring the total DMAc content to 10 mL, and then add the resulting solution to methyl tert-butyl ether (MTBE) (25 mL) pre-cooled to -20 °C. Add 8 seed crystals of intermediate, and stir the resulting slurry at -20 °C for 4 hours, then add another MTBE (5 mL). After stirring at -20 °C for another 4 hours, filter the slurry, and wash the resulting filter cake with 3:1 MTBE / DMAc (7.5 mL). After drying in a vacuum oven, 5-(2,2-dimethoxyethyl)-6-(1H-pyrazol-4-yl)pyrimidine-4-amine 8 (2.91 g, 54% yield) was obtained as a grayish-white solid.

[0181] Example 8b:

[0182]

[0183] Solid pyrazole-enamine 22 (5.56 g, 25 mmol, 1.0 equivalent) and NH4OAc (11.56 g, 150 mmol, 6.0 equivalent) were added to a 100-mL semi-jacketed glass reactor equipped with a screw cap and magnetic stirrer, followed by the addition of trimethyl orthoformate (TMOF) (50 mL, 9V). The reactor was purged with nitrogen and tightly sealed. The resulting slurry was stirred while the jacket temperature was raised to 88°C. The slurry was allowed to dissolve, yielding a brown solution. The solution was stirred overnight (approximately 20 hours) while maintaining the jacket temperature at 88°C. The mixture was cooled to 20°C and then transferred to a round-bottom flask and concentrated under vacuum to a brown liquid residue (17.9 g).

[0184] TMOF (9.0 mL) and NH4OAc (7.04 g, 91.3 mmol) were added to a portion of this brown liquid (10.6 g, approximately 61% of the initial feed). The mixture was heated in a sealed vial at 92 °C for 4 hours, then cooled to approximately 0 °C and stirred for 2 hours, followed by filtration to remove solids. The wet filter cake was washed with acetonitrile (2 × 5 mL), and the resulting filtrate was concentrated under vacuum. Acetonitrile (15 mL) was added to the concentrate, and the mixture was stirred at ambient temperature for 1.5 hours, followed by filtration to remove solids. The filter cake was washed with acetonitrile (5 mL), and the resulting filtrate was concentrated under vacuum to a brown liquid residue. The crude product was purified by silica gel chromatography (using 0%–70% methanol / CH2Cl2 as eluent) to give 2.1 g of a light brown solid. 1 ¹H-NMR (DMSO-d6) confirmed the presence of product 8 and approximately 8 w% acetic acid. Quantitative analysis was performed. 1 H-NMR (CD3OD) indicated 1.85 g of product 8, with a molar yield of 49%.

[0185] Example 8c:

[0186]

[0187] Pyrazole-enamine 22 (5 g) was mixed with formamidine acetate (14 g, 6.0 equivalents) and 7N NH3 in methanol (5 mL). The mixture was stirred and heated overnight in a sealed reactor, with the jacket temperature set at 120 °C. An additional 7 g of formamidine acetate (3 equivalents) and 7N NH3 in methanol (5 mL) were added to the resulting reaction mixture, and stirring was continued overnight, with the jacket temperature set at 120 °C. The reaction mixture was concentrated under vacuum, and the resulting residue was purified by passing it through a silica gel stopper (using 10%–100% methanol in acetonitrile as eluent) to give 2.7 g of 8 as a light beige solid (molar yield 48%).

[0188] Example 8d:

[0189]

[0190] Add 22 (5.0 g), toluene (20 mL), TMOF (6 mL), and acetic anhydride (6 mL) to a 100 mL reactor equipped with a top stirrer. Heat the mixture to 100 °C and stir under nitrogen for approximately 16 hours. Raise the jacket temperature to 145 °C and distill off approximately 15 mL of solution. Add toluene (15 mL) to the resulting mixture and adjust the batch temperature to 60 °C. Add ammonium acetate (8.8 g) to the solution and stir the mixture under nitrogen for 5 hours. Adjust the batch temperature to 20 °C and add water (10 mL). Cool the batch to 20 °C and discard the clear organic layer. Add potassium phosphate solution (0.5 M, 80 mL) to the reactor. Heat the reactor jacket to 145 °C and remove 5 mL of solution by distillation. Cool the batch to 60 °C and add approximately 2 mg of seed intermediate 8. Cool the mixture to -2 °C and add another 2 mg of seed crystals. Stir the mixture at this temperature for 14 hours. The resulting suspension was filtered through a polypropylene filter funnel and then washed twice with cold water (10 mL × 2). The brownish-red, sandy solid was dried by suction for 45 minutes to obtain 3.9 g of solid. KF titration showed 33% water. The purity was determined to be 61%, with a corrected yield of 41%. The product was analyzed by HPLC. 1 H NMR and mass spectrometry (ESI) + M+H (Expected value: 250.1, Found value: 250.1) is compared with the real sample to confirm the sample's identity.

