WO2025038910A1

WO2025038910A1 - Crystalline polymorph form a of a jak inhibitor and methods for its preparation

Info

Publication number: WO2025038910A1
Application number: PCT/US2024/042627
Authority: WO
Inventors: Gary Decrescenzo; John Springer; Jon P. Lawson; Jeffrey A. Scholten; Michelle A. Schmidt
Original assignee: Aclaris Therapeutics, Inc.
Priority date: 2023-08-16
Filing date: 2024-08-16
Publication date: 2025-02-20

Abstract

The present application relates to a method of preparing ethyl (R)-4-((1-(2-cyanoacetyl)piperidin-3-yl)amino)-1H-pyrrolo[2,3-b]pyridine-5-carboxylate (Compound 1). The process involves the addition of an ethyl carboxylate group, displacement of a halogen with a chiral amine, deprotection of the chiral, cyclic amine, and a subsequent coupling reaction with cyanoacetic acid. The displacement may be conducted in an autoclave at elevated pressure.

Description

CRYSTALLINE POLYMORPH FORM A OF A JAK INHIBITOR AND METHODS

FOR ITS PREPARATION

Cross-Reference to Related Applications

[0001] Tliis application claims the benefit of U.S. Provisional Application No.

63/533,050 filed August 16, 2023 and U.S. Provisional Application No. 63/606,795 filed

December 6, 202.3, each of which is hereby incorporated by reference in its entirety.

Summary of the Invention

[0002] In one aspect, the present disclosure provides a novel method of preparing

Compound 1 having the structure:

(Compound 1) comprising the

s ,teps o ct: (a) contac <ting n the compound i SM-01 , wi -th the compound . SM-02 in the presence

of a base to form the compound (b) contacting the compound STG-01 with ethyl chloroformate in the presence of a base to form the compound

contacting the compound STG-02 with an alcoholic HC1 solution to form the compound

STG-03 ; and (d) converting STG-03 to Compound 1 .

Brief Description of the Drawings

[0003] For a fuller understanding of the nature and advantages of the present invention, reference should be made to the following detailed description taken in connection with the accompanying drawings, in which:

[0004] FIG. 1A provides an image of crystalline Compound 1 under optical microscope. FIGs. IB and 1 C provide images of a single crystal used for the single crystal measurements used to simulate a PXRD pattern for Compound 1.

[0005] FIG. 2 is a representative PXRD pattern collected from a sample of Compound 1 Polymorph Form A.

[0006] FIG. 3 is a PXRD pattern simulated from measurements of a single crystal of Compound 1 Polymorph Form A.

[0007] FIG. 4 is a thermogravimetric analysis (TGA) curve and a differential scanning calorimetry (DSC) curve for Compound 1 .

[0008] FIG. 5 is dynamic vapor sorption (DA'S) isotherms for Compound 1 .

[0009] FIG. 6 is an FT-Raman spectrum for Compound 1.

[0010] FIG. 7 is a schematic diagram of the plug flow' reactor.

Detailed Description

[0011] Before the present compositions and methods are described, it is to be understood that the scope of the invention is not limited to these particular processes, compositions, or methodologies described, as these may vary. It is also to be understood that the terminology used in the description is for the purpose of describing the particular versions or embodiments only and is not intended to limit the scope of the present invention, which will be limited only by tire appended claims. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are incorporated by reference with respect to the aspect it is identified as describing. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

[0012] Compound 1, shown below as Formula I, is disclosed in U.S. Patent Application

Publication No. 20190135808A 1 (Example 117), which is hereby incorporated by reference with respect to its disclosure of and methods of synthesizing Compound 1. Compound 1, in its freebase form, has a chemical formula of C₁₈H₂₁N₅O₃ and a molecular weight of 355.40 g/mol.

[0013] As used herein, ‘‘Compound 1” refers to ethyl (R ) -4-(( 1 -(2 - cyanoacetyl)piperidin-3 -yl)amino)- Lff-pyrrolo[2,3 -b]pyridine-5-carboxylate .

Definitions

[0014] It must also be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to a “JAK inhibitor” is a reference to one or more JAK inhibitors and equivalents thereof known to those skilled in the art, and so forth.

[0015] As used herein, the term “about” means plus or minus 10% of the numerical value of the number with which it is being used. Therefore, about 50% means in the range of 45% to 55%. When used to describe temperature, “about” refers to the identified temperature plus or minus 5 degrees. When used to describe PXRD peaks, the term “about” refers to the identified 2θ peak plus or minus 0.2 degrees.

[0016] In any embodiment, the methods and compositions disclosed herein may comprise the recited steps and components. As used here, “comprise” is open language used to recite steps or components that are included in the recited method or composition but indicate that oilier elements may also be included, even though said elements are not explicitly recited. In any embodiment, tire methods and compositions disclosed herein may consist essentially of the recited steps and components. As used here, “consist essentially of’ is used to recite steps or components that are included in the recited method or composition and to indicate that other elements may also be included but said other elements would not materially affect the properties of the composition or the results of the method. In any embodiment, the methods and compositions disclosed herein may consist of the recited steps and components. As used here, “consist of’ is closed language used to recite steps or components that are included in the recited method or composition and that no other elements are included other than those explicitly recited. Any use of the term comprise or comprising may be replaced with “consisting essentially of’ or “consisting of.”

[0017] As used herein, two embodiments are “mutually exclusive” when one is defined to be something which is different from the other. For example, an embodiment wherein two groups combine to form a cycloalkyl is mutually exclusive with an embodiment in which one group is ethyl the other group is hydrogen. Similarly, an embodiment wherein one group is CH2 is mutually exclusive with an embodiment wherein the same group is NH.

[0018] As used herein, the term “pharmaceutically acceptable salt” refers to a salt prepared from an acid which is acceptable for administration to a patient. The term “pharmaceutically acceptable salts” embraces salts commonly used to form alkali metal salts and to form addition salts from free acids. Such salts can be derived from pharmaceutically- acceptable inorganic or organic acids.

[0019] When ranges of values are disclosed, and the notation “from nl ... to n2” or “between nl ... and n2” is used, where nl and n2 are the numbers, then unless otherwise specified, this notation is intended to include the numbers themselves and the range between them. This range may be integral or continuous between and including the end values. By way of example, the range “from 2 to 6 carbons” is intended to include two, three, four, five, and six carbons, since carbons come in integer units. Compare, by way of example, the range “from 1 to 3 pM (micromolar),” which is intended to include 1 pM, 3 pM, and everything in between to any number of significant figures (e.g., 1.255 pM, 2.1 pM, 2.9999 pM, etc.).

[0020] The term “halo,” or “halogen,” as used herein, alone or m combination, refers to fluorine, chlorine, bromine, or iodine,

[0021] The term “substantially free” as used herein, is used interchangeably with, the terms “below' the limit of detection” and “within the limit of detection”, alone or in combination, refers to a compound which is free from all other compounds within the limits of detection as measured by any means including nuclear magnetic resonance (NMR), gas chromatography/mass spectroscopy (GC/MS), or liquid chromatography/mass spectroscopy (LC/MS). [0022] Stereogenic centers exist in some of the compounds disclosed herein. These centers are designated by the symbols “R” or “S,” depending on the configuration of substituents around the stereogenic center. It should be understood that the invention encompasses all stereochemical isomeric forms, including diastereomeric, enantiomeric, atropisomeric, racemic and epimeric forms, as well as d- isomers and 1 -isomers, and mixtures thereof. Individual stereoisomers of compounds can be prepared synthetically from commercially available starting materials which contain fixed stereogenic centers or by- preparation of racemic mixtures of products followed by enantiomeric separation such as conversion to a mixture of diastereomers followed by separation or recrystallization, chromatographic techniques, direct separation of enantiomers on chiral chromatographic columns, or any other appropriate method known in the art. Starting compounds of particular stereochemical configuration are either commercially available or can be made and resolved by techniques known in the art. Additionally, the compounds disclosed herein may exist as geometric isomers. The present invention includes all cis, trans, syn, anti, enlgegen (E), and zusammen (2) isomers as well as the appropriate mixtures thereof. Additionally, compounds may exist as tautomers; all tautomeric isomers are provided by this invention. Additionally, the compounds disclosed herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like.

[0023] The term ‘'therapeutically acceptable salt,” as used herein, represents salts of the compound disclosed herein which are water or oil-soluble or dispersible and therapeutically acceptable as defined herein. The salts can be prepared during the final isolation and purification of the compounds or separately by reacting the appropriate compound m the form of the free base with a suitable acid. Representative acid addition salts include acetate, adipate, alginate, L-ascorbate, aspartate, benzoate, benzenesulfonate (besylate), bisulfate, butyrate, camphorate, camphorsulfonate, citrate, digluconate, formate, fumarate, gentisate, glutarate, glycerophosphate, glycolate, hemisulfate, heptanoate, hexanoate, hippurate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethansulfonate (isethionate), lactate, maleate, malonate, DL-mandelate, mesitylenesulfonate, methanesulfonate, naphthylenesulfonate, nicotinate, 2- naphthalene sulfonate, oxalate, pamoate, pectinate, persulfate, 3-phenylproprionate, phosphonate, picrate, pivalate, propionate, pyroglutamate, succinate, sulfonate, tartrate, L- tartrate, trichloroacetate, trifluoroacetate, phosphate, glutamate, bicarbonate, para- toluenesulfbnate (p-tosylate), and undecanoate. Examples of acids which can be employed to form therapeutically acceptable addition salts include inorganic acids such as hydrochloric, hydrobromic, sulfuric, and phosphoric, and organic acids such as oxalic, maleic, succinic, and citric.

Preparation of Compound 1

[0024] Ethyl (R) -4-((l-(2-cyanoacetyl)piperidin-3-yl)amino)-lH-pyrrolo[2,3- d]pyridine-5 -carboxylate or "Compound 1” as described herein can be prepared using methods illustrated in synthetic schemes and experimental procedures detailed below. Starting materials used to prepare compounds of the present invention are commercially available or can be prepared using routine methods known in the art. Representative procedures for the preparation of compounds of the invention are outlined in Schemes 1 -2 below. Solvents and reagents, whose synthetic preparations are not described below, can be purchased at Sigma-Aldrich or Fisher Scientific.

[0025] One embodiment of the present application relates to a method of preparing the compound of Formula (I’) having the structure

(Compound 1) according to the method depicted in Scheme 1 above. This method comprises the steps of: (a)

contacting the compound SM-02 in the presence of a base to

form the compound STG-01 . contacting the compound STG-01 with ethyl

chloroformate in the presence of a base to form the compound contacting the compound STG-02 with an alcoholic HC1 solution to form the compound

and converting STG-03 to Compound 1 .

[0026] In some embodiments, the compound SM-02 is triisopropylsilyl chloride.

