INHD3ITOR

This application claims the benefit of priority of U.S. Provisional Application 61 /531 ,896, filed September 7, 201 1 , which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

This invention relates to processes and intermediates for making { l-{ l-[3- fluoro-2-(trifluoromethyl)isonicotinoyl]piperidin-4-yl}-3-[4 -(7H-pyrrolo[2,3- d]pyrimidin-4-yl)-l H-pyrazol-l -yl]azetidin-3-yl}acetonitrile, useful in the treatment of diseases related to the activity of Janus kinases (JAK) including inflammatory disorders, autoimmune disorders, cancer, and other diseases.

BACKGROUND

Protein kinases (PKs) regulate diverse biological processes including cell growth, survival, differentiation, organ formation, morphogenesis, neovascularization, tissue repair, and regeneration, among others. Protein kinases also play specialized roles in a host of human diseases including cancer. Cytokines, low-molecular weight polypeptides or glycoproteins, regulate many pathways involved in the host inflammatory response to sepsis. Cytokines influence cell differentiation, proliferation and activation, and can modulate both pro-inflammatory and anti- inflammatory responses to allow the host to react appropriately to pathogens.

Signaling of a wide range of cytokines involves the Janus kinase family (JAKs) of protein tyrosine kinases and Signal Transducers and Activators of Transcription (STATs). There are four known mammalian JAKs: JAK1 (Janus kinase- 1), JAK2, JAK3 (also known as Janus kinase, leukocyte; JAKL; and L-JAK), and TYK2 (protein-tyrosine kinase 2).

Cytokine-stimulated immune and inflammatory responses contribute to pathogenesis of diseases: pathologies such as severe combined immunodeficiency (SCID) arise from suppression of the immune system, while a hyperactive or inappropriate immune/inflammatory response contributes to the pathology of autoimmune diseases (e.g., asthma, systemic lupus erythematosus, thyroiditis, myocarditis), and illnesses such as scleroderma and osteoarthritis (Ortmann, R. A., T. Cheng, et al. (2000) Arthritis Res 2(1 ): 16-32).

Deficiencies in expression of JAKs are associated with many disease states. For example, Jakl -/- mice are runted at birth, fail to nurse, and die perinatally (Rodig, S. J., M. A. Meraz, et al. (1998) Cell 93(3): 373-83). Jak2-/- mouse embryos are anemic and die around day 12.5 postcoitum due to the absence of definitive erythropoiesis.

The JAK/STAT pathway, and in particular all four JAKs, are believed to play a role in the pathogenesis of asthmatic response, chronic obstructive pulmonary disease, bronchitis, and other related inflammatory diseases of the lower respiratory tract. Multiple cytokines that signal through JAKs have been linked to inflammatory diseases/conditions of the upper respiratory tract, such as those affecting the nose and sinuses (e.g., rhinitis and sinusitis) whether classically allergic reactions or not. The JAK/STAT pathway has also been implicated in inflammatory diseases/conditions of the eye and chronic allergic responses.

Activation of JAK/STAT in cancers may occur by cytokine stimulation (e.g. IL-6 or GM-CSF) or by a reduction in the endogenous suppressors of JAK signaling such as SOCS (suppressor or cytokine signaling) or PIAS (protein inhibitor of activated STAT) (Boudny, V., and Kovarik, J., Neoplasm. 49:349-355, 2002).

Activation of STAT signaling, as well as other pathways downstream of JAKs (e.g., Akt), has been correlated with poor prognosis in many cancer types (Bowman, T., et al. Oncogene 19:2474-2488, 2000). Elevated levels of circulating cytokines that signal through JAK/STAT play a causal role in cachexia and/or chronic fatigue. As such, JAK inhibition may be beneficial to cancer patients for reasons that extend beyond potential anti-tumor activity.

JAK2 tyrosine kinase can be beneficial for patients with myeloproliferative disorders, e.g., polycythemia vera (PV), essential thrombocythemia (ET), myeloid metaplasia with myelofibrosis (MMM) (Levin, et al., Cancer Cell, vol. 7, 2005: 387- 397). Inhibition of the JAK2V617F kinase decreases proliferation of hematopoietic cells, suggesting JAK2 as a potential target for pharmacologic inhibition in patients with PV, ET, and MMM. Inhibition of the JAKs may benefit patients suffering from skin immune disorders such as psoriasis, and skin sensitization. The maintenance of psoriasis is believed to depend on a number of inflammatory cytokines in addition to various chemokines and growth factors (JCI, 1 13: 1664-1675), many of which signal through JAKs (Adv Pharmacol. 2000;47: 1 13-74).

JAKl plays a central role in a number of cytokine and growth factor signaling pathways that, when dysregulated, can result in or contribute to disease states. For example, IL-6 levels are elevated in rheumatoid arthritis, a disease in which it has been suggested to have detrimental effects (Fonesca, J.E. et al., Autoimmunity Reviews, 8:538-42, 2009). Because IL-6 signals, at least in part, through JAKl , antagonizing IL-6 directly or indirectly through JAKl inhibition is expected to provide clinical benefit (Guschin, D., N., et al Embo J 14: 1421, 1995; Smolen, J. S., et al. Lancet 371 :987, 2008). Moreover, in some cancers JAKl is mutated resulting in constitutive undesirable tumor cell growth and survival (Mullighan CG, Proc Natl Acad Sci U S A.106:9414-8, 2009; Flex E., et al.J Exp Med. 205:751-8, 2008). In other autoimmune diseases and cancers elevated systemic levels of inflammatory cytokines that activate JAK 1 may also contribute to the disease and/or associated symptoms. Therefore, patients with such diseases may benefit from JAKl inhibition. Selective inhibitors of JAKl may be efficacious while avoiding unnecessary and potentially undesirable effects of inhibiting other JAK kinases.

Selective inhibitors of JAKl , relative to other JAK kinases, may have multiple therapeutic advantages over less selective inhibitors. With respect to selectivity against JAK2, a number of important cytokines and growth factors signal through JAK2 including, for example, erythropoietin (Epo) and thrombopoietin (Tpo) (Parganas E, et al. Cell. 93:385-95, 1998). Epo is a key growth factor for red blood cells production; hence a paucity of Epo-dependent signaling can result in reduced numbers of red blood cells and anemia (Kaushansky K, NEJM 354:2034-45, 2006). Tpo, another example of a JAK2-dependent growth factor, plays a central role in controlling the proliferation and maturation of megakaryocytes - the cells from which platelets are produced (Kaushansky K, NEJM 354:2034-45, 2006). As such, reduced Tpo signaling would decrease megakaryocyte numbers (megakaryocytopenia) and lower circulating platelet counts (thrombocytopenia). This can result in undesirable and/or uncontrollable bleeding. Reduced inhibition of other JAKs, such as JAK3 and Tyk2, may also be desirable as humans lacking functional version of these kinases have been shown to suffer from numerous maladies such as severe-combined immunodeficiency or hyperimmunoglobulin E syndrome (Minegishi, Y, et al.

Immunity 25:745-55, 2006; Macchi P, et al. Nature. 377:65-8, 1995). Therefore a JAK 1 inhibitor with reduced affinity for other JAKs would have significant advantages over a less-selective inhibitor with respect to reduced side effects involving immune suppression, anemia and thrombocytopenia.

Due to the usefulness of JAK inhibitors, there is a need for development of new processes for making JAK inhibitors. This invention is directed towards this need and others.

SUMMARY

JAK inhibitors are described in U.S. Serial No. 13/043,986, filed March 9, 201 1 , which is incorporated herein by reference in its entirety, including { l -{ l -[3- fluoro-2-(trifluoromethyl)isonicotinoyl]piperidin-4-yl}-3-[4 -(7H-pyrrolo[2,3- d]pyrimidin-4-yl)-l H-pyrazol- l -yl]azetidin-3-yl }acetonitrile, which is depicted below as Formula I.

1

The present invention provides, inter alia, processes and intermediates for making the compound of Formula I. In particular, the present invention provides processes of making a compound of Formula II:

or a salt thereof, comprising reacting a compound of Formula III:

a salt thereof, with a compound

or a salt thereof, in the presence of a reducing agent to form the compound of Formula II or said salt thereof, provided said reducing agent is not sodium cyanoborodeutende; wherein P ¹ is a protecting group.

The present invention also provides processes of making a compound of Formula IV:

IV

or a salt thereof, comprising depro compound of Formula V:

V

or a salt thereof, to form a compound of Formula IV, or said salt thereof.

The present invention proc compound of Formula V:

or a salt thereof, comprising reacti of Formula VI:

VI

or a salt thereof, with a compound of Formula VII:

VII in the presence of a coupling agent to form the compound of Formula V, or said salt thereof.

The present invention furth pound of Formula V:

or a salt thereof.

DETAILED DESCRIPTION

The present invention provides a process of making a compound of Formula

II

or a salt thereof, comprising reacting a compound of Formula III:

III

or a salt thereof, with a compound

or a salt thereof, in the presence of a reducing agent to form the compound of Formula II, or said salt thereof, provided said reducing agent is not sodium

cyanoborodeuteride; wherein P ¹ is a protecting group.

In some embodiments, the compounds of Formula III and IV are preferably used as free bases and the compound of Formula II is produced preferably as a free base. As used herein, "free base" means the non-salt form of the compound.

In some embodiments, the reaction of compound III and compound IV is carried out in the presence of a tertiary amine (e.g., triethylamine). In some embodiments, the temperature of the reaction is < 30 °C. In some embodiments, the reaction is carried out in a suitable solvent. In some embodiments, the suitable solvent is dichloromethane.

Appropriate P ¹ protecting groups include, but are not limited to the protecting groups for amines delineated in Wuts and Greene, Protective Groups in Organic Synthesis, 4th ed., John Wiley & Sons: New Jersey, pages 696-887 (and, in particular, pages 872-887) (2007), which is incorporated herein by reference in its entirety. In some embodiments, P ¹ is benzyloxycarbonyl (Cbz), 2,2,2-trichloroethoxycarbonyl (Troc), 2-(trimethylsilyl)ethoxycarbonyl (Teoc), 2-(4- trifluoromethylphenylsulfonyl)ethoxycarbonyl (Tsc), t-butoxycarbonyl (BOC), 1 - adamantyloxycarbonyl (Adoc), 2-adamantylcarbonyl (2-Adoc), 2,4-dimethylpent-3- yloxycarbonyl (Doc), cyclohexyloxycarbonyl (Hoc), l , l -dimethyl-2,2,2- trichloroethoxycarbonyl (TcBOC), vinyl, 2-chloroethyl, 2-phenylsulfonylethyl, ally 1, benzyl, 2-nitrobenzyl, 4-nitrobenzyl, diphenyl-4-pyridylmethyl, Ν',Ν'- dimethylhydrazinyl, methoxymethyl, t-butoxymethyl (Bum), benzyloxymethyl (BOM), 2-tetrahydropyranyl (THP), tri(d. ₄ alkyl)silyl (e.g., tri(isopropyl)silyl), 1 , 1 - diethoxymethyl, -CH20CH ₂ CH ₂ Si(CH3)3 (SEM) or N-pivaloyloxymethyl (POM). In some embodiments, P ¹ is -CH ₂ OCH2CH ₂ Si(CH3)3.

The reducing agent can be any reducing agent suitable for use in reductive amination, including various borohydride and borane reducing agents, such as those in Ellen W. Baxter and Allen B. Reitz, Reductive Aminations of Carbonyl

Compounds with Borohydride and Borane Reducing Agents, Organic Reactions, Chapter 1 , pages 1 -57 (Wiley, 2002), which is incorporated herein by reference in its entirety. Non-limiting classes of appropriate reducing agents include borohydride, cyanoborohydride, tri(Ci.4 acyl)oxyborohydride (e.g., triacetoxyborohydride derivatives), 9-borobicyclo[3.3.1 ]nonane hydride, tri(Ci-4 alkyl)borohydride, and disopinocampteylcyanoborohydride derivatives, amino boranes, borane-pyridine complex, and alkylamine boranes. Non-limiting examples of appropriate reducing agents include sodium cyanoborohydride, sodium triacetoxyborohydride, sodium cyano-9-borobicyclo[3.3.1 ]nonane hydride, tetrabutylammonium cyanoborohydride, cyanoborohydride on a solid support, tetramethylammonium triacetoxyborohydride, sodium triacetoxyborohydride, lithium triethylborohydride, lithium tri(sec- butyl)borohydride, sodium disopinocampteylcyanoborohydride, catechol borane, borane tetrahydrofuran, sodium borohydride, potassium borohydride, lithium borohydride, palladium in the presence of hydrogen gas, 5-ethyl-2-methylpyridine borane (PEMB), 2-picoline borane or polymer-supported triacetoxyborohydride. In some embodiments, any of the aforementioned, and preferably sodium

cyanoborohydride, is used in combination with a titanium (IV) additive, dehydrating agent, or a zinc halide additive. In some embodiments, the reducing agent is a tetra(Ci-4 alkyl)ammonium cyanoborohydride or triacetoxyborohydride, an alkali metal cyanoborohydride or triacetoxyborohydride, or an alkaline earth

cyanoborohydride or triacetoxyborohydride. In some embodiments, the reducing agent is an alkali metal cyanoborohydride. In some embodiments, the reducing agent is selected from sodium cyanoborohydride and sodium triacetoxyborohydride. In some embodiments, the reducing agent is sodium triacetoxyborohydride. As used herein, a titanium (IV) additive is a Lewis acid containing a titanium (IV) metal (e.g., titanium tetrachloride, titanium isopropoxide, titanium ethoxide, and the like). In some embodiments, the process further comprisies deprotecting a compound of Formula II or said salt thereof, to form a" compound of Formula I:

I

or a salt thereof.

