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1. WO2020014605 - INHIBITEURS DE L'HISTONE DÉSACÉTYLASE

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INHIBITORS OF HISTONE DEACETYLASE

RELATED APPLICATIONS

[0001] This application claims the benefit of priority to U.S. Provisional Application No. 62/697498, filed July 13, 2018, the entire contents of which are incorporated herein by reference.

BACKGROUND

[0002] Inhibitors of histone deacetylases (HD AC) have been shown to modulate transcription and to induce cell growth arrest, differentiation and apoptosis. HD AC inhibitors also enhance the cytotoxic effects of therapeutic agents used in cancer treatment, including radiation and chemotherapeutic drugs. Marks, P., Rifkind, R. A., Richon, V. M., Breslow, R., Miller, T., Kelly, W. K. Histone deacetylases and cancer: causes and therapies. Nat Rev Cancer, 1, 194-202, (2001); and Marks, P. A., Richon, V. M., Miller, T., Kelly, W. K.

Histone deacetylase inhibitors. Adv Cancer Res, 91, 137-168, (2004). Moreover, recent evidence indicates that transcriptional dysregulation may contribute to the molecular pathogenesis of certain neurodegenerative disorders, such as Huntington's disease, spinal muscular atrophy, amyotropic lateral sclerosis, and ischemia. Langley, B., Gensert, J. M., Beal, M. F., Ratan, R. R. Remodeling chromatin and stress resistance in the central nervous system: histone deacetylase inhibitors as novel and broadly effective neuroprotective agents. Curr Drug Targets CNS Neurol Disord, 4, 41-50, (2005). A recent review has summarized the evidence that aberrant histone acetyltransferase (HAT) and histone deacetylases (HD AC) activity may represent a common underlying mechanism contributing to neurodegeneration. Moreover, using a mouse model of depression, Nestler has recently highlighted the therapeutic potential of histone deacetylation inhibitors (HDAC5) in depression. Tsankova,

N. M., Berton, O., Renthal, W., Kumar, A., Neve, R. L., Nestler, E. J. Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action. Nat

Neurosci, 9, 519-525, (2006).

[0003] There are 18 known human histone deacetylases, grouped into four classes based on the structure of their accessory domains. Class I includes HDAC1, HDAC2, HDAC3, and HD AC 8 and has homology to yeast RPD3. HDAC4, HDAC5, HDAC7, and HDAC9 belong to class Ila and have homology to yeast. HDAC6 and HD AC 10 contain two catalytic sites and are classified as class lib. Class III (the sirtuins) includes SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and SIRT7. HDAC11 is another recently identified member of the HD AC

family and has conserved residues in its catalytic center that are shared by both class I and class II deacetylases and is sometimes placed in class IV.

[0004] In contrast, HDACs have been shown to be powerful negative regulators of long term memory processes. Nonspecific HD AC inhibitors enhance synaptic plasticity as well as long-term memory (Levenson et al., 2004, J. Biol. Chem. 279:40545-40559; Lattal et al.,

2007, Behav Neurosci 121:1125-1131; Vecsey et al., 2007, J. Neurosci 27:6128; Bredy,

2008, Learn Mem 15:460-467; Guan et al., 2009, Nature 459:55-60; Malvaez et al., 2010, Biol. Psychiatry 67:36-43; Roozendaal et al., 2010, J. Neurosci. 30:5037-5046). For example, HD AC inhibition can transform a learning event that does not lead to long-term memory into a learning event that does result in significant long-term memory (Stefanko et al., 2009, Proc. Natl. Acad. Sci. USA 106:9447-9452). Furthermore, HDAC inhibition can also generate a form of long-term memory that persists beyond the point at which normal memory fails. HDAC inhibitors have been shown to ameliorate cognitive deficits in genetic models of Alzheimer’s disease (Fischer et al., 2007, Nature 447:178-182; Kilgore et al., 2010,

Neuropsychopharmacology 35:870-880). These demonstrations suggest that modulating memory via HDAC inhibition has considerable therapeutic potential for many memory and cognitive disorders.

[0005] Currently, the role of individual HDACs in long-term memory has been explored in two recent studies. Kilgore et al. 2010, Neuropsychopharmacology 35:870-880 revealed that nonspecific HDAC inhibitors, such as sodium butyrate, inhibit class I HDACs (HDAC1, HDAC2, HDAC3, HDAC8) with little effect on the class Ila HDAC family members (HDAC4, HDAC5, HDAC7, HDAC9). This suggests that inhibition of class I HDACs may be critical for the enhancement of cognition observed in many studies. Indeed, forebrain and neuron specific over expression of HDAC2, but not HDAC1, decreased dendritic spine density, synaptic density, synaptic plasticity and memory formation (Guan et al., 2009, Nature, 459:55-60). In contrast, HDAC2 knockout mice exhibited increased synaptic density, increased synaptic plasticity and increased dendritic density in neurons. These HDAC2 deficient mice also exhibited enhanced learning and memory in a battery of learning behavioral paradigms. This work demonstrates that HDAC2 is a key regulator of

synaptogenesis and synaptic plasticity. Additionally, Guan et al. showed that chronic treatment of mice with SAHA (an HDAC 1,2, 3, 6, 8 inhibitor) reproduced the effects seen in the HDAC2 deficient mice and recused the cognitive impairment in the HDAC2

overexpression mice.

[0006] The inhibition of the HDAC2 (selectively or in combination with inhibition of other class I HDACs) is an attractive therapeutic target. Such inhibition has the potential for enhancing cognition and facilitating the learning process through increasing synaptic and dendritic density in neuronal cell populations. In addition, inhibition of HDAC2 may also be therapeutically useful in treating a wide variety of other diseases and disorders.

SUMMARY

[0007] Provided herein are compounds of the Formula I:


and pharmaceutically acceptable salts and compositions thereof, wherein X, R 1 , R2 , R 3 , R 4 , q, and ring A are as described herein. The disclosed compounds and compositions modulate histone deacetylases (HD AC) (see e.g., Table 2 and 3), and are useful in a variety of therapeutic applications such as, for example, in treating neurological disorders, memory or cognitive function disorders or impairments, extinction learning disorders, fungal diseases or infections, inflammatory diseases, hematological diseases, neoplastic diseases, psychiatric disorders, and memory loss.

[0008] Certain compounds described herein have an increase in inhibitory activity in a cell lysate assay over direct comparators. For example, it was found that introducing aromatic substitutions at the 3-positon of the pyrrolidine (e.g., the phenyl and heteroaryl variables for R1) led to a significant increase in potency in an HDAC2 SH-SY5Y cell lysate assay when compared with counterparts possessing non-aromatic substitution at the pyrrolidine-3-position. See e.g., Table 4, where Compounds 19 and 20, each having an aromatic pyrimidinyl at R1, have greater potency then the non-cyclic, non-aromatic, Comparators A-C.

DETAILED DESCRIPTION

1. General Description of Compounds

[0009] Provided herein is a compound of the Formula I:


or a pharmaceutically acceptable salt thereof, wherein

ring A is phenyl or thiophenyl;

X is (CRaRb)t, O or NR5;

q and t are each independently 0, 1, 2, or 3;

R1 is phenyl or heteroaryl, each of which are optionally substituted with 1 to 3 groups selected from Rc;

R2 is halo, (Ci-C4)alkyl, (Ci-C4)alkoxy, or OH;

R is hydrogen or halo;

R4 is halo when ring A is phenyl and R4 is hydrogen when ring A is thiopheneyl;

R5 is hydrogen, (Ci-C4)alkyl, or (Ci-C4)alkylO(Ci-C4)alkyl;

Ra and Rb are each independently hydrogen, (Ci-C4)alkyl, halo(Ci-C4)alkyl, (Ci-C4)alkoxy, or halo; and

Rc is halo, (Ci-C4)alkyl, halo(Ci-C4)alkyl, (Ci-C4)alkoxy, halo(Ci-C4)alkoxy, (Ci-C4)alkylO(Ci-C4)alkyl, (Ci-C4)alkylNH(Ci-C4)alkyl, (Ci-C4)alkylN((Ci-C4)alkyl)2, -( -C4)alkylheteroaryl, or -(Ci-C4)alkylheterocyclyl, wherein said heteroaryl and heterocyclyl are each optionally and independently substituted with 1 to 3 groups selected from (Ci-C4)alkyl, halo(Ci-C4)alkyl, (Ci-C4)alkoxy, and halo.

2. Definitions

[0010] When used in connection to describe a chemical group that may have multiple points of attachment, a hyphen (-) designates the point of attachment of that group to the variable to which it is defined. For example, -(Ci-C4)alkylheteroaryl and -(Ci-C4)alkylheterocyclyl means that the point of attachment occurs on the (Ci-C4)alkyl residue.

[0011] The terms“halo” and“halogen” refer to an atom selected from fluorine

(fluoro, -F), chlorine (chloro, -Cl), bromine (bromo, -Br), and iodine (iodo, -I).

[0012] The term“alkyl” when used alone or as part of a larger moiety, such as “haloalkyl”, means a saturated straight-chain or branched monovalent hydrocarbon radical. Unless otherwise specified, an alkyl group typically has 1-6 carbon atoms, i.e., (Ci-C6)alkyl. [0013] The term“haloalkyl” includes mono, poly, and perhaloalkyl groups where the halogens are independently selected from fluorine, chlorine, bromine, and iodine.

[0014] “Alkoxy” means an alkyl radical attached through an oxygen linking atom, represented by -O-alkyl. For example,“(Ci-C4)alkoxy” includes methoxy, ethoxy, proproxy, and butoxy.

[0015] “Haloalkoxy” is a haloalkyl group which is attached to another moiety via an oxygen atom such as, e.g., but are not limited to -OCHF2 or -OCF3.

[0016] The term“heteroaryl” refers to a 5- to l2-membered (e.g., 5- or 6-membered) aromatic radical containing 1-4 heteroatoms selected from N, O, and S. A heteroaryl group may be mono- or bi-cyclic. Monocyclic heteroaryl includes, for example, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, etc. Bi-cyclic heteroaryls include groups in which a monocyclic heteroaryl ring is fused to one or more aryl or heteroaryl rings. Nonlimiting examples include indolyl, imidazopyridinyl, benzooxazolyl, benzooxodiazolyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, quinazolinyl, quinoxalinyl, pyrrolopyridinyl, pyrrolopyrimidinyl, pyrazolopyridinyl, thienopyridinyl, thienopyrimidinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. It will be understood that when specified, optional substituents on a heteroaryl group may be present on any substitutable position and, include, e.g., the position at which the heteroaryl is attached.

[0017] The term“heterocyclyl” means a 4- to l2-membered (e.g., 4- to 6-membered) saturated or partially unsaturated heterocyclic ring containing 1 to 4 heteroatoms

independently selected from N, O, and S. A heterocyclyl ring can be mononcyclic, bicyclic (e.g., a bridged, fused, or spiro bicyclic ring), or tricyclic. A heterocyclyl ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure.

Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, terahydropyranyl, pyrrolidinyl, pyridinonyl, pyrrolidonyl, piperidinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, morpholinyl, dihydrofuranyl, dihydropyranyl, dihydropyridinyl, tetrahydropyridinyl, dihydropyrimidinyl, oxetanyl, azetidinyl and tetrahydropyrimidinyl. The term“heterocyclyl” also includes, e.g., unsaturated heterocyclic radicals fused to another unsaturated heterocyclic radical or aryl or heteroaryl ring, such as for example, tetrahydronaphthyridine, indolinone,

dihydropyrrolotriazole, imidazopyrimidine, quinolinone, dioxaspirodecane. It will also be understood that when specified, optional substituents on a heterocyclyl group may be present

on any substitutable position and, include, e.g., the position at which the heterocyclyl is attached (e.g., in the case of an optionally substituted heterocyclyl or heterocyclyl which is optionally substituted).

[0018] The term“fused” refers to two rings that share two adjacent ring atoms with one another.

[0019] The term“spiro” refers to two rings that shares one ring atom (e.g., carbon).

[0020] The term“bridged” refers to two rings that share three ring atoms with one another.

[0021] Enantiomers are one type of stereoisomer that can arise from a chiral center or chiral centers. Enantiomers are pairs of stereoisomers whose mirror images are not superimposable, most commonly because they contain an asymmetrically substituted carbon atom or carbon atoms that acts as a chiral center(s).“R” and“S” represent the absolute configuration of substituents around one or more chiral carbon atoms, where each chiral center is assigned the prefix“R” or“S” according to whether the chiral center configuration is right- (clockwise rotation) or left-handed (counter clockwise rotation). If the turn is clockwise or right-handed about a chiral carbon, the designation is“R” for rectus. If the turn is counter clockwise or left-handed about a chiral carbon, the designation is“S” for sinister.

[0022] When a single enantiomer is named or depicted by structure, the depicted or named enantiomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight optically pure. Percent optical purity by weight is the ratio of the weight of the enantiomer over the weight of the enantiomer plus the weight of its optical isomer.

