Title of Invention

PYRROLOPYRIMIDINES USEFUL AS INHIBITORS OF PROTEIN KINASE

Abstract The present invention relates to compounds of formula (I) useful as inhibitors of protein kinases. The invention also provides pharmaceutically acceptable compositions comprising said compounds and methods of using the compositions in the treatment of various disease, conditions, or disorders.
Full Text WO 2006/096270 PCT/US2006/004019
PYRROLOPYRIMIDINES USEFUL AS INHIBITORS OF PROTEIN KINASE
TECHNICAL FIELD OF THE INVENTION
[0100] The present invention relates to compounds useful as inhibitors of Janus
kinases (JAK). The invention also provides pharmaceutically acceptable compositions
comprising the compounds of the invention and methods of using the compositions in
the treatment of various disorders.
BACKGROUND OF THE INVENTION
[0101] The Janus kinases (JAK) are a family of tyrosine kinases consisting of
JAKl,JAK2, JAK3 and TYK2. The JAKs play a critical role in cytokine signaling.
The down-stream substrates of the JAK family of kinases include the signal transducer
and activator of transcription (STAT) proteins. JAK/STAT signaling has been
implicated in the mediation of many abnormal immune responses such as allergies,
asthma, autoimmune diseases such as transplant rejection, rheumatoid arthritis,
amyotrophic lateral sclerosis and multiple sclerosis as well as in solid and hematologic
malignancies such as leukemias and lymphomas. JAK2 has also been implicated in
myeloproliferative disorders, which include polycythemia vera, essential
thrombocythemia, chronic idiopathic myelofibrosis, myeloid metaplasia with
myelofibrosis, chronic myeloid leukemia, chronic myelomonocytic leukemia, chronic
eosinophilic leukemia, hypereosinophilic syndrome and systematic mast cell disease.
[0102] The Rho-associated coiled-coil forming protein serine/threonine kinase
(ROCK) family are effectors of Ras-related small GTPase Rho. The ROCK family
includes pl60ROCK (ROCK-1), ROKRho-kinase/ROCK-II, protein kinase PKN,
and citron and citron kinase. ROCK has been implicated in various diseases and
disorders including hypertension, chronic obstructive pulmonary disease, cerebral

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vasospasm, coronary vasospasm, bronchial asthma, erectile dysfunction, glaucoma,
vascular smooth muscle cell proliferation, myocardial hypertrophy, malignoma,
ischemia/reperfusion-induced injury, endothelial dysfunction, Crohn's Disease and
colitis, neurite outgrowth, Raynaud's Disease, angina, Alzheimer's disease,
atherosclerosis, and cardiac hypertrophy and perivascular fibrosis.
[0103] Protein kinase A (PKA; also known as cAMP-dependent protein kinase)
is a tetrameric holoenzyme, which contains two catalytic subunits bound to a homo-
dimeric regulatory subunit (which acts to inhibit the catalytic sub-units). On binding of
cAMP (enzyme activation), the catalytic subunits dissociate from the regulatory
subunits to yield the active serine/threonine kinase. Three isoforms of the catalytic
subunit (C-, C- and C-) have been reported to date, with the C- subunit being the
most extensively studied, primarily because of its elevated expression in primary and
metastatic melanomas. PKA has been shown to regulate many vital functions including
energy metabolism, gene transcription, proliferation, differentiation, reproductive
function, secretion, neuronal activity, memory, contractility and motility.
[ 0104 ] Accordingly, there is a great need to develop compounds useful as
inhibitors of protein kinases, including JAK family, ROCK and PKA kinases. In
particular, it would be desirable to develop compounds that are useful as inhibitors of
JAK2 and JAK3.
SUMMARY OF THE INVENTION
[0105] It has now been found that compounds of this invention, and
pharmaceutically acceptable compositions thereof, are effective as inhibitors of protein
kinases, particularly the JAK family kinases. In certain embodiments, these
compounds are effective as inhibitors of JAK3 protein kinases. These compounds have
the general formula I:
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or a pharmaceutically acceptable salt thereof, wherein R1, R2, Z1, Z2, and Z3 are as
defined below.
