Wityak 2015 JMC Lead optimization towards PoC tools for HD with a 4-pyrazol-pyrimidine class of pan-JNK inhibitors (1)

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Journal of Medicinal Chemistry is published by the American Chemical Society. 1155Sixteenth Street N.W., Washington, DC 20036Published by American Chemical Society. Copyright © American Chemical Society.However, no copyright claim is made to original U.S. Government works, or worksproduced by employees of any Commonwealth realm Crown government in the courseof their duties.

Article

Lead Optimization Towards Proof of Concept Tools for Huntington?sDisease Within a 4-(1H-Pyrazol-4-yl)pyrimidine Class of pan-JNK InhibitorsJohn Wityak, Kevin F McGee, Michael P Conlon, Ren Hua Song, Bryan C Duffy, Brent Clayton, Michael

Lynch, Gwen Wang, Emily Freeman, James Haber, Douglas B. Kitchen, David D Manning, Jiffry Ismail, YuriKhmelnitsky, Peter C Michels, Jeff Webster, Macarena Irigoyen, Michele Luche, Monica Hultman, Mei Bai,

IokTeng D Kuok, Ryan Newell, Marieke Lamers, Philip Leonard, Dawn Yates, Kim Matthews, Lynette Ongeri,Steve Clifton, Tania Mead, Susan Deupree, Pat Wheelan, Kathyrn A Lyons, Claire Wilson, Alex Kiselyov,

Leticia Toledo-Sherman, Maria Beconi, Ignacio Muñoz-Sanjuan, Jonathan Bard, and Celia DominguezJ. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/jm5013598 • Publication Date (Web): 11 Mar 2015

Downloaded from http://pubs.acs.org on March 16, 2015

Just Accepted

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Muñoz-Sanjuan, Ignacio; CHDI Foundation Inc., Bard, Jonathan; CHDI Foundation Inc., Dominguez, Celia; CHDI Management Inc., Advisors to CHDI Foundation Inc.

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Lead Optimization Towards Proof of Concept Tools for Huntington’s Disease Within a 4-

(1H-Pyrazol-4-yl)pyrimidine Class of pan-JNK Inhibitors

John Wityak,f Kevin F. McGee,

a Michael P. Conlon,

a Ren Hua Song,

a Bryan C. Duffy,

a Brent

Clayton,a Michael Lynch,

a Gwen Wang,

a Emily Freeman,

a James Haber,

a Douglas B. Kitchen,

a

David D. Manning,a Jiffry Ismail,

a Yuri Khmelnitsky,

a Peter Michels,

a Jeff Webster,

a Macarena

Irigoyen,a Michele Luche,

a Monica Hultman,

a Mei Bai,

a IokTeng D. Kuok,

a Ryan Newell,

a

Marieke Lamers,b Philip Leonard,

b Dawn Yates,

b Kim Matthews,

b Lynette Ongeri,

b Steve

Clifton,b Tania Mead,

b Susan Deupree,

c Pat Wheelan,

c Kathy Lyons,

d Claire Wilson,

e Alex

Kiselyov,f Leticia Toledo-Sherman,

f Maria Beconi,

f Ignacio Muñoz-Sanjuan,

f Jonathan Bard,

f

and Celia Dominguezf

aAlbany Molecular Research Inc. (AMRI), 26 Corporate Circle, Albany, NY 12212-5098,

bBioFocus Discovery Services, Charles River Laboratories, Chesterford Research Park, CB10

1XL, UK, cTandem Labs, 2202 Ellis Road, Durham, NC 27703, dKathryn A. Lyons,

Pharmacokinetics Consultant to CHDI, P.O. Box 64, Holland, NY 14080, eEvotec, 114 Milton

Park, Abingdon, OX14 4SA, UK, fCHDI Foundation, Inc., 6080 Center Drive, Suite 100, Los

Angeles, CA 90045

Abstract

Through medicinal chemistry lead optimization studies focused on calculated properties and

guided by x-ray crystallography and computational modeling, potent pan-JNK inhibitors were

identified that showed sub-micromolar activity in a cellular assay. Using in vitro ADME

profiling data, 9t was identified as possessing favorable permeability and a low potential for

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efflux, but was rapidly cleared in liver microsomal incubations. In a mouse pharmacokinetics

study, compound 9t was brain penetrant after oral dosing, but exposure was limited by high

plasma clearance. Brain exposure at a level expected to support modulation of a

pharmacodynamic marker in mouse was achieved when the compound was co-administered with

the pan-cytochrome P450 inhibitor 1-aminobenzotriazole.

Introduction

The c-Jun N-terminal serine/threonine protein kinases (JNKs) are a mitogen-activated protein

kinase family that regulates signal transduction events in response to environmental stress. To

date, three distinct jnk genes have been identified (jnk1, jnk2, and jnk3), expressing 10 isoforms

and splice variants of JNK proteins. Whereas JNK1 and JNK2 are ubiquitously expressed, JNK3

is present primarily in brain, with lower expression found in testis, heart, and pancreatic β cells.1

Activation of JNK has been implicated in chronic neurodegenerative disorders such as

Parkinson’s and Alzheimer’s diseases.2,3 Genetic ablation of the murine jnk3 gene resulted in

mice that were resistant to the excitotoxic glutamate-receptor agonist kainic acid, leading to a

reduction in seizure activity.4 Recent reports describe orally bioavailable, ATP-competitive,

JNK inhibitors that have shown beneficial effects in vitro and in vivo.5,6 In addition, JNK

substrate-competitive peptides have shown beneficial effects in models of ischemia and

Alzheimer’s disease.7,8

Of particular interest were reports implicating increased JNK expression and activity in cellular9,

10, 11, 12. 13, 14 and in vivo models15,16 of Huntington’s disease (HD), an autosomal dominant,

progressive neurodegenerative disease that is characterized clinically by motor, cognitive, and

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behavioral deficits. In addition, a role for JNK3 in fast axonal transport (FAT) was demonstrated

in squid axoplasm perfused with mutant huntingtin protein, where JNK3 was shown to

phosphorylate kinesin-1 heavy chain and decrease FAT.17 Due to its reported role in neuronal

cell death, apoptosis, cargo transport, and its restricted tissue distribution, JNK3 is an attractive

target for potential therapeutic intervention in HD. We therefore desired a potent, selective, and

brain penetrant JNK3 inhibitor for proof of concept (POC) studies.

There have been many reports of JNK inhibitors from a wide variety of ATP competitive and

non-competitive chemotypes.18,19 Review of this literature revealed several compounds for

benchmarking efforts, the results of which are summarized in the Supplementary Information

section. Our minimum requirements for a POC compound is a pan-JNK inhibitor having > 100-

fold selectivity against p38 MAPK (itself a partially validated HD target of interest) and

adequate cellular potency and brain exposure to affect a pharmacodynamic (PD) marker.

Potential choices considered for a cellular assay were inhibition of phosphorylation of c-Jun or

ATF-2 substrates with reduction of phosphorylated c-Jun (p-c-Jun), or ATF-2 as the PD marker.

In addition, a POC compound would need to have adequate ADME properties, as determined in

solubility, permeability/efflux, and microsomal stability assays. Attesting to the challenge, none

of the benchmark compounds were judged suitable for advancement into mouse HD models.

Concurrent with these benchmarking studies, and to further facilitate identification of novel

starting points, a docking-based virtual screen was conducted based on the x-ray crystal structure

of JNK3 in complex with an imidazole-pyrimidine inhibitor (1pmq) from the Protein Data Bank

(PDB, www.rcsb.org). A compound library of approximately two hundred thousand compounds

from Asinex’s “privileged” collections was docked against a protein grid generated from the

1pmq structure. Of the 1100 virtual hits selected for wet screening a set of approximately 90

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were confirmed as actual hits. Among these, pyrazole 1 was identified as an attractive starting

point for medicinal chemistry and was advanced into hit to lead studies based upon favorable

JNK3 potency, chemical tractability, and a small base of published SAR including potent activity

in a cellular p-c-Jun assay.20 Profiling studies revealed 1 to be a pan-JNK inhibitor with

favorable permeability, but suffering a high rate of metabolism in mouse liver microsomes

(mLM) and poor selectivity against p38α.

Table 1. Activity Profile of Pyrazole 1.

JNK3

IC50 ± SD

(nM)

JNK1

IC50 ± SD

(nM)

JNK2

IC50 ± SD

(nM)

p38αααα IC50

± SD

(nM)

Caco-2

Papp A-B

(nm·sec-1

)

Caco-2

Papp B-A

(nm·sec-1

)

mLM Clint

(µµµµL/min/mg)

hLM Clint

(µµµµL/min/mg)

433 ± 208 737 ± 281 161 ± 77 24 ± 18 467 242 81.8 < 23.1

The x-ray crystal structure of human JNK3 in complex with 1 at 2.3 Å resolution confirmed the

mode of binding indicated by the docking studies, showing a single hydrogen bond between the

pyridine ring to the backbone NH of Met149 in the linker region of the protein (Figure 1). As

has been observed in several JNK3 structures, including 1pmq, a water molecule mediates a

hydrogen bond interaction between the pyrazole ring and the charged terminal amino group of

Lys93. The chlorophenyl substituent occupies the hydrophobic region I and appeared to cause

an induced-fit movement of the hydrophobic side chain of Met146 towards the back of the

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binding pocket, as compared to its position in the structure of JNK3 in complex with adenosine.

This movement further causes a perturbation in the side chain position of Ile124. We noted that

in the structures of JNK3 complexes in the PDB that the hydrophobic side chain of Met146 is

observed to occupy two predominant rotameric states depending of the hydrophobic nature of the

bound inhibitor.21,22 We postulated that inhibitors bearing a hydrophobic group such as in

pyrazole 1 may induce the side chain of Met146 to adopt the rotameric state mimicking the

corresponding pocket of p38, which could explain the lack of selectivity observed against p38.

An analysis and superposition of crystal structures of p38 and JNK3 with compounds of similar

chemotypes containing groups occupying the hydrophobic pocket reveals such similarity23,24.

This knowledge base informed our SAR exploration around this chemotype and resulted in the

design of compounds that would induce the engagement of the Met146 side chain as observed in

the adenosine structure, thus blocking the hydrophobic pocket of hydrophobic region 1. Docking

grids were prepared for JNK1, JNK2, JNK3, and p38; docking and scoring was used as a tool to

guide the medicinal chemistry efforts of the group.

A B

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Figure 1. 2Fo-Fc electron density map contoured at 1σ showing A) pyrazole 1 binding in the

JNK3 active site, B) a three dimensional schematic depicting the binding of pyrazole 1 (green) to

JNK3 (yellow) overlapped with the binding of adenosine in the JNK3 active site (aqua)

highlighting the alternate positions of Met146 and its effect of Ile124.

Synthesis of inhibitors

We chose to focus an SAR study around the 4-(pyrazol-4-yl)pyrimidine scaffold. Synthesis of

these pyrazoles was readily accomplished using a variation on the Knorr pyrazole synthesis

illustrated in Scheme 1. Alkylation of 4-methylpyrimidine 2 with ester 3 in the presence of

sodium hexamethyldisilazide gave a mixture of keto and enol tautomers 4 and 4’. Reaction with

dimethylformamide dimethylacetal (DMF-DMA) then afforded the intermediate enaminone,

which was followed by cyclization in the presence of hydrazine or a mono-substituted hydrazine

to give pyrazole 5. Oxidation using mCPBA then provided sulfone 6. For compounds in which

R2 is a hydrogen atom, the introduction of a tetrahydropyran (THP) protecting group at this

stage, giving 7, avoids the large excess of amine necessary in the subsequent amination step.

Protection in this way suppresses a competing dimerization process which was prominent with

poorly nucleophilic amines (NH2R1). Microwave assisted amination to provide 8 followed by

THP removal under acidic conditions affords 9. It should be noted that in every instance, the

regiochemistry of cyclization with a mono-substituted hydrazine was confirmed as the 2,3-

regioisomer (as depicted in 7-9) through Heteronuclear Multiple Bond Correlation (HMBC) and

NOE NMR experiments (see Supporting Information).

Scheme 1. General synthesis of pyrazolesa

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aReagents and conditions: (a) NaHMDS, THF, 60 °C, 4 d; (b) DMF-DMA, tol, 110 °C, 6 h, then

NH2NHR2, RT, 16 h; (c) mCPBA, CH2Cl2, 0 °C, 16 h; (d) 3,4-dihydro-2H-pyran, p-TsOH, RT, 10 min;

(e) NH2R1, dioxane, MW, 160 °C, 1 h; (f) HCl-dioxane, MeOH, RT, 2 h.

The synthesis of 3-trifluoromethyl pyrazole 9o required an alternative synthetic route due to the

poor reactivity of enol ether 10 (Scheme 2). Enol-ether 11a, prepared by standard methods, was

treated with triethyl orthoformate to provide enol ether 12. Cyclization with methyl hydrazine

provided pyrazole 13, which was converted to 2-thiomethylpyrimidine 14 following a two-step

cyclization procedure. Oxidation to the activated sulfone 15, followed by displacement with

excess trans-4-aminocyclohexanol gave 9o.

Scheme 2. Synthesis of 3-trifluoromethylpyrazole 9oa

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aReagents and conditions: (a) HC(OEt)3, Ac2O, reflux, 19 h; (b) NH2NHCH3, THF, -10 °C, 1.25 h; (c)

DMF-DMA, tol, 110 °C, 20 h; (d) methyl carbamimidothioate, NaOMe, i-PrOH, 12 h; (e) mCPBA,

CH2Cl2, 0 °C, 16 h; (f) NH2R1, dioxane, 160 °C, 1 h.

The synthesis of 5-chloropyrimidine 9mm is shown in Scheme 3. Cyclization of ethyl

acetoacetate 11b with S-methylisothiouronium sulfate gave pyrimidone 16 in good yield.

Chlorination using sulfuryl chloride provided chloride 17, which was further chlorinated using

phosphorus oxychloride to give dichloride 18. Regioselective hydrogenolysis of the 4-chloro-

substituent led to 5-chloropyrimidine 19. It should be noted that chloride 19 was quite volatile,

and caution must be exercised during solvent removal. Reaction of 19 with N-methoxy-N-

methyl-1-(trifluoromethyl)cyclopropanecarboxamide then gave ketone 20. Pyrazole formation

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using DMF•DMA followed by hydrazine provided pyrazole 21 in poor isolated yield. It was

likely that the presence of the chloride on the pyrimidine modulated reactivity. Several

subsequent steps required more forcing conditions, resulting in lower yields. Oxidization to

methylsulfone 22 using mCPBA, THP protection to give pyrazole 23, and methylsulfone

displacement using 4,4-difluorocyclohexylamine under microwave assisted heating afforded 24.

Deprotection under standard conditions completed the synthesis of 9mm in low overall yield.

Scheme 3. Synthesis of 5-chloropyrimidine 9mma

aReagents and conditions: (a) S-methyl isothiouronium sulfate, Na2CO3, H2O, RT, 16 h, 43%; (b) SO2Cl2,

FeCl3, AcOH, Ac2O, 100 °C, 36 h, 69%; (c) POCl3, DMA, 115 °C, 15 h, 75%; (d) H2, Pd-C, NaOH, H2O,

RT, 24 h, 75%; (e) N-methoxy-N-methyl-1-(trifluoromethyl)cyclopropanecarboxamide, NaHMDS, THF,

0 °C-RT, 16 h, 79%; (f) DMF-DMA, MeOH, 110 °C, 6 h; then NH2NH2, THF, RT, 16 h, 5%; (g)

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mCPBA, CH2Cl2, RT, 16 h, 49%; (h) 3,4-dihydro-2H-pyran, p-TsOH, 0 °C, 5 min, 99%; (i) 4,4-

difluorocyclohexylamine, DMSO, Et3N, MW, 130 °C, 3 h, 17%; (j) HCl-dioxane, MeOH, RT, 2 d, 85%.

Preparation of pyrimidine 25 is shown in Scheme 4. Reaction of cyclopropanecarboxylic acid 26

with N-methoxy methylamine afforded Wienreb amide 27, which was subsequently used to

acylate 2-chloro-4-methylpyridine to give 28 in good yield. Pyrazole formation to provide 29 and

protection as the THP to give 30 was followed by Buchwald–Hartwig reaction with 3,3-

difluorocyclobutylamine (31), giving aminopyridine 32. Removal of the THP under standard

conditions then afforded 25.

Scheme 4. Synthesis of 2-aminopyridine 25a

aReagents and conditions: (a) NH(OCH3)CH3 • HCl, EDC, HOBt, Et3N, CH2Cl2, RT, 90%; (b) LHMDS,

2-chloro-4-methylpyridine, THF, 55%; (c) DMF-DMA, MeOH, 110 °C, 6 h; then NH2NH2, THF, RT, 16

h, 68%; (d) 3,4-dihydro-2H-pyran, p-TsOH, 0 °C, 5 min, 95%; (e) 31, (tBu3P)2Pd(0), NaOtBu, dioxane,

130 °C, 16 h; then HCl, i-PrOH, RT, 2 d, 16%.