[0023] When a compound is depicted structurally without indicating the stereochemistry at a chiral center, the structure includes either configuration at the chiral center or, alternatively, any mixture of configurations at the chiral center stereoisomers.

[0024] “Racemate” or“racemic mixture” means a compound of equimolar quantities of two enantiomers, wherein such mixtures exhibit no optical activity, i.e., they do not rotate the plane of polarized light.

[0025] As used herein the terms“subject” and“patient” may be used interchangeably, and means a mammal in need of treatment, e.g., companion animals (e.g., dogs, cats, and the like), farm animals (e.g., cows, pigs, horses, sheep, goats and the like) and laboratory animals (e.g., rats, mice, guinea pigs and the like). Typically, the subject is a human in need of treatment.

[0026] Pharmaceutically acceptable salts as well as the neutral forms of the compounds described herein are included. For use in medicines, the salts of the compounds refer to non- toxic“pharmaceutically acceptable salts.” Pharmaceutically acceptable salt forms include pharmaceutically acceptable acidic/anionic or basic/cationic salts. Pharmaceutically acceptable basic/cationic salts include, the sodium, potassium, calcium, magnesium, diethanolamine, n-methyl-D-glucamine, L-lysine, L-arginine, ammonium, ethanolamine, piperazine and triethanolamine salts. Pharmaceutically acceptable acidic/anionic salts include, e.g., the acetate, benzenesulfonate, benzoate, bicarbonate, bitartrate, carbonate, citrate, dihydrochloride, gluconate, glutamate, glycollylarsanilate, hexylresorcinate, hydrobromide, hydrochloride, malate, maleate, malonate, mesylate, nitrate, salicylate, stearate, succinate, sulfate, tartrate, and tosylate.

[0027] The term“pharmaceutically acceptable carrier” refers to a non-toxic carrier, adjuvant, or vehicle that does not destroy the pharmacological activity of the compound with which it is formulated. Pharmaceutically acceptable carriers, adjuvants or vehicles that may be used in the compositions described herein include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat.

[0028] The terms“treatment,”“treat,” and“treating” refer to reversing, alleviating, reducing the likelihood of developing, or inhibiting the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed, i.e., therapeutic treatment. In other embodiments, treatment may be administered in the absence of symptoms. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors), i.e., prophylactic treatment. Treatment may also be continued after symptoms have resolved, for example to prevent or delay their recurrence.

[0029] The term“effective amount” or“therapeutically effective amount” includes an amount of a compound described herein that will elicit a biological or medical response of a subject e.g., between 0.01 - 100 mg/kg body weight/day of the provided compound, such as e.g., 0.1 - 100 mg/kg body weight/day.

5. Description of Exemplary Compounds

[0030] In a first embodiment, provided herein is a compound of the Formula I:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I.

[0031] In a second embodiment, provided herein is a compound of the Formula II:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I.

[0032] In a third embodiment, provided herein is a compound of the Formula III or Ilia:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I.

[0033] In a fourth embodiment, q in any one of Formula I, II, III, or Ilia is 0 or 1; and

2

R is halo when q is 1, wherein the remaining variables are as described above for Formula I. [0034] In a fifth embodiment, the compound of Formula I is of the Formula IV or IVa:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I.

[0035] In a sixth embodiment, R in any one of Formula I, II, III, Ilia, IV, or IVa is halo, wherein the remaining variables are as described above for Formula I, or the fourth embodiment. Alternatively, R in any one of Formula I, II, III, Ilia, IV, or IVa is fluoro, wherein the remaining variables are as described above for Formula I, or the fourth embodiment. In another alternative, R in any one of Formula I, II, III, Ilia, IV, or IVa is hydrogen, wherein the remaining variables are as described above for Formula I, or the fourth embodiment.

[0036] In a seventh embodiment, R4 in any one of Formula I, II, III, Ilia, IV, or IVa is fluoro, wherein the remaining variables are as described above for Formula I, or the fourth or sixth embodiment.

[0037] In an eighth embodiment, X in any one of Formula I, II, III, Ilia, IV, or IVa is (CRaRb)t, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, or seventh embodiment.

[0038] In an ninth embodiment, Ra and Rb in any one of Formula I, II, III, Ilia, IV, or IVa are each hydrogen, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, or eighth embodiment.

[0039] In a tenth embodiment, provided herein is a compound of the Formula V or Va:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I, or the fourth, sixth, or seventh embodiment.

[0040] In an eleventh embodiment, provided herein is a compound of the Formula VI or

Via:


or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I, or the fourth, sixth, seventh, or eighth embodiment.

[0041] In a twelfth embodiment, provided herein is a compound of the Formula VII or

Vila:


(Vila);

or a pharmaceutically acceptable salt thereof, wherein the variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, or ninth embodiment.

[0042] In a thirteenth embodiment, R1 in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is phenyl or 5- to 6-membered monocyclic heteroaryl, each of which is optionally substituted with one or more groups selected from Rc, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, or ninth embodiment. Alternatively, R1 in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is phenyl, pyridinyl, pyrazinyl, pyridazinyl, or pyrimidinyl, each of which is optionally substituted with 1 to 2 groups selected from Rc, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, or ninth embodiment. In another alternative, R1 in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is thiazolyl, thiadiazolyl, imidazolyl, pyrazolyl, or oxazolyl, each of which is optionally substituted with 1 to 2 groups selected from Rc, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, or ninth embodiment.

[0043] In a fourteenth embodiment, Rc in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is halo, (Ci-C4)alkyl, or (Ci-C4)alkylO(Ci-C4)alkyl, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, ninth or thirteenth embodiment. Alternatively, Rc in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is fluoro, methyl, or CH2OCH3, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, ninth or thirteenth embodiment. In another alternative, Rc in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is halo, halo(Ci-C4)alkyl, or (Ci-C4)alkyl, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, ninth or thirteenth embodiment. In another alternative, Rc in any one of Formula I, II, III, Ilia, IV, IVa, V, Va, VI, Via, VII, or Vila is fluoro, methyl, or CHF2, wherein the remaining variables are as described above for Formula I, or the fourth, sixth, seventh, eighth, ninth or thirteenth embodiment.

[0044] In a fifteenth embodiment, provided is a compound as described below in the Exemplification section. Pharmaceutically acceptable salts and free forms of the exemplified compounds are included.

4. Uses, Formulation and Administration

[0045] In some embodiments, the compounds and compositions described herein are useful in treating conditions associated with the activity of HD AC. Such conditions include for example, those described below.

[0046] Recent reports have detailed the importance of histone acetylation in central nervous system (“CNS”) functions such as neuronal differentiation, memory formation, drug addiction, and depression (Citrome, Psychopharmacol. Bull. 2003, 37, Suppl. 2, 74-88;

Johannessen, CNS Drug Rev. 2003, 9, 199-216; Tsankova et ah, 2006, Nat. Neurosci. 9, 519-525). Thus, in one aspect, the provided compounds and compositions may be useful in treating a neurological disorder. Examples of neurological disorders include: (i) chronic neurodegenerative diseases such as familial and sporadic amyotrophic lateral sclerosis (FALS and ALS, respectively), familial and sporadic Parkinson's disease, Huntington's disease, familial and sporadic Alzheimer's disease, multiple sclerosis, muscular dystrophy, olivopontocerebellar atrophy, multiple system atrophy, Wilson’s disease, progressive supranuclear palsy, diffuse Lewy body disease, fronto-temporal lobar degeneration (FTLD), corticodentatonigral degeneration, progressive familial myoclonic epilepsy, strionigral degeneration, torsion dystonia, familial tremor, Down's Syndrome, Gilles de la Tourette syndrome, Hallervorden-Spatz disease, diabetic peripheral neuropathy, dementia pugilistica, AIDS Dementia, age related dementia, age associated memory impairment, and amyloidosis-related neurodegenerative diseases such as those caused by the prion protein (PrP) which is associated with transmissible spongiform encephalopathy (Creutzfeldt- Jakob disease, Gerstmann-Straussler-Scheinker syndrome, scrapie, and kuru), and those caused by excess cystatin C accumulation (hereditary cy statin C angiopathy); and (ii) acute neurodegenerative disorders such as traumatic brain injury (e.g., surgery-related brain injury), cerebral edema, peripheral nerve damage, spinal cord injury, Leigh's disease, Guillain-Barre syndrome, lysosomal storage disorders such as lipofuscinosis, Alper's disease, restless leg syndrome, vertigo as result of CNS degeneration; pathologies arising with chronic alcohol or drug abuse including, for example, the degeneration of neurons in locus coeruleus and cerebellum, drug-induced movement disorders; pathologies arising with aging including degeneration of cerebellar neurons and cortical neurons leading to cognitive and motor impairments; and pathologies arising with chronic amphetamine abuse to including degeneration of basal ganglia neurons leading to motor impairments; pathological changes resulting from focal trauma such as stroke, focal ischemia, vascular insufficiency, hypoxic-ischemic

encephalopathy, hyperglycemia, hypoglycemia or direct trauma; pathologies arising as a negative side-effect of therapeutic drugs and treatments (e.g., degeneration of cingulate and entorhinal cortex neurons in response to anticonvulsant doses of antagonists of the NMDA class of glutamate receptor) and Wemicke-Korsakoff s related dementia. Neurological disorders affecting sensory neurons include Friedreich's ataxia, diabetes, peripheral neuropathy, and retinal neuronal degeneration. Other neurological disorders include nerve injury or trauma associated with spinal cord injury. Neurological disorders of limbic and cortical systems include cerebral amyloidosis, Pick's atrophy, and Rett syndrome. In another aspect, neurological disorders include disorders of mood, such as affective disorders and anxiety; disorders of social behavior, such as character defects and personality disorders; disorders of learning, memory, and intelligence, such as mental retardation and dementia. Thus, in one aspect the disclosed compounds and compositions may be useful in treating schizophrenia, delirium, attention deficit disorder (ADD), schizoaffective disorder,

Alzheimer's disease, Rubinstein-Taybi syndrome, depression, mania, attention deficit disorders, drug addiction, dementia, agitation, apathy, anxiety, psychoses, personality disorders, bipolar disorders, unipolar affective disorder, obsessive-compulsive disorders, eating disorders, post-traumatic stress disorders, irritability, adolescent conduct disorder and disinhibition.

[0047] Transcription is thought to be a key step for long-term memory processes (Alberini, 2009, Physiol. Rev. 89, 121-145). Transcription is promoted by specific chromatin modifications, such as histone acetylation, which modulate histone-DNA interactions (Kouzarides, 2007, Cell, 128:693-705). Modifying enzymes, such as histone

acetyltransferases (HATs) and histone deacetylases (HDACs), regulate the state of acetylation on histone tails. In general, histone acetylation promotes gene expression, whereas histone deacetylation leads to gene silencing. Numerous studies have shown that a potent HAT, cAMP response element-binding protein (CREB)-binding protein (CBP), is necessary for long-lasting forms of synaptic plasticity and long term memory (for review, see Barrett, 2008, Learn Mem 15:460-467). Thus, in one aspect, the provided compounds and compositions may be useful for promoting cognitive function and enhancing learning and memory formation.

[0048] The compounds and compositions described herein may also be used for treating fungal diseases or infections.

[0049] In another aspect, the compounds and compositions described herein may be used for treating inflammatory diseases such as stroke, rheumatoid arthritis, lupus erythematosus, ulcerative colitis and traumatic brain injuries (Leoni et ah, PNAS, 99(5); 2995-3000(2002); Suuronen et al. J. Neurochem. 87; 407-416 (2003) and Drug Discovery Today, 10: 197-204 (2005).

[0050] In yet another aspect, the compounds and compositions described herein may be used for treating a cancer caused by the proliferation of neoplastic cells. Such cancers include e.g., solid tumors, neoplasms, carcinomas, sarcomas, leukemias, lymphomas and the like. In one aspect, cancers that may be treated by the compounds and compositions described herein include, but are not limited to: cardiac cancer, lung cancer, gastrointestinal cancer, genitourinary tract cancer, liver cancer, nervous system cancer, gynecological cancer, hematologic cancer, skin cancer, and adrenal gland cancer. In one aspect, the compounds and compositions described herein are useful in treating cardiac cancers selected from sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyoma, fibroma, lipoma and teratoma. In another aspect, the compounds and compositions described herein are useful in treating a lung cancer selected from bronchogenic carcinoma (squamous cell, undifferentiated small cell, undifferentiated large cell, adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma, chondromatous

hamartoma, and mesothelioma. In one aspect, the compounds and compositions described herein are useful in treating a gastrointestinal cancer selected from esophagus (squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel (adenocarcinoma, lymphoma, carcinoid tumors, Kaposi’s sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), and large bowel (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma). In one aspect, the compounds and compositions described herein are useful in treating a

genitourinary tract cancer selected from kidney (adenocarcinoma, Wilm's tumor

[nephroblastoma], lymphoma, leukemia), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), and testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma). In one aspect, the compounds and compositions described herein are useful in treating a liver cancer selected from hepatoma (hepatocellular carcinoma), cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellular adenoma, and hemangioma.