[0106] These compounds, and pharmaceutically acceptable compositions
thereof, are useful for treating or lessening the severity of a variety of disorders,
including allergic disorders such as asthma and atopic dermatitis, autoimmune diseases
such as SLE lupus and psoriasis, conditions associated with organ transplantation,
myeloproliferative disorders, hypertension, chronic obstructive pulmonary disease and
proliferative disorders such as melanoma.
DETAILED DESCRIPTION OF THE INVENTION
Compounds and Definitions
[0107 ] Compounds of this invention include those described generally above,
and are further illustrated by the classes, subclasses, and species disclosed herein. As
used herein, the following definitions shall apply unless otherwise indicated. For
purposes of this invention, the chemical elements are identified in accordance with the
Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th
Ed. Additionally, general principles of organic chemistry are described in "Organic
Chemistry", Thomas Sorrell, University Science Books, Sausalito: 1999, and "March's
Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley &
Sons, New York: 2001, the entire contents of which are hereby incorporated by
reference.
[0108] As described herein, compounds of the invention may optionally be
substituted with one or more substituents, such as are illustrated generally above, or as
exemplified by particular classes, subclasses, and species of the invention. It will be
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appreciated that the phrase "optionally substituted" is used interchangeably with the
phrase "substituted or unsubstituted." In general, the term "substituted", whether
preceded by the term "optionally" or not, refers to the replacement of hydrogen radicals
in a given structure with the radical of a specified substituent. Unless otherwise
indicated, an optionally substituted group may have a substituent at each substitutable
position of the group, and when more than one position in any given structure may be
substituted with more than one substituent selected from a specified group, the
substituent may be either the same or different at every position.
[ 0109 ] As described herein, when the term "optionally substituted" precedes a
list, said term refers to all of the subsequent substitutable groups in that list. For
example, if X is halogen; optionally substituted C1-3alkyl or phenyl; X may be either
optionally substituted alkyl or optionally substituted phenyl. Likewise, if the term
"optionally substituted" follows a list, said term also refers to all of the substitutable
groups in the prior list unless otherwise indicated. For example: if X is halogen, C1-.
3alkyl or phenyl wherein X is optionally substituted by Jx, then both C1-3alkyl and
phenyl may be optionally substituted by Jx. As is apparent to one having ordinary skill
in the art, groups such as H, halogen, NO2, CN, NH2, OH, or OCF3 would not be
included because they are not substitutable groups.
[0110] Combinations of substituents envisioned by this invention are preferably
those that result in the formation of stable or chemically feasible compounds. The term
"stable", as used herein, refers to compounds that are not substantially altered when
subjected to conditions to allow for their production, detection, and preferably their
recovery, purification, and use for one or more of the purposes disclosed herein. In
some embodiments, a stable compound or chemically feasible compound is one that is
not substantially altered when kept at a temperature of 40°C or less, in the absence of
moisture or other chemically reactive conditions, for at least a week.
[0111] As described herein, a bond drawn from a substituent to the center of
one ring within a multiple-ring system (as shown below), represents substitution of the
substituent at any substitutable position in any of the rings within the multiple ring
system. For example, Figure a represents possible substitution in any of the positions
shown in Figure b.
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[ 0112 ] This also applies to multiple ring systems fused to optional ring systems
(which would be represented by dotted lines). For example, in Figure c, X is an
optional substituent both for ring A and ring B.

[ 0113 ] If, however, two rings in a multiple ring system each have different
substituents drawn from the center of each ring, then, unless otherwise specified, each
substituent only represents substitution on the ring to which it is attached. For example,
in Figure d, Y is an optionally substituent for ring A only, and X is an optional
substituent for ring B only.

[0114 ] The term "aliphatic" or "aliphatic group", as used herein, means a
straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon
chain that is completely saturated or that contains one or more units of unsaturation.
