Xinafoate salt of the JAK inhibitor compound

Abstract

To provide compounds and production methods thereof.SOLUTION: The present disclosure provides the compound 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2): and a production method thereof.SELECTED DRAWING: None

Description

[Background technology]

[0001] The novel salts of formula (I) of the present disclosure are expected to be useful for the treatment or prevention of conditions mediated solely or in part by Janus Kinases (or JAKs), a family of cytoplasmic protein tyrosine kinases including JAK1, JAK2, JAK3 and TYK2. Although multiple JAK kinases can be affected by a particular cytokine or signaling pathway, each JAK kinase is selective for the receptor of a particular cytokine. Studies suggest that JAK3 is associated with the common gamma chain (γc) of various cytokine receptors. In particular, JAK3 selectively binds to the receptors of IL-2, IL-4, IL-7, IL-9, IL-15 and IL-21 and is part of their cytokine signaling pathways. Kinase JAK1 specifically interacts with the receptors of cytokines IL-2, IL-4, IL-7, IL-9 and IL-21. Binding of certain cytokines to their receptors (e.g., IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21) leads to receptor oligomerization, bringing the cytoplasmic tails of the associated JAK kinases into close proximity and promoting trans-phosphorylation of tyrosine residues on the JAK kinases, which results in their activation.

[0002] Phosphorylated JAK kinases bind to various signal transducers and activators of transcription (STAT) proteins. These STAT proteins, which are DNA-binding proteins activated by phosphorylation of tyrosine residues, act as both signal transduction molecules and transcription factors, and ultimately bind to specific DNA sequences present in the promoters of cytokine-responsive genes (Non-Patent Document 1). JAK / STAT signaling is involved in mediating many abnormal immune responses, such as allergies, asthma, autoimmune diseases, such as graft (allograft) rejection, rheumatoid arthritis, amyotrophic lateral sclerosis, and multiple sclerosis, as well as solid and hematological malignancies, such as leukemia and lymphoma. For reviews of pharmaceutical intervention of the JAK / STAT pathway, see (Non-Patent Document 2), (Non-Patent Document 3), (Non-Patent Document 4), and (Non-Patent Document 5).

[0003] Given the importance of JAK kinases, compounds that modulate the JAK pathway may be useful for treating diseases or conditions involving lymphocyte, macrophage, or mast cell function (Non-Patent Document 6; Non-Patent Document 7). Conditions in which targeting the JAK pathway or modulating JAK kinases is believed to be therapeutically useful include leukemia, lymphoma, transplant rejection (e.g., islet graft rejection, bone marrow transplant applications (e.g., graft-versus-host disease), autoimmune diseases (e.g., diabetes), and inflammation (e.g., asthma, allergic reactions).

[0004] In view of the large number of conditions that would benefit from treatment involving modulation of the JAK pathway, it is apparent that new compounds and new forms of compounds that modulate the JAK pathway, as well as methods of using these compounds, should provide significant therapeutic benefits to a variety of patient types. [Prior art documents] [Non-patent literature]

[0005] [Non-Patent Document 1] Leonard et al.,(2000),J.Allergy Clin.Immunol.105:877-888 [Non-Patent Document 2] Frank,(1999),Mol.Med.5:432:456 [Non-Patent Document 3] Seidel et al.,(2000),Oncogene 19:2645-2656 [Non-Patent Document 4] Vijayakrishnan et al,Trends Pharmacol.Sci 2011,32,25-34 [Non-Patent Document 5] Flanagan et al,J.Med.Chem.2014,57,5023-5038 [Non-Patent Document 6] Kudlacz et al.,(2004)Am.J.Transplant 4:51-57 [Non-Patent Document 7] Changelian(2003)Science 302:875-878 Summary of the Invention [Means for solving the problem]

[0006] The present disclosure provides a compound of formula (I): [ka] The present invention relates to novel salts of the formula (I), pharmaceutical compositions containing the salts of formula (I), and methods of using the same.

[0007] Compounds of formula (I) are described in International Patent Application PCT / EP2018 / 051038, which discloses a class of JAK inhibitor compounds, including (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide (see Example 35). Additional JAK inhibitor compounds are described in International Patent Application PCT / EP2018 / 051038, including various salts of (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide.

[0008] Disclosed herein are compounds of formula (I) prepared as novel salts that are useful in treating conditions in which targeting the JAK pathway or inhibiting a JAK kinase, particularly JAK1, is beneficial.

[0009] In at least one embodiment, the disclosure includes a compound of formula (I) prepared as the xinafoic acid (1-hydroxy-2-naphthoic acid) salt (formula (Ia)). [ka] 4-{(2R)-1-[(3-{5-fluoro-2-[2-fluoro-3-(methanesulfonyl)anilino]pyrimidin-4-yl}-1H-indol-7-yl)amino]-3-methoxy-1-oxopropan-2-yl}-1-methylpiperazin-1-ium; 1-hydroxynaphthalene-2-carboxylate

[0010] The xinafoate salt of the present disclosure has a xinafoate stoichiometry of 1:1 (as shown above). Also disclosed herein is a method for preparing the xinafoate salt of formula (Ia). Also disclosed is a pharmaceutical composition comprising the xinafoate salt of formula (Ia) and a pharma- ceutically acceptable diluent, excipient, or carrier. In another embodiment, a method for treating a JAK-associated disorder in a subject in need thereof is disclosed, comprising administering to the subject an effective amount of the xinafoate salt of formula (Ia). In another embodiment, a xinafoate salt of formula (Ia) for use in treating a JAK-associated disorder is disclosed. In another embodiment, a pharmaceutical composition comprising the xinafoate salt of formula (Ia) for use in treating a JAK-associated disorder is disclosed. In another embodiment, a use of the xinafoate salt of formula (Ia) in the manufacture of a medicament for treating a JAK-associated disorder is disclosed. Also disclosed is a novel method for preparing the xinafoate salt of formula (Ia), as well as two novel intermediates: - 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2), as shown below: [ka] - 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride, as shown below: [ka] is also disclosed. [Brief description of the drawings]

[0011] [Figure 1] 4-{(2R)-1-[(3-{5-fluoro-2-[2-fluoro-3-(methanesulfonyl)anilino]pyrimidin-4-yl}-1H-indol-7-yl)amino]-3-methoxy-1-oxopropan-2-yl}-1-methylpiperazin-1-ium; 1-hydroxynaphthalene-2-carboxylate X-ray powder diffraction pattern (XRPD). DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0012] In some embodiments, solid forms of the compounds of formula (I) and (Ia) are disclosed. The term "solid form" includes polymorphs, crystalline salts, solvates, hydrates, and amorphous forms of the compounds of formula (I) and (Ia). According to at least one embodiment of the present disclosure, the salts of the present disclosure are crystalline. The salts can also exist in solvated and non-solvated forms, such as hydrated forms. It should be understood that the present disclosure encompasses all such solvated and non-solvated forms of the compounds of formula (I). The term "solvate" includes a crystal structure of the same chemical entity, but incorporating molecules of a solvent within the molecular packing of the crystal structure. The term "hydrate" includes a crystal structure of the same chemical entity, but incorporating molecules of water within the molecular packing of the crystal structure.

[0013] Compounds may exist in various crystal structure forms known as polymorphs.As used herein, "polymorph" is understood to mean a crystal form that has the same chemical composition but has different spatial arrangements of the molecules, atoms, and / or ions that form the crystal.Polymorphs have the same chemical composition but can have different geometric arrangements, and therefore can show different physical properties, such as density, hardness, melting point, flexibility, durability, stability, dissolution, etc.

[0014] It is generally known that solid materials can be characterized using conventional techniques such as X-ray powder diffraction (XRPD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, near infrared (NIR) spectroscopy, solution and / or solid state nuclear magnetic resonance spectroscopy, etc. The water content of such solid materials can be determined by Karl Fischer analysis.

