Canadian Patents Database / Patent 2813299 Summary

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(12) Patent Application: (11) CA 2813299
(54) English Title: PROTEIN KINASE INHIBITORS
(54) French Title: INHIBITEURS DE PROTEINES KINASES
(51) International Patent Classification (IPC):
  • C07D 487/04 (2006.01)
(72) Inventors :
  • LAURENT, ALAIN (Canada)
  • ROSE, YANNICK (Canada)
  • JAQUITH, JAMES B. (Canada)
(73) Owners :
  • PHARMASCIENCE INC. (Canada)
(71) Applicants :
  • PHARMASCIENCE INC. (Canada)
(74) Agent: NA
(74) Associate agent: NA
(45) Issued:
(22) Filed Date: 2013-04-17
(41) Open to Public Inspection: 2014-10-17
(30) Availability of licence: N/A
(30) Language of filing: English

English Abstract


The present invention relates to a novel family of inhibitors of protein
kinases.
In particular, the present invention relates to inhibitors of the members of
the
Tec and Src protein kinase families.


Note: Claims are shown in the official language in which they were submitted.

CLAIMS
1. A compound of Formula 1:
Image
wherein R1 is selected from the group consisting of:
1) hydrogen,
2) alkyl,
3) heteroalkyl,
4) carbocyclyl,
5) heterocyclyl, and
6) -C(O)R4;
wherein the alkyl, heteroalkyl, carbocyclyl and heterocyclyl may be further
substituted by the groups consisting of:
1) hydroxy,
2) alkoxy,
3) alkyl,
4) -OC(O)R4,
5) -OC(O)NR5R6,
6) -C(O)R4,
184


7) -C(O)NR5R6,
8) -NR5R6,
9) -NR2C(O)R4,
10) -NR2S(O)n R4 and
11) -NR2C(O)NR5R6;
wherein Y is Image
wherein Z is Image
wherein -YZW is Image
X1 and X2 are independently selected from the group consisting of hydrogen,
halogen and cyano;
n is an integer from 0 to 2;
m is an integer from 0 to 2;
m' is an integer from 0 to 2;
W is selected from the group consisting of:
1) alkyl,
2) aralkyl,
3) heteroaralkyl,
4) -OR3,

185

5) -OC(O)R4,
6) -OC(O)NR5R6,
7) -CH2O-R4,
8) -NR5R6,
9) -NR2C(O)R4,
10) -NR2S(O)n R4 and
11) -NR2C(C)NR5R6;
wherein the alkyl, aralkyl and heteraralkyl may be further substituted;
R2 is hydrogen or alkyl;
R3 is selected from the group consisting of: substituted or unsubstituted
alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted
alkynyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted carbocyclyl, heterocyclyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, substituted or unsubstituted aralkyl,

and substituted or unsubstituted heteroaralkyl;
R4 is selected from the group consisting of: substituted or unsubstituted
alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted
alkynyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted carbocyclyl, heterocyclyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, substituted or unsubstituted aralkyl,

and substituted or unsubstituted heteroaralkyl;
R5 and R6 are independently selected from the group consisting of: hydrogen,
alkyl, alkenyl, alkynyl, heteroalkyl, carbocyclyl, heterocyclyl, aryl and
heteroaryl;
alternatively R5 and R6 are fused to form a 3 to 8 membered heterocyclyl ring
system.
186

2. The compound of claim 1, wherein W is -OR3, and wherein R3 is
selected from the group consisting of: substituted or unsubstituted
aralkyl and substituted or unsubstituted heteroaralkyl.
3. The compound of claim 1, wherein W is selected from the group
consisting of:
Image
187


Image
4. The compound according to claim 1, wherein W is selected from the
group consisting of:
Image
5. The compound according to any one of claims 1 to 4, wherein R1 is
selected from the group consisting of:
Image
188


Image
6. The compound according to claim 5, wherein R1 is selected from the
group consisting of:
Image
7. The compound according to any one of claims 1 to 6, wherein Y is
selected from the group consisting of:
Image
8. The compound according to any one of claims 1 to 5, wherein Z is
selected from the group consisting of:
Image
9. The compound according to claim 8, wherein Z is:

189


10. The compound according to any one of claims 1 to 9, wherein -YZW is
selected from the group consisting of:
Image
11. A compound selected from the group consisting of:
Image

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Note: Descriptions are shown in the official language in which they were submitted.

CA 02813299 2013-04-17
PROTEIN KINASE INHIBITORS
FIELD OF INVENTION
The present invention relates to a novel family of inhibitors of protein
kinases. In particular, the present invention relates to inhibitors of the
members of the Tec and Src protein kinase families.
BACKGROUND OF THE INVENTION
Protein kinases are a large group of intracellular and transmembrane
signaling proteins in eukaryotic cells. These enzymes are responsible for
transfer of the terminal (gamma) phosphate from ATP to specific amino acid
residues of target proteins. Phosphorylation of specific tyrosine, serine or
threonine amino acid residues in target proteins can modulate their activity
leading to profound changes in cellular signaling and metabolism. Protein
kinases can be found in the cell membrane, cytosol and organelles such as
the nucleus and are responsible for mediating multiple cellular functions
including metabolism, cellular growth and division, cellular signaling,
modulation of immune responses, and apoptosis. The receptor tyrosine
kinases are a large family of cell surface receptors with protein tyrosine
kinase activity that respond to extracellular cues and activate intracellular
signaling cascades (Plowman et al. (1994) DN&P, 7(6):334-339).
Aberrant activation or excessive expression of various protein kinases are
implicated in the mechanism of multiple diseases and disorders
characterized by benign and malignant proliferation, excess angiogenesis, as
well as diseases resulting from inappropriate activation of the immune
system. Thus, inhibitors of select kinases or kinase families are expected to
be useful in the treatment of cancer, autoimmune diseases, and
inflammatory conditions including, but not limited to: solid tumors,
hematological malignancies, arthritis, graft versus host disease, lupus
erythematosus, psoriasis, colitis, illeitis, multiple sclerosis, uveitis,
coronary
artery vasculopathy, systemic sclerosis, atherosclerosis, asthma, transplant
rejection, allergy, dermatomyositis, pemphigus and the like.
1

CA 02813299 2013-04-17
Examples of kinases that can be targeted to modulate disease include
receptor tyrosine kinases such as members of the platelet-derived growth
factor receptor (PDGFR), vascular endothelial growth factor receptor (VEGFR)
families and intracellular proteins such as members of the Syk, SRC, and Tec
families of kinases.
Tec kinases are non-receptor tyrosine kinases predominantly, but not
exclusively, expressed in cells of hematopoietic origin (Bradshaw W. Cell
Signal. 2010,22:1175-84). The Tec family includes Tec, Bruton's tyrosine
kinase (Btk), inducible T-cell kinase (Itk), resting lymphocyte kinase
(RIk/Txk), and bone marrow-expressed kinase (Bmx/Etk). Btk is a Tec
family kinase which is important in B-cell receptor signaling. Btk is
activated
by Src-family kinases and phosphorylates PLC gamma leading to effects on
B-cell function and survival. Additionally, Btk is important in signal
transduction in response to immune complex recognition by macrophage,
mast cells and neutrophils. Btk inhibition is also important in survival of
lymphoma cells (Herman, SEM. Blood 2011, 117:6287-6289) suggesting that
inhibition of Btk may be useful in the treatment of lymphomas.
cSRC is the prototypical member of the SRC family of tyrosine kinases which
includes Lyn, Fyn, Lck, Hck, Fgr, Blk, Syk, Yrk, and Yes. cSRC is critically
involved in signaling pathways involved in cancer and is often over-expressed
in human malignancies (Kim LC, Song L, Haura EB. Nat Rev Clin Oncol. 2009
6(10):587-9). The role of cSRC in cell adhesion, migration and bone
remodeling strongly implicate this kinase in the development and progression
of bone metastases. cSRC is also involved in signaling downstream of
growth factor receptor tyrosine kinases and regulates cell cycle progression
suggesting that cSRC inhibition would impact cancer cell proliferation.
Additionally, inhibition of SRC family members may be useful in treatments
designed to modulate immune function. SRC family members, including Lck,
regulate T-cell receptor signal transduction which leads to gene regulation
events resulting in cytokine release, survival and proliferation. Thus,
2

CA 02813299 2013-04-17
inhibitors of Lck have been keenly sought as immunosuppressive agents with
potential application in graft rejection and T-cell mediated autoimmune
disease (Martin et al. Expert Opin Ther Pat. 2010, 20:1573-93).
Inhibition of kinases using small molecule inhibitors has successfully led to
several approved therapeutic agents used in the treatment of human
conditions. Herein, we disclose a novel family of kinase inhibitors. Further,
we demonstrate that modifications in compound substitution can influence
kinase selectivity and therefore the biological function of that agent.
PCT Publication Nos. W002/080926 and W002/76986 disclose
pyrazolopyrimidines as therapeutic agents. Btk is included in a long list of
biologically un-related kinases. No evidence of kinase inhibition or cellular
activity was disclosed in W002/080926 and exemplification centers on amide
and sulfonamide derivatives with a limited subset of unsubstituted 4-
phenoxyphenyl derivatives.
US Patent No. 7,514,444 discloses inhibitors of Btk. Compound 13 (PCI-
32765) of this patent has been reported to show ATP competitive binding to
a wide range of kinases including Btk, Lck, Lyn, cSRC, Jak, EGFR, KDR and
others (Honigberg, L.A, et al, The Bruton tyrosine kinase inhibitor PCI-32765
blocks B-cell activation and is efficacious in models of autoimmune disease
and B-cell malignancy,PNAS vol. 107 no. 29, 13075-13080). Specifically for
Btk, the acrylannide functionality of compound 13 is reported to covalently
bind the thiol moiety of Cys481, which is situated adjacent to the ATP binding

pocket of Btk, thus inducing "sustained" inhibition of Btk. However,
compound 13 also inhibits various kinases which also feature a Cys adjacent
to the ATP binding pocket, such as Bmx, Tec, Txk, Itk, EGFR, ErbB2, ErbB4,
Jak3 and Blk. Covalent binding to any of these kinases may diminish the
selective nature of this approach.
CDG-0834 belongs to a structurally unrelated family of compounds which
were recently reported to demonstrate significant Btk selectivity (Liu L., et
al,
3

CA 02813299 2013-04-17
Antiarthritis effect of a novel Bruton's tyrosine kinase (BTK) inhibitor in
rat
collagen-induced arthritis and mechanism-based
pharmacokinetic/pharmacodynamic modeling: relationships between
inhibition of BTK phosphorylation and efficacy. 3 Pharmacol Exp Ther. 2011
3u1;338(1):154-63). GDC-0834 was active in several animal models of
autoimmune disease. However, this compound failed in Phase 1 clinical trials
as a result of human specific metabolism (Liu L, et al, Significant species
difference in amide hydrolysis of GDC-0834, a novel potent and selective
Bruton's tyrosine kinase inhibitor, Drug Metab Dispos. 2011
Oct;39(10):1840-9).
Inhibition of EGFR has been related to the induction of severe rash with
multiple clinical compounds (Tan AR, et al, Markers in the epidermal growth
factor receptor pathway and skin toxicity during erlotinib treatment. Ann
Oncol. 2008 Jan;19(1):185-90). Similarly, inhibition of KDR (VEGFR2) has
been clinically related to hypertension (Howard R. Mellor, et
al.,Cardiotoxicity
Associated with Targeting Kinase Pathways in Cancer, Toxicological Sciences
120(1), 14-32 (2011). Therefore, the development of Btk inhibitors which
demonstrated greater kinase selectivity could potentially be useful in various

B-cell related indications which require acute and/or chronic dosing
regimens, such as cancer, inflammatory and autoimmune diseases.
The present invention relates to a family of potent and selective, non-
covalent Btk inhibitors which demonstrate cellular activity, oral exposure and

activity in animal models of inflammation and autoimmune disease. Kinase
selectivity and cellular potency are related to specific substitution patterns
on
the compounds. Synthetic methods are disclosed which provide compounds
on multi-gram scale.
4

CA 02813299 2013-04-17
SUMMARY OF THE INVENTION
The present invention relates to a novel family of kinase inhibitors.
Compounds of this class have been found to have inhibitory activity against
members of the Tec and Scr protein kinase families.
One aspect of the present invention is directed to a compound of Formula 1:
NH2 y_z_w
I ,N
N N
iR1
Formula 1
wherein
R1 is selected from the group consisting of:
1) hydrogen,
2) alkyl,
3) heteroalkyl,
4) carbocyclyl,
5) heterocyclyl,
6) -C(0)R4,
wherein the alkyl, heteroalkyl, carbocyclyl and heterocyclyl may be further
substituted by the groups consisting of:
1) hydroxy,
2) alkoxy,
3) alkyl,
4) -0C(0)R4,

CA 02813299 2013-04-17
5) -0C(0)NR5R6,
6) -C(0)R4,
7) -C(0)NR5R6,
8) -NR5R6,
9) -NR2C(0)R4,
10) -NR2S(0)nR4,
11) -NR2C(0)NR5R6;
Y is selected from:
(X2), sjsj
Z is selected from:
(x1)m,
Wherein -YZW is selected from:
(x2),, _________ w
(X)rn.
Xl and X2 are independently selected from hydrogen, halogen or cyano;
n is an integer from 0 to 2;
m is an integer from 0 to 2;
m' is an integer from 0 to 2;
6

CA 02813299 2013-04-17
W is independently selected from:
1) alkyl,
2) aralkyl,
3) heteroaralkyl,
4) -0R3,
5) -0C(0)R4,
6) -0C(0)NR5R6,
7) -CH2O-R4,
8) -NR5R6,
9) -NR2C(0)R4,
10) -NR2S(0)nR4,
11) -NR2C(0)NR5R6;
wherein the alkyl, aralkyl and heteraralkyl may be further substituted;
R2 is selected from hydrogen or alkyl;
R3 is selected from substituted or unsubstituted alkyl, substituted or
unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted carbocyclyl,
substituted or unsubstitutded heterocyclyl, substituted or unsubstituted aryl,

substituted or unsubstituted heteroaryl, substituted or unsubstituted aralkyl
or substituted or unsubstituted heteroaralkyl;
R4 is selected from substituted or unsubstituted alkyl, substituted or
unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted carbocyclyl,
substituted or unsubstitutded heterocyclyl, substituted or unsubstituted aryl,
7

CA 02813299 2013-04-17
substituted or unsubstituted heteroaryl, substituted or unsubstituted aralkyl
or substituted or unsubstituted heteroaralkyl;
R5 and R6 are independently selected from hydrogen, alkyl, alkenyl, alkynyl,
heteroalkyl, carbocyclyl, heterocyclyl, aryl, heteroaryl or R5 and R6 can be
fused to form a 3 to 8 membered heterocyclyi ring system.
Preferred embodiment includes compounds of Formula 1 where W is selected
from -0R3 and R3 is selected from substituted or unsubstituted aralkyl, or
substituted or unsubstituted heteroaralkyl.
Preferred embodiment includes compounds of Formula 1 where W is selected
from the group consisting of:
N
\\
F3C
1/
¨0 . 1 ¨0 I/ ¨0 1 Cl,ci ¨0
, ,
o/ \o
¨0 . ¨0(kip // N
=____/0 41 _oy V.K
, , , ,
r_eil
/--N ff-N
/ \NJ
/ -0 N
/ __________________ ej / __ CS
, _0 N s /e_
D t1$
D, __I /=--- \N
/
fi , _i 0 \
D _N
1 ¨0 N
/--% ---"- c ¨0/ N -----% ---
8

CA 02813299 2013-04-17
/(; 1
-0 N
0 / __ el
N
. k
HO z--N OH
eNc // N
HO %-N/1)---
/ -0 S -0 S----c
I ,or
I I
ií'
N.
N--
H .
Preferred embodiment includes compounds of Formula 1 where Fels selected
from the group consisting of:
JvW
JUVV
VVVV JVNAI
...,,'' ..., ..,
N
II
H, CH3, acetyl, zN, D3eLCD3 ,,
V-N, , (y= , =.õ..,NH
0 I
JWV
JvvV
0
,..../ \ .., NA0
Th\l"
N1,11 I\LIr,_, oN,I.r.0
0 0 0 H 0 , 'L)
I I I I I
VVVV
JVVV
VVVV
JUVV L,.... VVVV
Ns'V'A
1\1.r. rN) c jj LI\i, n 0
0 \ ___ /, 1 III rµk 11"
I I I I I I
9

CA 02813299 2013-04-17
sss\
JVVV $4,.., srVVV VVVV
JVW .AAIV VVVV
N
NH
0 --,/ OH OH OH OH OH CI OH <>
, , , , , , ,
or
Preferred embodiment includes compounds of Formula 1 where Y is selected
from the group consisting of:
F
F
1 o . civ 1 4. 0
\
Jsrrj , ' , or .

Preferred embodiment includes compounds of Formula 1 where Z is selected
from the group consisting of:
CI CN F
0\ 0 0 0 i \ l , or\
, , .
More preferred embodiment includes compounds of Formula 1 where W is
selected from the group consisting of:
N
\\
F3C
* *
¨0 ¨0
,
10H, ¨N
¨0
/---C.
N ¨0
N
, or
,
N
--a/ _____ (s___INI
=

CA 02813299 2013-04-17
More preferred embodiment includes compounds of Formula 1 where RI- is
selected from the group consisting of:
6,vv,
õsõ,,, õõõ, iss4 VW
, JVVV
NOW JVVV
OWN!
...WV ..........s`...,
VN
a _1 1 ,
, õ, 1 OH, H, O OH OH1 OH 0 ,or
.ftrw
.
More preferred embodiment includes compounds of Formula 1 where Z is
selected from the group consisting of:
F
More preferred embodiment includes compounds of Formula 1 where -YZW is
selected from the group consisting of:
1 lik 0 1 o Mk 0
F 446 W F 1110 W 441 W
F F or F
, .
Another aspect of the present invention provides a pharmaceutical
composition comprising an effective amount of a compound of Formula 1 and
a pharmaceutically acceptable carrier, diluent or excipient.
In another aspect of the present invention, there is provided a use of the
compound of Formula 1 as an inhibitor of protein kinase, more particularly,
as an inhibitor of Btk.
11

CA 02813299 2013-04-17
Another aspect of the present invention provides a method of modulating
kinase function, the method comprising contacting a cell with a compound of
the present invention in an amount sufficient to modulate the enzymatic
activity of a given kinase or kinases, such as Btk, thereby modulating the
kinase function.
Another aspect of the present invention provides a method of modulating the
target kinase function, the method comprising a) contacting a cell with a
compound of the present invention in an amount sufficient to modulate the
target kinase function, thereby b) modulating the target kinase activity and
signaling.
Another aspect of the present invention provides a probe, the probe
comprising a compound of Formula 1 labeled with a detectable label or an
affinity tag. In other words, the probe comprises a residue of a compound of
Formula 1 covalently conjugated to a detectable label. Such detectable
labels include, but are not limited to, a fluorescent moiety, a
chemiluminescent moiety, a paramagnetic contrast agent, a metal chelate, a
radioactive isotope-containing moiety, or biotin.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
The present invention relates to novel kinase inhibitors. These compounds
are found to have activity as inhibitors of protein kinases: including members

of the tyrosine kinases Aurora, SRC (more specifically Lck) and Tec (more
specifically Btk) kinase families.
Compounds of the present invention may be formulated into a
pharmaceutical composition which comprises an effective amount of a
compound of Formula 1 with a pharmaceutically acceptable diluent or carrier.
For example, the pharmaceutical compositions may be in a conventional
pharmaceutical form suitable for oral administration (e.g., tablets, capsules,

granules, powders and syrups), parenteral administration (e.g., injections
(intravenous, intramuscular, or subcutaneous)), drop infusion preparations,
inhalation, eye lotion, topical administration (e.g., ointment), or
12

CA 02813299 2013-04-17
suppositories. Regardless of the route of administration selected the
compounds may be formulated into pharmaceutically acceptable dosage
forms by conventional methods known to those skilled in the art.
The phrase "pharmaceutically acceptable" is employed herein to refer to
those ligands, materials, compositions, and/or dosage forms which are,
within the scope of sound medical judgment, suitable for use in contact with
the tissues of human beings and animals without excessive toxicity,
irritation, allergic response, or other problem or complication, commensurate
with a reasonable benefit/risk ratio.
The phrase "pharmaceutically acceptable carrier" as used herein means a
pharmaceutically acceptable material, composition, or vehicle, such as a
liquid or solid filler, diluent, excipient, solvent or encapsulating material.

Each carrier must be acceptable in the sense of being compatible with the
other ingredients of the formulation, including the active ingredient, and not

injurious or harmful to the patient. Some examples of materials which can
serve as pharmaceutically acceptable carriers include: (1) sugars, such as
lactose, glucose, and sucrose; (2) starches, such as corn starch, potato
starch, and substituted or unsubstituted 8-cyclodextrin; (3) cellulose, and
its
derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose, and
cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc;
(8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as
peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil,
and
soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as
glycerin, sorbitol, mannitol, and polyethylene glycol; (12) esters, such as
ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as
magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16)
pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl
alcohol; (20) phosphate buffer solutions; and (21) other non-toxic
compatible substances employed in pharmaceutical formulations.
The term "pharmaceutically acceptable salt" refers to the relatively non-
toxic,
inorganic and organic acid addition salts of the compound(s). These salts
13

CA 02813299 2013-04-17
can be prepared in situ during the final isolation and purification of the
compound(s), or by separately reacting a purified compound(s) in its free
base form with a suitable organic or inorganic acid, and isolating the salt
thus
formed. Representative salts include the hydrobromide, hydrochloride,
sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate, palmitate,
stearate, laurate, benzoate, lactate, phosphate, tosylate, citrate, maleate,
fumarate, succinate, tartrate, naphthylate, mesylate, glucoheptonate,
lactobionate, laurylsulphonate salts, and amino acid salts, and the like (See,

for example, Berge et al. (1977) "Pharmaceutical Salts", J. Pharm. Sci. 66:
1-19).
In other cases, the compounds of the present invention may contain one or
more acidic functional groups and, thus, are capable of forming
pharmaceutically acceptable salts with pharmaceutically acceptable bases.
The term "pharmaceutically acceptable salts" in these instances refers to the
relatively non-toxic inorganic and organic base addition salts of a
compound(s). These salts can likewise be prepared in situ during the final
isolation and purification of the compound(s), or by separately reacting the
purified compound(s) in its free acid form with a suitable base, such as the
hydroxide, carbonate, or bicarbonate of a pharmaceutically acceptable metal
cation, with ammonia, or with a pharmaceutically acceptable organic
primary, secondary, or tertiary amine. Representative alkali or alkaline earth

salts include the lithium, sodium, potassium, calcium, magnesium, and
aluminum salts, and the like. Representative organic amines useful for the
formation of base addition salts include ethylamine, diethylamine,
ethylenediamine, ethanolamine, diethanolamine, piperazine, and the like
(see, for example, Berge et al., supra).
As used herein, the term "affinity tag" means a ligand or group, linked either

to a compound of the present invention or to a protein kinase domain, that
allows the conjugate to be extracted from a solution.
The term "alkyl" refers to substituted or unsubstituted saturated hydrocarbon
groups, including straight-chain alkyl and branched-chain alkyl groups,
14

CA 02813299 2013-04-17
including haloalkyl groups such as trifluoromethyl and 2,2,2-trifluoroethyl,
etc. Representative alkyl groups include methyl, ethyl, n-propyl, isopropyl,
n-butyl, t-butyl, isobutyl, sec-butyl, (cyclohexyl)methyl, cyclopropylmethyl,
n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. The terms "alkenyl" and
"alkynyl" refer to substituted or unsubstituted unsaturated aliphatic groups
analogous in length and possible substitution to the alkyls described above,
but that contain at least one double or triple bond respectively.
Representative alkenyl groups include vinyl, propen-2-yl, crotyl, isopenten-2-
yl, 1,3-butadien-2-y1), 2,4-pentadienyl, and 1,4-pentadien-3-yl.
Representative alkynyl groups include ethynyl, 1- and 3-propynyl, and 3-
butynyl. In certain preferred embodiments, alkyl substituents are lower alkyl
groups, e.g., having from 1 to 6 carbon atoms. Similarly, alkenyl and alkynyl
preferably refer to lower alkenyl and alkynyl groups, e.g., having from 2 to 6

carbon atoms. As used herein, "alkylene" refers to an alkyl group with two
open valencies (rather than a single valency), such as -(Ch12)1-10- and
substituted variants thereof.
The term "alkoxy" refers to an alkyl group having an oxygen attached
thereto. Representative alkoxy groups include methoxy, ethoxy, propoxy,
tert-butoxy and the like. An "ether" is two hydrocarbons covalently linked by
an oxygen. Accordingly, the substituent of an alkyl that renders that alkyl an

ether is or resembles an alkoxy.
The term "alkoxyalkyl" refers to an alkyl group substituted with an alkoxy
group, thereby forming an ether.
The terms "amide" and "amido" are art-recognized as an amino-substituted
carbonyl and includes a moiety that can be represented by the general
formula:
0
A ,R10
N
i
R9