[0027] Any suitable base can be used to carry step (a) above. In one embodiment, the base is NaH.

[0028] In one embodiment, the base of step (a) is methyllithium, n-butyllithium, tert- butyllithium, or s'ec-butyllithiuin.

[0029] In one embodiment, the base of step (a) is sec-butyllithium.

[0030] The step of contacting the compound SM-01 with the compound SM-02 can be conducted in any suitable solvent. Suitable solvents include, without limitation, w-heptane, dichloromethane, tetrahydrofuran (THF), 2-methyltetrahydrofuran (2-MeTHF), acetonitrile, dimethylformamide (DMF), or dimethyl sulfoxide (DMSO). In one embodiment, the step of contacting the compound SM-01 with the compound SM-02 is conducted in THF.

[0031] Contacting STG-01 with ethyl chloroformate can be carried out in the presence of any suitable base. For example, suitable bases include, without limitation, methyllithium, n~ butyllithium, terr-butyllithiura, or sec-butyllithium. In one embodiment, the base of step (b) is sec-butyllithium. In some embodiments, contacting STG-01 with ethyl chlorofonnate may optionally include diethyl carbonate. In some embodiments, contacting STG-01 with ethyl chloroformate may optionally include N,N,N ', -tetramethylethylenediamine (TMEDA).

[0032] The step of contacting the compound STG-01 with ethyl chlorofonnate in the presence of a base can be carried out at a temperature of about 0 ºC to about -95 ºC for about 30 minutes to about 3 hours. In some embodiments, the contacting is carried out at a temperature of about -50 ºC to about -95 ºC for about 30 minutes to about 3 hours. In some embodiments, the contacting is carried out at a temperature of about -60 ºC to about -90 ºC for about 30 minutes to about 3 hours. In some embodiments, the contacting is carried out at about -60 ºC for about 30 minutes to about 3 hours. In some embodiment, the contacting is carried out at a temperature of about -90 ºC for about 30 minutes to about 3 hours,

[0033] In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the base at a temperature of 0 ºC to about -95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01-base mixture with ethyl chloroformate at a temperature of 0 ºC to about -95 ºC for 30 minutes to about 1.5 hours. In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the base at a temperature of -50 ºC to about -95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01-base mixture with ethyl chloroformate at a temperature of -50 ºC to about -95 ºC for 30 minutes to about 1 .5 hours.

[0034] In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the base at a temperature of 0 ºC to about ---95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01-base mixture with ethyl chlorofonnate at a temperature of 0 ºC to about -95 ºC for 30 minutes to about 1.5 hours under flow chemistry' conditions. In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the base at a temperature of -50 ºC to about -95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01-base mixture -with ethyl chlorofonnate at a temperature of -50 “C to about -95 ºC for 30 minutes to about 1.5 hours under flow chemistry' conditions.

[0035] In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the sec-butyllithium at a. temperature of -80 ºC to about -95 ºC tor about 30 minutes to about 1.5 hours and then contacting the STG-01 -sec-butyllithium mixture with ethyl chloroformate at a temperature of 0 ºC to about -95 ºC for 30 minutes to about 1.5 hours. In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the sec-butyllithium at a temperature of -80 ºC to about -95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01 -sec-butyllithium mixture with ethyl chloroformate at a temperature of ---80 ºC to about ---95 ºC for 30 minutes to about 1.5 hours.

[0036] In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the sec-butyllithmm at a temperature of -80 ºC to about -95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG-01-sec-butyllithium mixture with ethyl chloroformate at a temperature of 0 ºC to about -95 ºC for 30 minutes to about 1 .5 hours under flow chemistry conditions. In one embodiment, the step of contacting the compound of STG-01 involves contacting STG-01 with the vec-butyllithium at a temperature of -80 ºC to about --95 ºC for about 30 minutes to about 1.5 hours and then contacting the STG- 01-sec-butyllithium mixture with ethyl chlorofonnate at a temperature of -80 ºC to about -95 ºC for 30 minutes to about 1.5 hours under flow chemistry conditions.

[0037] The step of contacting the compound STG-01 with ethyl chloroformate can be conducted m any suitable solvent. Suitable solvents include, without limitation, tetrahydrofuran (THF), dichloromethane, hexane, pentane, benzene, n-heptane, or a mixture thereof. In one embodiment, the reaction is carried out in a solvent selected from the group consisting of THF, 2-MeTHF, hexane, n-heptane, cyclohexane, dimethoxyethane (DME), and mixtures thereof

[0038] Additionally, or alternatively, the method can further comprise contacting the compound STG-02 with an alcoholic HC1 solution to form the compound

STG-03

[0039] Contacting STG-02 to form STG-03 can be carried out with any suitable alcoholic HC1 solutions. Exemplary alcoholic HC1 solutions include, without limitation, an ethyl alcohol HC1 solution.

[0040] Contacting STG-02 to form STG-03 can be carried out with any suitable alcoholic HC1 solutions. Exemplary alcoholic HC1 solutions include, without limitation, an ethyl alcohol HCl solution. [0041] According to the present invention, the method can further comprise contacting

the compound STG-03 with a base to form the compound STG-04

[0042] Contacting STG-03 to form STG-04 can be carried out with any suitable base.

Exemplary bases include, without limitation, NaHCC₃ or K₃PO₄.

[0043] In one embodiment, the base is NaHCO₃.

[0044] In one embodiment, the base is K₃PO₄.

[0045] According to the present disclosure, the method can further comprise contacting

the compound STG-04 with in the presence of an amine base to form the

compound STG-05

[0046] Contacting STG-04 with INT-01 can be carried out in the presence of any suitable base. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), triethylamine, morpholine, piperidine, Na₂CO₃, or KF can be used as a base. In one embodiment, the amine base is diisopropylethylamine (DIPEA). In one embodiment, contacting STG-04 with INT-01 can be carried out in the presence of Pd(OAc)?., Xantphos, and K₃PO₄.

[0047] The step of contacting the compound STG-04 with INT-01 can be conducted in any suitable solvent. Suitable solvents include, without limitation, ethanol, acetonitrile, dimethyl sulfoxide (DMS), dimethylformamide (DMF), water, toluene, xylene, N,N’~ dimethyl acetamide (DM Ac). A-methylpyrrolidone (NMP), I) ME, and mixtures thereof In one embodiment, the reaction is carried out in ethanol. [0048] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted in an autoclave at elevated pressure.

[0049] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted at a temperature selected from the group consisting of about 80 ºC, about 90 ºC, about 100 ºC, about 110 ºC, about 120 ºC, about 130 ºC, about 140 ºC, or about 150 ºC. In one embodiment, the contacting the compound STG-04 with INT-01 is conducted at a temperature of about 120 ºC.

[0050] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted for about 10 hours to about 90 hours, about 12 hours to about 24 hours, about 24 hours to about 48 hours, or about 48 hours to about 72 hours. In one embodiment, the contacting is conducted for about 24 hours to about 48 hours.

[0051] According to the present invention, the method can further comprise contacting the compound STG-05 with an alcoholic HC1 solution to form the compound

[0052] Contacting STG-05 to form STG-06 can be carried out with any suitable alcoholic HC1 solutions. Exemplary alcoholic HC1 solutions include, without limitation, an ethyl alcohol HC1 solution.

[0053] According to the present invention, the method can further comprise contacting

the compound STG-06 with in dichloromethane in the presence of a coupling reagent and an amine base, thereby forming Compound 1.

[0054] According to the present invention, the method can further comprise contacting

the compound STG-06 with

in THF and ethanol in the presence of a coupling reagent and an amine base, thereby forming Compound 1, [0055] According to the present invention, the method can further comprise contacting

the compound STG-06 with

in THF in the presence of a coupling reagent and an amine base, thereby forming Compound 1.

[0056] Contacting STG-06 with INT-02 in dichloromethane can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, A-(3-dimethylaminopropyI)-N^'-ethylcarbodiimide hydrochloride, N,N'- dicyclohexylcarbodiirnide, N,N'diisopropylcarbodiimide, or N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is A’-(3-dimethylaminopropyl)-A'- ethylcarbodiimide hydrochloride.

[0057] Contacting STG-06 with INT-02 in THF and ethanol can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, N-(3 -di methylaminopropyl) -N'-ethylcarbodiimide hydrochloride, N^,N'- dicyclohexylcarbodiimide, N^,N'- diisopropylcarbodiimide, or N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is N- (3-dimethylaminopropyl)-N'- ethylcarbodiimide hydrochloride .

[0058] Contacting STG-06 with INT-02 in THF can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, N- (3-dimethylaminopropyl)-A^?'-ethylcarbodiimide hydrochloride, A',A"- dicyclohexylcarbodiimide, N,N' diisopropylcarbodiimide, or N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is N -(3-dimethylammopropyl)-N^'- ethylcarbodiirnide hydrochloride.

[0059] Contacting STG-06 with INT-02 in dichloromethane can be carried out in the presence of any one or more suitable amine bases. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropylethylamine (DIPEA).

[0060] Contacting STG-06 with INT-02 in THF and ethanol can be carried out in the presence of any one or more suitable amine bases. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropylethylamine (DIPEA).

[0061] Contacting STG-06 with INT-02 in THF can be carried out in the presence of any one or more suitable amine bases. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropylethylamine (DIPEA).

[0062] In some embodiments, contacting STG-06 with INT-02 in dichloromethane is conducted in the presence of hydroxybenzotriazole.

[0063] In some embodiments, contacting STG-06 with INT-02 in THF and ethanol is conducted in the presence of hydroxybenzotri azole.

[0064] In some embodiments, contacting STG-06 with INT-02 in THF is conducted in the presence of hydroxybenzotriazole.

[0065] In some embodiments, contacting STG-06 with INT-02 in dichloromethane is conducted in the presence of 2 -hydroxypyridine 1 -oxide (HOPO).

[0066] In some embodiments, contacting STG-06 with INT-02 in THF and ethanol is conducted in the presence of 2-hydroxypyridine 1 -oxide (HOPO).

[0067] In some embodiments, contacting STG-06 with INT-02 in THF is conducted in the presence of 2-hydroxypyridine 1 -oxide (HOPO).

[0068] In some embodiments. Compound 1 is prepared in an overall yield of at least about 25%, at least about 24%, at least about 23%, at least about 22%, at least about 2.1%, at least about 20%, at least about 19%, at least about 18%, at least about 17%, at least about 16%, at least about 15%, at least about 14%, at least about 13%, at least about 12%, at least about 11%, at least about 10%, at least about 9%, at least about 8%, at least about 7%, at least about 6%, at least about 5%, at least about 4%, at least about 3%, at least about 2%, or at least about 1%. [0069] In some embodiments, the method of preparing of Compound 1 results in an improved purity profile.