Unless otherwise specified, aliphatic groups contain 1-20 aliphatic carbon atoms. In
some embodiments, aliphatic groups contain 1-10 aliphatic carbon atoms. In other
embodiments, aliphatic groups contain 1-8 aliphatic carbon atoms. In still other
embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms, and in yet other
embodiments aliphatic groups contain 1-4 aliphatic carbon atoms. Suitable aliphatic
groups include, but are not limited to, linear or branched, substituted or unsubstituted
alkyl, alkenyl, or alkynyl groups. Further examples of aliphatic groups include methyl,
ethyl, propyl, butyl, isopropyl, isobutyl, vinyl, and sec-butyl.
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[ 0115 ] The term "cycloaliphatic" (or "carbocycle" or "cycloalkyl") refers to a
monocyclic C3-C8 hydrocarbon or bicyclic C8-C12 hydrocarbon that is completely
saturated or that contains one or more units of unsaturation, but which is not aromatic,
that has a single point of attachment to the rest of the molecule wherein any individual
ring in said bicyclic ring system has 3-7 members. Suitable cycloaliphatic groups
include, but are not limited to, cycloalkyl, cycloalkenyl, and cycloalkynyl. Further
examples of aliphatic groups include cyclopentyl, cyclopentenyl, cyclohexyl,
cyclohexenyl, cycloheptyl, and cycloheptenyl.
[0116] The term "heterocycle", "heterocyclyl", "heterocycloaliphatic", or
"heterocyclic" as used herein means non-aromatic, monocyclic, bicyclic, or tricyclic
ring systems in which one or more ring members are an independently selected
heteroatom. In some embodiments, the "heterocycle", "heterocyclyl",
"heterocycloaliphatic", or "heterocyclic" group has three to fourteen ring members in
which one or more ring members is a heteroatom independently selected from oxygen,
sulfur, nitrogen, or phosphorus, and each ring in the system contains 3 to 7 ring
members.
[0117] Further examples of heterocyclic rings include, but are not limited to,
the following monocycles: 2-tetrahydrofuranyl, 3-tetrahydrofuranyl,
2-tetrahydrothiophenyl, 3-tetrahydrothiophenyl, 2-morpholino, 3-morpholino,
4-morpholino, 2-thiomorpholino, 3-thiomorpholino, 4-thiomorpholino, 1-pyrrolidinyl,
2-pyrrolidinyl, 3-pynolidinyl, 1-tetrahydropiperazinyl, 2-tetrahydropiperazinyl,
3-tetrahydropiperazinyl, 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 1-pyrazolinyl,
3-pyrazolinyl, 4-pyrazolinyl, 5-pyrazolinyl, 1-piperidinyl, 2-piperidinyl, 3-piperidinyl,
4-piperidinyl, 2-thiazolidinyl, 3-thiazolidinyl, 4-thiazolidinyl, 1-imidazolidinyl,
2-imidazolidinyl, 4-imidazolidinyl, 5-imidazolidinyl, and the following bicycles: 3-1H-
benzimidazol-2-one, 3-(l-alkyl)-benzimidazol-2-one, indolinyl, tetrahydroquinolinyl,
tetrahydroisoquinolinyl, benzothiolane, benzodithiane, and l,3-dihydro-imidazol-2-one.
[0118] The term "heteroatom" means one or more of oxygen, sulfur, nitrogen,
phosphorus, or silicon (including, any oxidized form of nitrogen, sulfur, phosphorus, or
silicon; the quaternized form of any basic nitrogen or; a substitutable nitrogen of a
heterocyclic ring, for example N (as in 3,4-dihydro-2H-pyrrolyI), NH (as in
pyrrolidinyl) or NR+ (as in N-substituted pyrrolidinyl)).
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[ 0119 ] The term "unsaturated", as used herein, means that a moiety has one or
more units of unsaturation.
[ 0120 ] The term "alkoxy", or "thioalkyl", as used herein, refers to an alkyl
group, as previously defined, attached to the principal carbon chain through an oxygen
("alkoxy") or sulfur ("thioalkyl") atom.
[ 0121] The terms "haloalkyl", "haloalkenyl" and "haloalkoxy" means alkyl,
alkenyl or alkoxy, as the case may be, substituted with one or more halogen atoms.