CA 02813299 2013-04-17
wherein R9, le) are as defined above. Preferred embodiments of the amide
will not include imides, which may be unstable.
The terms "amine" and "amino" are art-recognized and refer to both
unsubstituted and substituted amines and salts thereof, e.g., a moiety that
can be represented by the general formulae:
R9 R9
1 .,,
¨14 or ¨N4.¨R '''
i
\R10 Rio'
wherein R9, 111 and R1 ' each independently represent a hydrogen, an alkyl,
an alkenyl, -(CH2)m-R8, or R9 and Rw taken together with the N atom to
which they are attached complete a heterocycle having from 4 to 8 atoms in
the ring structure; R8 represents an aryl, a cycloalkyl, a cycloalkenyl, a
heterocyclyl or a polycyclyl; and m is zero or an integer from 1 to 8. In
preferred embodiments, only one of R9 or Ftw can be a carbonyl, e.g., R9, R10,

and the nitrogen together do not form an imide. In even more preferred
embodiments, R9 and le) (and optionally R1w) each independently represent
a hydrogen, an alkyl, an alkenyl, or -(CH2)m-R8. In certain embodiments, the
amino group is basic, meaning the protonated form has a pKa > 7.00.
The term "aralkyl", as used herein, refers to an alkyl group substituted with
an aryl group, for example -(CH2)n-Ar.
The term "heteroaralkyl", as used herein, refers to an alkyl group substituted

with a heteroaryl group, for example -(CH2)n-Het.
The term "aryl" as used herein includes 5-, 6-, and 7-membered substituted
or unsubstituted single-ring aromatic groups in which each atom of the ring
is carbon. The term "aryl" also includes polycyclic ring systems having two
or more cyclic rings in which two or more carbons are common to two
adjoining rings wherein at least one of the rings is aromatic, e.g., the other

cyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls,
16

CA 02813299 2013-04-17
heteroaryls, and/or heterocyclyls. Aryl groups include benzene, naphthalene,
phenanthrene, phenol, aniline, anthracene, and phenanthrene.
The terms "carbocycle" and "carbocyclyl", as used herein, refer to a non-
aromatic substituted or unsubstituted ring in which each atom of the ring is
carbon. The terms "carbocycle" and "carbocycly1" also include polycyclic ring
systems having two or more cyclic rings in which two or more carbons are
common to two adjoining rings wherein at least one of the rings is
carbocyclic, e.g., the other cyclic rings can be cycloalkyls, cycloalkenyls,
cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls. Representative
carbocyclic groups include cyclopentyl, cyclohexyl, 1-cyclohexenyl, and 3-
cyclohexen-1-yl, cycloheptyl.
The term "carbonyl" is art-recognized and includes such moieties as can be
represented by the general formula:
0
AR"
X'
wherein X is a bond or represents an oxygen or a sulfur, and Rn represents a
hydrogen, an alkyl, an alkenyl, -(CH2)m-R8 or a pharmaceutically acceptable
salt. Where X is an oxygen and R11 is not hydrogen, the formula represents
an "ester". Where X is an oxygen, and Rfi is a hydrogen, the formula
represents a "carboxylic acid".
The terms "heteroaryl" includes substituted or unsubstituted aromatic 5- to
7-membered ring structures, more preferably 5- to 6-membered rings,
whose ring structures include one to four heteroatoms. The term
"heteroaryl" also includes polycyclic ring systems having two or more cyclic
rings in which two or more carbons are common to two adjoining rings
wherein at least one of the rings is heteroaromatic, e.g., the other cyclic
rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls,
and/or heterocyclyls. Heteroaryl groups include, for example, pyrrole, furan,
thiophene, imidazole, isoxazole, oxazole, thiazole, triazole, pyrazole,
pyridine, pyrazine, pyridazine and pyrimidine, and the like.
17

CA 02813299 2013-04-17
The term "heteroatom" as used herein means an atom of any element other
than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, and
sulfur.
The terms "heterocycly1" or "heterocyclic group" refer to substituted or
unsubstituted non-aromatic 3- to 10-membered ring structures, more
preferably 3- to 7-membered rings, whose ring structures include one to four
heteroatoms. The term terms "heterocyclyl" or "heterocyclic group" also
include polycyclic ring systems having two or more cyclic rings in which two
or more carbons are common to two adjoining rings wherein at least one of
the rings is heterocyclic, e.g., the other cyclic rings can be cycloalkyls,
cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls.
Heterocyclyl groups include, for example, tetrahydrofuran, tetrahydropyran,
piperidine, piperazine, pyrrolidine, morpholine, lactones, and lactams.
The term "hydrocarbon", as used herein, refers to a group that is bonded
through a carbon atom that does not have a =0 or =S substituent, and
typically has at least one carbon-hydrogen bond and a primarily carbon
backbone, but may optionally include heteroatoms. Thus, groups like
methyl, ethoxyethyl, 2-pyridyl, and trifluoromethyl are considered to be
hydrocarbyl for the purposes of this application, but substituents such as
acetyl (which has a =0 substituent on the linking carbon) and ethoxy (which
is linked through oxygen, not carbon) are not. Hydrocarbyl groups include,
but are not limited to aryl, heteroaryl, carbocycle, heterocycle, alkyl,
alkenyl,
alkynyl, and combinations thereof.
The terms "polycycly1" or "polycyclic" refer to two or more rings (e.g.,
cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or
heterocyclyls) in which two or more carbons are common to two adjoining
rings, e.g., the rings are "fused rings". Each of the rings of the polycycle
can
be substituted or unsubstituted.
As used herein, the term "probe" means a compound of the invention which
is labeled with either a detectable label or an affinity tag, and which is
18

CA 02813299 2013-04-17
capable of binding, either covalently or non-covalently, to a protein kinase
domain. When, for example, the probe is non-covalently bound, it may be
displaced by a test compound. When, for example, the probe is bound
covalently, it may be used to form cross-linked adducts, which may be
quantified and inhibited by a test compound.
The term "substituted" refers to moieties having substituents replacing a
hydrogen on one or more carbons of the backbone. It will be understood
that "substitution" or "substituted with" includes the implicit proviso that
such substitution is in accordance with permitted valence of the substituted
atom and the substituent, and that the substitution results in a stable
compound, e.g., which does not spontaneously undergo transformation such
as by rearrangement, cyclization, elimination, etc. As used herein, the term
"substituted" is contemplated to include all permissible substituents of
organic compounds. In a broad aspect, the permissible substituents include
acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic,
aromatic and non-aromatic substituents of organic compounds. The
permissible substituents can be one or more and the same or different for
appropriate organic compounds. For purposes of this invention, the
heteroatoms such as nitrogen may have hydrogen substituents and/or any
permissible substituents of organic compounds described herein which satisfy
the valences of the heteroatoms. Substituents can include, for example, a
halogen, a hydroxyl, a carbonyl (such as a carboxyl, an alkoxycarbonyl, a
formyl, or an acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a
thioformate), an alkoxyl, a phosphoryl, a phosphate, a phosphonate, a
phosphinate, an amino, an amido, an amidine, an imine, a cyano, a nitro, an
azido, a sulfhydryl, an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a
sulfonamido, a sulfonyl, a heterocyclyl, an aralkyl, or an aromatic or
heteroaromatic moiety. It will be understood by those skilled in the art that
the moieties substituted on the hydrocarbon chain can themselves be
substituted, if appropriate.
19

CA 02813299 2013-04-17
Compounds of the invention also include all isotopes of atoms present in the
intermediates and/or final compounds. Isotopes include those atoms having
the same atomic number but different mass numbers. For example, isotopes
of hydrogen include deuterium and tritium.
General Synthetic Methods
General Synthetic Method A:
Ulmann condensation of phenol 1-i with ester 1-ii provided intermediate 1-iii.

Saponification of intermediate 1-iii yielded intermediate 1-iv. Conversion of
intermediate 1-iv to its acid chloride, using for example oxalyl chloride and
DMF, provided intermediate 1-v. Condensation of intermediate 1-v with
malononitrile yielded intermediate 1-vi. Methylation of intermediate 1-vi with

TMS-diazomethane provided intermediate 1-vii. Condensation of 1-vii with
hydrazine yielded intermediate 1-viii. Condensation of intermediate 1-viii
with formamidine yielded intermediate 1-ix. Intermediate 1-ix was treated
with alcohol R101-I, under Mitsunobu conditions, to provide the desired
compounds or intermediates of general formula 1-x.

CA 02813299 2013-04-17
(X16. (X16
(X16.
\ ,õ...,,,vv Base, ligand, 1\'-/-w
TW
1 catalyst
/I- I
..f- NaOH
______________________________________________ ),
Y (x2)m OH 0 0
OH
7C)
EtO2C (X26 HO2C X2),
1-1 X
1-iii 1-iv
1-ii; X=I, Br
(X1),õ. (X1)m.
(x1),,=
t71\1 o W
oxalyl chloride --' malononitrile
.vi'm TMS-diazomethane ,j7W
1-iv i ¨(X2)m ' I ¨(X2)rn
0
1 \
CIOC)(X2)m HOCN Me0 CN
CN CN
1-v 1-vi 1-vii
_<------- )m,
0 \ ?
hydrazine / \ W
1-vii _______________________ .
NC -----0(2)m
/ \,NI
H2N N
H
1-viii
(X1) . (Xl)m
0____.
a m z'
c-- \ /
Ph3P, DIAD
W W
.. o. f rmamidine / \
1-viii _______ is. _________________________ 1
NH2 ' (X2)m NH2 ----(X2)m
RiOH
N 1 L
\ N N
N ' N I :
vi
R1
1-ix 1-x
Scheme 1
General Synthetic Method 13:
Benzoyl chlorides of formula 2-1 were condensed with malononitrile to
provide intermediate 2-11. Methylation of intermediate 2-11 with TMS-
21

CA 02813299 2013-04-17
diazomethane provided intermediate 2-iii. Condensation of intermediate 2-iii
with hydrazine provided intermediate 2-iv. Further condensation of
intermediate 2-iv with formamidine provided intermediate 2-v. Intermediate
2-v was treated with alcohol R1OH, under Mitsunobu conditions, to provide
intermediate 2-vi. Ullmann condensation of intermediate 2-vi with phenolic
intermediates 2-vii provided the desired compounds or intermediates of
general formula 2-viii.
X
X
X
X
TMS-diazomethane /1-=
.L1 )(2,r, malononitrile rjTh.._(x2) 1 ___(x26 hydrazine
( )
CN o CN NC--.)N
0 Cl
HO-1-'
CN NH
.''
CN H2 N
2-1; X=1, Br 2-ii; X=1, Br 2-111; X=1, Br 2-iv; X=1, Br
X
X / \
formamidine / \ Ph3P, D1AD,
2-iv NH2 -------(X-, )171 IsV , \
1:210H
N \ N N,
' R1
N N
2-v; X=1, Br 2-vi; X=1, Br
0 \ /
Base, ligand,
catalyst
2-vi _____________________ p.
NH2 --(X2)m
HOW
1 N \
1 ,N
(X1),õ, N N,
R1
2-vii 2-viii
Scheme 2a
22

CA 02813299 2013-04-17
Alternatively, intermediate 2-iv was treated with an alcohol of formula R101-
1,
under Mitsunobu conditions to provide intermediate 2-ix. Condensation of
intermediate 2-ix with formamidine provided intermediate 2-vi.
X
X X
NC Ph3P, DIAD, NC (X26 formamidine NH2
________________________________________________ k
\ RiOH
N N
NH I \ N
H2NN,/
H2N N
R1
2-iv; X=1, Br 2-ix; X=1, Br 2-vi; X=1, Br
Scheme 2b
In a similar manner, condensation of intermediate 2-iii with a hydrazine of
formula R1NIHNH2 provided intermediate 2-ix. Ullmann condensation of
intermediate 2-ix with phenolic intermediates 2-vii provided intermediates 2-
x. Condensation of intermediate 2-x with formamidine provided the desired
compounds or intermediates of general formula 2-viii.
23

CA 01281299 2013-04-17
Xa(xi)m.
, \ 0-
7 _(X2),, Base, ligand, \ W
-H1-c2N6 RiNHNH2 NC Ho w
0
. \
14
NC(X2)m
\
CN Ri
/'" H HN14
--
(X1),,, Ri
2-iii; X=1, Br 2-ix; X=1, Br
2-vii 2-x
-(X1)m'
0_ \ /
W
/ \ 2
formamidine
2-x ________________________ .
N \ N
I '
le---N
Ft1
2-viii
Scheme 2c
Alternatively, trimethyl orthoformate and ammonia can be used in place of
formamidine, for example, in the conversion of intermediate 2-x to
compounds of formula 2-vii.
Exemplification
The following synthetic methods are intended to be representative of the
chemistry used to prepare compounds of Formula 1 and are not intended to
be limiting.
Synthesis of Compound 1:
24

CA 02813299 2013-04-17
1 0
0 OBn OH K2CO3 0 OBn CuCI, Cs2CO3
___________________ r _____________________ ).
Benzyl bromide 0 0
OH OH 40 o'' Ir
EtO2C
3-a Br 3-b
0 OBn 0 OBn
NaOH oxalyl chloride
3-b __________ r id 0 _________ N ja 0
Mr ir
H020 CIOC
3-c 3-d
o IS o 010
3-d
DIPEA 0 TMS-diazomethane 0
malononitrile 0 40
'-.
HO Me0 CN --. CN
CN CN
3-e 3-f
0 * O,
hydrazine
41 NC 0 formamidine
NH2 O 0
3-f r ___________________________ r
i \isl . N '' , \ it
H2N N, L i ,N
H N N
H
3-g Compound 1
Scheme 3
Step 1: Intermediate 3-a
Benzyl bromide (27.0 ml, 227 mmol) was added drop wise to a stirred
suspension of resorcinol (25.0 g, 227 mmol) and potassium carbonate (31.4
g, 227 mmol) in acetone (150 ml) and the reaction was heated under reflux
overnight. Volatiles were removed under reduced pressure. Water and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.

CA 02813299 2013-04-17
Purification by silica gel chromatography provided intermediate 3-a as a
beige oil.
Step 2: Intermediate 3-b
To a solution of compound 3-a (15.0 g, 74.9 mmol) in 1,4-dioxane (200 ml)
were sequentially added ethyl 4-bromobenzoate (20.59 g, 90 mmol), N,N-
dimethylglycine (4.25 g, 41.2 mmol), copper(I) chloride(3.71 g, 37.5 mmol)
and cesium carbonate (61.0 g, 187 mmol). The reaction mixture was stirred
at reflux overnight and then cooled to room temperature. Water and ethyl
acetate were added, the organic layer was separated, washed with saturated
aqueous NaHCO3, brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediate 3-b as a colorless oil.
Step 3: Intermediate 3-c
To a solution of intermediate 3-b (17.5 g, 50.2 mmol) in THF (200 ml) and
Me0H (100 ml) was added 2N sodium hydroxide (100 ml, 200 mmol) and the
reaction was stirred at room temperature overnight. Volatiles were removed
under reduced pressure. 10% aqueous HCI and ethyl acetate were added to
the residue, the organic layer was separated, washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure to provide
intermediate 3-c as beige solid.
Step 4: Intermediate 3-d
To a suspension of intermediate 3-c (16.1 g, 50.3 mmol) in dichloromethane
(100 ml) were added DMF (0.1 ml, 1.29 mmol) and oxalyl chloride (4.4 ml,
50.3 mmol). The solution was stirred at room temperature for 2 hours.
Volatiles were removed under reduced pressure to provide intermediate 3-d
as beige solid.
26

CA 02813299 2013-04-17
Step 5: Intermediate 3-e
To a solution of intermediate 3-d (16.5 g, 48.9 mmol) in toluene (50 ml) and
THF (7 ml), cooled to -10 C, were added malononitrile (3.19 ml, 50.2 mmol)
and DIPEA (17.5 ml, 100 mmol) in toluene (50 mL), drop wise, over a period
of 30 minutes. After the addition was completed, the reaction was stirred for
1 hour at 0 C and room temperature overnight. Volatiles were removed
under reduced pressure. 1M aqueous HCI and ethyl acetate were added, the
organic layer was separated, washed with 1M HCI and brine, dried over
MgSO4, filtered and concentrated under reduced pressure to provide
intermediate 3-e as beige solid.
Step 6: Intermediate 3-f
To a solution of intermediate 3-e (18.1 g, 49.1 mmol) in acetonitrile (177 ml)

and methanol (19.0 ml), cooled to 0 C, were added DIPEA (10.3 ml, 59.0
mmol) and a 2M solution of (diazomethyl)trimethylsilane in hexanes (27.0
ml, 54.0 mmol). After the addition was completed, the reaction was stirred at
room temperature overnight. Acetic acid (0.56 ml, 9.83 mmol) was added,
the reaction was then stirred for 30 minutes and volatiles were removed
under reduced pressure. A saturated aqueous solution of NaHCO3 and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 3-f as yellow
solid.
Step 7: Intermediate 3-g
To a suspension of intermediate 3-f (8.05 g, 21.1 mmol) in ethanol (10.5 ml)
was added a solution of hydrazine monohydrate (2.76 ml, 56.8 mmol). The
reaction was stirred at 100 C for 1 hour and then cooled to room
temperature.= Water was added; a precipitate formed and was collected by
27

CA 02813299 2013-04-17
filtration, washed with diethyl ether and dried in vacuo to provide
intermediate 3-g as an off-white solid.
Step 8: Compound 1
Intermediate 3-g (8.0 g, 20.92 mmol) was added to a solution of
formamidine (58.4 ml, 1464 mmol) and the reaction was stirred at 180 C
for 2 hours and then cooled to room temperature. Water and ethyl acetate
were added; the organic layer was separated, washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure to provide
compound 1 as beige solid. MS (m/z) M+H=410.2
Synthesis of Compound 2:
O . o 40
.
o o
NH2 41k 40 Ph3P, DIAD NH2
410
N' \N N
OH N
i N' [.., 1 )1
N
H
6
uCompound 1 Compound 2
Scheme 4
To a solution of cyclopentanol (316 mg, 3.66 mmol) in THF was added
triphenylphosphine (961 mg, 3.66 mmol) and DIAD (712 pl, 3.66 mmol). The
yellow solution was stirred for 5 minutes, compound 1 (1.0 g, 2.44 mmol)
was added and the reaction was then stirred at room temperature overnight.
Volatiles were removed under reduced pressure. Purification by silica gel
chromatography provided compound 2 as an off-white solid. MS (m/z)
M+H=478.2
Synthesis of Compound 3:
28

CA 02813299 2013-04-17
,
o 0
NH2 * Ph3P, DIAD
OH NH2 40
N

N 41#
N
' N
N N'
Ny(31 N N
0
Compound 1
0
Compound 3
Scheme 5
To a solution of (S)-tert-butyl 3-hydroxypiperidine-1-carboxylate (5.65 g,
28.1 mmol) in THF was added triphenylphosphine (7.37 g, 28.1 mmol) and
DIAD (5.46 ml, 28.1 mmol). The yellow solution was stirred for 5 minutes,
compound 1 (10.0 g, 24.42 mmol) was added and the reaction was then
stirred at room temperature overnight. Volatiles were removed under
reduced pressure. Purification by silica gel chromatography provided
compound 3 as a white foam. MS (m/z) M+H= 593.1
Synthesis of Compound 4:
o
0
NH2 41, HCI
NH2 *
410
\ N
I N I ,N
N N N
LNH
0
Compound 4
Compound 3
Scheme 6
29

CA 02813299 2013-04-17
To a solution of compound 3 (1.88 g, 3.17 mmol) in dichloromethane was
added 4N HCI in 1,4-dioxane (19.82 ml, 79.0 mmol) and the reaction was
stirred at room temperature for 2 hours. Volatiles were removed under
reduced pressure. Purification by reverse phase chromatography eluting with
a 1% aqueous HCl/methanol gradient provided compound 4.2HCI as a white
solid. MS (m/z) M+H= 493.1
Synthesis of compound 5
0 = o,
0 0
TEA
NH2
4Ik 0 NH2
4410
N \
'N I N
N N 2HCI N N
òH
Compound 4 Compound 5
Scheme 7
To a solution of compound 4.2HCI (100 mg, 0.17 mmol) in dichloromethane
(2 ml) cooled to 0 C were sequentially added TEA (99 pl, 0.70 mmol) and
acryloyl chloride (17.6 mg, 0.19 mmol). The reaction was stirred at 0 C for 1
hour. A saturated aqueous solution of ammonium chloride was added, the
organic layer was separated, washed with brine, dried over MgSO4, filtered
and concentrated under reduced pressure. Purification by silica gel
chromatography provided compound 5 as a white solid. MS (m/z) M+H=
547.1
Synthesis of compound 6

CA 02813299 2013-04-17
ifh o,
0
TEA
NH2
NH2
0 =
41kN \ 11
CI N \ N
I ,
N'N N
2HCI
L\NH LN
Compound 4 Compound 6
Scheme 8
To a solution of compound 4.2HCI (1.8 g, 3.18 mmol) in dichloromethane (32
ml) cooled to 0 C were sequentially added TEA (1.77 ml, 12.73 mmol) and
acetyl chloride (249 pl, 3.50 mmol). The reaction was stirred at 0 C for 1
hour and room temperature overnight. A saturated aqueous solution of
ammonium chloride was added, the organic layer was separated, washed
with brine, dried over MgSO4, filtered and concentrated under reduced
pressure. Purification by reverse phase chromatography eluting with 1%
aqueous HCl/methanol gradient provided compound 6.11C1 as beige solid. MS
(m/z) M+H= 535.1
Synthesis of intermediate 9-d
31

CA 02813299 2013-04-17
Br
Br
Br
0 DIPEA ,
malononitrile (110 TMS-diazomethane SI
________________________________________________ A
CN =-. \ CN
0
HO
0 CI , CN
CN
9-a 9-b
Br Br
hydrazine
0 formamidine
9-b __________ A ' NH2 fa
NC \'N N \ N
NH N N
H
H2N
9-c 9-d
Scheme 9
Step 1: Intermediate 9-a
To a solution of 4-bromobenzoyl chloride (25.0 g, 114 mmol) in toluene (200
ml) and THF (30 ml), cooled to -10 C, were sequentially added malononitrile
(7.60 ml, 120.0 mmol) and DIPEA (39.8 ml, 228 mmol) in toluene (50 mL)
drop wise over a period of 1 hour. After the addition was completed, the
reaction was stirred for 1 hour at 0 C and room temperature overnight.
Volatiles were removed under reduced pressure. 1N HCI and ethyl acetate
were added to the residue, the organic layer was separated, washed twice
with 1N HCI and brine, dried over MgSO4, filtered and concentrated under
reduced pressure to provide intermediate 9-a as yellow solid.
Step 2: Intermediate 9-b
To a solution of intermediate 9-a (26.4 g, 106 mmol) in acetonitrile (300 ml)
and methanol (35.0 ml), cooled to 0 C, was added DIPEA (22.2 ml, 127
mmol) and a 2M solution of diazomethyl)trimethylsilane in hexanes (58.3 ml,
32

CA 02813299 2013-04-17
117 mmol). After the addition was completed, the reaction was stirred at
room temperature overnight. Acetic acid (1.21 ml, 21.2 mmol) was added,
the reaction was stirred for 30 minutes and volatiles were removed under
reduced pressure. A saturated aqueous solution of NaHCO3 and ethyl acetate
were added, the organic layer was separated, washed with brine, dried over
M9SO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediate 9-b as a yellow solid.
Step 3: Intermediate 9-c
To a suspension of intermediate 9-b (4.49 g, 17.07 mmol) in ethanol (8.5
ml) was added a solution of hydrazine monohydrate (2.23 ml, 46.1 mmol)
and the reaction was stirred at 100 C for 1 hour and then cooled to room
temperature. Volatiles were removed under reduced pressure to provide
intermediate 9-c as a yellow solid.
Step 4: Intermediate 9-d
Intermediate 9-c (4.49 g, 17.07 mmol) was added to a solution of
formamidine (40.8 ml, 1024 mmol) and the reaction was stirred at 180 C
for 3 hours and then cooled to room temperature. Ethanol was added; a
precipitate formed and was collected by filtration, dried in vacuo to provide
intermediate 9-d as a beige solid.
Synthesis of intermediate 10-a
Br
Ph3P, DIAD
9-d ______________________________ , NH2 .
OH
6 N 1 \
1 1 N
'
N N
10-a o
33