[0070] In some embodiments of the method, the method does not produce more than about 5.0% of an isomer other than Compound 1, about 4.0% of an isomer other than Compound 1 , about 3.0% of an isomer other than Compound 1, about 2.0% of an isomer other than Compound 1, about 1.0% of an isomer other than Compound 1, about 0.5% of an isomer other than Compound 1, about 0.25% of an isomer other than Compound 1, about 0.2%) of an isomer other than Compound 1, about 0. 15% of an isomer other than Compound I, about 0.1% of an isomer other than Compound 1, or about 0.05% of an isomer other than Compound 1.

[0071] In some embodiments of the method, the method does not produce more than about 1.0% of an isomer other than Compound 1 .

[0072] In some embodiments of the method, the method does not produce more than about 0.15% of an isomer other than Compound 1. [0073] In some embodiments, the method does not produce more than about 0.1% of an isomer other than Compound 1.

[0074] In some embodiments, the method does not produce more than about 0.05% of an isomer other than Compound 1.

[0075] In some embodiments, the method does not produce an isomer within the limit of detection other than Compound 1.

[0076] In some embodiments. Compound I is at ieast about 91% pure, at least about 92% pure, at least about 93% pure, at ieast about 94% pure, at least about 95% pure, at least about 96% pure, at least about 97% pure, at least about 98% pure, at least about 99% pure, at least about 99.1% pure, at least about 99.2% pure, at least about 99.3% pure, at least about 99.4% pure, at least about 99.5% pure, at least about 99.6% pure, at least about 99.6% pure, at least about 99.7% pure, at least about 99.8% pure, at least about 99.9% pure, or about 100% pure. [0077] In some embodiments, Compound 1 is at least about 95% pure.

[0078] In some embodiments. Compound 1 is at ieast about 99% pure.

[0079] In some embodiments. Compound 1 is at ieast about 99.8% pure.

[0080] In some embodiments. Compound 1 is about 100% pure.

[0081] In some embodiments, any individual impurity is present in an amount of less than about 0.95%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about 0.75%, less than about 0.7%, less than about 0.65%, less than about 0.6%, less than about

0.55%, less than about 0.5%, less than about 0.45%, less than about 0.4%, less than about

0.35%, less than about 0.3%, less than about 0.25%, less than about 0.2%, less than about

0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0082] In some embodiments, any individual impurity is present in an amount of less than about 0.15%.

[0083] In some embodiments, any individual impurity is present in an amount of less than about 0.1 %.

[0084] In some embodiments, any individual impurity is present in an amount of less than about 0.05%.

[0085] In some embodiments, any individual impurity is below the limit of detection.

[0086] In some embodiments, the total amount of the impurities is in an amount of less than about 10.0%, less than about 9.0%, less than about 8.0%, less than about 7.0%, less than about 6.0%, less than about 5.0%, less than about 4.0%, less than about 3.0%, less than about 2.0%, less than about 1.0%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about 0,75%, less than about 0,7%, less than about 0.65%, less than about 0.6%, less than about 0.55%, less than about 0.5%, less than about 0.45%, less than about 0.4%, less than about 0.35%, less than about 0.3%, less than about 0.25%, less than about 0.2%, less than about 0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0087] In some embodiments, the total amount of the impurities is in an amount of less than about 10.0%.

[0088] In some embodiments, the total amount of the impurities is in an amount of less than about 5 ,0%,

[0089] In some embodiments, the total amount of the impurities is in an amount of less than about 1.0%.

[0090] In some embodiments, the total amount of the impurities is in an amount of less than about 0.5%.

[0091] In some embodiments, the total amount of the impurities is in an amount of less than about 0.2%.

[0092] In some embodiments, the total amount of the impurities is below the limit of detection.

[0093] In some embodiments, the impurity is selected from an unreacted starting material, an unreacted intermediate, an impurity propagated from a side reaction, or a combination thereof. In some embodiments, the impurity is an unreacted starting material. In some embodiments, the impurity is an unreacted intermediate. In some embodiments, the impurity an impurity propagated from a side reaction.

[0094] In some embodiments, the impurity is selected from:

buty! (R)-4-((1-(2-cyanoacetyl)piperidin-3- isopropyl (R)-4-(piperidin-3-ylamino)-1 H- yl)amino)-iH-pyrrolo[2_;3-6]pyridine~5- pyrrolo[2,3-b]pyridine-5-carboxylate carboxylate

isopropyl (R)-4-((1 -(2- ethyl (R)-4-((l-(3-amino-3- cyanoacetyl)piperidin-3-yl)amino)-1 H- oxopropanoyl)piperidin-3-yl)amino)-1H- pyrrolo[2,3-6]pyridine-5-carboxylate pyrolo[2,3-bjpyridine-5-carboxylate

(R)-4-((1 -(3-amino-3- oxopropanoyl)piperidin-3-yl)amino)-5- (R)-4-((1”(2-cyanoacetyl)piperidin-3- (ethoxycarbonyl)-1H-pyrroio[2,3- y!)amino)-5-(ethoxycarbonyl)-1H- b]pyridine 7-oxide pyrroio[2,3-b]pyridine 7-oxide

1 -(4-chloro-1 -(triisopropylsily!)- tert-buty I (R)-3-((5-pentanoyl-1 H-

1 H-pyrrolo[2 , 3-b]pyrid in-5- 1 -(4-ch!oro-1 H-pyrroto[2_:3- pyrroio[2,3-b]pyndin-4- y!)pentan-1-one £>ipyridin-5-yi;pentan-1-one yl)amino)piperidine-1 -carboxylate

(R)-1 -(4-(piperidin-3-ylamino)-1 H- (R)-3-oxo-3-(3-((5-pentanoyi-1 H- pyrroio[2,3-b]pyridin-5-yl)pentan-1- pyrrolo[2 , 3-b]pyridi n-4- one hydrochloride yl)amino)piperid!n-1-yi)propanenitrile

1 -(4-chloro-1 -(tri isopropylsily l)-1 H- 1-(4-ch!oro-1H-pyrrolo[2,3- pyrrolo[2,3-&]pyrid!n-5-yi)-3- b]pyridin-5-yl)-3-methy!butan- methylbutan-1-one 1-one

tert-butyl (R)-3-((5-(3-methylbutanoy!)-1W- (R)-3-methyl-1-(4-(piperidin-3- pyrrolo[2,3-b]pyridin-4-yi)amino)piperid!ne- ylamino)-1H-pyrrolo[2,3-&]pyridin-5- 1 -carboxylate yl)butan-1-one hydrochloride

(R)-3-(3-((5-(3-methylbutanoyl)-1 H- 1 -(4-chloro- -1 -(triisopropylsilyl)- 1 H- pyrrolo[2,3-b]pyridin-4-yl)amino)piperidin-1- pyrroio[2,3-6]pyridm-5-yl)-2- y I )-3-oxo propane n it ri le methy!butan-1-one

1-(4-ch!oro-1H-pyrrolo[2,3- fert-buty! (3/?)-3-((5-(2-methylbutanoyl)- b]pyridin-5-yl)-2-methylbutan- 1 H-pyrrolo[2,3-.b]pyridin-4- 1-one yi)amino)piperidine-1 -carboxylate

2-methyl-1 -(4-(((R)-piperidin-3- 3-((3/^:?)--3--((5-(2-methylbutanoyl)-1 /-/- yl)amino)-1 H-pyrrolo[2,3-b]pyrid!n-5- pyrroio[2_!3-d!pyTidin-4-yi)amino)p!pendin-1- yl)butan-1-one hydrochloride yl)-3--oxopropanenitrHe

ethyl (R)-4-((1 -(2-cyanoacetyl)piperidin- ethyl 4-(((3R)-1 -(2-

3-y!)amino)-1-methy!-1/7-pyrrolo[2,3- cyanopropanoyl)pipendin-3-yl)amino)- b]pyridine-5-carboxylate 1 H-pyrrolo[2,3-t>]pyridine-5-carboxylate and a combination thereof.

[0095] Scheme 2 outlines another method of synthesizing Compound 1.

Scheme 2

[0096] Another embodiment of the present disclosure is directed to a method of preparing Compound 1 according to the route shown in Scheme 2.

[0097] In some embodiments, Compound 1 is prepared in an overall yield of at least about 25%, at least about 24%, at least about 23%, at least about 22%, at least about 21%, at least about 20%, at least about 19%, at least about 18%, at least about 17%, at least about 16%, at least about 15%, at least about 14%, at least about 13%, at least about 12%, at least about 1 1%, at least about 10%, at least about 9%, at least about 8%, at least about 7%, at least about 6%, at least about 5%, at least about 4%, at least about 3%, at least about 2%, or at least about 1%. [0098] In some embodiments, the method of preparing Compound 1 according to the route shown in Scheme 2 results in an improved purity profile.

[0099] In some embodiments of the method, the method does not produce more than about 5.0% of an isomer other than Compound 1 , about 4.0% of an isomer other than Compound 1, about 3.0% of an isomer other than Compound 1 , about 2.0% of an isomer other than Compound I, about 1.0% of an isomer other than Compound 1, about 0.5% of an isomer other than Compound 1, about 0.25% of an isomer other than Compound 1, about 0.2% of an isomer other than Compound 1 , about 0. 15% of an isomer other than Compound 1 , about 0. 1% of an isomer other than Compound I, or about 0.05% of an isomer oilier than Compound 1 .

[0100] In some embodiments of the method, the method does not produce more than about 1 .0% of an i somer other than Compound 1.

[0101] In some embodiments of the method, the method does not produce more than about 0.15% of an isomer other than Compound 1 .

[0102] In some embodiments, the method does not produce more than about 0.1% of an isomer other than Compound 1.

[0103] In some embodiments, the method does not produce more than about 0.05% of an isomer other than Compound 1.

[0104] In some embodiments, the method does not produce an isomer within the limit of detection other than Compound 1.

[0105] In some embodiments. Compound 1 is at least about 91% pure, at least about 92% pure, at least about 93% pure, at least about 94% pure, at least about 95% pure, at least about 96% pure, at least about 97% pure, at least about 98% pure, at least about 99% pure, at least about 99.1% pure, at least about 99.2% pure, at least about 99.3% pure, at least about 99.4% pure, at least about 99.5% pure, at least about 99.6% pure, at least about 99.6% pure, at least about 99.7% pure, at least about 99.8% pure, at least about 99.9% pure, or about 100% pure. [0106] In some embodiments. Compound 1 is at least about 95% pure.

[0107] In some embodiments. Compound 1 is at least about 99% pure.

[0108] In some embodiments. Compound 1 is at least about 99.8% pure.

[0109] In some embodiments, Compound 1 is about 100% pure.