The term "halogen" means F, Cl, Br, or I.
[0122] The term "aryl" used alone or as part of a larger moiety as in "aralkyl",
"aralkoxy", or "aryloxyalkyl", refers to monocyclic, bicyclic, and tricyclic ring systems
having a total of five to fourteen ring members, wherein at least one ring in the system
is aromatic and wherein each ring in the system contains 3 to 7 ring members. The
term "aryl" may be used interchangeably with the term "aryl ring". The term "aryl"
also refers to heteroaryl ring systems as defined herein below. Examples of aryl rings
would include phenyl, naphthyl, and the heteroaryl group listed below.
[0123] The term "heteroaryl", used alone or as part of a larger moiety as in
"heteroaralkyl" or "heteroarylalkoxy", refers to monocyclic, bicyclic, and tricyclic ring
systems having a total of five to fourteen ring members, wherein at least one ring in the
system is aromatic, at least one ring in the system contains one or more heteroatoms,
and wherein each ring in the system contains 3 to 7 ring members. The term
"heteroaryl" may be used interchangeably with the term "heteroaryl ring" or the term
"heteroaromatic".
[0124] Further examples of heteroaryl rings include the following monocycles:
2-furanyl, 3-furanyl, N-imidazolyl, 2-imidazolyl, 4-imidazolyl, 5-imidazolyl, 3-
isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-oxazolyl, 4-oxazolyl, 5-oxazolyl, N-pyrrolyl,
2-pyrrolyl, 3-pyrrolyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidinyl, 4-pyrimidinyl,
5-pyrimidinyl, pyridazinyl (e.g., 3-pyridazinyl), 2-thiazolyl, 4-thiazolyl, 5-thiazolyl,
tetrazolyl (e.g., 5-tetrazolyl), triazolyl (e.g., 2-triazolyl and 5-triazolyl), 2-thienyl,
3-thienyl, pyrazolyl (e.g., 2-pyrazolyl), isothiazolyl, 1,2,3-oxadiazolyl, 1,2,5-
oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,3-triazolyl, 1,2,3-thiadiazolyl, 1,3,4-thiadiazolyl,
1,2,5-thiadiazolyl, pyrazinyl, 1,3,5-triazinyl, and the following bicycles:
benzimidazolyl, benzofuryl, benzothiophenyl, indolyl (e.g., 2-indolyl), purinyl,
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quinolinyl (e.g., 2-quinolinyl, 3-quinolinyl, 4-quinolinyl), and isoquinolinyl (e.g.,
l-isoquinolinyl, 3-isoquinolinyl, or 4-isoquinolinyl).
[ 0125 ] An aryl (including aralkyl, aralkoxy, aryloxyalkyl and the like) or
heteroaryl (including heteroaralkyl and heteroarylalkoxy and the like) group may
contain one or more substituents. Suitable substituents on the unsaturated carbon atom
of an aryl or heteroaryl group are selected from those listed in the definition of Jx, JQ,
JR above; halogen; -R°; -ORo; -SR°; 1,2-methylenedioxy; 1,2-ethylenedioxy; phenyl
(Ph) optionally substituted with R°; -O(Ph) optionally substituted with R°;
-(CH2)1-2(Ph), optionally substituted with R°; -CH=CH(Ph), optionally substituted with
R°; -NO2; -CN; -N(R°)2; -NR°C(O)R°; -NR°C(S)R°; -NR°C(O)N(RO)2; -
NROC(S)N(R°)2; -NR°CO2R°; -NR°NR°C(O)R°; -NR°NRoC(0)N(Ro)2; -
NR°NR°CO2R0; -C(O)C(O)Ro; -C(O)CH2C(O)R°; -CO2R°; -C(O)R°; -C(S)R°; -
C(O)N(R°)2; -C(S)N(R°)2; -OC(O)N(R°)2; -OC(O)R°; -C(O)N(OR°) R°; -C(NOR°)
R°; -S(O)2R°; -S(O)3R°; -SO2N(R0)2; -S(O)R°; -NROSO2N(RO)2; -NRoSO2R0;