CA 02813299 2013-04-17
Scheme 10
To a solution of intermediate 9-d (1.0 g, 3.45 mmol) in THF was added
triphenylphosphine (1.35 g, 5.17 mmol), cyclopentanol (0.47 ml, 5.17 mmol)
and DIAD (1.0 ml, 5.17 mmol) and the reaction was then stirred at room
temperature overnight. Volatiles were removed under reduced pressure.
Purification by silica gel chromatography provided intermediate 10-a as white
solid. MS (m/z) M+H= 359.6
Synthesis of Compound 9
0 a
0 OH imidazole 0
OTBS Ph3P, DIAD, I. 0
w ____________________________________________ 1.
TBSCI CI
OH OH HO 40 OTBS
11-a 11-b
0 CI
to
TBAF 0
11-b _____ ).
OH
11-c
0 Os
0
cuci, CS2CO3,
10-a + 11-c > OH NH2 441k glik
CI
lel N N
Compound 9
a
Scheme 11
Step 1: Intermediate 11-a
34

CA 02813299 2013-04-17
To a solution of resorcinol (15.0 g, 136 mmol) in DMF (100 ml), cooled to
0 C, were added imidazole (19.48 g, 286 mmol) and tert-
butylchlorodimethylsilane (21.56 g, 143 mmol). The reaction was then stirred
at room temperature overnight. A saturated aqueous solution of ammonium
chloride and ethyl acetate were added; the organic layer was separated,
washed 3 times with a saturated aqueous solution of ammonium chloride and
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 11-a as a
colorless oil.
Step 2: Intermediate 11-b
To a solution of (4-chlorophenyl) methanol (1.52 g, 10.70 mmol) in THF (20
mL) were sequentially added intermediate 11-a (2.88 g, 12.84 mmol),
triphenylphosphine (3.37 g, 12.84 mmol) and DIAD (2.53 ml, 12.84 mmol)
drop wise at room temperature and the reaction was then stirred for 1 hour.
A saturated aqueous solution of ammonium chloride and ethyl acetate were
added, the organic layer was separated, washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediate 11-b as a colorless oil.
Step 3: Intermediate 11-c
Tetrabutylammonium fluoride trihydrate (3.93 g, 12.47 mmol) was added to
a solution of intermediate 11-b (2.9 g, 8.31 mmol) in THF (15 mL) and the
reaction was stirred at room temperature overnight. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 11-c as a colorless oil.
Step 4: Compound 9

CA 02813299 2013-04-17
A solution of intermediate 10-a (200 mg, 0.56 mmol), intermediate 11-c
(229 mg, 0.977 mmol), quinolin-8-ol (16.21 mg, 0.112 mmol), copper (I)
chloride (11.05 mg, 0.11 mmol) and cesium carbonate (546 mg, 1.67
mmol), in dimethylacetamide (1 ml), was degassed with argon for 10
minutes, heated in a sealed tube at 140 C overnight and then cooled to
room temperature. Water and ethyl acetate were added, the organic layer
was separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 9.HCI as a yellow solid. MS (m/z) M+H= 512.2
Synthesis of intermediate 12-a
Br
NH2 O
Ph3P, DIAD ,
9-d \,N
Me0H N'
\

Scheme 12
To a solution of intermediate 9-d (500 mg, 1.72 mmol) in THF (8.6 mL),
were sequentially added methanol (105 pl, 2.59 mmol), triphenylphosphine
(678 mg, 2.59 mmol) and DIAD (503 pl, 2.59 mmol) drop wise at room
temperature. The solution was then stirred at room temperature overnight.
A precipitate formed and was collected by filtration, dried in vacuo to
provide
intermediate 12-a as a white solid.
Synthesis of compound 16
36

CA 02813299 2013-04-17
O,
0
12-a + 3-a
CuCI, CS2CO3,
NH2 4Ik
OH ___________________________________
N
I ,N
N N
./
Compound 16
Scheme 13
A solution of intermediate 12-a (235 mg, 0.77 mmol), intermediate 3-a (271
mg, 1.35 mmol), quinolin-8-ol (22.4 mg, 0.15 mmol), copper (I) chloride
(15.3 mg, 0.15 mmol) and cesium carbonate (755 mg, 2.31 mmol) in
dimethylacetamide (1 ml) was degassed with nitrogen for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with 1% HCl/methanol gradient provided
compound 16=HCI as a beige solid. MS (m/z) M+H= 424.2
Synthesis of compound 17
37

CA 02813299 2013-04-17
is CHO 0 CHO
TEA, TBSCI NaBH4 0 OH
_______________________ v. ______________________ )..-
OH OTBS OTBS
14-a 14-b
Ph3P, DIAD, 10 0 411 TBAF0
0 i
14-b ________ ). CN l I. CN
OTBS OH
HO S
CN 14-c 14-d
0 . CN
CuCI, CS2CO3,
0
12-a + 14-d _____________ ).
OH NH2 410 ifk
0 N N ' \N
1 '
N N
\ Compound 17
Scheme 14
Step 1: Intermediate 14-a
To a solution of 3-hydroxybenzaldehyde (14.73 g, 121 mmol) in
dichloromethane (100 mL) were sequentially added triethylamine (25.08 ml,
181 mmol), tert-butylchlorodimethylsilane (20.0 g, 133 mmol) portion wise,
and the reaction was stirred at room temperature overnight. 10% aqueous
citric acid was added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 14-a as a
yellow oil.
Step 2: Intermediate 14-b
38

CA 02813299 2013-04-17
To a solution of intermediate 14-a (16.0 g, 67.7 mmol) in methanol (100 ml)
cooled to 0 C was added portion wise sodium borohydride (1.28 g, 33.8
mmol). After the addition was completed the reaction was stirred at room
temperature for 2 hours. Volatiles were removed under reduced pressure.
Water and ethyl acetate were added to the residue, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure to provide intermediate 14-b as a yellow oil.
Step 3: Intermediate 14-c
To a solution of intermediate 14-b (1.0 g, 2.09 mmol) in THF (42 mL) were
sequentially added 2-hydroxybenzonitrile (600 mg, 5.03 mmol),
triphenylphosphine (1.32 g, 5.03 mmol) and DIAD (991 pl, 5.03 mmol) drop
wise at room temperature; the reaction was stirred at reflux for 2 hours and
then cooled to room temperature. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 14-c as a colorless oil.
Step 2: Intermediate 14-d
To a solution of intermediate 14-c (1.22 g, 3.62 mmol) in THF (36.0 ml) was
added tetrabutylammonium fluoride trihydrate (946 mg, 3.62 mmol) and the
reaction was stirred at room temperature for 1 hour. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 14-d as a white solid.
Step 2: Compound 17
39

CA 02813299 2013-04-17
A solution of intermediate 12-a (200 mg, 0.6 mmol), intermediate 14-d (259
mg, 1.15 mmol), quinolin-8-ol (19.0 mg, 0.13 mmol), copper (I) chloride
(13.0 mg, 0.13 mmol) and cesium carbonate (643 mg, 1.97 mmol) in
dimethylacetamide (3.0 ml) was degassed with argon for 10 minutes, heated
in a sealed tube at 140 C overnight. After cooling to room temperature,
water and ethyl acetate were added, the organic layer was separated, the
aqueous layer was extracted twice with ethyl acetate, the combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
compound 17 as a white solid. MS (m/z) M+H= 449.3
Synthesis of compound 18:
N
LIAIH4 HOr- ---
Ojs----
N N Ph3P, DIAD, 0
s
14-b
0 OTBS
15-a 15-b
N
----
TBAF
S
15-b
OH
15-c
O,
CuCI, CS2CO3
4.0---\-
12-a +15-c ON NH2 S/, N
\
N
IW N -- 1 1 \
L ,N
/
N N
\ Compound 18
Scheme 15
Step 1: Intermediate 15-a
To a solution of ethyl 2-methylthiazole-5-carboxylate (5.82 g, 34.0 mmol) in
THF (170 m1), cooled to 0 C, was added a 1.0M solution of LiAIH4in THF
(34.0 ml, 34.0 mmol) and the reaction was slowly warmed to room
temperature and stirred overnight. Water (1.3 ml) was slowly added,
followed by 15% NaOH (1.3 mL). The solution was stirred for 2 hours at

CA 02813299 2013-04-17
room temperature then filtered over celite. The filtrate was concentrated
under reduced pressure to provide intermediate 15-a as a yellow oil.
Step 2: Intermediate 15-b
To a solution of intermediate 15-a (7.75 g, 34.5 mmol) and intermediate 11-
a (4.25 g, 32.9 mmol), in THF (33 mL), were sequentially added
triphenylphosphine (10.35 g, 39.5 mmol) and DIAD (7.68 ml, 39.5 mmol)
drop wise at room temperature. The reaction was then stirred for 18 hours.
Volatiles were removed in vacuo. Purification by silica gel chromatography
provided intermediate 15-b as a colorless oil.
Step 3: Intermediate 15-c
To a solution of intermediate 15-b (5.5 g, 16.39 mmol), in THF (82.0 ml),
was added a 1.0M solution of tetrabutylammonium fluoride in THF (16.4 ml,
16.4 mmol) and the reaction was stirred at room temperature for 30
minutes. A saturated aqueous solution of ammonium chloride and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgS0.4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 15-c as beige
solid.
Step 4: Compound 18
A solution of intermediate 12-a (200 mg, 0.65 mmol), intermediate 15-c
(146 mg, 0.65 mmol), quinolin-8-ol (19.0 mg, 0.13 mmol), copper (I)
chloride (13.0 mg, 0.13 mmol) and cesium carbonate (643 mg, 1.97 mmol)
in dimethylacetamide (6.5 ml) was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C for 2 hours and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
41

CA 02813299 2013-04-17
phase chromatography eluting with 1% HCl/methanol gradient provided
compound 18=2HCI as a beige solid. MS (m/z) M+H= 445.1
Synthesis of compound 15:
0 ilikt 0 CN
CuCI, Cs2CO3
10-a + 14-d __________________ v, NH2 O OOH
N N.' \
I t NN el N - Compound 15
a
Scheme 16
A solution of intermediate 10-a (200 mg, 0.56 mmol), intermediate 14-d
(156 mg, 0.68 mmol), quinolin-8-ol (16.2 mg, 0.11 mmol), copper (I)
chloride (11.0 mg, 0.11 mmol) and cesium carbonate (546 mg, 1.67 mmol)
in dimethylacetamide (5.5 ml) was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with 1% HCl/methanol gradient provided
compound 15=HCI as beige solid. MS (m/z) M+H= 503.3
Synthesis of intermediate 17-a
42

CA 02813299 2013-04-17
Br
NH2 .
Ph3P, DIAD
9-d N *' \
__________________________________ A I ,N
0/ )¨OH N N)Th
\_
17-a U0
Scheme 17
To a solution of intermediate 9-d (650 mg, 2.24 mmol), in THF (22.0 mL),
were sequentially added tetrahydro-2H-pyran-4-ol (320 pl, 3.36 mmol),
triphenylphosphine (881 mg, 3.36 mmol) and DIAD (653 pl, 3.36 mmol)
drop wise at room temperature. The solution was then stirred at 50 C
overnight. Volatiles were removed in vacuo. Purification by silica gel
chromatography provided intermediate 17-a as a white solid.
Synthesis of compound 22:
0 . CN
0
CuCI, Cs2CO3
17-a + 14-d OH __ ). NH2 44k 4411k
N
=NV "
i 1 ,N
N N Compound 22
a
0
Scheme 18
A solution of intermediate 17-a (200 mg, 0.53mmol), intermediate 14-d (181
mg, 0.80 mmol), quinolin-8-ol (15.5 mg, 0.11 mmol), copper (I) chloride
(11.5 mg, 0.11 mmol) and cesium carbonate (348 mg, 1.07 mmol) in
dimethylacetamide (5.3 ml) was degassed with argon for 10 minutes, heated
43

CA 02813299 2013-04-17
in a sealed tube at 140 C overnight and then cooled to room temperature.
Water and ethyl acetate were added, the organic layer was separated, the
aqueous layer was extracted twice with ethyl acetate, the combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with 1% HCl/methanol gradient provided compound 22=HCI as a beige
solid. MS (m/z) M+H= 519.2
Synthesis of compound 31:
Ph3P, DIAD, o TBAF 0 1.1
14-b CF3
CF3
OTBS OH
HO SI
CF3 19-a 19-b
0
CF3
CuCI, Cs2CO3, 0
12-a + 19-b
OH NH2
N \N
I '
/ N N ¨
\ Compound 31
Scheme 19
Step 1: Intermediate 19-a
To a solution of intermediate 14-b (10.0 g, 41.9 mmol) in THF (210 mL)
were sequentially added 2-(trifluoromethyl)phenol (6.80 g, 41.9 mmol),
triphenylphosphine (13.2 g, 50.33 mmol) and DIAD (9.79 ml, 50.3 mmol)
drop wise at room temperature. The reaction was then stirred at room
temperature overnight. Saturated aqueous ammonium chloride and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
44

CA 02813299 2013-04-17
Purification by silica gel chromatography provided intermediate 19-a as a
colorless oil.
Step 2: Intermediate 19-b
To a solution of intermediate 19-a (13.9 g, 36.3 mmol) in THF (182.0 ml)
was added a 1.0M solution of tetrabutylammonium fluoride in THF (36.3 ml,
36.3 mmol) and the reaction was stirred at room temperature for 1 hour.
Saturated aqueous ammonium chloride and ethyl acetate were added, the
organic layer was separated, washed with brine, dried over MgSO4, filtered
and concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 19-b as colorless oil.
Step 3: Compound 31
A solution of intermediate 12-a (200 mg, 0.66 mmol), intermediate 19-b
(265 mg, 0.98 mmol), quinolin-8-ol (19.0 mg, 0.13 mmol), copper (I)
chloride (25.5 mg, 0.13 mmol) and cesium carbonate (429 mg, 1.31 mmol)
in dimethylacetamide (6.5 ml) was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with 1% HCl/methanol gradient provided
compound 31.HCI as white solid. MS (m/z) M+H= 492.1
Synthesis of compound 32:

CA 02813299 2013-04-17
0 41,
o 0F3
Cul, Cs2CO3
10-a + 19-b OH __ lw- NH2 ft 441k
N N -' \
I 'N
4101 N N Compound 32
a
Scheme 20
A solution of intermediate 10-a (200 mg, 0.55 mmol), intermediate 19-b
(225 mg, 0.83 mmol), quinolin-8-ol (16.2 mg, 0.11 mmol), copper (I) iodide
(22.0 mg, 0.11 mmol) and cesium carbonate (364 mg, 1.17 mmol) in
dimethylacetamide (5.5 ml) was degassed with argon for 10 minutes, heated
in a sealed tube at 140 C overnight and then cooled to room temperature.
Water and ethyl acetate were added, the organic layer was separated, the
aqueous layer was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with 1% HCl/methanol gradient provided compound 32.HCI as beige
solid. MS (m/z) M+H= 546.1
Synthesis of compound 36:
0 41kt u3
0
cul, Cs2CO3
17-a + 19-b OH __ 11. NH2 0 O
1 1 N
'
N N Compound 36 1 / o
0
Scheme 21
46

CA 02813299 2013-04-17
A solution of intermediate 17-a (200 mg, 0.53 mmol), intermediate 19-b
(215 mg, 0.80 mmol), quinolin-8-ol (15.5 mg, 0.11 mmol), copper (I) iodide
(20.3 mg, 0.11 mmol) and cesium carbonate (348 mg, 1.06 mmol) in
dimethylacetamide (5.3 ml) was degassed with argon for 10 minutes, heated
in a sealed tube at 140 C overnight and then cooled to room temperature.
Water and ethyl acetate were added, the organic layer was separated, the
aqueous layer was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Puriflcation by reverse phase chromatography
eluting with 1% HCl/methanol gradient provided compound 36=HCI as beige
solid. MS (m/z) M+H= 562.2
Synthesis of compound 20:
F3 0 F3 0
to 0 Ph3P, DIAD, 0 TBAF 0
HO __________________ ).. i.
OTBS
CF3 las OTBS OH
11-a 22-b
HO 22-a
0 . CF3
0
CuCI, Cs2CO3,
12-a + 22-b ' NH
OH 2 40 O
N N \
i I N
1
' 101 N N
\ Compound 20
Scheme 22
Step 1: Intermediate 22-a
To a solution of 2-(trifluoromethyl)phenylmethanol (1.43 g, 8.10 mmol) in
THF (8.10 mL) were sequentially added intermediate 11-a (2.0 g, 8.91
mmol), triphenylphosphine (2.55 g, 9.72 mmol) and DIAD (1.89 ml, 9.72
47

CA 02813299 2013-04-17
mmol) drop wise at room temperature. The reaction was then stirred
overnight at room temperature. Saturated aqueous ammonium chloride and
ethyl acetate were added, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 22-a as a
colorless oil.
Step 2: Intermediate 22-b
Tetrabutylammonium fluoride trihydrate (1.81 g, 5.75 mmol) was added to a
solution of intermediate 22-a (2.2 g, 5.75 mmol) in THF (23 mL) and the
reaction was stirred at room temperature for 1 hour. Saturated aqueous
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 22-b as a colorless oil.
Step 3: Compound 20
A solution of intermediate 12-a (200 mg, 0.65 mmol), intermediate 22-b
(309 mg, 1.15 mmol), quinolin-8-ol (19.1 mg, 0.13 mmol), copper (I)
chloride (13.0 mg, 0.13 mmol) and cesium carbonate (429 mg, 1.31 mmol),
in dimethylacetamide (6.5 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 20.1-1CI as beige solid. MS (m/z) M+H= 492.1
Synthesis of compound 29:
48

CA 02813299 2013-04-17
0 =
cF3
0
Cul, Cs2CO3
10-a + 22-b OH __ 1.- NH2 O 4411k
N N'' \N
I
0 N N Compound 29
a
Scheme 23
A solution of intermediate 10-a (200 mg, 0.55 mmol), intermediate 22-b
(225 mg, 0.83 mmol), quinolin-8-ol (16.2 mg, 0.11 mmol), copper (I) iodide
(21.2 mg, 0.11 mmol) and cesium carbonate (364 mg, 1.11 mmol), in
dimethylacetamide (5.5 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 29=HCI as beige solid. MS (m/z) M+H= 546.2
Synthesis of compound 23:
0 =
cF3
0
Cul, Cs2CO3
17-a + 22-b OH __ ii. NH2 0 40
N N \N
I N
Ol / N _.....) Compound
23
0
Scheme 24
49

CA 02813299 2013-04-17
A solution of intermediate 17-a (200 mg, 0.53 mmol), intermediate 22-b
(215 mg, 0.80 mmol), quinolin-8-ol (15.5 mg, 0.11 mmol), copper (I) iodide
(20.4 mg, 0.11 mmol) and cesium carbonate (348 mg, 1.07 mmol), in
dimethylacetamide (5.3 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 23.1-1CI as beige solid. MS (m/z) M+H= 562.1
Synthesis of compound 30:
NC
=
0
OH
K2CO3 10 =
=
OH Br 4101 OH
CN 25-a
CN
0
Cul, Cs2CO3,
12-a + 25-a ________________ = OH NH2 4Ik
\
N
40 N N
Compound 30
Scheme 25
Step 1: Intermediate 25-a
To a solution of 2-(bromomethypbenzonitrile (1.0 g, 5.10 mmol) and
resorcinol (2.81 g, 25.5 mmol) in acetone (51.0 mL) was added cesium

CA 02813299 2013-04-17
carbonate (3.32 g, 10.20 mmol) and the reaction was then stirred at reflux
for 2 hours. Volatiles were removed under reduced pressure. Saturated
aqueous ammonium chloride and ethyl acetate were added, the organic layer
was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 25-a as white solid.
Step 2: Compound 30
A solution of intermediate 12-a (200 mg, 0.65 mmol), intermediate 25-a
(222 mg, 0.98 mmol), quinolin-8-ol (19.1 mg, 0.13 mmol), copper (I) iodide
(25.0 mg, 0.13 mmol) and cesium carbonate (429 mg, 1.31 mmol), in
dimethylacetamide (6.5 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 30=HCI as beige solid. MS (m/z) M+H= 449.4
Synthesis of compound 12:
0 410 CN
CuCI, Cs2CO3 0
10-a + 25-a ___________________ s NH2 fa O
OH
N N
I 1' .1 .' N N - Compound 12
a
Scheme 26
51

CA 02813299 2013-04-17
A solution of intermediate 10-a (200 mg, 0.55 mmol), intermediate 25-a
(220 mg, 0.98 mmol), quinolin-8-ol (16.2 mg, 0.11 mmol), copper (I)
chloride (11.0 mg, 0.11 mmol) and cesium carbonate (546 mg, 1.67 mmol),
in dimethylacetamide (5.5 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 12=HCI as a beige solid. MS (m/z) M+H= 503.2
Synthesis of compound 35:
0 . CN
Cul, Cs2CO3 0
17-a + 25-a __________________ D.- NH2 . 0
OH
N I N.' \N '
11101 .7N
N ¨ Compound 35
o
0
Scheme 27
A solution of intermediate 17-a (200 mg, 0.55 mmol), intermediate 25-a
(181.0 mg, 0.80 mmol), quinolin-8-ol (15.5 mg, 0.11 mmol), copper (I)
iodide (20.3 mg, 0.11 mmol) and cesium carbonate (348 mg, 1.07 mmol), in
dimethylacetamide (5.3 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
52

CA 02813299 2013-04-17 .
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 35=HCI as beige solid. MS (m/z) M+H= 519.2
Synthesis of compound 10:
OMe OMe
0 . OTBS Ph3P, DIAD, 110 0 40 TBAF I* 0 0
_____________________ 3.
OTBS OH
OH HO 1.1
OMe
28-b
11-a 28-a
O,
OMe
0
I, 410
10-a + 28-b CuCCs2CO3, 1.. NH2 O
OH
N INV \N
I '
aCompound 10
Scheme 28
Step 1: Intermediate 28-a
To a solution of (3-methoxyphenyl)methanol (1.38 g, 10.0 mmol) in THF
(20.0 mL) were sequentially added intermediate 11-a (2.69 g, 12.0 mmol),
triphenylphosphine (3.15 g, 12.0 mmol) and DIAD (2.36 ml, 12.0 mmol)
drop wise at room temperature and the reaction was then stirred overnight
at room temperature. A saturated aqueous solution of ammonium chloride
and ethyl acetate were added, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 28-a as a
colorless oil.
53

CA 02813299 2013-04-17
Step 2: Intermediate 28-b
Tetrabutylammonium fluoride trihydrate (2.88 g, 9.14 mmol) was added to a
solution of intermediate 28-a (2.1 g, 6.10 mmol) in THF (10 mL) and the
reaction was stirred at room temperature overnight. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 28-b as a colorless oil.
Step 3: Compound 10
A solution of intermediate 10-a (200 mg, 0.65 mmol), intermediate 28-b
(225 mg, 0.97 mmol), quinolin-8-ol (16.2 mg, 0.11 mmol), copper (I)
chloride (11.0 mg, 0.1 mmol) and cesium carbonate (546 mg, 1.67 mmol),
in dimethylacetamide (5.5 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 10.1-1C1 as a yellow solid. MS (m/z) M+H= 508.1
Synthesis of intermediate 29-i
54

CA 02813299 2013-04-17
0 01
Et01=184. H2N)L= , N
,
HC(0)0Et 0 toluene, reflux 0
29-a 29-c
29-b
29-c LiAIH4 Ho, j--\\_
29-d
F OMe
BBr3 F OH Base F OH
TBDMSCI
=
OMe OH OTBDMS
29-e 29-f 29-g
F =
TBAF
29-g Ph3P, DIAD F
HOJ , N
OTBDMS
S¨ OH
29-d 29-h 29-i
Scheme 29
Step 1: Intermediate 29-b
Ethyl chloroacetate, 29-a (50.0 g, 0.41 mol), and ethyl formate (30.2 g, 0.41
mol) were taken in anhydrous toluene (500 mL) and cooled to 0 C. Sodium
ethoxide (35.1 g, 0.49 mol) was added portion wise. The reaction mixture
was stirred at 0 C for 5 hours and then at room temperature overnight. The
reaction mixture was quenched with water (250 mL) and washed twice with
diethyl ether. The aqueous layer was cooled to 0 C and acidified to pH 4-5
using 1 N HCI. The aqueous layer was extracted twice with diethyl ether; the
combined organic layers were dried over MgSO4 filtered and concentrated
under reduced pressure to provide intermediate 29-b as beige Oil.