[0110] In some embodiments, any individual impurity' is present in an amount of less than about 0.95%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about

0.75%, less than about 0.7%, less than about 0.65%, less than about 0.6%, less than about

0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0111] In some embodiments, any individual impurity is present in an amount of less than about 0.15%.

[0112] In some embodiments, any individual impurity is present in an amount of less than about 0.1 %.

[0113] In some embodiments, any individual impurity is present in an amount of less than about 0.05%.

[0114] In some embodiments, any individual impurity is below the limit of detection.

[0115] In some embodiments, the total amount of the impurities is in an amount of less than about 10.0%, less than about 9.0%, less than about 8.0%, less than about 7.0%, less than about 6.0%, less than about 5.0%, less than about 4.0%, less than about 3.0%, less than about 2.0%, less than about 1.0%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about 0.75%, less than about 0.7%, less than about 0.65%, less than about 0.6%, less than about 0.55%, less than about 0.5%, less than about 0.45%, less than about 0.4%, less than about 0.35%, less than about 0.3%, less than about 0.25%, less than about 0.2%, less than about 0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0116] In some embodiments, the total amount of the impurities is m an amount of less than about 10.0%.

[0117] In some embodiments, the total amount of the impurities is in an amount of less than about 5.0%.

[0118] In some embodiments, the total amount of the impurities is in an amount of less than about 1 .0%.

[0119] In some embodiments, the total amount of the impurities is in an amount of less than about 0.5%. [0120] In some embodiments, the total amount of the impurities is in an amount of less than about 0,2%,

[01211 In some embodiments, the total amount of the impurities is below the limit of detection.

[0122] In some embodiments, the impurity is selected from an unreacted starting material, an unreacted intermediate, an impurity propagated from a side reaction, or a combination thereof. In some embodiments, the impurity is an unreacted starting material. In some embodiments, the impurity is an unreacted intermediate. In some embodiments, the impurity is an impurity propagated from a side reaction.

[0123] In some embodiments, the impurity is selected from:

b uty I (R)-4-((1 -(2-cyanoacetyl)piperidin-3- isopropyi (R)-4-(piperid in-3-ylam ino)-1 H- yl)amino)-1H-pyrrolo[2,3-b]pyridine-5- pyrrolo[2_;3-b]pyridine-5-carboxylate carboxylate

isopropyl (R)-4-((1-(2- ethyl (R)-4-((1 -(3-amino-3- cyanoacetyl)piperidin-3-yl)amino)-1W- oxopropanoyl)piperidin-3-yl)amino)-1H- pyrrolo[2,3-b]pyridine-5-carboxylate pyrralo[2,3-b]pyridine-5-carboxylate

(R)-4-((1 -(3-amino-3- oxopropanoy!)piperidin-3-yl)amino)-5- (R)-4-((1-(2-cyanoacety!)piperidin-3- (ethoxycarbony!)-1H"pyrroio[2,3- yl)amino)-5-(ethoxycarbonyl)-1H- b]pyridine 7-oxide py rro lo[2 , 3-b] pyridine 7 -oxid e

1 -(4-chloro-1 -(triisopropylsily!)- tert-butyl (R)-3-((5-pentanoyl-1 H-

1 H-pyrrolo[2,3-b]pyridin-5- 1 -(4-chloro-1 H-pyrrolo[2,3- pyrrolo[2,3-b]pyridin-4- yl)pentan-1-one b]pyridin-5-yl)pentan-1-one yl)amino)piperidine-1 -carboxylate

(R)-1-(4-(piperidin-3-ylamino)-1H- (R)-3-oxo-3-(3-((5-pentanoyl-1H- pyrrolo[2,3-6]pyridin-5-yl)pentan-1- pyrrolo[2,3-b]pyridin-4- one hydrochloride yl)amino)piperidin-1-yl)propanenitrile

1 -(4-chloro-1 -(triisopropylsilyl)- 1 H- 1 -(4-chloro-1 H-pyrrolo[2,3- pyrrolo[2,3-b]pyridin-5-yl)-3- b]pyridirk5-yl)-3-rnethylbutafi- methylbutan-1-one 1-one

tert-butyl (R)-3-((5-(3-methylbutanoyl)-1 H- (R)-3-methyl-1 -(4-(piperidin-3- pyrrolo[2,3-6]pyridin-4-yl)amino)piperidine- ylamino)-1 H-pyrrolo[2,3-bjpyridin-5- 1 -carboxylate yl)butan-1-one hydrochloride

(R)-3-(3-((5-(3-methylbutanoyl)-1 /7- 1 -(4-chloro-1 -(triisopropylsilyl)- 1 H- pyrrolo[2,3-b]pyridin-4-yl)amino)piperidin-1- pyrroio[2,3-b]pyridin-5-yl)-2- yl)-3-oxopropanenitrile methylbutan-1 -one

1-(4-chlorO"1H-pyrrolo[2,3- tert-butyl (3R)-3~((5-(2-methy!butanoy!)- b]pyridin-5-y!)-2-methylbutan- 1H-pyrroio[2,3-b]pyridin-4~ 1-one yl)amino)piperidine-1 -carboxylate

2-methyi-1-(4-(((R)-piperidin-3- 3-((3/?)-3-((5-(2-methylbutanoyl)-1H- yl)amino)-1H-pyrrolo[2,3-b]pyridin-5- pyrrolo[2,3-b]pyridin-4-yl)amino)piperidin-1 - yl)butan-1-one hydrochloride yi)-3-oxopropanenitrile

ethyl (R)-4-((1 -(2-cyanoacetyl)piperidin- ethyl 4-(((3R)-1-(2- 3-yi)amino)-1 -methyl- 1 H-pyrroio[2,3- cyanopropanoyl)piperidir!-3-yl)amino)- b]pyridine-5-carboxylate 1H-pyrrolo[2.3-b]pyridine-5-carboxylate arid a combination thereof.

[0124] Another embodiment of the present disclosure is directed to a method of preparing Compound 1 comprising the steps of: (a) contacting the compound with an alcoholic HC1 solution to form the compound

STG-03 ; and (d) converting STG-03 to Compound 1. [0125] Contacting STG-02 to form STG-03 can be earned out with any suitable alcoholic HC1 solutions. Exemplary alcoholic HC1 solutions include, without limitation, an ethyl alcohol HC1 solution.

[0126] According to the present invention, the method can further comprise contacting

tlie compound STG-03 with a base to form the compound STG-04

[0127] Contacting STG-03 to form STG-04 can be carried out with any suitable base.

Exemplary’ bases include, without limitation, NaHCO₃ or K₃PO₄.

[0128] In one embodiment, the base is NaHCO₃.

[0129] In one embodiment, the base is K₃PO₄.

[0130] According to the present disclosure, the method can further comprise contacting

the compound STG-04 with INT-01 in the presence of an amine base to form the

compound STG-05

[0131] Contacting STG-04 with INT-01 can be carried out in the presence of any suitable base. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), tnethylamme, morpholine, piperidine, Na₂CO₃, or KF can be used as a base. In one embodiment, the amine base is diisopropylethylamme (DIPEA). In one embodiment, contacting STG-04 with INT-01 can be earned out in the presence of Pd(OAc)₂., Xantphos, and K₃PO₄.

[0132] The step of contacting the compound STG-04 with INT-01 can be conducted m any suitable solvent. Suitable solvents include, without limitation, ethanol, acetonitrile, dimethyl sulfoxide (DMS), dimethylformamide (DMF), water, toluene, xylene, AaV- dimethyl acetamide (DMAc), N-metbylpyrrolidone (NMP), I) ME, and mixtures thereof. In one embodiment, the reaction is carried out in ethanol.

[0133] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted in an autoclave at elevated pressure.

[0134] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted at a temperature selected from the group consisting of about 80 °C, about 90 °C, about 100 °C, about 110 °C, about 120 °C, about 130 °C, about 140 °C, or about 150 °C. In one embodiment, the contacting the compound STG-04 with INT-01 is conducted at a temperature of about 120 °C.

[0135] In some embodiments, contacting the compound STG-04 with INT-01 can be conducted for about 10 hours to about 90 hours, about 12 hours to about 24 hours, about 24 hours to about 48 hours, or about 48 hours to about 72 hours. In one embodiment, the contacting is conducted for about 24 hours to about 48 hours.

[0136] According to the present invention, the method can further comprise contacting the compound STG-05 with an alcoholic HC1 solution to form the compound

STG-06

[0137] Contacting STG-05 to form STG-06 can be earned out with any suitable alcoholic HC1 solutions. Exemplary alcoholic HC1 solutions include, without limitation, an

:thyl alcohol HC1 solution.

[0138] According to the present invention, the method can further comprise contacting

the compound STG-06 with

in dichloromethane in the presence of a coupling reagent and an amine base, thereby forming Compound 1 . [0139] According to the present invention, the method can further comprise contacting

the compound STG-06 with INT-02 in THF and ethano| in presence of a coupling reagent and an amine base, thereby forming Compound 1.

[0140] According to the present invention, the method can further comprise contacting

the compound STG-06 with in THF in the presence of a coupling reagent and an amine base, thereby forming Compound 1.

[0141] Contacting STG-06 with INT-02 in dichloromethane can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, A-(3-dimethylaminopropyl)-,N'-ethylcarbodiimide hydrochloride, AyV- dicyclohexylcarbodiimide, N,N'diisopropylcarbodiimide, or N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is N'-(3-dimethylaminopropyl)-N'- ethylcarbodiimide hydrochloride.

[0142] Contacting STG-06 with INT-02 in THF and ethanol can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, A^,-(3-dimethylaminopropyl)-A'^/ -ethylcarbodiimide hydrochloride, AyV- dicyclohexylcarbodiimide, N,N'-diisopropylcarbodiimide, or ,N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is A’-(3-dimethylaminopropyl)-A”- ethylcarbodiimide hydrochloride.

[0143] Contacting STG-06 with INT-02 in THF can be carried out in the presence of any one or more suitable coupling reagents. Suitable coupling reagents include, without limitation, A-(3-dimethylaminopropyl)-A⁷' -ethylcarbodiimide hydrochloride, N,N'- dicycloliexylcarbodimiide, N,N'-diisopropylcarbodiimide, or N,N'-di-tert-butyicarbodiimide can be used. In one embodiment, the coupling reagent is N-(3-dimethylaminopropyl)~A”~ ethylcarbodiimide hydrochloride.

[0144] Contacting STG-06 with INT-02 in dichloromethane can be carried out in the presence of any one or more suitable anime bases. Suitable amine bases include, without limitation, diisopropylethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropylethylamine (DIPEA). [0145] Contacting STG-06 with INT-02 in THF and ethanol can be carried out in the presence of any one or more suitable amine bases. Suitable amine bases include, without limitation, diisopropyiethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropyiethylamine (DIPEA).