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Results and Discussion

Based upon the binding mode of 1, we expected to gain potency through the addition of an amine

containing substituent at the pyrimidine 2-position. This would complete the double hinge

hydrogen bond interaction with Met149 and would introduce the possibly of gaining favorable

interactions with residues in the sugar region. Our SAR investigation began with preparation of

a series of analogs in which the R3 group was fixed as 4-chlorophenyl with the incorporation of a

small set of amines at the 2-position (Table 2). The incorporation of a 2-amino moiety on the

pyrimidine resulted in a one to two order of magnitude improvement in JNK3 activity relative to

1, with 4-hydroxycyclohexylamine 9c showing potent activity but little selectivity against JNK1,

JNK2, or p38α. The lack of selectivity against JNK1 and JNK2 was expected, as the ATP

binding site of the JNK isoforms are highly conserved (98% homology), with the only residue

differences being Met115 in JNK1/3 versus Leu77 in JNK2, and Leu144 in JNK2/3 versus

Ile106 in JNK1. Several groups have used these differences to gain some degree of selectivity

among the JNK isoforms.25,26,27,28,29 The lack of selectivity against p38 was also predicted since

the chlorophenyl substituent had been preserved and was expected to occupy the hydrophobic

region I, as depicted in Figure 1, in both the JNKs and p38.

Table 2. JNK and p38α Potency of (4-Chlorophenyl)pyrazol-3-yl Derivativesa

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Cmpd R1 JNK3

IC50 ± SD

(nM)

JNK1

IC50 ± SD

(nM)

JNK2

IC50 ± SD

(nM)

p38αααα IC50

± SD

(nM)

9a

36 ± 9.3 119 ± 15.5 26 ± 2.1 6.2 ± 1.6

9b

81 ± 18 269 ± 50.2 62 ± 15 113 ± 74.1

9c

5.4 ± 1.7 26 ± 13 15 ± 2.8 3.2 ± 1.5

9d

14 ± 6.2 32 ± 9.3 19 ± 2.6 14 ± 5.5

aValues accompanied by standard deviation were averaged from at least two independent experiments.

The next set of analogs kept the trans-4-hydroxycyclohexylamine at R1 constant and probed the

R3 position (Table 3). Most significantly, selectivity against p38α was achieved by replacing the

3-aryl moiety with saturated groups. tert-Butyl derivative 9e was the most potent compound of

this set, showing an IC50 value of 13 nM. Compounds 9f-h were also potent JNK3 inhibitors,

affording inhibition constants of approximately 20 nM. Cyclopropyl 9i gave up 2-fold potency

to this group, with tetrahydropyran 9j another 2-fold less potent. The importance of a lipophilic

substituent at R3 to potency was further established by the order of magnitude loss seen with

pyrazole 9k. As expected, little selectivity was observed against the JNK1 or JNK2 isoforms.

Table 3. JNK and p38α Potency of trans-4-Hydroxycyclohexylamine Derivativesa

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Cmpd R3 JNK3

IC50 ± SD

(nM)

JNK1

IC50 ± SD

(nM)

JNK2

IC50 ± SD

(nM)

p38αααα IC50

± SD

(nM)

9e

13 ± 1.0 16 ± 3.5 17 ± 0.0 > 10000

9f

16 ± 3.5 22 ± 3.5 24 ± 7.8 5560

9g

22 ± 4.6 24 ± 0.71 28 ± 4.9 > 10000

9h

26 ± 1.1 22 ± 2.8 28 ± 1.4

5940 ± 1420

9i

42 ± 4.9 26 ± 2.8 43 ± 5.6 > 10000

9j

73 ± 28 33 ± 8.1 51 ± 10 7450 ± 2295

9k H 487 ± 57.8 266 ± 99.7 550 ± 106 NTb


bNT indicates not tested.

Noting the generally favorable selectivity against p38α for this set, we obtained a co-

structure of JNK3 with pyrazole 9e at 2.3 Å resolution (Figure 2). Inspection of the structure

revealed the expected double hinge interaction of the N1 pyrimidine and NH-linker moiety with

the carbonyl and NH of Met149, and a water-mediated hydrogen bonding interaction with the

side chain of Lys93. The cyclohexyl ring pointed towards the solvent interphase and occupied

the hydrophobic region II, with its hydroxyl substituent forming a hydrogen bond to Gln155.

Unexpectedly, the pyrazole had rotated about the pyrazole pyrimidine bond, bringing the tert-

butyl group and the cyclohexanol in close proximity due to an apparent favourable

intramolecular hydrophobic contact. In this “horseshoe” conformation the tert-butyl group

occupied the sugar pocket and made hydrophobic interactions with Val78, Ala91, and Leu206.

Interestingly, since no portion of compound 9e occupied the hydrophobic region I, this allowed

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the side chain of Met146 to populate its “natural” adenosine-bound rotamer, and thus occupy the

hydrophobic region I, leading to favorable selectivity against p38. The relatively weak JNK3

activity of 9k, which is devoid of a hydrophobic moiety at R3, highlights the importance of the

placement of a hydrophobic moiety in the ribose pocket, aiding intramolecular stabilization of

the horseshoe conformation.

A B

Figure 2. 2Fo-Fc electron density map contoured at 1σ showing A) 9e binding in the JNK3

active site, B) a three dimensional schematic showing the binding of 9e (pink) to JNK3 (aqua)

overlapped with the binding of 1 (green) in the JNK3 active site (yellow).

Compounds 9e and 9j were taken into in vitro ADME assays (Table 4). Both compounds

showed low solubility, were rapidly metabolized in mLM, and had good stability in human liver

microsomal incubations (hLM). Permeability and P-gp mediated efflux were determined in an

MDCK-MDR1 transfected cell line. Tetrahydropyran 9e displayed good permeability but had

moderate to high P-gp efflux, whereas 9j showed low permeability accompanied by moderate to

high efflux.

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Table 4. Results of In Vitro ADME Profiling

Cmpd

No.

JNK3

IC50

(nM)

Aq. Sol.

(mg/mL)

mLM Clint

(µµµµL/min/

mg)

hLM Clint

(µµµµL/min/

mg)

MDCK

Papp A-B

(nm-s-1

)

MDCK

-MDR1

EER

9e 13 0.028 498.8 < 23.1 253 9

9j 73 0.037 39.8 < 23.1 38 14

Our strategy to improve efflux to an acceptable level was to reduce the number of hydrogen bond

donors. Tactics included alkylation of the pyrazole ring and replacement of the cyclohexanol

moiety, resulting in the compounds of Table 5. Alkylation of the pyrazole as in compounds 9l-o

in all cases resulted in high permeability and a low effective efflux ratio (EER), but other than

for 9m, loss of JNK3 potency was observed. This may be due to the loss of a productive

interaction of the pyrazole moiety with Lys93, or the introduction of a possibly unfavorable

interaction as in the case of trifluoroethyl 9n. Replacement of the cyclohexanol moiety with

groups that did not bear a hydrogen bond donor as in 9p-u also had acceptable permeability, low

EER, and retained acceptable JNK3 potency, with the one notable exception being 3-

methoxypropyl 9s. The permeability and efflux data indicated that efflux was not the result of

specific recognition by the transporter of the pyrazole’s free NH and suggest that P-gp efflux

may be avoided in this series by simply keeping the hydrogen bond donor count to 2 or less.

With regard to JNK potency these results appeared to point to the need for a cyclic or α-

branched alkyl substituent such as isopropyl to maximize hydrophobic interactions with residues

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in the sugar pocket. Of particular interest was pyrimidine 33, which was not a JNK3 inhibitor, a

surprising result, given the potency of pyridine 1. Docking studies support these results, as

docking of compound 33 with grids derived from the X-ray structure of JNK3 in complex with

either 9e or 1 did not generate acceptable binding poses. We propose that in the absence of an

alkyl amino group at the pyrimidine 2-position, internal energy stabilization of the isopropyl

group is no longer present, and thus no rotamer of the pyrazole-pyrimidine group is favored.

Table 5. Permeability and Efflux Profiling of Selected JNK Inhibitorsa

9

N N

R3

N

N

NH

R1

R2

33

HN N

N

N

Cmpd R1 R

2 R

3

JNK3

IC50 ±

SD (nM)

Aq. Sol.

(mg/mL)

MDCK

Papp A-B

(nm-s-1

)

MDCK-

MDR1

EER

9l

113 ± 16 0.040 428 0.5

9m

24 ± 6.2 0.043 466 1.5

9n

339 ± 98 0.060 291 0.7

9o

CH3 CF3 219 ± 14 0.058 494 1.6

9p

H

110 ± 16 0.031 203 1.9

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9q

H

24 ± 4.0 0.0026 107 2.2

9r

H

13 ± 0.0 0.034 321 1.2

9s

H

493 ± 45 0.036 NTb NT

9t

H

94 ± 22 0.0039 265 1.8

9u

H

16 ± 2.5 0.018 166 5.3

33 --- --- --- > 100000 0.018 NT NT


bNT indicates not tested.

Another round of SAR was carried out to further investigate the R1 position while keeping the R3

position as either 1-methylcyclopropyl or 1-trifluoromethylcyclopropyl. As all compounds thus

far showed poor metabolic stability, we hoped to identify compounds having improved stability

in microsomal incubations. Bearing in mind our desire to attain compounds with blood-brain

barrier permeability, we attempted to keep the hydrogen bond donor count to two or less,

maintain the polar surface area (PSA) to less than 90, and hold the cLogP in the range of 2-4.

Keeping R3 as 1-trifluoromethylcyclopropyl, compounds 9v-y ranged in activity, with IC50

values of 66 nM (cyclopentyl 9w) to 237 nM (cyclopropylmethyl 9y). None of these analogs

was as potent as cyclohexyl 9q (IC50 = 24 nM), whose potency was surprising when compared to

9f or 9g, both of which can make an additional hydrogen bonding interaction of the hydroxyl

moiety with the side chain of Gln155. These findings suggest that these additional interactions

come at some cost, presumably from desolvation. The potencies of cyclic ethers 9z-bb were also

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unexpected when compared to 9q and 9w; it was postulated that these ether moieties might also

interact with Gln155, which can flip to present either a hydrogen bond donor or acceptor to the

ligand. The complete lack of potency of 9cc was especially surprising. Docking studies of 9cc

with the grid generated from the crystal structure of JNK3 with structurally similar 9e generated

several favorable ‘horseshoe-shaped” ligand binding poses showing good overlay with the x-ray

position and binding interactions of 9e. The data in table 6 shows a correlation of JNK3 potency

with the lipophilicity of R1; we speculate that the oxetanyl moiety was not sufficiently lipophilic

to provide the necessary hydrophobic shielding to drive a productive double hinge hydrogen

bonding interaction. Next investigated were the 4- and 3-piperidines 9dd-hh, however, none of

these showed potent JNK3 activity, with the most potent compound, trifluoroethyl 9ff, having

attenuated basicity, suggesting that basicity in this region is not well-tolerated. Replacement of

the monocyclic R1 with a much larger multi-ring substituted aniline moiety as in 9ii showed

potency consistent with literature reports;5 however, ligand efficiency, PSA, and solubility

suffered relative to the other potent compounds from this series. The isomeric tertiary alcohols

9jj and 9kk were approximately 4-fold less potent than 9g. The final three compounds from

Table 6 examined the effect of fluorination of the cyclobutyl moiety (9ll), comparison with its

pyridinyl analog (25), and the effect of chlorination at the 5-position of the pyrimidine ring

(9mm). Fluorination of the cyclobutyl resulted in a 10-fold loss of potency when compared to

9v. Comparison of pyrimidine 9ll with pyridine 25 demonstrated that this change results in no

significant difference with respect to JNK3 potency. In addition, both compounds showed

similar selectivity (10-fold) against p38α (data not shown). Literature precedent indicated that

incorporation of a 5’-chloro group on a related pyrimidine scaffold helps to improve JNK3

potency by ca. 2 fold.30 A 5-chlorinated analog of 9t (9mm) was prepared in an attempt to

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encourage the “horseshoe” conformation and improve activity, but this instead resulted in a 4-

fold potency loss, which may be explained by the chloro-substituent obstructing co-planarity of

the pyrimidine and pyrazole rings. Metabolic stability of this series continued to be poor, with

typical half-life values of < 20 min in mouse liver microsomes.

Table 6. JNK3 Potency of 3-Cyclopropylpyrazolesa

Cmpd R1 R

4 R

5

JNK3

IC50 ±

SD (nM)

Aq. Sol.

(mg/mL) PSA cLogP

9v

H CF3 90 ± 29 0.0058 66 2.6

9w

H CF3 66 ± 5.8 0.0032 66 3.2

9x

H CF3 111 ± 23 0.0028 66 4.3

9y

H CH3 237 ± 35 0.029 66 2.8

9z

H CF3 120 ± 30 76 1.3

9aa

H CF3 151 ± 35 0.018 76 2.0

9bb

H CF3 742 ± 123

0.046 76 1.5

9cc

H CF3 > 100000 0.034 63 1.9

9dd

H CF3 2632 ±

486 0.054 70 2.3

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9ee

H CH3 1890 ±

416 0.038 78 1.5

9ff

H CF3 298 ± 69 0.016 70 2.6

9gg

H CF3 19118 ±

1427 0.045 78 2.0

9hh

H CF3 2398 ±

350 0.048 78 2.0

9ii

H CF3 109 ± 12 0.0019 110 3.8

9jj

H CF3 77 ± 27 0.059 87 2.2

9kk

H CF3 81 ± 28 0.0010 87 2.2

9ll

H CF3 793 ± 100

0.007 66 2.0

25a

--- --- 964 ± 157

0.015 54 2.4

25b S

N

--- --- 78 ± 38 0.0002 95 4.6

9mm

Cl CF3 441 ± 92 66 3.6


Activity in cellular assays

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In a rat model of HD, increased phosphorylation of c-Jun, accompanied by an increase in protein

aggregates and a loss of DARPP-32 immunoreactivity was observed after lentiviral-mediated

expression of htt171-82Q.31 Presumably, a reduction in the activation of c-Jun would result in

neuroprotection and phenotypic improvements. To support compound prioritization for

subsequent in vivo testing and to aid in estimating the dose required to modulate a p-c-Jun

pharmacodynamic endpoint, compounds were tested in a cellular assay to assess JNK-mediated

phosphorylation of c-Jun. The cell-based assay was conducted at Life Technologies (Carlsbad,

CA) using their LanthaScreen technology. In this assay TNF-α was used to stimulate JNK

activation in HeLa cells stably expressing GFP-c-Jun 1–79. Phosphorylation was determined by

measuring the TR-FRET signal between a terbium-labeled anti-p-c-Jun antibody and GFP after

lysis of the cells. Given the challenge of achieving compound exposure in the brain necessary to

modulate p-c-Jun levels in vivo, we held the assumption that a sub-500 nanomolar IC50 against

cellular c-Jun activation would be desirable. As shown in Table 7, despite nanomolar

biochemical potency of 9c, and double-digit nanomolar potency for many of the other

compounds, the cellular potency of these inhibitors was disappointing. Notable was the potency

of 25b (IC50 = 0.5 µM), which was the only aminopyridine in this set. This finding prompted

testing of several other aminopyridines from our collection; however, none showed sub-

micromolar potency in the c-Jun assay (data not shown). The activity of SP600125 (34)32 is

included in Table 7 as an assay standard; its potency was consistent with prior literature values.

Difficulty in efficiently translating the biochemical potency of JNK inhibitors to potency against

c-Jun phosphorylation in a cellular context is well-documented. Upon exposure to activating

stimuli, c-Jun is rapidly phosphorylated. In addition, the c-jun transcription response element is

constitutively occupied and this phosphorylation occurs while the proteins are bound to the c-jun

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promoter, activating transcription, and leading to c-Jun induction.33 Conversely, there have been

several JNK inhibitors with reported sub-micromolar cell-based activity; however, when we

attempted to recapitulate these results in either the Life Technologies assay, or in an internally

developed NIH3T3-cell-based c-Jun MSD assay (data not shown), we were unable to reasonably

match the published potencies. It is perhaps of interest to note that the potency of a recently

reported covalent inhibitor JNK-IN-11 (35)34 was an exception. In the Life Technologies assay,

35 showed an IC50 of 0.1 uM and had similar translation of biochemical to cellular potency as

some of the other inhibitors studied. Unfortunately, this compound potently inhibited a number

of other kinases, including p38, when tested at 1 µM concentration in selectivity profiling

conducted at Cerep (see Supporting Information). As stated earlier, this activity would be a

potential confound in interpretation of efficacy results. In addition, it cannot be ruled out that the

potent inhibition of p-c-Jun observed may be the result of off-target activity against a variety of

kinase families.

Due in part to the cellular c-Jun results, compounds were also tested in a second cellular assay,

the LPS-induced TNF-α secretion assay in PBMC conducted at Cerep (Celle l'Evescaul, France).

It is known that LPS activates the JNKs to induce TNF-α production,35 and that this can be

suppressed in macrophages by 34.36 The compounds in Table 7 showed markedly better potency

and translation against this readout. Dexamethasone is included as the assay positive standard,

and its potency was as expected. Interestingly, the dual JNK/p38 inhibitor 9c was approximately

equipotent with JNK inhibitor 9r. The expectation was that significantly improved activity

might have resulted from potent inhibition of these two MAPK families. Aminopyridine 25b

was also one of the more potent compounds in this assay. These results, while encouraging, do

little to advance JNK inhibition as an HD therapeutic strategy, but may become relevant if a

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connection between elevated TNF-α and HD disease progression can be established. At present

they demonstrate that the compounds can cross cell membranes and modulate functional activity

within a cell at a concentration that might reasonably be achievable in brain.