[0015] The solid forms described herein provide XRPD patterns substantially similar to those shown in the figures, with various 2-theta (2θ) values ​​as shown in the tables contained herein. Those skilled in the art will understand that XRPD patterns or diffractograms are obtained with one or more measurement errors depending on the recording conditions, such as the device or machine used. Similarly, it is generally known that the intensity of an XRPD pattern may vary depending on the measurement conditions or sample preparation, as a result of preferred orientation. Those skilled in the art of XRPD will further be aware that the relative intensity of peaks may also be affected by particles with sizes greater than 30 μm and non-unitary aspect ratios. Those skilled in the art will understand that the position of reflections may also be affected by the exact height at which the sample is located within the diffractometer, and also by the zero calibration of the diffractometer. The planarity of the surface of the sample may also have a slight effect.

[0016] In view of these considerations, the diffraction pattern data presented should not be considered absolute (Jenkins, R & Snyder, RL 'Introduction to X-Ray Powder Diffractometry' John Wiley & Sons 1996; Bunn, CW (1948), 'Chemical Crystallography', Clarendon Press, London; Klug, HP & Alexander, LE (1974), 'X-Ray Diffraction Procedures'). It should also be understood that the solid forms embodied herein are not limited to those that provide XRPD patterns identical to those shown in the figures, and that any solid form that provides an XRPD pattern substantially the same as that shown in the figures is within the scope of the corresponding embodiments. Those skilled in the art of XRPD will be able to judge the substantial identity of the XRPD patterns. In general, the measurement error of the diffraction angle in XRPD is about 2θ (±0.2°), and this degree of measurement error should be taken into account when analyzing the X-ray powder diffraction patterns in the figures and when reading the data contained in the tables contained herein.

[0017] Form A In at least one embodiment, Form A of 4-{(2R)-1-[(3-{5-fluoro-2-[2-fluoro-3-(methanesulfonyl)anilino]pyrimidin-4-yl}-1H-indol-7-yl)amino]-3-methoxy-1-oxopropan-2-yl}-1-methylpiperazin-1-ium; xinafoate salt of 1-hydroxynaphthalene-2-carboxylate is disclosed.

[0018] In some embodiments, Form A is characterized by providing an X-ray powder diffraction (XRPD) pattern substantially as shown in FIG.

[0019] In some embodiments, Form A has an XRPD pattern comprising at least one peak expressed in 2-theta (±2°) selected from the peaks set forth in Table 1. It will be understood that 2-theta values ​​in X-ray powder diffraction patterns may vary slightly from machine to machine or from sample to sample, and therefore quoted values ​​should not be construed as absolute.

[0020] In some embodiments, Form A has the following 2θ value measured using CuKα radiation: 15.0 ° and 21.0 ° and 22.6 ° The present invention is characterized by providing at least one of the following:

[0021] In some embodiments, Form A has the following 2θ values ​​measured using CuKα radiation: 8.2, 8.9, 11.2, 14.2, 15.0, 15.3, 16.2, 17.5, 21.0, 22.6, 23.0, 23.7, 24.6, and 26.2. ° The present invention is characterized by providing at least one of the following:

[0022] In some embodiments, the crystallinity of Form A is greater than about 60%, such as greater than about 80%, e.g., greater than about 90%, and in at least one embodiment, greater than about 95%. In yet other embodiments, the crystallinity is greater than about 98%.

[0023] According to a further aspect of the present disclosure, (i) dissolving 5-((5-methyl-2-((3,4,5-trimethylphenyl)amino)pyrimidin-4-yl)amino)-benzo[d]oxazol-2(3H)-one free base in a suitable solvent such as DMSO; (ii) dissolving xinafoic acid in a suitable solvent, such as DMSO; (iii) mixing the two solutions; (iv) optionally seeding with crystals of the xinafoate salt of 5-((5-methyl-2-((3,4,5-trimethylphenyl)amino)pyrimidin-4-yl)amino)-benzo[d]oxazol-2(3H)-one; (v) crystallizing the xinafoate salt of 5-((5-methyl-2-((3,4,5-trimethylphenyl)amino)pyrimidin-4-yl)amino)-benzo[d]oxazol-2(3H)-one; (vi) isolating the xinafoate salt of 5-((5-methyl-2-((3,4,5-trimethylphenyl)amino)pyrimidin-4-yl)amino)-benzo[d]oxazol-2(3H)-one; A method for preparing Form A is provided, comprising:

[0024] According to a further aspect of the present disclosure, there is provided a process for the preparation of two novel intermediates 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2) and 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride, comprising: (i) dissolving lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate in distilled water at pH 4; (ii) dissolving L-(+)-tartaric acid in distilled water; (iii) mixing the two solutions from step (i) and step (ii) in a suitable solvent, such as ethanol, to induce crystallization; (iv) stirring the mixture of step (iii) at room temperature for 20 hours; (v) adding a suitable solvent, such as ethanol, to the mixture of step (iv) and filtering after cooling to give the product 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium(2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2); (vi) collecting the product of step (v) and drying under reduced pressure for 72 hours; (vii) dissolving the product of step (vi) in distilled water; (viii) performing cationic ion exchange on the product of step (vii); (ix) eluting the product of step (viii) with 2M HCl and evaporating the solution to dryness to induce crystallization of 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride; A method is provided that includes:

[0025] Pharmaceutical Compositions & Methods of Use The novel salts herein may be administered by inhalation as finely divided solid particles without any additional excipients, diluents or carriers. In at least one embodiment, a pharmaceutical composition is disclosed that comprises Form A in association with a pharma- ceutically acceptable diluent or carrier.

[0026] Compositions of the present disclosure may be in a form suitable for administration by inhalation (eg, as a fine powder or liquid aerosol) or by insufflation using an appropriate device (eg, as a fine powder).

[0027] The compositions of the present disclosure can be obtained by conventional procedures using conventional pharmaceutical excipients well known in the art. For example, compositions intended for inhalation may contain, for example, finely divided lactose or other suitable excipients in an amount up to about 90 w / w% of the composition.

[0028] If necessary, the novel salts can be milled or micronized prior to formulation to provide a uniform particle size distribution. For example, Form A can be milled to provide an average particle size of about 1 μm to 3 μm. Suitable milling and micronization methods are well known (Midoux et al., (1999), Powder Technology, 104:113-120).

[0029] Form A of the present disclosure is expected to be useful in the treatment of diseases or medical conditions mediated solely or in part by JAK, particularly JAK1, i.e., Form A may be used to provide a JAK inhibitory effect in a warm-blooded animal in need of such treatment. For example, Form A of the present disclosure may be used to inhibit JAK kinase in vivo as a therapeutic approach to the treatment or prevention of diseases mediated completely or in part by JAK kinase activity (referred to herein as "JAK kinase-mediated diseases"). Non-limiting examples of JAK kinase mediated diseases that may be treated or prevented include obstructive, restrictive or inflammatory airway diseases of whatever type, etiology or pathogenesis, in particular obstructive, restrictive or inflammatory airway diseases, including asthma, in particular atopic asthma, allergic asthma, non-atopic asthma, bronchial asthma, non-allergic asthma, emphysematous asthma, exercise-induced asthma, emotion-induced asthma, extrinsic asthma caused by environmental factors, infectious asthma associated with bacterial, fungal, protozoan and / or viral infections, bronchiolitis, cough variant asthma, drug-induced asthma, and the like, seasonal allergic rhinitis, perennial allergic rhinitis, vasomotor rhinitis, acute, chronic, ethmoid, frontal maxillary, and other asthma-related diseases, as described above. Rhinitis or sinusitis of various etiologies, including but not limited to sinusitis including maxillary or sphenoid sinusitis; chronic obstructive pulmonary disease (COPD), chronic obstructive pulmonary disease (COLD), chronic obstructive airway disease (COAD) or small airway obstruction, including but not limited to chronic bronchitis, emphysema, bronchiectasis, cystic fibrosis, obliterative bronchiolitis; treatment of bronchitis, particularly including acute bronchitis, acute laryngobronchitis, chronic bronchitis, dry bronchitis, wet bronchitis, infectious asthmatic bronchitis, staphylococcal or streptococcal bronchitis, and vesicular bronchitis.

[0030] Thus, in one aspect of the disclosure, there is disclosed a method of treating a JAK kinase mediated disease in a subject in need thereof, comprising administering to the subject an effective amount of the xinafoate salt of the compound of formula (Ia), or an effective amount of Form A. Also disclosed is a method of treating a JAK kinase mediated disease in a subject in need thereof, comprising administering to the subject a pharma- ceutically acceptable composition comprising an effective amount of the compound of formula (Ia), or an effective amount of Form A.