-N(OR°)R°; -C(=NH)-N(R°)2; or -(CH2)o-2NHC(0)R° wherein each independent
occurrence of R° is selected from hydrogen, optionally substituted C1-6 aliphatic, an
unsubstituted 5-6 membered heteroaryl or heterocyclic ring, phenyl, -O(Ph), or
-CH2(Ph), or, notwithstanding the definition above, two independent occurrences of R°,
on the same substituent or different substituents, taken together with the atom(s) to
which each R° group is bound, form a 5-8-membered heterocyclyl, aryl, or heteroaryl
ring or a 3-8-membeied cycloalkyl ring having 0-3 heteroatoms independently selected
from nitrogen, oxygen, or sulfur. Optional substituents on the aliphatic group of R° are
selected from NH2, NH(C1-4aliphatic), N(C1-4aliphatic)2, halogen, C1-4aliphatic, OH,
O(C1-4aliphatic), NO2, CN, CO2H, CO2(C1-4aliphatic), O(haloC1-4aliphatic), or haloC1-
4aliphatic, wherein each of the foregoing C1-4aliphatic groups of R° is unsubstituted
[0126] An aliphatic or heteroaliphatic group, or a non-aromatic heterocyclic
ring may contain one or more substituents. Suitable substituents on the saturated
carbon of an aliphatic or heteroaliphatic group, or of a non-aromatic heterocyclic ring
are selected from those listed above for the unsaturated carbon of an aryl or heteroaryl
group and additionally include the following: =0, =S, =NNHR*, =NN(R*)2,
=NNHC(O)R*, =NNHCO2(alkyI), =NNHSO2(alkyl), or =NR*, where each R* is
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independently selected from hydrogen or an optionally substituted C1-6 aliphatic.
Optional substituents on the aliphatic group of R* are selected from NH2, NH(C1-4
aliphatic), N(C1-4 aliphatic)2, halogen, C1-4 aliphatic, OH, 0(C1-4 aliphatic), NO2, CN,
CO2H, C02(C1-4 aliphatic), O(halo C1-4 aliphatic), or halo(C1-4 aliphatic), wherein each
of the foregoing C1-4aliphatic groups of R* is unsubstituted.
[0127] Optional substituents on the nitrogen of a non-aromatic heterocyclic ring
include those listed in the definition of 3Q and R7 herein; -R+, -N(R+)2, -C(O)R+,
-CO2R+, -C(O)C(O)R+, -C(O)CH2C(O)R+, -SO2R+, -SO2N(R+)2, -C(=S)N(R+)2,
-C(=NH)-N(R+)2, or -NR+SO2R+; wherein R+ is hydrogen, an optionally substituted C1-
6 aliphatic, optionally substituted phenyl, optionally substituted -O(Ph), optionally
substituted -CH2(Ph), optionally substituted -(CH2)1-2(Ph); optionally substituted -
CH=CH(Ph); or an unsubstituted 5-6 membered heteroaryl or heterocyclic ring having
one to four heteroatoms independently selected from oxygen, nitrogen, or sulfur, or,
notwithstanding the definition above, two independent occurrences of R+, on the same
substituent or different substituents, taken together with the atom(s) to which each R+
group is bound, form a 5-8-membered heterocyclyl, aryl, or heteroaryl ring or a 3-8-
membered cycloalkyl ring having 0-3 heteroatoms independently selected from
nitrogen, oxygen, or sulfur. Optional substituents on the aliphatic group or the phenyl
ring of R+ are selected from NH2, NH(C1-4 aliphatic), N(C1-4aliphatic)2, halogen, C1-4
aliphatic, OH, O(C1-4 aliphatic), NO2, CN, CO2H, CO2(C1-4 aliphatic), O(halo C1-4
aliphatic), or halo(C1-4 aliphatic), wherein each of the foregoing C1-4aliphatic groups of
R+ is unsubstituted.