Table 7. Cellular Activity of Selected JNK Inhibitorsa

Cmpd JNK3 IC50

(nM)

p38αααα

IC50

(nM)

p-c-Jun

IC50 (µµµµM)

Ratio p-c-

Jun/JNK3

LPS-

TNF-αααα

IC50 (µµµµM)

Ratio

TNF-

αααα/JNK3

9c 5 16 8.0 1600 0.081 16

9r 13 4574 2.5 192 0.093 7

9f 16 5559 2.2 138 0.45 28

9m 24 3052 1.6 67 5.8 242

9q 24 >10000 2.0 83 0.89 37

25b 78 NT 0.51 7 0.15 2

9t 94 6084 > 10 NA 0.18 2

9ii 109 >10000 3.0 28 0.18 2

9x 111 >10000 2.7 24 0.35 3

9z 121 >10000 > 10 NA 1.5 12

34 59 >10000 2.8 48 0.89 15

35 0.5b NT 0.1 200 NT NA

dexamethasone NT NT NT --- 0.0051 ---

aNT indicates not tested. NA indicates not calculated.

bValue from Ref 33.

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ADME-PK

In preparation for planned in vivo pharmacodynamic evaluation in mice of a p-c-Jun biomarker,

several of the compounds from Tables 3, 5, and 6 were profiled for microsomal stability;

however, despite the structural diversity queried, all showed rapid rates of metabolism in both

mouse and rat liver microsomes (data not shown). From these studies 9t emerged as an early

example of a compound having met most of our criteria for progression into further studies. The

JNK3 potency (IC50 = 94 nM), cellular potency (IC50 = 180 nM, LPS-TNF-α assay), cellular

permeability (MDCK-WT Papp A-B = 265 nm-s-1), and P-gp-mediated efflux (EER = 1.8) of 9t

were acceptable. While its stability in mLM was poor/moderate (Clint = 142 mL/min.mg), its

rate of disappearance was slower than most compounds tested from this series. When assayed at

10 µM in receptor panels of 144 diverse and 75 kinase targets, 9t showed > 50% of control

specific binding in 9 out of the 219 assays: adenosine A3 (51%), Na+ channel (83%),

norepinephrine transporter (92%), CDC2/CDK1 (79%), CDK2 (77%), CDK5 (72%), GSK3β

(82%), HGK (54%), and JNK1 (97%). The full report can be found in the Supporting

Information section.

As a follow-up to the receptor profiling study, IC50 values were determined against CDK5 and

GSK3β, since these are targets implicated in HD (Table 8). While activity against these would

not affect a p-c-Jun readout, they might impact an efficacy readout in an HD model. The data

suggests that selectivity against these kinases, which have relatively close homology to JNK3,

may be difficult to achieve with this chemotype, although the selectivity observed for 9m shows

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that > 50-fold is possible. This level of selectivity was possibly driven by favorable hydrophobic

interactions of the R2 isopropyl moiety with Leu206 in JNK3 and, assuming a similar binding

conformation with GSK3β and CDK5, unfavorable, or less favorable, interactions with Cys199

(GSK3β) and Ala143 (CDK5).

Table 8. CDK5 and GSK3β Inhibition of Selected JNK3 Inhibitors

Cmpd

JNK3

IC50 (nM)

CDK5

IC50 (nM)

GSK3ββββ

IC50 (nM)

9j 73 1100 260

9u 16 87 280

9m 24 1400 1800

9t 88 430 380

In a mouse BBB penetration study, 9t was dosed as an i.v. bolus in mouse at 5 mpk. It showed a

brain to plasma ratio of 1.8 : 1, reaching a Cmax in brain of 1967 ng-eq/mg at a Tmax of 0.25 h.

Clearance of the compound was rapid; the half-life was approximately 15 min. By 2 hours the

brain concentration had fallen to 100 ng-eq/mg. Considering the high rate of microsomal

metabolism noted for the series, attempts were made to identify specific site(s) of metabolism. A

metabolite identification study of 9t in mLM revealed extensive metabolism involving both the

R1 cyclohexyl and R3 cyclopropyl groups. While it was not possible to quantify the relative

abundance of metabolites due to unknown ionization efficiencies of the various species, clear

evidence was obtained demonstrating R1 and R3 hydroxylation(s), dehydration(s), and

dealkylation to the 2-aminopyrimidine (structures of these putative metabolites and their

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respective extracted single ion mass chromatograms can be found in the Supporting Information

section).

Thus far, the incorporation of hydrophobic groups at both R1 and R3 necessary to achieve a level

of biochemical potency that might translate into sub-micromolar cellular potency was

incompatible with metabolic stability in mouse. Anticipating that metabolism issues might

dictate the need to proceed into an in vivo pharmacodynamic proof of concept study with a high

clearance compound, we undertook an in vitro cytochrome P450-mediated metabolism

suppression study of 9t in mLM. Using the cytochrome P450 (CYP450) inhibitors listed in Table

9, the objective was to identify which CYP450 isoforms were principally responsible for

metabolism as evidenced by reduction in the rate of clearance. Table 9 lists the specific

inhibitors of human CYP450 isoforms studied and the results are summarized in Figure 3. The

results from co-administration of each inhibitor with 9t suggest that human CYP450-2B6-like,

human CYP450-2C19-like, and human CYP450-3A4-like activities are mainly responsible for

its metabolism in mLM. It is important to caution that the CYP450 isoforms in mouse are not

well-characterized, and that the precise CYP450 isoforms being inhibited in mLM by this panel

of human CYP450 inhibitors is unknown. The CYP450-3A4/5 inhibitor ketoconazole was

particularly effective at slowing the rate of clearance when dosed at both 3x and 30x its Ki. In

addition, pan-CYP450 inhibition using SKF-525a was more effective than inhibition of any

individual isoform; it strongly suppressed the rate of metabolism when co-administered at 3x Ki.

Table 9. Human CYP450 Inhibitors for Metabolism Suppression Study

Human CYP450

Isoform Selective

Inhibitor Ki (µM)

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1A2 α-Naphthoflavone 0.01

2B6 Clopidogrel 0.5

2D6 Quinidine 0.2

2C8 Montelukast 0.07

2C9 Sulfaphenazole 0.3

2C19 Ticlopidine 1.2

3A4/5 Ketoconazole 0.09

Figure 3. Suppression of metabolism of 9t in mLM incubations by co-administration with

known inhibitors of human CYP450 isoforms.

These in vitro findings were then extended demonstrating that in vivo suppression of CYP450-

mediated metabolism of 9t could result in enhanced brain exposure after oral dosing in mice.

Thus, 9t was dosed orally at 30 mpk to one cohort, a second cohort was co-administered 30 mpk

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9t with 50 mpk orally of the CYP450-3A4 inhibitor ketoconazole, and a third group was co-

administered 30 mpk 9t and 30 mpk orally of 1-aminobenzotriazole (1-ABT), a potent pan-

CYP450 inhibitor (Figure 4). The brain concentration at 8 h was approximately 100-fold

improved with 1-ABT co-administration relative to administration of 9t alone. The

concentration of 9t in brain was 7.3 µM by 0.5 h post-dose and remained above this level

through 4 h, reaching a Cmax of 11.4 µM at 1 h, and then falling to 4.8 µM at 8 h. Working back

from this exposure level and assuming that a brain concentration would likely need to be at some

multiple of the cellular IC50 value, we felt confident that if elevated levels of TNF-α could be

correlated with HD disease progression, 9t would have the potency necessary to go forward as a

PD tool.

It is important to note that co-administration with the CYP450 inhibitor did not increase BBB

permeability or alter the brain to plasma ratio; it only served to decrease clearance, thus

improving exposure to all tissues. The plasma exposure of 9t was also similarly improved (not

shown). For a highly metabolized compound such as 9t, suppression of metabolism 1) improved

exposure to levels that might allow modulation of a PD marker in brain; 2) ensures that PD

activity can be attributed to the parent compound and directly linked to JNK inhibition; 3) since

1-ABT has been shown to be relatively non-toxic in a rat toxicology study,37 it may permit a

highly metabolized compound to enter into a mouse HD efficacy study requiring chronic dosing.

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Figure 4. Brain concentrations of 9t over time in mice dosed orally with A) 30 mpk 9t (▲), B)

30 mpk 9t co-administered with 50 mpk ketoconazole (◊), C) 30 mpk 9t co-administered with 30

mpk 1-ABT (♦).

Conclusions

Despite numerous reports of JNK inhibitors, there remains a need for sharp tools having

sufficient cellular potency and pharmacokinetic profile to support in vivo proof of concept

studies in models of Huntington’s disease. With a focus on identification of compounds having

calculated properties aligned with BBB penetration for HD, we have expanded the scope of the

SAR of the 1H-pyrazol-4-yl)pyrimidine chemotype through incorporation of new substituents

that bind in the sugar pocket, while significantly expanding the SAR with respect to binding in

0.01

0.1

1

10

100

0 2 4 6 8 10 12 14 16 18 20 22 24

Bra

in C

on

c ( µµ µµ

M)

Time (hr) post 9t dose

9t 30 mg/kg PO

9t 30 mg/kg PO + keto 50 mg/kg PO

9t 30 mg/kg PO + 1-ABT 30 mg/kg PO

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hydrophobic region II. Through our studies, a binding model to rationalize the observed

selectivity for JNK3 versus p38 was established, one which favors small groups at R3 that allow

Met146 of JNK3 to occupy hydrophobic region I. Three different cellular assays were used to

stratify compounds for further studies. In two different assays used to assess the activity of

compounds against a p-c-Jun readout, only the irreversible inhibitor 34 showed a level of activity

consistent with a pharmacodynamic tool. While 34 has the necessary level of cellular potency, its

permeability in an MDCK-MDR1 assay, and its kinase selectivity were insufficient (see

Supporting Information). In an LPS-TNF-α secretion assay, all compounds showed a much

improved translation of biochemical potency, with most showing sub-micromolar IC50 values.

Our focus on calculated properties resulted in compounds showing low efflux, leading to the

identification of 9t as a brain penetrant pan-JNK inhibitor in mouse. All compounds from this

chemotype were highly and rapidly metabolized, showing high in vivo clearance in mouse;

however, this liability could be overcome through in vivo pan-CYP450 inhibition. Additional

studies will be needed to establish a correlation between TNF-α levels and HD disease

progression to demonstrate whether 9t is suitable for oral dosing in pharmacodynamic and

efficacy models.

Experimental Section

Unless otherwise noted, reagents and solvents were used as received from commercial suppliers.

All non-aqueous reactions were carried out under an atmosphere of dry nitrogen (unless

otherwise noted). Proton nuclear magnetic resonance spectra were obtained on a Bruker

AVANCE 300 spectrometer at 300 MHz or Bruker AVANCE 500 spectrometer at 500 MHz.

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Spectra are given in ppm (δ) and coupling constants, J values, are reported in hertz (Hz).

Tetramethylsilane was used as an internal standard for 13C and 1H nuclear magnetic resonance.

Mass spectra were obtained on either a Perkin Elmer Sciex 100 mass spectrometer (APCI),

Varian 1200L single quadrapole mass spectrometer (ESI) or a Waters Acquity SQD (ESI and

APCI). LC–MS analyses were obtained using a Varian 1200L single quadrapole mass

spectrometer (ESI, HP-LCMS) or a Waters Acquity SQD (ESI and APCI, UP-LCMS). HPLC

analyses were obtained using a Grace Alltima C18 column, 3µ, (7 × 53 mm) with UV detection

at 254 nm (unless otherwise noted) using standard solvent gradient program (Methods 1–5). All

final compounds were of ≥95% purity as assessed by 1H NMR and using one of the analytical

HPLC methods noted above.

Method 1

Time

(min)

Flow

(mL/min)

%A %B

0.0 3.0 90.0 10.0

5.0 3.0 0.0 100.0

6.0 3.0 0.0 100.0

A = 95% Water/Acetonitrile with 0.05% v/v Trifluoroacetic Acid

B = 95% Acetonitrile/Water with 0.05% v/v Trifluoroacetic Acid

Method 2

Time

(min)

Flow

(mL/min)

%A %B

0.0 3.0 70.0 30.0

5.0 3.0 0.0 100.0

6.0 3.0 0.0 100.0



Method 3

Time

(min)

Flow

(mL/min)

%A %B

0.0 3.0 100.0 0.0

10.0 3.0 0.0 100.0

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11.0 3.0 0.0 100.0



Method 4

Time

(min)

Flow

(mL/min)

%A %B

0.0 3.0 100.0 0.0

5.0 3.0 0.0 100.0

6.0 3.0 0.0 100.0



Method 5

Time

(min)

Flow

(mL/min)

%A %B

0.0 0.75 90.0 10.0

20.0 0.75 0.0 100.0

25.0 0.75 0.0 100.0

A = Water with 0.01% v/v Trifluoroacetic Acid

B = Acetonitrile with 0.01% v/v Trifluoroacetic Acid

hJNK3αααα1, p38αααα and ββββ In Vitro Kinase Assays for Compound IC50 Determinations

Compounds were prepared as 10 mM stocks in 100% DMSO from fresh powder. The compound

stock solution was serially diluted 1:3 in DMSO for a 10-point concentration dose response in

duplicate and transferred to assay plates with a final DMSO assay concentration of one percent.

Control compounds such as JNK inhibitor JNK-40138 (36) and p38 inhibitor SB 23906339 (37)

were also included in each test plate to monitor assay performance.

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Figure 5. Structures of assay standards 36 and 37.

The Kinase Glo® assay platform from Promega (Cat. # V6714) was used to determine

compound IC50 for hJNK3α1. In this format, ATP in the reaction is measured after the addition

of the Kinase-Glo® Reagent. The assay was performed at room temperature in 384-well plates

(Corning Cat. # 3572). Each well received 8 nM JNK3α1 (Invitrogen, Cat. # PR6983A), 2 µM

ATF-2 (BPS Biosciences, Cat. # 40520), and 1 µM ATP (Cell Signaling Technology, Cat. #

9804) in 50 mM Tris-HCl pH 7.5, 2 mM EGTA, 2 mM DTT, and 10 mM MgCl2 and test

compounds in a 20 µL final reaction volume. The kinase reaction was initiated with the addition

of JNK3α1 kinase and incubated 30 minutes prior to the addition of the Kinase-Glo® Reagent as

per manufacture’s recommendation. The plate was incubated for an additional 15 minutes at

room temperature and luminescence was measured in an Analyst GT reader (Molecular Devices,

using the default luminescence settings). The luminescence produced is inversely related to

kinase activity. Data were analyzed by calculating the percent of inhibition and each IC50 was

determined using the 4-parameter logistic equation (model 205, Excel fit -IDBS curve-fitting

software).

The γ32P-ATP radioactive assay platform was used to determine compound IC50 for human p38α

and β isoforms. The assay was performed at room temperature in 96-well plates (Corning, Cat.

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#3363). Each well received 10 nM hp38α or 40 nM hp38β (Millipore), 2 or 3 µM ATF-2

respectively (BPS Biosciences), 50 µM ATP (Cell Signaling Technology, Cat. # 9804) and 1.125

µCi γ-32P-ATP (PerkinElmer, Cat. # BLU502A250UC) in 50 mM Tris-HCl pH 7.5, 2 mM

EGTA, 2 mM DTT, and 10 mM MgCl2 and test compounds in a 20 µL final reaction volume.

The kinase reaction was initiated with the addition of the p38α or β kinase and incubated 30

minutes for the hp38α assay and 40 minutes for the hp38β. Reactions were terminated with the

addition of 150 μL of 150 mM phosphoric acid to each well. The reaction mixture was

transferred to a pretreated- Immobilon filter plate based on manufacture’s recommendation

(Millipore, Cat. # MAIPNOB50). After vacuum filtration, the filter plate was washed four times

with 300 μL of 150 mM phosphoric acid. After the final wash, the membrane was allowed to air

dry at room temperature, 50 µL of EcoScint scintillation cocktail (National Diagnostics Cat. #

LS-271) was added, and radioactivity measured using a TriLux reader (Perkin Elmer). Data were

analyzed by calculating the percent of inhibition and each IC50 was determined using the 4-

parameter logistic equation (model 205, Excel fit-IDBS software).

Compound Synthesis

4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-N-(cyclopropylmethyl)pyrimidin-2-amine (9a)

Preparation of 1-(4-Chlorophenyl)-2-(2-(methylthio)pyrimidin-4-yl)ethenol/ethanone (4

and 4’). To a stirred solution at 0 °C of 2 (2.10 g, 15.0 mmol) and methyl 4-chlorobenzonate

(3b, 2.64 g, 15.0 mmol) in THF (30.0 mL) was added lithium hexamethyldisilazide (30 mL of a

1.0 M solution in THF, 30.0 mmol) and after the addition was complete the reaction mixture was

warmed to room temperature. After 16 h the reaction mixture was quenched with saturated

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ammonium chloride solution and the layers were separated. The aqueous layer was extracted

using ethyl acetate (2 × 25 mL). The combined organic phase was washed with 1.0 N

hydrochloric acid, water, saturated sodium chloride, dried (MgSO4), filtered, and concentrated

under reduced pressure. The residue was triturated using heptane/methylene chloride to provide a

mixture of (Z)-1-(4- chlorophenyl)-2-(2-(methylthio)pyrimidin-4-yl)ethanol (4) and 1-(4-

chlorophenyl)-2-(2- (methylthio)pyrimidin-4-yl)ethanone (4’), 2.56:1 ratio, 4.09 g, 98%

combined yield, as a bright yellow crystalline solid: 1H NMR (300 MHz, CDCl3) δ 2.51 (s,

1.17H), 2.62 (s, 3H), 4.34 (s, 0.78H), 5.96 (s, 1H), 6.66 (d, J = 5.4 Hz, 1H), 6.97 (d, J = 5.1 Hz,

0.39H), 7.38–7.42 (m, 2H), 7.43–7.47 (m, 0.78H), 7.75–7.79 (m, 2H), 7.98 (d, J = 8.7 Hz,

0.78H), 8.32 (d, J = 5.4 Hz, 1H), 8.46 (d, J = 5.1 Hz, 0.39H), 14.60 (br s, 1H); MS (APCI) m/z

279 [M + H]+.