[0031] In one embodiment, a xinafoate salt of the compound of formula (Ia) is also disclosed for use in treating a JAK kinase-mediated disease in a subject in need thereof. In another embodiment, a pharma- ceutically acceptable composition comprising a xinafoate salt of the compound of formula (Ia) is disclosed for use in treating a JAK kinase-mediated disease in a subject in need thereof. In one embodiment, Form A is also disclosed for use in treating a JAK kinase-mediated disease in a subject in need thereof. In another embodiment, a pharma- ceutically acceptable composition comprising Form A is disclosed for use in treating a JAK kinase-mediated disease in a subject in need thereof.

[0032] In one embodiment, the use of the xinafoate salt of the compound of formula (Ia) in the manufacture of a medicament for use in treating a JAK kinase mediated disease in a subject in need thereof is also disclosed.In one embodiment, the use of Form A in the manufacture of a medicament for use in treating a JAK kinase mediated disease in a subject in need thereof is also disclosed.

[0033] In one aspect of the disclosure, a method of treating asthma in a subject in need thereof is disclosed, comprising administering to the subject an effective amount of a xinafoate salt of the compound of formula (Ia), or an effective amount of Form A. Also disclosed is a method of treating asthma in a subject in need thereof, comprising administering to the subject a pharma- ceutically acceptable composition comprising an effective amount of a xinafoate salt of the compound of formula (Ia), or an effective amount of Form A.

[0034] In one embodiment, a xinafoate salt of the compound of formula (Ia) is also disclosed for use in treating asthma in a subject in need thereof. In another embodiment, a pharma- ceutically acceptable composition comprising a xinafoate salt of the compound of formula (Ia) is disclosed for use in treating asthma in a subject in need thereof. In one embodiment, Form A is also disclosed for use in treating asthma in a subject in need thereof. In another embodiment, a pharma-ceutically acceptable composition comprising Form A is disclosed for use in treating asthma in a subject in need thereof.

[0035] In one embodiment, the use of the xinafoate salt of the compound of formula (Ia) in the manufacture of a medicament for use in treating asthma in a subject in need thereof is also disclosed.In one embodiment, the use of Form A in the manufacture of a medicament for use in treating asthma in a subject in need thereof is also disclosed.

[0036] Thus, in one aspect of the disclosure, there is disclosed a method of treating COPD in a subject in need thereof, comprising administering to the subject an effective amount of a xinafoate salt of the compound of formula (Ia), or an effective amount of Form A. Also disclosed is a method of treating COPD in a subject in need thereof, comprising administering to the subject a pharma- ceutically acceptable composition comprising an effective amount of a xinafoate salt of the compound of formula (Ia), or an effective amount of Form A.

[0037] In one embodiment, the xinafoate salt of the compound of formula (Ia) is also disclosed for use in treating COPD in a subject in need thereof. In another embodiment, a pharma- ceutically acceptable composition comprising the xinafoate salt of the compound of formula (Ia) is disclosed for use in treating COPD in a subject in need thereof. In one embodiment, Form A is also disclosed for use in treating COPD in a subject in need thereof. In another embodiment, a pharma- ceutically acceptable composition comprising Form A is disclosed for use in treating COPD in a subject in need thereof.

[0038] In one embodiment, the use of the xinafoate salt of the compound of formula (Ia) in the manufacture of a medicament for use in treating COPD in a subject in need thereof is also disclosed.In one embodiment, the use of Form A in the manufacture of a medicament for use in treating COPD in a subject in need thereof is also disclosed. EXAMPLES

[0039] The present disclosure is further illustrated by the following examples, which are intended to detail some embodiments of the present disclosure. These examples are not intended to limit, and should not be construed to limit, the scope of the present disclosure. It will be apparent that the present disclosure can be practiced other than as specifically described herein. In light of the teachings herein, numerous modifications and variations of the present disclosure are possible, and therefore are within the scope of the present disclosure.

[0040] We have found that the novel salts of formula (I) have advantageous properties compared to the free base compound of formula (I), for example, the xinafoate salt has advantageous mechanical and physicochemical properties (i.e., non-hygroscopicity).

[0041] In the examples, unless otherwise stated: (i) Yields are given for illustration only and are not necessarily maximum attainable. (ii) NMR data, where given, are in the form of delta values ​​of major characteristic protons given in parts per million (ppm) using perdeuterio dimethylsulfoxide (DMSO-d6) as the solvent unless otherwise stated, and the following abbreviations have been used: s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet; br, broad line. (iii) Chemical symbols have their usual meaning and SI units and symbols are used. (iv) Solvent ratios are given as volume:volume (v / v). (v) X-ray powder diffraction analysis was carried out as described in the Examples. (vi) in the examples set forth below, the moles and yields given relate to 100% w / w raw materials and reagents and therefore take into account the purity of the materials used.

[0042] Example 1 Intermediate 1: 7-nitro-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-indole Step 1 A solution of NaOH (599 g, 14986.55 mmol) in water (1500 mL) was added to a stirred mixture of 7-nitro-1H-indole (243 g, 1498.65 mmol) and tetrabutylammonium hydrogen sulfate (50.9 g, 149.87 mmol) in DCM (3000 mL) over 5 min under air at 25° C. The resulting mixture was stirred for 20 min at 25° C. 4-Methylphenylsulfonyl chloride (371 g, 1948.25 mmol) was added under air and the resulting mixture was stirred for 16 h at 25° C. The reaction mixture was diluted with DCM (2000 mL) and washed successively with water (2×500 mL), 10% aqueous K2CO3 (2×500 mL), and 1 M HCl (2×500 mL) and saturated NaCl (2×500 mL). The organic layer was dried over Na2SO4, filtered and evaporated. When about 200 mL of DCM remained, EtOAc (500 mL) was added. The solvent was removed under reduced pressure. When about 200 mL of EtOAc remained, MTBE (1000 mL) was added. The precipitate was collected by filtration, washed with MTBE (1000 mL) and dried under vacuum to give 7-nitro-1-tosyl-1H-indole (402 g, 85%) as a white solid. 1 H NMR(300MHz,DMSO-d6)δ 2.39(s,3H),7.09(d,1H),7.40-7.55(m,3H),7.75-7.85(m,3H),7.95-8.00(m,1H),8.06(d,1H). m / z(ES+), [M+H] + =317.

[0043] Step 2 Bromine (81 mL, 1580 mmol) was added dropwise to 7-nitro-1-tosyl-1H-indole (50 g, 158 mmol) in CCl4 (1000 mL) at 80° C. The resulting solution was stirred at 80° C. for 6 h. The mixture was cooled to room temperature, concentrated in vacuo, and the residue was washed with EtOAc to give 3-bromo-7-nitro-1-tosyl-1H-indole (53 g, 85%) as a brown solid. 1H NMR(300MHz,DMSO-d6)δ 2.41(s,3H),7.55-7.62(m,2H),7.57(t,1H),7.85-7.92(m,3H),7.96(d,1H),8.49(s,1H). m / z(ES-), [MH] + =393.

[0044] Step 3 A solution of 3-bromo-7-nitro-1-tosyl-1H-indole (200 g, 506 mmol), 4,4,4',4',5,5,5',5'-octamethyl-2,2'-bi(1,3,2-dioxaborolane) (193 g, 759 mmol), potassium acetate (99 g, 1012 mmol) and PdCl2(dppf) (18.5 g, 25.3 mmol) in 1,4-dioxane (1500 mL) was degassed three times with nitrogen and the reaction mixture was stirred for 8 h at 90° C. The mixture was cooled to room temperature and concentrated in vacuo. The solid was treated with water, filtered, washed with methanol and dried in vacuum to give 7-nitro-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-indole (150 g, 67%) as a grey solid. 1 H NMR(400MHz,CDCl3)δ 1.41(s,12H),2.47(s,3H),7.38-7.43(m,3H),7.66(d,1H),7.87(d,2H),8.24(s,1H),8.29 -8.32(d,1H). m / z(ES+),[M+H] + =443.