In some embodiments, the compound of Formula I is initially produced as a free base from the free base form of the compound of Formula II.

In some embodiments, the deprotecting involves reacting the compound of Formula II with a suitable deprotecting agent. In some embodiments, the deprotecting comprises treating with boron trifluoride etherate, followed by treating with aqueous ammonium hydroxide. In some embodiments, the deprotection is carried out in a suitable solvent at a temperature of < 30 °C, < 20 °C, < 10 °C, or < 5 °C. In some embodiments, the suitable solvent is acetonitrile.

In some embodiments, the process of deprotecting the compound of Formula II to form the compound of Formula I, further comprises reacting the compound of Formula I with adipic acid to form the adipate salt.

In some embodiments, the process further comprises:

(a) heating the compound of Formula I in methanol at reflux to form a mixture;

(b) after (a), adding methyl isobutyl ketone to the mixture;

(c) after (b), removing a portion of solvent by distillation at an internal temperature of 40 °C to 50 °C to form a concentrated mixture;

(d) after (c), adding methanol to the concentrated mixture to form a diluted mixture; (e) after (d), heating the diluted mixture at reflux to form a mixture;

(f) after (e), adding methyl isobutyl ketone to the mixture;

(g) after (f), removing a portion of solvent by distillation at an internal temperature of 40 °C to 50 °C to form a concentrated mixture;

(h) after (g), adding adipic acid and methanol to the concentrated mixture;

(i) after (h), heating the mixture at reflux; and

(j) after (i), removing a portion of solvent by distillation at an internal temperature of 40 °C to 50 °C to form a concentrated mixture;

(k) after (j), adding heptane to the mixture; and

(1) after (k), stirring the mixture at room temperature to form the adipic acid salt of the compound of Formula I.

Treatment of the compound of Formula II to remove the P ¹ group can be accomplished by methods known in the art for the removal of particular protecting groups for amines, such as those in Wuts and Greene, Protective Groups in Organic Synthesis, 4th ed., John Wiley & Sons: New Jersey, pages 696-887 (and, in particular, pages 872-887) (2007), which is incorporated herein by reference in its entirety. For example, in some embodiments, the P ¹ group is removed by treating with fluoride ion (e.g., treating with tetrabutylammonium fluoride), hydrochloric acid, pyridinium p- toluenesulfonic acid (PPTS), or a Lewis acid (e.g., lithium tetrafluoroborate)). In some embodiments, the treating comprises treating with lithium tetrafluoroborate, followed by treating with ammonium hydroxide (e.g., when P ¹ is 2- (trimethylsilyl)ethoxymethyl). In some embodiments, the treating comprises treating with base (e.g., P ¹ is N-pivaloyloxymethyl). In some embodiments, the base is an alkali metal hydroxide. In some embodiments, the base is sodium hydroxide. In some embodiments, the treating comprises treating with sodium hydroxide or ammonia in a solvent such as methanol or water.

In some embodiments, the compound of Formula IV, or a salt thereof, is produced by a process comprising deprotecting a compound of Formula V:

V

or a salt thereof.

In some embodiments, the compound of Formula V is used preferably as a free base and the compound of Formula IV is produced preferably as a free base.

In some embodiments, the deprotecting comprises reacting with aqueous acid.

In some embodiments, the acid is hydrochloric acid.

In some embodiments, an excess of aqueous acid is used relative to the compound of Formula V. In some embodiments, an excess of 5, 6, 7, 8, 9, or 10 equivalents of aqueous acid is used relative to the compound of Formula V. In some embodiments, an excess of 6, 7, 8, 9, or 10 equivalents or more of aqueous acid is used relative to the compound of Formula V. In some embodiments, an excess of 7, 8, 9, or 10 equivalents or more of aqueous acid is used relative to φε compound of Formula V. In some embodiments, an excess of 8, 9, or 10 equivalents or more of aqueous acid is used relative to the compound of Formula V. In some embodiments, an excess of 9 or 10 equivalents or more of aqueous acid is used relative to the compound of Formula V. In some embodiments, an excess of 9 equivalents or more of aqueous acid is used relative to the compound of Formula V. In some

embodiments, the deprotection is carried out in acetonitrile solvent at a temperature of < 30 °C, < 20 °C, < 10 °C, or < 5 °C.

Other appropriate deprotecting conditions include, but are not limited to, those in Wuts and Greene, Protective Groups in Organic Synthesis, 4th ed., John Wiley & Sons: New Jersey, pages 696-887 (and, in particular, pages 872-887) (2007), which is incorporated herein by reference in its entirety.

In some embodiments, the compound of Formula V is produced by a process comprising reacting a compound of Formula VI: VI

a salt thereof, with a compound of Formula or a salt thereof, in the presence of a coupling agent.

Appropriate coupling agents are any of the well-known coupling agents for coupling an amine to an acid to form an amine. Non-limiting examples include carbodiimides (e.g., Ν,Ν'-dicyclohexylcarbodiimide (DCC), Ν,Ν'- diisopropylcarbodiimide (D1C), l-ethyl-3-(3-dimethylaminopropyl, or

dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC hydrochloride)) carbodiimide (EDC), or Ι ,Γ-carbonyldiimidazole (CDI)), a carbodiimide regent in the presence of 1-hydroxybenzotriazole (HOBt) or hydrate thereof, phosphonium-based coupling agents (e.g., benzotriazol-l-yloxy-tris(dimethylamino)-phosphonium hexafluorophosphate (BOP), (benzotriazol-l-yloxy)tripyrrolidinophosphonium hexafluorophosphate (P BOP), (7-azabenzotriazol- 1 -y loxy )-tris- pyrrolidinophosphonium hexafluorophosphate (PyAOP),

bromotripyrrolidinophosphonium hexafluorophosphate (PyBrOP), bis(2-oxo-3- oxazolidinyl)phosphinic chloride (BOP-C1)), aminium-based reagents (e.g., O- (benzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HBTU), O- (benzotriazol-l-yl)- Ν,Ν,Ν',Ν'-tetramethyluronium tetrafluoroborate (TBTU), 3- (diethylphosphoryloxy)-l,2,3-benzotriazin-4(3H)-one (DEPBT), 0-(7- azabenzotriazol-l -yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU), 0-(6-chlorobenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HCTU), and 0-(7-azabenzotriazol- 1 -yl)-N,N,N',N'-tetramethy luronium

tetrafluoroborate (TATU)), uronium-based reagents (0-(5-norbornene-2,3- dicarboximido)-N,N,N',N'-tetramethyluronium tetrafluoroborate (TNTU), and 0-(N- succinimidyl)-l ,l ,3,3-tetramethyluronium tetrafluoroborate (TSTU), 0-(3,4-dihydro- 4-oxo-l ,2,3-benzotriazine-3-yl)-N,N,N',N'-tetramethyluronium tetrafluoroborate (TDBTU)), 0-(l ,2-dihydro-2-oxo-l-pyridyl-N,N,N',N'-tetramethyluronium tetrafluoroborate (TPTU), or 0-[(ethoxycarbonyl)cyano-methyleneamino]-N,N,N',N'- tetramethyluronium tertafluoroborate (TOTU)), other regents including, but not limited to, 3-(diethylphosphoryloxy)-l ,2,3-benzotriazin-4(3H)-one (DEPBT), carbonyldiimidazole (CDI), Ν,Ν,Ν',Ν'-tertamethylchloroformamidium

hexafluorophosphate (TCFH), or propylphosphonic anhydride solution. In some embodiments, the coupling agent is benzotriazol-l-yloxy-tris(dimethylamino)- phosphonium hexafluorophosphate (BOP).

In some embodiments, the compounds of Formulas V, VI, and VII are, preferably, in their non-salt forms.

In some embodiments, the reaction of the compound of Formula VI and VII is carried out in the presence of a tertiary amine (e.g., triethylamine). In some embodiments, the reaction is carried out in dimethylformamide (DMF) at a temperature of < 30 °C, < 20 °C, or < 15 °C. In some embodiments, the coupling agent is present in > 1.05, > 1.1 , or > 1.2 equivalents relative to the compound of Formula VI.

The present invention also und of Formula V:

or a salt thereof, which is a useful intermediate in the processes described above.

In some embodiments, the compound of Formula V is a free base.

The processes described herein can be monitored according to any suitable method known in the art. For example, product formation can be monitored by spectroscopic means, such as nuclear magnetic resonance spectroscopy (e.g., Ή or ¹³ C), infrared spectroscopy, or spectrophotometry (e.g., UV-visible); or by chromatography such as high performance liquid chromatograpy (HPLC) or thin layer chromatography (TLC) or other related techniques.

As used herein, the term "reacting" is used as known in the art and generally refers to the bringing together of chemical reagents in such a manner so as to allow their interaction at the molecular level to achieve a chemical or physical transformation. In some embodiments, the reacting involves two reagents, wherein one or more equivalents of second reagent are used with respect to the first reagent. The reacting steps of the processes described herein can be conducted for a time and under conditions suitable for preparing the identified product.

Preparation of compounds can involve the protection and deprotection of various chemical groups. The need for protection and deprotection, and the selection of appropriate protecting groups can be readily determined by one skilled in the art. The chemistry of protecting groups can be found, for example, in Greene, et al., Protective Groups in Organic Synthesis, 4d. Ed., Wiley & Sons, 2007, which is incorporated herein by reference in its entirety. Adjustments to the protecting groups and formation and cleavage methods described herein may be adjusted as necessary in light of the various substituents.

The reactions of the processes described herein can be carried out in suitable solvents which can be readily selected by one of skill in the art of organic synthesis. Suitable solvents can be substantially nonreactive with the starting materials

(reactants), the intermediates, or products at the temperatures at which the reactions are carried out, e.g., temperatures which can range from the solvent's freezing temperature to the solvent's boiling temperature. A given reaction can be carried out in one solvent or a mixture of more than one solvent. Depending on the particular reaction step, suitable solvents for a particular reaction step can be selected. In some embodiments, reactions can be carried out in the absence of solvent, such as when at least one of the reagents is a liquid or gas.

Suitable solvents can include halogenated solvents such as carbon tetrachloride, bromodichloromethane, dibromochloromethane, bromoform, chloroform, bromochloromethane, dibromomethane, butyl chloride, dichloromethane, tetrachloroethylene, trichloroethylene, 1 , 1,1 -trichloroethane, 1 , 1 ,2-trichloroethane, 1 , 1-dichloroethane, 2-chloropropane, α,α,α-trifluorotoluene, 1 ,2-dichloroethane, 1 ,2- dibromoethane, hexafluorobenzene, 1 ,2,4-trichlorobenzene, 1 ,2-dichlorobenzene, chlorobenzene, fluorobenzene, mixtures thereof and the like.

Suitable ether solvents include: dimethoxymethane, tetrahydrofuran, 1 ,3- dioxane, 1 ,4-dioxane, furan, diethyl ether, ethylene glycol dimethyl ether, ethylene glycol diethyl ether, diethylene glycol dimethyl ether, diethylene glycol diethyl ether, triethylene glycol dimethyl ether, anisole, t-butyl methyl ether, mixtures thereof and the like.

Suitable protic solvents can include, by way of example and without limitation, water, methanol, ethanol, 2-nitroethanol, 2-fluoroethanol, 2,2,2- trifluoroethanol, ethylene glycol, 1 -propanol, 2-propanol, 2-methoxyethanol, 1 - butanol, 2-butanol, i-butyl alcohol, t-butyl alcohol, 2-ethoxyethanol, diethylene glycol, 1-, 2-, or 3- pentanol, neo-pentyl alcohol, t-pentyl alcohol, diethylene glycol monomethyl ether, diethylene glycol monoethyl ether, cyclohexanol, benzyl alcohol, phenol, or glycerol.