Preparation of 4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-2-(methylthio)pyrimidine (5). A

stirred solution of 4 and 4’ (1.00 g, 3.59 mmol) and DMF•DMA (0.640 g, 5.38 mmol) in toluene

(10 mL) was heated at reflux for 18 h. After this time the reaction mixture was cooled to room

temperature and concentrated under reduced pressure. To the resulting residue was added

anhydrous hydrazine (0.235 g, 7.18 mmol) and ethanol (9.0 mL) and the mixture was stirred at

room temperature for 16 h. After this time the mixture was concentrated under reduced pressure

and the residue was recrystallized using ethyl acetate/heptane to provide 2-methylthiopyrimidine

5 (0.822 g, 85%) as an off-white solid: 1H NMR (300 MHz, CDCl3) δ 2.43 (s, 3H), 2.99 (br s,

1H), 6.84 (d, J = 5.1 Hz, 1H), 7.42–7.50 (m, 4H), 8.21 (s, 1H), 8.35 (d, J = 5.1 Hz, 1H); MS

(ESI) m/z 303 [M + H]+.

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Preparation of 4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-2-(methylsulfonyl)pyrimidine (6).

To a stirred suspension at 0 °C of 5 (0.773 g, 2.56 mmol) in methylene chloride (12.0 mL) was

added m-CPBA (1.18 g, 5.11 mmol) portion-wise and then the reaction mixture was warmed to

room temperature. After 16 h a saturated sodium bicarbonate solution (20 mL) was added to the

reaction mixture and then stirred for 5 min. The organic layer was separated. The aqueous layer

was extracted with ethyl acetate (2 × 15 mL). The combined organic phase was washed with

sodium thiosulfate, saturated sodium chloride and dried (MgSO4), filtered, and concentrated

under reduced pressure to provide 2-(methylsulfonyl)pyrimidine 6 (0.847 g, 99%) as an off-

white solid: mp 194–195 °C; 1H NMR (500 MHz, CDCl3) δ 3.23 (s, 3H), 4.95 (br s, 1H), 7.33

(d, J = 5.0 Hz, 1H), 7.45–7.50 (m, 4H), 8.34 (s, 1H), 8.69 (d, J = 5.0 Hz, 1H); MS (APCI) m/z

335 [M + H]+.

Preparation of 4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-N-(cyclopropylmethyl)pyrimidine-

2-amine (9a). A microwave tube charged with a stir bar and suspension of 6 (0.300 g, 0.90

mmol), cyclopropanemethylamine (0.128 g, 1.80 mmol) in dioxane (3.0 mL) was irradiated (400

W, 130 °C) for 30 min. After this time the reaction mixture was concentrated under reduced

pressure. The residue was purified using flash column chromatography (silica gel; 40-80% ethyl

acetate/heptanes, gradient elution) to provide 9a (0.118 g, 41%) as an off-white solid: mp 221–

222 °C; 1H NMR (500 MHz, DMSO-d6) d 0.12 (br s, 2H), 0.94–0.83 (m, 2H), 0.94–0.83 (m,

1H), 2.86 (br s, 2H), 6.58 (s, 1H), 6.95 (s, 1H), 7.56–7.41 (m, 4H), 8.04–8.32 (m, 2H), 13.30–

13.38 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 162.1, 157.8, 140.2, 132.1 (low intensity),

131.1, 130.9, 130.6, 128.2, 127.8, 117.9, 117.4, 44.8, 10.8, 3.1; HRMS: Calcd. for C17H16ClN5:

326.1172, Found: 326.1180; HPLC: Method 1, tR = 3.24 min, (> 99% AUC).

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4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-N-(cyclohexylmethyl)pyrimidine-2-amine (9b).

The compound was prepared using a method similar to that described for the preparation of 9a,

0.164 g, 50% as a white solid: mp 222–223 °C; 1H NMR (500 MHz, DMSO-d6) δ 0.73 (br s,

2H), 1.11 (br s, 3H), 1.33–1.60 (m, 6H), 2.80 (br s, 2H), 6.59–6.65 (br s, 1H), 6.87 (s, 1H), 7.41–

7.56 (m, 4H), 8.03–8.31 (m, 2H), 13.29–13.37 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ

162.4, 157.8, 140.2, 133.3 (low intensity), 131.1, 130.8, 130.5, 128.2, 127.7, 117.9, 117.4, 46.6,

37.0, 30.3, 26.1, 25.3; HRMS: Calcd. for C20H22ClN5: 368.1642, Found: 368.1646; HPLC:

Method 1, tR = 3.85 min, (> 99% AUC).

trans-4-(4-(3-Chlorophenyl)-1H-pyrazol-4-yl)-pyrimidin-2-ylamino)cyclohexanol (9c). The

compound was prepared using a method similar to that described for the preparation of 9a, with

the addition of an extra preparative HPLC purification step after flash column chromatography

(Phenomenex Luna 10µ C18(2) 100Å column (21.2 × 250 mm); 10–60% then 60–100% [95:5

CH3CN:H2O]/[95:5 H2O:CH3CN, 0.05% TFA], gradient elution, integration at 254 nm) and then

washed using saturated sodium bicarbonate, 0.114 g, 17% as a white solid: mp 248–250 °C; 1H

NMR (500 MHz, DMSO-d6) δ 1.10–1.16 (m, 4H), 1.62–1.73 (m, 4H), 3.25–3.40 (br s, 2H), 4.48

(br s, 1H), 6.66 (br s, 1H), 6.85 (s, 1H), 7.46–7.55 (m, 4H), 8.13 (d, J = 5.5 Hz, 1H), 8.27 (br s,

1H), 13.34 (br s, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.2, 160.1, 157.4, 148.3, 140.5,

133.2, 132.4, 131.2, 130.6, 128.0, 117.8, 106.6, 68.4, 48.4, 34.0, 30.3; HRMS: Calcd. for

C19H20ClN5O: 370.1435, Found: 370.1425; HPLC: Method 1, tR = 2.60 min, (> 99% AUC).

4-(3-(4-Chlorophenyl)-1H-pyrazol-4-yl)-N-(pyridine-2-yl)pyrimidin-2-amine (9d). The

compound was prepared using a method similar to that described for the preparation of 9a, 0.032

g, 5% as an off-white solid: mp 246–247 °C; 1H NMR (500 MHz, DMSO-d6) δ 6.96–7.01 (m,

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2H), 7.47–7.57 (m, 5H), 7.65 (d, J = 8.0 Hz, 1H), 8.18–8.47 (m, 3H), 9.85 (br s, 1H), 13.47–

13.60 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 160.3, 158.6, 158.5, 158.0, 157.9, 157.7,

152.1, 152.0, 151.9, 145.6, 145.5, 145.2, 139.0, 138.6, 133.0, 130.7, 128.5, 117.1, 112.8, 110.9;

HRMS: Calcd. for C18H13ClN6: 349.0968, Found: 349.0976; HPLC: Method 1, tR = 2.99 min, (>

99% AUC).

trans-4-(4-(3-tert-Butyl-1H-pyrazol-4-yl)-pyrimidin-2-ylamino)cyclohexanol (9e). The

compound was prepared using a method similar to that described for the preparation of 9a,

0.189g, 38% as a white solid: mp 232–234 °C; 1H NMR (500 MHz, CD3OD) δ 1.35–1.39 (m,

4H), 1.46–1.52 (m, 9H), 1.96–1.98 (m, 2H), 2.02–2.05 (m, 2H), 3.30–3.32 (m, 2H), 3.57–3.58

(m, 1H), 3.89 (br s, 1H), 6.71–6.76 (m, 1H), 7.78–7.94 (m, 1H), 8.12 (d, J = 5.0 Hz, 1H); 13C

NMR (125 MHz, CD3OD) δ 29.93, 30.56, 32.05, 33.76, 35.17, 50.30, 70.70, 109.9, 118.3, 142.9,

151.9, 158.3, 162.8, 164.4; HRMS: Calcd. for C17H25N5O: 316.2137, Found: 316.2149; HPLC:

Method 1, tR = 2.30 min, (98.6% AUC).

trans-4-(4-(3-(1-Methylcyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-ylamino)cyclohexanol

(9f). The compound was prepared using a method similar to that described for the preparation of

9a, 0.125 g, 40% as an off-white solid: mp; no clear melt observed; 1H NMR (500 MHz, DMSO-

d6) d 0.73–0.83 (m, 2H), 0.92–0.94 (m, 2H), 1.23–1.30 (m, 2H), 1.38–1.44 (m, 5H), 1.86–1.93

(m, 4H), 3.46 (s, 2H), 3.71 (br s, 1H), 4.11 (br s, 1H), 7.25 (d, J = 6.5 Hz, 1H), 8.29–8.38 (m,

2H), 8.50–8.69 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 166.5, 153.4, 151.7, 145.6, 139.9,

116.2, 105.7, 67.5, 48.8, 33.5, 29.8, 24.0, 13.6, 13.4; HRMS: Calcd. for C17H23N5O: 314.1981,

Found: 314.1983; HPLC: Method 1, tR = 2.18 min, (97.5% AUC).

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trans-4-(4-(3-(1-(Trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9g). The compound was prepared using a method similar to that

described for the preparation of 9a, 0.064 g, 19% as a white solid: mp 239–240 °C; 1H NMR

(500 MHz, DMSOd6) δ 1.21–1.33 (m, 6H), 1.44–1.53 (m, 2H), 1.80–1.88 (m, 4H), 3.38–3.41

(m, 1H), 3.81 (br s, 1H), 4.52 (d, J = 5.4 Hz, 1H), 6.74 (br s, 1H), 6.81–6.83 (m, 1H), 8.02–8.28

(m, 2H), 13.19–13.56 (m, 1H); 19F {1H} (282 MHz, CDCl3) δ –67.27; 13C NMR (125 MHz,

DMSO-d6) δ 161.5, 159.4, 157.6, 143.8, 139.9, 130.9, 120.3, 106.3, 68.3, 48.2, 34.2, 30.5, 11.3;

HRMS: Calcd. for C17H20F3N5O: 368.1698, Found: 368.1691; HPLC: Method 3, tR = 3.57 min,

(> 99% AUC).

trans-4-(4-(3-Cyclobutyl-1H-pyrazol-4-yl)pyrimidin-2-ylamino)cyclohexanol (9h). The

compound was prepared using a method similar to that described for the preparation of 9a, 0.167

g, 53% as a light yellow solid: mp; no clear melt observed; 1H NMR (500 MHz, DMSO-d6) d

1.28–1.46 (m, 4H), 1.92–2.03 (m, 6H), 2.31–2.36 (m, 4H), 3.48 (br s, 1H), 3.69–3.94 (m, 1H),

4.32 (m, 1H), 5.50 (br s, 1H), 7.20 (br s, 1H), 8.24 (br s, 1H), 8.50 (br s, 2H), 13.18 (br s, 1H);

13C NMR (125 MHz, DMSO-d6) δ 167.1, 152.9, 152.1, 145.0, 138.7, 114.4, 105.4, 67.5, 49.8,

33.6, 32.4, 29.7, 27.8, 18.1; HRMS: Calcd. for C17H23N5O: 314.1981, Found: 314.1981; HPLC:

Method 1, tR = 2.30 min, (98.4% AUC).

4-(3-Cyclopropyl-1H-pyrazol-4-yl)-N-isopropylpyrimidin-2-amine (9i). The compound was

prepared using a method similar to that described for the preparation of 9a, 0.116 g, 33% as a

white solid: mp 225–226 °C; 1H NMR (500 MHz, DMSO-d6) δ 0.85–1.00 (m, 4H), 1.16–1.30

(m, 4H), 1.81–1.84 (m, 2H), 1.89–1.92 (m, 2H), 2.89 (br s, 1H), 3.35–3.40 (m, 1H), 3.63 (br s,

1H), 4.51 (d, J = 4.5 Hz, 1H), 6.74 (br s, 1H), 6.82 (d, J = 5.5 Hz, 1H), 7.93–8.24 (m, 1H), 8.15

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(s, 1H), 12.56–12.68 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.5, 157.6, 151.8, 144.7,

139.5, 130.0, 117.6, 117.2, 105.4, 68.4, 49.1, 34.2, 30.2, 8.5, 8.0, 7.1; HRMS: Calcd. for

C16H21N5O: 300.1824, Found: 300.1833; HPLC: Method 1, tR = 2.09 min, (> 99% AUC).

trans-4-(4-(3-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9j). The compound was prepared using a method similar to that

described for the preparation of 9a, 0.077 g, 23% as a white powder: mp 229 °C; 1H NMR (300

MHz, DMSO-d6) δ 1.05–1.40 (m, 4H), 1.60–2.00 (m, 8H), 3.55–4.05 (m, 7H), 4.55–4.61 (m,

1H), 6.78 (d, J = 4.5 Hz, 2H), 7.95–8.30 (m, 2H), 12.84–12.96 (m, 1H); 13C NMR (125 MHz,

DMSO-d6) δ 161.7, 160.6, 157.7, 153.9, 146.2, 139.4, 130.3, 115.3, 105.8, 68.3, 67.3, 48.5, 34.3,

33.3, 31.9, 31.3, 30.3; HRMS: Calcd. for C18H25N5O2: 344.2087, Found: 344.2090; HPLC:

Method 1, tR = 1.98 min, (> 99% AUC, integration at 230 nm).

trans-4-(4-(1-cyclopentyl-3-cyclopropyl-1H-pyrazol-4-yl)pyrimidin-2-ylamino)cyclohexanol

(9l). The compound was prepared using a method similar to that described for the preparation of

9a, 0.155g, 59% as a white foam: mp No clear melt observed; 1H NMR (500 MHz, CDCl3) δ

0.60–0.63 (m, 2H), 1.08–1.12 (m, 2H), 1.25–1.33 (m, 2H), 1.40 (br s, 1H), 1.41–1.49 (m, 2H),

1.67–1.71 (m, 2H), 1.81–1.86 (m, 1H), 1.96–2.03 (m, 4H), 2.06–2.10 (m, 4H), 2.17–2.19 (m,

2H), 3.66–3.70 (m, 1H), 3.48–3.91 (m, 1H), 4.88 (d, J = 3.9 Hz, 1H), 5.03–5.09 (m, 1H), 6.79 (d,

J = 5.0 Hz, 1H), 7.89 (s, 1H), 8.21 (d, J = 5.0 Hz, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.6,

159.4, 157.3, 141.9, 137.9, 119.1, 107.1 (low intensity), 68.4, 58.4, 48.7, 34.2, 32.4, 30.3, 24.3,

7.7, 5.4; HRMS: Calcd. for C21H29N5O: 368.2450, Found: 368.2455; HPLC: Method 1, tR = 3.09

min, (98.3% AUC).

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trans-4-(4-(1-Isopropyl-3-(1-methylcyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9m). The compound was prepared using a method similar to that

described for the preparation of 9a, 0.085 g, 33% as a white solid: mp; no clear melt observed;

1H NMR (500 MHz, DMSO-d6) δ 0.67 (br s, 2H), 0.92 (br s, 2H), 1.17–1.33 (m, 4H), 1.42 (d, J

= 6.5 Hz, 6H), 1.45 (s, 3H), 1.82–1.89 (m, 4H), 3.36–3.41 (m, 1H), 3.80 (br s, 1H), 4.51 (d, J =

5.5 Hz, 1H), 4.91– 4.96 (m, 1H), 6.73 (br s, 1H), 7.84 (s, 1H), 8.17 (br s, 1H); 13C NMR (125

MHz, DMSO-d6) δ 161.7, 159.6, 157.5, 144.1, 138.3, 117.9, 106.8, 68.4, 49.1, 48.5, 34.3, 30.5,

24.2, 22.5, 15.0, 11.2; HRMS: Calcd. for C20H29N5O: 356.2450, Found: 356.2463; HPLC:

Method 1, tR = 3.63 min, (> 99% AUC).

trans-4-(4-(3-Cyclopropyl-1-(2,2,2-trifluoroethyl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9n). The compound was prepared using a method similar to that

described for the preparation of 9a, 0.251 g, 57% as a white foam: mp No clear melt observed;

1H NMR (500 MHz, DMSO-d6) δ 0.58–0.64 (m, 2H), 1.13–1.15 (m, 2H), 1.18–1.33 (m, 4H),

1.82–1.95 (m, 5H), 3.36–3.41 (m, 1H), 3.71 (br s, 1H), 4.50 (d, J = 2.5 Hz, 1H), 5.15 (q, J = 9.0

Hz, 2H), 6.84 (d, J = 5.0 Hz, 1H), 7.93 (s, 1H), 8.23 (s, 1H); 19F {1H} NMR (282 MHz, CDCl3)

δ –68.75; 13C NMR (125 MHz, DMSO-d6) δ 161.6, 158.7, 157.6, 143.9, 139.7, 123.7 (q, J =

280.4 Hz), 120.4, 107.5 (low intensity), 68.4, 49.5 (q, J = 34.0 Hz), 48.7, 34.2, 30.3, 7.7, 5.2;

HRMS: Calcd. for C18H22F3N5O: 382.1855, Found: 382.1848; HPLC: Method 1, tR = 2.75 min,

(98.7% AUC).