[0051] In some embodiments, the compounds described herein relate to treating, a bone cancer selected from osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochondroma

(osteocartilaginous exostoses), benign chondroma, chondroblastoma, chondromyxofibroma, osteoid osteoma and giant cell tumors.

[0052] In one aspect, the compounds and compositions described herein are useful in treating a nervous system cancer selected from skull (osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningio sarcoma, gliomatosis), brain (astrocytoma, medulloblastoma, glioma, ependymoma, germinoma [pinealoma], glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), and spinal cord (neurofibroma, meningioma, glioma, sarcoma).

[0053] In one aspect, the compounds and compositions described herein are useful in treating a gynecological cancer selected from uterus (endometrial carcinoma), cervix

(cervical carcinoma, pre-tumor cervical dysplasia), ovaries (ovarian carcinoma [serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma], granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma,

melanoma), vagina (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma (embryonal rhabdomyosarcoma), and fallopian tubes (carcinoma).

[0054] In one aspect, the compounds and compositions described herein are useful in treating a skin cancer selected from malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Karposi's sarcoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, keloids, and psoriasis.

[0055] In one aspect, the compounds and compositions described herein are useful in treating an adrenal gland cancer selected from neuroblastoma.

[0056] In one aspect, the compounds and compositions described herein are useful in treating cancers that include, but are not limited to: leukemias including acute leukemias and chronic leukemias such as acute lymphocytic leukemia (ALL), Acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML) and Hairy Cell Leukemia; lymphomas such as cutaneous T-cell lymphomas (CTCL),

noncutaneous peripheral T-cell lymphomas, lymphomas associated with human T-cell lymphotrophic virus (HTLV) such as adult T-cell leukemia/lymphoma (ATLL), Hodgkin's disease and non-Hodgkin's lymphomas, large-cell lymphomas, diffuse large B-cell lymphoma (DLBCL); Burkitf s lymphoma; mesothelioma, primary central nervous system (CNS) lymphoma; multiple myeloma; childhood solid tumors such as brain tumors, neuroblastoma, retinoblastoma, Wilm's tumor, bone tumors, and soft-tissue sarcomas, common solid tumors of adults such as head and neck cancers (e.g., oral, laryngeal and esophageal), genito urinary cancers (e.g., prostate, bladder, renal, uterine, ovarian, testicular, rectal and colon), lung cancer, breast cancer, pancreatic cancer, melanoma and other skin cancers, stomach cancer, brain tumors, liver cancer and thyroid cancer.

[0057] In one aspect, provided herein is a method of treating a subject suffering from a neurological disorder, memory or cognitive function disorder or impairment, extinction learning disorder, fungal disease or infection, inflammatory disease, hematological disease, psychiatric disorders, and neoplastic disease, comprising administering to the subject an effective amount a compound described herein, or a pharmaceutically acceptable salt thereof, or the composition comprising a compound described herein.

[0058] Also provided herein is a method of treating a subject suffering from (a) a cognitive function disorder or impairment associated with Alzheimer’s disease, posterior cortical atrophy, normal-pressure hydrocephalus, Huntington’s disease, seizure induced memory loss, schizophrenia, Rubinstein Taybi syndrome, Rett Syndrome, depression, Fragile X, Lewy body dementia, vascular dementia, vascular cognitive impairment (VCI),

Binswanger’s Disease, fronto-temporal lobar degeneration (FTLD), ADHD, dyslexia, major depressive disorder, bipolar disorder and social, cognitive and learning disorders associated with autism, traumatic brain injury (TBI), chronic traumatic encephalopathy (CTE), multiple sclerosis (MS), attention deficit disorder, anxiety disorder, conditioned fear response, panic disorder, obsessive compulsive disorder, posttraumatic stress disorder (PTSD), phobia, social anxiety disorder, substance dependence recovery, Age Associated Memory Impairment (AAMI), Age Related Cognitive Decline (ARCD), ataxia, Parkinson’s disease, or Parkinson’s disease dementia; or (b) a hematological disease selected from acute myeloid leukemia, acute promyelocytic leukemia, acute lymphoblastic leukemia, chronic myelogenous leukemia, myelodysplastic syndromes, and sickle cell anemia; or (c) a neoplastic disease; or (d) a disorder of learning extinction selected from fear extinction and post-traumatic stress disorder; or (e) hearing loss or a hearing disorder; or (f) fibrotic diseases, such as pulmonary fibrosis, renal fibrosis, cardiac fibrosis, and scleroderma; or (g) bone pain in patients with cancer; or (h) neuropathic pain; comprising administering to the subject an effective amount a compound described herein, or a pharmaceutically acceptable salt thereof, or the composition comprising a compound described herein.

[0059] Also provided is a method of treating a subject suffering from Alzheimer's disease, Huntington's disease, frontotemporal dementia, Friedreich's ataxia, post-traumatic stress disorder (PTSD), Parkinson’s disease, or substance dependence recovery, comprising administering to the subject an effective amount a compound described herein, or a pharmaceutically acceptable salt thereof, or the composition comprising a compound described herein.

[0060] Also provided is a compound described herein, or a pharmaceutically acceptable salt thereof, or a provided composition, for treating one or more of the disclosed conditions.

[0061] Also provided is a compound described herein, or a pharmaceutically acceptable salt thereof, or a provided composition, for the manufacture of a medicament for treating one or more of the disclosed conditions.

[0062] Subjects may also be selected to be suffering from one or more of the described conditions prior to treatment with a compound described herein, or a pharmaceutically acceptable salt thereof, or a provided composition.

[0063] The present disclosure also provides pharmaceutically acceptable compositions comprising a compound described herein, or a pharmaceutically acceptable salt thereof; and a pharmaceutically acceptable carrier. These compositions can be used to treat one or more of the conditions described above.

[0064] Compositions described herein may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir. The term "parenteral" as used herein includes subcutaneous, intravenous, intramuscular, intra- articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques. Liquid dosage forms, injectable preparations, solid dispersion forms, and dosage forms for topical or transdermal administration of a compound are included herein.

[0065] It should also be understood that a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, the judgment of the treating physician, and the severity of the particular disease being treated. The amount of a provided compound in the composition will also depend upon the particular compound in the composition.

EXEMPLIFICATION

[0066] As depicted in the Examples below, in certain exemplary embodiments, compounds are prepared according to the following general procedures. It will be

appreciated that, although the general methods depict the synthesis of certain compounds of the present invention, the following general methods, and other methods known to one of ordinary skill in the art, can be applied to all compounds and subclasses and species of each of these compounds, as described herein.

General Information

[0067] Spots were visualized by UV light (254 and 365 nm). Purification by column and flash chromatography was carried out using silica gel (200-300 mesh). Solvent systems are reported as the ratio of solvents.

[0068] NMR spectra were recorded on a Bruker 400 (400 MHz) spectrometer. 1H chemical shifts are reported in d values in ppm with tetramethylsilane (TMS, = 0.00 ppm) as the internal standard. See, e.g., the data provided in Table 1.

[0069] LCMS spectra were obtained on an Agilent 1200 series 6110 or 6120 mass spectrometer with ESI (+) ionization mode. See, e.g., the data provided in Table 1.

Example 1


[0070] Synthesis of 1949-A. A mixture of 6-chloro-3-nitropyridin-2-amine (4.58 g, 26.4 mmol), 2,4-difluorophenylboronic acid (5.00 g, 31.7 mmol) and Cs2C03 (25.73 g, 79.2 mmol) in dioxane/H20 (100 mL/l0 mL) was treated with Pd(PPh3)4 (1.10 g, 0.95 mmol) under a N2 atmosphere. The mixture was stirred at 100 °C for 2 h and then concentrated in vacuo. The residue was dissolved with EtOAc (200 mL) and the resulting solution was washed with brine (100 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 7 : 1 ~ 5 : 1) to give 1949-A (4.0 g, 61%) as a yellow solid. MS 252.1 [M + H]+.

[0071] Synthesis of 1949-B. A solution of 1949-A (4.0 g, 15.94 mmol) in pyridine (60 mL) was cooled to 0 °C and then phenyl carbonochloridate (7.50 g, 47.81 mmol) was added dropwise. After the addition was completed, the mixture was heated to 50 °C and stirred at 50 °C for 4 h. The mixture was then concentrated in vacuo , and the residue was purified by column chromatography on silica gel (PE : DCM = 3: 2 - 1 : l) to give 1949-B (7.1 g, 91%) as a yellow solid. MS 492.1 [M + H]+.

[0072] Synthesis of 1949-C. A mixture of 1949-B (140 mg, 0.29 mmol), 2-pyrrolidin-3-yl-pyridine (51 mg, 0.34 mmol) and Cs2C03 (279 mg, 0.86 mol) in acetonitrile (5 mL) was stirred at room temperature for 3 h. The mixture was then diluted with water (10 mL) and extracted with EtOAc (10 mL x 3). The combined organic layers were washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was

purified by Prep-TLC (DCM : EtOAc = 1 : 1) to give 1949-C (70 mg, 57%) as a yellow solid. MS 426.2 [M + H]+.

[0073] Synthesis of Compound 1. A mixture of 1949-C (70 mg, 0.16 mmol) and Pd/C (70 mg) in MeOH/EtOAc (3 mL/3 mL) was stirred at room temperature for 1 h under a H2 atmosphere. The Pd/C was then removed by filtration through Celite, the filtrate was concentrated and the residue was purified by Prep-TLC (DCM : MeOH = 20 : 1) to give

Compound 1 (30 mg, 47%) as a yellow solid. MS 396.2 [M + H]+.

[0074] Compounds 2-6 were synthesized in a similar manner using the appropriately substituted amine variant of the reagent used to synthesize Compound 1.

[0075] Compound 2. 40 mg, 54 %, a white solid.

[0076] Compound 3. 48 mg, 52 %, a white solid.

[0077] Compound 4. 70 mg, 69 %, a white solid.

[0078] Compound 5. 109 mg, 97 %, a white solid (prepared from commercially available chiral building blocks).

[0079] Compound 6. 95 mg, 73 %, a gray solid (prepared from commercially available chiral building blocks).

Example 2


[0080] Synthesis ofl981-A. A mixture of zinc dust (840 mg, 12.9 mmol) and Celite (180 mg) in a sealed flask was heated under vacuum with a heat gun for 5 min. The flask was purged with N2 and cooled to room temperature. To the mixture was added anhydrous DMA (5.5 mL) followed by a mixture of TMSC1 and l,2-dibromoethane (0.3 mL, v/v=7/5). The mixture was stirred at room temperature for 15 min under a N2 atmosphere, whereupon a solution of tert-butyl 3-iodopyrrolidine-l-carboxylate (3.10 g, 10.4 mmol) in DMA (5.5 mL) was added. The resulting mixture was stirred at room temperature for 4 h under N2, and then the mixture was used taken on to the next step directly as 1981-A. The concentration of 1981-A was about 0.85 mol/L in DMA.

[0081] Synthesis ofl981-B. A mixture of 2-bromopyrimidine (1.1 g, 6.92 mmol), Cul (197 mg, 1.04 mmol) and Pd(dppf)2Cl2 (452 mg, 0.55 mmol) in DMA (10 mL) under a N2 atmosphere was treated with 1981-A (10.0 mL). The resulting mixture was stirred at 85 °C for 48 h under a N2 atmosphere, and then the mixture was diluted with water (50 mL) and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc =10 : 1— 1 : 1) to give 1981-B (320 mg, 19%) as a yellow oil. MS 194.3 [M -56 + H]+.

[0082] Synthesis of 1981-C. To a solution of 1981-B (320 mg, 1.29 mmol) in DCM (6 mL) was added TFA (2 mL) dropwise. The reaction mixture was stirred at room temperature for 1 h, whereupon the solution was concentrated in vacuo to give 1981-C as a crude product which was used directly in the next step without further purification. MS 150.3 [M + H]+.

[0083] Synthesis ofl981-D. A mixture of 1981-C (1.29 mmol, crude product from last step) and 1949-B (352 mg, 0.72 mmol) in DMSO (10 mL) was stirred at room temperature for 10 min, then Na2C03 (760 mg, 7.17 mmol) was added and the reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (30 mL) and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM : MeOH = 40 : 1) to give 1981-D (205 mg, 67%) as a yellow solid. MS 427.1 [M + H]+.

[0084] Synthesis of Compound 7. A mixture of 1981-D (205 mg, 0.48 mmol) and Pd/C (205 mg) in MeOH/EtOAc (5 mL/5 mL) was stirred at room temperature for 50 min under a H2 atmosphere. The Pd/C was removed by filtration through Celite, the filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 25 : 1) to give Compound 7 (130 mg, 68%) as a brown solid. MS 397.2 [M + H]+.

[0085] Chiral-separation of Compound 7. The enantiomers of racemic Compound 7 (100 mg, 0.25 mmol) was separated by chiral chromatographic separation (Column:

Chiralpak OJ-3; Solvent: MeOH; Flow rate: 2 mL/min; RT8EI = 2.287 min, RT8E2 = 2.553 min) to give the first eluting peak Enantiomer 1 (Compound 8E1) (40 mg, 40%) as a yellow solid (MS 397.2 [M+H]+) and the second eluting peak Enantiomer 2 (Compound 8E2) (20 mg, 20%) as a yellow solid. MS 397.2 [M+H]+. Stereochemistry was randomly assigned.