[0146] Contacting STG-06 with INT-02 in THF can be earned out in the presence of any one or more suitable amine bases. Suitable amine bases include, without limitation, diisopropyiethylamine (DIPEA), triethylamine, morpholine, or piperidine. In one embodiment, the amine base is diisopropyiethylamine (DIPEA).

[0147] In some embodiments, contacting STG-06 with INT-02 in dichloromethane is conducted in the presence of hydroxybenzotriazole.

[0148] In some embodiments, contacting STG-06 with INT-02 in THF and ethanol is conducted in the presence of hydroxybenzotriazole ,

[0149] In some embodiments, contacting STG-06 with INT-02 in THF is conducted in tlie presence of hydroxybenzotriazole.

[0150] In some embodiments, contacting STG-06 with INT-02 in dichloromethane is conducted in the presence of 2. -hydroxypyridine 1 -oxide (HOPO).

[0151] In some embodiments, contacting STG-06 with INT-02 in THF and ethanol is conducted in the presence of 2-hydroxypyridine 1 -oxide (HOPO).

[0152] In some embodiments, contacting STG-06 with INT-02 in THF is conducted in the presence of 2-hydroxypyridine 1 -oxide (HOPO).

[0153] In some embodiments. Compound 1 is prepared in an overall yield of at least about 25%, at least about 24%, at least about 23%, at least about 22%, at least about 21%, at least about 20%, at least about 19%, at least about 18%, at least about 17%, at least about 16%, at least about 15%, at least about 14%, at least about 13%, at least about 12%, at least about 11%, at least about 10%, at least about 9%, at least about 8%, at least about 7%, at least about 6%, at least about 5%, at least about 4%, at least about 3%, at least about 2%, or at least about 1%. [0154] In some embodiments, the method of preparing Compound I results in an improved purity profile.

[0155] In some embodiments of tire method, the method does not produce more than about 5.0% of an isomer other than Compound 1, about 4,0% of an isomer other than Compound 1, about 3.0% of an isomer other than Compound 1, about 2.0% of an isomer other than Compound 1, about 1.0% of an isomer oilier than Compound I, about 0.5% of an isomer other than Compound I, about 0.25% of an isomer other than Compound 1, about 0.2% of an isomer other than Compound 1 , about 0. 15% of an isomer other than Compound 1 , about 0. 1% of an isomer other than Compound 1, or about 0.05% of an isomer other than Compound 1 .

[0156] In some embodiments of the method, the method does not produce more than about 1.0% of an isomer other than Compound 1.

[0157] In some embodiments of the method, the method does not produce more than about 0.15% of an isomer other than Compound 1 .

[0158] In some embodiments, the method does not produce more than about 0.1% of an isomer other than Compound 1.

[0159] In some embodiments, the method does not produce more than about 0.05% of an isomer other than Compound 1.

[0160] In some embodiments, the method does not produce an isomer within the limit of detection other than Compound 1.

[0161] In some embodiments. Compound 1 is at least about 91% pure, at least about 92% pure, at least about 93% pure, at least about 94% pure, at least about 95% pure, at least about 96% pure, at least about 97% pure, at least about 98% pure, at least about 99% pure, at least about 99. 1% pure, at least about 99.2% pure, at least about 99.3% pure, at least about 99.4% pure, at least about 99.5% pure, at least about 99.6% pure, at least about 99.6% pure, at least about 99.7% pure, at least about 99.8% pure, at least about 99.9% pure, or about 100% pure . [0162] In some embodiments, Compound 1 is at least about 95% pure.

[0163] In some embodiments, Compound 1 is at least about 99% pure.

[0164] In some embodiments. Compound 1 is at least about 99.8% pure.

[0165] In some embodiments. Compound 1 is about 100% pure.

[0166] In some embodiments, any individual impurity is present in an amount of less than about 0.95%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about 0.75%, less than about 0.7%, less than about 0.65%, less than about 0.6%, less than about

0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0167] In some embodiments, any individual impurity is present m an amount of less than about 0.15%.

[0168] In some embodiments, any individual impurity is present in an amount of less than about 0.1%. [0169] In some embodiments, any individual impurity is present in an amount of less than about 0.05%.

[0170] In some embodiments, any individual impurity is below the limit of detection.

[0171] In some embodiments, the total amount of the impurities is in an amount of less than about 10.0%, less than about 9.0%, less than about 8.0%, less than about 7.0%, less than about 6.0%, less than about 5.0%, less than about 4.0%, less than about 3.0%, less than about 2.0%, less than about 1.0%, less than about 0.9%, less than about 0.85%, less than about 0.8%, less than about 0,75%, less than about 0,7%, less than about 0.65%, less than about 0.6%, less than about 0.55%, less than about 0.5%, less than about 0.45%, less than about 0.4%, less than about 0.35%, less than about 0.3%, less than about 0.25%, less than about 0.2%, less than about 0.15%, less than about 0.1%, less than about 0.05%, or less than about 0.01%.

[0172] In some embodiments, the total amount of the impurities is in an amount, of less than about 10.0%.

[0173] In some embodiments, the total amount of the impurities is in an amount of less than about 5.0%.

[0174] In some embodiments, the total amount of the impurities is in an amount of less than about 1.0%.

[0175] In some embodiments, the total amount of the impurities is in an amount of less than about 0.5%.

[0176] In some embodiments, the total amount of the impurities is in an amount of less than about 0.2%.

[0177] In some embodiments, the total amount of the impurities is below the limit of detection.

[0178] In some embodiments, the impurity is selected from an unreacted starting material, an unreacted intermediate, an impurity propagated from a side reaction, or a combination thereof. In some embodiments, the impurity is an unreacted starting material. In some embodiments, the impurity is an unreacted intermediate. In some embodiments, the impurity is an impurity propagated from a side reaction.

[0179] In some embodiments, the impurity is selected from:

butyl (R)-4-((1-(2-cyanoacetyl)piperidin-3- isopropyl (R)-4-(piperidin-3-ylamino)-1 H- y1)amino)-iH-pyrrolo[2_;3-b]pyridine-5- pyrrolo[2,3-b]pyridine-5-carboxylate carboxylate

isopropyl (R)-4-((1 -(2- ethyl (R)-4-((l-(3-amino-3- cyanoacetyl)piperidin-3-yl)amino)-1 H- oxopropanoyl)piperidin-3-yl)amino)-1H- pyrrolo[2,3-b]pyridine-5-carboxylate pyrolo[2,3-bjpyridine-5-carboxylate

1

-(4-chloro-1 -(triisopropyisiiyl)- tert-buty I (R)-3-((5-pentanoyl-1 H-

1 H-pyrrolo[2 , 3-£>]pyrid in-5- 1 -(4-ch!oro-1 H-pyrroto[2_:3- pyrroio[2,3-b]pyndin-4- y!)pentan-1-one £>ipyridin-5-yi;pentan-1-one yl)amino)piperidine-1 -carboxylate

2-methyl-1 -(4-(((R)-piperidin-3- 3-((3R)-3~((5-(2-methylbutanoyl)-1 H- yl)amino)-1H-pyrrolo[2,3-b]pyridin-5- pyrrolo[2,3-b]pyridin-4-yl)amino)piperidin -1 - yi)butan-1-one hydrochloride yl)-3-oxopropanenitrile

ethyl (R)-4-((1 -(2-cyanoacetyl)piperidin- ethyl 4-(((3/?)-1-(2- 3-yi)amino)-1-methyi-1/7-pyrrolo[2,3- cyanopropanoyl)piperidin-3-yl)amino)- t>]pyridine-5-carboxylate 1H-pyrroio[2,3-b]pyridine-5-carboxylate and a combination thereof.

Crystalline Polymorph Form A of Compound 1

[0180] Polymorphism is the ability of solid materials to exist in two or more crystalline forms with different arrangements or conformations of the constituents in the crystal lattice. Polymorphism and pseudomorphism are very common amongst drags and are responsible for differences in many properties. While convention dictates selection of the lowest energy- polymorph for incorporation into a formulation due to its chemical stability, considerations must be given to the excipients in the formulation to achieve desired chemical and physical stability and therefore efficacy. Disclosed herein is a particularly useful polymorph of Compound 1, named polymorph Form A, which can be used to prepare or incorporated into topical formulations for treatment of AD, vitiligo, and alopecia areata.

[0181] Therefore, in one aspect, the present disclosure provides crystalline polymorph Form A of Compound 1. Crystalline polymorph Form A of Compound 1 is a non-solvated colorless rhombic-dipyramidal crystalline solid. Images of said crystals are shown in FIGs. 1A, IB, and 1C. Crystalline polymorph Form A of Compound 1 may be characterized as such by- powder X-ray diffraction (PXRD) wherein the pattern resulting from the analysis comprises significant peaks at characteristic 2-theta angles. Form A may be characterized, for example, by a significant peak at about 10.50º20. A PXRD pattern of Form A of Compound 1 may further have a significant peak of about 18.86º20. A PXRD pattern of Form A of Compound 1 may further have a significant peak at about one or more of about 9.69º20, about 14.O1º20, and about 25,85 20. Yet further, a PXRD pattern of Form A of Compound 1 may additionally have significant peaks at one or more of about 4.67º20, about 9.33º20, about 9.55º20, and about 27.46º20. Parameters that may be used to analyze Compound 1 by PXRD may be found in the Characterization Methods section below.

[0182] As stated above, cry stalline Form A of Compound 1 is non-solvated crystalline form of Compound 1. In addition to characterization by PXRD, Crystalline Form A of Compound 1 may be also characterized by one or more of therm ogravimetric analysis (TGA), differentia] scanning calorimetry (DSC), and Fourier Transform-Raman (FT-Raman). TGA thermograms, DSC curves, and FT-Raman spectra collected for particular batches of crystalline Form A of Compound 1 are described in the Examples. However, in general, crystalline Form A of Compound 1 may be characterized by a water loss of less than about 1 wt. % when analyzed by TGA. When analyzed via DSC, crystalline Form A of Compound 1 may undergo a phase transition (as evidenced by an endotherm in the DSC) at about 196 ºC to about 197ºC. [0183] Crystalline polymorph Form A of Compound 1 may be characterized by a FT- Raman spectra comprising a significant peak at about 1499.7 cm’¹. A FT-Raman spectra of Form A of Compound 1 may further have a significant peak at about 31.867 cm"¹. A FT-Raman spectra of Form A of Compound 1 may further have a significant peak at one or more of about 28.008 cm'¹, about 27,729 cm'¹, about 20,742 cm'¹, and about 19.862 cm"⁵. A FT-Raman spectra of Form A of Compound 1 may further have a significant peak at one or more of about 17.799 cm'¹, about 17.727 cm'¹, about 17.47 cm'¹, and about 16.713 cm'¹.