[0045] Intermediate 2: 2-Fluoro-3-(methylsulfonyl)aniline Step 1 To 3-bromo-2-fluoroaniline (5 g, 26.31 mmol), N1,N2-dimethylethane-1,2-diamine (0.464 g, 5.26 mmol) and sodium iodide (7.89 g, 52.63 mmol) in 1,4-dioxane (10 mL) was added copper(I) iodide (1.002 g, 5.26 mmol) in one portion over 1 min under nitrogen at 25 °C. The resulting suspension was stirred at 110 °C for 1 day. The reaction mixture was filtered through Celite and concentrated in vacuo. The crude product was purified by flash silica chromatography using a gradient of 5-30% EtOAc in petroleum ether as the mobile phase. Pure fractions were evaporated in vacuo to give 2-fluoro-3-iodoaniline (5.00 g, 80%) as a brown oil. 1 H NMR(400MHz,DMSO-d6)δ 5.32(bs,2H),6.59-6.83(m,2H),6.83-6.93(m,1H). m / z(ES+), [M+H] + =238.

[0046] Step 2 To 2-fluoro-3-iodoaniline (5.00 g, 21.10 mmol), sodium methanesulfinate (3.23 g, 31.64 mmol), N1,N2-dimethylethane-1,2-diamine (0.558 g, 6.33 mmol) in DMSO (20 mL) under nitrogen was added copper(I) iodide (0.402 g, 2.11 mmol). The resulting suspension was stirred at 95° C. for 18 h. The reaction mixture was diluted with EtOAc (50 mL) and washed with water (50 mL) and brine (50 mL). The organic layer was dried over Na2SO4, filtered and evaporated in vacuo. The residue was purified by preparative TLC using EtOAc / petroleum ether 1:1 to give 2-fluoro-3-(methylsulfonyl)aniline (3.20 g, 80%) as a colorless oil that solidified upon standing. 1 H NMR(400MHz,CDCl3)δ 3.20(s,3H),3.96(bs,2H),6.97-7.13(m,2H),7.20-7.31(m,1H).m / z(ES+),[M+H] +=190.

[0047] Intermediate 18: 3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-amine Step 1 A solution of potassium carbonate (40.9 mL, 678.28 mmol) was placed in a 1 L reactor equipped with a thermometer and nitrogen inlet. The mixture was degassed with N2 three times at room temperature (23 °C). 7-Nitro-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-indole, intermediate 1 (100 g, 226.09 mmol), 2,4-dichloro-5-fluoropyrimidine (49.1 g, 293.92 mmol) and methyl THF (1000 mL) were added and stirred at room temperature for 10 minutes. The resulting mixture was degassed with nitrogen three times. Dichloro[1,1'-bis(diphenylphosphino)ferrocene]palladium dichloromethane adduct (9.23 g, 11.30 mmol) was added to the reaction mixture and the resulting mixture was degassed, backfilled again (3xN2) and stirred at 23°C overnight to give a yellow precipitate. Heptane (500 mL) was added to the reaction mixture at room temperature and stirred for 10 min. Stirring was then stopped and the precipitate was allowed to settle. The reaction mixture was cooled to 5°C and stirred for 1 h. The precipitate was filtered through a fritted funnel and washed with water until the water was pH neutral (13 vol, displacement wash, 1.3 L). The filter cake was then washed with room temperature EtOAc / heptane mixture 1:1 (5x2 volumes, 1 L), heptane (2x200 mL, 2x2 volumes) and the solid was dried under vacuum at 35°C overnight to give 3-(2-chloro-5-fluoropyrimidin-4-yl)-7-nitro-1-tosyl-1H-indole (97 g, effective yield 89%). 1 H NMR(400MHz,DMSO-d6)δ 2.41(s,3H),7.51(d,2H),7.69(t,1H),7.95(d,2H),8.01(dd,1H),8.75(d,1H),8.81(dd,1H),9.01(d,1H).m / z(ES+),[M+H] + =447.2.

[0048] Step 2 3-(2-chloro-5-fluoropyrimidin-4-yl)-7-nitro-1-tosyl-1H-indole (89.5 g, 200.30 mmol), 2-fluoro-3-(methylsulfonyl)aniline hydrochloride, intermediate 2 (54.2 g, 240.36 mmol), Pd2(dba)3 (9.17 g, 10.01 mmol) and 2'-(dicyclohexylphosphino)-N,N-dimethyl-[1,1'-biphenyl]-2-amine (7.88 g, 20.03 mmol) were added to a 2 L reactor under nitrogen. Degassed 2-methyltetrahydrofuran (1000 mL) and a solution of cesium carbonate (137 g, 420.62 mmol) in water (450 mL) were added at room temperature and the reaction mixture was degassed (x7). The reaction was then heated to 72.6° C. and stirred overnight. The reaction was cooled to 4-5° C. and stirred for at least 30 minutes. The solid was filtered through a Buchner funnel, washed with cold 2-methyltetrahydrofuran (300 mL, 3 volumes), water (3×300 mL, 3 volumes) and a 1:2 EtOAc / heptane mixture (3×300 mL, 3 volumes) and dried under vacuum at 40° C. to give 5-fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1-tosyl-1H-indol-3-yl)pyrimidin-2-amine (77.89 g, 65% effective yield) as a brown solid. 1 H NMR(400MHz,DMSO-d6)δ 2.56-2.64(m,3H),3.42(d,3H),7.52-7.64(m,4H),7.73(t,1H),7.98-8.0 9(m,3H),8.22(t,1H),8.71(s,1H),8.79(d,1H),8.94(d,1H),9.89(s,1H). m / z(ES+), [M+H] + =600.2.

[0049] Step 3 5-Fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1-tosyl-1H-indol-3-yl)pyrimidin-2-amine (97.7 g, 129.87 mmol) was placed in a 5 L reactor at room temperature. A mixture of THF (100 mL) and 3.8 M NaOH (aq) (1000 mL) was added to give a brown insoluble mixture. The mixture was heated to reflux at 75° C. and stirred over the weekend. THF (10 vol) and heptane (10 vol) were added to the reaction mixture. It was then allowed to cool to 17° C. over 40 min, stirred for 60 min, and the solids were filtered through a Buchner funnel. The filter cake was washed with 1M citic acid (500 mL, until pH neutral), water (5x300 mL, until pH neutral), and then heptane / EtOAc (4x400 mL). The solid was dried under vacuum to give 5-fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1H-indol-3-yl)pyrimidin-2-amine (55.0 g, 95%). 1 H NMR(400MHz,DMSO-d6)δ 3.27-3.38(m,3H),7.30(t,1H),7.47(t,1H),7.64(t,1H),8.11-8.29(m,3H),8.52(d,1H),8.98(d,1H),9.60(s,1H),12.57(s,1H). m / z(ES+), [M+H] + =446.2.

[0050] Step 4 To a stirred suspension of 5-fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1H-indol-3-yl)pyrimidin-2-amine (59.5 g, 123.5 mmol, 92.5% Wt) in THF / EtOH 2:1 (600 mL) was added 10% Pd / C (12.0 g, 123.5 mmol, 50% wet) and a solution of ammonium formate (46.8 g, 741.4 mmol) in water (50 mL) at room temperature and under nitrogen. The reaction mixture was slowly heated to 70° C. and stirred for 30 minutes. 12 g of activated charcoal was added and the mixture was stirred for 15 minutes. The reaction mixture was cooled to 40° C. and filtered through a Buchner funnel (paper) under nitrogen. The filter cake was washed with THF / EtOH (160 mL). The filtrate was concentrated to 4 volumes and the resulting slurry was cooled to room temperature and filtered under nitrogen. The solid was washed with water (2 volumes), ethanol (2 volumes) and dried under nitrogen / vacuum at 40° C. to give 3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-amine (44.3 g, 86%) as a light brown solid. 1 H NMR(400MHz,DMSO-d6)δ 3.28(s,3H),5.20(bs,2H),6.43(dd,1H),6.78(t,1H),7.44(t,1H),7.57-7.63(m,1H),7 .66(d,1H),8.09-8.25(m,2H),8.38(d,1H),9.34(s,1H),11.57(s,1H).m / z(ES+),[M+H] + =416.3.