[0086] Compounds 9-21 were synthesized in a similar manner using appropriately substituted boronic acid and bromine variants of reagents used to synthesize Compound 7.

[0087] Compound 9. 11 mg, 54%, a yellow solid.

[0088] Compound 10. 11 mg, 47%, a white solid.

[0089] Compound 11. 34 mg, 70%, a white solid.

[0090] Compound 12. 18 mg, 48%, a white solid.

[0091] Compound 13. 34 mg, 61%, a light yellow solid.

[0092] Compound 15. 14 mg, 47%, a white solid.

[0093] Compound 16. 35 mg, 63%, an off-white solid.

[0094] Compound 17. 25 mg, 45%, a white solid.

[0095] Compound 18. 30 mg, 52 %, an off-white solid.

[0096] Compound 19. 15 mg, 28%, a light yellow solid.

[0097] Compound 20. 11 mg, 47 %, a light yellow solid.

[0098] Compound 21. 17 mg, 41%, a light yellow solid.

Example 3. Synthesis of 14-El and 14-E2


[0099] Synthesis of 2147-A. To a mixture of ieri-butyl 3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-2,5-dihydro-lH-pyrrole-l-carboxylate (33.6 g, 113.9 mmol), 2-bromo-5-fluoropyrimidine (20 g, 113.6 mmol) and K2C03 (47.l g, 341 mmol) in dioxane/H20 (500 mL/50 mL) was added PdCl2(dppf)2 (4.6 g, 5.7 mmol) under a nitrogen atmosphere. The resulting mixture was stirred at 100 °C for 2 h and then concentrated in vacuo. The residue was dissolved with EtOAc (500 mL) and the solution was washed with brine (200 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10: 1 to 5 : 1) to give 2147-A (25.5 g, 85 %) as a gray solid. MS 210.1 [M - 55]+.

[00100] Synthesis of2147-B. To a solution of 2147-A (1.0 g, 6.0 mmol) in DCM (30 mL) was added TFA (10 mL) dropwise at 0 °C. The resulting solution was stirred at room temperature for 1 h, whereupon the solvent was removed in vacuo to give 2147-B as a crude product which was used directly in the next step. MS 166.1 [M + H]+.

[00101] Synthesis of2147-D. A solution of 1954-A (1.87 g, 7.45 mmol) in DMF (15 mL) was cooled to 0 °C and then was treated with NaH (60% in mineral oil) (596 mg, 14.9 mmol). The reaction mixture was stirred at 0 °C for 30 min, then CDI (1.20 g, 7.45 mmol) was added and stirring was continued at 0 °C for another 30 min. A solution of 2147-B in DMF was added to the reaction mixture, and stirring was continued at 0 °C for 1 h. The mixture was then quenched with water (100 mL) and extracted with EtOAc (50 mL x 3). The combined organic layers were washed with brine (50 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography (DCM : EtOAc = 15 : 1 to 2 : 1) to give 2147-D (2.3 g, 70 %) as a yellow solid. MS 443.2 [M + H]+.

[00102] Synthesis of 14. A mixture of 2147-D (2.3 g, 5.2 mmol) and Pd/C (2.3 g) in MeOH/EtOAc (50 mL/50 mL) was stirred at room temperature for 1 h under a H2

atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography (DCM : MeOH = 20 : 1) to give Compound 14 (1.14 g, 53%) as a white solid. MS 415.2 [M + H]+.

[00103] Chiral-separation of 14-El and 14-E2. The enantiomers of 14 (1.14 g, 2.75 mmol) were separated by chiral SFC separation (Column: Chiralcel OD-3; Solvent: MeOH; Flow rate: 2 mL/min; RTT-2I47-EI = 1.849 min, RTT-2I47-e2 = 2.175 min) to give Compound 14-El Isomer 1 (410 mg, 36%) as a yellow solid (MS 415.2 [M+H]+) and Compound 14-E2 (360 mg, 31%) as a yellow solid. MS 415.2 [M+H]+ Isomer 2.

Example 4. Synthesis of 19-El & 19-E2


[00104] Synthesis of 2145-A. A mixture of 1981-A (1.7 g, 6.8 mmol) and Pd/C (850 mg) in EtOAc (80 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was removed by filtration through Celite. The filtrate was concentrated in vacuo to give 2145-A (1.6 g, 94%) as colorless oil. MS 194.2 [M -55]+

[00105] Synthesis of 2145-B. To a solution of 2145-A (1.3 g, 5.22 mmol) in DCM (18 mL) was added TFA (6 mL) drop wise at 0 °C. The reaction mixture was allowed to warm to room temperature and was stirred at room temperature for 1 h, whereupon the reaction mixture was concentrated in vacuo. The crude residue was dissolved in DMF (5mL) and treated with TEA (1.58 g, 15.66 mmol) to give 2145-B as a solution used to next step directly. MS 150.0 [M + H]+.

[00106] Synthesis of 2145-C. A mixture of 6-chloro-3-nitropyridin-2-amine (50.0 g, 289.0 mmol), 4-fluorophenylboronic acid (48.5 g, 346.8 mmol) and K2C03 (119.6 g, 867 mmol) in dioxane/H20 (1000 mL/lOO mL) was treated with Pd(PPh3)4 (5.0 g, 4.33 mmol) under a N2 atmosphere. The mixture was stirred at 95 °C for 4 h and then concentrated in vacuo. The residue was dissolved with EtOAc (2000 mL) and the solution was washed with brine (700 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 - 5 : 1) to give 2145-C (36 g, 54%) as a yellow solid. MS 233.1 [M + H]+.

[00107] Synthesis of2145-E. A solution of 2145-C (1.0 g, 4.35 mmol) in DMF (20 mL) was cooled to 0 °C and treated with NaH (60% in mineral oil)(2l0 mg, 5.22 mmol). The reaction mixture was stirred at 0 °C for 30 min, then CDI (846 mg, 5.22 mmol) was added into above mixture, and stirring was continued at 0 °C for another 30 min to give a solution as 2145-D. The solution of 2145-B was added into the solution of 2145-D at 0 °C and stirred for 1 h. The reaction mixture was poured into water (420 mL), then extracted with EtOAc (50 mL x 3), washed with brine (50 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (DCM : MeOH = 100 : 1 ~ 30 : 1) to give 2145-E (1.2 g, 56.3%) as yellow oil. MS 409.1 [M + H]+.

[00108] Synthesis of 19. A mixture of 2145-E (1.2 g, 2.94 mmol) and Pd/C (1.2 g) in MeOH/ EtOAc (20 mL/20 mL) was stirred at room temperature for 1 h under a ¾

atmosphere. Pd/C was removed by filtration through Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (DCM : MeOH = 100 : 1 ~ 15 : 1) to give 19 (700 mg, 63%) as a off-white solid. MS 379.4 [M + H]+.

[00109] Chiral-separation of 19-El and 19-E2. The enantiomers of 19 (700 mg, 1.85 mmol) were separated by chiral SFC (Column: Chiralpak AD-3; Solvent: MeOH; Flow rate: 1.5 mL/min; RTT_2I45-E2 = 5.544 min, to give 19-E2 (230 mg, 32.8%) as a white solid, and RTT_2145-EI = 4.009 min, to give 19-El (260 mg, 37.1%) as a white solid. MS 379.4 [M+H]+.

Example 5. Alternative Synthesis of 19-El & 19-E2


[00110] Synthesis of 2145-F. A solution of 2145-C (5.83 g, 25.0 mmol) in DMF (100 mL) was cooled to 0 °C and was treated with NaH(60% in mineral oil)(l.4 g, 35 mmol). The reaction mixture was stirred at 0 °C for 30 min, then CDI (4.86 g, 30 mmol) was added into above mixture and stirring was continued at 0 °C for another 30 min to give a solution as 2145-D. Then a solution of 1981-B (9.26 g, 37.5 mmol) and TEA (18.93 g, 187.5 mmol) in DMF (40 mL) was added into the solution of 2145-D at 0 °C and the resulting reaction mixture was stirred at 0 °C for 1 h. The reaction mixture was then poured into water (420 mL) and stirred for 10 min. The precipitate was collected by filtered and the cake washed with water (150 mL), then acetone (150 mL). Finally, the cake was concentrated to dryness to give 2145-F (9.5 g, 94%) as a light yellow solid. MS 407.1 [M + H]+.

[00111] Synthesis of 19. A mixture of 2145-F (8.5 g, 20.9 mmol) and Pd/C (8.5 g) in MeOH/DCM (250 mL/200 mL) was stirred at room temperature for 3 h under a H

atmosphere. Pd/C was removed by filtration through Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (DCM : MeOH = 100 : 1 ~ 15 : 1) to give 19 (4.1 g, 50%) as a light yellow solid. MS 379.4 [M + H]+.

[00112] Compounds 46, 50 and 51 were synthesized in a similar manner as 19 by using appropriately substituted boronic acid and aryl bromide reagents.

[00113] Compound 46. 100 mg, 63%, a lighty yellow solid.

[00114] Chiral-separation of 50 and 51. The enantiomers of 19 were separated by chiral SFC (Column: Chiralpak AD-3; Solvent: MeOH; Flow rate: 1.5 mL/min; RTso = 3.267 min, and RT = 5.375 min.

[00115] Compound 50. 200 mg, 29%, a white solid.

[00116] Compound 51. 230 mg, 33%, a white solid.

Example 6. Synthesis of 20-El and 20-E2


[00117] Synthesis of 2292-A. A mixture of 2-bromo-5-fluoropyrimidine (20 g, 113.6 mmol), tert-butyl 3-(4, 4,5, 5-tetramethyl- 1,3, 2-dioxaborolan-2-yl)-2, 5-dihydro- lH-pyrrole-l-carboxylate (33.7 g, 113.6 mmol) and K2CO3 (47.0 g, 340.8 mmol) in dioxane/H20 (500 mL/50 mL) were treated with Pd(dppf)2Cl2 (4.64 g, 5.7 mmol) under a N2 atmosphere. The reaction mixture was stirred at 90 °C for 3 h and then concentrated in vacuo. The residue was dissolved with EtOAc (200 mL) and the solution was washed with brine (100 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : DCM = 1 : 1 to DCM) to give 2292-A (25.5 g, 85%) as a gray solid. MS 210.1 [M - 55]+.

[00118] Synthesis of 2292-B. A mixture of 2292-A (11.7 g, 44.1 mmol) in DCM (100 mL) was treated with TLA (30 mL) at 0 °C. The reaction mixture was allowed to warm to room temperature and was stirred at room temperature for 1 h. The solution was then concentrated in vacuo, and the residue was dissolved in DMF (50 mL) and treated with TEA (13.4 g, 132.3 mmol) to give 2292-B as a solution used directly in the next step. MS 165.1 [M + H]+.

[00119] Synthesis of2292-C. A solution of 2145-C (9.32 g, 40.0 mmol) in DMF (100 mL) was cooled to 0 °C and then was treated with NaH (60% in mineral oil)(L92 g, 48.0 mmol). The reaction mixture was stirred at 0 °C for 30 min, then CDI (7.13 g, 44.0 mmol) was added into above mixture and stirring was continued at 0 °C another 30 min to give a solution as 2145-D. Then a solution of 2292-B was added into above mixture at 0 °C and the resulting mixture was stirred at 0 °C for 1 h. The reaction mixture was then poured into water (450 mL) and stirred for 10 min. The precipitate was collected by filtration and the cake washed with water (150 mL), then acetone (150 mL). Finally, the cake was concentrated to dryness to give 2292-C (12.2 g, 70%) as a light yellow solid. MS 424.9 [M + H]+.

[00120] Synthesis of 20. A solution of 2292-C (12.2 g, 28.6 mmol) and Pd/C (12.2 g) in MeOH/DCM (400 mL/300 mL) was stirred at room temperature for 2.5 h under a H2 atmosphere. Pd/C was removed by filtration through Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (DCM to DCM : EA = 1 : 1) to give 20 (6.8 g, 60%) as a yellow solid. MS 397.0 [M + H]+.

[00121] Chiral-separation of 20-El and 20-E2. The enantiomers of 20 (360 mg, 0.91 mmol) were separated by chiral SFC (Column: Chiralcel OJ-3; Solvent: MeOH; Flow rate:

1.5 mL/min; RTT_2292-E2 = 2.862 min, to give 20-E2 (100 mg, 28%) as a white solid, and RTV 2292-El = 2.338 min, to give 20-El (88 mg, 25%) as a white solid. MS 397.0 [M+H]+.

Example 7

N-N


[00122] Synthesis of 2007-A. A solution of tert-butyl 3-hydroxypyrrolidine-l-carboxylate (821 mg, 4.75 mmol) in THF (10 mL) was treated with 3-bromopyridazine (500 mg, 3.16

mmol) and KOH (798 mg, 4.25 mmol) at room temperature. The reaction mixture was then heated to 70 °C and stirred at 70 °C for 16 h. The mixture was then diluted with water (20 ml), and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : PE = 10 : 1) to give 2007-A (70 mg, 8%) as a yellow oil. MS 288.2 [M + H]+.