[0184] Crystalline polymorph Form A of Compound 1 may be characterized by a PXRD pattern comprising a significant peak at a 2G angle of about 10.50º and characterized by a FT-Raman spectra comprising a significant, peak at about 1499.7 cm'¹. Crystalline polymorph Form A of Compound 1 may be further characterized by a PXRD comprising a significant peak at 20 angle of about 18,86º and a FT-Raman spectra further comprising a significant peak at about 31.867 cm'¹. Crystalline polymorph Form A of Compound 1 may be further characterized by a PXRD comprising a significant peak at a 20 angle at one or more of about 9.69º, about 14.01º, and about 25.85º and a FT-Raman spectra further comprising a significant peak at one or more of about 28.008 cm'¹, about 27,729 cm"⁵, about 2.0.742 cm'⁵, and about 19.862 cm"¹. Crystalline polymorph Form A of Compound 1 may be further characterized by a PXRD comprising a significant peak at a 20 angle at one or more of about 9.33º, about 9.55º, and about 27.46º and a FT-Raman spectra further comprising a significant peak at one or more of about 17.799 cm^-1, about 17.727 cm^-1, about 17.47 cm^-1, and about 16.713 cm^-1.

[0185] In various embodiments, crystalline polymorph Form A of Compound 1 may be further characterized by a PXRD pattern substantially as shown in FIG. 2 or FIG. 3. Crystalline polymorph Form A of Compound I may also be characterized by one or more of 1) a DSC thermograms exhibiting an endotherm at about 196.8ºC; 2) a water loss as measured by thermogravimetric analysis of about 0.7 wt. %; and 3) an FT-Raman spectra as substantially shown in FIG. 6.

[0186] Compound 1 produced by any of the methods disclosed herein can be used to produce crystalline polymorph Form A of Compound 1 by the methods disclosed in W02022/067106.

Characterization Methods

[0187] X-Ray Data Collection: A single, rod-like crystal (0.050 x 0.0932 x 0.38 mm), as shown in FIG. 1 A, IB, and 1C, was mounted on a MiTeGen™ cryo-loop. Preliminary analysis and data collection were performed at temperature of 200 K using copper Ka radiation ( 1.54184 A) with a Broker APEX II Duo™ diffractometer equipped with a IpS Cu source and an Oxford Crystalstream™ low temperature device.

[0188 ] X-Ray Structure Determination: Data from X-Ray Data Collection (above) was integrated using an orthorhombic unit cell. The structure was determined and refined using the Broker SHELXTL software package, using the space group P 2₁ 2₁2₁, with Z=4 for the formula unit, C₁₈H₂₁N₅O₃.

[0189] Simulated PXRD: The program Mercury 4.0 was used to analyze the structural coordinates. The command “calculate powder pattern” was used to create a representative PXRD pattern. The h, k, 1, and 26 values were identified using the software and compared with experimental data. Values tor d-spacing were generated using Apex3 v. 2019.1 software.

[0190] Powder X-Ray Diffraction: A ~50 mg sample of Compound 1, Form A was ground to a uniform, fine powder in an agate mortar and pestle and carefully packed into a sample holder. The PXRD measurements were conducted at room temperature using a PANalytical X’Pert Pro MPD diffractometer. PXRD measurements were conducted using Ni- filtered copper CuKa radiation with a wavelength of 1.54 A over an angle range of 20 = 4º- 42º and a step size of 0.02º. [0191] Differential Scanning Calorimetry (DSC): DSC was conducted with a TA instruments Q100 or Q2000 differential scanning calorimeter equipped with an autosampler and a refrigerated cooling system under 30 mL/min N₂ purge. DSC thermograms of samples were obtained at 10 ºC/min in crimped Ai pans.

[0192] Thennogravimetric Analysis: TGA thermograms were obtained with a TA Instruments Q50 thennogravimetric analyzer under 40 mL/min N₂ purge in Pt or Al pans. TGA thermograms of samples were obtained at 10 ºC/min in crimped Al pans. TGA analysis with IR Off-Gas Detection (TGA-IR) was conducted with a TA Instruments Q5000 thennogravimetric analyzer interfaced to a Nicolet 6700 FT-IR spectrometer equipped with an external TGA-IR module with a gas flow cell and DTGS detector. TGA was conducted under 60 mL/min N₂ flow and heating rate of 15 ºC/min in Pt or Al pans. IR spectra were collected at 4 cm ^-1 resolution and 32 scans at each time point.

[0193] FT-Raman Spectroscopy: Raman spectra were collected with a Nicolet

NXR9650 or NXR 960 spectrometer equipped with 1064 nm Nd:YVO₄ excitation laser, InGaAs and liquid N₂-cooied Ge detectors, and a microstage. All spectra were acquired at 4 cm^-1 resolution, 64-128 scans, using Happ-Genzel application function and 2 -level zero-filling. [0194] To facilitate a better understanding of the embodiments of the present invention, the following examples of preferred or representative embodiments are given. In no way should the following examples be read to limit, or to define, the scope of the invention.

EXAMPLES

[0195] Synthetic Scheme

[0196] Example 1: X-Ray Structure Determination and PXRD Analysis of Crystalline Polymorph Form A of Compound 1: Crystalline polymorph Form A of Compound 1 was formed by the methods disclosed in W02022/067106. Integration of the data collected from the single crystal of Compound 1 yielded a total of 54,767 reflections to a maximum 0 angle of 71.09º, of which 3,222 were independent and 3,213 were greater than 2o(F2). The final cell constants of a=5.0232 A, b=9.3308 A, and c ~ 37.863 A with a volume of 1774.7 A³ are based on the refinement of the xyz-centroids of reflections above 20 o(I) . The calculated density was 1.330 g/cm³.

[0197] Table 1 below provides those peaks detected as significant as well as the corresponding d-spacing for both experimental data as well as simulated data calculated from measurements of a single crystal .

Table 1

[0198] Table 2 below provides the peaks and their intensities of the FT-Raman spectrum.

Table 2

[0199] FIG. 2 and FIG. 3 provide representative PXRD patterns of the experimental data collected on a bulk sample of Compound 1 and a simulated PXRD pattern calculated using measurements from a single Compound 1 crystal. FIG. 4 provides representative TGA-IR and DSC curves for Compound 1, illustrating a 0.7 wt. % loss of water from 35ºC to 225ºC and a sharp endotherm with an onset at 196.8ºC, respectively. FIG. 5 provides the results of DVS analysis on a batch of Compound L revealing that the bulk material has low moisture uptake. FIG. 6 provides a representative FT-Raman spectrum of Compound 1.

[0200] Example 2: Preparation of Ethyl 4-Chloro- 1H-pyrrolo[2,3-b]pyridine-5- carboxylate Hydrochloride (STG-03)

[0201] In a jacketed reactor (20 L), 4-chloro-lH-pyrrolo[2.,3-b]pyridine (SM-0I, 1.8 kg, 1.0 eq.) was combined with anhydrous THF (48.0 kg, 30 vol.) and stirred at temperature

(25 -.t 5 ºC) under a nitrogen atmosphere. The reaction mass was cooled (-20 ± 5 ºC), and triisopropylsilyl chloride (2.7 kg, 1.2 eq.) was added while the temperature was maintained. To the reaction mixture, sec-butyllithium (6.3 kg, 1 ,0 eq., 12% wt in cyclohexane) was dosed in segments over a 2-hour period with the reaction temperature not exceeding - 15 ºC. The reach on mixture was monitored by HPLC. The reaction mixture continued to stir at temperature (-15 ± 5 ºC) overnight. HPLC indicated the reaction was complete to provide 4-chloro-l- (triisopropylsilyl)-lH-pyrrolo[2,3-b]pyridine (STG-01 ). The reaction mass was filtered and placed is a cylinder under nitrogen. To enhance plug flow reactor operation, 2-MeTHF (15% w/w) was added to the filter reaction mass from the previous step. The plug flow reactor was cooled to temperature (-55 ± 5 ºC), and the filtered reaction mass was pumped into the plug flow reactor, along with sec-butyllithium (12% wt in cyclohexane, 1.5 eq., 7 parts by vol.), which was diluted with heptane (3 parts by vol.). Ethyl chloroformate (1.75 eq., 3 parts by vol.), which was diluted with THF (2 parts by vol.), was introduced into reaction loop 2 with a residence time of 36 minutes. The effluent was directed to a stirring solution of aqueous ammonium chloride (8 vol., 10% w/v) at 25 ± 5 ºC under nitrogen. HPLC of the reaction mixture indicated ethyl 4-chloro-l-(triisopropylsilyl)- 1H-pyrrolo[2,3-d]pyridine-5- carboxylate (STG-02) was obtained. FIG. 7 depicts the schematic diagram of the plug flow reactor.

[0202] The reaction mass in the aqueous ammonium chloride solution was charged with MTBE (4 vol.), stirred, allowed to settle, and the layers were separated. MTBE (3 vol.) was added to the aqueous layer, stirred, allowed to settle, and the layers were separated. The organic layers were combined, washed with potable water (4 vol .) and aqueous sodium chloride (10% w/v, 5 vol.). The organic layer was reduced by distillation (2 vol.). Ethanol (3 vol.) was added to the organic layer, and the organic layer was reduced by vacuum distillation (2 vol.). The addition of ethanol (3 vol.) to the organic layer was repeated followed by concentration byvacuum distillation (2 vol.). Ethanol (2 vol.) was added followed by the addition of ethanolic HC1 (3.3 M, 5 vol.) before stirring overnight. The resulting solids were filtered and washed with ethanol (1 vol.). The wet cake was dried in a vacuum oven overnight at 45 ± 5 ºC to obtain ethyl 4-chloro-1H-pyrrolo[2,3-b]pyridine-5-carboxylate hydrochloride, a pale brown solid (2.17 kg, 72%). ¹H NMR (300 MHz, CDCh), 5 ppm: 10.79 (s, 1H), 8.89 (s, 1H), 7.50 - 7.44 (d, J 3.6 Hz, 1H), 6.79 - 6.75 (d, ./ 3.6 Hz, 1H), 4.52 - 4.41 (q, J = 7.2, 7.2, 7.1 Hz, 2H), 1.48 - 1.42. (t, ./= 7.2, 7.1 Hz, 3H)

[0203] Example 3: Preparation of Ethyl 4-ChIoro-1H pyrroIo[2,3-b]pyridine-5- carboxylate (STG-04)

[0204] In a jacketed reactor (100 L), ethyl 4-chloro-lH-pyrrolo[2,3-d]pyridine-5- carboxylate hydrochloride (2.1 kg, 8.31 mol, 1 .0 eq., Example 2, STG-03) was combined with