Suitable aprotic solvents can include, by way of example and without limitation, tetrahydrofuran (THF), Ν,Ν-dimethylformamide (DMF), N,N- dimethylacetamide (DMA), l ,3-dimethyl-3,4,5,6-tetrahydro-2(l H)-pyrimidinone (DMPU), l ,3-dimethyl-2-imidazolidinone (DMI), N-methylpyrrolidinone (NMP), formamide, N-methylacetamide, N-methylformamide, acetonitrile, dimethyl sulfoxide, propionitrile, ethyl formate, methyl acetate, hexachloroacetone, acetone, ethyl methyl ketone, ethyl acetate, sulfolane, N,N-dimethylpropionamide, tetramethylurea, nitromethane, nitrobenzene, or hexamethylphosphoramide.

Suitable hydrocarbon solvents include benzene, cyclohexane, pentane, hexane, toluene, cycloheptane, methylcyclohexane, heptane, ethylbenzene, m-, o-, or p- xylene, octane, indane, nonane, or naphthalene.

The reactions of the processes described herein can be carried out at appropriate temperatures which can be readily determined by the skilled artisan. Reaction temperatures will depend on, for example, the melting and boiling points of the reagents and solvent, if present; the thermodynamics of the reaction (e.g., vigorously exothermic reactions may need to be carried out at reduced temperatures); and the kinetics of the reaction (e.g., a high activation energy barrier may need elevated temperatures). "Elevated temperature" refers to temperatures above room temperature (about 22 °C).

The reactions of the processes described herein can be carried out in air or under an inert atmosphere. Typically, reactions containing reagents or products that are substantially reactive with air can be carried out using air-sensitive synthetic techniques that are well known to the skilled artisan. In some embodiments, preparation of compounds can involve the addition of acids or bases to affect, for example, catalysis of a desired reaction or formation of salt forms such as acid addition salts.

Example acids can be inorganic or organic acids. Inorganic acids include hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, and nitric acid. Organic acids include formic acid, acetic acid, propionic acid, butanoic acid, benzoic acid, 4-nitrobenzoic acid, methanesulfonic acid, p-toluenesulfonic acid,

benzenesulfonic acid, tartaric acid, trifluoroacetic acid, propiolic acid, butyric acid, 2- butynoic acid, vinyl acetic acid, pentanoic acid, hexanoic acid, heptanoic acid, octanoic acid, nonanoic acid and decanoic acid.

Example bases include lithium hydroxide, sodium hydroxide, potassium hydroxide, lithium carbonate, sodium carbonate, and potassium carbonate. Some example strong bases include, but are not limited to, hydroxide, alkoxides, metal amides, metal hydrides, metal dialkylamides and arylamines, wherein; alkoxides include lithium, sodium and potassium salts of methyl, ethyl and t-butyl oxides; metal amides include sodium amide, potassium amide and lithium amide; metal hydrides include sodium hydride, potassium hydride and lithium hydride; and metal dialkylamides include sodium and potassium salts of methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, trimethylsilyl and cyclohexyl substituted amides.

The intermediates and products may also include salts of the compounds disclosed herein. As used herein, the term "salt" refers to a salt formed by the addition of an acceptable acid or base to a compound disclosed herein. In some embodiments, the salts are pharmaceutically acceptable salts. As used herein, the phrase "pharmaceutically acceptable" refers to a substance that is acceptable for use in pharmaceutical applications from a toxicological perspective and does not adversely interact with the active ingredient. Pharmaceutically acceptable salts, including mono- and bi- salts, include, but are not limited to, those derived from organic and inorganic acids such as, but not limited to, acetic, lactic, citric, cinnamic, tartaric, succinic, fumaric, maleic, malonic, mandelic, malic, oxalic, propionic, hydrochloric, hydrobromic, phosphoric, nitric, sulfuric, glycolic, pyruvic, methanesulfonic, ethanesulfonic, toluenesulfonic, salicylic, benzoic, and similarly known acceptable acids. Lists of suitable salts are found in Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, Pa., 1985, p.

1418 and Journal of Pharmaceutical Science, 66, 2 (1977), each of which is incorporated herein by reference in their entireties.

Upon carrying out preparation of compounds according to the processes described herein, the usual isolation and purification operations such as concentration, filtration, extraction, solid-phase extraction, recrystallization, chromatography, and the like may be used, to isolate the desired products.

In some embodiments, the compounds of the invention, and salts thereof, are substantially isolated. By "substantially isolated" is meant that the compound is at least partially or substantially separated from the environment in which it was formed or detected. Partial separation can include, for example, a composition enriched in the compound of the invention. Substantial separation can include compositions containing at least about 50%, at least about 60%, at least about 70%, at least about

80%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% by weight of the compound of the invention, or a salt thereof. Methods for isolating compounds and their salts are routine in the art.

Uses

The compound of Formula I, { l -{ l -[3-fluoro-2- (trifluoromethyl)isonicotinoyl]piperidin-4-yl}-3-[4-(7H-pynO lo[2,3-d]pyrimidin-4- yl)-l H-pyrazol-l -yl]azetidin-3-yl}acetonitrile, is an inhibitor of JAK (e.g., JA 1 , JA 2). JAK inhibitors are useful in treating various JAK-associated diseases or disorders. Examples of JAK-associated diseases include diseases involving the immune system including, for example, organ transplant rejection (e.g. , allograft rejection and graft versus host disease). Further examples of JAK-associated diseases include autoimmune diseases such as multiple sclerosis, rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, type 1 diabetes, lupus, psoriasis, inflammatory bowel disease, ulcerative colitis, Crohn's disease, myasthenia gravis, immunoglobulin nephropathies, myocarditis, autoimmune thyroid disorders, chronic obstructive pulmonary disease (COPD), and the like. In some embodiments, the autoimmune disease is an autoimmune bullous skin disorder such as pemphigus vulgaris (PV) or bullous pemphigoid (BP). Further examples of JAK-associated diseases include allergic conditions such as asthma, food allergies, eszematous dermatitis, contact dermatitis, atopic dermatitis (atropic eczema), and rhinitis. Further examples of JAK-associated diseases include viral diseases such as Epstein Barr Virus (EBV), Hepatitis B, Hepatitis C, HIV, HTLV 1 , Varicella-Zoster Virus (VZV) and Human Papilloma Virus (HPV).

Further examples of JAK-associated disease include diseases associated with cartilage turnover, for example, gouty arthritis, septic or infectious arthritis, reactive arthritis, reflex sympathetic dystrophy, algodystrophy, Tietze syndrome, costal athropathy, osteoarthritis deformans endemica, Mseleni disease, Handigodu disease, degeneration resulting from fibromyalgia, systemic lupus erythematosus, scleroderma, or ankylosing spondylitis.

Further examples of JAK-associated disease include congenital cartilage malformations, including hereditary chrondrolysis, chrondrodysplasias, and pseudochrondrodysplasias (e.g., microtia, enotia, and metaphyseal

chrondrodysplasia).

Further examples of JAK-associated diseases or conditions include skin disorders such as psoriasis (for example, psoriasis vulgaris), atopic dermatitis, skin rash, skin irritation, skin sensitization (e.g., contact dermatitis or allergic contact dermatitis). For example, certain substances including some pharmaceuticals when topically applied can cause skin sensitization. In some embodiments, coadministration or sequential administration of at least one JAK inhibitor of the invention together with the agent causing unwanted sensitization can be helpful in treating such unwanted sensitization or dermatitis. In some embodiments, the skin disorder is treated by topical administration of at least one JAK inhibitor of the invention.

Further examples of JAK-associated diseases or conditions include those characterized by solid tumors (e.g., prostate cancer, renal cancer, hepatic cancer, pancreatic cancer, gastric cancer, breast cancer, lung cancer, cancers of the head and neck, thyroid cancer, glioblastoma, Kaposi's sarcoma, Castleman's disease, uterine leiomyosarcoma, melanoma etc.), hematological cancers (e.g., lymphoma, leukemia such as acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML) or multiple myeloma), and skin cancer such as cutaneous T-cell lymphoma (CTCL) and cutaneous B-cell lymphoma. Example CTCLs include Sezary syndrome and mycosis fungoides. Other examples of JA -associated diseases or conditions include pulmonary arterial hypertension.

Other examples of JAK-associated diseases or conditions include

inflammation-associated cancers. In some embodiments, the cancer is associated with inflammatory bowel disease. In some embodiments, the inflammatory bowel disease is ulcerative colitis. In some embodiments, the inflammatory bowel disease is Crohn's disease. In some embodiments, the inflammation-associated cancer is colitis- associated cancer. In some embodiments, the inflammation-associated cancer is colon cancer or colorectal cancer. In some embodiments, the cancer is gastric cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor (GIST),

adenocarcinoma, small intestine cancer, or rectal cancer.

JAK-associated diseases can further include those characterized by expression of: JAK2 mutants such as those having at least one mutation in the pseudo-kinase domain {e.g., JAK2V617F); JAK2 mutants having at least one mutation outside of the pseudo-kinase domain; JAK 1 mutants; JAK3 mutants; erythropoietin receptor (EPOR) mutants; or deregulated expression of CRLF2.

JAK-associated diseases can further include myeloproliferative disorders (MPDs) such as polycythemia vera (PV), essential thrombocythemia (ET), myelofibrosis with myeloid metaplasia (MMM), primary myelofibrosis (PMF), chronic myelogenous leukemia (CML), chronic myelomonocytic leukemia (CMML), hypereosinophilic syndrome (HES), systemic mast cell disease (SMCD), and the like. In some embodiments, the myeloproliferative disorder is myelofibrosis (e.g., primary myelofibrosis (PMF) or post polycythemia vera/essential thrombocythemia myelofibrosis (Post-PV Post-ET MF)). In some embodiments, the myeloproliferative disorder is post- essential thrombocythemia myelofibrosis (Post-ET MF). In some embodiments, the myeloproliferative disorder is post polycythemia vera myelofibrosis (Post-PV MF).

Other examples of JAK-associated diseases or conditions include ameliorating the dermatological side effects of other pharmaceuticals by administration of the compound of the invention. For example, numerous pharmaceutical agents result in unwanted allergic reactions which can manifest as acneiform rash or related dermatitis. Example pharmaceutical agents that have such undesirable side effects include anti-cancer drugs such as gefitinib, cetuximab, erlotinib, and the like. The compounds of the invention can be administered systemically or topically (e.g., localized to the vicinity of the dermatitis) in combination with (e.g., simultaneously or sequentially) the pharmaceutical agent having the undesirable dermatological side effect. In some embodiments, the compound of the invention can be administered topically together with one or more other pharmaceuticals, where the other pharmaceuticals when topically applied in the absence of a compound of the invention cause contact dermatitis, allergic contact sensitization, or similar skin disorder.

Accordingly, compositions of the invention include topical formulations containing the compound of the invention and a further pharmaceutical agent which can cause dermatitis, skin disorders, or related side effects.

Further JAK-associated diseases include inflammation and inflammatory diseases. Example inflammatory diseases include sarcoidosis, inflammatory diseases of the eye (e.g., iritis, uveitis, scleritis, conjunctivitis, or related disease),

inflammatory diseases of the respiratory tract (e.g., the upper respiratory tract including the nose and sinuses such as rhinitis or sinusitis or the lower respiratory tract including bronchitis, chronic obstructive pulmonary disease, and the like), inflammatory myopathy such as myocarditis, and other inflammatory diseases. In some embodiments, the inflammation disease of the eye is blepharitis.

Further JAK-associated diseases include ischemia reperfusion injuries or a disease or condition related to an inflammatory ischemic event such as stroke or cardiac arrest, endotoxin-driven disease state (e.g., complications after bypass surgery or chronic endotoxin states contributing to chronic cardiac failure), anorexia, cachexia, fatigue such as that resulting from or associated with cancer, restenosis, sclerodermitis, fibrosis, conditions associated with hypoxia or astrogliosis such as, for example, diabetic retinopathy, cancer, or neurodegeneration, and other inflammatory diseases such as systemic inflammatory response syndrome (SIRS) and septic shock.

Other JAK-associated diseases include gout and increased prostate size due to, e.g., benign prostatic hypertrophy or benign prostatic hyperplasia, as well as bone resorption diseases such as osteoporosis or osteoarthritis, bone resorption diseases associated with: hormonal imbalance and/or hormonal therapy, autoimmune disease (e.g. osseous sarcoidosis), or cancer (e.g. myeloma).