[0051] Intermediate 28: Methyl 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate 1-Methylpiperazine (100 g, 988.4 mmol) and potassium carbonate (164 g, 1186 mmol) were slurried in dry acetonitrile (800 mL) under nitrogen. Methyl 2-bromo-3-methoxypropanoate (201 g, 988.4 mmol) was added to the slurry over 40 min at 50-60 °C. The resulting mixture was heated at 61 °C under nitrogen for 23 h and then cooled to 20 °C. The solid was filtered. The filtrate was evaporated to an oily residue, which was dissolved in 1 M HCl (1000 mL). The pH was then adjusted to 1 with 4 M HCl (ca. 300 mL). The resulting solution was extracted with DCM (200 mL). The aqueous solution was basified to pH 9 with saturated Na2CO3 (1000 mL) and extracted with DCM (2x500 mL). The pH of the aqueous phase was then raised to 10-11 with sodium hydroxide and extracted with DCM (2x500 mL). The four organic phases were combined and evaporated in vacuo to give methyl 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (181 g, 85%). 1 H NMR(400MHz,CDCl3)δ 2.07(s,3H),2.14-2.34(m,4H),2.39-2.52(m,4H),3.14(s,3H),3.22(dd,1H),3.42(dd,1H),3.48-3.56(m,4H).

[0052] Intermediate 48: Lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate To a solution of methyl 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate, intermediate 28 (1.93 g, 8.92 mmol) in THF (5 mL) was added a solution of lithium hydroxide (0.321 g, 13.39 mmol) in water (5 mL). A few drops of MeOH were added until the reaction mixture became clear. The reaction was heated at 40° C. for 24 h. The organics were evaporated in vacuo. The residue was diluted with water and lyophilized (x3) to give lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (1.92 g, 103%) as a solid. 1H NMR(500MHz,D2O)δ 2.06(s,3H),2.48(bs,8H),2.99(t,1H),3.20(s,3H),3.46-3.57(m,2H).

[0053] Synthesis of the free base compound of formula (Ia) Lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate, Intermediate 48 (430 mg, 2.06 mmol), 2-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)-1,1,3,3-tetramethylisouronium hexafluorophosphate (V) (785 mg, 2.06 mmol) and DIPEA (1.068 mL, 6.11 mmol) were dissolved in DMF (10 mL) and stirred at room temperature for 5 min before the addition of 3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-amine, Intermediate 18 (635 mg, 1.53 mmol).

[0054] The reaction was stirred at room temperature for 2 hours, then diluted with DCM (75 mL) and 5% Na2CO3 (aq) (50 mL), shaken and the phases separated. The aqueous phase was extracted with DCM (2x50 mL). The combined organic phase was dried over a phase separator, filtered and evaporated in vacuum. The compound was purified by preparative HPLC on an XBridge C18 column (10 μm, 250x50 mm) using a gradient of 15-65% acetonitrile in H2O / ACN / NH3 95 / 5 / 0.2 buffer over 20 minutes at a flow rate of 100 mL / min. The compound was detected by UV at 220 nm. The product peak was collected and lyophilized. It was then crystallized from acetonitrile and the solid was collected by filtration, washed with a minimal amount of acetonitrile and dried in vacuum.

[0055] The enantiomers were separated by chiral-SFC on a CelluCoat (250x30mm, 5μm) column using 25% IPA / DEA 100:0.5 in CO2 at 150 bar with a flow rate of 140mL / min. The enantiomers were detected by UV at 270nm. The first eluting enantiomer was collected and lyophilized to give N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide.

[0056] The second eluting enantiomer was collected and lyophilized. The residue was recrystallized by stirring the suspension in EtOH / water (3:1) (5 mL) heated to 70° C. with an oil bath and seeding. The oil bath temperature was then set to 23° C. and the suspension was allowed to slowly reach room temperature. Stirring was continued for 5 days to give a milky slurry containing short needles intermixed with longer needles. The suspension was heated to 70° C. with stirring, then heating and stirring were stopped and the mixture was allowed to slowly reach room temperature (2x). Only good long needles. The suspension was allowed to stand for another week without stirring. The solid was filtered and dried in vacuum at 40° C. to give (R)—N-(3-(5-fluoro-2-(2-fluoro-3-(methylsulfonyl)phenylamino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide (186 mg, 20%, 99.4% ee) as white needles. 1 H NMR(500MHz,DMSO-d6)δ 2.14(s,3H),2.23-2.45(m,4H),2.57-2.67(m,2H),2.69-2.78(m,2H),3.26-3.34(m,6H),3.50(t,1H),3.67(dd,1H),3.79(d d,1H),7.03(t,1H),7.4-7.55(m,2H),7.62(t,1H),8.13-8.33(m,3H),8.44(d,1H),9.46(s,1H),9.84(s,1H),11.48(s,1H). 19F NMR(470MHz,DMSO-d6)δ -120.52,-147.75.m / z(ES+),[M+H] + =600.5.

[0057] Synthesis of the xinafoate salt of formula (Ia) (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide (345 g, 563.82 mmol) was placed in a 10 L reactor with ethyl acetate (20 vol) (7 L) and methanol (4 vol) (1.4 L) ("SM solution"). The jacket temperature was set to 65° C. 1-Hydroxy-2-naphthoic acid (106 g, 563.82 mmol) was dissolved in methanol (1,5 vol) (0.7 L) and ethyl acetate (1,5 vol) (0.7 L) in a 2 L reactor and heated to 50° C. The xinafoic acid solution was polish filtered through Celite to remove insoluble material and rinsed with EtOAc / MeOH (2:1, 150 ml). The SM solution was polish filtered through Celite filter and SM was crystallized by cooling in the receiving vessel rather than in the filter. Filtration time was 30 min for approximately 9 L. The SM suspension was recharged to the reactor and heated to 65° C. to redissolve. The xinafoic acid solution was added to the 20 L reactor and the jacket temperature was set to 70° C. The solution (SM solution + xinafoic acid solution) was seeded with crystalline material of (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide and crystallization started immediately. A stream of nitrogen air was passed through the headspace to the condenser to distill off the MeOH. Ethyl acetate (2 L) was added over 5 min to compensate for losses to the azeotrope and approximately 3 L was distilled off. The distillation was allowed to reach completion (5 L collected). A cooling gradient was started from 75°C to 10°C over 600 min, then held at 10°C. The solid was filtered using a P3 sintered glass funnel. Filtration was very fast. The solid was washed through the reactor with ethyl acetate (2 L) and left in the funnel to dry under a stream of nitrogen air. The solid was transferred to a drying vat and dried in a vacuum oven at 40°C. Mass start: 426g (4-{(2R)-1-[(3-{5-fluoro-2-[2-fluoro-3-(methanesulfonyl)anilino]pyrimidin-4-yl}-1H-indol-7-yl)amino]-3-methoxy-1-oxopropan-2-yl}-1-methylpiperazin-1-ium; 1-hydroxynaphthalene-2-carboxylate (420 g, 95%) was obtained as an off-white crystalline solid. 1H NMR(400MHz,DMSO)δ 0.97(s,0H),1.78(s,0H),2.29(s,3H),2.58-3.03(m,8H),3.09(s,7H),3.37-3.72(m,3H),3.83(s,0H),6.69-6.97(m,2H) ),7.11-7.36(m,4H),7.42(s,1H),7.54(t,2H),7.86-8.16(m,4H),8.24(s,1H),9.26(s,1H),9.86(s,1H),11.52(s,1H).

[0058] For XRPD, powder X-ray diffraction was recorded using a Theta-Theta Bruker D8 Advance (X-ray wavelength 1.5418 Å, nickel filtered Cu radiation, voltage 40 kV, filament emission 40 mA) with samples mounted on a silicon single crystal (SSC) wafer mount. A 2.5° Soller slit and a 3 mm anti-scatter slit were used and the sample was rotated during the measurement. A step width of 0.02° and a step width of 0.04° s -1 The sample was scanned from 2 to 50° 2-theta using a LynxEye 3° PSD detector (10.5 mm detector slit) with a measurement time of time / step.