CA 02813299 2013-04-17
Step 2: Intermediate 29-c
To a solution of ethyl 2-chloro-3-oxopropanoate, 29-b (34.7 g, 230 mmol), in
toluene (250 ml) was added thioacetamide (26.0 g, 346.0 mmol), the
reaction was stirred at 90 C overnight and then cooled to room temperature,
diluted with water (300 mL) and then neutralized to pH 7 with a saturated
aqueous solution of NaHCO3. Ethyl acetate was added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 29-c as beige oil.
Step 4: Intermediate 29-d
To a solution of intermediate 29-c (22.2 g, 130.0 mmol) in THF (430 ml)
cooled to 0 C was added a 1.0 M solution of LiAIH4in THF (91.0 ml, 91.0
mmol) and the solution was slowly warmed to room temperature and stirred
for 2 hours. Water (3.5 ml) was slowly added, followed by 3.5 ml 15% NaOH
(3.5 ml) and water (10.5 ml) and the mixture was stirred for 1 hour. The
reaction was filtered over celite and volatiles were removed in vacuo to
provide intermediate 29-d as yellow oil.
Step 5: Intermediate 29-f
To a solution of 1-fluoro-3,5-dimethoxybenzene (12.5 g, 80 mmol) in
dichloromethane (80 ml), cooled to OK, was added 1.0 M solution of boron
tribromide in dichloromethane (200 ml, 200 mmol), drop wise over a period
of 30 minutes. The reaction was stirred for 1 hour at 0 C and then slowly
warmed to room temperature and stirred for 18 hours. The reaction was
cooled to 0 C and quenched by the slow addition of Me0H and water. After
stirring at room temperature for 1 hour the mixture was filtered and volatiles

were removed in vacuo. Ethyl acetate was added to the residue; a precipitate
formed and was collected by filtration to provide intermediate 29-f as an
orange solid.
56

CA 02813299 2013-04-17
Step 6: Intermediate 29-g
To a solution of intermediate 29-f (10.25 g, 80.0 mmol) in DMF (50 ml),
cooled to 0 C, was added imidazole (5.99 g, 88.0 mmol) and tert-
butylchlorodimethylsilane (13.27 g, 88.0 mmol). The reaction was then
stirred at room temperature overnight. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed 3 times with a saturated aqueous solution of ammonium
chloride and brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediate 29-g as a yellow oil.
Step 7: Intermediate 29-h
To a solution of intermediate 29-g (8.0 g, 33.1 mmol) and intermediate 29-d
(4.70 g, 36.4 mmol) in THF (20 ml) were sequentially added
triphenylphosphine (12.15 g, 46.3 mmol) and DIAD (9.0 ml, 46.3 mmol) at
room temperature and the reaction was then stirred at room temperature
overnight. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 29-h as a yellow oil.
Step 8: Intermediate 29-i
To a solution of intermediate 29-h (6.0 g, 16.97 mmol) in THF (85 ml) was
added a 1.0 M solution of TBAF in THF (16.97 ml, 16.97 mmol) and the
reaction was stirred at room temperature for 1 hour. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Diethyl ether was added to the
residue; a precipitate formed and was collected by filtration to provide
intermediate 29-i as white solid.
57

CA 02813299 2013-04-17
Synthesis of intermediate 30-b
F = OH Ph3P/DIAD
TBAF
HON N
OTBS OTBS OH
29-g 30-a 30-b
Scheme 30
Step 1: Intermediate 30-a
To a solution of intermediate 29-g (9.0 g, 37.1 mmol) and 2-
(methylpyrimidin-5-yl)methanol (4.61 g, 37.1 mmol) in THF (37 ml) were
sequentially added triphenylphosphine (11.69 g, 44.6 mmol) and DIAD (9.39
ml, 48.3 mmol) at room temperature and the reaction was then stirred at
room temperature for 4 days. Volatiles were removed under reduced
pressure. Purification by silica gel chromatography provided intermediate 30-
a as a yellow solid.
Step 2: Intermediate 30-b
To a solution of intermediate 30-a (12.5 g, 35.9 mmol) in THF (72 ml) was
added a 1.0 M solution of TBAF in THF (35.9 ml, 35.9 mmol) and the reaction
was stirred at room temperature for 1 hour. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 30-b as a white solid.
Synthesis of intermediate 31-d
58

CA 02813299 2013-04-17
LiAIH4
31-a 31-b
F = OH Ph3P, DD F =01
TBAF
F tio
OTBS % OTBS OH
29-g 31-c 31-d
Scheme 31
Step 1: Intermediate 31-b
To a solution of methyl 6-methylnicotinate 31-a (20.10 g, 133 mmol) in THF
(90 ml) cooled to 0 C was added drop wise a 1.0 M solution of LiAIH4 in THF
(100 ml, 100 mmol) and the reaction was then stirred at 0 C for 1 hour.
Water (3.8 ml) was slowly added, followed by 15% NaOH (3.5 ml) and water
(11.4 ml) and the mixture was stirred at room temperature for 1 hour. The
reaction was filtered over celite and volatiles were removed in vacuo to
provide intermediate 31-b as a yellow oil.
Step 2: Intermediate 31-c
To a solution of intermediate 29-g (13.2 g, 54.5 mmol) and intermediate 31-
b (7.38 g, 59.9 mmol) in THF (50 ml) were sequentially added
triphenylphosphine (21.43 g, 82.0 mmol) and DIAD (17.10 ml, 87.0 mmol)
at room temperature and the reaction was then stirred at room temperature
for 1 hour. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 31-c as a colorless oil.
Step 3: Intermediate 31-d
59

CA 02813299 2013-04-17
To a solution of intermediate 31-c (7.6 g, 21.87 mmol) in THF (44 ml) was
added tetrabutylammonium fluoride trihydrate (5.72 g, 21.87 mmol) and the
reaction was stirred at room temperature for 1 hour. Saturated aqueous
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 31-d as white solid.
Synthesis of intermediate 32-f
O rN\\ NaBH4, CaC,I2 OrN1\\ /OH
\--/
32-a 32-b
¨0
PPTS
0, / 0, ¨N\\ _)
0 DIBALH
\-1 OH
HO
32-b 32-c 32-d
F io OH Ph3P, DIAD TBAF
TBSO 40. ____________ - HO 40
OTBS 32-d 0 0
N /
29-g 32-e 0
o 32-f 0
Scheme 32
Step 1: Intermediate 32-b
To a solution of dimethyl pyridine-2,5-dicarboxylate (13.0 g, 66.6 mmol) in a
mixture of THF (110 mL) and ethanol (110 mL) was added calcium chloride
(29.6 g, 266 mmol). After stirring at room temperature for 30 minutes the
reaction was cooled to 0 C and sodium borohydride (3.78 g, 100 mmol) was
added portion wise. After the addition was completed the reaction was stirred

CA 02813299 2013-04-17
at room temperature overnight. A saturated aqueous solution of ammonium
chloride and dichloromethane were added, the organic layer was separated
and the aqueous phase was extracted twice with dichloromethane. The
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure to provide intermediate 32-
b as a yellow solid.
Step 2: Intermediate 32-c
To a solution of intermediate 32-b (1.70 g, 10.17 mmol) in dichloromethane
(203 mL) was added 3,4-dihydro-2H-pyran (4.28 g, 50.8 mmol) and PPTS
(2.56 g, 10.17 mmol) and the reaction was stirred at room temperature
overnight. Water was added and the organic layer was separated, washed
with brine, dried over MgSO4, filtered and concentrated under reduced
pressure to provide intermediate 32-c as a white solid.
Step 3: Intermediate 32-d
To a solution of intermediate 32-c (2.56 g, 10.17 mmol) in THF (51 ml)
cooled to 0 C was added drop wise a 1.0 M solution of DIBALH in hexane
(23.39 ml, 23.39 mmol) and the reaction was then stirred at 0 C for 1.5 hour
and room temperature overnight. Water (1.0 ml) was slowly added, followed
15% NaOH (3.5 ml) and water (2.3 ml) and the mixture was stirred at room
temperature for 30 minutes. The reaction was filtered over celite and
volatiles were removed under reduced pressure. Purification by silica gel
chromatography provided intermediate 32-d as a yellow oil.
Step 4: Intermediate 32-e
To a solution of intermediate 29-g (1.57 g, 6.51 mmol) and intermediate 32-
d (2.56 g, 7.17 mmol) in THF (7 ml) were sequentially added
triphenylphosphine (2.56 g, 9.77 mmol) and DIAD (2.04 ml, 10.42 mmol) at
room temperature and the reaction was then stirred at room temperature
61

CA 02813299 2013-04-17
overnight. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 32-e as a yellow solid.
Step 5: Intermediate 32-f
To a solution of intermediate 32-e (2.2 g, 4.91 mmol) in THF (9.8 ml) was
added a 1.0 M solution of TBAF in THF (4.91 ml, 4.91 mmol) and the reaction
was stirred at room temperature for 1 hour. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 32-f as a white solid.
Synthesis of intermediate 33-a
-o
riY1 y
W
F 0
=MCP BA _ F 1Wa& 0,....)-
OTBS OH
31-c 33-a
Scheme 33
To a solution of intermediate 31-c (424 mg, 1.82 mmol) in dichloromethane
(9.0 ml) was added m-CPBA (538 mg, 2.18 mmol) and the reaction was
stirred at room temperature for 4 hours. A saturated aqueous solution of
NaHCO3 and dichloromethane were added, the organic layer was separated,
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediate 33-a as a white solid.
Synthesis of intermediate 34-d
62

CA 02813299 2013-04-17
N N
tBuONa ,,E
.,.,1
F 0 F K2c03 F 0 F id o
toluene/DMPU F=

0 0 N HC!
F ir N
1 ___________________________________________________________________ \
MOMCIN
OH OMOM HO r¨, \.... OMOM OH
N
34-a 34-b I 34-c 34-d
Scheme 34
Step 1: Intermediate 34-b
To a solution of 3,5-difluorophenol (15.0 g, 115 mmol) in acetone (200 ml)
was added K2CO3 (23.90 g, 173 mmol) and bromomethyl methyl ether
(15.85 g, 127 mmol). The reaction was then stirred at room temperature
overnight and filtered. The filtrate was concentrated under reduced pressure
to provide intermediate 34-b as a colorless oil. ,
Step 2: Intermediate 34-c
To a solution of (1-methyl-1H-imidazol-5-y1) methanol (3.1 g, 27.6 mmol)
and intermediate 34-b (4.01 g, 23.04 mmol) in toluene (25.0 ml) and DMPU
(25.0 ml) was added sodium 2-methylpropan-2-olate (4.43 g, 46.1 mmol).
The reaction was stirred overnight at 80 C and then cooled to room
temperature. A saturated aqueous solution of ammonium chloride and ethyl
acetate were added, the organic layer was separated, washed twice with a
saturated aqueous solution of ammonium chloride and brine, dried over
MgSO4, filtered and concentrated in vacuo. Purification by silica gel
chromatography provided intermediate 34-c as beige oil.
Step 3: Intermediate 34-d
To a solution of intermediate 34-c (3.2 g, 12.02 mmol) in Me0H (25.0 ml)
was added 4N HCI in dioxane (10.95 ml, 361.0 mmol) and the reaction was
stirred overnight at room temperature. Volatiles were removed in vacuo.
63

CA 02813299 2013-04-17
Diethyl ether was added to the residue; a precipitate formed and was
collected by filtration to provide intermediate 34-d-FICI as a white solid.
Synthesis of intermediate 35-d
LiAIH4 HOJS
35-a 35-b
tBua
F F
toluONene/DMPU
HCI
, N
OMOM OMOM OH
34-h 35-c 35-d
Scheme 35
Step I: Intermediate 35-b
To a solution of 1,2-dimethy1-1H-imidazole-5-carbaldehyde (1.0 g, 8.06
mmol) in THF (40.3 mL) cooled to 0 C was added drop wise a 1.0 M solution
of LiAlHain THF (6.04 ml, 6.04 mmol) and the reaction was then stirred at
room temperature for 1 hour. Water (250 uL) was slowly added, followed by
15% NaOH (250 uL) and water (750 uL) and the mixture was stirred at room
temperature for 1 hour. The reaction was filtered over celite and volatiles
were removed in vacuo to provide intermediate 35-b as a white solid.
Step 2: Intermediate 35-c
To a solution of intermediate 35-b (1.50 g, 11..89 mmol) and intermediate
34-b (2.07 g, 11.89 mmol) in DMPU (11.89 mL) and toluene (11.89 mL) was
added sodium 2-methylpropan-2-olate (3.43 g, 35.7 mmol) at room
temperature. The reaction was stirred overnight at 80 C and then cooled to
room temperature. A saturated aqueous solution of ammonium chloride and
ethyl acetate were added, the organic layer was separated, washed with
64

CA 02813299 2013-04-17
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 35-c as a
yellow oil.
Step 3: Intermediate 35-d
To a solution of intermediate 35-c (3.30 g, 11.77 mmol) in Me0H (36.2 mL)
was added 4N HCI in dioxane (10.7 mL, 353 mmol) and the reaction was
stirred at room temperature overnight. Volatiles were removed under
reduced pressure. Diethyl ether was added to the residue; a precipitate
formed and was collected by filtration to provide intermediate 35-d=HCI as a
white solid.
Synthesis of intermediate 36-f
N ,N
n ,'-O-
-H
__________________________ .athj ,-SH
OH KSCN HON H2W04, H20.
2
HO,..f
-N
0H0 Acetic acid ?
?
0 0
36-a 112N---- WI
36-b
= 114
36-c 36-d
N N
tBuONa o j-
F 401 F F HCI F 0
toluene/DMPU
01 N
__________________________________________________ ..
IW-
36-d
OMOM OMOM 0 OH 0
34-b 36-e 0 36-f
It
Scheme 36
Step 1: Intermediate 36-c

CA 02813299 2013-04-17
To a suspension of 2-(benzyloxy)ethanamine HCI, 36-b (2.08 g, 11.10
mmol), and 2,5-bis(hydroxymethyl)-1,4-dioxane-2,5-diol 36-a (2.00 g,
11.10 mmol) in iPrOH (8 mL), were sequentially added potassium
thiocyanate (1.62 g, 16.7 mmol) and acetic acid (2.03 mL, 35.5 mmol) drop
wise. The mixture was stirred at room temperature overnight. Water was
added; a precipitate formed and was collected by filtration to provide
intermediate 36-c as a white solid.
Step 2: Intermediate 36-d
To a solution of intermediate 36-c (1.5 g, 5.67 mmol) and H2W04 (14 mg,
0.057 mmol) in Me0H (22.7 mL) at 40 C was added H202 (1.85 mL, 18.16
mmol) drop wise. The mixture was stirred at reflux overnight and then
cooled to room temperature. Volatiles were removed under reduced
pressure. Purification by silica gel chromatography provided intermediate 36-
d as a colorless oil.
Step 3: Intermediate 36-e
To a solution of intermediate 36-d (1.46 g, 6.32 mmol) and intermediate 34-
b (1.0 g, 5.74 mmol) in DMPU (11.48 ml) and toluene (11.48 ml) was added
sodium 2-methylpropan-2-olate (1.10 g, 11.48 mmol) at room temperature.
The reaction was stirred overnight at 80 C and then cooled to room
temperature. A saturated aqueous solution of ammonium chloride and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 36-e as a
colorless oil.
Step 4: Intermediate 36-f
To a solution of intermediate 36-e (400 mg, 1.03 mmol) in Me0H (10.4 mL)
was added 4N HCI in dioxane (2.50 mL, 10.0 mmol) the reaction was stirred
66

CA 02813299 2013-04-17
at room temperature overnight. Volatiles were removed under reduced
pressure to provide intermediate 364.1-1C1 as a white solid.
Synthesis of intermediates 37-f and 37-f'
SiMe3 SiMe3
N r r_N r
NaBH4
NaH (:).M + N HOõ.N, +
N
Me3S1 ' Oji 0) HO,(Ntl
H (3'CI 0 ,)
37-a 37-h 37-b 37-c 37-d
SiMe3 SiMe3
TMS
(
0
tBuONa
F toluene/DMPU --N N,---- \
F 0 F K2CO3 F io cc:
.
F F =

0-- \
OH Br 0
OBn 37-c + 37-d
w- to
L-TMS
34-a 37-d 0 37-e 0 37-e'
0 40
TMS
(
0
(N____\\ N,:-- \
r
37-e + 37e'
H2, Pd/C N
----.- +
F i, o
W F 0
1.1 ---\---TMS
HO 374 HO 37-f
Scheme 37
Step 1: Intermediates 37-b and 37-b'
To a solution of 1H-imidazole-5-carbaldehyde, 37-a (3.0 g, 31..2 mmol), in
DMF (20 ml) was added a 60% dispersion of NaH in mineral oil (1.25 g, 31.2
mmol) portion wise. After stirring for 30 minutes at room temperature, (2-
(chloromethoxy)ethyl)trimethylsilane (5.73 g, 34.3 mmol) was added and
the reaction was then was stirred at room temperature overnight. A
saturated aqueous solution of ammonium chloride and ethyl acetate were
added, the organic layer was separated, washed with brine, dried over
67

CA 02813299 2013-04-17
MgSO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediates 37-b and 37-b' as an
inseparable mixture.
Step 2: Intermediates 37-c and 37-c'
To a solution of intermediates 37-b and 37-b' (3.2 g, 14.14 mmol) in THF
(56.6 ml) was added NaBH4 (535 mg, 14.14 mmol) at room temperature.
The reaction was stirred overnight at room temperature and then cooled to
0 C. A saturated aqueous solution of ammonium chloride and ethyl acetate
were added, the organic layer was separated and the aqueous phase was
extracted twice with ethyl acetate. The combined organic extracts were
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure to provide intermediate 37-c and 37-c' as an inseparable
mixture.
Step 3: Intermediate 37-d
To a solution of 3,5-difluorophenol (8.0 g, 61.4 mmol) in acetone (100 ml)
was added potassium carbonate (17.0 g, 123.0 mmol) and potassium iodide
(1.021 g, 6.15 mmol). The reaction was heated to 65 C and benzyl bromide
(8.03 g, 67.6 mmol) was added. The reaction was then stirred overnight at
65 C, cooled to room temperature and filtered. Volatiles were removed in
vacuo. A saturated aqueous solution of ammonium chloride and ethyl acetate
were added to the residue, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated in vacuo. Purification by
silica gel chromatography provided intermediate 37-d as a colorless oil.
Step 4: Intermediate 37-e and 37-e'
To a solution of intermediates 37-c and 37-c' (1.0 g, 4.38 mmol) and
intermediate 37-d (877 mg, 3.98 mmol) in DMPU (7.96 ml) and toluene
(7.96 ml) was added sodium 2-methylpropan-2-olate (765 mg, 3.98 mmol)
at room temperature. The reaction was stirred overnight at 80 C and then
68

CA 02813299 2013-04-17
cooled to room temperature. A saturated aqueous solution of ammonium
chloride and ethyl acetate were added, the organic layer was separated,
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediates 37-e and 37-e' as an inseparable mixture.
Step 5: Intermediates 37-f and 37-f'
A methanol solution of intermediate 37-e and 37-e' (140 mg, 0.32 mmol)
was treated with 10% palladium on carbon (70 mg, 0.045 mmol) and purged
with H2. The solution was stirred under H2 (1 atm) for 2 hours before being
filtered through celite. The filtrate was concentrated in vacuo to provide
intermediate 37-f and 37-f' as an inseparable mixture.
Synthesis of intermediates 38-e and 38-e'
69

CA 02813299 2013-04-17
Me3Si Me3Si
N
i
O HO,Z¨N¨

N
isi'---
N NaBH4
NaH H o) + )+ <o
---- ___________________________________________ a
OyfN '
H
H 38-h
Me3Si,...,,O.,.C1 N--( N--(
4 38-h 38-c 38-d 'l
SiMe3 SiMe3 y
38-a "H NO
TMS
(o
tBuOK ( N--7----
F 0 F toluene/DMPU N--('
F
r)N 0
_____________________ . +
F
0 0 --\-_
38-c + 38-c' TMS
0
tw- 0
37-d 00:1 0 38-d 0 38-d'
40 I.
TMS
(o
(N4 N=---
H2, Pd/C rk,N r ,./../N---\0
38-d + 38-d _______ . +
F00 F 40 0 --\__.
TMS
OH 38-e HO 38-e'
Scheme 38
Step 1: Intermediates 38-b and 38-b'
To a solution of 1H-imidazole-5-carbaldehyde (5.0 g, 45.4 mmol) in DMF (20
mL) was added a 60% dispersion of NaH mineral oil (1.81 g, 45.4 mmol)
portion wise. After stirring for 30 minutes at room temperature, (2-
(chloromethoxy)ethyl)trimethylsilane (9.08 g, 54.5 mmol) was added and
the reaction was then stirred at room temperature overnight. A saturated
aqueous solution of ammonium chloride and ethyl acetate were added, the
organic layer was separated, washed with brine, dried over MgSO4, filtered
and concentrated under reduced pressure. Purification by silica gel

CA 02813299 2013-04-17
chromatography provided intermediates 38-b and 38-h' as an inseparable
mixture.
Step 2: Intermediates 38-c and 38-c'
To a solution of intermediate 38-b and 38-b' (7.0 g, 29.1 mmol) in THF
(116.0 ml) was added NaBH4 (1.10 g, 29.1 mmol) at room temperature. The
reaction was stirred overnight at room temperature and then cooled to 0 C.
A saturated aqueous solution of ammonium chloride and ethyl acetate were
added, the organic layer was separated and the aqueous phase was
extracted twice with ethyl acetate. The combined organic extracts were
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure to provide intermediates 38-c and 38-c' as an inseparable
mixture.
Step 3: Intermediate 38-d and 38-d'
To a solution of intermediate 38-c and 38-c' (1.0 g, 4.13 mmol) and
intermediate 37-d (826 mg, 3.75 mmol) in DMPU (7.50 ml) and toluene
(7.50 ml) was added sodium 2-methylpropan-2-olate (721 mg, 7.50 mmol)
at room temperature. The reaction was stirred overnight at 80 C and then
cooled to room temperature. A saturated aqueous solution of ammonium
chloride and ethyl acetate were added, the organic layer was separated,
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediates 38-d and 38-d' as an inseparable mixture.
Step 4: Intermediates 38-e and 38-e'
A methanol solution of intermediates 38-d and 38-d' (200 mg, 0.45 mmol)
was treated with 10% palladium on carbon (96 mg, 0.045 mmol) and purged
with H2. The solution was stirred under H2 (1 atm) for 2 hours before being
filtered through celite. The filtrate was concentrated in vacuo to provide
intermediate 38-e and 38-e' as an inseparable mixture.
71

CA 02813299 2013-04-17
Synthesis of intermediate 39-b
F = OH Ph3P, DD F = F
TBAF
HON
OTBS \ c \ OTBS OH
29-g 39-a 39-b
Scheme 39
Step 1: Intermediate 39-a
To a solution of intermediate 29-g (4.20 g, 17.3 mmol) and pyrimidin-5-
ylmethanol (1.90 g, 17.3 mmol) in THF (35 mL) were sequentially added
triphenylphosphine (5.91 g, 22.5 mmol) and DIAD (4.38 mL, 22.5 mmol) at
room temperature and the reaction was then stirred at room temperature for
3 hours. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 39-a as a white solid.
Step 2: Intermediate 39-b
To a solution of intermediate 39-a (5.80 g, 17.3 mmol) in THF (35 mL) was
added a 1.0 M solution of TBAF in THF (17.3 ml, 17.3 mmol) and the reaction
was stirred at room temperature for 1 hour. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 39-b as a white solid.
Synthesis of intermediate 40-b
72

CA 02813299 2013-04-17
rN,n
F OH Ph3P, DIAD F = 0,,N)
TBAF F =
ON)
HO
OTBS \ OTBS OH
29-g 40-a 40-b
Scheme 40
Step 1: Intermediate 40-a
To a solution of intermediate 29-g (4.62 g, 19.1 mmol) and pyrazin-2-
ylmethanol (2.10 g, 19.1 mmol) in THF (38 mL) were sequentially added
triphenylphosphine (7.50 g, 28.6 mmol) and DIAD (5.19 ml, 26.7 mmol) at
room temperature and the reaction was then stirred at room temperature
overnight. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 40-a as a colorless oil.
Step 2: Intermediate 40-b
To a solution of intermediate 40-a (3.40 g, 10.2 mmol) in THF (20 mL) was
added a 1.0 M solution of TBAF in THF (10.2 ml, 10.2 mmol) and the reaction
was stirred at room temperature for 1 hour. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 40-b as a white solid.
Synthesis of intermediate 41-b
F = OH Ph3P, DIAD F io 0 lel
TBAF F = 0 I.
HO
OTBS OTBS OH
29-g 41-a 41-b
73

CA 02813299 2013-04-17
Scheme 41
Step 1: Intermediate 41-a
To a solution of intermediate 29-g (2.60 g, 10.7 mmol) and benzyl alcohol
(1.39 g, 12.9 mmol) in THF (20 mL) were sequentially added
triphenylphosphine (3.94 g, 15.02 mmol) and DIAD (2.92 mL, 15.0 mmol) at
room temperature and the reaction was then stirred at room temperature
overnight. Volatiles were removed under reduced pressure. Purification by
silica gel chromatography provided intermediate 41-a as colorless oil.
Step 2: Intermediate 41-b
To a solution of intermediate 41-a (1.40 g, 4.21 mmol) in THF (10 ml) was
added a 1.0 M solution of TBAF in THF (4.63 ml, 4.63 mmol) and the reaction
was stirred at room temperature overnight. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 41-b as a colorless oil.
Synthesis of intermediate 42-d
74

CA 02813299 2013-04-17
Boc
NNH NaBH3CN HN,NH2
0=0 ______________________
HCI HCI
,N
H2N , Boc
42-a 42-b 42-c
Br Br
TEA
NC NC
0
N
CN 42-c
H2N
9-b 42-d
Scheme 42
Step 1: Intermediate 42-b
To a solution of cyclopentanone (10.00 g, 119.0 mmol) in Me0H (594 mL),
were added tert-butyl hydrazinecarboxylate (16.50 g, 125.0 mmol) and the
reaction was stirred overnight at room temperature. Volatiles were removed
under reduced pressure to provide intermediate 42-b as a white solid.
Step 2: Intermediate 42-c
To a solution of intermediate 42-b (10.00 g, 50.40 mmol) in THF (50.4 mL)
and Me0H (50.4 mL) was added sodium cyanoborohydride (3.80 g, 60.5
mmol) portion wise. The reaction was refluxed under argon for 10 minutes,
and then cooled to room temperature. 6N NCI (25 mL) was added, the
mixture was refluxed for 3 hours, cooled to room temperature and stirred
overnight. The reaction was filtered to remove inorganic insoluble material
and the filtrate was concentrated under reduced pressure and azeotroped
three times with toluene. The residue was dissolved in hot isopropanol,
cooled to room temperature, diluted with ether and then cooled to 0 C. A
precipitate formed and was collected by filtration to provide intermediate 42-
c=FICI as a white solid.