(4-(3-Isopropyl-1H-pyrazol-4-yl)-N-(trans-4-methoxycyclohexyl)-pyrimidin-2-amine (9r).


0.044 g, 19% as a white solid: mp 190–191 °C; 1H NMR (500 MHz, DMSO-d6) δ 1.17–1.31 (m,

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10H), 1.94 (d, J = 11.0 Hz, 2H), 2.03 (d, J = 11.0 Hz, 2H), 3.08–3.14 (m, 1H), 3.30 (s, 3H),

3.66–3.72 (m, 1H), 3.87–4.09 (m, 1H), 6.77–6.79 (m, 2H), 7.93–8.31 (m, 1H), 8.13 (d, J = 3.0

Hz, 1H), 12.73–12.89 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.6, 160.7, 157.7, 148.7,

139.3, 130.1, 115.9, 114.7, 105.5, 77.9, 55.0, 49.0, 30.3, 30.0, 26.4, 24.8, 22.4, 21.7; HRMS:

Calcd. for C17H25N5O: 316.2137, Found: 316.2132; HPLC: Method 1, tR = 2.62 min, (98.5%

AUC).

trans-4-(4-(3-Isopropyl-1H-pyrazol-4-yl)pyrimidin-2-ylamino)cyclohexanecarbonitrile (9u).


0.077 g, 25% as a white solid: mp 219–220 °C; 1H NMR (500 MHz, DMSO-d6) δ 1.29–1.35 (m,

8H), 1.51–1.58 (m, 2H), 1.94–1.97 (m, 2H), 2.07–2.09 (m, 2H), 2.66–2.71 (m, 1H), 3.71 (br s,

1H), 3.84–4.06 (m, 1H), 6.79 (d, J = 5.0 Hz, 1H), 6.90 (br s, 1H), 7.93–8.27 (m, 1H), 8.14 (d, J =

5.0 Hz, 1H), 12.74–12.89 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.5, 160.8, 157.6,

156.1, 148.8, 139.4, 130.2, 123.0, 116.0, 114.8, 105.8, 48.0, 30.6, 28.2, 26.6, 24.8, 22.5, 21.8;

HRMS: Calcd. for C17H22N6: 311.1984, Found: 311.1984; HPLC: Method 1, tR = 2.74 min,

(>99% AUC).

N-(Cyclopropylmethyl)-4-(3-(1-methylcyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine

(9y). The compound was prepared using a method similar to that described for the preparation of

9a, 0.064 g, 25% as a white solid: mp 158–160 °C; 1H NMR (500 MHz, DMSO-d6) δ 0.20–0.22

(m, 2H), 0.38–0.44 (m, 2H), 0.70–0.82 (m, 2H), 0.87–0.89 (m, 2H), 1.06–1.11 (m, 1H), 1.34–

1.38 (m, 3H), 3.22 (br s, 2H), 6.88–6.94 (m, 2H), 7.92–8.20 (m, 2H), 12.72–12.95 (m, 1H); 13C

NMR (125 MHz, DMSO-d6) δ 162.2, 159.6, 157.6, 153.7, 146.3, 139.7, 130.4, 118.1, 117.2,

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106.1, 44.8, 24.4, 24.2, 14.6, 13.8, 12.3, 11.1, 3.1; HRMS: Calcd. for C15H19N5: 270.1719,

Found: 270.1718; HPLC: Method 1, tR = 3.47 min, (> 99% AUC).

N-(1-Ethylpiperidin-4-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1Hpyrazol-4-yl)pyrimidin-

2-amine (9dd). The compound was prepared using a method similar to that described for the

preparation of 9a, 0.058 g, 19% as a crystalline white solid: mp 220–222 °C (dec); 1H NMR (500

MHz, DMSO-d6) d 0.90–1.10 (m, 3H), 1.23–1.40 (m, 2H), 1.40–1.60 (m, 4H), 1.74–1.95 (m,

4H), 2.25–2.39 (m, 2H), 2.80–2.92 (m, 2H), 3.85 (br s, 1H), 6.70–6.85 (m, 2H), 8.10–8.30 (m,

2H), 13.20–13.60 (m, 1H); 19F{1H} (282 MHz, DMSO-d6) δ –67.27 (s); 13C NMR (125 MHz,

DMSO-d6) δ 161.7, 159.2, 157.8, 126.2 (q, J = 274.2 Hz), 120.4, 106.5, 52.1, 51.7, 47.4, 31.8,

20.4, 12.3, 11.4; HRMS: Calcd. for C18H23F3N6: 381.2015, Found: 381.2029; HPLC: Method 1,

tR = 1.94 min, (97.3% AUC).

trans-4-(4-(1-Methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9o)

Preparation of 3-(Ethoxymethylene)-1,1,1-trifluoropentane-2,4-dione 13. A stirred solution

of 1,1,1-trifluoropentane-2,4-dione 12 (12.7 g, 82.4 mmol), acetic anhydride (8.41 g, 82.4

mmol), and triethyl orthoformate (24.4 g, 164.8 mmol) were heated at reflux for 19 h. After this

time the reaction mixture was cooled to room temperature and concentrated under reduced

pressure. The residue was vacuum distilled under reduced pressure to provide 13 (6.01 g, 35%)

(55:45 mixture of E,Z isomers by NMR integration) as a red oil: bp 70–85 °C at 2 mm Hg; 1H

NMR (300 MHz, CDCl3) δ 1.40–1.49 (m, 3H), 2.32 (s, 1.35H), 2.42 (s, 1.65H), 4.30–4.40 (m,

2H), 7.69 (s, 0.55H), 7.96 (s, 0.45H); 19F{1H} NMR (282 MHz, CDCl3) δ –76.43, –71.92.

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Preparation of 1-(1-Methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)ethanone 14. To a stirred

solution at –10 °C of methyl hydrazine (0.657 g, 14.3 mmol) in THF (500 mL) was added a

solution of E- and Z- 3-(ethoxymethylene)-1,1,1-trifluoropentane-2,4-dione 20 (3.00 g, 14.3

mmol) in THF (250 mL) dropwise over 1 h. After the addition was complete the resulting

reaction mixture was stirred at –10 °C for 1.25 h, then allowed to warm to room temperature

over 1 h. After this time the reaction mixture was concentrated under reduced pressure, and the

residue was purified using flash column chromatography (silica gel; 20–85% ethyl

acetate/heptanes, gradient elution) to provide 14 (1.92 g, 70%) as a light-yellow solid: mp 79–80;

1H NMR (300 MHz, CDCl3) δ 2.48 (s, 3H), 3.99 (s, 3H), 7.93 (s, 1H); MS (ESI) m/z 253 [M +

H]+.

Preparation of 4-(1-Methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-2-(methylthio)pyrimidine

15. A stirred solution of 1-(1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)ethanone 14 (0.850 g,

4.42 mmol) and DMF•DMA (1.05 g, 8.85 mmol) in toluene (10 mL) was heated at reflux for 18

h. After this time additional DMF•DMA (1.05 g, 8.85 mmol) was added and heating at reflux

was continued for an additional 2 h. After this time the reaction mixture was concentrated under

reduced pressure, the residue was treated with methyl carbamimidothioate•½H2SO4 (0.923 g,

6.64 mmol) and sodium methoxide (30 wt.%, 1.17 mL, 6.64 mmol) in 2-propanol (20 mL), and

the resulting reaction mixture was heated at reflux for 12 h. After this time the reaction mixture

was cooled to room temperature, acidified to pH 3 with 1 N hydrochloric acid and extracted with

ethyl acetate (2 × 50 mL). The combined organic layers were washed with aqueous saturated

sodium chloride solution (30 mL), dried (Na2SO4), filtered, and concentrated under reduced

pressure. The residue was purified using flash column chromatography (silica gel; 25–85% ethyl

acetate/heptanes, gradient elution) to provide 15 (0.097 g, 8%) as a golden oil: 1H NMR (300

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MHz, CDCl3) δ 2.59 (s, 3H), 4.00 (s, 3H), 7.17 (d, J = 5.1 Hz, 1H), 8.11 (s, 1H), 8.51 (d, J = 5.1

Hz, 1H); 19F{1H} NMR (282 MHz, CDCl3) δ -60.42; LC-MS (ESI) m/z 275 [M + H]+.

Preparation of 4-(1-Methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-2-(methylsulfonyl)-

pyrimidine 16. The title compound was prepared by a similar method described for the

preparation of 6. 0.098 g, 92% as a white solid: 1H NMR (300 MHz, CDCl3) δ 3.39 (s, 3H), 4.05

(s, 3H), 7.70 (d, J = 5.1 Hz, 1H), 8.31 (s, 1H), 8.87 (d, J = 5.1 Hz, 1H); 19F{1H} NMR (282

MHz, CDCl3) δ –60.69; MS (ESI) m/z 307 [M + H]+.

Preparation of Trans-4-(4-(1-Methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)pyrimidin-2-

ylamino)cyclohexanol (9o). The compound was prepared using a method similar to that

described for the preparation of 9a, 0.061 g, 56% as an off-white powder: mp 191–192 °C; 1H

NMR (300 MHz, DMSO-d6) δ 1.10–1.35 (m, 4H), 1.80–1.92 (m, 4H), 3.38 (br s, 1H), 3.73 (br s,

1H), 3.96 (s, 3H), 4.51 (d, J = 4.5 Hz, 1H), 6.74 (br d, J = 4.8 Hz, 1H), 6.92 (br s, 1H), 8.24 (br

d, J = 4.8 Hz, 1H), 8.55 (br s, 1H); 19F {1H} NMR (282 MHz, DMSO-d6) δ –59.26; 13C NMR

(125 MHz, DMSO-d6) δ 161.6, 158.5, 156.9, 134.4, 122.4, 120.3, 119.5, 105.7, 68.4, 48.5, 34.2,

30.2; HRMS: Calcd. for C15H18F3N5O: 342.1542, Found: 342.1536; HPLC: Method 1, tR = 2.47

min, (98.4% AUC).

N-(4,4-Difluorocyclohexyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-

yl)pyrimidin-2-amine (9t)

Preparation of 2-Methylsulfonyl)-4-(1-(tetrahydro-2H-pyran-2-yl)-3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidine (6t). To a stirred solution of 2-

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(methylsulfonyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1Hpyrazol-4-yl)pyrimidine (6t) (1.06 g,

3.19 mmol) in 3,4-dihydropyrane (5.0 mL) was added p-toluenesulfonic acid (0.061 g, 0.32

mmol) at room temperature. After 10 min the reaction mixture was concentrated under reduced

pressure. The residue was partitioned between saturated sodium bicarbonate and chloroform, and

separated. The combined organics were dried (MgSO4), filtered and concentrated under reduced

pressure. The residue was purified using flash column chromatography (silica gel; 5-20% ethyl

acetate/methylene chloride, gradient elution) to provide 7t (1.03 g, 78%) as an off-white solid:

1H NMR (500 MHz, CDCl3) δ 1.34–1.41 (m, 2H), 1.28–1.73 (m, 5H), 2.00–2.05 (m, 2H), 2.13–

2.16 (m, 1H), 3.36 (s, 3H), 3.69–3.74 (m, 1H), 4.09–4.12 (m, 1H), 5.41 (dd, J = 9.5, 2.5 Hz, 1H),

7.82 (d, J = 5.0 Hz, 1H), 8.44 (s, 1H), 8.82 (d, J = 5.0 Hz, 1H); 19F {1H} (282 MHz, CDCl3) δ –

68.45 (s); MS (ESI) m/z 417 [M + H]+.

Preparation of N-(4,4-Difluorocyclohexyl)-4-(1-tetrahydro-2H-pyran-2-yl)-3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine (8t). The compound was

prepared from 7t using a method similar to that described for the preparation of 9a to provide 8t

(0.178 g, 47%) as an off-white solid: 1H NMR (300 MHz, CDCl3) δ 1.20–1.25 (m, 2H), 1.46–

1.47 (m, 2H), 1.61–1.71 (m, 6H), 2.01–2.14 (m, 8H), 3.67–3.76 (m, 1H), 4.04–4.11 (m, 2H),

5.12 (br s, 1H), 5.41 (dd, J = 9.3, 3.0 Hz, 1H), 6.93 (d, J = 5.4 Hz, 1H), 8.16 (s, 1H), 8.25 (d, J =

5.4 Hz, 1H); 19F {1H} (282 MHz, CDCl3) δ –68.42 (s), –68.39 (s); MS (ESI) m/z 472 [M + H]+.

Preparation of N-(4,4-Difluorocyclohexyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-

1Hpyrazol-4-yl)pyrimidin-2-amine (9t, CHDI-00372893). To a stirred solution of 8t (0.178 g,

0.38 mmol) in methanol (3.0 mL) was added hydrochloric acid (0.283 mL of a 4.0 M solution in

dioxane, 1.13 mmol,) at room temperature. After 1.5 h the reaction mixture was concentrated

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under reduced pressure. The residue was basified with sodium bicarbonate solution and the

precipitate was collected by filtration. This solid was purified by trituration with methylene

chloride followed by methanol to provide 9t (0.052 g, 13%) as a white solid: 1H NMR (300

MHz, DMSO-d6) δ 1.21–1.26 (m, 2H), 1.43–1.66 (m, 4H), 1.84–2.09 (m, 6H), 3.95–4.14 (m,

1H), 6.87 (d, J = 5.1 Hz, 1H), 6.99 (br s, 1H), 8.05–8.31 (m, 2H), 13.23–13.59 (m, 1H); 19F{1H}

(282 MHz, CDCl3) δ –67.22 (s), –67.56 (s); 13C NMR (125 MHz, DMSO-d6) δ 161.5, 159.3,

158.9, 157.8, 143.7, 140.0, 130.9, 125.6, 123.7, 121.8, 120.3, 106.7, 106.5, 46.3, 31.6 (t, J = 23.9

Hz), 28.0, 27.9, 21.3, 11.5, 11.2; HRMS: Calcd. for C17H18F5N5: 388.1561, Found: 388.1554;

HPLC: Method 1, tR = 3.22 min, (97.4% AUC).

trans-4-((4-(1H-Pyrazol-4-yl)pyrimidin-2-yl)amino)cyclohexanol (9k). The compound was

prepared using a method similar to that described for the preparation of 9t, 0.0658 g, 58% as a

white solid: mp 217–218 °C; 1H NMR (500 MHz, DMSO-d6) 1.24–1.33 (m, 4H), 1.81–1.89 (m,

4H), 3.33– 3.40 (m, 1H), 3.67–3.75 (m, 1H), 4.51 (d, J = 4.5 Hz, 1H), 6.74 (d, J = 8.0 Hz, 1H),

6.81 (d, J = 5.5 Hz, 1H), 8.02 (br s, 1H), 8.17 (d, J = 4.5 Hz, 1H), 8.32 (br s, 1H), 13.42 (br s,

1H); 13C NMR (125 MHz, DMSO-d6) δ 161.4, 158.9, 157.5, 137.4, 128.0, 120.5, 104.8, 68.1,

48.5, 33.8, 30.0; HRMS: Calcd. for C13H17N5O: 260.1511, Found: 260.1510; HPLC: Method 4,

tR = 2.30 min., (98.2% AUC).

N-Cyclohexyl-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine

Dihydrochloride (9q). The compound was prepared using a method similar to that described for

the preparation of 9t, 0.158 g, 94% as a crystalline yellow-brown solid: 1H NMR (500 MHz,

DMSO-d6) δ 1.19–1.89 (m, 15H), 4.10 (s, 1H), 7.19 (s, 1H), 8.25–8.35 (m, 2H), 8.62 (s, 1H); 19F

{1H} (282 MHz, DMSO-d6) δ –67.36 (s); 13C NMR (125 MHz, DMSO-d6) δ 166.0, 153.5,

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146.3, 143.5, 136.6, 126.0 (q, J = 274.2 Hz), 118.4, 106.1, 48.9, 32.0, 24.8, 24.1, 20.6, 11.4;

HRMS: Calcd. for C17H20F3N5: 352.1749, Found: 352.1757; HPLC: Method 1, tR = 3.36 min,

(98.7% AUC).

N-Cyclobutyl-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine

(9v). The compound was prepared using a method similar to that described for the preparation of

9t, 0.096 g, 87% as a white solid: mp; no clear melt observed; 1H NMR (300 MHz, DMSO-d6) δ

1.27 (br s, 2H), 1.53 (br s, 2H), 1.60–1.74 (m, 2H), 2.00–2.10 (m, 2H), 2.27–2.30 (m, 2H), 4.64

(br s, 1H), 7.15 (d, J = 6.3 Hz, 1H), 8.28 (d, J = 6.3 Hz, 1H), 8.52 (br s, 2H), 13.74 (br s, 1H); 19F

{1H} (282 MHz, DMSO-d6) δ –67.37 (s); 13C NMR (125 MHz, DMSO-d6) δ 165.6, 153.2,

146.8, 143.5, 136.3, 126.0 (q, J = 273.8 Hz), 118.5, 106.3, 45.4, 30.0, 20.8, 14.5, 11.4; HRMS:

Calcd. for C15H16F3N5: 324.1436, Found: 324.1446; HPLC: Method 1, tR = 3.00 min, (98.5%

AUC).