Further JA -associated diseases include a dry eye disorder. As used herein, "dry eye disorder" is intended to encompass the disease states summarized in a recent official report of the Dry Eye Workshop (DEWS), which defined dry eye as "a multifactorial disease of the tears and ocular surface that results in symptoms of discomfort, visual disturbance, and tear film instability with potential damage to the ocular surface. It is accompanied by increased osmolarity of the tear film and inflammation of the ocular surface." Lemp, "The Definition and Classification of Dry Eye Disease: Report of the Definition and Classification Subcommittee of the

International Dry Eye Workshop", The Ocular Surface, 5(2), 75-92 April 2007, which is incorporated herein by reference in its entirety. In some embodiments, the dry eye disorder is selected from aqueous tear-deficient dry eye (ADDE) or evaporative dry eye disorder, or appropriate combinations thereof. In some embodiments, the dry eye disorder is Sjogren syndrome dry eye (SSDE). In some embodiments, the dry eye disorder is non-Sjogren syndrome dry eye (NSSDE).

Further JAK-associated diseases include conjunctivitis, uveitis (including chronic uveitis), chorioditis, retinitis, cyclitis, sclieritis, episcleritis, or iritis. Other JAK-associated diseases include respiratory dysfunction or failure associated wth viral infection, such as influenza and SARS.

Examples

The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of noncritical parameters which can be changed or modified to yield essentially the same results.

Example 1. Synthesis of 4-(lH-pyrazol-4-yl)-7-((2- (trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-rf]pyrimidine (5)

C ₆ H_CIN ₃ C ₁₂ H _le CIN ₃ OSi C ₁₃ H ₂ 3BN ₂ 03

Mol. Wt: 266.14

CissHjsNsOijSi C ₁₆ H ₂₁ N ₅ OSi

Mol. Wt.: 387.55 Mol. Wt.: 315.45

Step 1. 4-Chlow-7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3- d]pyrimidine (3)

To a flask equipped with a nitrogen inlet, an addition funnel, a thermowell, and the mechanical stirrer was added 4-chloro-7H-pyirolo[2,3-c/]pyrirnidine (1, 600 g, 3.91 mol) and N,N-dimethylacetimide (DMAC, 9.6 L) at room temperature. The mixture was cooled to 0 - 5 °C in an ice/brine bath before solid sodium hydride (NaH, 60 wt%, 174 g, 4.35 mol, 1.1 equiv) was added in portions at 0 - 5 °C. The reaction mixture turned into a dark solution after 15 minutes. Trimethylsilylethoxymethyl chloride (2, SEM-C1, 763 mL, 4.31 mol, 1.1 equiv) was then added slowly via an addition funnel at a rate that the internal reaction temperature did not exceed 5 °C. The reaction mixture was then stirred at 0 - 5 °C for 30 minutes. When the reaction was deemed complete determined by TLC and HPLC, the reaction mixture was quenched by water (1 L). The mixture was then diluted with water (12 L) and methyl tert-b ty] ether (MTBE) (8 L). The two layers were separated and the aqueous layer was extracted with MTBE (8 L). The combined organic layers were washed with water (2 x 4 L) and brine (4 L) and solvent switched to 1-butanol. The solution of crude product (3) in 1 -butanol was used in the subsequent Suzuki coupling reaction without further purification. Alternatively, the organic solution of the crude product (3) in MTBE was dried over sodium sulfate (Na2SC>4). The solvents were removed under reduced pressure. The residue was then dissolved in heptane (2 L), filtered and loaded onto a silica gel (S1O2, 3.5 Kg) column eluting with heptane (6 L), 95% heptane/ethyl acetate (12 L), 90% heptane/ethyl acetate (10 L), and finally 80% heptane/ethyl acetate (10 L). The fractions containing the pure desired product were combined and concentrated under reduced pressure to give 4-chloro-7-((2-

(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-i/]pyrimidi ne (3, 987 g, 1 109.8 g theoretical, 88.9% yield) as a pale yellow oil which partially solidified to an oily solid on standing at room temperature. For 3: Ή NMR (DMSO-af ₆ , 300 MHz) δ 8.67 (s, 1 H), 7.87 (d, 1 H, J = 3.8 Hz), 6.71 (d, 1 H, J= 3.6 Hz), 5.63 (s, 2H), 3.50 (t, 2H, J= 7.9 Hz), 0.80 (t, 2H, J= 8.1 Hz), 1.24 (s, 9H) ppm; ¹³ C NMR (DMSO-cfe, 100 MHz) δ 151.3, 150.8, 150.7, 131.5, 1 16.9, 99.3, 72.9, 65.8, 17.1 , -1 .48 ppm;

C,2H,8ClN ₃ OSi (MW 283.83), LCMS (EI) m/e 284/286 (M ⁺ + H).

Step 2. 4-(lH-Pyrazol-4-yl)-7-((2-(trimethylsilyl)ethoxy)methyl)-7H- pyrwlo[2,3- d] pyrimidine (5)

To a reactor equipped with the overhead stirrer, a condenser, a thermowell, ' and a nitrogen inlet was charged water (¾0, 9.0 L), solid potassium carbonate (K ₂ C0 ₃ , 4461 g, 32.28 mol, 2.42 equiv), 4-chloro-7-((2-

(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-cT]pyrimidi ne (3, 3597 g, 12.67 mol), 1 -( 1 -ethoxyethyl)-4-(4,4,5,5-tetramethyl- 1 ,3,2-dioxaborolan-2-y I)- 1 H-pyrazole (4, 3550 g, 13.34 mol, 1.05 equiv), and 1-butanol (27 L) at room temperature. The resulting reaction mixture was degassed three timed backfilling with nitrogen each time before being treated with tetrakis(triphenylphosphine)palladium(0) (Pd(PPli3)4, 46 g, 0.040 mol, 0.003 equiv) at room temperature. The resulting reaction mixture was heated to gentle reflux (about 90 °C) for 1 - 4 hours. When the reaction was deemed complete determined by HPLC, the reaction mixture was gradually cooled down to room temperature before being filtered through a Ceiite bed. The Ceiite bed was washed with ethyl acetate (2 x 2 L) before the filtrates and washing solution were combined. The two layers were separated, and the aqueous layer was extracted with ethyl acetate (12 L). The combined organic layers were concentrated under reduced pressure to remove solvents, and the crude 4-(l-(l-ethoxyethyl)-lH-pyrazol-4-yl)-7- ((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-c/]pynmidi ne (6) was directly charged back to the reactor with tetrahydrofuran (THF, 4.2 L) for the subsequent acid- promoted de-protection reaction without further purification.

To a suspension of crude 4-(l -(l -ethoxyethyl)-lH-pyrazol-4-yl)-7-((2- (trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-c/]pyrimidine (6), made as described above, in tetrahydrofuran (THF, 4.2 L) in the reactor was charged water (Η ₂ 0, 20.8 L), and a 10% aqueous HC1 solution (16.2 L, 45.89 mol, 3.44 equiv) at room temperature. The resulting reaction mixture was stirred at 16 - 30 °C for 2 - 5 hours. When the reaction was deemed complete by HPLC analysis, the reaction mixture was treated with a 30% aqueous sodium hydroxide (NaOH) solution (4 L, 50.42 mol, 3.78 equiv) at room temperature. The resulting reaction mixture was stirred at room temperature for 1 - 2 hours. The solids were collected by filtration and washed with water (2 x 5 L). The wet cake was charged back to the reactor with acetonitrile (21.6' L), and resulting suspension was heated to gentle reflux for 1 - 2 hours. The clear solution was then gradually cooled down to room temperature with stirring, and solids were precipitated out from the solution with cooling. The mixture was stirred at room temperature for an additional 1 - 2 hours. The solids were collected by filtration, washed with acetonitrile (2 x 3.5 L), and dried in oven under reduced pressure at 45 - 55 °C to constant weight to afford 4-( 1 H-pyrazol-4-yl)-7-((2- (trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-i/]pyrimidine (5, 3281.7 g, 3996.8 g theoretical, 82.1 % yield) as white crystalline solids (99.5 area% by HPLC). For 5: Ή NMR (DMSO-i/ ₆ , 400 MHz) δ 13.41 (br. s, 1 H), 8.74 (s, 1 H), 8.67 (br. s, 1 H), 8.35 (br. s, 1 H), 7.72 (d, l H, J= 3.7 Hz), 7.10 (d, 1 H, J= 3.7 Hz), 5.61 (s, 2H), 3.51 (t, 2H, J= 8.2 Hz), 0.81 (t, 2H, J= 8.2 Hz), 0.13 (s, 9H) ppm; C ₁₅ H ₂ iN ₅ OSi (MW, 315.45), LCMS (El) mle 316 (M ⁺ + H).

Example 2. terf-Butyl 3-(cyanomethylene)azetidine-l-carboxylate (13)

C ₁₃ H ₁₃ N C ₅ H ₅ CIO C ₁₆ H ₁₈ CINO

Mol. Wt: 183.25 Mol. Wt: 92.52 Mol. Wt: 275.77

'BuOK/THF C ₁₀ H ₁₄ N ₂ O ₂

Mol. Wt: 194.23

Step 1. 1 -Benzhydrylazetidin-3-ol hydrochloride (9)

A solution of diphenylmethanamine (7, 2737 g, 15.0 mol, 1.04 equiv) in methanol (MeOH, 6 L) was treated with 2-(chloromethyl)oxirane (8, 1330 g, 14.5 mol) from an addition funnel at room temperature. During the initial addition a slight endotherm was noticed. The resulting reaction mixture was stirred at room temperature for 3 days before being warmed to reflux for an additional 3 days. When TLC showed that the reaction was deemed complete, the reaction mixture was first cooled down to room temperature and then to 0 - 5 °C in an ice bath. The solids were collected by filtration and washed with acetone (4 L) to give the first crop of the crude desired product (9, 1516 g). The filtrate was concentrated under reduced pressure and the resulting semisolid was diluted with acetone (1 L). This solid was then collected by filtration to give the second crop of the crude desired product (9, 221 g). The crude product, l -benzhydrylazetidin-3-ol hydrochloride (9, 1737 g, 3998.7 g theoretical, 43.4 % yield), was found to be sufficiently pure to be used in the subsequent reaction without further purification. For 9: 'H MR (DMSO-C/ ₆ , 300 MHz), δ 12.28 (br. d, 1 H), 7.7 (m, 5H), 7.49 (m, 5H), 6.38 (d, 1H), 4.72 (br. s, 1 H), 4.46 (m, 1 H), 4.12 (m, 2H), 3.85 (m, 2H) ppm; C,6H, ₈ ClNO (free base of 9, Ci ₆ Hi ₇ NO MW, 239.31 ), LCMS (EI) m/e 240 (M ⁺ +. H). Step 2. tert-Butyl 3-hydroxyazetidine-l -carboxylate (10)

A suspension of l-benzhydrylazetidin-3-ol hydrochloride (9, 625 g, 2.27 mol) in a 10 % solution of aqueous sodium carbonate (Na2C0 ₃ , 5 L) and dichloromethane (CH2CI2, 5 L) was stirred at room temperature until all solids were dissolved. The two layers were separated, and the aqueous layer was extracted with dichloromethane (CH2CI2, 2 L). The combined organics extracts were dried over sodium sulfate

(Na2SC>4) and concentrated under reduced pressure. This resulting crude free base of 9 was then dissolved in THF (6 L) and the solution was placed into a large Parr bomb. Di-teri-butyl dicarbonate (BOC ₂ 0, 545 g, 2.5 mol, 1.1 equiv) and 20 % palladium (Pd) on carbon (125 g, 50 % wet) were added to the Parr bomb. The vessel was charged to 30 psi with hydrogen gas (¾) and stirred under steady hydrogen atmosphere (vessel was recharged three times to maintain the pressure at 30 psi) at room temperature for 18 h. When HPLC showed that the reaction was complete (when no more hydrogen was taken up), the reaction mixture was filtered through a Celite pad and the Celite pad was washed with THF (4 L). The filtrates were concentrated under reduced pressure to remove the solvent and the residue was loaded onto a Biotage 150 column with a minimum amount of dichloromethane (CH2CI2). The column was eluted with 20 - 50 % ethyl acetate in heptane and the fractions containing the pure desired product (10) were collected and combined. The solvents were removed under reduced pressure to afford terr-butyl 3-hydroxyazetidine-l - carboxylate (10, 357 g, 393.2 g theoretical, 90.8% yield) as colorless oil, which solidified upon standing at room temperature in vacuum. For 10: 'iTNMR (CDCI3, 300 MHz), δ 4.56 (m 1 H), 4.13 (m, 2H), 3.81 (m, 2H), 1.43 (s, 9H) ppm.