[0191] Example 8e:

[0192]

[0193] Program A:Add 0.281 g of 22, 1.4 mL of methanol, and 2.8 equivalences of dimethylformamide dimethyl acetal to a 20 mL scintillation bottle equipped with a stir bar. Cap the bottle and stir the mixture for 4 hours in a bottle holder warmed to 60 °C. Add 0.420 g of ammonium formate to the bottle, cap the bottle again, and stir at 60 °C for 23 hours. Use a nitrogen stream to remove most of the methanol from the mixture. Cool the mixture and add 2 mL of potassium phosphate solution (0.5 M) to the remaining oily residue. Briefly stir the resulting mixture, add another 1 mL of potassium phosphate solution, and a white suspension forms immediately. Stir this suspension for 5 minutes and then filter. Wash the bottle and filter cake twice with water (1 mL), and then wash the filter cake three times with 1 mL of methyl tert-butyl ether to promote water removal. After 5 minutes of suction drying, the solid was transferred to a warm (60°C) vial and further dried with a nitrogen stream for 5 minutes to give 0.132 g of a brownish-red solid. The first batch of product was 72.1% w / w product (quantitative NMR) and approximately 22% water (KF titration). The aqueous solutions were combined and cooled to 0°C for 24 hours. A second, smaller batch of product was separated by filtration and dried by suction drying for 20 minutes to give 0.018 g of a second batch of product, 91% w / w (quantitative NMR). The combined yield of the precipitated solid was 35%.

[0194] Program B: Add 2-propanol (10 mL, 5 volumes) and dimethylformamide dimethylacetal (1.2 mL, 1.1 equivalents) to enamine 22 (2.0 g, 1.0 equivalents). Stir the mixture at 80-85°C for 2 hours, then partially cool. Add ammonium formate (1.75 g, 3.0 equivalents) to the mixture, and stir the resulting mixture at 80-85°C for 20 hours. Add potassium phosphate solution (0.5 M, 10 mL, 5 volumes) to the mixture, and concentrate the resulting mixture at 85°C to approximately 5 volumes. Add water (10 mL, 5 volumes), and concentrate again at 85°C to approximately 5 volumes. Cool the mixture to 50°C, then add seed crystal 8 (approximately 5 mg). Cool the mixture to 20°C, stir for 1 hour, and then filter. The filter cake was washed with water (5 mL, 2.5 wt%), then with MBTE (5 mL, 2.5 wt%), and then vacuum dried for 1 hour to give 1.373 g of grayish-white solid 8 (93.0 wt%, purity determined, yield corrected to 57%).

[0195] Without further description, it is believed that those skilled in the art can use the foregoing description and illustrative examples to manufacture and utilize the compounds of the present invention and practice the claimed methods. It should be understood that the foregoing discussion and examples present only a detailed description of certain preferred embodiments. It will be apparent to those skilled in the art that various modifications and equivalents can be made without departing from the spirit and scope of the invention.

Claims

1. A method for preparing a compound having formula E: The method involves making a compound having formula B: Compounds having formula C: or mixtures thereof The steps of reacting with formamidin or its salt, or with trialkyl orthoformate and an ammonium source, or with dimethylformamide dimethyl acetal and an ammonium source; Where R 1 Selected from H and protecting group (PG), and each of R 3 It is C1-C 10 Alkyl, C2-C 10 alkenyl, aryl, or two R 3 Together with the oxygen atoms to which they are attached, they form 5-7 membered heterocycles that can be optionally substituted.

2. The method as described in claim 1, wherein, R 1 It is H.

3. The method as described in claim 1, wherein, R 1 It is a protective base.

4. The method of claim 3, wherein, R 1 It is a protecting group, which is benzyl.

5. The method according to any one of claims 1-4, wherein, R 3 It is a methyl group.

6. The method according to any one of claims 1-4, wherein, R 3 It is an ethyl group.

7. The method according to any one of claims 1-4, wherein, The method includes reacting a compound having formula B with formamidin or a salt thereof, or with a trialkyl orthoformate, or with dimethylformamide dimethyl acetal.

8. The method according to any one of claims 1-4, wherein, The method includes reacting a compound having formula C with formamidin or a salt thereof, or with a trialkyl orthoformate, or with dimethylformamide dimethyl acetal.

9. The method according to any one of claims 1-4, wherein, This reaction is carried out in a proton solvent.

10. The method of claim 9, wherein, The proton solvent is methanol or n-butanol.

11. The method according to any one of claims 1-4, wherein, This reaction is carried out in an aprotic solvent.

12. The method of claim 11, wherein, The aprotic solvent is toluene.

13. The method according to any one of claims 1-4, wherein, The method includes the step of reacting a compound having formula B with formamidine or a salt thereof.

14. The method of claim 13, wherein, The formamidine or its salt is formamidine acetate.

15. The method according to any one of claims 1-4, wherein, The method includes the step of reacting a compound having formula B with ammonium acetate and trimethyl orthoformate.

16. A method for preparing a compound having Formula 7: The method includes making a compound having formula 6a: The steps of reacting with formamidin or its salt; or with trimethyl orthoformate; or with dimethylformamide dimethylacetal; Where R 1 Selected from H or protecting group (PG).

17. The method of claim 16, wherein, R 1 It is H.

18. The method of claim 16, wherein, R 1 It is a protecting group, which is benzyl (Bn).

19. A method for preparing a compound having formula 6a: The method includes making a compound having Formula 5: The steps involved in the reaction with an ammonium source; Where R 1 Selected from H or protecting group (PG).

20. The method of claim 19, wherein, R 1 It is H.

21. The method of claim 19, wherein, R 1 It is a protecting group, which is benzyl (Bn).

22. The method according to any one of claims 19-21, wherein, The ammonium source is selected from ammonium formate, ammonium chloride, and ammonium acetate.

23. A compound represented by the following structure: or its salt Bn is a benzyl group.

24. A compound represented by the following structure: Or its salt.

25. A compound represented by the following structure: or its salt Bn is a benzyl group.

26. A compound represented by the following structure: Or its salt.

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