N-Cyclopentyl-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine

(9w). The compound was prepared using a method similar to that described for the preparation of

9t, 0.143 g, 90% as a white solid: mp; no clear melt observed; 1H NMR (300 MHz, DMSO-d6)

δ 1.28 (br s, 2H), 1.50–1.61 (m, 6H), 1.71–1.73 (m, 2H), 1.94–1.96 (m, 2H), 4.48 (br s, 1H), 7.19

(d, J = 6.3 Hz, 1H), 8.31 (d, J = 6.6 Hz, 1H), 8.45–8.59 (m, 2H), 13.92 (br s, 1H); 19F {1H} (282

MHz, DMSO-d6) δ –67.39 (s); 13C NMR (125 MHz, DMSO-d6) δ 165.8, 153.7, 146.4, 143.2,

136.5, 126.0 (q, J = 272.9 Hz), 118.5, 106.0, 52.3, 32.0, 23.0, 20.7, 11.4; HRMS: Calcd. for

C16H18F3N5: 338.1593, Found: 338.1595; HPLC: Method 1, tR = 3.19 min, (> 99% AUC).

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N-Cycloheptyl-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine

(9x). The compound was prepared using a method similar to that described for the preparation of

9t, 0.079 g, 50% as an off-white solid: mp; no clear melt; 1H NMR (300 MHz, DMSO-d6) δ 1.27

(br s, 2H), 1.42–1.70 (m, 12H), 1.88–1.95 (m, 2H), 4.27 (br s, 1H), 7.16 (d, J = 6.0 Hz, 1H), 8.30

(d, J = 6.3 Hz, 1H), 8.35 (br s, 1H), 8.52–8.57 (m, 1H), 13.49 (br s, 1H); 19F {1H} (282 MHz,

DMSO-d6) δ –67.35 (s); 13C NMR (125 MHz, DMSO-d6) δ 165.9, 153.3, 146.5, 136.4, 126.0 (q,

J = 274.2 Hz), 118.6, 106.0, 51.2, 34.1, 27.5, 23.0, 20.6, 11.4; S: Calcd. for C18H22F3N5:


N-(Tetrahydro-2H-pyran-4-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-

yl)pyrimidin-2-amine Hydrochloride (9z). The compound was prepared using a method

similar to that described for the preparation of 9t, 0.057 g, 28% as a white solid: mp; no clear

melt observed; 1H NMR (500 MHz, DMSO-d6) δ 1.26 (br s, 2H), 1.50 (br s, 2H), 1.54–1.62 (m,

2H), 1.83 (d, J = 11.0 Hz, 2H), 3.35–3.39 (m, 2H), 3.90 (d, J = 11.0 Hz, 2H), 4.23 (br s, 3H),

7.11 (br s, 1H), 8.00 (br s, 1H), 8.29 (d, J = 6.0 Hz, 1H), 8.50 (br s, 1H); 19F {1H} (282 MHz,

CDCl3) δ –67.55 (s); 13C NMR (125 MHz, DMSO-d6) δ 165.7, 153.7, 146.9, 143.5, 136.6, 126.1

(q, J = 274.2 Hz), 118.5, 106.4, 65.6, 46.5, 32.0, 20.6, 11.5; HRMS: Calcd. for C16H18F3N5O:

354.1542, Found: 354.1544; HPLC: Method 1, tR = 2.48 min, (97.6% AUC).

N-(Tetrahydro-2H-pyran-3-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-

yl)pyrimidin-2-amine (9aa). The compound was prepared using a method similar to that

described for the preparation of 9t, 0.089 g, 80% as a white solid: mp 228–230 °C; 1H NMR

(300 MHz, DMSOd6) δ 1.29 (br s, 2H), 1.50 (br s, 2H), 1.54–1.74 (m, 3H), 1.93–1.95 (m, 1H),

3.30 (br s, 1H), 3.30 (br s, 1H), 3.34 (br s, 1H), 3.70–3.73 (m, 1H), 3.81–3.86 (m, 1H), 4.22 (br s,

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1H), 7.24 (br s, 1H), 8.32–8.64 (m, 3H); 19F {1H} (282 MHz, CDCl3) δ –67.46 (s); 13C NMR

(125 MHz, DMSO-d6) δ 165.8, 154.0, 146.7, 143.3, 136.7, 126.0 (q, J = 272.9 Hz), 118.3, 106.4,

69.7, 66.9, 46.4, 28.3, 23.6, 20.9, 11.3, 11.2; HRMS: Calcd. for C16H18F3N5O: 354.1542, Found:

354.1536; HPLC: Method 1, tR = 2.69 min, (98.7% AUC).

Preparation of N-(tetrahydrofuran-3-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-

4-yl)pyrimidin-2-amine Hydrochloride (9bb). The compound was prepared using a method

similar to that described for the preparation of 9t, 129.4 mg, 52% as a white solid: 1H NMR (300

MHz, DMSO-d6): δ 1.29 (m, 2H), 1.52 (m, 2H), 1.88–1.98 (m, 1H), 2.19–2.31 (m, 1H), 3.65–

3.68 (m, 1H), 3.69–3.72 (m, 1H), 3.80–3.94 (m, 2H), 4.68 (m, 1H), 7.23 (d, J = 6.3 Hz, 1H),

8.35 (d, J = 6.3 Hz, 1H), 8.60 (bs, 2H); 19F {1H} (282 MHz, DMSO-d6) δ –67.33 (s); 13C NMR

(125 MHz, DMSO-d6) δ 164.8, 153.9, 147.0, 142.6, 136.1, 125.6 (q, J = 274.2 Hz), 118.2, 106.1,

71.7, 65.8, 51.1, 31.6, 20.1, 11.0; HRMS: Calcd. for C15H16F3N5O: 340.1385, Found: 340.1385;

HPLC: Method 1, tR = 2.52 min, (> 99% AUC).

N-(Oxetan-3-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridin-2-amine

(9cc). The compound was prepared using a method similar to that described for the preparation

of 9t, 0.024 g, 46% as a yellow solid: mp; no clear melt; 1H NMR (500 MHz, DMSO-d6) δ 1.23

(s, 2H), 1.51–1.53 (m, 2H), 3.51 (br s, 2H), 4.16–4.20 (m, 1H), 4.22–4.27 (m, 1H), 4.27–4.47 (m,

1H), 5.08 (br s, 1H), 6.77 (br s, 1H), 6.92 (s, 1H), 7.89 (br s, 1H), 8.29 (br s, 1H); 19F {1H} (282

MHz, CDCl3) δ –67.16; MS (ESI) m/z 325 [M + H]+.; HRMS: Calcd. for C15H15F3N4O:


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4-(3-(1-Methylcyclopropyl)-1H-pyrazol-4-yl)-N-(piperidin-4-yl)pyrimidin-2-amine

Dihydrochloride (9ee). The compound was prepared using a method similar to that described

for the preparation of 9t, 0.033 g, 39% as an off-white solid: mp; no clear melt; 1H NMR (500

MHz, DMSO-d6) δ 0.85–0.95 (m, 4H), 1.38 (s, 3H), 1.75–1.83 (m, 2H), 2.05–2.10 (m, 2H),

3.00–3.10 (m, 2H), 3.30–3.36 (m, 2H), 7.20 (d, J = 5.5 Hz, 1H), 8.20 (br s, 1H), 8.33 (d, J = 5.5

Hz, 1H), 8.81 (br s, 1H), 8.97 (br s, 1H); HRMS: Calcd. for C16H22N6: 299.1984, Found:

299.1992; HPLC: Method 1, tR = 2.34 min, (> 99% AUC).

N-(1-(2,2,2-Trifluoroethyl)piperidin-4-yl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-

pyrazol-4-yl)pyrimidin-2-amine Dihydrochloride (9ff)

Preparation of 2,2,2-Trifluoro-1-(1,4-dioxa-8-azaspiro[4.5]decan-8-yl)ethanone (37). To a

stirred solution at 0 °C of 1,4-dioxa-8-azaspiro[4.5]decane (38) (20.0 g, 0.140 mol),

triethylamine (28.3 g, 0.279 mol), and DMAP (0.86 g, 0.007 mol) in dichloromethane (490 mL)

was added trifluoroacetic anhydride (32.3 g, 0.154 mol) dropwise over 20 min. After the addition

was complete the reaction mixture was stirred at 0 °C for 1 h, then warmed to room temperature

over 4 h. After this time the reaction was quenched with saturated aqueous sodium bicarbonate

(100 mL) and separated. The organic layer was washed with water (100 mL), saturated sodium

chloride (100 mL), dried (Na2SO4), filtered, and concentrated under reduced pressure. The

yellow oil was dissolved in hot ethyl acetate (200 mL) and precipitate was filtered. The solution

was cooled to room temperature, passed through a plug of silica gel and the filtrate was

concentrated under reduced pressure to afford 37 (32.4 g, 97%) as a yellow oil, which

crystallized to a waxy solid upon standing: 1H NMR (300 MHz, CDCl3) δ 1.76 (t, J = 6.0 Hz,

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4H), 3.67 (t, J = 5.7 Hz, 2H), 3.77 (t, J = 6.0 Hz, 2H), 4.00 (s, 4H); 19F {1H} (282 MHz, CDCl3)

δ –68.91 (s); MS (ESI) m/z 240 [M + H]+.

Preparation of 8-(2,2,2-Trifluoroethyl)-1,4-dioxa-8-azaspiro[4.5]decane (39). To a stirred

solution of BH3-THF complex in THF (1.0 M; 69.0 mL, 69.0 mmol) was added a solution of 37

(15.0 g, 62.7 mmol) in THF (69.0 mL) dropwise over 10 min. The resulting reaction solution

was heated at reflux for 30 min, cooled to room temperature, an additional portion of BH3-THF

complex in THF (1.0 M; 69.0 mL, 69.0 mmol) was added, and the reaction mixture was heated at

reflux for 24 h. After this time the reaction mixture was cooled to room temperature, carefully

quenched with methanol (100 mL), and the resulting reaction mixture was heated to reflux for 30

min. After this time the reaction mixture was cooled to room temperature and concentrated under

reduced pressure to provide 39 (7.50 g, 53%) as a light yellow oil: 1H NMR (300 MHz, CDCl3) δ

1.73–1.77 (m, 4H), 2.74–2.79 (m, 4H), 3.01 (q, J = 9.6 Hz, 2H), 3.96 (s, 4H); 19F {1H} (282

MHz, CDCl3) δ –69.27 (s); MS (ESI) m/z 226 [M + H]+.

Preparation of 1-(2,2,2-Trifluoroethyl)piperidin-4-one oxime (40). A stirred solution of 39

(7.43 g, 32.9 mmol) in a 1.0 M hydrochloric acid (125 mL) was heated at reflux for 6 h. After

this time the reaction mixture was cooled in an ice/water bath, the solution was made basic (pH

9) with saturated sodium carbonate, and extracted with MTBE (3 × 150 mL). The combined

organics were washed with saturated sodium chloride, dried (Na2SO4), filtered, and concentrated

under reduced pressure to prove the crude ketone (4.71 g, 79%). The crude ketone was taken up

in absolute ethanol (130 mL) and treated with sodium acetate (3.20 g, 39.0 mmol) and

hydroxylamine hydrochloride (2.17 g. 31.2 mmol). The resulting reaction mixture was stirred at

room temperature for 18 h. After this time the reaction mixture was concentrated under reduced

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pressure, the residue was partitioned between ethyl acetate (200 mL) and water (200 mL), and

separated. The organic layer was washed with saturated sodium chloride, dried (Na2SO4),

filtered, and concentrated under reduced pressure to provide 40 (4.59 g, 90%) as a clear,

colorless oil: 1H NMR (300 MHz, CDCl3) δ 2.37 (t, J = 6.3 Hz, 2H), 2.67 (t, J = 6.3 Hz, 2H),

2.70–2.84 (m, 4H), 3.05 (q, J = 9.6 Hz, 2H), 7.86 (s, 1H); 19F {1H} (282 MHz, CDCl3) δ –69.26

(s); Note: Could not obtain adequate ionization for a mass spectrum.

Preparation of 1-(2,2,2-Trifluoroethyl)piperidin-4-amine (36). A Parr bottle charged with a

solution of 40 (3.51 g, 17.9 mmol) in absolute ethanol (45.0 mL) was purged with nitrogen and

Raney nickel catalyst (Grade 2800 50 wt. % slurry in water) (1.8 mL) was added to the solution.

The reactor bottle was purged with hydrogen (3×), the pressure was maintained at 30–40 psi, and

shaken for 72 h at room temperature. After this time the reaction bottle was purged with

nitrogen, the catalyst was carefully removed over a pad of Celite, and the filtrate was

concentrated under reduced pressure to afford 36 (2.28 g, 70%) as a light-yellow oil: 1H NMR

(300 MHz, CDCl3) δ 1.42–1.50 (m, 2H), 1.70–1.86 (m, 2H), 1.90 (br s, 2H), 2.30–2.47 (m, 2H),

2.59–2.72 (m, 1H), 2.80-3.05 (m, 4H); 19F {1H} (282 MHz, CDCl3) δ –69.05 (s); Note: Could

not obtain adequate ionization for a mass spectrum.

Preparation of N-(1-(2,2,2-Trifluoroethyl)piperidin-4-yl)-4-(3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine Dihydrochloride (9ff).

The compound was prepared using a method similar to that described for the preparation of 9t

using 36 as the amine, 0.113 g, 30% as an off-white powder: mp 84–87 °C; 1H NMR (500 MHz,

DMSO-d6) δ 1.25 (s, 2H), 1.51 (s, 2H), 1.65–2.10 (m, 6H), 2.80–3.00 (m, 2H), 3.10–4.90 (m,

6H), 7.26 (d, J = 5.5 Hz, 1H), 8.38 (d, J = 5.5 Hz, 1H), 8.66 (br s, 1H), 8.88 (br s, 1H); 19F {1H}

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NMR (282 MHz, DMSO-d6) δ –62.0 to –63.1 (m), –67.3 (s); 13C NMR (125 MHz, DMSO-d6) δ

165.8, 153.8, 147.0, 143.2, 136.8, 126.0 (q, J = 274.2 Hz), 124.2, 121.9, 118.5, 106.6, 54.6, 54.3,

53.6, 53.3, 51.3, 45.5, 29.9, 28.6, 20.8, 11.4; HRMS: Calcd. for C18H20F6N6: 435.1732, Found:

435.1726; HPLC: Method 1, tR = 2.60 min, (98.7% AUC).

(S)-N-(Piperidin-3-yl)-4-(3-(1-trifluoromethyl)cyclopropyl)-1Hpyrazol-4-yl)pyrimidin-2-

amine (9gg). The compound was prepared using a method similar to that described for the

preparation of 9t, 0.045 g, 45% as a white solid: mp 204–205 °C; 1H NMR (300 MHz, DMSO-

d6) δ 1.24 (s, 2H), 1.38–1.44 (m, 2H), 1.53 (s, 2H), 1.59–1.62 (m, 1H), 1.83–1.88 (m, 1H), 2.32–

2.46 (m, 2H), 2.72–2.78 (m, 1H), 2.99–3.03 (m, 1H), 3.86 (br s, 1H), 6.72 (br s, 1H), 6.85 (d, J =

5.1 Hz, 1H), 8.20 (s, 2H), 13.30 (br s, 1H); 19F {1H} (282 MHz, DMSO-d6) δ –67.37 (s); HRMS:

Calcd. for C16H19F3N6: 353.1702, Found: 353.1688; HPLC: Method 1, tR = 2.65 min, (> 99%

AUC).

(R)-N-(Piperidin-3-yl)-4-(3-(1-trifluoromethyl)cyclopropyl)-1Hpyrazol-4-yl)pyrimidin-2-

amine (9hh). The compound was prepared using a method similar to that described for the

preparation of 9t, 0.052 g, 38% as a white solid: mp 204–205 °C;1H NMR (500 MHz, DMSO-

d6) δ 1.24 (s, 2H), 1.37–1.43 (m, 2H), 1.53 (s, 2H), 1.60–1.62 (m, 1H), 1.83–1.85 (m, 1H), 2.34–

2.44 (m, 2H), 2.77 (d, J = 12.0 Hz, 1H), 3.00–3.02 (m, 1H), 3.88 (br s, 1H), 6.71 (br s, 1H), 6.85

(d, J = 4.5 Hz, 1H), 8.19 (s, 2H), 13.30 (br s, 1H); 19F {1H} (282 MHz, DMSO-d6) δ –67.37 (s);

13C NMR (125 MHz, DMSO-d6) δ 161.7, 159.3, 157.9, 140.7, 134.3, 126.2 (q, J = 274.2 Hz),

120.3, 106.5, 51.5, 47.1, 45.7, 30.7, 25.0, 20.4 (q, J = 35.2 Hz), 11.4; HRMS: Calcd. for

C16H19F3N6: 353.1702, Found: 353.1705; HPLC: Method 1, tR = 2.02 min, (> 99% AUC).