Step 3. tert-Butyl 3-oxoazetidine-l -carboxylate (11)

A solution of tert-b ty\ 3-hydroxyazetidine-l -carboxylate (10, 50 g, 289 mmol) in ethyl acetate (400 mL) was cooled to 0 °C. The resulting solution was then treated with solid TEMPO (0.5 g, 3.2 mmol, 0.01 1 equiv) and a solution of potassium bromide ( Br, 3.9 g, 33.2 mmol, 0.1 15 equiv) in water (60 mL) at 0 - 5 °C. While keeping the reaction temperature between 0 - 5 °C a solution of saturated aqueous sodium bicarbonate (NaHCCb, 450 mL) and an aqueous sodium hypochlorite solution ( aCIO, 10 - 13 % available chlorine, 450 mL) were added. Once the solution of sodium hypochlorite was added, the color of the reaction mixture was changed immediately. When additional amount of sodium hypochlorite solution was added, the color of the reaction mixture was gradually faded. When TLC showed that all of the starting material was consumed, the color of the reaction mixture was no longer changed. The reaction mixture was then diluted with ethyl acetate (EtOAc, 500 mL) and two layers were separated. The organic layer was washed with water (500 mL) and the saturated aqueous sodium chloride solution (500 mL) and dried over sodium sulfate ( a ₂ SC>4). The solvent was then removed under reduced pressure to give the crude product, /erf-butyl 3-oxoazetidine-l-carboxylate (11, 48 g, 49.47 g theoretical, 97% yield), which was found to be sufficiently pure and was used directly in the subsequent reaction without further purification. For crude 11: 'HNMR (CDCI ₃ , 300 MHz), δ 4.65 (s, 4H), 1.42 (s, 9H) ppm. Step 4. tert-Butyl 3-(cyanomethylene)azetidine-l-carboxylate (13)

Diethyl cyanomethyl phosphate (12, 745 g, 4.20 mol, 1.20 equiv) and anhydrous tetrahydrofuran (THF, 9 L) was added to a four-neck flask equipped with a thermowell, an addition funnel and the nitrogen protection tube at room temperature. The solution was copied with an ice-methanol bath to - 14 °C and a l .O M solution of potassium teri-butoxide (f-BuO ) in anhydrous tetrahydrofuran (THF, 3.85 L, 3.85 mol, 1.1 equiv) was added over 20 minutes keeping the reaction temperature below - 5 °C. The resulting reaction mixture was stirred for 3 hours at - 10 °C and a solution of l -/er/-butoxycarbonyl-3-azetidinone (11, 600 g, 3.50 mol) in anhydrous tetrahydrofuran (THF, 2 L) was added over 2 h keeping the internal temperature below - 5 °C. The reaction mixture was stirred at - 5 to - 10 °C over 1 hour and then slowly warmed up to room temperature and stirred at room temperature for overnight. The reaction mixture was then diluted with water (4.5 L) and saturated aqueous sodium chloride solution (NaCl, 4.5 L) and extracted with ethyl acetate (EtOAc, 2 x 9 L). The combined organic layers were washed with brine (6 L) and dried over anhydrous sodium sulfate (Na ₂ S0 ₄ ). The organic solvent was removed under reduced pressure and the residue was diluted with dichloromethane (CH2CI2, 4 L) before being absorbed onto silica gel (S1O2, 1.5 Kg). The crude product, which was absorbed on silica gel, was purified by flash column chromatography (Si0 ₂ , 3.5 Kg, 0 - 25% EtOAc/hexanes gradient elution) to afford terf-butyl 3-(cyanomethylene)azetidine-l - carboxylate (13, 414.7 g, 679.8 g theoretical, 61 % yield) as white solid. For 13: Ή NMR (CDC , 300MHz), 6 5.40 (m, 1H), 4.70 (m, 2H), 4.61 (m, 2H), 1.46 (s, 9H) ppm; C,oH, N ₂ 02 (MW, 194.23), LCMS (EI) mle 217 (M ⁺ + Na).

Example 3. (3-Fluoro-2-(trifluoromethyl)pyridin-4-yl)(l,4-dioxa-8- a

Step 1. 1 ,4-Dioxa-8-azaspiro[4.5]decane (15)

To a 30 L reactor equipped with a mechanic stirrer, an addition funnel and a septum was charged sodium hydroxide (NaOH, 1.4 kg, 35 mol) and water (7 L, 3.13 kg, 17.43 mol). To the solution thus obtained was added l ,4-dioxa-8- azaspiro[4.5]decane hydrochloric acid (14, 3.13 kg, 17.43 mol). The mixture was stirred at 25 °C for 30 minutes. Then the solution was saturated with sodium chloride (1.3 kg) and extracted with 2-methyl-tetrahydrofuran (3 x 7 L). The combined organic layer was dried with anhydrous sodium sulfate (1.3 kg), filtered and concentrated under reduced pressure (70 mmHg) at 50 °C. The yellow oil thus obtained was distilled under reduced pressure (80 mmHg, bp: 1 15 °C to 120 °C) to give compound 15 (2.34 kg, 16.36 mol, 93.8%) as a clear oil, which was used directly in the subsequent coupling reaction.

Step 2. (3-Fluoro-2-(trifluoromethyl)pyridin-4-yl) (1, 4-dioxa-8-azaspiro[ 4, 5]decan-8- yl)methanone (17)

To a dried 100 L reactor equipped with a mechanic stirrer, an addition funnel, a thermometer and a vacuum outlet were placed 3-fluoro-2- (trifluoromethyl)isonicotinic acid (16, 3.0 kg, 14.35 mol), benzotriazol-1- yloxytris(dimethylamino)phosphonium hexafluorophosphate (BOP reagent, 7.6 kg, 17.2 mol, 1.20 equiv) in dimethy lformamide (DMF, 18 L). To the resulting solution was added l ,4-dioxa-8-azaspiro[4.5]decane (15, 2.34 kg, 16.36 mol, 1.14 equiv) with stirring over 20 minutes. Triethylamine (Et ₃ N, 4 L, 28.67 mol, 2.00 equiv) was then added over 1 hour. The temperature was kept between 5 °C and 10 °C during the additions. The dark brown solution thus obtained was stirred for 12 hours at 20 °C and then chilled to 10 °C. With vigorous stirring, 18 L of saturated sodium bicarbonate solution and 36 L of water were sequentially added and the temperature was kept under 15 °C. The precipitation (filter cake) thus obtained was collected by filtration. The aqueous phase was then saturated with 12 kg of solid sodium chloride and extracted with EtOAc (2 x 18 L). The combined organic layer was washed with saturated sodium bicarbonate solution (18 L), and water (2 x 18 L) in sequence. The filter cake from the previous filtration was dissolved back in the organic phase. The dark brown solution thus obtained was washed twice with 18 L of water each and then concentrated under reduced pressure (40 - 50 °C, 30 mm Hg) to give 5.0 kg of the crude product as viscous brown oil. The crude product 17 obtained above was dissolved in EtOH (8.15 L) at 50 °C. Water (16.3 L) was added over 30 minutes. The brown solution was seeded, cooled to 20 °C over 3 hours with stirring and stirred at 20 °C for 12 h. The precipitate formed was filtered, washed with a mixture of EtOH and water (EtOH : H ₂ 0 = 1 : 20, 2 L) and dried under reduced pressure (50 mmHg) at 60 °C for 24 hours to afford (3-fluoro-2-(trifluoromethyl)pyridin-4-yl)(l ,4-dioxa-8- azaspiro[4,5]decan-8-yl)methanone (17, 3.98 kg, 1 1.92 mol, 83.1%) as a white powder. For 17: Ή NMR (300 MHz, (CD ₃ ) ₂ SO) δ 8.64 (d, ³ J _HH = 4.68 Hz, 1 H, NCH in pyridine), 7.92 (dd, ³ J _HH = 4.68 Hz, ⁴ J _HF = 4.68 Hz, 1 H, NCCH in pyridine), 3.87- 3.91 (m, 4 H, OCH ₂ CH ₂ 0), 3.70 (br s, 2 H, one of NCH ₂ in piperidine rine, one of another NCH ₂ in piperidine ring, both in axial position), 3.26 (t, HH ⁼ 5.86 Hz, 2 H, one of NCH ₂ in piperidine rine, one of another NCH ₂ in piperidine ring, both in equatorial position), 1.67 (d, _HH = 5.86 Hz, 2 H, one of NCCH ₂ in piperidine ring, one of another NCCH ₂ in piperidine ring, both in equatorial position), 1.58 (br s, 2 H, one of NCCH ₂ in piperidine ring, one of another NCCH ₂ in piperidine ring, both in axial position) ppm; ^,3 C NMR (75 MHz, (CD ₃ ) ₂ SO) δ 161.03 (N-C=0), 151.16 (d, 'JCF = 266.03 Hz, C-F), 146.85 (d, V _CF = 4.32 Hz, NCH in pyridine), 135.24 (d, ² J _CF = 1 1.51 Hz, C-C=0), 135.02 (quartet, V _CF = 34.57 Hz, NCCF ₃ ), 128.24 (d, V _CF = 7.48 Hz, NCCH in pyridine), 1 19.43 (dxquartet, 'JcF = 274.38 Hz, V _CF = 4.89 Hz, CF ₃ ), 106.74 (OCO), 64.60 (OCCO), 45.34 (NC in piperidine ring), 39.62(NC in piperidine ring), 34.79(NCC in piperidine ring), 34.10 (NCC in piperidine ring) ppm; ¹⁹ F NMR (282 MHz, (CD ₃ ) ₂ SO) δ -64.69 (d, V _FF = 15.85 Hz, F ₃ C), -129.26 (dx quartet, ⁴ J _FF = 15.85 Hz, ⁴ J _FH = 3.96 Hz, FC) ppm; CuHnF^C (MW, 334.27), LCMS (EI) m/e 335.1 (M ⁺ + H). Example 4. (3-Fluoro-2-(trifluoromethyI)pyridin-4-yl) (l,4-dioxa-8- azaspiro|4,5]decan-

17 18

C _M H ₁₄ F ₄ N20, C ₁₂ H ₁₀ F ₄ N ₂ O2 Mol. Wt: 334.27 Mol. Wt: 290.21

In a 5 L 4-necked round bottom flask equipped with a mechanical stirrer, a thermocouple, an addition funnel and a nitrogen inlet was placed (3-fluoro-2- (trifluoromethyl)pyridin-4-yl)(l ,4-dioxa-8-azaspiro[4,5]decan-8-yl)methanone (17, 100 g, 0.299 mol) in acetonitrile (ACN, 400 mL) at room temperature. The resultant solution was cooled to below 10 °C. To the reaction mixture was added 6.0 N aqueous hydrochloric acid (HCl, 450 mL, 2.70 mol, 9.0 equiv), while the internal temperature was kept below 10 °C. The resulting reaction mixture was then warmed to room temperature and an additional amount of 6.0 N aqueous hydrochloric acid (HCl, 1050 mL, 6.30 mol, 21.0 equiv) was slowly introduced to the reaction mixture at room temperature in 8 hours via the addition funnel. The reaction mixture was then cooled to 0 °C before being treated with 30% aqueous sodium hydroxide (NaOH, 860 mL, 8.57 mmol, 28.6 equiv) while the internal temperature was kept at below 10 °C. The resulting reaction mixture was subsequently warmed to room temperature prior to addition of solid sodium bicarbonate (NaHC0 ₃ , 85.0 g, 1.01 mol, 3.37 equiv) in 1 hour. The mixture was then extracted with EtOAc (2 x 1.2 L), and the combined organic phase was washed with 16% aqueous sodium chloride solution (2 x 800 mL) and concentrated to approximately 1.0 L by vacuum distillation. Heptane (2.1 L) was added to the residue, and the resulting mixture was concentrated to 1.0 L by vacuum distillation. To the concentrated mixture was added heptane (2.1 L). The resulting white slurry was then concentrated to 1.0 L by vacuum distillation. To the white slurry was then added methyl fert-butyl ether (MTBE, 1.94 L). The white turbid was heated to 40 °C to obtain a clear solution. The resulting solution was concentrated to about 1.0 L by vacuum distillation. The mixture was stirred at room temperature for 1 hour. The white precipitate was collected by filtration with pulling vacuum. The filter cake was washed with heptane (400 mL) and dried on the filter under nitrogen with pulling vacuum to provide compound 18 (78.3 g, 90.1%) as an off-white solid. For 18: Ή NMR (300 MHz, (CD ₃ ) ₂ SO) δ 8.68 (d, ³ J _HH = 4.69 Hz, 1 H, NCH in pyridine), 7.97 (dd, ³ J _HH = 4.69 Hz, V _HF = 4.69 Hz, 1 H, NCCH in pyridine), 3.92 (br s, 2 H, one of NCH2 in piperidine rine, one of another NC¾ in piperidine ring, both in axial position), 3.54 (t, V _HH = 6.15 Hz, 2 H, one of NCH2 in piperidine rine, one of another NCH2 in piperidine ring, both in equatorial position), 2.48 (t, HH = 6.44 Hz, 2 H, NCCH ₂ ), 2.34 (t, _HH = 6.15 Hz, 2 H, NCCH ₂ ) ppm; ¹³ C NMR (75 MHz, (CD ₃ ) ₂ SO) δ 207.17 (C=0), 161.66 (N-C=0), 151.26 (d, 'J _CF = 266.89 Hz, C-F), 146.90 (d, _CF = 6.05 Hz, NCH in pyridine), 135.56 (C-C=0), 134.78 -135.56 (m, NCCF ₃ ), 128.27 (d, V _CF = 7.19 Hz, NCCH in pyridine), 1 19.52 (d* quartet, V _C F = 274.38 Hz, V _CF = 4.89 Hz, CF ₃ ), 45.10 (NC in piperidine ring) ppm, one carbon

(NCC in piperidine ring) missing due to overlap with (CD ₃ ) ₂ SO; ¹⁹ F NMR (282 MHz, (CD ₃ ) ₂ SO) δ -64.58 (d, V _FF = 15.85 Hz, F ₃ C), -128.90 (dxquartet, V _FF =1 5.85 Hz, F _H = 4.05 Hz, FC) ppm; (MW, 290.21 ), LCMS (EI) m/e 291.1 (M ⁺ + H).