2-MeTHF (22 L, 10 vol.) and stirred under nitrogen at 30 ± 5 ºC. To the reaction mass, an aqueous solution of potassium phosphate tribasic (1.76 kg, 8.31 moi, 1.0 eq.) was added in portions every 5 minutes. The slurry was stirred at 30 ± 5 ºC (40 - 45 min.) and was then allowed to settle (20 - 25 min.), and the layers were separated. To the aqueous layer, 2-MeTHF (2.1 L, 1 vol.) was added, stirred, and allowed to settle. The organic layers were combined and washed twice with potable water (2.1 L, 1 vol.) and aqueous sodium chloride (10%, 2 vol.), separated, and the organic layer was concentrated by vacuum distillation (2 vol.). Ethanol (15.1 L, 7 vol.) was charged, stirred, and concentrated by vacuum distillation (2 vol.), which generated a slurry. A sample of the slurry was evaluated by proton NMR to confirm tire swap from 2-MeTHF to ethanol was complete (0.13% 2-MeTHF by wt.). The slurry was filtered to collect solids. The wet cake was rinsed with ethanol (2.1 L, 1 vol.), dried in a vacuum oven (45 ± 5 ºC, 60 - 70 hours) with a nitrogen bleed to obtain ethyl 4-chloro-1H -pyrrolo[2,3%]pyridine- 5-carboxylate as a pale yellow solid (1.73 kg, 92.7%). ’H NMR (300 MHz, DMSO-d₆), δ ppm: 12.38 (s, 1H), 8.69 (s, 1H), 7.75-7.66 (d, J= 3.6 Hz, 1H), 6.69 - 6.60 (d, J= 3.6 Hz, 1H), 4.41 - 4.28 (q, 7.2, 7.2, 6.9 Hz, 2H), 1.39 - 1.29 (t, 7.2, 7.1 Hz, 3H)

[0205] Example 4: preparation of Ethyl (R )-4-((l-(tert-Butoxycarbonyl)piperidin-

3-yi)amino)-1H- pyrrolo[2,3-b]pyridine-5-carboxylate (STG-05)

[0206] In a jacketed reactor (100 L), ethyl 4-chloro-lH-pyrrolo[2,3-d]pyridine-5- carboxylate (1.7 kg, 1 eq., Example 3, STG-04), (R)-tert-Butyl 3-aminopiperidine-l-

carboxylate (2.53 kg, 1 .6 eq.), ethanol (5,4 kg, 4 vol), and A’AMiisopropylethylamine (2.9 kg, 3.0 eq.) were combined and agitated under nitrogen. The reaction mass was warmed to 120 ± 5 ºC for 35 - 40 hours. The reaction mass was cooled to 50 ± 5 ºC over 2 hours and sampled for HPLC analysis. HPLC results indicated the reaction was complete (0.05% SM remaining). The reaction mass was cooled (25 ± 5 ºC) over time (50 - 60 mm). Ethanol was charged (5,4 kg, 4 vol) and the reaction mass was -warmed (65 ± 5 ºC), and water (34.0 kg, 25 vol.) was charged over time (1.5 - 2.5 h). Solids were formed, the reach mass was cooled (25 ± 5 ºC), agitated overtime (1 - 2 h), and solids were filtered. The wet cake was washed with water (8.5 kg, 6.5 vol.), dried on the filter (25 - 50 min). In a jacketed reactor (100 L), the wet cake was charged and combined with ethanol and water ( 17 L, 1 : 1, 6.7 kg EtOH and 8.5 kg water) before agitating at 25 ± 5 ºC over 20 - 40 min. The reaction mass was filtered, washed with ethanol and water (4 L, 1: 1 , 1 .6 kg EtOH and 2.4 kg water), dried in a vacuum oven (50 ± 5 ºC) over time (55 - 65 h) to obtain ethyl (/?)-4-((l-(terf-butoxycarbonyl)piperidm-3-yl)amino)-lH- pyrrolo[2,3%]pyridine-5-carboxylate as a pale yellow solid (2.3 kg, 78%). ¹H NMR (300 MHz, DMSO-d₆), δ ppm: 11.7 (s, 1H). 8.97-8.94 (d, J = 7.6 Hz, 1H), 8.55 (s, 1H), 7.22 - 7.20 (q, J-= 2.6, 0.5, 2.6 Hz, 1H), 6.62 (bs, 1H), 4.28 - 4.11 (m, 3H), 3.73 - 3.35 (m, 3H), 3.31-3.16 (m, 1H), 2.07-1.91 (m, IH), 1,81 - 1.61 (m, 21 1). 1.60 - 1.48 (bs, 1H), 1.47 - 1.34 (m, 3H), 1.33 -

1.25 (• . ./ 7.1, 7.1 Hz, 3H), 1.23 - 1.06 (m. 6H)

[0207] Example 5: Preparation of Ethyl ( R)-4-(Piperidin-3-ylamino)-1H - pyrroIo[2,3-b]pyridine-5-carboxyIate Dihydrochloride Salt (STG-06)

[0208] In a jacketed reactor (100 L), ( R)-4-((l-(tert-butoxycarbonyl)pipendin-3~ yl)amino)-1H -pyrro1o[2,3-b>]pyridine-5-carboxylate (2.3 kg, 1.0 eq., Example 4, STG-05) and ethanol (11 .5 L, 5 vol.) were combined, agitated under nitrogen, and cooled (5 ± 5 ºC). To the reaction mass, ethanolic hydrochloride (11.5 L, 3.3 M, 6.4 eq.) was charged over time (20-40 min) maintaining reaction mass temperature < 6 ºC. Upon the complete addition of the ethanolic hydrochloride, the reaction mass was wanned (35 ± 5 ºC) and continued to stir overnight. A sample of the reaction mass was analyzed by HPLC. HPLC results indicated the reaction was complete (0.2 % SM). The reaction mass was filtered and dried in a vacuum oven (50 ± 5 ºC), with a nitrogen bleed, overnight to obtain ethyl (R )-4-(piperidin-3-ylamino)-lH- pyrrolo[2,3-b ]pyridme-5-carboxylate di-hydrochloride as an off-white solid (2.07 kg, 96%). Tl NMR (300 MHz, DMSO-d₆), δ ppm: 12.92. (bs, 1H), 10.31 - 10.01 (bs, 1H), 9.65 - 9.35 (d, J = 8.2 Hz, 2H), 8.65 - 8.60 (m, 1H), 7.49 - 7.41 (m, 1H), 7.41 - 7.33 (m, 1H), 4.78 - 4.59 (m.

1H), 4.41 - 4.29 (q, J= 7.1, 7.0, 7.1 Hz, 2H), 3.48 - 3.37 (m, 2H), 3.31 - 3.18 (m, 1H), 3.13 - 2.79 (m, 2H), 2.24 - 2.10 (m, 1H), 2.08 - 1.70 (m, 3H), 1.41 - 1.29 (t, J 7.1, 7.1 Hz, 3H) [0209] Example 6: Preparation of Ethyl (R )-4-((l-(2-cyanoacetyl)piperidin-3- yl)amino)-lH -pyrrolo[2,3-i]pyridine-5-carboxylate (STG-06)

[0210] In a jacketed reactor (100 L), ethyl (R )-4-(piperidin-3-ylamino)-lH- pyrrolo[2,3-b ]pyridme-5-carboxylate di-hydrochloride (2.07 kg, 1 .0 eq.. Example 5, STG-06), 2 -hydroxypyridine 1 -oxide (1.0 kg, 1.6 eq., HOPO), l-(3-dimethylaminopropyl)-3- ethylcarbodiimide hydrochloride (1.8 kg, 1.6 eq., EDC HCI), cyanoacetic acid (0.8 kg, 1.6 eq.), and THF (20 L, 10 vol.) were combined and agitated under nitrogen over time (20 - 40 min) at 20 i 5 ºC. To the reaction mass, diisopropylethylamine (2.6 L, 2.6 eq.) was added, and and the reaction was warmed (50 ± 5 ºC) and continued to agitate overnight. HPLC of the reaction mass provided results that the starting material was consumed. The reaction mass was cooled (25 ± 5 ºC) over time (1 - 2 h). The reaction mass was charged into a jacketed reactor containing agitated water (40 L, 20 vol.) at temperature (25 ± 5 ºC) over time (90 - 100 min). The jacket reactor containing the reaction mass was rinsed with THF (2 L , 1 vol.) and charged into the jacketed reactor containing water, which agitated over time (19 - 21 h) at 25 ± 5 ºC. The reaction mass was cooled (10 ± 5 ºC) over time (50 - 70 min) and filtered. The wet cake was washed twice with water (5 L, 2.5 vol.), washed with ethanol (2 L, 1 vol.), dried under filter vacuum (3 - 4 h), dried in a vacuum oven (< 50 ºC) overtime (15 - 20 h) to obtain ethyl (R )-4- ((1 -(2-cya.noacetyl)piperidin-3-yl)amino)-1H -pyrroIo[2,3-h]pyridine-5-carboxylate as a pale yellow solid (1.56 kg, 77%). ¹H NMR (300 MHz, DMSO-d₆), δ ppm: 11.76 (bs, 1H), 8.92 - 8.81 (dd, J = 8.4, 8.2 Hz, 1H), 8.59 - 8.55 (d, J= 3.0 Hz, 1H), 7.28 - 7.20 (m, 1H), 6.74 - 6.67 (m, 1H), 4.39 - 4.21 (q, J= 7.2, 7.2, 7.1 Hz, 3H), 4.21-4.0 (m, 2H), 4.05 - 3.07 (m, 4H), 2.17 - 1.99 (m, 1H), 1.82 - 1.51 (m, 3H), 1.37 - 1.28 (t, J= 7.2, 7.2 Hz, 3H)

[0211] Example 7: Preparation of Ethyl (^)-4-((l-(2-cyanoacetyI)piperidin-3- yl)amino)-lH -pyrrolo[2,3-b]]pyridme-5-carboxylate (Compound 1)