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N-(4-(3-(6-Methylpyridin-3-yl)-1H-1,2,4-triazol-1-yl)phenyl)-4-(3-(1-

trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine Hydrochloride (9ii). The

compound was prepared using a method similar to that described for the preparation of 9t, 0.106

g, 70% as a yellow solid: mp No clear melt;1H NMR (500 MHz, DMSO-d6) δ 1.27–1.31 (m,

2H), 1.54–1.56 (m, 2H), 2.71 (s, 3H), 7.21 (d, J = 5.0 Hz, 1H), 7.82 (br s, 1H), 7.87 (d, J = 9.0

Hz, 2H), 8.02 (d, J = 9.0 Hz, 2H), 8.31 (s, 1H), 8.52 (d, J = 5.0 Hz, 1H), 8.75 (br s, 1H), 9.24 (s,

1H), 9.39 (s, 1H), 9.75 (s, 1H); 19F {1H} (282 MHz, CDCl3) δ –67.27 (s, 3F); 13C NMR (125

MHz, DMSO-d6) δ 160.1, 158. 5, 157.0, 156.5, 154.4, 143.9, 141.1, 140.1, 138.3, 134.7, 130.4,

128.0, 127.2 (q, J = 274.2 Hz), 126.9, 120.1, 119.9, 119.8, 109.3, 33.9, 20.4, 20.2, 19.4, 11.3;

HRMS: Calcd. for C25H20F3N9: 504.1872, Found: 504.1882; HPLC: Method 1, tR = 3.09 min, (>

99% AUC).

trans-1-Methyl-4-((4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-

yl)amino)cyclohexanol (9jj)

Preparation of (cis)-4-amino-1-methylcyclohexanol (41). A mixture of (cis)-4-

(dibenzylamino)-1-methylcyclohexanol (42) (2.60 g, 8.40 mmol) and palladium hydroxide on

carbon (50% water, 20 wt%, 1.17 g, 1.10 mmol) in ethanol (90 mL) was stirred at ambient

temperature under hydrogen (balloon pressure) for 15 h. After this time, the reaction was filtered

through diatomaceous earth and washed with ethanol. The filtrate was concentrated under

reduced pressure to afford 41 as a white solid: 1H NMR (500 MHz, CDCl3) 1.22 (s, 3H),

1.40–1.48 (m, 7H), 1.64–1.69 (m, 4H), 2.60–2.63 (m, 1H); MS (ESI) m/z 130 [M + H]+.

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Preparation of trans-1-Methyl-4-((4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-

yl)pyrimidin-2-yl)amino)cyclohexanol (9jj). The compound was prepared using a method

similar to that described for the preparation of 9t using amine 41, 0.0620 g, 54% as a white solid:

mp 220– 222 °C; 1H NMR (500 MHz, DMSO-d6) δ 1.14 (s, 3H), 1.23–1.27 (m, 2H), 1.38–1.45

(m, 5H), 1.51–1.59 (m, 3H), 1.78–1.81 (m, 2H), 3.91 (br s, 1H), 4.23 (s, 1H), 6.72 (br s, 1H),

6.83 (d, J = 5.0 Hz, 1H), 8.03–8.28 (m, 2H), 13.20 (br s, 0.65H, tautomer), 13.56 (br s, 0.35H,

tautomer); 13C NMR (125 MHz, DMSO-d6) δ 160.7, 158.3, 156.8, 142.8, 139.0, 129.9, 119.3,

105.4, 67.1, 46.8, 36.8, 27.9, 25.5, 10.3; HRMS: Calcd. for C18H22F3N5O: 382.1855, Found:

382.1853; HPLC: Method 4, tR = 2.90 min., (> 99% AUC).

(cis)-1-methyl-4-((4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-

yl)amino)cyclohexanol (9kk). The compound was prepared using a method similar to that

described for the preparation of 9t, 0.0820 g, 55% as a white solid: mp 230–232 °C; 1H NMR

(500 MHz, CDCl3) δ 1.11 (s, 3H), 1.20–1.26 (m, 2H), 1.31–1.36 (m, 2H), 1.44 (br s, 1H), 1.51–

1.70 (m, 7H), 3.78 (br s, 1H), 3.98 (s, 1H), 6.74–6.82 (m, 2H), 8.18 (s, 1H), 8.27 (s, 1H), 13.19

(s, 1H); 13C NMR (125 MHz, DMSO-d6) δ 161.6, 159.3, 158.9, 157.7, 143.7, 139.9, 134.9,

130.8, 120.4, 106.3, 66.4, 48.5, 37.4, 31.1, 27.8, 11.5, 11.2; HRMS: Calcd. for C18H22F3N5O:

382.1855, Found: 382.1853; HPLC: Method 5, tR = 15.47 min., (> 99% AUC).

N-(3,3-Difluorocyclobutyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-

yl)pyrimidin-2-amine (9ll). The compound was prepared using a method similar to that

described for the preparation of 9t, 0.035 g, 16% over 2-steps, as a light brown solid: 1H NMR

(500 MHz, DMSO-d6) δ 1.26 (m, 2H), 1.51 (br s, 2H), 2.68–2.78 (m, 2H), 2.93–3.01 (m, 2H),

4.44 (br s, 1H), 7.10 (d, J = 5.5 Hz, 1H), 8.13–8.42 (m, 3H); 13C NMR (125 MHz, DMSO-d6) δ

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127.2, 125.0, 121.6, 119.5, 119.4, 119.2, 117.2, 42.3, 42.1, 41.9, 35.6, 35.5; HRMS: Calcd. for

C15H14F5N5: 360.1248, Found: 360.1242; HPLC: Method 4, tR = 3.47 min., (97.9% AUC).

N-(3,3-Difluorocyclobutyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridin-

2-amine Hydrochloride (25)

Preparation of tert-butyl (3,3-difluorocyclobutyl)carbamate. To an ice-cold, stirred solution

of tert-butyl (3-oxocyclobutyl)carbamate in CH2Cl2 (18 mL) was added diethylaminosulfur

trifluoride (1.8 mL, 13.5 mmol) and the mixture allowed to slowly warm to room temperature

over 4 h. The reaction was quenched using saturated NaHCO3. The layers were separated and the

organic layer was washed with water, dried (Na2SO4), filtered, and concentrated under reduced

pressure. The residue was purified using flash column chromatography (silica gel; 50% ethyl

acetate/heptanes) to provide tert-butyl (3,3-difluorocyclobutyl)carbamate (770 mg, 70%) as an

off-white solid: 1H NMR (300 MHz, CDCl3): δ 1.45 (s, 9H), 2.41–2.53 (m, 2H), 2.91–3.00 (m,

2H), 3.94 (m, 1H), 4.62 (m, 1H).

Preparation of 3,3-difluorocyclobutanamine hydrochloride (31). To a stirred solution of tert-

butyl (3,3-difluorocyclobutyl)carbamate (770 mg, 3.71 mmol) in ethyl acetate (2 mL) was added

hydrochloric acid (18.6 mL of a 4 N solution in dioxane, 74.4 mmol). After 20 h, the solvent was

removed under reduced pressure to provide 31 (406 mg, 76%) as a light brown solid: 1H NMR

(300 MHz, DMSO-d6): δ 2.77–2.99 (m, 4H), 3.57–3.66 (m, 1H), 8.52 (bs, 3H).

Preparation of 2-(2-chloropyridin-4-yl)-1-(1-(trifluoromethyl)cyclopropyl)ethanone (28).

To a cold (-15 to -10 °C), stirred solution of 2-chloro-4-methylpyridine (3.24 g, 25.4 mmol) in

THF (90 mL) was added lithium hexamethyldisilazide (52.1 mL of a 1.0 M solution in THF,

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52.1 mmol) dropwise so as to maintain an internal reaction temperature between -10 to -5 °C.

After 30 minutes, a solution of N-methoxy-N-methyl-1-

(trifluoromethyl)cyclopropanecarboxamide (27, 5.00 g, 25.4 mmol) in THF (40 mL) was added

dropwise. The reaction mixture was then allowed to slowly warm to room temperature overnight.

The reaction was quenched with saturated ammonium chloride solution (100 mL) and the layers

were separated. The aqueous layer was extracted with ethyl acetate (3 × 50 mL). The combined

organic extracts were washed with saturated sodium chloride, dried (Na2SO4), filtered, and

concentrated under reduced pressure. The residue was purified using flash column

chromatography (silica gel; 0–100% ethyl acetate/heptanes, gradient elution) to provide 2-(2-

chloropyridin-4-yl)-1-(1-(trifluoromethyl)cyclopropyl)ethanone 28 (3.69 g, 55%) as a light

yellow oil: 1H NMR (300 MHz, CDCl3): δ 1.40–1.60 (m, 4H), 4.07 (s, 2H), 7.04 (d, J = 5.1 Hz,

1H), 7.17 (s, 1H), 8.34 (d, J = 5.1 Hz, 1H); MS (ESI) m/z 264 [M + H]+.

Preparation of 2-chloro-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridine

(29). A stirred solution of 2-(2-chloropyridin-4-yl)-1-(1-(trifluoromethyl)cyclopropyl)ethanone

28 (2.52 g, 9.58 mmol) in DMF•DMA (10 mL) was heated to 80 °C for 1 h. The reaction mixture

was then cooled to room temperature and concentrated under reduced pressure. The resulting

residue was dissolved in EtOH (50 mL). Hydrazine (0.36 mL, 11.5 mmol) and diisopropylamine

(2.5 mL, 14.4 mmol) were then added, and the resulting mixture was stirred at room temperature

for 2 days. Afterwards, the resulting solids were isolated by filtration, washed with cold EtOH

(30 mL), and dried under vacuum to provide the desired product as an off-white solid (0.56 g).

The filtrate was concentrated under reduced pressure and the residue triturated with CH2Cl2. A

pale yellow solid was isolated by filtration and confirmed to be desired product. The solids were

combined to provide 2-chloro-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridine

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29 (1.84 g, 67%). 1H NMR (500 MHz, DMSO-d6): δ 1.22 (s, 2H), 1.50 (s, 2H), 7.62 (d, J = 5.5

Hz, 1H), 7.68 (s, 1H), 8.33 (bs, 1H), 8.39 (d, J = 5.5 Hz, 1H), 13.45 (s, 1H).

Preparation of 2-chloro-4-(1-(tetrahydro-2H-pyran-2-yl)-3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridine (30). A mixture of 2-chloro-4-(3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyridine 29 (1.78 g, 6.20 mmol) and p-toluene

sulfonic acid monohydrate in 3,4-dihydro-2H-pyran (10 mL) was stirred at room temperature for

1 h. The reaction mixture was then concentrated under reduced pressure. The residue was

purified using flash column chromatography (silica gel; 0–75% ethyl acetate/heptanes, gradient

elution) to provide 30 (2.32 g, quantitative) as a mixture of regioisomers (85:15) and as a viscous

yellow oil: 1H NMR (500 MHz, CDCl3): δ 1.06–1.13 (m, 2H), 1.41–1.76 (m, 5H), 1.95–2.17 (m,

3H), 3.63–3.75 (m, 1H), 4.08–4.15 (m, 1H), 5.40–5.43 (m, 0.85H), 5.66–5.68 (m, 0.15H), 7.37–

7.42 (m, 1H), 7.46–7.47 (m, 1H), 7.79–7.85 (m, 1H), 8.35–8.40 (m, 1H).

Preparation of N-(3,3-Difluorocyclobutyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-

pyrazol-4-yl)pyridin-2-amine Hydrochloride (25). To a reaction vial containing 2-chloro-4-(1-

(tetrahydro-2H-pyran-2-yl)-5-(1-(trifluoromethyl)-cyclopropyl)-1H-pyrazol-4-yl)pyridine (30)

(0.519 g, 1.40 mmol), 3,3-difluorocyclobutanamine hydrochloride (31) (0.220 g, 1.54 mmol),

bis(tri-tert-butylphosphine)-palladium (0) (0.072 g, 0.140 mmol) and sodium tert-butoxide

(0.336 g, 3.50 mmol) was added degassed dioxane (4 ml) at room temperature under argon. The

reaction mixture was sparged with argon for 5 min; the vial was sealed and then heated at 130 °C

overnight. After this time the reaction mixture was cooled to room temperature, diluted with

ethyl acetate (50 mL), washed with water (2×25 mL), saturated sodium chloride (25 mL), dried

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(Na2SO4), filtered, and concentrated under reduced pressure. The residue was purified using

flash column chromatography (silica gel; 0–75% ethyl acetate/heptanes, gradient elution) to

provide a pale yellow semi-solid (0.107 g). A mixture of the semi-solid (0.100 g, 0.220 mmol) in

a 5–6 M solution of hydrogen chloride in 2-propanol (10 mL) was stirred at room temperature

for 2 d. After this time, the solvent was removed under reduced pressure. The residue was

lyophilized from acetonitrile/water to provide 25 (0.088 g, 16%, for 2 steps) as a light yellow-

brown solid: 1H NMR (500 MHz, DMSO-d6) δ 1.25 (m, 2H), 1.58–1.61 (m, 2H), 2.74–2.84 (m,

2H), 3.17–2.25 (m, 2H), 4.27 (m, 1H), 7.19–7.21 (m, 2H), 7.95 (d, J = 7.5 Hz, 1H), 8.42 (s, 1H),

9.51 (br s, 1H), 13.65 (br s, 1H); 13C NMR (125 MHz, DMSO-d6) δ 150.0, 134.1, 125.4, 119.4,

117.2, 117.1, 115.4, 115.0, 109.8, 105.9, 40.3, 40.1, 39.9, 34.6, 34.5, 34.4; HRMS: Calcd. for

C16H15F5N4: 359.1295, Found: 359.1297; HPLC: Method 4, tR = 3.34 min., (98.9% AUC).

Preparation of 4-(3-Isopropyl-1H-pyrazol-4-yl)pyrimidine (33). A solution of 2-

(methylsulfonyl)-4-(3-(isopropyl)-1H-pyrazol-4-yl)pyrimidine (6p) (0.265 g, 0.996 mmol) in 1:1

ethanol/chloroform (12.0 mL) was treated with sodium borohydride (0.171 g, 4.52 mmol) at

room temperature. After 2 h the reaction was carefully quenched with deionized water (2 mL,

caution: hydrogen gas evolution!) and the resulting reaction mixture was stirred for an additional

30 min at room temperature. After this time the reaction mixture was diluted with ethyl acetate

(150 mL), washed with saturated aqueous sodium chloride, dried (Na2SO4), filtered, and

concentrated under reduced pressure. The residue was purified using flash column

chromatography (silica gel; 0–10% methanol/methylene chloride, gradient elution) to provide 33

(0.105 g, 56%) as a white solid: mp 152–154 °C; 1H NMR (500 MHz, DMSO-d6) δ 1.23–1.29

(m, 6H), 3.79–4.04 (m, 1H), 7.71 (d, J = 5.5 Hz, 1H), 8.10–8.45 (m, 1H), 8.65 (d, J = 5.5 Hz,

1H), 9.06 (d, J = 1.0 Hz, 1H), 12.90–13.04 (m, 1H); 13C NMR (125 MHz, DMSO-d6) δ 160.2,

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158.4, 156.6, 149.7, 139.6, 117.3, 114.5, 25.2, 21.8; HRMS: Calcd. for C10H12N4: 189.1140,

Found: 189.1135; HPLC: Method 1, tR = 2.81 min, (> 99% AUC).

5-Chloro-N-(4,4-difluorocyclohexyl)4-(3-(1-(trifluoromethyl)cyclopropyl)-1Hpyrazol-4-

yl)pyrimidin-2-amine (9mm)

Preparation of 6-Methyl-2-(methylthio)pyrimidin-4(3H)-one (16). To a stirred solution of 2-

methyl-2-thiourea sulfate (24.5 g, 176 mmol) in water (420 mL) were added sodium carbonate

(34.0 g, 320 mmol) and ethyl acetoacetate (11b, 20.8 g, 160 mmol) at room temperature. After

16 h the solid was collected by filtration, washed with ice water (5 mL), and dried under reduced

pressure at 40 °C to provide 16 (10.7 g, 43%) as a white solid: 1H NMR (300 MHz, DMSO-d6) δ

2.16 (s, 3H), 2.46 (s, 3H), 5.94 (s, 1H), 12.44 (br s, 1H).

Preparation of 5-Chloro-6-methyl-2-(methylthio)pyrimidin-4(3H)-one (17). To a stirred

suspension of 16 (10.7 g, 68.7 mmol) and acetic anhydride (10.9 g, 103 mmol) in acetic acid

(220 mL) was added ferric chloride (10.9 g, 103 mmol), and sulfuryl chloride (14.1 g, 104.4

mmol) dropwise at room temperature. After the addition was complete the resulting reaction

mixture was heated at 100 °C for 18 h. After this time the reaction mixture was cooled to room

temperature and another portion of sulfuryl chloride (3.3 g, 25.0 mmol) was added and the

reaction mixture was heated to 100 °C for an additional 18 h. After this time the reaction mixture

was cooled to room temperature, concentrated under reduced pressure, and the residue was

triturated with acetone to provide 17 (9.06 g, 69%) as an off-white solid: 1H NMR (300 MHz,

DMSO-d6) δ 2.32 (s, 3H), 2.48 (s, 3H), 12.10 (br s, 1H); MS (ESI) m/z 194 [M + H]+.