[00123] Synthesis of2007-B. To a solution of 2007-A (70 mg, 0.26 mmol) in DCM (6 mL) was added TFA (2 mL) dropwise. The reaction mixture was stirred at room temperature for 1 h, whereupon the solvent was removed in vacuo to give 2007-B as a crude product which was used directly in the next step without further purification.

[00124] Synthesis of2007-C. A mixture of 1949-B (71.0 mg, 0.14 mmol) and 2007-B (0.26 mmol, crude product from last step) in DMSO (5 mL) was stirred at room temperature for 10 min, then was treated with Na2C03 (276 mg, 2.6 mmol). The resulting reaction mixture was stirred at room temperature for 2 h, whereupon the mixture was diluted with water (20 mL) and extracted with EtOAc (10 mL x 3). The combined organic layer was washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : PE = 5 : 1) to give 2007-C (40 mg, 45%) as a yellow solid. MS 443.2 [M + H]+.

[00125] Synthesis of 22. A mixture of 2007-C (40 mg, 0.09 mmol) in MeOH (6 mL) was treated with Raney-Ni (20 mg) and stirred at room temperature for 30 min under a H2 atmosphere. The Raney-Ni was then removed by filtration through Celite, the filtrate was concentrated and the residue was purified by Prep-TLC (DCM : MeOH = 10 : 1) to give 22 (18 mg, 48%) as a pink solid. MS 413.2 [M + H]+.

Example 8


F F

[00126] Synthesis of 2008- A. A solution of tert-butyl 3-hydroxypyrrolidine-l-carboxylate (375 mg, 3.32 mmol) in THF (10 mL) was treated with 2-bromopyrimidine (350 mg, 3.22 mmol) and t-BuOK (1.08 g, 9.66 mmol) at room temperature. The reaction mixture was then heated to 70 °C, and was stirred at 70 °C for 3 h. The mixture was then diluted with water (30 ml ), and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : PE = 10 : 1) to give 2008-A (400 mg, 48%) as a colorless oil. MS 288.2 [M + H]+.

[00127] Synthesis of2008-B. To a solution of 2008-A (400 mg, 1.51 mmol) in DCM (6 mL) was added TFA (2 mL) dropwise. The resulting reaction mixture was stirred at room temperature for 1 h, whereupon the solvent was removed in vacuo to give 2008-B as a crude product which was used directly in the next step without further purification. MS 188.2 [M + H]+.

[00128] Synthesis of2008-C. A mixture of 1949-B (370.0 mg, 0.76 mmol) and 2008-B (1.51 mmol, crude product from last step) in DMSO (10 mL) was stirred at room temperature for 10 min, then was treated with Na2C03 (800 mg, 7.55 mmol). The resulting reaction mixture was stirred at room temperature for 2 h, whereupon the mixture was diluted with water (30 mL) and extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (30 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : PE = 5: 1) to give 2008-C (250 mg, 75%) as a yellow solid. MS 443.2 [M + H]+.

[00129] Synthesis of 23. A mixture of 2008-C (200 mg, 0.45 mmol) in MeOH (8 mL) was treated with Pd/C (200 mg), and the reaction mixture was stirred at room temperature for 1 h under a H2 atmosphere. The Pd/C was then removed by filtration through Celite, the filtrate was concentrated and the residue was purified by Prep-TLC (DCM : MeOH = 10 : 1) to give 23 (84 mg, 42%) as an off-white solid. MS 413.2 [M + H]+.

Example 9


[00130] Synthesis of 2058-A. A mixture of zinc dust (896 mg, 13.8 mmol) and anhydrous DMA (3 mL) was treated with TMSC1 and l,2-dibromoethane (0.24 mL, v/v= 7/5), and the resulting reaction mixture was stirred at room temperature for 20 min under a N2 atmosphere. A solution of tert-butyl 3-(iodomethyl)pyrrolidine-l-carboxylate (3.3 g, 10.6 mmol) in anhydrous DMA (4 mL) was then added, and the resulting reaction mixture was stirred at room temperature for 16 h under a N2 atmosphere. The mixture was then used directly in the next step as 2058-A. The concentration of 2058-A was about 1.0 mol/L in DMA.

[00131] Synthesis of 2058-B. A mixture of 2-bromopyrimidine (734 mg, 4.61 mmol), Cul (87 mg, 0.46 mmol) and Pd(PPh3)4 (266 mg, 0.23 mmol) in anhydrous DMA (15 mL) under a N2 atmosphere was treated with 2058-A (6.0 mL). The resulting mixture was stirred at 60 °C for 48 h under a N2 atmosphere. The mixture was then diluted with water (50 mL) and extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (30 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : DCM = 1 : 1) to give 2058-B (500 mg, 41%) as a yellow solid. MS 264.2 [M + H]+.

[00132] Synthesis of 2058-C. To a solution of 2058-B (500 mg, 1.9 mmol) in DCM (10 mL) was added TFA (3 mL) dropwise. The reaction mixture was stirred at room temperature for 1 h, whereupon the solution was concentrated in vacuo to give 2058-C as a crude product which was used directly in the next step without further purification. MS 164.2 [M + H]+.

[00133] Synthesis of 2058-D. A mixture of 2058-C (1.9 mmol, crude product from last step) and 1949-B (518 mg, 1.05 mmol) in DMSO (15 mL) was stirred at room temperature for 10 min, then was treated with Na2C03 (1.11 g, 10.5 mmol), and the resulting reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (50 mL) and extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (30 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM : EtOAc = 1 : 2) to give 2058-D (400 mg, 86%) as a yellow solid. MS 441.2 [M + H]+.

[00134] Synthesis of 24. A mixture of 2058-D (400 mg, 0.91 mmol) and Pd/C (400 mg) in MeOH/EtOAc (10 mL/l0 mL) was stirred at room temperature for 1 h under a H2 atmosphere. The Pd/C was removed by filtration through Celite, the filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 25 : 1) to give 24 (250 mg, 67%) as a yellow solid. MS 411.2 [M + H]+.

[00135] Chiral-separation of 24. The enantiomers of 24 (250 mg, 0.61 mmol) were separated by chiral chromatographic separation (Column: Chiralpak AD-3; Solvent: MeOH; Flow rate: 2 mL/min; RT24EI = 2.893 min, RT24E2 = 3.892 min) to give Enantiomer 1 (25E1) (62 mg, 25%) as a yellow solid (MS 411.2 [M+H]+) and Enantiomer 2 (25E2) (90 mg, 36%) as a yellow solid. MS 411.2 [M+H]+. Stereochemistry was randomly assigned.

[00136] Compounds 26-28 were synthesized in a similar manner using the appropriately substituted bromine variants of the reagent used to synthesize 23.

[00137] Compound 26. 20 mg, 21%, a yellow solid.

[00138] Compound 27. 110 mg, 59%, a white solid.

[00139] Compound 28. 20 mg, 54%, a light yellow solid.

Example 10


[00140] Synthesis of 2106-A. To a solution of 2-bromopyrimidine (50.0 g, 314.5 mmol) in DCM (600 mL) under nitrogen atmosphere was added H-BuLi (150 mL, 377.5 mmol) dropwise at -78 °C and stirred at -78 °C for 2 h under nitrogen atmosphere. Then ieri-butyl 3-oxopyrrolidine-l-carboxylate (70 g, 377.5 mmol) in DCM (200 mL) was added into above mixture dropwise at -78 °C. The resulting mixture was warmed to room temperature for 3 h. The mixture was quenched with saturated NH4Cl (200 mL), extracted with DCM (400 mL x 3). The combined organic layers were washed with brine (200 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 2106-A (9.0 g, 11%) as a light yellow solid. MS 266.2 [M+H]+.

[00141] Synthesis of 2106-B. To a solution of 2106-A (9.0 g, 34.0 mmol) in DCM (50 mL) was added DAST (18 mL) dropwise at -78 °C and the solution was warmed to room temperature for 1 h under nitrogen atmosphere. The solvent was concentrated and the residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 2106-B (2.2 g, 24%) as a brown solid. MS 268.2 [M+H]+.

[00142] Synthesis of 2106-C. To a solution of 2106-B (2.2 g, 8.21 mmol) in DCM (20 mL) was added TFA (8 mL) dropwise at 0 °C. Then the solution was stirred at room temperature for 1 h. The solvent was removed in vacuo to give 2106-C as a crude product which was directly used in the next step. MS 168.2 [M+H]+.

[00143] Synthesis of 2106-D. A mixture of 1949-B (2.6 g, 5.47 mmol) and 2106-C (8.21 mmol, crude product from last step) in DMSO (40 mL) was stirred at room temperature for 10 min, and then Na2C03 (5.8 g, 54.7 mmol) was added into above mixture. The resulting mixture continued to stir at room temperature for 2 h. The mixture was diluted with water (200 mL), extracted with EtOAc (100 mL x 3). The combined organic layers were washed

with brine (50 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 2106-D (2.0 g, 82%) as a yellow solid. MS 445.0 [M+H]+.

[00144] Synthesis of 29. A mixture of 2106-D (12.0 g, 27.0 mmol) and Raney-Ni (2.0 g) in MeOH (20 mL) was stirred at room temperature for 1 h under H2 atmosphere. Raney-Ni was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 29 (8.0 g, 71%) as a yellow solid. MS 415.2 [M+H]+.

[00145] Chiral-separation of 29-El and 29-E2. The enantiomers of Compound 29 (8.0 g, 19.3 mmol) were separated by chiral SFC (Column: Chiralcel OX-3; Solvent: MeOH; Flow rate: 1.5 mL/min; RT2IO6-EI = 2.814 min, RTT_2IO6-E2 = 4.362 min) to give 29-El (1.2 g, 11%) as a yellow solid (MS 415.2 [M+H]+) and 29-E2 (1.3 g, 12%) as a yellow solid. MS 415.2 [M+H]+.

[00146] Compound 45 was synthesized in a similar manner as 29 by using 2-(5-fluorothiophen-2-yl)-4,4,5,5-tetramethyl-l,3,2-dioxaborolane as a reagent.

[00147] Compound 45. 90 mg, 19%, a yellow solid.

Example 11


[00148] Synthesis of 1984-A. A solution of 2-bromo-5-methylthiazole (1.0 g, 5.59 mmol) in THF (20 mL) under a N2 atmosphere was treated with nBuLi (2.7 mL, 6.70 mmol) dropwise at -78°C, and the resulting reaction mixture was stirred at -78°C for 1 h. A solution of tert-butyl 3-oxopyrrolidine-l-carboxylate (1.2 g, 6.70 mmol) in THF (10 mL) was then added to the reaction mixture dropwise at -78 °C. The reaction mixture was then allowed to warm to room temperature, and was stirred at room temperature for 3 h. The mixture was diluted with saturated aqueous NH4Cl (40 mL), and extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04

and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 1984-A (760 mg, 48%) as a light yellow solid. MS 285.2 [M+H]+.

[00149] Synthesis of 1984-B. A solution of 1984-A (660 mg, 2.32 mmol) in DCM (10 mL) was cooled to 0 °C and treated with pyridine (1.09 g, 13.94 mmol), followed by dropwise addition of SOCl2 (414 mg, 3.48 mmol). The resulting reaction mixture was then heated to 45 °C and stirred at 45 °C for 16 h. The mixture was then diluted with water (20 ml), and extracted with DCM (30 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 ~ 1: 5) to give 1984-B (120 mg, 19%) as a brown oil. MS 266.2 [M+H]+.

[00150] Synthesis of 1984-C. A mixture of 1984-B (100 mg, 0.38 mmol) and Pd/C (100 mg) in MeOH (6 mL) was stirred at room temperature for 1 h under a H2 atmosphere. The Pd/C was then removed by filtration through Celite, the filtrate was concentrated and the residue was purified by Prep-TLC (EtOAc : PE = 5 : 1) to give 1984-C (90 mg, 88%) as a light brown oil. MS 269.2 [M+H]+.

[00151] Synthesis of 1984-D. To a solution of 1984-C (90 mg, 0.34 mmol) in DCM (3 mL) was added TFA (1 mL) dropwise. The resulting reaction mixture was stirred at room temperature for 1 h, whereupon the solvent was removed in vacuo to give 1984-D as a crude product which was used directly in the next step without further purification. MS 169.2

[M+H]+.

[00152] Synthesis of 1984-E. A mixture of 1949-B (93 mg, 0.19 mmol) and 1984-D (0.34 mmol, crude product from last step) in DMSO (5 mL) was treated with Na2C03 (200 mg,

1.89 mmol), and the resulting reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (20 mL), and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : PE = 5: 1) to give 1984-E (80 mg, 95%) as a yellow solid. MS 446.2 [M+H]+.