Example 5. 3-[4-(7-{[2-(Trimethylsilyl)ethoxy]methyl}-7H-pyrrolo[2,3- rf]pyrimidin-4-yl)-lH-pyrazol-l-yl]azetidin-3-yl}acetonitril e dihydrochloride (20)

Mol. Wt: 315.45 Mol. W 509.68 Mol. Wt: 482.28

Step 1. tert-But l 3-(cyanomethyl)-3-(4-(7-((2-(trimethylsilyl)ethoxy)methyl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-lH-pyrazol-l-yl)azetidine-l-ca rboxylate (19)

In a dried 30 L reactor equipped with a mechanic stirrer, a thermometer, an addition funnel and a vacuum outlet were placed 4-(lH-pyrazol-4-yl)-7-((2-

(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-i/]pyrimidi ne (5, 4.50 kg, 14.28 mol), terf-butyl 3-(cyanomethylene)azetidine-l -carboxylate (13, 3.12 kg, 16.08 mol, 1.126 equiv) in acetonitrile (9 L) at 20 ± 5 °C. To the resultant pink suspension was added l ,8-diazabicyclo[5.4.0]undec-7-ene (DBU, 225 mL, 1.48 mol, 0.10 equiv) over 40 minutes. The batch temperature was kept between 10 °C and 20 °C during addition. The brown solution obtained was stirred at 20 °C for 3 hours. After the reaction was complete, water (18 L) was added with stirring over 80 minutes at 20 °C. The mixture was seeded and the seeded mixture was stirred at room temperature for 12 hours. The solids were collected by filtration and the filter cake was washed with a mixture of acetonitrile and water (1 : 2, 9 L) and dried in a vacuum oven with nitrogen purge for 12 hours at 60 °C to provide the crude product (19, 7.34 kg) as a light yellow powder. The crude product obtained above was dissolved in methyl teri-butyl ether (MTBE, 22 L) at 60 °C in a 50 L reactor equipped with a mechanic stirrer, a thermometer, an addition funnel and a septum. Hexanes (22 L) was added over 1 hour at 60 °C. The solution was then seeded, cooled to 20 °C over 3 hours and stirred at 20 °C for 12 hours. The precipitation was collected by filtration. The resultant cake was washed with a mixture of MTBE and hexane (1 : 15, 3 L) and dried in a vacuum oven for 10 hours at 50 °C to provide the compound 19 (6.83 kg, 13.42 mol, 94.0%) as a white powder. For 19: Ή NMR (400 MHz, CDCI ₃ ) δ 8.87 (s, 1 H), 8.46 (d, J = 0.6 Hz, 1 H), 8.36 (d, J= 0.7 Hz, 1 H), 7.44 (d, J= 3.7 Hz, 1 H), 6.82 (d, J = 3.7 Hz, I H), 5.69 (s, 2H), 4.57 (d, J= 9.6 Hz, 2Η), 4.32 (d, J= 9.5 Hz, 2H), 3.59 - 3.49 (m, 2H), 3.35 (s, 2H), 1.49 (s, 9H), 0.96 - 0.87 (m, 2H), -0.03 - -0.10 (s, 9H) ppm; ¹³ C NMR (101 MHz, CDC1 ₃ ) δ 157.22, 153.67, 153.24, 151.62, 142.13, 130.16, 129.67, 124.47, 1 16.72, 1 15.79, 102.12, 82.54, 74.23, 68.01, 60.25, 58.23, 29.65, 29.52, 19.15, -0.26 ppm; C25H35N7O3S1 (MW, 509.68), LCMS (EI) mle 510.1 (M ⁺ + H).

Step 2. 3-[4-(7-{[2-(Trimethylsilyl)ethoxy]methyl}-7H-pyrrolo[2,3-d] pyrimidin-4-yl)- lH-pyrazol-l-yl]azetidin-3-yl}acetonitrile dihydrochloride (20)

In a 2 L 4-necked round bottom flask equipped with a mechanical stirrer, a thermocouple, an addition funnel and a nitrogen inlet was added compound 19 (55.0 g, 0.108 mol) and methanol (MeOH, 440 mL) at 20 ± 5 °C. The resulting white turbid was stirred for 20 minutes at room temperature to provide a light yellow solution. A solution of hydrochloric acid (HC1) in isopropanol (5.25 M, 165 mL, 0.866 mol, 8.02 equiv) was then added to the reaction mixture via the addition funnel in 5 minutes. The resulting reaction mixture was then heated to 40 °C by a heating mantle. After 2 hours at 40 °C, water (165 mL, 9.17 mol, 84.8 equiv) was added to the reaction mixture via the addition funnel to provide a light green solution at 40 °C. Methyl tert- butyl ether (MTBE, 440 mL) was added to the resulting mixture via the addition funnel at 40 °C. The resulting mixture was slowly cooled to 10 °C. The solids were collected by filtration and washed with MTBE (2 x 220 mL). The white solids were dried in the filter under nitrogen with a pulling vacuum for 18 hours to afford compound 20 (52.2 g, KF water content 5.42%, yield 94.9%). For 20: Ή NMR (400 MHz, (CD ₃ ) ₂ SO) δ 10.39 (brs, I H), 10.16 (brs, IH), 9.61 (s, IH), 9.12 (s, I H), 9.02 (s, I H), 8.27 - 8.21 (d, J= 3.8 Hz, I H), 7.72 - 7.66 (d, J= 3.8 Hz, I H), 5.82 (s, 2H), 4.88 - 4.77 (m, 2H), 4.53 - 4.44 (m, 2H), 4.12 (s, 2H), 3.69 - 3.60 (m, 2H), 0.98 - 0.89 (m, 2H), 0.01 (s, 9H) ppm; ¹³ C NMR (101 MHz, (CD ₃ ) ₂ SO) δ 151.25, 146.45, 145.09, 140.75, 133.38, 132.44, 1 16.20, 1 16.09, 1 12.79, 102.88, 73.07, 66.14, 59.16, 53.69, 26.44, 17.15, -1.36 ppm; C ₂ oH29Cl ₂ N ₇ OSi (free base of 20, C ₂₀ H ₂₇ N ₇ OSi, MW 409.56), LCMS (EI) mle 410.2 (M ⁺ + H). Example 6. 2-(l-(l-(3-Fluoro-2-(trifluoromethyl)isonicotinoyl)piperidin -4-yl)-3- (4-(7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-rf]p yrimidin-4-yl)-lH- pyrazo

In a 100 L dried reactor equipped with a mechanical stirrer, a thermocouple, a condenser, and a nitrogen inlet was added (20, 3.24 kg, 6.71 5 mol) and

dichloromethane (32 L) at 20 ± 5 °C. The mixture was stirred at room temperature for 10 minutes before being treated with triethylamine (TEA, 1.36 kg, 13.44 mol, 2.00 equiv) at an addition rate which keeping the internal temperature at 15 -30 °C.

Compound 18 (2.01 kg, 6.926 mol, 1.03 equiv) was then added to the reactor at room temperature. After 10 minutes, sodium triacetoxyborohydride (NaBH(OAc)3, 2.28 kg, 10.75 mol, 1.60 equiv) was added portion wise to the reactor in 1 hour while the internal temperature was kept at 15 - 30 °C. The resulting. reaction mixture was stirred at 15 - 30 °C for an additional one hour. Once the reductive amination reaction is deemed complete, the reaction mixture was treated with a 4% aqueous sodium bicarbonate solution ( aHCCh, 32 L) to adjust the pH to 7 - 8. After stirring for 30 minutes at room temperature, the two phases were separated. The aqueous phase was extracted with dichloromethane (29 L). The combined organic phase was sequentially washed with 0.1 N aqueous hydrochloric acid solution (16 L), 4% aqueous sodium bicarbonate solution (16 L), 8% aqueous sodium chloride solution (2 x 16 L). The resultant organic phase was partially concentrated and filtered. The filtrate was subjected to solvent exchange by gradually adding acetonitrile (65 L) under vacuum. The white solids were collected by filtration, washed with acetonitrile (10 L) and dried at 40 - 50 °C in a vacuum oven with nitrogen purge to afford compound 21 (4.26 kg, 6.23 mol, 92.9%). For 21: Ή NMR (500 MHz, (CD ₃ ) ₂ SO) δ 8.84 (s, 1 H), 8.76 (s, 1H), 8.66 (d, J =4.7 Hz, 1H), 8.43 (s, 1H), 7.90 (t, J= 4.7 Hz, 1H), 7.78 (d, .7=3.7 Hz, 1H), 7.17 (d,J= 3.7 Hz, 1H),5.63 (s, 2H), 4.07 (dt,J= 11.1, 4.9 Hz, 1H), 3.75 (d, J= 7.8 Hz, 2H), 3.57 (dd, J= 10.2, 7.8 Hz, 2H), 3.55 (s, 2h), 3.52 (dd, J= 8.5, 7.4 Hz,2H), 3.41 (dq,J= 13.3,4.3 Hz, 1H), 3.26 (t, J= 10.0 Hz, 1H), 3.07 (ddd, J = 13.1,9.4,3.2 Hz, 1H), 2.56 (dt,J=8.5, 4.7 Hz, 1H), 1.81-1.73 (m, 1H), 1.63 (m, 1H), 1.29 (m, 1H), 1.21 (m, 1H), 0.82 (dd,J= 8.5, 7.4 Hz, 2H), -0.12 (s, 9H) ppm; ^l3 CNMR(101 MHz, (CD ₃ ) ₂ SO) δ 161.68,(154.91, 152.27), 153.08, 152.69, 151.53, 147.69, 140.96, (136.19, 136.02), (136.48, 136.36, 136.13, 136.0, 135.78, 135.66, 135.43, 135.32), 131.43, 130.84, 129.03,(126.17, 123.42, 120.69), 117.99, 122.77, 118.78, 114.71, 102.02, 73.73, 67.04, 62.86, 61.88, 58.51, 45.63, 30.03, 29.30, 28.60, 18.52, 0.00 ppm; C32H37F4N9O2S1 (MW, 683.77), LCMS (EI) mle 684.2 (M ⁺ + H).