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Preparation of 4,5-Dichloro-6-methyl-2-(methylthio)pyrimidine (18). A stirred suspension of

17 (6.67 g, 35.0 mmol), phosphorus oxychloride (83.8 g, 55.0 mmol) and N,N-dimethylaniline

(6.21 g, 5.3 mmol) was heated at 115 °C for 15 h. After this time the reaction mixture was cooled

to room temperature, concentrated under reduced pressure, and the residue was poured into an

ice water. After stirring for several minutes, the aqueous mixture was neutralized with a saturated

sodium bicarbonate and extracted with methylene chloride (3 × 50 mL). The combined organics

were dried (Na2SO4), filtered, and concentrated under reduced pressure. A major portion of the

N,N-dimethylaniline was removed by vacuum distillation (10 mm Hg/80 °C oil bath) and the

residue was purified using flash column chromatography (silica gel; 0–50% methylene

chloride/heptane, gradient elution) to provide 18 (5.46 g, 75%) as an off-white solid: 1H NMR

(300 MHz, CDCl3) δ 2.55 (s, 3H), 2.58 (s, 3H).

Preparation of 5-Chloro-4-methyl-2-(methylthio)pyrimidine (19). A Parr bottle charged with

a suspension of prepared 18 (5.30 g, 25.3 mmol) and palladium on carbon (50% wet, 10% Pd,

1.06 g) in a 0.68 M sodium hydroxide solution (100 mL) was degassed and backfilling with

hydrogen twice and then the resulting mixture was shaken under a hydrogen atmosphere (25-30

psi) at room temperature for 24 h. After this time the reaction mixture was filtered through a pad

of celite and the filter cake was washed with methylene chloride. The combined organics was

dried (MgSO4), filtered and distill (760 mm Hg, oil bath 60 to 75 °C) to provide 19 (3.33 g, 75%)

as a clear colorless oil: 1H NMR (300 MHz, CDCl3) δ 2.53 (s, 3H), 2.54 (s, 3H), 8.36 (s, 1H);

MS (ESI) m/z 175 [M + H]+.

Preparation of 2-(5-Chloro-2-(methylthio)pyrimidin-4-yl)-1-(1-(trifluoromethyl)-

cyclopropyl)ethenol (20). To a stirred solution at 0 °C of 19 (1.51 g, 8.6 mmol) in THF (18.0

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mL) was added sodium hexamethyldisilazide (18 mL of a 1.0 M solution in THF, 17.6 mmol)

and the resulting reaction mixture was held at 0 °C for 2 h. After this time a solution of N-

methoxy-N-methyl-1-(trifluoromethyl)cyclopropanecarboxamide (1.70 g, 8.6 mmol) in THF (5

mL) was added dropwise and then the resulting reaction mixture was warmed to room

temperature. After 16 h the reaction mixture was quenched with saturated ammonium chloride,

the layers were separated, and the aqueous layer was extracted with ethyl acetate (3 × 20 mL).

The combined organics were washed with saturated sodium chloride (15 mL), dried (MgSO4),

filtered and concentrated under reduced pressure. The residue was purified using flash column

chromatography (silica gel; 2-5% ethyl acetate/heptanes, gradient elution) to provide 20 (2.10 g,

79%) as a light yellow solid: 1H NMR (300 MHz, CDCl3) δ 1.31–1.35 (m, 2H), 1.42–1.45 (m,

2H), 2.55 (s, 3H), 6.10 (d, J = 0.9 Hz, 1H), 8.27 (s, 1H), 14.76 (s, 1H); 19F {1H} (282 MHz,

CDCl3) δ –66.80; MS (ESI) m/z 311 [M + H]+.

Preparation of 5-Chloro-2-(methylthio)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1Hpyrazol-4-

yl)pyrimidine (21). A stirred solution of 20 (2.10 g, 6.8 mmol) in DMF•DMA (11 mL) and

methanol (2.5 mL) was refluxed at 110 °C for 6 h. After this time the reaction mixture was

cooled to room temperature, hydrazine hydrate (4.0 mL, 50–60%) was added, and the resulting

reaction mixture was stirred at room temperature for 16 h. After this time the reaction mixture

was concentrated under reduced pressure and the residue was purified using flash column

chromatography (silica gel; 2-5%, 40% ethyl acetate/heptanes, gradient elution) to provide 21

(0.104 g, 5%) as an orange solid: 1H NMR (300 MHz, CDCl3) δ 1.26–1.30 (m, 2H), 1.44–1.48

(m, 2H), 2.57 (s, 3H), 8.17 (s, 1H), 8.52 (s, 1H); 19F {1H} (282 MHz, CDCl3) δ –68.90; MS

(ESI) m/z 333 [M – H]-.

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Preparation of 5-Chloro-2-(methylsulfonyl)-4-(3-(1-(trifluoromethyl)cyclopropyl)-1H-

pyrazol-4-yl)pyrimidine (22). To a stirred suspension at 0 °C of 21 (0.178 g, 0.53 mmol) in

methylene chloride (2.5 mL) was added m-CPBA (75%, 0.193 g, 1.12 mmol) portion-wise and

then the reaction mixture was warmed to room temperature. After 16 h the reaction mixture was

diluted with methylene chloride, saturated sodium bicarbonate (20 mL) and saturated sodium

thiosulfate were added, and the resulting reaction mixture was stirred for 15 min. After this time

the organic layer was separated and the aqueous layer was extracted with 3:1 chloroform/IPA (2

× 15 mL). The combined organics were washed with saturated sodium thiosulfate, saturated

sodium chloride, dried (MgSO4), filtered and concentrated under reduced pressure. The residue

was purified using flash column chromatography (silica gel; 50-100% ethyl acetate/heptanes,

gradient elution) to provide 22 (0.096 g, 49%) as a light yellow solid: 1H NMR (300 MHz,

CDCl3) δ 1.23–1.34 (m, 2H), 1.39–1.50 (m, 2H), 3.40 (s, 3H), 8.30 (s, 1H), 8.63 (s, 1H), 9.19 (s,

1H); 19F {1H} (282 MHz, CDCl3) δ –63.11, –62.88; MS (ESI) m/z 367 [M + H]+.

Preparation of 5-Chloro-2-(methylsulfonyl)-4-(1-(tetrahydro-2H-pyran-2-yl)-3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidine (23). To an ice-cooled stirred

solution of 22 (0.126 g, 0.34 mmol) in 3,4-dihydropyrane (2.0 mL) was added p-toluenesulfonic

acid (0.032 g, 0.02 mmol). After 5 min the reaction mixture was concentrated under reduced

pressure, the residue was partitioned between saturated sodium bicarbonate and chloroform, and

separated. The organics were dried (MgSO4), filtered and concentrated under reduced pressure.

The residue was purified using flash column chromatography (silica gel; 50-80% ethyl

acetate/heptane, gradient elution) to provide 23 (0.125 g, > 99%) as a light yellow oil: 1H NMR

(300 MHz, CDCl3) δ 1.59–1.85 (m, 5H), 2.04–2.06 (m, 1H), 2.16–2.19 (m, 1H), 3.31 (s, 3H),

3.50–3.58 (m, 1H), 3.63–3.77 (m, 1H), 3.98–4.05 (m, 1H), 4.08–4.19 (m, 1H), 4.88–4.92 (m,

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1H), 5.43–5.79 (m, 1H), 8.37–8.46 (m, 1H), 8.84 (d, J = 4.5 Hz, 1H); 19F {1H} (282 MHz,

CDCl3) δ –68.65, –68.13; MS (APCI) m/z 451 [M + H]+.

Preparation of 5-Chloro-N-(4,4-difluorocyclohexyl)-4-(1-tetrahydro-2H-pyran-2-yl)-3-(1-

(trifluoromethyl)cyclopropyl)-1H-pyrazol-4-yl)pyrimidin-2-amine (24). A sealed microwave

tube charged with a stirred suspension of 23 (0.150 g, 0.33 mmol), 4,4-difluorocyclohexanamine

hydrochloride (0.118 g, 0.66 mmol) and triethylamine (0.088 g, 0.83 mmol) in DMSO (2.0 mL)

was heated at 130 °C for 3 h with microwave irradiation. After this time the reaction mixture was

cooled to room temperature, poured into water (10 mL), and was extracted with methylene

chloride (3 × 15 mL). The combined organics was washed with saturated sodium chloride, dried

(MgSO4), filtered and concentrated under reduced pressure. The residue was purified using flash

column chromatography (silica gel; 30-50% ethyl acetate/heptanes, gradient elution) to provide

24 (0.029 g, 17%) as a yellow solid: 1H NMR (500 MHz, CDCl3) δ 1.21–1.32 (m, 6H), 1.57–

1.93 (m, 6H), 2.03–2.09 (m, 6H), 3.63–3.73 (m, 1H), 4.01 (br s, 1H), 4.07–4.12 (m, 1H), 4.90–

4.92 (m, 1H), 5.40–5.70 (m, 1H), 8.01–8.12 (m, 1H), 8.24 (d, J = 5.5 Hz, 1H); 19F {1H} (282

MHz, CDCl3) δ –68.45 (s), –68.59 (s); MS (ESI) m/z 506 [M + H]+.

Preparation of 5-Chloro-N-(4,4-difluorocyclohexyl)4-(3-(1-(trifluoromethyl)cyclopropyl)-

1H-pyrazol-4-yl)pyrimidin-2-amine (9mm, CHDI-00391118). To a stirred solution of 24

(0.028 g, 0.06 mmol) in methanol (2.0 mL) was added hydrochloric acid (0.500 mL of a 5 to 6 M

solution in IPA, ~0.25 mmol,) at room temperature. After 2 d the reaction mixture was

concentrated under reduced pressure. The residue was basified with sodium bicarbonate solution

and the precipitate was collected by filtration to provide 9mm (0.020 g, 85%) as an off-white

solid: 1H NMR (500 MHz, DMSO-d6) δ 1.28–1.42 (m, 4H), 1.56–1.62 (m, 2H), 1.84–1.89 (m,

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4H), 2.05–2.07 (m, 2H), 3.95 (br s, 1H), 7.87–8.15 (m, 1H), 8.32 (s, 1H), 13.23–13.61 (m, 1H);

19F {1H} (282 MHz, CDCl3) δ –67.82 (s), –67.56 (s); HRMS: Calcd. for C17H17ClF5N5:

422.1171, Found: 422.1159; HPLC: Method 2, tR = 19.65 min, (97.3% AUC).

Molecular Modeling

Virtual Screening: Docking based virtual screening was performed according to methods

described for Glide.40, 41 The structure of Jnk3 in complex with an imidazole-pyrimidine

inhibitor (1pmq) was downloaded from Protein Data Bank (PDB) and prepared using protein

preparation wizard in Maestro (Maestro, version 9.0, Schrodinger, LLC, New York, NY, 2009.

Ligands were prepared using LigPrep (LigPrep, version 2.3, Schrodinger, LLC, New York, NY,

2009) using the OPLS-2005 force field and ionization states at physiological pH (+/- 2) derived

with Epic (Epic, version 2.0, Schrodinger, LLC, New York, NY, 2009). Molecular docking was

performed with Glide (Glide, version 5.5, Schrodinger, LLC, New York, NY, 2009) with HTVS

precision scoring function. Virtual hit selection was done using a combination of ligand ranking

based on Glide gscore, Glide emodel, and careful visual inspection for the fulfillment of key

hydrogen bonding and hydrophobic interactions between the ligand and the protein.

Glide Ligand Docking: Having obtained JNK3 complexes with imidazole 1 and analog

9e, which represented a better representation of the JNK3 binding states with structurally-related

compounds, grids were prepared for these two structures for use in Glide docking. All ligands

were energy minimized using the OPLS-2005 force field in Macromodel (Macromodel, version

9.7, Schrodinger, LLC, New York, NY, 2009) prior to docking. Molecular docking was

performed with Glide (Glide, version 5.5, Schrodinger, LLC, New York, NY, 2009) with the

standard precision scoring function. Assessment of docking pose quality and likelihood was done

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by visual inspection based on a knowledge-base of Glide gscores and Glide emodel rankings

generated for a set of JNK3 inhibitor benchmarks from the literature as well as pyrazole

compounds from the medicinal chemistry efforts.

X-Ray Crystallography Studies

JNK3-Adenosine Co-Crystallization. The hanging drop vapor diffusion method was

used for JNK3 co-crystallization with adenosine. JNK3 protein (1 µL, ~8.5 mg/mL) containing

25 mM HEPES pH 6.9, 5% v/v glycerol, 5 mM DTT, 125 mM NaCl and 1 mM adenosine was

mixed with a precipitant solution containing 20-25% PEG 3350 and 0.18-0.24 M potassium

fluoride. JNK3 crystals in complex with adenosine were obtained through micro seeding using

JNK3/AMP-PNP seeds and crystals appeared within one week at 20 °C. X-ray diffraction data

were collected in-house using a Rigaku Micromax 007HF rotating anode X-ray generator and a

Rigaku R-Axis IV++ image plate detector. Prior to data collection, the crystals were flash-cooled

to 100 K in the precipitant solution. Data were indexed and reduced with MOSFLM and

SCALA (CCP4) in the orthorhombic P212121 space group. The structure was determined by the

molecular replacement method using PDB entry 3G9L with MOLREP (CCP4). Refinement and

model building were performed using REFMAC5 and COOT, respectively (CCP4). Clear

electron density for the adenosine molecule was observed after one round of refinement. After

alternating cycles of model building, water addition and refinement the JNK3-adenosine

complex had a final Rcryst = 25.6% and Rfree = 31.1%.

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JNK3-Adenosine Crystal Soaking Experiment with 1. A 50 mM stock solution of each

CHDI inhibitor compound was prepared in DMSO. JNK3-adenosine co-crystals were

transferred from their growth drop to a drop containing 23% PEG 3350, 0.2 M potassium

fluoride, 10% v/v DMSO and 5 mM CHDI ligand. Crystals were extremely sensitive to drying

out and were transferred using a large 0.5 mm diameter, 20 µm loop which would hold a

relatively large volume of precipitant solution and prevent crystal damage. Soaks were

performed with pyrazole 1 for 7 days, 24 hours, 3 days and 3 hours, respectively. Prior to data

collection the crystals were flash-cooled to 100 K in the soak solution. All ligand soak data sets

were collected in-house as described above and structures were also solved as described above.

The topology files for each inhibitor were generated using JLIGAND (CCP4). The JNK3-1

complex had a final Rcryst = 24.7% and Rfree = 31.9%. Soaking with 9e was conducted in a

similar manner. The JNK3-9e complex had a final Rcryst = 26.3% and Rfree = 32.4%.

Kinetic Solubility Assay. The assay was run using the following materials and reagents:

Tamoxifen, Sigma (Cat # T-5648); Verapamil, Sigma (Cat # V-4629); DMSO, Sigma (Cat #

472301); phosphate buffered saline (PBS), Sigma (Cat # D8537); 0.45 µm PVDF filters, Titan

Sun Sri (Cat # 44504-PV); 2 mL 96-well plate, Whatman (Cat # 7701-5200); 96 well plates (UV

compatible, non-polystyrene, clear bottom), Costar (Cat # 3635); Spectramax PLUS UV/VIS

spectrophotometer, Molecular Devices.

Stock solutions (10 mM) of each compound were prepared in DMSO and 10 µL of 10 mM

stock solution was transferred into a well in a 2 mL 96-well plate containing 990 µL of PBS (pH

7.4) in triplicate (theoretical concentration of 100 µM). The plate was sealed and incubated in an

incubator shaker for 1 hour at 25 oC while shaking at 200 rpm. Samples were filtered through a

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0.45 µm hydrophilic PVDF 96-well filter plate mounted on a 2 mL 96-well plate by

centrifugation at 3,600 rpm for 10 min. Filtered samples were then measured in a 96-well UV

plate. Standards were prepared by initially preparing a 200 µM solution from the 10 mM stock

(e.g. 20 µL of 10 mM stock solution in 960 µL DMSO) and then performing a 1:1 serial dilution

in a 96-well UV plate. PBS with 1 % v/v DMSO was used as a blank. The UV plate was

scanned using a UV/Vis spectrophotometer at a wavelength of 280 nm. Compound solubility

was determined by comparing the absorbance value of the filtrate to the standard calibration

curve of the compound and measured in µM of compound dissolved in PBS with 1 % v/v

DMSO.

Acknowledgment

The authors would like to thank John Mangette for obtaining 13C NMR and HRMS data

on all new compounds.

Supporting Information Available:

Included are experimental descriptions of in vitro liver microsomal stability assays and

permeability/efflux assays in MDCK cells. A description of the metabolite identification in

mouse liver microsomes and a mouse pharmacokinetic study of 9t co-administered with CYP450

inhibitors are provided. Also shown are Cerep selectivity panels showing the activity of 9t at 10

µM concentration against diverse enzyme, kinase and receptor targets. This is followed by

Cerep kinase panel results of 34 at 10 µM and a summary of JNK inhibitor benchmark profiling.

This material is available free of charge via the Internet at http://pubs.acs.org.

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Corresponding Author Information

J. W.: phone; 310-342-5518; email; [email protected].

Abbreviations Used

JNK, c-Jun N-terminal kinase; HD, Huntington’s disease; FAT, Fast axonal transport; POC,

Proof of concept; p38 MAPK, p38 Mitogen activated protein kinase; ATF-2, Activating

transcription factor 2; PD, Pharmacodynamic; PK, pharmacokinetics; ADME, adsorption

distribution metabolism excretion; mLM, Mouse liver microsomes; hLM, Human liver

microsomes; MDCK-MDR1, Madin-Darby canine kidney cells expressing the MDR1 gene;

PDB, Protein data bank; HMBC, Heteronuclear Multiple Bond Correlation; NOE, Nuclear

Overhauser effect; P-gp, P-Glycoprotein

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Table of Contents Graphic

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1

N NH

N

Cl

9t

N NH

N

N

F3C

NH

F

FSAR

ADME-PK

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