[00153] Synthesis of 30. A mixture of 1984-E (80 mg, 0.18 mmol) and Pd/C (80 mg) in MeOH (5 mL) was stirred at room temperature for 1 h under a H2 atmosphere. The Pd/C was then removed by filtration through Celite, the filtrate was concentrated and the residue was purified by Prep-TLC (EtOAc : MeOH = 15 : 1) to give 30 (44 mg, 59%) as a yellow solid. MS 416.2 [M+H]+.

Example 12 Synthesis of 31


[00154] Synthesis of 1954-A. A mixture of 6-chloro-3-nitropyridin-2-amine (4.58 g, 26.4 mmol), 2,4-difluorophenylboronic acid (5.00 g, 31.7 mmol) and K2C03 (10.9 g, 79.2 mmol) in dioxane/H20 (100 mL/l0 mL) was treated with Pd(PPh3)4 (1.10 g, 0.95 mmol) under a nitrogen atmosphere. The mixture was stirred at 100 °C for 3 h and then concentrated in vacuo. The residue was dissolved with EtOAc (200 mL) and the solution was washed with brine (100 mL x 3). The organic layer was dried over anhydrous Na2S04 and then

concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 7 : 1 to 5 : 1) to give 1954-A (4.0 g, 61%) as a yellow solid. MS 252.1 [M + H]+.

[00155] Synthesis of 1954-B. To a stirred solution of 1954-A (4.0 g, 15.94 mmol) in pyridine (60 mL) was added phenyl carbonochloridate (7.50 g, 47.81 mmol) dropwise at 0 °C. After the addition was completed, the mixture was stirred at 50 °C for 4 h. The mixture was concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : DCM = 3: 2 to 1 : 1) to give 1954-B (7.1 g, 91%) as a yellow solid. MS 492.1 [M +

H]+.

[00156] Synthesis of 1954-C. To a mixture of zinc dust (449 mg, 6.9 mmol) in anhydrous DMA (2 mL) was added TMSC1 and l,2-dibromoethane (0.24 mL, v/v= 7/5), and the reaction mixture was stirred at room temperature for 20 min under a nitrogen atmosphere. Then a solution of tert-butyl 3-(iodomethyl)pyrrolidine-l-carboxylate (1.65 g, 5.3 mmol) in anhydrous DMA (1.5 mL) was added into above mixture, and the resulting mixture was stirred at room temperature for 16 h under a nitrogen atmosphere. The mixture was used directly in the next step as 1954-C. The concentration of 1954-C was about 1.0 mol/L in DMA.

[00157] Synthesis of 1954-D. To a mixture of 3-bromopyrimidine (243 mg, 1.54 mmol), Cul (30 mg, 0.15 mmol) and Pd(PPh3)4 (89 mg, 0.077 mmol) in anhydrous DMA (6 mL) under nitrogen atmosphere was added 1954-C (2.0 mL). The resulting mixture was stirred at 60 °C for 72 h under a nitrogen atmosphere. The mixture was then diluted with water (20 mL) and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM :EtOAc = 2 : 1) to give 1954-D (180 mg, 44%) as a yellow solid. MS 263.2 [M + H]+.

[00158] Synthesis of 1954-E. To a solution of 1954-D (160 mg, 0.69 mmol) in DCM (6 mL) was added TFA (2 mL) drop wise at 0 °C. The resulting reaction mixture was stirred at room temperature for 1 h, then was concentrated in vacuo to give 1954-E as a crude product which was directly used in the next step. MS 163.2 [M + H]+.

[00159] Synthesis of 1954-F. A mixture of 1954-E (0.69 mmol, crude product from previous step) and 1954-B (188 mg, 0.38 mmol) in DMSO (6 mL) was stirred at room temperature for 10 min, then Na2C03 (403 mg, 3.8 mmol) was added into above mixture and the resulting reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (30 mL) and extracted with EtOAc (10 mL x 3). The combined organic layers were washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM : EtOAc = 1 : 2) to give 1954-F (110 mg, 66%) as a yellow solid. MS 440.1 [M + H]+.

[00160] Synthesis of Compound 31. A mixture of 1954-F (110 mg, 0.25 mmol) and Pd/C

(110 mg) in MeOH/EtOAc (5 mL/5 mL) was stirred at room temperature for 50 min under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 30 : 1) to give 31 (45 mg, 44%) as a yellow solid. MS 410.1 [M + H]+.

[00161] Compound 33 was synthesized in a similar manner as 31 by using ie/ -butyl 3-iodopyrrolidine-l-carboxylate and 2-bromo-5-methylpyrimidine as reagents.

[00162] Compound 33. 38 mg, 41%, a light yellow solid.

[00163] Compound 48 was synthesized in a similar manner as 31 by using tert- butyl 3-iodopyrrolidine-l-carboxylate, 2-bromopyrimidine and 2-fluorophenylboronic acid as reagents.

[00164] Compound 48. 38 mg, 41%, a light yellow solid.

Example 13 Synthesis of Compound 32


[00165] Synthesis of 1985-A. A mixture of 2-bromo-5-methyl-l, 3, 4-thiadiazole (700 mg, 3.89 mmol), ie/t-butyl 3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-2,5-dihydro-lH-pyrrole-l-carboxylate (1.15 g, 3.89 mmol) and Na2C03 (l.2 g, 11.7 mmol) in dioxane (40 mL) was treated with PdCl2(dppf)2 (l59 mg, 0.2 mmol) under a nitrogen atmosphere. The reaction mixture was stirred at 90 °C for 3 h and then concentrated in vacuo. The residue was dissolved with EtOAc (30 mL) and the solution was washed with brine (10 mL x 3). The combined organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to 1 : 1) to give 1985-A (400 mg, 39%) as a yellow solid. MS 268.1 [M + H]+.

[00166] Synthesis of 1985-B A mixture of 1985-A (400 mg, 1.5 mmol) and Pd/C (400 mg) in EtOAc (10 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was then removed by filtration through a pad of Celite. The filtrate was concentrated and the residue was purified by Prep-TLC (EA: PE = 3 : 1) to give 1985-B (300 mg, 74%) as yellow solid. MS 270.2 [M+H]+.

[00167] Synthesis of 1985-C. A solution of 1985-B (300 mg, 1.1 mmol) in DCM (10 mL) was cooled to 0 °C and then TFA (4 mL) was added dropwise at 0°C. The resulting solution was stirred at room temperature for 1 h, whereupon the solvent was removed in vacuo to give 1985-C as a crude product which was used directly in the next step. MS 170.2 [M+H]+.

[00168] Synthesis of 1985-D. A mixture of 1954-B (300 mg, 0.6 mmol) and 1985-C (1.1 mmol, crude product from previous step) in DMSO (10 mL) was treated with Na2C03 (636 mg, 6.0 mmol) and the resulting mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (50 mL), extracted with EtOAc (50 mL x 3). The combined combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EA : PE = 5 : 1) to give 1985-D (150 mg, 56%) as a yellow solid. MS 447.2 [M+H]+.

[00169] Synthesis of 32 A mixture of 1985-D (150 mg, 0.34 mmol) and Pd/C (150 mg) in

MeOH (6 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was then removed by filtration through a pad of Celite. The filtrate was concentrated and the residue was purified by Prep-TLC (EA: MeOH = 15 : 1) to give 32 (83 mg, 55%) as yellow solid.

MS 417.2 [M+H]+.

[00170] Compound 37 was synthesized in a similar manner as 32 by using the

appropriately substituted aryl bromide reagent. Compound 37. 65 mg, 58%, a light yellow solid.

Example 14 Synthesis of Compound 34


[00172] Synthesis of 2060-A. A solution of l/ -imidazole (115 mg, 1.69 mmol) in DMF (5 mL) was cooled to 0 °C and treated with NaH (60% in mineral oil, 122 mg, 3.1 mmol). The reaction mixture was stirred at 0 °C for 10 min, then tert- butyl 3-(iodomethyl)pyrrolidine-l-carboxylate (687 mg, 2.21 mmol) was added and the reaction mixture was warmed to 40 °C and stirred at 40 °C for 3 h. The mixture was thendiluted with water (30 mL) and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by

Prep-TLC (DCM : MeOH = 30 : 1) to give 2060-A (105 mg, 25%) as a colorless oil. MS 197.2 [M + H]+.

[00173] Synthesis of2060-B. To a solution of 2060-A (201 mg, 0.80 mmol) in DCM (6 mL) was added TFA (2 mL) drop wise at 0 °C. The resulting reaction mixture was allowed to warm to room temperature and was stirred at room temperature for 1 h, then was

concentrated in vacuo to give 2060-B as a crude product which was directly used in the next step. MS 151.2 [M + H]+.

[00174] Synthesis of 2060-C. A mixture of 2060-B (0.80 mmol, crude product from previous step) and 1954-B (216 mg, 0.44 mmol) in DMSO (6 mL) was stirred at room temperature for 10 min, then Na2C03 (471 mg, 4.44 mmol) was added into above mixture and stirred at room temperature for 2 h. The mixture was diluted with water (20 mL) and extracted with EtOAc (10 mL x 3). The combined organic layers were washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM : MeOH = 30 : 1) to give 2060-C (147 mg, 78%) as a yellow solid. MS 429.1 [M + H]+.

[00175] Synthesis of 34. A mixture of 2060-C (124 mg, 0.29 mmol) and Pd/C (124 mg) in

MeOH/EtOAc (5 mL/5 mL) was stirred at room temperature for 2 h under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 20 : 1) to give 34 (53 mg, 43%) as a white solid. MS 399.2. [M + H]+.

[00176] Compounds 35 was synthesized in a similar manner as 34 by using pyrazole as a reagent.

[00177] Compound 35. 60 mg, 64%, a white solid.

Example 16 Synthesis of Compound 41


[00178] Synthesis of 2200-A. To a mixture of thiophen-2-ylboronic acid (14.1 g, 110 mmol), 6-chloro-3-nitropyridin-2-amine (17.3 g, 100 mmol) and K2C03 (41.4 g, 300 mmol) in dioxane/H20 (500 mL/50 mL) was added Pd(PPh3)4 (5.8 g, 5.0 mmol) under a nitrogen atmosphere. The reaction mixture was stirred at 100 °C for 2 h and then concentrated in vacuo. The residue was dissolved with EtOAc (200 mL) and the solution was washed with brine (100 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10: 1 to 5 : 1) to give 2200-A (20.4 g, 84 %) as a yellow solid. MS 222.0 [M + H]+.

[00179] Synthesis of 2200-B. To a stirred solution of 2200-A (4.42 g, 20 mmol) in pyridine (80 mL) was added phenyl carbonochloridate (3.12 g, 60 mmol) dropwise at 0 °C. After the addition was completed, the mixture was stirred at 50 °C for 4 h. The mixture was then concentrated in vacuo , and the residue was purified by column chromatography on silica gel (PE : DCM = 3: 2 to 1 : 1) to give 2200-B (8.57 g, 93%) as a yellow solid. MS 462.1 [M + H]+.

[00180] Synthesis of2200-D. A mixture of 2200-C (108 mg, 0.44 mmol) and Pd/C (108 mg) in EtOAc (15 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (EtOAc : PE = 1 : 5) to give 41 (100 mg, 92%) as a white solid. MS 250.1 [M + H]+

[00181] Synthesis of2200-E. To a solution of 2200-D (100 mg, 0.40 mmol) in DCM (3 mL) was added TFA (1 mL) dropwise at °C. The resulting solution was stirred at room temperature for 1 h, and then the solvent was removed in vacuo to give 2200-E as a crude product which was used directly in the next step. MS 194.1 [M + H]+.

[00182] Synthesis of 2200-F. A mixture of 2200-E (0.4 mmol, crude product from previous step) and 2200-B (103 mg, 0.22 mmol) in DMSO (6 mL) was stirred at room temperature for 10 min, then Na2C03 (234 mg, 2.2 mmol) was added and the reaction mixture was stirred at room temperature for 2 h. The mixture was diluted with water (30 mL) and extracted with EtOAc (10 mL x 3). The combined organic layers were washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (DCM : EtOAc = 1 : 1) to give 2200-F (80 mg, 91%) as a yellow solid. MS 397.0 [M + H]+.

[00183] Synthesis of 41. A mixture of 2200-F (80 mg, 0.20 mmol) and Raney-Ni (80 mg) in MeOH (15 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Raney-Ni was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 20 : 1) to give 41 (43 mg, 58%) as a brown solid. MS 367.2 [M + H]+

[00184] Compound 42 was synthesized in a similar manner as 41 by using methyl magnesium bromide and appropriately substituted boronic acid reagent.

[00185] Compound 42. 23 mg, 31%, a yellow solid.

Example 17 Synthesis of 43 and 44


[00186] Synthesis of 2332-A. A mixture of 2147-A (1.0 g, 3.8 mmol) and Pd/C (1.0 g) in EtOAc (20 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (PE : EtOAc =5 : 1 to 3 : 1) to give 2332-A (1.0 g, 99%) as a white solid. MS 268.1 [M + H]+.