CA 02813299 2013-04-17
Step 3: Intermediate 42-d
To a solution of intermediate 9-b (3.00 g, 11.4 mmol) and TEA (3.50 mL,
25.1 mmol) in Et0H (11.4 mL) was added intermediate 42-c=HCI (1.86 g,
13.7 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 42-d as a white solid.
Synthesis of intermediate 43-e
Boc Boc
NI' NH
HN
H Pd/CNH HCI HNNH2
0\ 2 . _______________ . HCI
N,
H2N Boc
43-a 43-b 43-c 43-d
Br Br
TEA
NC NC
0
N
CN 43-d
H2N
9-b 43-e
0
Scheme 43
76

CA 02813299 2013-04-17
Step 1: Intermediate 43-b
To a solution of dihydro-2H-pyran-4-(3H)-one (15.0 g, 150.0 mmol) in Me0H
(749 mL), were added tert-butyl hydrazinecarboxylate (20.79 g, 157.0
mmol) and the reaction was stirred overnight at room temperature. Volatiles
were removed under reduced pressure to provide intermediate 43-b as a
white solid.
Step 2: Intermediate 43-c
A methanol solution of intermediate 43-b (32.1 g, 150.0 mmol) was treated
with 10% palladium on carbon (6.39 g, 3.00 mmol), acetic acid (100 pL) and
purged with H2. The solution was stirred under H2 (1 atm) overnight before
being filtered through celite. The filtrate was concentrated in vacuo to
provide intermediate 43-c as a white solid.
Step 3: Intermediate 43-d
To a solution of intermediate 43-c (32.4 g, 150 mmol) in Me0H (300 mL)
was added 4N HCI in 1,4-dioxane (300 ml, 1200 mmol) and the reaction was
stirred at room temperature for 5 hours. Diethyl ether was added and a
precipitate formed which was collected by filtration to provide intermediate
43-d=HCI as a white solid.
Step 4: Intermediate 43-e
To a solution of intermediate 9-b (5.00 g, 19.0 mmol) and TEA (5.30 mL,
38.0 mmol) in Et0H (19.0 mL) was added intermediate 43-c=FICI (3.48 g,
22.81 mmol) and the reaction was then stirred for 2 hours at 100 C.
Volatiles were removed under reduced pressure. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added to the residue,
the organic layer was separated, washed with brine, dried over MgSO4,
77

CA 02813299 2013-04-17
filtered and concentrated under reduced pressure to provide intermediate 43-
e as a yellow solid.
Synthesis of intermediate 44-d
Boc
NNH
0
H _________________________ A. I
V\ NaBH3CN
HCI HN,NH2
_________________________________________________ p riN
N,
H2N, Boc
44-a 44-b 44-c
Br Br
SI ilk
TEA
NC ________________________________________ A NC
0 I \ N
44-c
CN
H2N "....,,_
9-b 44-d
Scheme 44
Step 1: Intermediate 44-b
tert-Butyl hydrazinecarboxylate (7.60 g, 57.5 mmol) was added to acetone
(50 mL) and the reaction was stirred overnight at room temperature.
Volatiles were removed under reduced pressure to provide intermediate 44-b
as a white solid.
Step 2: Intermediate 44-c
To a solution of intermediate 44-b (9.90 g, 57.5 mmol) in THF (57.5 mL) and
Me0H (57.5 mL) was added sodium cyanoborohydride (4.34 g, 69.0 mmol)
portion wise. The reaction was refluxed under nitrogen for 10 minutes, and
then cooled to room temperature. 6N HCI (30 mL) was added, the mixture
was refluxed for 3 hours, cooled to room temperature and stirred overnight.
78

CA 02813299 2013-04-17
The reaction was filtered to remove inorganic insoluble material and the
filtrate was concentrated under reduced pressure and azeotroped three times
with toluene for complete water removal. The residue was dissolved in hot
isopropanol, cooled to room temperature, diluted with ether and then cooled
to 0 C. A precipitate formed and was collected by filtration to provide
intermediate 44-c=HCI as a white solid.
Step 3: Intermediate 44-d
To a solution of intermediate 9-b (12.61 g, 47.9 mmol) and TEA (14.70 mL,
105.0 mmol) in Et0H (96.0 ml) was added intermediate 44-c.HCI (6.36 g,
57.5 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 44-d as a white solid.
Synthesis of intermediate 45-a
Br Br
TEA
NC __________________________________________________ . NC410
/ 0 \
I N
CN) NHNH2 N
H2N
/)----
9-b 45-a
Scheme 45
To a solution of intermediate 9-b (2.0 g, 7.60 mmol) and TEA (2.12 ml, 15.2
mmol) in Et0H (7.60 mL) was added tert-butylhydrazine hydrochloride (1.13
g, 9.12 mmol) and the reaction was then stirred for 2 hours at 100 C.
Volatiles were removed under reduced pressure. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added to the residue,
79

CA 02813299 2013-04-17
the organic layer was separated, washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure to provide intermediate 45-
a as a yellow solid.
Synthesis of intermediate 46-a
Br Br
TEA
NC NC
0 \ N
CN 0-NHNH2
H2N
9-b 46-a
Scheme 46
To a solution of intermediate 9-b (1.45 g, 5.53 mmol) and TEA (1.54 mL,
11.1 mmol) in Et0H (15.0 mL) was added cyclohexylhydrazine hydrochloride
(1.00 g, 6.64 mmol) and the reaction was then stirred for 2 hours at 100 C.
Volatiles were removed under reduced pressure. A saturated aqueous
solution of ammonium chloride and ethyl acetate were added to the residue,
the organic layer was separated, washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure to provide intermediate 46-
a as a yellow solid.
Synthesis of intermediate 47-a
Br Br
TEA
NC NC
0 I \ N
CN HO H2 H2N Nv_
9-b 47-a OH

CA 02813299 2013-04-17
Scheme 47
To a solution of intermediate 9-b (2.00 g, 7.60 mmol) and TEA (1.27 mL,
9.12 mmol) in Et0H (7.60 mL) was added 2-hydroxyethylhydrazine (618 pL,
9.12 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure to provide intermediate 47-a as a white
solid.
Synthesis of intermediate 48-c
cK)OH NaOH
H2NOH
Hydrazine
48-a 48-b
Br Br
TEA
NC NC
0
N
48-b
CN H2N
9-b 48-c OH
Scheme 48
Step 1: Intermediate 48-b
To a mixture of sodium hydroxide (7.37 g, 184.0 mmol) and hydrazine
monohydrate (46.10 g, 921.0 mmol) heated to 95 C, was added 1-chloro-2-
methylpropan-2-ol (20.00 g, 184.0 mmol). The reaction was stirred
overnight at 95 C and then cooled to room temperature. Volatiles were
81

CA 02813299 2013-04-17
removed under reduced pressure. THF (40 mL) and diethyl ether (40 mL)
were added to the residue; a precipitate formed which was removed by
filtration. The filtrate was concentrated under reduced pressure to provide
intermediate 48-b as a colorless oil.
Step 2: Intermediate 48-c
To a solution of intermediate 9-b (4.45 g, 16.9 mmol) and TEA (4.71 mL,
33.8 mmol) in Et0H (15.0 mL) was added intermediate 48-b (1.76 g, 16.9
mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles were
removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure to provide intermediate 48-c as a white
solid.
Synthesis of intermediate 49-c
NaOH
H2N
NOH
Hydrazine
49-a 49-b
Br TEA Br
1101 410
NC N
0
N
49-h
H2C
CN N
9-b 49-c OH
Scheme 49
82

CA 02813299 2013-04-17
Step 1: Intermediate 49-b
To a mixture of sodium hydroxide (1.15 g, 28.8 mmol) and hydrazine
monohydrate (7.20 g, 144.0 mmol) heated to 95 C, was added 3-bromo-1-
propanol (4.00 g, 28.8 mmol) and the reaction was stirred overnight at 95 C
and then cooled to room temperature. Volatiles were removed under reduced
pressure. Ethanol was added to the residue; a precipitate formed and was
removed by filtration. The filtrate was concentrated under reduced pressure
and 1M HCI in diethyl was added to the residue. After stirring for 15 minutes
a precipitate formed and was collected by filtration to provide intermediate
49-b=HCI as a white solid.
Step 2: Intermediate 49-c
To a solution of intermediate 9-b (1.12 g, 4.28 mmol) and TEA (1.19 mL,
8.56 mmol) in Et0H (10.0 mL) was added intermediate 49-b=FICI (650 mg,
5.13 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure to provide intermediate 49-c as a white
solid.
Synthesis of intermediate 50-c
83

CA 02813299 2013-04-17
Boc
n OH FIN,N
NaBH3CN H2N,INH HCI
_____________________________ _ ____________________ .
H007
H
HCI
r-
OH N

H2NõBoc OH OH OH OH
36-a 50-a 50-b
Br Br
01 0
TEA
___________________________ .
NC 7 NC
CN 50-b N
H2N
9-b OH 50-c
Scheme 50
Step 1: Intermediate 50-a
Dihydroxyacetone dimer (15.0 g) and tert-butyl hydrazinecarboxylate (22.01
g) were dissolved in ethanol (500 mL) and this solution was stirred at room
temperature for 2 days. After the reaction mixture was concentrated under
reduced pressure, the resulting residue was recrystallized from ethyl acetate
to provide intermediate 50-a as a white solid.
Step 2: Intermediate 50-b
To a solution of intermediate 50-a (10.0 g, 49.0 mmol) in THF (49.0 mL) and
Me0H (49.0 mL) was added sodium cyanoborohydride (3.69 g, 58.8 mmol)
portion wise. The reaction was refluxed under nitrogen for 10 minutes, and
then cooled to room temperature. 6N HCI (40 mL) was added, the mixture
was refluxed for 3 hours, cooled to room temperature and stirred overnight.
The reaction was filtered to remove inorganic insoluble material and the
84

CA 02813299 2013-04-17
filtrate was concentrated under reduced pressure and azeotroped three times
with toluene to provide intermediate 50-b=HCI as a white solid.
Step 3: Intermediate 50-c
To a solution of intermediate 9-b (10.70 g, 40.9 mmol) and TEA (12.5 mL,
90.0 mmol) in Et0H (40.9 mL) was added intermediate 50-13.1-1C1 (7.00 g,
49.1 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 50-c as a beige solid.
Synthesis of intermediate 51-a
Br Br
O fa
Ph3P, DIAD
NC ________________________________ v NC
l \ N l \ N
H2N [\il HC:Y>C0 H2N
LC)
9-c 51-a
Scheme 51
To a solution of intermediate 9-c (1.40 g, 5.32 mmol) and 3-methyloxetan-3-
yl)methanol (1.08 g, 10.64 mmol) in THF (5.3 mL) were sequentially added
triphenylphosphine (1.67 g, 6.39 mmol) and DIAD (1.13 mL, 5.85 mmol) at
room temperature and the reaction was then stirred at room temperature for
4 days. Volatiles were removed under reduced pressure. Purification by silica
gel chromatography provided intermediate 51-a as a white solid.
Synthesis of intermediate 52-a

CA 02813299 2013-04-17
NC Br Br
Ph3P, DIAD NC
H2N /\N H
OH 2N
1\1 rN N,N
0)
9-c 52-a 170
Scheme 52
To a solution of intermediate 9-c (500 mg, 1.90 mmol) and 3-
morpholinopropan-1-ol (263 pl, 1.90 mmol) in THF (19.0 ml) cooled to 0 C
were sequentially added triphenylphosphine (498 mg, 1.90 mmol) and DIAD
(370 pl, 1.90 mmol). The reaction was stirred at 0 C for 1 hour and room
temperature overnight. Volatiles were removed under reduced pressure.
Purification by silica gel chromatography provided intermediate 52-a as a
white foam.
Synthesis of intermediate 53-a
Br Br
NH2 = NH2
N Ph3P, DIAD
,N N
N N N iN\
r-N\ 10
F10--/
9-d 53-a
Scheme 53
To a solution of intermediate 9-d (3.00 g, 10.3 mmol) and N-(2-
hydroxyethyl)morpholine (1.88 ml, 15.1 mmol) in THF (103 ml) cooled to
0 C were sequentially added triphenylphosphine (4.07 mg, 15.1 mmol) and
86

CA 02813299 2013-04-17
DIAD (3.02 ml, 15.5 mmol). The reaction was stirred at 50 C overnight.
Volatiles were removed under reduced pressure. Purification by silica gel
chromatography provided intermediate 53-a as a white solid.
Synthesis of intermediate 54-a
Br Br
= 110+
Ph3P, DIAD NC
NC
\ /
H2NNN OH H2N N
9-c 54-a
Scheme 54
To a solution of intermediate 9-c (500 mg, 1.90 mmol) and 2-(pyrrolidin-1-
yl)ethanol (219 mg, 1.90 mmol) in THF (9.5 ml) cooled to 0 C were
sequentially added triphenylphosphine (498 mg, 1.90 mmol) and DIAD (370
pl, 1.90 mmol). The reaction was stirred at 0 C for 1 hour and room
temperature for 30 minutes. Volatiles were removed under reduced pressure.
Purification by silica gel chromatography provided intermediate 54-a as
yellow solid.
Synthesis of Compound 65:
Br
0 0 it
H2N N)-(OH 0
Cul, Cs2CO3 NH2
I'
N 31-d
N N
bo
17-a Compound 65
87

CA 02813299 2013-04-17
Scheme 55
To a solution of intermediate 17-a (321 mg, 0.85 mmol) and intermediate
31-d (200 mg, 0.85 mmol) in 1,4-dioxane (4.30 ml) were sequentially added
N,N-dimethylglycine (265 mg, 2.57 mmol), copper(I) iodide (163 mg, 0.85
mmol) and cesium carbonate (1.12 g, 3.43 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided compound
65.2HCI as a white solid.
Synthesis of Compound 85
40 0
Br 0 0 411t
0
NC * Cul, Cs2CO3 tN
HC(OMe)3
=
/ \ N
H2N
_______________________________________________ =
/
H2N m 31-d NC N
NH3 N
N
'
)\ H2N N
44-d 56-a Compound
85
Scheme 56
Step 1: Intermediate 56-a
To a solution of intermediate 44-d (5.00 g, 16.4 mmol) and intermediate 31-
d (4.20 g, 18.0 mmol) in 1,4-dioxane (54.6 ml) were sequentially added
N,N-dimethylglycine (3.80 g, 36.9 mmol), copper(I) iodide (2.34 g, 12.29
mmol) and cesium carbonate (21.35 g, 65.5 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
88

CA 02813299 2013-04-17
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 56-a.HCI as a white solid.
Step 2: Compound 85
Intermediate 56-a=FICI (3.13 g, 6.84 mmol) and trimethyl orthoformate (48.7
ml, 445.0 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with
ammonia (7.0 N in Me0H) (48.9 ml, 342.0 mmol). The mixture was stirred at
room temperature for 3 days and volatiles were removed under reduced
pressure. Purification by reverse phase chromatography eluting with a 1%
aqueous HCl/methanol gradient provided compound 85.2HCI as a white solid.
MS (m/z) M+H= 485.2
Synthesis of Compound 91:
Br Oil 0 0 0 =
N0 L
0
NC Cul, Cs2CO3
HC(OMe)3 40
_______________________________________________ =
H \ N \
¨2..N N- 33-a NC N NH3 N
\
H2N
)
0
43-e 57-a 0
Compound 91
Scheme 57
Step 1: Intermediate 57-a
To a solution of intermediate 43-e (192 mg, 0.55 mmol) and intermediate
33-a (190 mg, 0.66 mmol) in 1,4-dioxane (2.8 ml) were sequentially added
N,N-dimethylglycine (129 mg, 1.24 mmol), copper(I) iodide (79 mg, 0.42
mmol) and cesium carbonate (722 mg, 2.21 mmol). The reaction mixture
89

CA 02813299 2013-04-17
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 57-a as a yellow foam.
Step 2: Compound 91
Intermediate 57-a (286 mg, 0.55 mmol) and trimethyl orthoformate (3.94
ml, 36.0 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (3.96 ml, 27.7 mmol). The mixture was stirred at room
temperature for 3 days and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 91.HCI as white solid. MS (m/z)
M+H= 543.1
Synthesis of Compound 101:
Br
0
NC 0
Cul, Cs2CO3HC(OMe)3
/\ 0 1. 0
NH2'
H2N NN NH3 "N
32-f
\
N NiN OH
NC NN
43-eH2N 58-a o Compound 101
o
Scheme 58

CA 02813299 2013-04-17
Step 1: Intermediate 58-a
To a solution of intermediate 43-e (400 mg, 1.15 mmol) and intermediate
32-f (384 mg, 1.15 mmol) in 1,4-dioxane (2.8 ml) were sequentially added
N,N-dimethylglycine (267 mg, 2.59 mmol), copper(I) iodide (165 mg, 0.86
mmol) and cesium carbonate (1.50 g, 4.61 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure to provide intermediate 58-a as a beige foam.
Step 2: Compound 101
Intermediate 58-a (690 mg, 1.15 mmol) and trimethyl orthoformate (8.18
ml, 74.8 mmol) were heated at 110 C for 4 days. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (8.21 ml, 57.5 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 101.2HCI as a white solid. MS
(m/z) M+H= 543.1
Synthesis of Compound 128:
F
Br 0 F
0 =
ii, 1\1I)-LOH
NC / Cul, Cs2CO3 0 lei 0 HC(OMe)3
1
L
m
NH2
H2N * 0
\ __________ = .,,,-., NH3 / \ N
32-f N-- 1 '` N
N ' 1 \
.) 40
,--cAH L 1 ,N OH
N\
NC N 7---
\ ,
44-d N 59-a Compound 128
H2N ?---
91

CA 02813299 2013-04-17
Scheme 59
Step 1: Intermediate 59-a
To a solution of intermediate 44-d (261 mg, 0.85 mmol) and intermediate
32-f (285 mg, 0.85 mmol) in 1,4-dioxane (2.8 ml) were sequentially added
N,N-dimethylglycine (198 mg, 1.92 mmol), copper(I) iodide (122 mg, 0.64
mmol) and cesium carbonate (1.11 g, 3.42 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure to provide Purification by reverse phase
chromatography eluting with a 1% aqueous HCl/methanol gradient provided
intermediate 59-a.HCI as a beige foam.
Step 2: Compound 128
Intermediate 59-a (405 mg, 0.85 mmol) and trimethyl orthoformate (6.08
ml, 55.6 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (6.11 ml, 42.8 mmol). The mixture was stirred at room
temperature for 3 days and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 128.2HCI as a white solid. MS
(m/z) M+H= 501.1
Synthesis of Compound 78:
92

CA 02813299 2013-04-17
F
Br 1 0 F
Nj=LOH 0
NC 11 Cul, Cs2CO3 o Si o HC(OMe)3
OTh---\-
_______________________________________________ r
\ *
Ly---\N NH3 NI-12 . S7/ N
H2N /N-N 29-i 40 S--c \
1, 1 ,N
NC\ N N N\
,
7----
N
44-d H2N ------ 60-a
Compound 78
Scheme 60
Step 1: Intermediate 60-a
To a solution of intermediate 44-d (300 mg, 0.98 mmol) and intermediate
29-i (259 mg, 1.08 mmol) in 1,4-dioxane (3.9 ml) were sequentially added
N,N-dimethylglycine (304 mg, 2.95 mmol), copper(I) iodide (187 mg, 0.98
mmol) and cesium carbonate (961 mg, 2.95 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 60-a=HCI as a beige foam.
Step 2: Compound 78
Intermediate 60-a=HCI (265 mg, 0.57 mmol) and trimethyl orthoformate
(1.87 ml, 17.16 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (5.7 ml, 11.44 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
93

CA 02813299 2013-04-17
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 78.2HCI as beige solid. MS (m/z)
M+H= 491.2
Synthesis of Compound 58:
F
Br O=
I 0
N,)-(OH
NH2 /1 NH2 Os S(/ N
Cul, Cs2CO3 \
1 1 N 1 I N
'
N N)....,.., 29-i N 14)....._,
U U
10-a Compound 58
Scheme 61
To a solution of intermediate 10-a (3.96 g, 11.1 mmol) and intermediate 29-i
(2.91 g, 12.2 mmol) in 1,4-dioxane (55.3 ml) were sequentially added N,N-
dimethylglycine (3.42 g, 33.2 mmol), copper(I) iodide (2.10 g, 11.07 mmol)
and cesium carbonate (10.82 g, 33.2 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided compound
58.2HCI as a beige solid. MS (m/z) M+H= 517.2
94

CA 02813299 2013-04-17
Synthesis of Compound 117:
F
F
Br 0 0 .
.Ij=(OH OTh"----\-
0 el 0
NC Cul, Cs2CO3 HC(OMe)3
/ \k, _____________ 1- 0 NH2 it ____________________________________ s,,,N
H2N N.- s__c NH3 \
29-i N -- \
NC N NI N'IN1
OH \ , N \_.4......
H2N N\.___1(
OH
48-c OH 62-a Compound 117
Scheme 62
Step 1: Intermediate 62-a
To a solution of intermediate 48-c (200 mg, 0.59 mmol) and intermediate
29-1 (157 mg, 0.65 mmol) in 1,4-dioxane (1.50 ml) were sequentially added
N,N-dimethylglycine (92 mg, 0.89 mmol), copper(I) iodide (57 mg, 0.29
mmol) and cesium carbonate (583 mg, 1.79 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 62-a=HCI as a beige solid.
Step 2: Compound 117
Intermediate 62-a=HCI (322 mg, 0.65 mmol) and trimethyl orthoformate (3.0
ml, 19.57 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with
ammonia (7.0 N in Me0H) (1.85 ml, 13.0 mmol). The mixture was stirred at
room temperature overnight and volatiles were removed under reduced
pressure. Purification by reverse phase chromatography eluting with a i%

CA 02813299 2013-04-17
aqueous HCl/methanol gradient provided compound 117=2HCI as a white
solid. MS (m/z) M+H= 521.1
Synthesis of Compound 100:
F
F
Br 1 0 0 40 0 o=
46, -N 0OH 0 Y\N
S/, N
NC Cul, Cs2CO3 S---c HC(OMe)3
NH2
__________________ r _________________________ r-
/ \ \
\
NH3 N N
, "
H2N N,"m 29-i NC N , nu I ,
N,-.
H2N ---/ N JOH
OH OH
50-c 63-a Compound 100
Scheme 63
Step 1: Intermediate 63-a
To a solution of intermediate 50-c (1.42 g, 4.21 mmol) and intermediate 29-i
(1.10 g, 4.63 mmol) in 1,4-dioxane (16.8 ml) were sequentially added N,N-
dimethylglycine (1.30 g, 12.6 mmol), copper(I) iodide (802 mg, 4.21 mmol)
and cesium carbonate (4.12 g, 12.63 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided intermediate 63-
a=HCI as a white solid.
Step 2: Compound 100
Intermediate 63-a=HCI (577 mg, 1.16 mmol) and trimethyl orthoformate
(3.82 ml, 35.0 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (3.30 ml, 23.32 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
96