[ 0128 ] As detailed above, in some embodiments, two independent occurrences
of R° (or R+, or any other variable similarly defined herein), are taken together with the
atom(s) to which each variable is bound to form a 5-8-membered heterocyclyl, aryl, or
heteroaryl ring or a 3-8-membered cycloalkyl ring having 0-3 heteroatoms
independently selected from nitrogen, oxygen, or sulfur. Exemplary rings that are
formed when two independent occurrences of R° (or R+, or any other variable similarly
defined herein) are taken together with the atom(s) to which each variable is bound
include, but are not limited to the following: a) two independent occurrences of R° (or
R+, or any other variable similarly defined herein) that are bound to the same atom and
are taken together with that atom to form a ring, for example, N(R°)2, where both
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occurrences of R° are taken together with the nitrogen atom to form a piperidin-1-yl,
piperazin-1-yl, or morpholin-4-yl group; and b) two independent occurrences of R° (or
R+, or any other variable similarly defined herein) that are bound to different atoms and
are taken together with both of those atoms to form a ring, for example where a phenyl

t
group is substituted with two occurrences of OR°

these two

occurrences of Ro are taken together with the oxygen atoms to which they are bound to

It will be
form a fused 6-membered oxygen containing ring:

appreciated that a variety of other rings can be formed when two independent
occurrences of R° (or R+, or any other variable similarly defined herein) are taken
together with the atom(s) to which each variable is bound and that the examples
detailed above are not intended to be limiting.
[0129] An alkyl or aliphatic chain can be optionally interrupted with another
atom or group. This means that a methylene unit of the alkyl or aliphatic chain is
optionally replaced with said other atom or group. Examples of such atoms or groups
would include, but are not limited to, -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-,
-C(O)-, -C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-, wherein R is defined herein.
Unless otherwise specified, the optional replacements form a chemically stable
compound. Optional interruptions can occur both within the chain and at either ends of
the chain; both at the point of attachment and also at the terminal end. Two optional
replacements can also be adjacent to each other within a chain. Unless otherwise
specified, if the replacement or interruption occurs at the terminal end, the replacement
atom is bound to an H on the terminal end. For example, if -CH2CH2CH3 were
optionally interrupted with -O-, the resulting compound could be -OCH2CH3,
-CH2OCH3, or -CH2CH2OH.
[0130] Unless otherwise stated, structures depicted herein are also meant to
include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or
conformational)) forms of the structure; for example, the R and S configurations for
each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E)
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conformational isomers. Therefore, single stereochemical isomers as well as
enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the
present compounds are within the scope of the invention.
[0131] Unless otherwise stated, all tautomeric forms of the compounds of the
invention are within the scope of the invention. Additionally, unless otherwise stated,
structures depicted herein are also meant to include compounds that differ only in the
presence of one or more isotopically enriched atoms. For example, compounds having
the present structures except for the replacement pf hydrogen by deuterium or tritium,
or the replacement of a carbon by a 13C- or 14C-enriched carbon are within the scope of
this invention. Such compounds are useful, for example, as analytical tools or probes
in biological assays.