[0059] [Table 1]

[0060] Example 2 From the crystal structure of the free base compound of formula (Ia) (performed using single crystal X-ray diffraction, SXRD), it was determined that the form is a non-stoichiometric hydrate. This was further supported by gravimetric vapor sorption analysis (GVS), as water uptake of 2% w / w was observed between 0 and 80% relative humidity, and the compound exhibited a weight loss of 5% w / w between room temperature (RT) and 120°C.

[0061] Therefore, a salt screen was performed and from the 20 counterions tested, three salts (phosphate, sulfate and xinafoate) were scaled up (5 g) and further analyzed. The phosphate and sulfate salts showed less crystallinity compared to the xinafoate salt, with weight losses of 3.2% w / w at RT-120° C. (sulfate) and 5.4% w / w at RT-120° C. (phosphate). As these two salts showed such unfavorable solid state properties compared to xinafoic acid, which were similar or worse than the free base, gravimetric sorption analysis was not performed on them.

[0062] The crystal structure (from SXRD) of the xinafoate salt showed that the salt is a 1:1 salt, which is the anhydrous form rather than a non-stoichiometric hydrate of the free base compound of formula (Ia). The simulated powder pattern from SXRD was overlaid with the experimental powder X-ray diffraction data (PXRD) and showed that the single crystal structure is the same as the bulk.

[0063] Independently, polymorph screening showed that the non-stoichiometric hydrate of the free base compound of formula (Ia) was the most stable form identified under ambient conditions and the chance of obtaining the anhydrous free form should be considered very low. Screening involving over 110 solvent and non-solvent based screening experiments was carried out at Almac. The xinafoate salt was found to be the non-hygroscopic form of the compound of formula (1a), exhibiting an absorption of 0.2% w / w between 0-80% relative humidity and a weight loss of 0.2% w / w when the compound was heated between RT and 120°C, whereas the free base compound of formula (Ia) was found to be slightly hygroscopic, exhibiting an absorption of 1.7% w / w between 0-80% relative humidity and a weight loss of 5% w / w from room temperature (RT) to 120°C.

[0064] [Table 2]

[0065] Example 3 An alternative synthesis of the xinafoate salt of formula (Ia) is further described below: [ka] Step 1: 2-Fluoro-3-(methylsulfonyl)aniline (2) To the inerted reactor were added 2-fluoro-3-bromoaniline (1) (930 g, 1 eq, 4.9 mol) and sodium methanesulfinate (3 eq, 1.5 kg), followed by DMSO (5 L). The reactor contents were inerted 5 times and stirred at 20-30 °C for 30 min. Copper(I) iodide (0.2 eq, 187 g) and 1,2-dimethylethylenediamine (0.4 eq, 173 g) were added to the reactor and then inerted 3 times. The reaction mixture was stirred at 110-120 °C for 17 h after which it was deemed ready for work-up. The mixture was cooled to 20-30 °C and water (10 L) was added followed by ethyl acetate (10 L). The mixture was stirred for 30 min, the organic layer was separated and the aqueous phase was extracted twice with ethyl acetate (2 x 10 L). The combined organic phase was evaporated to dryness and dissolved in 2 L of ethyl acetate. The crude product solution was filtered through a short silica column and the column was washed with 10 L of a 1:1 mixture of ethyl acetate / petroleum ether. The eluate was then concentrated to 2 L. To this solution was slowly added heptane (1 L) over 2 h at 20-30 °C. The precipitated product was filtered and dried under reduced pressure at 40-50 °C to give 0.6 kg, 65% of the desired product. [ka]

[0066] Step 2: 7-Nitro-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-indole (4) To the inerted reactor were added 3-bromo-7-nitro-1-(p-tolylsulfonyl)indole (3) (1.2 kg, 3 mol) and bis(pinacolato)diborane (1.14 kg, 4.5 mol, 1.5 equiv.), followed by potassium acetate (590 g, 6 mol, 2 equiv.). The reactor contents were then inerted and 8.4 L of 1,4-dioxane was added. The reactor was inerted three times, followed by the addition of Pd(PPh3)4 (0.01 equiv., 35 g). The reaction mixture was heated to 95-100 °C and stirred for 18 h. An HPLC sample was taken and the mixture was cooled to 20-30 °C. 2-Methyl-THF (8.4 L) and 8.4 L of water were added to the reaction mixture, which was then stirred for 30 min. The organic layer was separated and washed three times with 10% sodium chloride (aqueous) (8.4 L). The organic solution was evaporated to dryness and co-evaporated with acetonitrile (6 L). Finally, 6 L of acetonitrile was added and the mixture was stirred at 20-30 °C for 2 h, then cooled to 0-5 °C, stirred for 2 h, and filtered. The filtered product was dried under reduced pressure at 40-50 °C to give 1 kg (75%) of the desired product (4).

[0067] Step 3: 3-(2-chloro-5-fluoropyrimidin-4-yl)-7-nitro-1-tosyl-1H-indole (6) To the inerted reactor were added 7-nitro-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-indole (4) (1 kg, 2.26 mol) and 2,4-dichloro-5-fluoropyrimidine (5) (442 g, 1.2 eq.), followed by 4 L of 2-MeTHF. A solution of potassium carbonate (937 g) (3 eq.) in 2 L of water was charged to the reactor, which was then inerted 5 times. The catalyst Pd(dppf)Cl2-DCM (92 g, 0.05 eq.) (113 mmol) was added to the reactor, which was then inerted 3 times, and the mixture was stirred at 20-30 °C for 17 h. A sample was taken for LCMS, and 4 L of n-heptane was added to the reactor over 2 h at 20-30 °C. After stirring the precipitate for an additional 30 min, the product was filtered and washed with water (7 L) until the filtrate was neutral (pH 7-8). The wet filter cake was slurried in ethyl acetate (3 L) (3 volumes) and filtered. Finally, the filter cake was washed with 1 L of ethyl acetate and dried under reduced pressure at 40-50 °C to give 0.9 kg (89%) of the desired product (6). [ka]

[0068] Step 4: 5-Fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1-tosyl-1H-indol-3-yl)pyrimidin-2-amine (7) To the inerted reactor, Pd2(dba)3 (124 g) (0.05 eq.) and DavePhos (106 g) (0.1 eq.) were added, followed by 2-methyltetrahydrofuran (3 L). The reactor was inerted three times and stirred at 20-30 °C for 30 min. 3-(2-chloro-5-fluoropyrimidin-4-yl)-7-nitro-1-tosyl-1H-indole (6) (1 eq., 1.2 kg, 2.7 mol) and 2-fluoro-3-(methylsulfonyl)aniline hydrochloride (2) (1 eq., 610 g, 2.7 mol) were added to the reactor, followed by 2-methyltetrahydrofuran (3 L). Cesium carbonate (1.1 eq., 970 g) in water (2.4 L) was then added to the reactor, which was then inerted again three times. Once deemed complete, the reaction mixture was stirred at 75-80°C for 18 hours. The reaction mixture was cooled to 20-30°C and the precipitated product was filtered. The filter cake was washed with 2-methyltetrahydrofuran (5 L), then with water (5 L) and finally with acetone (5 L). The product was dried under reduced pressure at 40-50°C to give 1.3 kg of the desired product (7) (80%). 1 H NMR(400MHz,DMSO)δ 2.40(s,3H),3.32(s,3H),7.43-7.54(m,4H),7.65(t,1H),7.93(dd,3H) ,8.13(t,1H),8.57-8.66(m,1H),8.69(d,1H),8.84(d,1H),9.79(s,1H).

[0069] Step 5: 5-Fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1-tosyl-1H-indol-3-yl)pyrimidin-2-amine (8) To the inerted reactor was added 5-fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1-tosyl-1H-indol-3-yl)pyrimidin-2-amine (7) (1.10 kg, 1 equiv., 1.84 mol), followed by THF (5.5 L). 4 M aqueous NaOH (2.2 L) was added to the reactor and the resulting mixture was stirred at 65-70 °C for 45 h, after which complete hydrolysis was achieved. MTBE (6.6 L) was added over 3 h with stirring at 15-25 °C, resulting in a fine precipitate. The mixture was filtered and the filter cake was washed with water until neutral. Finally the cake was washed with methanol (2.2 L). The desired product was dried under reduced pressure at 40-50 °C to give 0.70 kg (84%) of the desired product (8). 1 H NMR(400MHz,DMSO)δ 3.33(s,3H),7.30(t,1H),7.47(t,1H),7.64(ddd,1H),8.06-8.26(m,3H),8.51(d,1H),8.97(d,1H),9.60(s,1H),12.56(s,1H).