CA 02813299 2013-04-17
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 100.2HCI as white solid. MS
(m/z) M+H= 523.2
Synthesis of Compound 113:
0 0 4, 0
,49
s.õN NH2
sõNi NH2 =41k
$,//N
Bu Tsa N N N\,11
N \ N IsLN \.N
OH 0, 0 0
Compound 100 ti\(. 64-a Compound 113
Scheme 64
Step 1: Intermediate 64-a
To a solution of compound 100 (198.0 mg, 0.38 mmol) in THF cooled to -
C was slowly added a 2.5 M solution of n-butyllithium in THF (304 pl,
0.76 mmol). After stirring for 30 minutes, para-toluenesulfonyl chloride (72.0

mg, 0.38 mmol) in THF (2 ml) was added. The reaction was stirred at 60 C
overnight and then cooled to room temperature. Water and ethyl acetate
were added, the organic layer was separated, washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediate 64-a as beige foam.
Step 2: Compound 113
To a solution of intermediate 64-a (85.0 mg, 0.12 mmol) in THF cooled to -
10 C was slowly added a 2.5 M solution of n-butyllithium in THF (110.0 pl,
0.27 mmol). The reaction was stirred at 60 C overnight and then cooled to
room temperature. Water and ethyl acetate were added, the organic layer
was separated, washed with brine, dried over MgSO4, filtered and
97

CA 02813299 2013-04-17
concentrated under reduced pressure. Purification by silica gel
chromatography provided compound 113 as pale yellow foam. MS (m/z)
M+H= 505.2
Synthesis of Compound 125:
Br
0 o,0 4.
4410
0 0
Cul, Cs2C0 NC 3 HC(OMe)3
NC NH2
S,/,1%1
I \ N I \,N NH3 N".
29-i I ,N
H2N N
H2N
oI N NL7C0
51-a 65-a Compound 125
Scheme 65
Step 1: Intermediate 65-a
To a solution of intermediate 51-a (300 mg, 0.86 mmol) and intermediate
29-i (262 mg, 0.95 mmol) in 1,4-dioxane (1.50 ml) were sequentially added
N,N-dimethylglycine (267 mg, 2.59 mmol), copper(I) iodide (165 mg, 0.86
mmol) and cesium carbonate (845 mg, 2.59 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 65-a as a beige foam.
Step 2: Compound 125
Intermediate 65-a (120 mg, 0.23 mmol), trimethyl orthoformate (260 pl, 2.3
mmol) and PTSA (catalytic) were stirred at room temperature for 1 hour.
Excess trimethyl orthoformate was removed in vacuo and the residue was
98

CA 02813299 2013-04-17
treated with 7.0 N ammonia in Me0H (652 pl, 4.6 mmol). The mixture was
stirred at room temperature for 3 days and volatiles were removed under
reduced pressure. Purification by silica gel chromatography provided
compound 125 as a white solid. MS (m/z) M+H= 533.2
Synthesis of Compound 54:
Br
0
0 0
NH2 410
')'OH
NH2
N Cul, Cs2CO3
I
NN
N NI)Th
29-i N )ThN
0
0
17-a
Compound 54
Scheme 66
To a solution of intermediate 17-a (1.20 g, 3.21 mmol) and intermediate 29-1
(844 mg, 3.53 mmol) in DMF (16.0 ml) were sequentially added N,N-
dimethylglycine (992 mg, 9.62 mmol), copper(I) iodide (611 mg, 3.21 mmol)
and cesium carbonate (4.18 g, 12.83 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided compound
54.2HCI as a yellow solid. MS (m/z) M+H= 533.1
Synthesis of Compound 55:
99

CA 02813299 2013-04-17
F F
Br I V 0 . o=
411 -'NOH
* 0 0
NC Cul, Cs2CO3 =:---\¨ formamidine NH2
/ \ ______________ ' NC Si/14 ----0-
H2N NN 29-1 " \
1 111
H2N N N
.._
52-a 67-a Compound 55
Scheme 67
Step 1: Intermediate 67-a
To a solution of intermediate 52-a (397.0 mg, 1.00 mmol) and intermediate
29-1 (268 mg, 1.12 mmol) in 1,4-dioxane (5.0 ml) were sequentially added
N,N-dimethylglycine (157 mg, 1.53 mmol), copper(I) iodide (97.0 mg, 050
mmol) and cesium carbonate (995 mg, 3.05 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure to provide intermediate 67-
a as beige foam.
Step 2: Compound 55
Formamide (2.84 ml, 71.3 mmol) was added to intermediate 67-a (559 mg,
1.0 mmol) and the reaction was stirred at 180 C for 2 hours. Water and
ethyl acetate were added, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 55.3HCI as beige solid. MS (m/z)
M+H= 576.2
Synthesis of Compound 52:
100

CA 02813299 2013-04-17
F
Br OH
0 40
N 0
NH2 41k 441k ,---"\--
N \ N 0 NH2 * SerNI
I'
N N\ Cs2CO3, Cul I N I
---1 29-1 N rµl_
N--\ ---1
53-a (...__ ) (N--) Compound 52
0
LO
Scheme 68
To a solution of intermediate 53-a (1.0 g, 2.48 mmol) and intermediate 29-i
(771 mg, 3.22 mmol) in DMAC (12.4 ml) were sequentially added quinolin-8-
ol (36.0 mg, 0.24 mmol), copper(I) iodide (47.0 mg, 0.24 mmol) and cesium
carbonate (808 mg, 2.48 mmol) and the reaction was heated at 140 C for 2
hours. A saturated aqueous solution of ammonium chloride and ethyl acetate
were added, the organic layer was separated and the aqueous phase was
extracted twice with ethyl acetate. The combined organic extracts were
washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by reverse phase chromatography eluting with
a 1% aqueous HCl/methanol gradient provided compound 52.3HCI as white
solid. MS (m/z) M+H= 562.1
Synthesis of Compound 57:
F F
Br i 0 0* 0=
0 0
11 fh
NC / H NC l formamide * --'----\
, Cr¨ \ NH2
N ____________________________________________ p.
1 CulCs2CO3
H2N N=N 29-i I \,N S(/
14-- . \
i ,N I
H2N N,
'---1 N NI,
µ----1
--J
54-a 69-a Compound 57
101

CA 02813299 2013-04-17
Scheme 69
Step 1: Intermediate 69-a
To a solution of intermediate 54-a (425.0 mg, 1.18 mmol) and intermediate
29-1 (282 mg, 1.18 mmol) in 1,4-dioxane (5.9 ml) were sequentially added
N,N-dimethylglycine (182 mg, 1.77 mmol), copper(I) iodide (112 mg, 0.59
mmol) and cesium carbonate (1.15 g, 3.54 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgS0.4, filtered and concentrated
under reduced pressure to provide intermediate 69-a as a beige foam.
Step 2: Compound 57
Formamide (5.53 ml, 139.0 mmol) was added to intermediate 69-a (600 mg,
1.15 mmol) and the reaction was stirred at 180 C for 4 hours. Water and
ethyl acetate were added, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 57.3HCI as beige solid. MS (m/z)
M+H= 546.2
Synthesis of Compound 102:
Br O 0 0 *
0
LrN
NC Cul, Cs2CO3 I 1
ts( HC(OMe)3 NH,
N
H2N N=N 30-b NC NH3
I ,N
H2N
44-d
70-a Compound 102
Scheme 70
102

CA 02813299 2013-04-17
Step 1: Intermediate 70-a
To a solution of intermediate 44-d (4.00 g, 13.1 mmol) and intermediate 30-
b (3.38 g, 14.4 mmol) in 1,4-dioxane (43.7 ml) were sequentially added
N,N-dimethylglycine (3.04 g, 29.5 mmol), copper(I) iodide (1.87 g, 9.83
mmol) and cesium carbonate (17.08 g, 52.4 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 70-a=HCI as beige foam.
Step 2: Compound 102
Intermediate 70-a=HCI (3.80 g, 7.68 mmol) and trimethyl orthoformate (54.6
ml, 499.0 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (54.8 ml, 384.0 mmol). The mixture was stirred at room
temperature for 2 days and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 10/0 aqueous
HCl/methanol gradient provided compound 102.2HCI as white solid. MS
(m/z) M+H= 486.2
Synthesis of Compound 129:
103

CA 02813299 2013-04-17
F F
Br 1 0 0 0 o o =
-N o
2qj-OH L'
NC = Cul, Cs2CO3 0 I I
Thµl HC(OMe)3 NH2 ik
/--N
___________________ y __...
i\ m N , \ N--:"--c
\
H2N Ny¨ 30-b NC ,,, ,' NI-13 is I ,N
N
N N,
/-'-. H2N .-- i\---
45-a 71-a Compound 129
Scheme 71
Step 1: Intermediate 71-a
To a solution of intermediate 45-a (350 mg, 1.10 mmol) and intermediate
30-b (283 mg, 1.20 mmol) in 1,4-dioxane (4.3 ml) were sequentially added
N,N-dimethylglycine (1.07 g, 3.29 mmol), copper(I) iodide (209 mg, 1.10
mmol) and cesium carbonate (985 mg, 3.02 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 71-a=HCI as a beige solid.
Step 2: Compound 129
Intermediate 71-a=HCI (403.0 mg, 0.85 mmol) and trimethyl orthoformate
(6.07 ml, 55.5 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (6.07 ml, 42.7 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
104

CA 02813299 2013-04-17
HCl/methanol gradient provided compound 129.2HCI as beige solid. MS
(m/z) M+H= 500.1
Synthesis of Compound 106:
F F
Br 1 0 0 Si 0 0*
,4
'-)LOH . 0
L'N
NC it cui,c.2.3
tst HC(OMe)3 NH2
_________________________________________________ /
/ N N \ NI-----
H2N NN
.- 30-b NC N N NH3
\ N1_ l ,N
INI___,
/c H2N
43-e 72-a Compound 106
Scheme 72
Step 1: Intermediate 72-a
To a solution of intermediate 43-e (350 mg, 1.00 mmol) and intermediate
30-b (260 mg, 1.10 mmol) in 1,4-dioxane (4.0 ml) were sequentially added
N,N-dimethylglycine (312 mg, 3.02 mmol), copper(I) iodide (192 mg, 1.00
mmol) and cesium carbonate (985 mg, 3.02 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 72-a.HCI as a beige solid.
Step 2: Compound 106
Intermediate 72-a=HCI (263 mg, 0.52 mmol) and trimethyl orthoformate
(1.72 ml, 15.8 mmol) were heated at 110 C for 2 hours. Excess trimethyl
105

CA 02813299 2013-04-17
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (46.2 ml, 324 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 106.2HCI as a beige solid. MS
(m/z) M+H= 528.1
Synthesis of Compound 114:
Br 9 0 el 0 0*
N,2cOH 0
trN
NC Cul, Cs2CO3 110 I I
HC(OMe)3 NH2 fk
N \
H2N /N-N 30-b NC N
N NH3
M11
OH A-
H2N
OH
49-c 73-a Compound 114
Scheme 73
Step 1: Intermediate 73-a
To a solution of intermediate 49-c (250 mg, 0.78 mmol) and intermediate
30-b (201 mg, 0.85 mmol) in 1,4-dioxane (3.1 ml) were sequentially added
N,N-dimethylglycine (241 mg, 2.33 mmol), copper(I) iodide (148 mg, 0.78
mmol) and cesium carbonate (761 mg, 2.33 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 73-a=FICI as a beige solid.
106

CA 02813299 2013-04-17
Step 2: Compound 114
Intermediate 73-a=FICI (106 mg, 0.22 mmol) and trimethyl orthoformate
(737 pl, 6.74 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (2.24 ml, 4.49 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 114.2HCI as a beige solid. MS
(m/z) M+H= 502.2
Synthesis of Compound 130:
F
F
Br 1 0 0 lei 0 0 =
Nji,.OH0 \
H2N Irl
NC 11 Cul, Cs2CO3 f*1 HC(OMe)3 NH240 N---;"-k
'N NC N
\ OH \ 30-b NH3 Isr" \
' N
,
N I ,N
rJ0H H2N Z-----/
OH (
OH OH
50-c 74-a Compound 130
Scheme 74
Step 1: Intermediate 74-a
To a solution of intermediate 50-c (300 mg, 0.89 mmol) and intermediate
30-b (229 mg, 0.97 mmol) in 1,4-dioxane (890 pl) were sequentially added
N,N-dimethylglycine (275 mg, 2.67 mmol), copper(I) iodide (169 mg, 0.89
mmol) and cesium carbonate (870 mg, 2.67 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
107

CA 02813299 2013-04-17
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 74-a=HCI as beige solid.
Step 2: Compound 130
A solution of intermediate 74-a (125 mg, 0.25 mmol), trimethyl orthoformate
(836 pl, 7.65 mmol) and PTSA (catalytic) was stirred at room temperature
for 3 hours. Excess trimethyl orthoformate was removed in vacuo and the
residue was treated with ammonia (7.0 N in Me0H) (2.55 ml, 5.10 mmol).
The mixture was stirred at room temperature for 2 days and volatiles were
removed under reduced pressure. Purification by reverse phase
chromatography eluting with a 1% aqueous HCl/methanol gradient provided
compound 130.2HCI as a white solid. MS (m/z) M+H= 518.1
Synthesis of Compound 97:
F F
fa
Br 1 ?I O= o,
it
--=.-\ 0
----\-
NC Cul, Cs2CO3 HC(OMe)3 NH2 iii
-.........*. C _____________________ I.
/ \ \/N , \ /
H2N V'm 36-f I ,N CNNo I NH3 ,N Co
N N
)\ HN2N N)Th N
U
0 0 \--0) irk
43-e 75-a Compound 97
Scheme 75
Step 1: Intermediate 75-a
To a solution of intermediate 43-e (101 mg, 0.29 mmol) and intermediate
36-f (110 mg, 0.32 mmol) in 1,4-dioxane (1.4 ml) were sequentially added
N,N-dimethylglycine (90 mg, 0.87 mmol), copper(I) iodide (56 mg, 0.29
mmol) and cesium carbonate (381 mg, 1.17 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated and the aqueous phase was extracted twice with ethyl acetate.
108

CA 02813299 2013-04-17
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 75-a as a beige solid.
Step 2: Compound 97
Intermediate 75-a (160 mg, 0.26 mmol), trimethyl orthoformate (1.86 ml,
17.09 mmol) and TFA (catalytic) were heated at 110 C for 1 hour. Excess
trimethyl orthoformate was removed in vacuo and the residue was treated
with 7.0 N ammonia in Me0H (1.87 ml, 13.14 mmol). The mixture was
stirred at 50 C overnight and volatiles were removed under reduced
pressure. Purification by reverse phase chromatography eluting with a 1 70
aqueous HCl/methanol gradient provided compound 97.2HCI as a beige solid.
MS (m/z) M+H= 636.1
Synthesis of Compound 99:
F F
0 46 0 .
0 0
NH2 OH2 Pd/C NH2 fit
---=--\-
_____________________________________ ).
NV r "N N ,N NV i 1 "N N N
I ,)
N N 0 N N HO
o a
* 0
Compound 97 Compound 99
Scheme 76
A solution of compound 97.2HCI (100 mg, 0.15 mmol) in ethyl acetate was
treated with 10% palladium on carbon (32 mg, 0.015 mmol) and purged with
H2. The solution was stirred under H2(1 atm) for 1 hour before being filtered
through celite. The filtrate was concentrated in vacuo. Purification by
reverse
109

CA 02 8132 9 9 2 013-0 4-17
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided compound 99.2HCI as white solid. MS (m/z) M+H= 546.2
Synthesis of Compound 93:
F F
Br 1 9 0 * o 0 *
NJ-OH
NC 41 Cul, Cs2CO3 4. -------% *
___________________ w
NC N - + NC N.--,,/N---/
H2N N-- 37-f + 37-f 1 \,N r , \,N
N 0
H2N )_____\ 1 N
\-
H2N
SiMe3 -0)
43-e 77-a 77-a'
F
0.
F
0 ft
0 0
HC(OMe)3 NH2 * -":---"\--- NH2 *
77-a + 77-a' --1.- N / N + , -_/
NH3 N "*" i " N N
L 1 N r -z N ' \
I 14
l'i, o N'
1 N
SiMe3
77-h 77-h'
F
O,
HCI NH2 * 0
---\-- õ,
77-h + 77-b' ---0,- / HNrµ
N
l " ,N
N l'I)_Th
U
0
Compound 93
Scheme 77
Step 1: Intermediates 77-a and 77-a'
To a solution of intermediate 43-e (115 mg, 0.33 mmol) and intermediates
37-f and 37-f' (123 mg, 0.36 mmol) in 1,4-dioxane (1.6 ml) were
sequentially added N,N-dimethylglycine (102 mg, 0.99 mmol), copper(I)
iodide (63 mg, 0.33 mmol) and cesium carbonate (431 mg, 1.32 mmol). The
110

CA 02813299 2013-04-17
reaction mixture was stirred at reflux overnight, cooled to room temperature,
diluted with ethyl acetate and filtered over celite. A saturated aqueous
solution of ammonium chloride was added to the filtrate, the organic layer
was separated and the aqueous phase was extracted twice with ethyl
acetate. The combined organic extracts were washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediate 77-a and 77-a' as an
inseparable mixture.
Step 2: Intermediates 77-b and 77-b'
A solution of intermediates 77-a and 77-a' (100 mg, 0.16 mmol), trimethyl
orthoformate (2.0 ml, 18.28 mmol) and PTSA (catalytic) was stirred at room
temperature for 1 hour. Excess trimethyl orthoformate was removed in vacuo
and the residue was treated with 7.0 N ammonia in Me0H (2.0 ml, 14.1
mmol). The mixture was stirred at room temperature for 3 days and volatiles
were removed under reduced pressure. Purification by silica gel
chromatography provided intermediates 77-b and 77-b' as an inseparable
mixture.
Step 3: Compound 93
4N HCI in 1,4-dioxane (2 mL) was added to intermediates 77-b and 77-b' (60
mg, 0.09 mmol) band the mixture was stirred for 1 hour at room
temperature. Volatiles were removed under reduced pressure. Purification by
reverse phase chromatography eluting with a 1% aqueous HCl/methanol
gradient provided compound 93.2HCI as a white solid. MS (m/z) M+H= 502.2
Synthesis of Compound 118:
111

CA 02813299 2013-04-17
F F
Br 1 On 0 * 0 .
NC 11 Cut, Cs2CO3 *--------\-- *
/ \
___________________ ).
N NC r-.N m e'' + NC \
I
H2N N-- 38-e +38-e' 1 ",N 1 1 N
a N 0
H2N __ )__\ 1
SiMe3 N
I-12N
\
0 --0) \---0)
43-e 78-a 78-a'
F F
0 10 0 .
0 0
HC(OMe)3 NH2 4* -----\--- n, + NH2 4* ,---=\-
(:)/"SiMe3
78-a + 78-a' 0- N r II N.--/
NH3 N ' , \
r '( N" \
I N'N NK \
N Q t`l..Th I N
SiMe3
78-b 78-b'
F
0 .
0
HCI NH2 . ------'\
78-b + 78-b' 1. ' HN ,,, N
N \
Th\I r4)____I
Compound 118
Scheme 78
Step 1: Intermediates 78-a and 78-a'
To a solution of intermediate 43-e (276.0 mg, 0.79 mmol) and intermediates
38-e and 38-e' (340 mg, 0.87 mmol) in 1,4-dioxane (795 pl) were
sequentially added N,N-dimethylglycine (246 mg, 2.38 mmol), copper(I)
iodide (151 mg, 0.79 mmol) and cesium carbonate (1.03 g, 3.18 mmol). The
reaction mixture was stirred at reflux overnight, cooled to room temperature,
diluted with ethyl acetate and filtered over celite. A saturated aqueous
solution of ammonium chloride was added to the filtrate, the organic layer
was separated and the aqueous phase was extracted twice with ethyl
112

CA 02813299 2013-04-17
acetate. The combined organic extracts were washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure. Purification by
silica gel chromatography provided intermediate 78-a and 78-a' as an
inseparable mixture.
Step 2: Intermediates 78-b and 78-b'
A solution of intermediates 78-a and 78-a' (90 mg, 0.14 mmol), trimethyl
orthoformate (1.03 ml, 9.45 mmol) and TFA (catalytic) was stirred at room
temperature for 1 hour. Excess trimethyl orthoformate was removed in vacuo
and the residue was treated with 7.0 N ammonia in Me0H (1.03 ml, 7.27
mmol). The mixture was stirred at room temperature overnight and volatiles
were removed under reduced pressure to provide intermediates 78-b and 78-
b' as an inseparable mixture.
Step 3: Compound 118
4N HCI in 1,4-dioxane (2.82 mL) was added to intermediates 78-b and 78-b'
(60 mg, 0.09 mmol) and the mixture was stirred overnight at room
temperature. Volatiles were removed under reduced pressure. Purification by
reverse phase chromatography eluting with a 1% aqueous HCl/methanol
gradient provided compound 118.2HCI as a white solid. MS (m/z) M+H=
516.2
Synthesis of Compound 90:
F F
Br 1 ?I 0O 0 fa
41,
NC Cul, Cs2CO3 0HC(OMe)3 NH2 * ---\----
/ \
NC ,N,.// NH3 N ''. \
H2N N'N 34-d 1 \ N L I N
H N
H2N N\
M
OH OH OH
47-a 79-a Compound 90
113

CA 02813299 2013-04-17
Scheme 79
Step 1: Intermediate 79-a
To a solution of intermediate 79-a (310 mg, 1.0 mmol) and intermediate 34-
d (313 mg, 1.21 mmol) in 1,4-dioxane (2.5 ml) were sequentially added N,N-
dimethylglycine (156 mg, 1.51 mmol), copper(I) iodide (96.0 mg, 0.50
mmol) and cesium carbonate (1.31 g, 4.04 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided intermediate 79-
a as a beige solid.
Step 2: Compound 90
Intermediate 79-a (280 mg, 0.62 mmol) and trimethyl orthoformate (2.05
ml, 18.7 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (1.78 ml, 12.5 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1 /0 aqueous
HCl/methanol gradient provided compound 90.2HCI as a beige solid. MS
(m/z) M+H= 476.2
Synthesis of Compound 103:
114

CA 02813299 2013-04-17
F F
Br 1 0 0 * AO o O*
NC Cul, Cs2CO3 fl Cr---:\ HC(OMe)3 NH2 . -.---;-
-\,,
_________________________________________________ s
N / N
/ \ NC ,...- ---./ NH3 N , \
H2N N'N 34-d =
1 N L I ,N
6 14
H2N o ,N N)._...,
U
46-a 80-a Compound 103
Scheme 80
Step 1: Intermediate 80-a
To a solution of intermediate 46-a (300 mg, 0.87 mmol) and intermediate
34-d (247 mg, 0.95 mmol) in 1,4-dioxane (2.1 ml) were sequentially added
N,N-dimethylglycine (134 mg, 1.30 mmol), copper(I) iodide (83 mg, 0.43
mmol) and cesium carbonate (1.13 g, 3.48 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided intermediate 80-
a=FICI as a beige solid.
Step 2: Compound 103
Intermediate 80-a=HCI (65.0 mg, 0.13 mmol) and trimethyl orthoformate(3.0
ml, 4.01 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (378 pl, 2.65 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
115

CA 02813299 2013-04-17
HCl/methanol gradient provided compound 103.2HCI as a white solid. MS
(m/z) M+H= 514.2
Synthesis of Compound 120:
Br O * 410 o *
NC Cul, Cs2003 = HC(OMe)3 NH2 10
N
N
HN N NC NH3'N 35-d i I JA
\,N1
H2N
42-d 81-a Compound 120
Scheme 81
Step 1: Intermediate 81-a
To a solution of intermediate 42-d (176 mg, 0.53 mmol) and intermediate
35-d (145 mg, 0.53 mmol) in 1,4-dioxane (3.5 ml) were sequentially added
N,N-dimethylglycine (123 mg, 1.19 mmol), copper(I) iodide (76 mg, 0.40
mmol) and cesium carbonate (693 mg, 2.13 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated, and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 81-a.HCI as a yellow foam.
116