[00187] Synthesis of 2332-B. A solution of 2332-A (1.0 g, 3.7 mmol) in DCM (21 mL) was cooled to 0 °C and TFA (7 mL) was added dropwise at 0 °C. The reaction mixture was allowed to warm to room temperature and was stirred at room temperature for 1 h. The solvent was then removed in vacuo , and the residue was dissolved in DMF (7 mL) and treated with TEA (1.01 g, 10 mmol) to give 2332-B as a solution used to next step directly. MS 168.1 [M + H]+.

[00188] Synthesis of 2332-C. To a solution of thiophene (20.0 g, 238 mmol) in THF (500 mL) under nitrogen atmosphere was added //-BuLi (100 mL, 250 mmol) dropwise at -78 °C and the reactin was stirred at -78 °C for 1 h under a nitrogen atmosphere. Then N-fluorobenzenesulfonimide (78.8 g, 250 mmol) in THF (300 mL) was added into above mixture dropwise at -78 °C and warmed to room temperature for 1 h. Then the reaction mixture was cooled to -78 °C, and another portion of //-BuLi (100 mL, 250 mmol) was added dropwise at -78 °C and stirred at -78 °C for 1 h. Finally, 2-isopropoxy-4,4,5,5-tetramethyl- l,3,2-dioxaborolane (46.5 g, 250 mmol) in THF (200 mL) was added into above mixture dropwise at -78 °C, and the reaction mixture was allowed to warm to room temperature and stirred for 16 h. The mixture was poured into cooled saturated NH4Cl (2000 mL), extracted with PE (400 mL x 3), and the combined organic layers were washed with brine (400 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo to give 2332-C (32 g) as a crude product used to next step directly. MS 229.0 [M+H]+.

[00189] Synthesis of 2332-D. A mixture of 6-chloro-3-nitropyridin-2-amine (18.9 g, 109.6 mmol), 2332-C (30 g, crude product from previous step) and K2C03 (45.37 g, 328.8 mmol) in dioxane/H20 (400 mL/40 mL) was treated with Pd(PPh3)4 (2.0 g) under a nitrogen

atmosphere. The mixture was stirred at 95 °C for 3 h and then concentrated in vacuo. The residue was dissolved with EtOAc (500 mL) and the solution was washed with brine (200 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo.

The residue was purified by column chromatography on silica gel (PE : DCM = 10 : 1 to 2 :

1) to give 2332-D (9.0 g, 34%(two steps)) as a yellow solid. MS 240.0 [M + H]+.

[00190] Synthesis of2332-F. A solution of 2332-D (820 mg, 3.43 mmol) in DMF (10 mL) was cooled to 0 °C and treated with NaH (60% in mineral oil) (275 mg, 6.86 mmol). The reaction mixture was stirred at 0 °C for 30 min, then CDI (556 mg, 3.43 mmol) was added into above mixture and stirring continued at 0 °C for another 30 min. Finally, the solution of 2332-B was added into above mixture at 0 °C and stirred for 1 h. The mixture was then quenched with water (60 mL) and extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (30 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (DCM : EtOAc = 15 : 1 to 2 : 1) to give 2332-F (1.18 g, 80 %) as a yellow solid. MS 433.0 [M + H]+.

[00191] Synthesis of T-2332. A mixture of 2332-F (1.18 g, 2.7 mmol) and Raney-Ni (1.2 g) in MeOH (20 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Raney-Ni was removed by filtration through apad of Celite. The filtrate was concentrated in vacuo and the residue was purified by column chromatography on silica gel (DCM : MeOH = 50 : 1 to 20 : 1) to give T-2332 (850 mg, 77%) as a red solid. MS 403.0 [M + H]+.

[00192] Chiral-separation of 43 and 44. T-2332 (850 mg, 2.11 mmol) was separated by chiral separation (Column: Chiralcel OJ-3; Solvent: MeOH; Flow rate: 2 mL/min; RT43 = 2.141 min, RT44 = 2.689 min) to give 43 (300 mg, 35%) as a light purple solid (MS 403.0 [M+H]+) and 44 (190 mg, 22%) as a white solid. MS 403.0 [M+H]+.

Example 18 Synthesis of Compound 52 & 53


[00193] Synthesis of 2303-A. 2 -chloro-5-fluoropyrimidine (50 g, 378.0 mmol) was stirred in a solution of HBr in AcOH (33 wt %, 250 mL) at 40 °C for 16 h. The reaction mixture was then cooled to room temperature and the precipitate was collected by filtrate. The filter cake was dissolved in EtOAc (500 mL) and basified to pH = 9 with saturated Na2C03. The resulting mixture was extracted with EtOAc (500 mL x 2). The combined organic layers were washed with brine (100 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. PE (20 mL) was added into the residue and the precipitate was collected by filtration, then dried in vacuo to give 2303-A (35.0 g, 53%) as a light brown solid. MS 177.2 [M+H]+.

[00194] Synthesis of 2303-B. To a solution of 2303-A (5.0 g, 28.4 mmol) in DCM (70 mL) was added n-BuLi (13.6 mL, 34.1 mmol) dropwise at -78 °C and the reaction mixture was stirred for 1 h under N2 atmosphere. Then a solution of SM-A (6.3 g, 34.1 mmol) in DCM (20 mL) was added into the mixture dropwise. The resulting mixture was warmed to room temperature and stirred for 3 h. The mixture was then diluted with saturated NH4Cl (100 mL), extracted with DCM (100 mL x 3). The combined organic layer was washed with brine (100 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 2303-B (550 mg) as a crude product. The crude product was purified by Prep-HPLC to give 2303-B (177 mg, 2.2%) as a brown solid. MS 284.2 [M+H]+.

[00195] Synthesis of2303-C. A solution of 2303-B (1.6 g, 5.63 mmol) in DCM (50 mL) was treated with DAST (3.2 mL) dropwise at -78 °C under a N2 atmosphere. Then the solution was warmed to room temperature and stirred for 2 h. The reaction was then quenched with ice water, extracted with DCM (30 mL x 3). The combined organic layer was washed with brine (100 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 :

1 ~ 1 : 1) to give 2303-C (850 mg, 53%) as a brown solid. MS 286.2 [M+H]+.

[00196] Synthesis of2303-D. To a solution of 2303-C (850 mg, 2.98 mmol) in DCM (30 mL) at 0 °C was added TFA (4 mL) dropwise. Then the solution was allowed to warm to room temperature and was stirred at room temperature for 1 h. The solvent was removed in vacuo to give 2303-D as a crude product which was used directly in the next step.

[00197] Synthesis of2303-E. To a solution of SM-B (1.2 g, 2.48 mmol) and 2303-D (1.1 g, crude product from last step) in DMSO (50 mL) was added Na2C03 (3.2 g, 29.8 mmol). The mixture was stirred at room temperature for 2 h. The mixture was diluted with water (200 mL), extracted with EtOAc (100 mL x 3). The combined organic layers were washed with brine (100 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (PE : EtOAc = 1 : 5) to give 2303-E (680 mg, 61%) as a yellow solid. MS 445.2 [M+H]+.

[00198] Synthesis of 52 and 53. A mixture of 2303-E (680 mg, 1.53 mmol) and Raney-Ni (680 mg) in MeOH (10 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Raney-Ni was then removed by filtration through the Celite. The filtrate was concentrated and the residue was purified by Prep-TLC (EA : MeOH = 10 : 1) to give T-2303 (600 mg, 94%) as a yellow solid. The enantiomers were separated by chiral SFC (Column: Chiralcel OJ-3; Solvent: MeOH; Flow rate: 1.5 mL/min; RTs2 = 1.869 min, RT53 = 2.848 min) to give 52 (250 mg, 41%) as a yellow solid . MS 415.2 [M+H]+. 53 (240 mg, 40%) as a yellow solid. MS 415.2 [M+H]+.

Example 19 Synthesis of Compound 54 and 55


[00199] Synthesis of 2294-A. To a solution of 3-bromopyridazine (50.0 g, 314.5 mmol) in DCM (400 mL) was added n-BuLi (2.5 M in hexane)(l50 mL) dropwise at -78°C under a N2 atmosphere and the reaction mixture was stirred at -78°C for 1 h. Then a solution of tert-butyl 3-oxopyrrolidine-l-carboxylate (69.7 g, 377.0 mmol) in DCM (200 mL) was added into the above mixture and the mixture was warmed to room temperature and stirred for 3 h. The reaction mixture was poured into saturated NH4Cl (300 mL), then extracted with DCM (400 mL x 3), washed with brine (300 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to EtOAc) to give 2294-A (7.0 g) as a crude product. MS 266.2 [M+H]+.

[00200] Synthesis of 2294-B. A solution of 2294-A (7.0 g, crude product from last step) in DCM (100 mL) was cooled to -78 °C and treated with DAST (3.0 mL) dropwise, and the reaction mixture was then allowed to warm to room temperature and stirred at room temperature for 2 h. The mixture was then diluted with water (100 mL), extracted with DCM (50 mL x 3). The combined organic layer was washed with brine (80 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (EtOAc : PE = 10 : 1 ~ 1 : 1) to give 2294-B (2.5 g, 3%)(two steps) as a brown solid. MS 268.2 [M+H]+.

[00201] Synthesis of 2294-C. A solution of 2294-B (2.5 g, 9.4 mmol) in DCM (24 mL) was cooled to 0 °C and treated with TFA (8 mL). The reaction mixture was allowed to warm to room temperature following the addition, and was stirred at room temperature for 1 h. The solution was concentrated in vacuo to give 2294-C as a crude product which was used directly in the next step. MS 168.2 [M+H]+.

[00202] Synthesis of2294-D. A solution of SM-A (2.5 g, 5.3 mmol) and 2294-C (9.4 mmol, crude product from last step) in DMSO (50 mL) was treated with Na2C03 (5.5 g, 52.2 mmol). The reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (150 mL), extracted with EtOAc (100 mL x 3), and the combined organic layers were washed with brine (100 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (EtOAc to EtOAc : MeOH = 30 : 1) to give 2294-D (1.4 g, 82%) as a yellow solid. MS 427.2 [M+H]+.

[00203] Synthesis of T-2294. A mixture of 2294-D (1.4 g, 3.3 mmol) and Raney-Ni (1.0 g) in DCM/MeOH (10 mL/l0 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Raney-Ni was then removed by filtration through Celite. The filtrate was concentrated and the residue was purified by column chromatography on silica gel (EtOAc to EtOAc : MeOH = 10 : 1) to give T-2294 (800 mg, 61%) as a gray solid. MS 397.2 [M+H]+.

[00204] Chiral-separation of 55. T-2294 (800 mg, 2.02 mmol) was separated by chiral SFC (Column: Chiralcel OJ-3; Solvent: MeOH; Flow rate: 2 mL/min; RT55 = 2.599 min) to give 55 (226 mg, 17%) as a yellow solid, (RT54 = 1.854 min) to give 54 (226 mg, 17%) as a yellow solid.. MS 397.2 [M+H]+.

Example 20 Synthesis of 39 and 40


[00205] Synthesis of2201-A. To a solution of thiophene (20.0 g, 238 mmol) in THF (400 mL) was added n-BuLi (2.5 M in hexane)(l00 mL) dropwise at -78 °C and the reaction mixture was stirred at -78 °C for 1 h. Then a solution of NFSI (78.8 g, 250 mmol) in THF (400 mL) was added into the above solution dropwise at -78 °C, and the reaction mixture was warmed to room temperature and stirred for 1 h. Then the reaction mixture was cooled again to -78 °C another portion of n-BuLi (2.5 M in hexane)(l00 mL) was added dropwise into the above mixture at -78 °C and stirring was continued at -78 °C for 1 h. Finally, a solution of 2-isopropoxy-4,4,5,5-tetramethyl-l,3,2-dioxaborolane (46.5 g, 250 mmol) in THF (200 mL) was added into above solution dropwise at -78 °C. The reaction mixture was warmed to room temperature for 16 h. The reaction mixture was poured into saturated NH4Cl (1000 mL), then extracted with PE (300 mL x 3), and washed with brine (300 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo to give 2201-A (32 g) as a crude product. MS 147.1 [M - 82]+.

[00206] Synthesis of 2201 -B. A mixture of 6-chloro-3-nitropyridin-2-amine (18.9 g, 109.6 mmol), 2201-A (32 g, crude product from last step) and K2C03 (45.4 g, 328.8 mmol) in dioxane/H20 (400 mL/40 mL) was added Pd(PPh3)4 (2.0 g, 1.73 mmol) under N2 atmosphere. The mixture was stirred at 95 °C for 4 h and then concentrated in vacuo. The residue was dissolved with EtOAc (300 mL) and the solution was washed with brine (100 mL x 3). The organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : DCM = 10 : 1 - 2 : 1) to give 2201-B (9.0 g, 34%) as a yellow solid. MS 240.1 [M + H]+.

[00207] Synthesis of2201-C. A stirred solution of 2201-B (460 mg, 1.92 mmol) in pyridine (10 mL) was treated with phenyl carbonochloridate (900 mg, 5.77 mmol) dropwise. After the addition was completed, the mixture was stirred at 55 °C for 2 h. The mixture was concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE: DCM = 20 : 1 - 1 : 3) to give 2201-C (700 mg, 76%) as a yellow solid. MS 479.8 [M+H]+.