[0070] Step 6: 3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-amine (9) A 25 L inerted reactor preheated to 55° C. was charged with 5-fluoro-N-(2-fluoro-3-(methylsulfonyl)phenyl)-4-(7-nitro-1H-indol-3-yl)pyrimidin-2-amine (8) (578 g, 1.26 mol), followed by THF (8.5 L). To this suspension was added ammonium formiate (475 g, 7.53 mol) in 2.3 L of water, followed by Pd / C (170 g, 80 mmol Pd) and finally 4.3 L of ethanol in 5 min. The final mixture was heated from room temperature to 43° C. The reaction was started by the addition of ethanol with gas evolution evident. The conversion was complete within 1 h as monitored by UPLC-MS. The reaction mixture was hot filtered to remove the Pd / C. The reactor was rinsed with 3 L of hot THF / ethanol 2:1 (55° C.), which was also collected through the filter. The filtrate was evaporated to a semi-solid mixture, which was triturated with 2.5 L of ethanol overnight under nitrogen. The product was filtered and dried in vacuum at 40° C. Yield: 508 g, assay 100%. mp: 236C (onset DSC), HRMS (ESI + ):[M+H] + m / z C 19 H 15 Calculated value of F2N5O2S: 416.0987; measured value: 416.0996. 1 H NMR(400MHz,DMSO)δ 3.29(s,3H),5.20(s,2H),6.44(d,1H),6.79(t,1H),7.45(t,1H),7.56- 7.75(m,2H),8.08-8.25(m,2H),8.39(d,1H),9.35(s,1H),11.58(s,1H). 19 F NMR(376MHz,DMSO)δ -147.61,-120.58. [ka]

[0071] Step 7: Methyl 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (10) To a glass reactor under nitrogen was added potassium carbonate (396 g, 1.3 equiv.), followed by 1.8 L of dry acetonitrile, Sigma-Aldrich 34851N (0.004% water) and 1-methylpiperazine (99%, 234 g, 2.3 mol, 1.05 equiv.). The jacket was set to 60° C. To the resulting slurry was added methyl 2-bromo-3-methoxypropanoate (448 g, 97%, 2.2 mol, 300 ml) in 200 ml of dry acetonitrile at 60° C. over 1 h, keeping the reaction temperature below reflux. After 19 h, 99% conversion was evidenced by NMR. After 24 h the reaction was worked up. The reactor contents were filtered through a Celite dish filter. The filter cake was washed with 500 ml of acetonitrile and the combined organics were evaporated to an oil. The crude product oil was dissolved in 1 L of isopropyl acetate and extracted with 200 ml of water to remove salts. The product is very soluble in water and a backwash with isopropyl acetate is required to recover the material (this water wash can be omitted as it results in a lot of extra work and results in only slightly improved product purity). The combined isopropyl acetate extracts were evaporated under reduced pressure at 60° C. This gave the title compound (10) as a yellow oil (471 g, 99% w / w, 98% yield). 1 H NMR(400MHz,CDCl3)δ 2.16(s,3H),2.33(m,4H),2.55(m,4H),3.23(s,3H),3.31(dd,1H),3.51(dd,1H),3.60(dd,1H),3.61(s,3H). 13 C NMR(101MHz,CDCl3)δ 45.97,50.01,51.32,55.20,59.09,67.03,70.71,170.85 .HRMS(ESI + ):[M+H] + m / z C 10 H 21 Calculated N2O3 217.1552; measured 217.1547.

[0072] Step 8: Lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (11) To a solution of 87 g LiOHxHO (98%) (1.07 equiv.) in 1 L of pure water in a 5 L reactor under nitrogen was added a solution of methyl 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (441 g, 2000 mmol) in 1 L of THF and 300 ml of methanol. The reaction mixture was heated at 40° C. for 72 h, after which complete conversion was evidenced by NMR. The reaction mixture was evaporated to an oil, which solidified as a foam after drying in vacuum at 40° C. to give the title compound (11) (435 g, 97% w / w, 93% yield). 1 H NMR(400MHz,CDCl3)δ 2.24(s,3H),2.45(m,4H),2.64(m,4H),3.02(dd,1H),3.63(dd,1H),3.72(dd,1H). 13 C NMR(101MHz,DMSO)δ 45.9,49.76,55.01,57.91,70.18,72.18..HRMS(ESI + ):[M acid +H] + m / z C9H 19 Calculated N2O3 203.1396; measured 203.1388.

[0073] Step 9: Chromatography The eleven enantiomers (180 g, 865 mmol) were separated by chiral supercritical fluid chromatography using Lux Cellulose-4 (5 μm, 250×50 mm) with a mobile phase of 25% MeOH / NH3 100 / 0.5 in CO2 at 120 bar, 30° C., and detection at 215 nm. The second eluting compound was collected and evaporated to give the title compound (R)-3-methoxy-2-(4-methylpiperazin-1-yl)propanoic acid (80 g, 99.6% ee).

[0074] Step 9a: Salt division (R)-3-Methoxy-2-(4-methylpiperazin-1-yl)propanoic acid L-(+)-tartrate In a stirred reactor under nitrogen, lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate (208 g, 1 mol) was dissolved in 625 ml of distilled water and the pH was adjusted to 4 with 3.8 M HCl (340 ml). The temperature was increased from ambient to 33°C. L-(+)-tartaric acid (145 g, 0.97 mol) was dissolved in 170 ml of distilled water and added to the previous solution followed by 300 ml of ethanol (99.5% w / w). Crystallization could be induced by adding seeds, but stirring overnight at room temperature (20-21°C) also induced crystallization. Prior to filtration, 200 ml of ethanol (99.5% w / w) was slowly added, the reaction mixture was cooled to 10°C and stirring was continued for 1 hour. The product was filtered and washed with 300 ml of cold ethanol (99.5% w / w). The collected product crystals were dried in vacuum at 40° C. for 72 hours. Yield 144 g, Mw=388.37 (2 waters of crystallization by x-ray crystallography), 0.37 mol, 74%. mp 139° C. (peak, DSC). 1 H NMR(400MHz,D2O)δ 2.98(s,3H),δ 2.84(s,3H),δ 3.45-3.71(m,8H),δ 3.84(t,1H),δ 3.92(dd,2H),δ 4.53(s,4H),δ 4.79(s,4H)+additional water from solvent. Crystal data. C 13 H 28 N2O 11 , M r =388.37, orthorhombic, P212121(No.19), a=7.1515(4)Å, b=13.9607(7)Å, c=17.6138(11)Å, α=β=γ=90 ° , V=1758.56(17)Å 3 , T = 100(2)K, Z = 4, Z' = 1, μ(CuKα) = 1.109, 10608 measured reflections, 3096 unique (R int = 0.0898), which were used in all calculations. The final wR2 was 0.2209 (all data) and R1 was 0.0670 (I > 2(I)).