CA 02813299 2013-04-17
Step 2: Compound 120
Intermediate 81-a=HCI (259 mg, 0.53 mmol) and trimethyl orthoformate
(3.78 ml, 34.6 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (3.80 ml, 26.6 mmol). The mixture was heated at 60 C
for 5 hours and volatiles were removed under reduced pressure. Purification
by reverse phase chromatography eluting with a 1% aqueous HCl/methanol
gradient provided compound 120.2HCI as a white solid. MS (m/z) M+H=
514.2
Synthesis of intermediate 82-c:
Br Br
Br 11 0 DIPEA =
TMS-diazomethane =CI malononitrile
CN CN
HO Me0
CN CN
82-a 82-b 82-c
Scheme 82
Step 1: Intermediate 82-b
To a solution of 4-bromo-2-fluorobenzoyl chloride (16.27 g, 68.5 mmol) in
toluene (85 ml) and THF (8.5 ml), cooled to -10 C, were sequentially added
malononitrile (4.75 g, 71.9 mmol) and DIPEA (23.93 ml, 137.0 mmol) in
toluene (25 mL) drop wise over a period of 1 hour. After the addition was
completed, the reaction was stirred for 2 hours at 0 C and room temperature
for an additional 2 hours. Volatiles were removed under reduced pressure.
1N HCI and ethyl acetate were added to the residue; the organic layer was
separated, washed twice with 1N HCI and brine, dried over MgSO4, filtered
and concentrated under reduced pressure to provide intermediate 82-b as a
yellow solid.
117

CA 02813299 2013-04-17
=
Step 2: Intermediate 82-c
To a solution of intermediate 82-b (18.29 g, 68.5 mmol) in acetonitrile (247
ml) and methanol (27.4 ml), cooled to 0 C, was added DIPEA (14.36 ml,
82.0 mmol) and a 2M solution of diazomethyl)trimethylsilane in hexanes
(37.7 ml, 75.0 mmol). After the addition was completed, the reaction was
stirred at room temperature overnight. Acetic acid (1.17 ml, 20.5 mmol) was
added, the reaction was stirred for 30 minutes and volatiles were removed
under reduced pressure. A saturated aqueous solution of NaHCO3 and ethyl
acetate were added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 82-c as a
yellow solid.
Synthesis of Intermediate 83-a:
Br Br
TEA
441k
NC
NC 43-d
0 \ N
CN H2N N
82-c 83-a
0
Scheme 83
To a solution of intermediate 82-c (2.0 g, 7.12 mmol) and TEA (1.98 ml,
14.23 mmol) in Et0H (3.50 ml) was added intermediate 43-cl=FICI (1.30 g,
8.54 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure to provide intermediate 83-a as a
yellow solid.
118

CA 02813299 2013-04-17
Synthesis of Compound 60:
Br 0 I. 0 0 =
NJOH0 40 0 N
NH2 41k s,õN
NC F Cul, Cs2CO3
Formamide
I "'N NC N N
H2N
N 1_
29-i
H2N
U0
83-a 84-a Compound 60
Scheme 84
Step 1: Intermediate 84-a
To a solution of intermediate 83-a (2.60 g, 7.12 mmol) and intermediate 29-1
(1.00 g, 4.18 mmol) in 1,4-dioxane (20.9 ml) were sequentially added N,N-
dimethylglycine (646 mg, 6.27 mmol), copper(I) iodide (398 mg, 2.09 mmol)
and cesium carbonate (4.09 g, 12.5 mmol). The reaction mixture was stirred
at reflux overnight, cooled to room temperature, diluted with ethyl acetate
and filtered over celite. A saturated aqueous solution of ammonium chloride
was added to the filtrate, the organic layer was separated, and the aqueous
phase was extracted twice with ethyl acetate. The combined organic extracts
were washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediate 84-a as a beige solid.
Step 2: Compound 60
Formamide (11.7 ml, 293 mmol) was added to intermediate 84-a (2.18 g,
4.18 mmol) and the reaction was stirred at 180 C overnight. Water and
ethyl acetate were added, the organic layer was separated, washed with
brine, dried over MgSO4, filtered and concentrated under reduced pressure.
119

CA 02813299 2013-04-17
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 60.2HCI as white solid. MS (m/z)
M+H= 551.2
Synthesis of Compound 73:
F
F
Br 0 el 0 0 =
I 0 0
F /N---z/ NH2 . --)---\
1\1 N
NC
Cul, Cs2CO3 HC(OMe)3 F F
_________________ ).
I N m ' _________________ N1LT
\ NC N
1 \,N
\ Nr NH3
H2N N 34-d y..,.\ H2N N
(--()I
83-a 85-a Compound 73
Scheme 85
Step 1: Intermediate 85-a
To a solution of intermediate 83-a (2.60 g, 7.12 mmol) and intermediate 34-
d (1.0 g, 4.18 mmol) in 1,4-dioxane (20.9 ml) were sequentially added N,N-
dimethylglycine (646 mg, 6.27 mmol), copper(I) iodide (398 mg, 2.09 mmol)
and cesium carbonate (4.09 g, 12.5 mmol). The reaction mixture was stirred
at reflux overnight, cooled to room temperature, diluted with ethyl acetate
and filtered over celite. A saturated aqueous solution of ammonium chloride
was added to the filtrate, the organic layer was separated, and the aqueous
phase was extracted twice with ethyl acetate. The combined organic extracts
were washed with brine, dried over MgSO4, filtered and concentrated under
reduced pressure. Purification by silica gel chromatography provided
intermediate 85-a as a beige solid.
Step 2: Compound 73
Intermediate 85-a (195.0 mg, 0.38 mmol) and trimethyl orthoformate (1.26
ml, 11.59 mmol) were heated at 110 C for 3 hours. Excess trimethyl
120

CA 02813299 2013-04-17
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (3.86 ml, 7.72 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 73.HCI as white solid. MS (m/z)
M+H= 534.1
Synthesis of Compound 95:
F
F
Br 0 el 0 0 .
0
4k ,NIOH 40 1 N
NH2
/N
NC F Cul, Cs2CO3
__________________ > F ., HC(OMe)3
__________________________________________________ N . O_:21 " F
I \, H2N N NC ,,, 1
NH3
31-d \ Nr. [,,, ,N
H2N
N
11)____,
(--)1,
U0 U0
83-a 86-a Compound 95
Scheme 86
Step 1: Intermediate 86-a
To a solution of intermediate 83-a (200 mg, 0.54 mmol) and intermediate
31-d (177 mg, 0.65 mmol) in 1,4-dioxane (3.65 ml) were sequentially added
N,N-dimethylglycine (127 mg, 1.23 mmol), copper(I) iodide (7.8 mg, 0.41
mmol) and cesium carbonate (714 mg, 2.19 mmol). The reaction mixture
was stirred at reflux overnight, cooled to room temperature, diluted with
ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated, and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
121

CA 02813299 2013-04-17
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 86-a=HCI as a beige solid.
Step 2: Compound 95
Intermediate 86-a=HCI (284 mg, 0.54 mmol) and trimethyl orthoformate
(3.90 ml, 35.6 mmol) were heated at 110 C for 1 hour. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (3.91 ml, 27.4 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 95.2HCI as white solid. MS (m/z)
M+H= 545.2
Synthesis of Intermediate 87-a:
Br Br
4101 TEA O
,.
F NC F
NC 42-c
0 I \ N
CN I-12N N
82-c 87-a a
Scheme 87
To a solution of intermediate 82-c (1.00 g, 3.56 mmol) and TEA (1.09 ml,
7.83 mmol) in Et0H (3.50 ml) was added intermediate 42-c (583 mg, 4.27
mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles were
removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, filtered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 87-a as beige solid.
122

CA 02813299 2013-04-17
Synthesis of Compound 92:
F
F
Br 0 el 0 0 =
. ''N -)LOH 40 r\,N
/N--Zi NH2 10
NC F Cul, Cs2CO3 F
_________________ 1.- HC(OMe)3
F
NC "
I \,N K1 NH3
34-d \ Nr L I pi
H2N f \l,..,_ N NL
c-J H2N 0
U
87-a 88-a Compound 92
Scheme 88
Step 1: Intermediate 88-a
To a solution of intermediate 87-a (452 mg, 1.29 mmol) and intermediate
34-d (368 mg, 1.42 mmol) in 1,4-dioxane (5.20 ml) were sequentially added
N,N-dimethylglycine (400 mg, 3.88 mmol), copper(I) iodide (247 mg, 1.29
mmol) and cesium carbonate (1.26 g, 3.88 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated, and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided intermediate 88-
a=HCI as a beige solid.
Step 2: Compound 92
Intermediate 88-a=HCI (124.0 mg, 0.25 mmol) and trimethyl orthoformate
(935 pi, 7.63 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (2.54 ml, 5.09 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
123

CA 02813299 2013-04-17
HCl/methanol gradient provided compound 92.2HCI as a beige solid. MS
(m/z) M+H= 518.2
Synthesis of intermediate 89-a:
Br Br
401
_____________________________________________________ , *
F TEA NC F
NC 44-c
0 l \ N
CN H2N N
)----
82-c 89-a
Scheme 89
To a solution of intermediate 82-c (2.0 g, 7.12 mmol) and TEA (2.18 ml,
15.65 mmol) in Et0H (7.12 ml) was added intermediate isopropylhydrazine
hydrochloride (944 mg, 8.54 mmol) and the reaction was then stirred for 2
hours at 100 C. Volatiles were removed under reduced pressure. A
saturated aqueous solution of ammonium chloride and ethyl acetate were
added to the residue, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated under reduced pressure.
Purification by silica gel chromatography provided intermediate 89-a as a
beige solid.
Synthesis of Compound 98:
F
F
Br 0OO 0 =
1 0 0
iii .--14).1''ON 40 Cr\,N
F
F /N --S HC(OMe)3 NH2 . .----\-- m
NC Cul, Cs2CO3
, N F
l \,N NC õI 1
\ NH3 i_ ,N
34-d N :. N\
H2N Nj H2N---
1."--
89-a 90-a Compound 98
124

CA 02813299 2013-04-17
Scheme 90
Step 1: Intermediate 90-a
To a solution of intermediate 89-a (400 mg, 1.24 mmol) and intermediate
34-d (352 mg, 1.36 mmol) in 1,4-dioxane (4.9 ml) were sequentially added
N,N-dimethylglycine (383 mg, 3.71 mmol), copper(I) iodide (236 mg, 1.24
mmol) and cesium carbonate (1.21 g, 3.71 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated, and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by reverse phase chromatography
eluting with a 1% aqueous HCl/methanol gradient provided intermediate 90-
a=FICI as beige solid.
Step 2: Compound 98
Intermediate 90-a=HCI (208 mg, 0.45 mmol) and trimethyl orthoformate
(1.47 ml, 13.4 mmol) were heated at 110 C for 3 hours. Excess trimethyl
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (4.48 ml, 8.96 mmol). The mixture was stirred at room
temperature for 3 days and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 98.2HCI as a beige solid. MS
(m/z) M+H= 492.2
Synthesis of Intermediate 91-d:
=
125

CA 02813299 2013-04-17
Br Br
Br Br F F is
F 0 oxalyl chloride F 0
________________ ).- malononitrile =TMS-diazomethane
NaOH
CN CN
HO '=-= Me0
0 OH 0 Cl CN CN
91-a 91-b 91-c 91-d
Scheme 91
Step 1: Intermediate 91-b
To a suspension of 4-bromo-3-fluorobenzoic acid (15.0 g, 68.5 mmol) in
dichloromethane (342.0 ml) was added DMF (106.0 pl, 1.37 mmol) and
oxaly1y1 chloride (8.99 ml, 103.0 mmol). The solution was then stirred at
room temperature for 3 hours. Volatiles were removed under reduced
pressure to provide intermediate 91-b as a yellow solid.
Step 2: Intermediate 91-c
To a solution of intermediate 91-b (16.27 g, 68.5 mmol) in toluene (85.0 ml)
and THF (8.5 ml) cooled to -10 C were sequentially added malononitrile
(4.75 g, 71.9 mmol) and DIPEA (23.93 ml, 137 mmol) drop wise over a
period of 15 minutes. The reaction was stirred at 0 C for 2 hours and room
temperature for an additional 2 hours. Volatiles were removed under reduced
pressure. Ethyl acetate and 1N HCI were added, the organic layer was
separated, washed with brine, dried over MgSO4, filtered and concentrated in
vacuo to provide intermediate 91-c as a yellow solid.
Step 3: Intermediate 91-d
To a solution of intermediate 91-c (18.29 g, 68.5 mmol) in acetonitrile
(247.0 ml) and Me0H (27.4 ml) cooled to 0 C were sequentially added
DIPEA (14.36 ml, 82.0 mmol) and a 2M solution of TMS-Diazomethane in
hexanes (37.7 ml, 75.0 mmol). The reaction was then stirred for 5 hours at
room temperature. Acetic acid (1.17 ml, 20.55 mmol) was then added and
the reaction was stirred for an additional 30 minutes. Volatiles were removed
126

CA 02813299 2013-04-17
under reduced pressure. A saturated aqueous solution of NaHCO3 and ethyl
acetate was added, the organic layer was separated, washed with brine,
dried over MgSO4, filtered and concentrated in vacuo. Purification by silica
gel
chromatography provided intermediate 91-d as a beige solid.
Synthesis of Intermediate 92-a:
Br Br
F
TEA
NC NC
0
43-d
CN
H2N I \N
91-d 92-a
Scheme 92
To a solution of intermediate 91-d (2.0 g, 7.12 mmol) and TEA (1.98 ml,
14.23 mmol) in Et0H (3.50 ml) was added intermediate 43-d.HCI (1.30 g,
8.54 mmol) and the reaction was then stirred for 2 hours at 100 C. Volatiles
were removed under reduced pressure. A saturated aqueous solution of
ammonium chloride and ethyl acetate were added to the residue, the organic
layer was separated, washed with brine, dried over MgSO4, ffitered and
concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 92-a as a beige solid.
Synthesis of Compound 59:
127

CA 02813299 2013-04-17
Br 0 I. 0 0
0
F 0
j=LOH
8,711
Cul, Cs2CO3
Formamide NH2
NC
I "'NI NC \"N
__________________________________________________ N
29-i N I ,N
N
-12N N)..Th
H2N
U0
92-a 93-a Compound 59
Scheme 93
Step 1: Intermediate 93-a
To a solution of intermediate 92-a (2.60 g, 7.12 mmol) and intermediate 29-1
(1.0 g, 4.18 mmol) in 1,4-dioxane (20.90 ml) were sequentially added N,N-
dimethylglycine (646 mg, 6.27 mmol), copper(I) iodide (398 mg, 2.09 mmol)
and cesium carbonate (4.09 g, 12.54 mmol). The reaction mixture was
stirred at reflux overnight, cooled to room temperature, diluted with ethyl
acetate and filtered over celite. A saturated aqueous solution of ammonium
chloride was added to the filtrate, the organic layer was separated, and the
aqueous phase was extracted twice with ethyl acetate. The combined organic
extracts were washed with brine, dried over MgSO4, filtered and concentrated
under reduced pressure. Purification by silica gel chromatography provided
intermediate 93-a as a beige solid.
Step 2: Compound 59
Formamide (11.67 ml, 293.0 mmol) was added to intermediate 93-a (2.18 g,
4.18 mmol) and the reaction was stirred at 180 C overnight then cooled to
room temperature. Water and ethyl acetate were added, the organic layer
was separated, washed with brine, dried over Mg504, filtered and
concentrated under reduced pressure. Purification by reverse phase
128

CA 02813299 2013-04-17
chromatography eluting with a 1% aqueous HCl/methanol gradient provided
compound 59.2HCI as a yellow solid. MS (m/z) M+H= 551.1
Synthesis of Compound 72:
F
F
Br 0 Si 0 o =
F 0 F
th
F -7`0H
N-(/ .- it
NH, ,..N N
NC
Cul, Cs2CO3 HC(OMe)3
i "N NC N m
34-d \ NI NH3
N)_Th
H2N
H2N
(---1;)
U0 U0
92-a 94-a Compound 72
Scheme 94
Step 1: Intermediate 94-a
To a solution of intermediate 92-a (291.0 mg, 0.79 mmol) and intermediate
34-d (227.0 mg, 0.87 mmol) in 1,4-dioxane (3.2 ml) were sequentially
added N,N-dimethylglycine (247.0 mg, 2.39 mmol), copper(I) iodide (152.0
mg, 0.79 mmol) and cesium carbonate (780 mg, 2.39 mmol). The reaction
mixture was stirred at reflux overnight, cooled to room temperature, diluted
with ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated, and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided intermediate 94-a=FICI as a beige solid.
Step 2: Compound 72:
Intermediate 94-a=HCI (56.0 mg, 0.11 mmol) and trimethyl orthoformate
(363 pl, 3.32 mmol) were heated at 110 C for 3 hours. Excess trimethyl
129

CA 02813299 2013-04-17
orthoformate was removed in vacuo and the residue was treated with 7.0 N
ammonia in Me0H (1.10 ml, 2.21 mmol). The mixture was stirred at room
temperature overnight and volatiles were removed under reduced pressure.
Purification by reverse phase chromatography eluting with a 1% aqueous
HCl/methanol gradient provided compound 72.2HCI as a white solid. MS
(m/z) M+H= 534.2
Synthesis of Compound 68:
F
Br
0 411t
, 0=

0--......,
, \N
NH2 4410 N)-LOH NH2 *
---j
N \ Cul, Cs2CO3 N.:
N
l , _____________ 0, N'"N
N N)_\ I ,
\--__)
.
0 39-b N
U
0
17-a Compound 68
Scheme 95
To a solution of intermediate 17-a (300.0 mg, 0.80 mmol) and intermediate
39-b (177.0 mg, 0.80 mmol) in 1,4-dioxane (3.6 ml) were sequentially
added N,N-dimethylglycine (372.0 mg, 3.61 mmol), copper(I) iodide (229.0
mg, 1.20 mmol) and cesium carbonate (1.04 g, 3.21 mmol). The reaction
mixture was stirred at reflux overnight, cooled to room temperature, diluted
with ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated, and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided compound 68.2HCI as a beige solid. MS (m/z) M+H= 514.2
130

CA 02813299 2013-04-17
Synthesis of Compound 69:
F
Br
0 .
I 0 0
----)r-N
NH2 * N).LOH NH2 40 N\j,_
N \ N Cul, Cs2CO3
I, \
N N)__\ L I ,N
U0 40-b N
)
0
17-a Compound 69
Scheme 96
To a solution of intermediate 17-a (300.0 mg, 0.80 mmol) and intermediate
40-b (177.0 mg, 0.80 mmol) in 1,4-dioxane (3.6 ml) were sequentially
added N,N-dimethylglycine (372.0 mg, 3.61 mmol), copper(I) iodide (229.0
mg, 1.20 mmol) and cesium carbonate (1.04 g, 3.21 mmol). The reaction
mixture was stirred at reflux overnight, cooled to room temperature, diluted
with ethyl acetate and filtered over celite. A saturated aqueous solution of
ammonium chloride was added to the filtrate, the organic layer was
separated, and the aqueous phase was extracted twice with ethyl acetate.
The combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% aqueous HCl/methanol gradient
provided compound 69.2HCI as a beige solid. MS (m/z) M+H= 514.2
Synthesis of Compound 63:
131

CA 02813299 2013-04-17
Br
0
NH2 Os0
111j-LOH 0
NH2 4410 4110
INV \ Cul, Cs2CO3
1 'N N
N 1 'N
0 41-b N
0
17-a Compound 63
Scheme 97
A solution of intermediate 17-a (437 mg, 1.17 mmol), intermediate 11-c
(255 mg, 1.17 mmol), quinolin-8-ol (34 mg, 0.23 mmol), copper (I) iodide
(44.0 mg, 0.23 mmol) and cesium carbonate (761 mg, 2.33 mmol), in
dimethylacetamide (1.2 ml), was degassed with argon for 10 minutes,
heated in a sealed tube at 140 C overnight and then cooled to room
temperature. Water and ethyl acetate were added, the organic layer was
separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by reverse
phase chromatography eluting with a 1% HCl/methanol gradient provided
compound 63.1-1CI as a yellow solid. MS (m/z) M+H= 512.2
Synthesis of Compound 67:
132

CA 02813299 2013-04-17
N
i
F0 Br K2CO3 F Br Cul, DEA, Pd(PPh3)2Cl2 F 0 NI\
_________________ * __
MOMCI Vi 1 Nr
----_:-----XN1
OH OMOM OMOM
I
98-a 98-b 98-c 98-d
N N
F I F i
H2 Pd/C N HCI
40 N
98-d ______________ )= 1
OMOM OH
98-e 98-f
F
Br
0 49
0 0
NH2 O
NH2 41* N / N
..--- -...../
NI ' \N Cul
I'
N NI)Th . I ,N
98-f N NI)______\
S---.0)
U
17-a 0 compound 67
Scheme 98
Step 1: Intermediate 98-b
To a solution of 3-bromo-5-fluorophenol, 98-a (25.00 g, 131.0 mmol), in
acetone (654 ml) were sequentially added K2CO3 (27.10 g, 196.0 mmol) and
chloro(methoxy)methane (11.59 g, 144.0 mmol). The reaction was stirred at
room temperature for 2 hours and then filtered. The filtrate was concentrated
under reduced pressure to provide intermediate 98-b as a yellow oil.
Step 2: Intermediate 98-d
To a solution of intermediate 98-b (2.00 g, 8.51 mmol) in DMF (17.02 ml),
were sequentially added diethylamine (975 pl, 9.36 mmol), copper(I)iodide
(65 mg, 0.34 mmol) and 5-ethyny1-1-methyl-1H-imidazole 98-c (948 mg,
133

CA 02813299 2013-04-17
8.93 mmol). After copper(I)iodide has completely dissolved,
Dichlorobis(triphenylphosphine)palladium(II) (119 mg, 0.17 mmol) was
added and the reaction was then stirred at 100 C overnight and then cooled
to room temperature. Water and ethyl acetate were added, the organic layer
was separated, the aqueous layer was extracted twice with ethyl acetate, the
combined organic extracts were washed with brine, dried over MgSO4,
filtered and concentrated under reduced pressure. Purification by silica gel
chromatography provided intermediate 98-d as a beige solid
Step 3: Intermediate 98-e
A solution of intermediate 98-d (600.0 mg, 2.3 mmol) in methanol was
treated with 10% palladium on carbon (245.0 mg, 0.01 mmol) and purged
with H2. The solution was stirred under H2 (1 atm) overnight before being
filtered through celite. The filtrate was concentrated in vacuo to provide
intermediate 98-e as a yellow oil.
Step 4: Intermediate 98-f
To a solution of intermediate 98-e (2.4 g, 9.08 mmol) in Me0H (17 ml) was
added 4N HCI in dioxane (2.76 ml, 91 mmol). The reaction mixture was
stirred at room temperature for 2 hours. Volatiles were removed under
reduced pressure, diethyl ether was added to the residue; a precipitate
formed and was collected by filtration to provide intermediate 98-f=HCI as a
white solid.
Step 5: Compound 67
A solution of intermediate 17-a (292 mg, 0.78 mmol), intermediate 98-f=HCI
(200 mg, 0.78 mmol), tetramethylheptane-3,5-dione (287 mg, 1.56 mmol),
copper (I) iodide (148 mg, 0.78 mmol) and cesium carbonate (762 mg, 2.33
mmol), in NMP (3.9 ml), was degassed with argon for 10 minutes, heated in
a sealed tube at 120 C overnight and then cooled to room temperature,
diluted with ethyl acetate and filtered over celite. A saturated aqueous
134

CA 02813299 2013-04-17
solution of ammonium chloride was added to the filtrate, the organic layer
was separated, and the aqueous phase was extracted twice with ethyl
acetate. The combined organic extracts were washed with brine, dried over
MgSO4, filtered and concentrated under reduced pressure. Purification by
reverse phase chromatography eluting with a 1% HCl/methanol gradient
provided compound 67.2HCI as a yellow solid. MS (m/z) M+H= 514.3
Compounds 7, 8, 11, 13, 14, 19, 21, 24 to 28, 33, 34, 37 to 51, 53, 56, 61,
62, 64, 66, 70, 71, 74-77, 79 to 84, 86 to 89, 94, 96, 104, 105, 107 to 112,
115, 116, 119, 121, 122, 123, 124, 126, 127, 131, 132, and 133 were
prepared using similar methods to those described above.
Table 1 summarizes representative compound of Formula 1.
Table 1: Example Compounds of Formula 1
Compound Structure MS (m/z)
o,
0
1 NH2 * [M+H]=410.2
N.-- \ O
1 ,N
N N
H
o,
0
NH2 4It
2
40 [M+H]=478.2
N' 1 \
I N
N N),õ_,
U
135

CA 02813299 2013-04-17
o,
0
NH2 *
0[M+H]=593.1
3 N \
L 1 ,N
NN,_____
e
0--.
o,
0
NH2 *
4
* [M+H]=493.1
N" \N
1
N N,
òH
o,
0
NH2 *

N" * [M+H]=547.1
I \N
'
N N
136

CA 02813299 2013-04-17
o,
0
NH2 44*
6 fh[M+H]=535.1
N -' \ N
I '
N N
o,
0
NH2 4.
O[M+Hr=563.1
N N
----\
0 =
0
NH2 4k
8 N '' , \ O [M+H]=563.1
I ,N
N N
L\N---e
i----
137

CA 02813299 2013-04-17
,
0
NH2 4.
=
9 ci [M+H]=512.2
N \
I
N N
o,
0
NH2 it
[M+H]=508.1
, \ ¨0
I ,N
N N
0
NH2 410
*
11 0, [M+H]=508.2
\N
I '
N
o*
CN
0
NH2 41i =
12 [M+H]=503.2
N' \N
N N
138

CA 02813299 2013-04-17
o,
0
NH2. .
13 [M+Hr=478.2
N \N
I '
N NL
U
0 =
NH2 44* S N
14 [M+Hr=485.2
N' \N
I '
U
o,
0 CN
NH2. .
15 [M+Hr=503.3
N' \N
l ,
N NL
U
o,
0
16 NH2 0 fb [M+H]=424.2
N' \N
l ,
N N
\
139

CA 02813299 2013-04-17
o,
CN
0
17 NH2 fi fa [M+H]=449.3
N' , \
L 1 ,N
1\1 N
\
o,
18 NH2 40 0--)..______.
[M+H]=445.1
N
N' \N
N l N'
\
o =
om_-.//____\
19 NH2 4. N
S- [M+H]=431.4
N" , \
L 1 ,N
r\I NI
\
o,
CF3
0
20 NH2 44, 401 [M+H]=492.1
N", \
L 1 ,N
'N N
\
140

CA 02813299 2013-04-17
o,
0
NH2 .