Example 7. 2-(3-(4-(7H-P rrolo[2,3-rflpyrimidin-4-yl)-lH-pyrazol-l-yl)-l-(l-(3- fluoro-2-(trifluoromethyl)isonicotinoyl)piperidin-4-yl)azeti din-3-yl)acetonitrile

(22)

21 22

C ₃ 2H ₃₇ F ₄ N ₉ 0 ₂ Si C26H23F4N9O

Mol. Wt: 683.77 Mol. Wt: 553.51

To a 250 mL 4-necked round bottom flask equipped with a mechanical stirrer, a thermocouple, an addition funnel and a nitrogen inlet was added compound 21 (9.25 g, 13.52 mmol, F water content 3.50%) and acetonitrile (74 mL) at 20 ± 5 °C. The resulting white slurry was cooled to below 5 °C. Boron trifluoride diethyl etherate (BF ₃ -OEt2, 6.46 mL, 51.37 mmol, 3.80 equiv) was then added at a rate while the internal temperature was kept at.below 5.0 °C. The reaction mixture was then warmed to 20 ± 5 °C. After stirring at 20 ± 5 °C for 18 hours, the reaction mixture was cooled to 0 - 5 °C and an additional amount of BF3 OE12 (0.34 mL, 2.70 mmol, 0.2 equiv) was introduced to the reaction mixture at below 5.0 °C. The resulting reaction mixture was warmed to 20 ± 5 °C, and kept stirring at room temperature for an additional 5 hours. The reaction mixture was then cooled to 0 - 5 °C before water (12.17 mL, 0.676 mol, 50 equiv) was added. The internal temperature was kept at below 5.0 °C during addition of water. The resultant mixture was warmed to 20 ± 5 °C and kept stirring at room temperature for 2 hours. The reaction mixture was then cooled to 0 - 5 °C and aqueous ammonium hydroxide (NH4OH, 5 N, 121.7 mmol, 9.0 equiv) was added. During addition of aqueous ammonium hydroxide solution, the internal temperature was kept at below 5.0 °C. The resulting reaction mixture was warmed to 20 ± 5 °C and stirred at room temperature for 20 hours. Once the SEM-deprotection was deemed complete, the reaction mixture was filtered, and the solids were washed with EtOAc (9.25 mL). The filtrates were combined and diluted with EtOAc (74 mL). The diluted organic solution was washed with 13% aqueous sodium chloride solution (46.2 mL). The organic phase was then diluted with EtOAc (55.5 mL) before being concentrated to a minimum volume under reduced pressure. EtOAc (120 mL) was added to the residue, and the resulting solution was stirred at 20 ± 5 °C for 30 minutes. The solution was then washed with 7% aqueous sodium bicarbonate solution (2 x 46 mL) and 13% aqueous sodium bicarbonate solution (46 mL). The resultant organic phase was diluted with EtOAc (46 mL) and treated with water (64 mL) at 50 ± 5 °C for 30 minutes. The mixture was cooled to 20 ± 5 °C and the two phases were separated. The organic phase was treated with water (64 mL) at 50 ± 5 °C for 30 minutes for the second time. The mixture was cooled to 20 ± 5 °C and the two phases were separated. The resultant organic phase was concentrated to afford crude compound 22 (free base), which was further purified by column chromatography

(S1O2, 330 g, gradient elution with 0 - 10% of MeOH in EtOAc) to afford analytically pure free base (22, 7.00 g, 93.5 %) as an off-white solid. For 22: Ή NMR (400 MHz, (CD ₃ ) ₂ SO)812.17 (d, J = 2.8 Hz, 1H), 8.85 (s, 1H), 8.70 (m, 2H), 8.45 (s, 1H), 7.93 (t, .7=4.7 Hz, 1H), 7.63 (dd, J= 3.6, 2.3 Hz, 1H), 7.09 (dd,J=3.6, 1.7 Hz, 1H), 4.10 (m, 1H), 3.78 (d,J=7.9Hz, 2H), 3.61 (t,J=7.9 Hz, 1H), 3.58 (s, 2H), 3.46 (m, 1H), 3.28 (t,J= 10.5 Hz, 1H),3.09 (ddd,J= 13.2, 9.5,3.1 Hz, 1H), 2.58 (m, 1H), 1.83- 1.75 (m, 1H), 1.70 - 1.63 (m, 1H), 1.35-1.21 (m, 2H) ppm; ^l3 C NMR (101 MHz, (CD ₃ ) ₂ SO)5160.28,(153.51, 150.86), 152.20, 150.94, 149.62, (146.30, 146.25), 139.48,(134.78, 134.61), (135.04, 134.92, 134.72, 134.60, 134.38, 134.26, 134.03, 133.92), 129.22, 127.62, 126.84, 121.99, 122.04,(124.77, 122.02, 119.19, 116.52), 117.39, 113.00, 99.99, 61.47, 60.49, 57.05, 44.23, 28.62, 27.88, 27.19 ppm;

C26H23F4 9O (MW, 553.51), LCMS (EI)m/e 554.1 (M ⁺ + H).

Example 8. 2-(3-(4-(7H-Pyrrolo[2,3-i/]pyrimidin-4-yl)-lH-pyrazol-l-yl)- l-(l-(3- fluoro-2-(trifluoromethyl)isonicotinoyl)piperidin-4-yl)azeti din-3-yl)acetonitrile a

C26H23F4 9O crude salt

Mol. Wt: 553.51 CazH^NgOs

Mol. Wt: 699.66

Stepl. 2-(3-(4-(7H-Pyrrolo[2,3-d]pyrimidin-4-yl)-lH-pyrazol-l-yl)-l -(l-(3-fluoro-2' (trifluoromethyl)isonicotinoyl)piperidin-4-yl)azetidin-3-yl) acetonitrile adipate crude salt (24)

The process of making compound 22 in Example 7 was followed, except that the final organic phase was concentrated by vacuum distillation to the minimum volume to afford crude compound 22, which was not isolated but was directly used in subsequent adipate salt formation process. To the concentrated residue which containing crude compound 22 was added methanol (200 mL) at room temperature. The mixture was the concentrated by vacuum distillation to a minimum volume. The residue was then added methanol (75 mL) and the resulting solution was heated to reflux for 2 hours. Methyl isobutyl ketone (MIB , 75 mL) was added to the solution and the resulting mixture was distilled under vacuum to about 30 mL while the internal temperature was kept at 40 - 50 °C. Methanol (75 mL) was added and the resulting mixture was heated to reflux for 2 hours. To the solution was added MIBK (75 mL). The mixture was distilled again under vacuum to about 30 mL while the internal temperature was kept at 40 - 50 °C. To the solution was added a solution of adipic acid (23, 2.15 g, 14.77 mmol) in methanol (75 mL). The resultant solution was then heated to reflux for 2 hours. MIBK (75 mL) was added. The mixture was distilled under vacuum to about 60 mL while the internal temperature was kept at 40 - 50 °C. Heating was stopped and heptane (52.5 mL) was added over 1 - 2 hours. The resultant mixture was stirred at 20 ± 5 °C for 3 - 4 hours. The white precipitates were collected by filtration, and the filter cake was washed with heptane (2 x 15 mL). The solid was dried on the filter under nitrogen with a pulling vacuum at 20 ± 5 °C for 12 hours to provide compound 24 (crude adipate salt, 8.98 g, 12.84 mmol., 95.0%). For 24: Ή NMR (400 MHz, (CD ₃ ) ₂ SO) δ 12.16 (s, 1 H), 12.05 (brs, 2H), 8.85 (s, 1 H), 8.72 (s, 1H), 8.69 (d, 7 = 4.7 Hz, 1H), 8.45 (s, 1 H), 7.93 (t, 7= 4.7 Hz, 1 H), 7.63 (dd, J= 3.6, 2.3 Hz, 1 H), 7.09 (dd, 7= 3.6, 1.7 Hz, 1H), 8 4.1 1 (dt, 7= 1 1.0, 4.4 Hz, 1 H), 3.77 (d, 7= 7.8 Hz, 2H), 3.60 (t, 7= 7.8 Hz, 2H), 3.58 (s, 2H), 3.44 (dt, 7= 14.4, 4.6 Hz, 1 H), 3.28 (t, 7= 10.4 Hz, 1 H), 3.09 (ddd, 7= 13.2, 9.6, 3.2 Hz, 1 H), 2.58 (tt, 7 = 8.6, 3.5 Hz, 1 H), 2.28 - 2.17 (m, 4H), 1.83 - 1.74 (m, 1 H), 1.67 (d, 7= 1 1.0 Hz, 1 H), 1.59 - 1.46 (m, 4H), 1.37 - 1.21 (m, 2H) ppm; ^,3 C NMR (101 MHz, (CD ₃ ) ₂ SO) δ 174.38, 160.29, (153.52, 150.87), 152.20, 150.94, 149.63, (146.30, 146.25), 139.48, (134.79, 134.62), (135.08, 134.97, 134.74, 134.62, 134.38, 134.28, 134.04, 133.93), 129.21 , 127.62, 126.84, 122.05, (124.75, 122.02, 1 19.29, 1 16.54), 1 17.39, 1 13.01 , 99.99, 61.47, 60.50, 57.06, 44.24, 33.42, 30.70, 28.63, 27.89, 27.20, 24.07 ppm; C32H33F4N9O5 (Mol. Wt: 699.66; 24: C26H23F N9O, MW 553.51 ), LCMS (EI) mle 554.0 (M ⁺ + H). Step 2. 2-(3-(4-(7H-Pyrrolo[2,3-d]pyrimidin-4-yl)-lH^yrazol-l-yl)-l- (l-(3-fluoro-2- (trifluoromethyl)isonicotinoyl)piperidin-4-yl)azetidin-3-yl) acetonitrile adipate (25) In a 100 L dried reactor equipped with a mechanical stirrer, a thermocouple, an addition funnel and a nitrogen inlet was added compound 24 (3.40 kg, 4.86 mol) and acetone (23.8 L). The resulting white turbid was heated to 55 - 60 °C to provide a clear solution. The resultant solution was filtered through an in-line filter to another 100 L reactor. Heptane (23.8 L) was filtered through an in-line filter to a separated 50 L reactor. The filtered heptane was then charged to the acetone solution in the 100 L reactor at a rate while the internal temperature was kept at 55 - 60 °C. The reaction mixture in the 100 L reactor was then cooled to 20 ± 5 °C and stirred at 20 ± 5 °C for 16 hours. The white precipitates were collected by filtration and the cake was washed with heptane (2 x 5.1 L) and dried on the filter under nitrogen with a pulling vacuum. The solid was further dried in a vacuum oven at 55 - 65 °C with nitrogen purge to provide compound 25 (3.1 1 kg, 92.2%) as white to off-white powder. For 25: Ή NMR (400 MHz, (CD ₃ ) ₂ SO) δ 12.16 (s, 1 H), 12.05 (brs, 2H), 8.85 (s, 1 H), 8.72 (s, 1H), 8.69 (d, J = 4.7 Hz, 1 H), 8.45 (s, 1 H), 7.93 (t, J= 4.7 Hz, 1H), 7.63 (dd, J = 3.6, 2.3 Hz, 1 H), 7.09 (dd, J = 3.6, 1.7 Hz, 1 H), δ 4.1 1 (dt, J= 1 1.0, 4.4 Hz, l H), 3.77 (d, J= 7.8 Hz, 2H), 3.60 (t, J= 7.8 Hz, 2H), 3.58 (s, 2H), 3.44 (dt, J= 14.4, 4.6 Hz, 1 H), 3.28 (t, J= 10.4 Hz, 1H), 3.09 (ddd, J= 13.2, 9.6, 3.2 Hz, 1H), 2.58 (tt, J= 8.6, 3.5 Hz, 1 H), 2.28 - 2.17 (m, 4H), 1.83 - 1.74 (m, 1 H), 1.67 (d, J= 1 1.0 Hz, 1 H), 1.59 - 1.46 (m, 4H), 1.37 - 1.21 (m, 2H) ppm; ¹³ C NMR (101 MHz, (CD ₃ ) ₂ SO) δ 174.38, 160.29, (153.52, 150.87), 152.20, 150.94, 149.63, (146.30, 146.25), 139.48, (134.79, 134.62), (135.08, 134.97, 134.74, 134.62, 134.38, 134.28, 134.04, 133.93), 129.21 , 127.62, 126.84, 122.05, (124.75, 122.02, 1 19.29, 1 16.54), 1 17.39, 1 13.01 , 99.99, 61.47, 60.50, 57.06, 44.24, 33.42, 30.70, 28.63, 27.89, 27.20, 24.07 ppm;

C ₃ 2H33F _{4 9} 0 ₅ ( Mol. Wt: 699.66; free base: C26H23F4 9O (MW, 553.51 ), LCMS (EI) mle 554.0 (M ⁺ + H).

Example A: In vitro JAK Kinase Assay

The compound of Formula I herein was tested for inhibitory activity of JAK targets according to the following in vitro assay described in Park et ai, Analytical Biochemistry 1999, 269, 94-104. The catalytic domains of human JA 1 (a.a. 837- 1 142) and JAK2 (a.a. 828-1 132) with an N-terminal His tag were expressed using baculovirus in insect cells and purified. The catalytic activity of JAK1 and JAK.2 was assayed by measuring the phosphorylation of a biotinylated peptide. The

phosphorylated peptide was detected by homogenous time resolved fluorescence (HTRF). IC50S of compounds were measured for each kinase in the 40 microL reactions that contain the enzyme, ATP and 500 nM peptide in 50 mM Tris (pH 7.8) buffer with 100 mM NaCl, 5 mM DTT, and 0.1 mg/mL (0.01 %) BSA. For the 1 mM IC50 measurements, ATP concentration in the reactions was 1 mM. Reactions were carried out at room temperature for 1 hr and then stopped with 20 μL· 45 mM EDTA, 300 nM SA-APC, 6 nM Eu-Py20 in assay buffer (Perkin Elmer, Boston, MA).