[00208] Synthesis of2201-D. To a solution of 2201-C (106 mg, 0.22 mmol) and 2145-B (200 mg, 0.40 mmol) in DMSO (10 mL) was added Na2C03 (233 mg, 2.2 mmol). The reaction mixture was stirred at room temperature for 2 h. The mixture was diluted with water (30 mL), extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (PE : EA = 1 : 5) to give 2201-D (75 mg, 82%) as a yellow solid. MS 415.2 [M+H]+.

[00209] Synthesis of T-2201. To a solution of 2201-D (75 mg, 0.18 mmol) and Raney-Ni (75 mg) in DCM/MeOH (3 mL/5 mL) was stirred at room temperature for 0.5 h. Raney-Ni was removed by filtration through the Celite. The filtrate was concentrated and the residue was purified by Prep-TLC (EA : MeOH = 10 : 1) to give T-2201 (15 mg, 22%) as a gray solid. MS 385.2 [M+H]+.

[00210] Chiral-separation of 39 and 40. T-2201 (1.0 g, 2.6 mmol) was separated by chiral separation (Column: Chiralcel OJ-3; Solvent: MeOH; Flow rate: 1.5 mL/min; RT39 = 2.225 min, RT4O = 2.667 min) to give 39 (300 mg, 30%) as a brown solid (MS 385.0 [M+H]+) and 40 (300 mg, 30%) as a purple solid. MS 385.0 [M+H]+.

[00211] Compound 49 was synthesized in a similar manner as 39 and 40 by using the appropriately substituted boronic acid and aryl bromide reagents. Compound 49. 30 mg,

23%, a yellow solid.

Example 22 Synthesis of 36


[00213] Synthesis of 2066-A. A solution of 2475-B (400 mg, 1.7 mmol) in THF (10 mL) was treated with FDA (2.6 mL, 5.2 mmol) dropwise at -78 °C under a nitrogen atmosphere and stirred for 1 h at -78 °C. Then a solution of ie/ -butyl 3-oxoazetidine-l-carboxylate (414 mg, 2.2 mmol) in THF (5 mL) was added into above mixture dropwise at -78 °C and then the reaction mixture was allowed to warm to room temperature and stirred for 16 h. The mixture was diluted with saturated NH4Cl (40 mL), extracted with EtOAc (30 mL x 3). The combined organic layers were washed with brine (30 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was was purified by column chromatography on silica gel (PE : EtOAc = 3 : 1 to EtOAc) to give 2066-A (380 mg, 84%) as a colorless oil. MS 264.2 [M+H]+.S nf¾es7s of 2066-B A mixture of 2066-A (380 mg, 1.4 mmol) and Pd/C (380 mg) in EtOAc (10 mL) was stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was then removed by filtration through a pad of Celite. The filtrate was concentrated to in vacuo and the residue was purified by column chromatography on silica gel (PE : EtOAc = 3 : 1 to EtOAc) give 2066-B (300 mg, 79%) as a colorless oil. MS 266.2 [M+H]+.

[00215] Synthesis of2066-C. To a solution of 2066-B (150 mg, 0.57 mmol) in DCM (6 mL) was added TFA (2 mL) drop wise at 0 °C. The reaction mixture was allowed to warm to room temperature and was stirred at room temperature for 1 h. The solution was concentrated in vacuo to give 2066-C as a crude product which was directly used in the next step. MS 166.2 [M + H]+.

[00216] Synthesis of 2066-D. A mixture of 2066-C (0.57 mmol, crude product from previous step) and 1954-B (154 mg, 0.32 mmol) in DMSO (6 mL) was stirred at room temperature for 10 min, then Na2C03 (339 mg, 3.2 mmol) was added and the reaction mixture was stirred at room temperature for 2 h. The mixture was then diluted with water (20 mL) and extracted with EtOAc (10 mL x 3). The combined organic layers were washed with brine (10 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by Prep-TLC (EtOAc : MeOH = 40 : 1) to give 2066-D (100 mg, 73%) as a yellow solid. MS 443.1 [M + H]+.

[00217] Synthesis of 36. A mixture of 2066-D (100 mg, 0.23 mmol) and Pd/C (100 mg) in MeOH/EtOAc (5 mL/5 mL) was stirred at room temperature for 50 min under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Prep-TLC (DCM : MeOH = 30 : 1) to give 36 (40 mg, 42%) as a yellow solid. MS 413.0 [M + H]+.

Example 23 Synthesis of Compound 47


[00218] Synthesis of2341-A. To a solution of 2-(l-(/eri-butoxycarbonyl)pyrrolidin-3-yl)acetic acid (1.15 g, 5.0 mmol), HOBt (810 mg, 6.0 mmol) and EDCI (1.44 g, 7.5 mmol) in DCM (20 mL) was added DIPEA ( 1.94 g, 15.0 mmol) and stirred at room temperature for 30 min under a nitrogen atmosphere. Then a solution of prop-2-yn-l -amine (413 mg, 7.5 mmol) in DCM (10 mL) was added into above mixture and the resulting mixture was stirred at room temperature for 24 h. The mixture was diluted with DCM (30 mL), washed with 0.5 N HC1 (20 mL x 2), saturated NaHC03 (20 mLx 2) and brine (20 mL x 2). The organic layer was

dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to 2 : 1) to give 2341-A (1.0 g, 75%) as color oil. MS 211.0 [M -55]+.

[00219] Synthesis of2341-B. A solution of 2341-A (580 mg, 2.2 mmol) in acetonitrile (20 mL) was treated with gold trichloride (50 mg, 0.075 mmol) and the reaction mixture was stirred at 45 °C for 72 h under a nitrogen atmosphere. The mixture was concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to 1 : 1) to give 2341-B (380 mg, 66 %) as colorless oil. MS 267.0 [M + H]+.

[00220] Synthesis of2341-C. A solution of 2341-B (380 mg, 1.4 mmol) in DCM (12 mL) was cooled to 0 °C and then TFA (4 mL) was added dropwise. Following the addition the reaction was allowed to warm to room temperature and was stirred at room temperature for 1 h. The reaction mixture was then concentrated in vacuo to give 2341-C as a crude product. Then the residue was dissolved in DMF (6 mL) and was treated with TEA (424 mg, 4.2 mmol) to give 2341-C as a solution which was used directly in the next step. MS 167.0 [M + H]+.

[00221] Synthesis of2341-D. A solution of 1954-A (252 mg, 1.0 mmol) in DMF (5 mL) was cooled to 0 °C and was treated with NaH (60% in mineral oil, 80 mg, 2.0 mmol). The reaction was stirred at 0 °C for 30 min, then CDI (162 mg, 1.0 mmol) was added and the reaction mixture was stirred at 0 °C for another 30 min. Finally, the solution of 2341-C was added into the above mixture at 0 °C and the mixture was stirred at 0 °C for 1 h. The mixture was quenched with water (50 mL) and extracted with EtOAc (20 mL x 3). The combined organic layers were washed with brine (20 mL x 3), dried over anhydrous Na2S04 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE : EtOAc = 10 : 1 to 1 : 2) to give 2341-D (280 mg, 63%) as a yellow solid. MS 444.1 [M + H]+.

[00222] Synthesis of 47. A mixture of 2341-D (280 mg, 0.63 mmol) and Pd/C (280 mg) in MeOH/EtOAc (10 mL/l0 mL) were stirred at room temperature for 1 h under a H2 atmosphere. Pd/C was removed by filtration through a pad of Celite. The filtrate was concentrated in vacuo and the residue was purified by Pre-HPLC to give 47 (220 mg, 85%) as a light yellow solid. MS 414.2 [M + H]+.

Table 1




















HDAC2 and HDAC1 Enzymatic Assay (HDAC2 and HDAC1 IC50 data)

[00223] The following describes an assay protocol for measuring the deacetylation of a peptide substrate by HDAC2 or HDAC1.

[00224] HD AC protein composition and respective substrate peptides are summarized below.

[00225] Assay set up:

[00226] HD AC reactions are assembled in 384 well plates (Greiner) in a total volume of

20 DL as following:

[00227] HDAC proteins are pre-diluted in the assay buffer comprising: lOOmM HEPES, pH 7.5, 0.1% BSA, 0.01% Triton X-100, 25mM KC1 and dispensed into 384 well plate (lOuL per well).

[00228] Test compounds are serially pre-diluted in DMSO and added to the protein samples by acoustic dispensing (Labcyte Echo). Concentration of DMSO is equalized to 1% in all samples.

[00229] Control samples (0% -inhibition in the absence of inhibitor, DMSO only) and l00%-inhibition (in the absence of enzyme) are assembled in replicates of four and used to calculate the % -inhibition in the presence of compounds.

[00230] At this step compounds can be pre-incubated with enzyme if desired.

[00231] The reactions are initiated by addition of lOuL of the FAM-labeled substrate peptide pre-diluted in the same assay buffer. Final concentration of substrate peptide is luM (HDAC 1-2). The reactions are allowed to proceed at room temperature. Following incubation, the reactions are quenched by addition of 50 DL of termination buffer (100 mM HEPES, pH7.5, 0.01% Triton X-100, 0.1% SDS). Terminated plates are analyzed on a microfluidic electrophoresis instrument (Caliper LabChip® 3000, Caliper Life

Sciences/Perkin Elmer) which enables electrophoretic separation of de-acetylated product from acetylated substrate. A change in the relative intensity of the peptide substrate and product is the parameter measured. Activity in each test sample is determined as the product to sum ratio (PSR): P/(S+P), where P is the peak height of the product, and S is the peak height of the substrate. Percent inhibition (Pmh) is determined using the following equation:

Pinh— (PSRo%inh PSRcompound)/(PSRo%inh PSRl00%inh)* 100 , 1P which: PSRcompound IS the product/sum ratio in the presence of compound, PSRo%inh is the product/sum ratio in the absence of compound and the PSRioo%inh is the product/sum ratio in the absence of the enzyme. To determine IC50 of compounds (50%-inhibition) the %-inh data (R^ versus compound concentration) are fit by a 4 parameter sigmoid dose-response model using XLfit software (IDBS).

[00232] The results of this assay for certain compounds are reported in Table 2, below. In the table,“A” indicates a IC50 value of less than 0.5 mM;“B” a IC50 value from 0.5 pM to 1.0 pM;“C” a IC50 value of greater than 1.0 pM and less than or equal to 2.0 pM; and“D” indicates an IC50 value of greater than 2.0 pM. NT = Not Tested.

Table 2





HDAC2 Enzymatic Inhibition Assay in SH-SY5Y Cell Lysate with an Exogenous

Substrate

[00233] SH-SY5Y cells (Sigma) were cultured in Eagle’s Modified Essential Medium supplemented with 10% fetal bovine serum and pen/strep. Twenty-four hours prior to compound dosing 20 uL of cells were plated in white 384 well plates at a density of 1,500 cells/well. Compounds were serially diluted in neat DMSO and then diluted 1:100 v/v into media without FBS and mixed. Media was removed from the plated cells and the diluted compounds in serum free media (1% v/v final DMSO) were added and incubated at 37°C for five hours. Ten uL of HDAC-Glo 2 reagent with 0.1% Triton X-100 was then added, the plate was mixed and allowed to develop at room temperature for 100 minutes. Plates were then read with a Spectramax LMax luminometer employing a 0.4s integration time. Dose response curves were constructed with normalized data where CI-994 at 100 uM was defined as 100% inhibition and DMSO alone as 0% inhibition.

[00234] The results of this assay for certain compounds are reported in Table 3, below. In the table,“A” indicates a IC50 value of less than 0.5 mM;“B” a IC50 value from 0.5 pM to 1.0 pM;“C” a IC50 value of greater than 1.0 pM and less than or equal to 2.0 pM; and“D” indicates an IC50 value of greater than 2.0 pM. NT = Not Tested.

Table 3







Comparison of pyrrolidine rings substituted at the 3-position with heteroaromatic rings or methylene-linked heteroaromatic rings to pyrrolidines substituted with non-aromatic groups at the 3-position for pyrrolidine ureas

[00235] Table 4 below shows direct comparison of the activity levels between certain compounds possessing non-aromatic substitution at the pyrrolidine-3-position and inventive compounds possessing aromatic substitution at the 3-position of the pyrrolidinyl motif (i.e.,

R1 with or without spacer group X). As shown by the data, an increase in potency in the HDAC2 SH-SY5Y cell lysate assay results when the non-cyclic, non-aromatic substituents for R1 in Comparators A-C are replaced with the aromatic pyrimidinyl in Compounds 19 and 20. A similar trend is seen for other compounds in Table 4. Compound 20 with a 5-F-pyrimidine directly linked to the 3-position is >2-fold more potent than Comparator A.

Table 4




[00236] The contents of all references (including literature references, issued patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated herein in their entireties by reference. Unless otherwise defined, all technical and scientific terms used herein are accorded the meaning commonly known to one with ordinary skill in the art.