21 [M+H]=494.2
N \N
I ,
N
U
0
o,
CN
0
NH2 4.
0
22
N [M+Hr=519.2
' \
L I ,N
N )....ThN
U
0
o,
CF3
0
NH2 4. 40
23[M+H]=562.1
N' \N
I ,
N N)_Th
U
0
141

CA 02813299 2013-04-17
0
NH2 *
24 [M+H]=501.2
,N
N N
0
0 =
0 CN
NH2 410 4419
25 N \N [M+H]=560.2
'
N N1)
UTh(
0
0 = CF3
0
NH2 44*
26 \ N [M+H]=603.1
I ,
N
0
142

CA 02813299 2013-04-17
0 =
OTh-
S
NH2 \N*
27 N' \ N [M+H]'=542.2
I'
N N_
UN5(
0
O * CN
0
NH2 O41Ik
28 N' \ N [M+H]4=560.2
I'
N N3.
Urs1(
0
O fal CF3
0
NH2 * *
29 [M+H]'=546.2
N' \
L 1 N
U
o,
CN
0
30 NH2 ii
O [M+H]4=449.4
N' , \
1 ,N
N N
\
143

CA 02813299 2013-04-17
o,
CF3
0
31 NH2 * 44Ik [M+H]=492.1
N' \N
1 ,
N N
\
o,
0 CF3
NH2 .
44k
32 [M+H]=546.1
N' \
1 ,N
N N
b
o,
0 CF3
NH2 =
=
33 NJ' \
l [M+Hr=603.1
L ,N
N N
oN-{
0
o,
NH2 * S N
34 [M+H]=488.3
N' \N
1.l ,
N N\
-----\
N---
144

CA 02813299 2013-04-17
o,
0
NH2. NC 44Ik
35 [M+H]=519.2
\
I ,N
N N'
K)
o,
0
NH2 * F3C =
36 [M+H]=562.2
N \N
I'
N 14),Th
0
o,
NH2 441k
37 N [M+Hr=499.1
N' \N
1 '
c----i
145

CA 02813299 2013-04-17
44k
NH2
38 [M+Hr=515.1
\
L ,N
ymN
fi
NH2
39 [M+Hr=514.2
,N
Nv_
o,
NH2 441
L ,N [M+Hr=543.1
(N--)
\--N1
146

CA 02813299 2013-04-17
0--)1
NH2 41*
41 N \N [M+Hr=522.1
N'
o,
NH2 44
42 N \ N [M+H]=521.2
N#
0¨\
( µj
NH2
43 [M+H]=500.2
,N
N
147

CA 02813299 2013-04-17
o,
NH2 0--\ 4* US)
NI/
44 NI \ [M+H]=530.1
I N
'
N Niv
-------\
--C)
o,
0
45 NH2 0 40 [M+H]=452.1
NI' \N
I '
N N
/'0
F
o,
46 NH2 44k N [M+H]=519.1
N' \
/ N
'
N NI)._.....\
U0
148

CA 02813299 2013-04-17
fi
)
S
NH2
47
L ,N [M+Fi]=542.1
1%1
/C)
fk
NH2 10
48 [M+Hr=498.2
N
,N
N N)_Th
U0
0 =
NH2
49 , [M+H]=600.1
L ,N
Thµl r=L
0-<
149

CA 02813299 2013-04-17
4Ik
, S
50 NH2 =[M+H]=503.2
r%V \
,N
N
o,
NH2 Os
51 [M+H]=500.2
N
'
N N
L\NH
o,
NH2 S N
52 [M+H]=562.1
N'N
I'
N N\
\-0
150

CA 02813299 2013-04-17
o,
OTh---
N
NH2
53[M+H]=544.2
N'' \N
I'
N rµI___
----NO0
F
0 =
0
NH2. --==---- \-
54
sN/1µ1 [M+Hr=533.1
/
N- \
l N1
, 1
N N)___\
---'0)
F
o,
OTh-\--
SK./N
NH2 41
[M+H]=576.2
N.-- \N
1'
N N___
-\----N3
151

CA 02813299 2013-04-17
F
o,
0-Al__
NH2 . N [M+H1=532.2
56
N'
N 1 '
N N
- F
o,
NH2 41*
[M+H]=546.2
57 \
NV \N
1 '
N N\
----\
Nc13
F
o,
58 NH2
OTh.,__.\
N1 [M+H]=517.2
=
1
N"
152

1 '
_.---1
152

CA 02813299 2013-04-17
*
NH2 40. SN
59
[M+Hr=551.1
\N
'
N Nym
O*
60 NH2
[M+H]=551.2
N" \N
'
N N)Th
o*
61NH2 O[M+H]=463.2
S,,K/N
N" \
N'N
153

CA 02813299 2013-04-17
0 4Ik
F
0---\-
SK/
NH2 441, N
1 [M+H]=533.2
62
N' \N
I'
N Ny.Th
--- )0
F
o,
0
NH2 40 gli [M+H]=512.2
63
N' \
I N
'
N NI)...Th
U
0
F
0 . .V
64
S/
NH2 41* 1\1 [M+H]=535.2
\
N \ N
l ,
N NI).._\
U0
154

CA 02813299 2013-04-17
F
o,
0
65 NH2 O [M+Hr=527.2
N'/ \N
I '
U0
F
o,
66 NH2 O O [M+H]=510.2
N'' \N
I'
N N)___\
\--- )0
F
o,
67 NH2 Ok [M+H]=514.3
,.N ,..,N
N./\N
I'
N )...____\N
----0)
155

CA 02813299 2013-04-17
F
o,
0
68 NH2 411
-f-)=1 [M+Hr=514.2
N7 \N N-j
1 IV'
N
O
F
0 .
OThr__N
69 NH2 44, Nj_ [M+Hr=514.2
N7 \N
1 '
---- )0
0 49
NH2 4.OTh----\
S/I\I
70 F \ [M+Hr=533.2
N' \N
1 NI
N
O
156

CA 02813299 2013-04-17
F
o,
0
NH2 4.1
-_
71 _-:--.\.- N [M+H]=516.1
.1µ1
\
N
N N'
O
F
F 0 .
72 NH2 0 ,N.,N1
[M+H]=534.2
N \ N
l ,
N N),.._\
\--- )0
F
0 =
,,õNõN
73 NH2 . [M+Hr=534.1
F
N-- \N
I'
N N1).Th
Q
157

CA 02813299 2013-04-17
F
o,
0
NH2 .
74 --:-.---- A [M+H]=558.2
r.-11 N
I\V \N
I / ----
N 11
a
0
F
NH2 410 46:1D [M+Hr=518.1
N '7 \
1\1 1 'IV
N
o
0
F
o,
0
NH2 . _--,-L--_ AN [M+Hr=592.1
76
I\
N V \ ./'
N
No 0
0
158

CA 02813299 2013-04-17
F
0
0
NH2 ilk
77 -----\ [M+Hr=570.2
N \
I N Or`c',N1 N NI
F
o,
78 NH2 0 8/1=1
1 [M+H]=491.2
N \N
1 '
N N\
7.----
F
o,
79 NH2 0 NIN [M+Hr=474.2
r=V \
L I ,N
Th N\
7----
159

CA 02813299 2013-04-17
F
0 4,
NH2 11*

80 [M+H]=511.2
N 1 \N \1N
N I N'
o
0
F
o,
OTh--\-
81 NH2 O S/N1
1 [M+H]=493.2
N-' \
I'N
N N\._
----\
OH
F
o,
O OTh,...._\
82 NH2 _.
,,N.,1\1 [M+H]=500.2
I '
N N)........,
..---]
160

CA 02813299 2013-04-17
F
o,
0
NH2 10
83 ------\-- [M+H]=560.2
N /N1
NV \ r
N I N
N 0
0
F
o,
0)------
84 NH2 O
N¨ [M+H]=511.2
I
N' \N '
N N).....,..,
U
F
o,
O\_\
NH2

\ [M+H]=485.2
85 NH2 4111 N--
N' \N
I '
N N\_
7----
161

CA 02813299 2013-04-17
F
0
NH2 441i
86 [M+H]=511.2
IµV \N N\/
I NI'
O
F
0
0
NH2 441) ---_,:--\_. [M+Fir=530.2
87
N /NI
N \N r
N 1 N'
o
0
F
o,
0
88 NH2 411
/ \
N
[M+Hr=487.2
N'' \N
1 ,
N N\_
-----\
OH
162

CA 02813299 2013-04-17
F
89 NH2 O
F [M+H]'=536.1
\N
I'
N N)Th
Q
_
F
O,
0--\&._
, N
90 NH2 441 N [M+H]'=476.2
N' \N
iN '
Nv
----A
OH
F
O,
0
NH2 0
91 [M+Hr=543.1
N' \
1_ 1 ,N
i=I N
a
0
163

CA 02813299 2013-04-17
F
o,
,..,
92 NvI \N F N" NH2 411 [M+H]=518.2
'
ci
F
0 40
0
NH2 *
93 -7---\ [M+H]=502.2
N'' \ H N
r\i/'
I N'N
N
o
0
F
NH2
94
0
O0.
DD / \N
[M+H]'=529.2
N". \
1 N,N
N
O
164

CA 02813299 2013-04-17
F
o,
0
NH2 O , \ [M+H]=545.2
95 F / N
N'
IN
'
N
F
o,
0
/ \
N
96 NH2 O
[M+H]=501.2
N'I \N
,
N N\____,
\----OH
F
o,
0
NH2 =-,_-__
[M+H]=636.1
97 N /N
rµV " c
I N
N
0
a
0
=
165

CA 02813299 2013-04-17
F

NH2 411 0-N
98 [M+Hr=492.2
N-- F --N
iµ N'
F
o,
0
NH2 fh
99 __--_-\. [M+H]=546.2
NI." \
N I N r--
N HO-)
O
F
O,
SK/i`l
100 NH2 O
\ [M+H]=523.2
NV \
I N '
N
(
OH
166

CA 02813299 2013-04-17
F
o,
0
101 H2N *
/ \ N [M+H]=543.1
N' \N
I ' OH
N NI)......_\
U0
F
o,
0
102 NH2 O N [M+H]4=486.2
-/-"--\
N'
IN N'-c
'
N>
s-
F
o,
0--y,N
103 NH2 * N [M+H]=514.2
N' \
N N),___\
U
167

CA 02813299 2013-04-17
F
o,
0-).1..____
104 NH2 44* N [M+Hr=507.2
N ' \N
I

N'
N\_____
\--OH
F
O,
105 NH2 IA ,NN [M+Hr=494.1
F
N' \N
I '
N
---\
OH
_
F
O,
0)__
_
NH N
2 41
106 N-----c [M+H]=528.1
N' \N
I '
N Nim
'---- )0
168

CA 02813299 2013-04-17
F
o,
107 NH2 O
N'-'- [M+H]=512.2
N-' \
L I ,N
N 1`1)_,
U
F
o,
0
NH2 4
108 7----NI_____ [M+H]=530.2
N' \ N
I ,N
N N
o
0
_
F
o,
109 NH2 O
N' Sy/NI
N
I [M+H]=541.3
\
1 '
N 1)____/CI
C
OH
169

CA 02813299 2013-04-17
o,
0
110 NH2 [M+H]=488.1
N
I '
N
OH
fk
0
/ \ N
111 NH2 410 [M+H]=515.1
NN
I '
N
HO
o,
OTh==.\
112 NH2 40 . [M+H]=504.1
f\V
L ,N
HO
170

CA 02813299 2013-04-17
F
0 *
113 NH2 40 SK/ N [M+Hr=505.2
1
N' \N
I '
N
0
0
F
O,
0
----)--N
114 NH2 *
Nc [M+Hr=502.2
N' "N
I ,
N r`I.,..,,
\--OH
F
0 =
0
115 NH2 O [M+Hr=490.1
----______
N N
1 '
N N\_
---"\
OH
171

CA 02813299 2013-04-17
F
,
OTh..._:Th_
116 NH2 Os ,,.-N.,N [M+H]=490.2
N7 \N
I

N '
r`l...._,
V_OH
F
0 =
OTh"¨¨\¨
117 NH2 * SK/N1
\ [M+Hr=521.1
N7 \N
I '
HO
F
O,
0
NH2 41i
118 [M+Hr=516.2
L
N1 V 'N HI\J7/N
1
N NI'
172

CA 02813299 2013-04-17
F
o,
0
119 NH2fa [M+Hr=528.2
/-----\N
Ni "N N---;;.1\
N N'
F
0 =
0
120 NH2 41*--1 [M+H]=514.2
N ' \ N
I 'N
N
c-J
F
O,
OTh____\
121 NH2 * N1z/ N [M+Hr=518.1
N'
I ,N
N N\ i
'----/---
HO
173

CA 02813299 2013-04-17
F
O,
122 NH2 .N'-- [M+H]=516.1
N" \N
I '
HO
F
0 =
0
123 NH2 * i---Isl...___ [M+H]=488.2
N \ N
I ,N
N N\
/----
F
o,
0
124 NH2 fa
'.-----.-I [M+H]=530.1
N' , \
L 1 ,N \
1\1 N
\--70
174

CA 02813299 2013-04-17
F
o,
0
125 NH2 110 ...--..1 _-\- [M+H]=533.2
SK/N
N' \N
1 , \
N N7
F
o,
0
126 NH2 4) [M+H]=527.2
/ \ N
N' , \
,N
N N
--i0
F
o,
NH2 =127
S.,,i//N [M+Hr=505.2
1
Nv \N
I '
N 1=1\__
/ \---
175

CA 02813299 2013-04-17
F
0 =
0
128 NH2 * [M+Hr=501.1
N'i \
I ,N
N N\
1--
F
O,
)N--
129 0 0
-----N
H2N
[M+H]=500.1
---
N' \N
I '
F
o,
0---)__
N
130 NH2 * Ni."-c [M+H]=518.1
N' \
1 ,N
N NOH
C
OH
176

CA 02813299 2013-04-17
F
o,
OTh----\-
131 NH2 0 S(/11
\ [M+H]=497.2
NV \N
I'
N 1\1\
D3Ct-CD3
F
0 4. DD
0"--\
132 NH2 40 S,,//N [M+H]=493.2
\
N ' \N
I =
7----
F
0 =
0
133 NH2 Os ft [M+H]=470.1
N-- \
I 'N
N N\
7-----
177

CA 02813299 2013-04-17
Kinase Binding
Btk Kinase Inhibition Assay
Fluorescence polarization-based kinase assays were performed in 384 well-
plate format using histidine tagged recombinant human full-length Bruton
Agammaglobulinemia Tyrosine Kinase (Btk) and a modified protocol of the
KinEASE TM FP Fluorescein Green Assay supplied from Millipore. Kinase
reaction were performed at room temperature for 60 minutes in presence of
250 DM substrate, 10 OM ATP and variable test article concentrations. The
reaction was stopped with EDTA/kinase detection reagents and the
polarization measured on a Tecan 500 instrument. From the dose-response
curve obtained, the 1050 was calculated using Graph Pad Prisms using a
non linear fit curve. The Km for ATP on each enzyme was experimentally
determined and the Ki values calculated using the Cheng-Prusoff equation
(see: Cheng Y, Prusoff WH. (1973) Relationship between the inhibition
constant (K1) and the concentration of inhibitor which causes 50 per cent
inhibition (IA of an enzymatic reaction". Biochem Pharmacol 22 (23): 3099-
108).
k1 values are reported in Tables 2:
178

CA 02813299 2013-04-17
Table 2: Inhibition of Btk
Comp 1(1 Comp ki Comp Ici Comp lc, Comp ki
ound (nM) ound (nM) ound (nM) ound (nM) ound (nM)
1 a 31 a 61 a 91 a 121 a
2 a 32 a 62 a 92 a 122 a
3 a 33 a 63 a 93 a 123 a
4 a 34 a 64 a 94 - 124 a
a 35 a 65 a 95 a 125 a
6 a 36 a 66 a 96 a 126 a
7 a 37 a 67 a 97 a 127 a
8 a 38 a 68 a 98 a 128 a
9 a 39 a 69 a 99 a 129 a
a 40 a 70 a 100 a , 130 a
11 a 41 a 71 a 101 a 131
12 a 42 a 72 a 102 a 132 -
13 a 43 a 73 a 103 a 133 -
14 a 44 a 74 a 104 a
a 45 b 75 a 105 a
16 a 46 a 76 a 106 a
17 a 47 a 77 a 107 a
18 a 48 a 78 a 108 a
19 a 49 a 79 a 109 a
a 50 a 80 a 110 a
21 a 51 a 81 a 111 a
22 a 52 a 82 a 112 a
23 a 53 a 83 a 113 a
24 a 54 a 84 a 114 a
a 55 a 85 a 115 a .
26 a 56 - 86 a 116 a
27 a 57 a 87 a 117 a
28 a 58 a 88 a 118 a
29 a 59 a 89 - 119 a
a 60 a 90 a 120 a
a - Less than 100 nM; b - less than 1000 nM, c - more than 1000 nM
179

CA 02813299 2013-04-17
Splenic Cell Proliferation Assay
Splenocytes were obtained from 6 week old male CD1 mice (Charles River
Laboratories Inc.). Mouse spleens were manually disrupted in PBS and
filtered using a 70um cell strainer followed by ammonium chloride red blood
cell lysis. Cells were washed, resuspended in Splenocyte Medium (HyClone
RPMI supplemented with 10% heat-inactivated FBS, 0.5X non-essential
amino acids, 10mM HEPES, 50uM beta mercaptoethanol) and incubated at 37
C, 5% CO2 for 2h to remove adherent cells. Suspension cells were seeded in
96 well plates at 50,000 cells per well and incubated at 37 C, 5% CO2 for lh.
Splenocytes were pre-treated in triplicate with 10,000 nM curves of Formula
1 compounds for 1h, followed by stimulation of B cell proliferation with
2.5ug/m1 anti-IgM F(ab1)2 (Jackson ImmunoResearch) for 72h. Cell
proliferation was measured by Cell Titer-Glo Luminescent Assay (Promega).
EC50 values (50% proliferation in the presence of compound as compared to
vehicle treated controls) were calculated from dose response compound
curves using GraphPad Prism Software.
EC50 values are reported in Table 3:
180

CA 02813299 2013-04-17
Table 3: Inhibition of splenic cell proliferation
Compo EC50 Comp EC50 CornEC50 Comp EC50 Comp EC50
poun
und (nM) ound (nM) d (nM) ound (nM) ound (nM)
1 b 31 b 61 b 91 a 121 b
2 b 32 a 62 a 92 a 122 b
3 b 33 a 63 a 93 b 123 a
4 b 34 b 64 a 94 a 124 b
a 35 a 65 a 95 a 125 a
6 a 36 a 66 b 96 a 126 b
7 b 37 a 67 b 97 b 127 a
8 a 38 a 68 a 98 a 128 a
9 b 39 b 69 a 99 b 129 a
b 40 b 70 a 100 a 130 b
11 b 41 b 71 a 101 a 131
12 b 42 a 72 b 102 a 132 -
13 a 43 b 73 a 103 a 133 -
14 a 44 a 74 b 104 a
a 45 b 75 a 105 b
16 b 46 a 76 b 106 a
17 b 47 a 77 a 107 , a
18 a 48 a 78 a 108 a
19 b 49 a 79 a 109 , a
a 50 a 80 b 110 b
21 a 51 a 81 a 111 b
22 a 52 a 82 a 112 b
23 a 53 a 83 b 113 a
24 a 54 a 84 a 114 b
a 55 a 85 a 115 b
26 a 56 b 86 b 116 a
27 a 57 b 87 a 117 a
28 a 58 a 88 a 118 b
29 a 59 a 89 a 119 b
a 60 a 90 b 120 a
a - Less than 100 nM; b - less than 1000 nM, c - more than 1000 nM
181

CA 02813299 2013-04-17
Methods: Mouse Arthus
Mouse Arthus studies were conducted as reported in Braselmann S, Taylor V,
Zhao H, Wang S, Sylvain C, Baluom M, Qu K, Herlaar E, Lau A, Young C,
Wong BR, Lovell S, Sun T, Park G, Argade A, Jurcevic S, Pine P, Singh R,
Grossbard EB, Payan DG, Masuda ES: R406 an orally available spleen
tyrosine kinase inhibitor blocks fc receptor signaling and reduces immune-
complex mediated inflammation. J Pharmacol Exp Ther, 2006, 319:998-
1008.
In summary, female Balb/c mice (6-7 weeks on arrival) were habituated to
the animal facility for at least 4 days. On the day of the experiment, animals

were pre-treated (t= minus 1 h) with compound or vehicle alone by gavage
(PO). At t=0, animals were injected intravenously (IV; 0.1 mL/mouse) with
saline containing chicken ovalbumin and Evan's blue (10 mg/mL of each).
Ten minutes later (t= 10 min), animals were anesthesized with isoflurane,
the dorsal surface was shaved and rabbit anti-chicken ovalbumin antibody
was then injected intradermally at one site on the right side of the animal
(25 pg in 30 pL). The same amount of isotype control antibody was then
injected on the left side.
The animals were then returned to their home cage and skin punches (8
mm) were collected from each injection site four hours later. The samples
were placed in 1 mL formamide overnight at 80 degrees C (1 skin biopsy per
1 mL formamide in a glass tube). The amount of Evan's blue in the
formamide solution was then assessed by spectrophotometry (630 nm) as a
measure of serum extravasation into the dermis.
Compounds 14, 15, 24, 46, 50, 54, 58, 59, 62, 71, 78, 79, 82, 85, 90, 100,
102, 103, 106, 107, 108, 117, and 125 demonstrated efficacy when
administered by oral gavages at 30 mg/kg.
Mouse CIA model was performed using the methods described by Trentham
DE, Townes AS, Kang AH. Autoimmunity to Type II Collagen: An
Experimental Model of Arthritis. J Exp Med 1977; 857-868, and Bendele AM.
182

CA 02813299 2013-04-17
Animal Models of Rheumatoid Arthritis. 3 Musculoskel Interact 2001; 377-
385.
In summary, male B1OR111 mice (7-9 wks on arrival) were habituated to the
animal facility for at least 4 days. On experimental day 0 mice were
anaesthetized with isoflurane and the dorsal surface was shaved. Collagen,
emulsified in Freund's complete adjuvant (CFA) supplemented with additional
mycobacterium tuberculosis (TB) H37Ra, was injected intradermally at the
base of the tail (0.15 mL / animal; 2 mg/mL collagen and 2.5 mg/mL TB in
CFA). This CFA treatment was repeated on day 15.
From day 15 to the end of the study animals were scored daily for signs of
arthritis. On the first day of disease (RA Day 1) animals were recruited to
the
study and grouped using a balanced design based on arthritis score. Once
recruited, animals were weighed and dosed twice daily by gavage (PO, BID).
Recruited animals were then scored twice a week on RA days 1, 5, 8 and 12.
At the end of the study (RA day 12) animals were weighed and scored.
Compounds 14, 58, 78, 85 and 102 demonstrated efficacy when
administered by oral gavages at 30 mg/kg (BID).
183

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