[0212] To a jacketed reactor (20 L), ethyl (R)-4-((l-(2-cyanoacetyl)piperidin-3- yl)amino)-lJf-pyrro1o[2,3~Z>]pyridine-5-carboxylate (1.56 kg, 1.0 eq, Example 6, STG-07) was combined with aqueous ethanol (20%, 19.6 L, 14 vol.) and agitated at 25 ± 5 ºC) overtime (15 - 25 min). The reaction mass was warmed to 70 ± 5 ºC) over time (1 - 2 h). To the reaction mass, activated carbon (0. 14 kg, 10% w/w) was added with continued heating for 2 - 3 h). The warm reaction mass was filtered through a jacket celite pad filter, wanned and under vacuum. The jacketed celite pad filter was washed with aqueous ethanol (20%, 2.8 L, 2 vol.) at temperature 70 i 5 ºC. The filtrates were charged to a jacketed reactor (100 L) at 70 i 5 ºC with agitation and under nitrogen. The reaction mass was cooled (40 ± 5 ºC) over time (3 - 4 h) and held at temperature (40 ± 5 ºC) over time (6 - 7 h). The reaction mass was cooled (25 ± 5 ºC) over time (3 - 4 h) and held at temperature 25 ± 5 ºC) over 11 - 13 h). The reaction was cooled to 10 ± 5 ºC over 2 - 3 h and held at that temperature for 5 - 6 h). Hie reaction mass was cooled (5 ± 5 ºC) over time (1 - 2 hrs.) and held at temperature (5 ± 5 ºC) overnight. The reaction mass was filtered, washed with ethanol (1.5 L, 1 vol.), washed with ethanol again (3.0 L, 2 vol.), and dried in a vacuum oven (50 ± 5 ºC) over time (45 -52 h) with a nitrogen bleed to obtain ethyl (7?)-4“((l-(2-cyaiioacetyl)piperidin-3-yl)aniino)-lH-pyrrolo[2,3-/?]pyridine~5~ carboxylate as a crystalline off-white solid (1.2.3 kg, 87%). ^rH NMR (300 MHz, DMSO-de), 5 ppm: 11.73 (bs, 1H), 8.92 - 8.81 (dd, J= 8.5, 8.2 Hz, 1H), 8.58 - 8.55 (d, J= 2.9 Hz, 1H), 7.27 - 7.21 (m, 1H), 6.74 - 6.66 (m, 1H), 4.38 - 4.21 (m, 3H), 4.21 - 4.05 (m, 2H), 4.05 - 3.06 (m, 4H), 2.17 -1.98 (m, 1H), 1.84 - 1.51 (m, 3H), 1.38 - 1.2.7 (t, J= 7.2, 7.2 Hz, 3H)

[0213] Although the present invention has been described in considerable detail with reference to certain preferred embodiments thereof, other versions are possible. Therefore, the spirit and scope of the appended claims should not be limited to the description and the preferred versions contained within this specification.

Claims

1 . A method for the preparation of Compound 1 having the structure:

(Compound 1) comprising the steps of:

(a) contacting the compound SM-01 , with the compound

the presence of a

base to form the compound STG-01 .

_contacting the compound STG-01 with ethyl chloroformate in the presence of a base to form the compound

(d) converting STG-03 to Compound 1.

2. The method according to claim 1, further comprising contacting the compound STG-03

with a base to form the compound

3. The method according to claim 2, further comprising contacting the compound STG-04 with in the presence of an amine base to form the compound

STG-05

4. The method according to claim 3, wherein said contacting is conducted in an autoclave at elevated pressure.

5. The method according to claim 3, further comprising contacting the compound STG-05

with an alcoholic HC1 solution to form the compound

6. The method according to claim 5, further comprising contacting the compound STG-06

with

in dichloromethane in the presence of a coupling reagent and an amine base, and thereby forming Compound 1 .

7. The method according to claim 5, further comprising contacting the compound STG-06

with INT-02 in THF and ethanol in the presence of a coupling reagent and an amine base, and thereby forming Compound 1.

8. The method according to claim 5, further comprising contacting the compound STG-06

with in THF in the presence of a coupling reagent and an amine base, and thereby forming Compound 1 .

9. The method according to claim 1 , wherein the method results m an improved purity' profile.

10. A method of preparing Compound 1 according to the route shown in Scheme 2.

11. The method of claim 10, wherein the method of preparing Compound 1 according to the route shown in Scheme 2 results in an improved purity profile.

12. A method for the preparation of Compound 1 having the structure:

(Compound 1) comprising the steps of

(a) contacting the compound

alcoholic HC1 solution to form

the compound STG-03

(b) converting STG-03 to Compound 1 .

13. The method according to claim 12, further comprising contacting the compound STG-03

with a base to form the compound

14. The method according to claim 13, further comprising contacting the compound STG-04 with SNT-O1 in the presence of an amine base to form tire compound

STG-05

15. The method according to claim 14, wherein said contacting is conducted in an autoclave at elevated pressure.

16. The method according to claim 14, further comprising contacting the compound STG-05

with an alcoholic HC1 solution to form the compound

17. The method according to claim 16, further comprising contacting the compound STG-06

with 1NT-02 in dichloromethane in the presence of a coupling reagent and an amine base, and thereby forming Compound 1 .

18. The method according to claim 16, further comprising contacting the compound STG-06

with 1NT-02 in THF and ethanol in the presence of a coupling reagent and an amine base, and thereby forming Compound 1.

19. The method according to claim 16, further comprising contacting the compound STG-06

with 1NT-02 in THF in the presence of a coupling reagent and an amine base, and thereby forming Compound 1 .

20. The method according to claim 12, wherein the method results in an improved purity profile.

21. The method of any one of claims 1, 10, or 12, wherein the method does not produce more than about 1 .0% of an isomer than Compound 1.

22. The method of any one of claims 1, 10, or 12, wherein the method does not produce more than about 0.15% of an isomer than Compound 1 .

23. The method of any one of claims 1, 10, or 12, wherein the method does not produce more than about 0.1% of an isomer than Compound 1.

24. The method of any one of claims 1, 10, or 12, wherein the method does not produce more than about 0.05% of an isomer than Compound 1 .

25. Tie method of any one of claims 1, 10, or 12, wherein the method does not produce an isomer within the limit of detection oilier than Compound 1.

26. The method of any one of claims 1 , 10, or 12, wherein Compound 1 is at least about 95% pure.

27. The method of any one of claims 1, 10, or 12, wherein Compound 1 is at least about 99% pure.

28. The method any one of claims 1, 10, or 12, wherein Compound 1 is at least about 99.8% pure.

29. The method any one of claims 1, 10, or 12, wherein Compound 1 is about 100% pure.

30. The method of any one of claims 1, 10, or 12, wherein any individual impurity is present in an amount of less than about 0.15%.

31. The method of any one of claims 1, 10, or 12, wherein any individual impurity is present in an amount of less than about 0.1%.

32. Hie method of any one of claims 1, 10, or 12, wherein any individual impurity is present in an amount of less than about 0.05%.

33. In some embodiments, any individual impurity is below the limit of detection.

34. Hie method of any one of claims 1, 10, or 12, wherein the total amount of tire impurities is in an amount of less than about 1.0%,

35. The method of any one of claims 1, 10, or 12, wherein the total amount of the impurities is in an amount of less than about 0.5%.

36. The method of any one of claims 1, 10, or 12, wherein the total amount of the impurities is in an amount of less than about 0.2%,

37. In some embodiments, the total amount of the impurities is below the limit of detection.

38. The method of any one of claims 1 , 10, or 12, wherein the impurity is selected from an unreacted starting material, an unreacted intermediate, an impurity propagated from a side reaction, or a combination thereof.

39. The method of any one of claims I , 10, or 12, wherein the impurity is selected from:

butyl (R)-4-((1 -(2-cyanoacety!)piperidin-3- isopropyl (R)-4-(piperidin-3-ylamino)-1 H- yl)amino)-1 H-pyrrolo[2,3-L’]pyridine-5- pyrrolo[2,3-b]pyridine-5-carboxylate carboxylate

isopropyl (R)-4-((1-(2- ethyl (R)-4-((1-(3-amino-3- cyanoacetyl)piperidin-3-yl)amino)-1W- oxopropanoyl)piperidin-3-yl)amino)-1H- pyrrolo[2,3-b]pyridine-5-carboxylate pyrroto[2,3-bjpyrid!ne-5-carboxyiate

(R)-4-((1-(3-amino-3- oxopropanoyl)piperidin-3-yl)amino)-5- (R)-4-((1-(2-cyanoacetyl)piperidin-3-

(ethoxycarbonyl)-1H-pyrrolo[2,3- yl)amino)-5-(ethoxycarbonyl)-1 H- jbjpyridine 7-oxide pyrrolo[2,3-b]pyridine 7-oxide

1-(4-chloro-1-(triisopropylsilyl)-

1 H-pyrrolo[2,3-b]pyridin-5- 1 -(4-chloro-1 H-pyrr olo[2,3- yl)pentan-1-one bjpyrid in-5-y l)pentan-1 -one

tert-butyl (R)-3-((5-pentanoyl-1 H- (R)-1-(4-(piperidin-3-ylamino)-1H- pyrrolo[2,3-b]pyridin-4- pyrrolo[2,3-b]pyridin-5-yl)pentan-1 yi)amino)piperidine-1 -carboxylate one hydrochloride

(R)-3-oxo-3-(3-((5-pentanoyl-1 H- 1 -(4-chloro-1 -(triisopropylsilyl)- 1 H- pyrrolo[2,3-6]pyridin-4- pyrrolo[2,3-b]pyridin-5-yi)-3- yl)amino)piperidin-1-yl)propanenitrile methylbutan-1-one

1 -(4-chloro-1 H-pyrrolo[2,3- tert-butyl (R)-3-((5-(3-methylbutanoyl)-1 H- b]pyridin-5-yl)-3-methylbutan- pyrrolo[2,3-b]pyridin-4-yl)amino)piperidine- 1-one 1 -carboxylate

(R)-3-methyl-1-(4-(piperidin-3- (R)-3-(3-((5-(3-methylbutanoyl)-1 H- ylamino)-1H-pyrrolo[2,3-b]pyridin-5- pyrrolo[2,3-/?]pyridin-4-yi)amino)piperidin-1 - yi)butan-1 -one hydrochloride yl)-3-oxopropanenitrile

1 -(4-chloro-1 -(triisoprapylsilyl)-! H~ 1 -(4-chloro-1 H-pyrralo[2,3- pyrrolo[2,3-b]pyridin-5-yl)-2- b]pyridin-5-yl)-2-methylbutan-

fert-butyl (3R)-3-((5-(2-methylbutanoyl)- 2-methyl-1-(4-(((f?)-piperidin-3-

1 H-pyrrolo[2 ,3-6]pyridin-4- yl)amino)-1H-pyrrolo[2,3-b]pyridin-5- yl)amino)piperidine-1 -carboxylate yl)butan-1-one hydrochloride

3-((3R)-3-((5-(2-methyibutanoyl)-1H- ethyl (R)-4-((1-(2-cyanoacetyl)piperldin- pyrroio[2,3-b]pyridin-4-yl)amino)piperidin-1 - 3-yl)amlno)-1-methyl-1H-pyrrolo[2_i3- yl)-3-oxopropanenltrlle b]pyridine-5-carboxylate

ethyl 4-(((3R)-1-(2- cyanopropanoyl)piperidin-3-yl)amino)-

1H-pyrrolo[2,3-b]pyridine-5-carboxylate _?

_{a combination} thereof.