[0075] Step 9b: (R)-3-Methoxy-2-(4-methylpiperazin-1-yl)propanoic acid bishydrochloride (12) 40 g of the L-(+)-tartrate salt of (R)-3-methoxy-2-(4-methylpiperazin-1-yl)propanoic acid was dissolved in 200 ml of warm distilled water and loaded onto 300 ml of Dowex 50WX2-100 cationic ion exchange resin (approximately 200 g in its H form) in a column (washed with distilled water until neutral). The column was eluted with distilled water (approximately 700 ml, 2-3 column volumes) until completely neutral after loading. The amino acid was then eluted with 2 M HCl (900 ml) (3 column volumes) to give 28 g, 90% (dry weight) of the amino acid HCl salt as an oil, which crystallized immediately. There was no detector coupled to the ion exchange, so some material may still be present on the column. NMR. Assay 93%, water content 2.24% (KF). 21 g of product was dissolved in 5 volumes of refluxing absolute ethanol (3 volumes are sufficient if the material is non-crystalline) (100 ml) and left to cool to ambient temperature. Once crystallization was complete, 3 volumes of MTBE (60 ml) were slowly added to reduce the solubility of the salt. The product was filtered and dried under vacuum at 40° C. for 17 hours. Melting point 141.6 (DSC, onset, 3 C / min). Water content 6.12% (6.18% 1 water of crystallization molecule) NMR assay 97.5%. Yield 70%, 14 g. The salt has solubility in ethanol, which makes it not a perfect solvent for the recryst, but water is added to the salt. The mother liquor contains a missing 30%, which can be recovered. 1 H NMR(400MHz,D2O)δ 2.99(s,3H),δ 3.33(s,3H),δ 3.53(t,2H),δ 3.66(m,2H),δ 3.85(t,2H),δ 3.96(m,1),δ 3.98(d,2H),δ 4.32(t,1H),δ 4.79(s,2H)+additional water from solvent. [ka]

[0076] Step 10: (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide (13) A 10 L inerted cryo reactor was charged at room temperature with (R)-3-methoxy-2-(4-methylpiperazin-1-yl)propanoic acid, 2HCl (12) (430 g, 1187.6 mmol) followed by 3 L of DMF (6 volumes). To the light brown solution was added 3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-amine (9) (449 g, 1079.6 mmol). The resulting dark brown clear solution was cooled to -20°C (jacket set at -30°C). Pyridine (1.3 L) was added to the reactor in 5 min. No significant exotherm was observed. At -20°C, propanephosphonic anhydride (T3P) (1.9 L, 3239 mmol) in DMF was added very slowly without exceeding -13°C. The jacket was set to -40°C due to the exothermic reaction. The addition was completed after 75 min. After 2 / 3 of the addition, a sample was taken and SFC-MS was run, showing almost complete conversion. Complete conversion after complete addition. Final analysis UPLC-MS. The reaction mixture was quenched by slow addition of water at -15°C for 1 h. The quenched mixture was stirred at -15°C for an additional 30 min. In a larger reactor, 8.5% NaHCO3 (14 L) was prepared in advance and cooled to +5°C to minimize foaming. The cooled quenched reaction mixture was slowly transferred to the reactor containing 8.5% NaHCO3 (14 L) by applying a short tube under pressure. After 1 hour of addition, an additional 18 L of saturated bicarbonate solution was added, which caused the product to begin to precipitate from a clear solution. The precipitated product mixture was stirred at +5° C. for 30 minutes. The clayey crude product was filtered. The filtered product was incomplete and the procedure took a significant amount of time to carry out. The product was dried under vacuum at 40° C. for 72 hours. Yield 665 g, assay of 87% (81%).

[0077] 665 g of the dried crude material (assay 87%) was placed in an inerted reactor and 13 L of acetonitrile was added. The mixture was stirred at reflux starting at ambient temperature. Acetonitrile (2 L) was added to improve the solubility of the product. The non-clear solution was clarified, which initiated some crystallization. Filtration was difficult and the insoluble material clogged the filter. When clogging occurred, the product solution in the filter had to be transferred back to the reactor. In total, the volume doubled during the filtration, which took a long time. The clarified organics were transferred to another reactor and the volume reduced to 13 L. Crystallization was initiated from reflux (clear solution) by slow cooling to 5° C. over 24 hours. The product was filtered and washed with 2 volumes of cold acetonitrile. The product was dried overnight under vacuum at 40° C. Yield: 364 g, 63%, purity 98% (NMR) HRMS(ESI + ):[M+H] + m / z C 28 H 31 Calculated value of F2N7O4S: 600.2204; measured value: 600.2199. 1 H NMR(400MHz,DMSO)δ 2.14(s,3H),2.35(s,4H),2.55-2.68(m,2H),2.68-2.85(m,2H),3.29(s,3H),3.30(s,3H),3.51(t,1H),3.67(dd,1H),3.79(d d,1H),7.04(t,1H),7.39-7.57(m,2H),7.62(td,1H),8.11-8.33(m,3H),8.44(d,1H),9.46(s,1H),9.88(s,1H),11.53(s,1H).

[0078] Step 11: (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamidoxinafoate (14) (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamide (13) (345 g, 563.82 mmol) was placed in an inerted 10 L reactor. Ethyl acetate (7 L, 20 vol) and methanol (1.4 L, 4 vol) were added. The mixture was heated to 65° C. until everything was dissolved. The solution was hot polish filtered through a Celite filter. Crystallization occurred in the filtrate. The filtrate, which was a slurry, was returned to the reactor and heated to 60° C. until completely redissolved. 1-Hydroxy-2-naphthoic acid (106 g, 563.82 mmol) was placed in an inerted 2 L reactor. Methanol (0.7 L, 1.5 vol) and ethyl acetate (0.7 L, 1.5 vol) were added and the mixture was heated to 50° C. until everything was dissolved. The solution was polish filtered and the filter was rinsed with EtOAc / MeOH (2:1, 150 ml). The resulting solution was added to a 10 L reactor at 60° C. to give a clear solution that was stirred for 10 min. The solution was seeded with crystalline material (7 g) from a previous batch. Crystallization started immediately. With a nitrogen flow through the headspace, the solvent was distilled at ambient pressure and a jacket temperature of 75° C. until the reflux temperature exceeded 70° C. 5 L of distillate was collected and EtOAc (2 L) was added to the reactor to compensate for volume loss. The reactor was slowly cooled to 10° C. over 10 h and the temperature was maintained for 4 h. The solid was filtered and washed with a reactor containing ethyl acetate (2 L). The solid was dried under vacuum at 40° C. (R)-N-(3-(5-fluoro-2-((2-fluoro-3-(methylsulfonyl)phenyl)amino)pyrimidin-4-yl)-1H-indol-7-yl)-3-methoxy-2-(4-methylpiperazin-1-yl)propanamidoxinafoate (14) (420 g, 95% yield) was obtained as an off-white crystalline solid. Purity (NMR) 97.7% 1H NMR (400 MHz, DMSO) δ 2.29 (s, 3H), 2.58 - 3.03 (m, 8H), 3.09 (s, 7H), 3.37 - 3.72 (m, 3H), 6.69 - 6.97 (m, 2H), 7.11 - 7.36 (m, 4H), 7.42 (s, 1H), 7.54 (t, 2H), 7.86 - 8.16 (m, 4H), 8.24 (s, 1H), 9.26 (s, 1H), 9.86 (s, 1H), 11.52 (s, 1H). 19F NMR (376 MHz, DMSO) δ -147.71, -120.45. Melting point: 189 °C (DSC, peak) HRMS (ESI + ): [M + H] + m / z C 28 H 31 F2N7O4S calculated value 600.2204; measured value 600.2199 (parent) Furthermore, the present invention includes the following aspects. 1. Formula (I):

Chemical Structure

change

change

Claims

1. Compound 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2): 【Chemistry 1】

2. Compound 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride: 【Chemistry 2】

3. A process for the preparation of 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2) and 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride comprising the steps of: (i) dissolving lithium 3-methoxy-2-(4-methylpiperazin-1-yl)propanoate in distilled water at pH 4; (ii) dissolving L-(+)-tartaric acid in distilled water; (iii) mixing the two solutions from step (i) and step (ii) in ethanol to induce crystallization; (iv) stirring the mixture of step (iii) at room temperature for 20 hours; (v) adding ethanol to the mixture of step (iv) and filtering after cooling to give the product 4-[(1R)-1-carboxy-2-methoxyethyl]-1-methylpiperazin-1-ium(2R,3R)-3-carboxy-2,3-dihydroxypropanoate hydrate (1:1:2); (vi) collecting the product of step (v) and drying under reduced pressure for 72 hours; (vii) dissolving the product of step (vi) in distilled water; (viii) performing cationic ion exchange on the product of step (vii); (ix) eluting the product of step (viii) with 2M HCl and evaporating the solution to dryness to induce crystallization of 1-[(1R)-1-carboxy-2-methoxyethyl]-4-methylpiperazine-1,4-diium dichloride; The method includes:

Images