Binding to the Europium labeled antibody took place for 40 minutes and HTRF signal was measured on a Fusion plate reader (Perkin Elmer, Boston, MA). The compound of Example 1 and the adipic acid salt had an IC50 at JA 1 of < 5 nM (measured at 1 mM ATP) with a JAK2/JAK1 ratio of > 10 (measured at 1 mM ATP).

Example B: Cellular Assays

Cancer cell lines dependent on cytokines and hence JAK/STAT signal transduction, for growth, can be plated at 6000 cells per well (96 well plate format) in RPMI 1640, 10% FBS, and 1 nG/mL of appropriate cytokine. Compounds can be added to the cells in DMSO/media (final concentration 0.2% DMSO) and incubated for 72 hours at 37 °C, 5% C0 ₂ . The effect of compound on cell viability is assessed using the CellTiter-Glo Luminescent Cell Viability Assay (Promega) followed by TopCount (Perkin Elmer, Boston, MA) quantitation. Potential off-target effects of compounds are measured in parallel using a non-JAK driven cell line with the same assay readout. All experiments are typically performed in duplicate.

The above cell lines can also be used to examine the effects of compounds on phosphorylation of JA kinases or potential downstream substrates such as STAT proteins, Akt, Shp2, or Erk. These experiments can be performed following an overnight cytokine starvation, followed by a brief preincubation with compound (2 hours or less) and cytokine stimulation of approximately 1 hour or less. Proteins are then extracted from cells and analyzed by techniques familiar to those schooled in the art including Western blotting or ELISAs using antibodies that can differentiate between phosphorylated and total protein. These experiments can utilize normal or cancer cells to investigate the activity of compounds on tumor cell survival biology or on mediators of inflammatory disease. For example, with regards to the latter, cytokines such as IL-6, IL-12, IL-23, or IFN can be used to stimulate JA activation resulting in phosphorylation of STAT protein(s) and potentially in transcriptional profiles (assessed by array or qPCR technology) or production and/or secretion of proteins, such as IL- 17. The ability of compounds to inhibit these cytokine mediated effects can be measured using techniques common to those schooled in the art.

Compounds herein can also be tested in cellular models designed to evaluate their potency and activity against mutant JAKs, for example, the JA 2V617F mutation found in myeloid proliferative disorders. These experiments often utilize cytokine dependent cells of hematological lineage (e.g. BaF/3) into which the wild- type or mutant JAK kinases are ectopically expressed (James, C, et al. Nature

434: 1 144-1 148; Staerk, J., et al. JBC 280:41893-41899). Endpoints include the effects of compounds on cell survival, proliferation, and phosphorylated JAK, STAT, Akt, or Erk proteins.

Certain compounds herein can be evaluated for their activity inhibiting T-cell proliferation. Such as assay can be considered a second cytokine (i.e. JAK) driven proliferation assay and also a simplistic assay of immune suppression or inhibition of immune activation. The following is a brief outline of how such experiments can be performed. Peripheral blood mononuclear cells (PBMCs) are prepared from human whole blood samples using Ficoll Hypaque separation method and T-cells (fraction 2000) can be obtained from PBMCs by elutriation. Freshly isolated human T-cells can be maintained in culture medium (RPMI 1640 supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin) at a density of 2 x 10 ⁶ cells/ml at 37 °C for up to 2 days. For IL-2 stimulated cell proliferation analysis, T-cells are first treated with Phytohemagglutinin (PHA) at a final concentration of 10 μg/mL for 72h. After washing once with PBS, 6000 cells/well are plated in 96-well plates and treated with compounds at different concentrations in the culture medium in the presence of 100 U/mL human IL-2 (ProSpec-Tany TechnoGene; Rehovot, Israel). The plates are incubated at 37 °C for 72h and the proliferation index is assessed using CellTiter-Glo Luminescent reagents following the manufactory suggested protocol (Promega; Madison, Wl).

Example C: In vivo anti-tumor efficacy

Compounds herein can be evaluated in human tumor xenograft models in immune compromised mice. For example, a tumorigenic variant of the ΓΝΑ-6 plasmacytoma cell line can be used to inoculate SC1D mice subcutaneously (Burger, R., et al. Hematol J. 2:42-53, 2001 ). Tumor bearing animals can then be randomized into drug or vehicle treatment groups and different doses of compounds can be administered by any number of the usual routes including oral, i.p., or continuous infusion using implantable pumps. Tumor growth is followed over time using calipers. Further, tumor samples can be harvested at any time after the initiation of treatment for analysis as described above (Example B) to evaluate compound effects on JA activity and downstream signaling pathways. In addition, selectivity of the compound(s) can be assessed using xenograft tumor models that are driven by other know kinases (e.g. Bcr-Abl) such as the K562 tumor model.

Example D: Murine Skin Contact Delayed Hypersensitivity Response Test

Compounds herein can also be tested for their efficacies (of inhibiting JAK targets) in the T-cell driven murine delayed hypersensitivity test model. The murine skin contact delayed-type hypersensitivity (DTH) response is considered to be a valid model of clinical contact dermatitis, and other T-lymphocyte mediated immune disorders of the skin, such as psoriasis (Immunol Today. 1998 Jan; 19(l ):37-44). Murine DTH shares multiple characteristics with psoriasis, including the immune infiltrate, the accompanying increase in inflammatory cytokines, and keratinocyte hyperproliferation. Furthermore, many classes of agents that are efficacious in treating psoriasis in the clinic are also effective inhibitors of the DTH response in mice (Agents Actions. 1993 Jan;38( l -2): 1 16-21 ).

On Day 0 and 1 , Balb/c mice are sensitized with a topical application, to their shaved abdomen with the antigen 2,4,dinitro-fluorobenzene (DNFB). On day 5, ears are measured for thickness using an engineer's micrometer. This measurement is recorded and used as a baseline. Both of the animals' ears are then challenged by a topical application of DNFB in a total of 20 (10 μL· on the internal pinna and 10 μΐ- on the external pinna) at a concentration of 0.2%. Twenty-four to seventy-two hours after the challenge, ears are measured again. Treatment with the test compounds is given throughout the sensitization and challenge phases (day -1 to day 7) or prior to and throughout the challenge phase (usually afternoon of day 4 to day 7). Treatment of the test compounds (in different concentration) is administered either systemicaily or topically (topical application of the treatment to the ears). Efficacies of the test compounds are indicated by a reduction in ear swelling comparing to the situation without the treatment. Compounds causing a reduction of 20% or more were considered efficacious. In some experiments, the mice are challenged but not sensitized (negative control).

The inhibitive effect (inhibiting activation of the JAK-STAT pathways) of the test compounds can be confirmed by immunohistochemical analysis. Activation of the JAK-STAT pathway(s) results in the formation and translocation of functional transcription factors. Further, the influx of immune cells and the increased proliferation of keratinocytes should also provide unique expression profile changes in the ear that can be investigated and quantified. Formalin fixed and paraffin embedded ear sections (harvested after the challenge phase in the DTH model) are subjected to immunohistochemical analysis using an antibody that specifically interacts with phosphorylated STAT3 (clone 58E12, Cell Signaling Technologies). The mouse ears are treated with test compounds, vehicle, or dexamethasone (a clinically efficacious treatment for psoriasis), or without any treatment, in the DTH model for comparisons. Test compounds and the dexamethasone can produce similar transcriptional changes both qualitatively and quantitatively, and both the test compounds and dexamethasone can reduce the number of infiltrating cells. Both systemicaily and topical administration of the test compounds can produce inhibitive effects, i.e., reduction in the number of infiltrating cells and inhibition of the transcriptional changes. Example E: In vivo anti-inflammatory activity

Compounds herein can be evaluated in rodent or non-rodent models designed to replicate a single or complex inflammation response. For instance, rodent models of arthritis can be used to evaluate the therapeutic potential of compounds dosed preventatively or therapeutically. These models include but are not limited to mouse or rat collagen-induced arthritis, rat adjuvant-induced arthritis, and collagen antibody- induced arthritis. Autoimmune diseases including, but not limited to, multiple sclerosis, type I-diabetes mellitus, uveoretinitis, thyroditis, myasthenia gravis, immunoglobulin nephropathies, myocarditis, airway sensitization (asthma), lupus, or colitis may also be used to evaluate the therapeutic potential of compounds herein. These models are well established in the research community and are familiar to those schooled in the art (Current Protocols in Immunology, Vol 3., Coligan, J.E. et al, Wiley Press.; Methods in Molecular Biology: Vol. 225, Inflammation Protocols., Winyard, P.G. and Willoughby, D.A., Humana Press, 2003.).

Example F: Animal Models for the Treatment of Dry Eye, Uveitis, and

Conjunctivitis

Agents may be evaluated in one or more preclinical models of dry eye known to those schooled in the art including, but not limited to, the rabbit concanavalin A (ConA) lacrimal gland model, the scopolamine mouse model (subcutaneous or transdermal), the Botulinumn mouse lacrimal gland model, or any of a number of spontaneous rodent auto-immune models that result in ocular gland dysfunction (e.g. NOD-SCID, MRL/lpr, or NZB/NZW) (Barabino et al., Experimental Eye Research 2004, 79, 613-621 and Schrader et al., Developmental Opthalmology, Karger 2008, 41 , 298-312, each of which is incorporated herein by reference in its entirety).

Endpoints in these models may include histopathology of the ocular glands and eye (cornea, etc.) and possibly the classic Schirmer test or modified versions thereof (Barabino et al.) which measure tear production. Activity may be assessed by dosing via multiple routes of administration (e.g. systemic or topical) which may begin prior to or after measurable disease exists.

Agents may be evaluated in one or more preclinical models of uveitis known to those schooled in the art. These include, but are not limited to, models of experimental autoimmune uveitis (EAU) and endotoxin induced uveitis (EIU). EAU experiements may be performed in the rabbit, rat, or mouse and may involve passive or activate immunization. For instance, any of a number or retinal antigens may be used to sensitize animals to a relevant immunogen after which animals may be challenged ocuarly with the same antigen. The EIU model is more acute and involves local or systemic administration of lipopolysaccaride at sublethal doses. Endpoints for both the EIU and EAU models may include fundoscopic exam, histopathology amongst others. These models are reviewed by Smith et al. (Immunology and Cell Biology 1998, 76, 497-512, which is incorporated herein by reference in its entirety). Activity is assessed by dosing via multiple routes of administration (e.g. systemic or topical) which may begin prior to or after measurable disease exists. Some models listed above may also develop scleritis/episcleritis, chorioditis, cyclitis, or iritis and are therefore useful in investigating the potential activity of compounds for the therapeutic treatment of these diseases.

Agents may also be evaluated in one or more preclinical models of conjunctivitis known those schooled in the art. These include, but are not limited to, rodent models utilizing guinea-pig, rat, or mouse. The guinea-pig models include those utilizing active or passive immunization and/or immune challenge protocols with antigens such as ovalbumin or ragweed (reviewed in Groneberg, D.A., et al., Allergy 2003, 58, 1 101-1 1 13, which is incorporated herein by reference in its entirety). Rat and mouse models are similar in general design to those in the guinea- pig (also reviewed by Groneberg). Activity may be assessed by dosing via multiple routes of administration (e.g. systemic or topical) which may begin prior to or after measurable disease exists. Endpoints for such studies may include, for example, histological, immunological, biochemical, or molecular analysis of ocular tissues such as the conjunctiva. Example G: In vivo protection of bone

Compounds may be evaluated in various preclinical models of osteopenia, osteoporosis, or bone resorption known to those schooled in the art. For example, ovariectomized rodents may be used to evaluate the ability of compounds to affect signs and markers of bone remodeling and/or density (W.S.S. Jee and W. Yao, J Musculoskel. Nueron. Interact., 2001 , 1 (3), 193-207, which is incorporated herein by reference in its entirety). Alternatively, bone density and architecture may be evaluated in control or compound treated rodents in models of therapy (e.g. glucocorticoid) induced osteopenia (Yao, et al. Arthritis and Rheumatism, 2008, 58(6), 3485-3497; and id. 58(1 1 ), 1674-1686, both of which are incorporated herein by reference in its entirety). In addition, the effects of compounds on bone resorption and density may be evaluable in _. the rodent models of arthritis discussed above (Example E). Endpoints for all these models may vary but often include histological and radiological assessments as well as immunohisotology and appropriate biochemical markers of bone remodeling.

A number of embodiments of the invention have been described.

Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.