[0132] The present invention relates to a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:
wherein
R1 is H, -NO2, -CN, -OCF3, halogen, or ammo; or C1-6aliphatic, C3-7cycloaliphatic,
C1-6alkoxy, or C1-4haloalkyl optionally substituted with 0-10 JR groups;
R2 is H, -NO2, -CN, -OCF3, halogen, or amino; or C1-6aliphatic, C3-7cycloaliphatic,
C1-6alkoxy, or C1-4thaloalkyl optionally substituted with 0-10 JR groups;
Z1 is C1-6aliphatic or C1-10cycloaliphatic optionally substituted with 0-10 Jz groups; if
the bond between Z1 and C is a double bond, then Z1 may also be =0, =NR, or
=C(R)2;
Z2 is H or halogen; or C1-10haloalkyl, C1-4haloalkoxy, Y, -(Vn)-CN, -(Vn)-NO2,
-(Vn)-OH, -(Vn)-(C1-6aliphatic), -(Vn)(C1-4heterocyclyl), -(Vn)-(C1-6aryl),
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-(Vn)-(5-10 membered heteroaryl), or -(Vn)-(C1-10cycloaliphatic) optionally
substituted with 0-10 Jz groups; or
Z1 and Z2, together with the carbon atom to which they are attached, form ring Q;
Z3 is H or C1-6alkcyl optionally substituted with 0-3 Jz groups; or
Z1, Z2, and Z3, together with the carbon atom to which they are attached, form an 6-14
membered saturated, partially saturated, or unsaturated bicyclic ring having 0-3
heteroatoms; wherein
if the bond between Z1 and C is a triple bond, then Z2 is absent; and
if the bond between Z1 and C is a double bond or a triple bond, then Z3 is absent;
Q is a 3-8 membered saturated or partially saturated monocyclic ring having 0-3
heteroatoms selected from nitrogen, oxygen, or sulfur, wherein said Q is
optionally and independently fused to Q1 or Q2; or to both Q1 and Q2; wherein
said Q is optionally substituted with 0-4 JQ groups;
Q1 is a 3-8 membered saturated, partially saturated, or unsaturated monocyclic ring
having 0-3 heteroatoms selected from nitrogen, oxygen, or sulfur, wherein said
Q1 group is optionally substituted with 0-4 JQ groups;
Q2 is a 3-8 membered saturated, partially saturated, or unsaturated monocyclic ring
having 0-3 heteroatoms selected from nitrogen, oxygen, or sulfur wherein said
Q2 group is optionally substituted with 0-4 JQ groups;
R is H, optionally substituted C1-6 aliphatic, C3-10 cycloaliphatic, C6-10 aryl, 5-14
membered heteroaryl, or 5-14 membered heterocyclyl; or two R groups, on the
same substituent or different substituents, together with the atom(s) to which
each R group is bound, form an optionally substituted 3-14 membered saturated,
partially unsaturated, or fully unsaturated monocyclic, bicyclic, or tricyclic ring
having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur
wherein said R is optionally substituted with 0-10 JR groups;
each JQ and Jz substituent on an unsaturated carbon atom is independently selected
from hydrogen, -OCF3, C1-6haloalkyl, N(R)2, OR, halogen, Y, -(Vn)-CN,
-(Vn)-NO2, -(Vn)-OH, -(Vn)(C1-6aliphatic), -(C1-10cycloaliphatic)-C(0)R,
-(C1-10cycloaliphatic)-(C1-12heterocyclyl);-(Vn)-(C1-12heterocyclyl), -(Vn)-
(C1-10aryl), -(Vn)-(5-10 membered heteroaryl), -(Vn)-(C1-10cycloaliphatic);
wherein each JQ and Jz is optionally substituted with up to 10 JR groups;
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each JQ and Jz substituent on a saturated carbon atom is selected from those listed
above for an unsaturated carbon and also the following: =O, =NN(Ra)2,
=NNHC(O)Ra, =NNHCO2(C1-4alkyl), =NNHSO2(C1-4alkyl), and =NRa wherein
each JQ and Jz is optionally substituted with up to 10 JR groups;
each JQ and Jz substituent on a nitrogen atom is independently selected from hydrogen,
Y, -(Vn)-CN, -(Vn)-NO2, -(Vn-OH, -(Vn)-(C1-6aliphatic), -(C1-10cycloaliphatic)-
C(O)R,-(C1-10cycloaliphatic)-(C3-12heterocyclyl),-(Vn)-(C3-12heterocyclyl),
-(Vn)-(C6-10aryl), -(Vn)-(5-10 membered heteroaryl), -(Vn)-(C3-10cycloaliphatic);
wherein two Jz groups, on the same substituent or different substituents,
together with the atom(s) to which each Jz group is bound, can optionally form
an optionally substituted 3-14 membered saturated, partially unsaturated, or
fully unsaturated monocyclic, bicyclic, or tricyclic ring having 0-4 heteroatoms
independently selected from nitrogen, oxygen, or sulfur; wherein each JQ and Jz
is optionally substituted with up to 10 JR groups;
JR is selected from halogen, -N(Rb)2 SRb, ORb, oxo, C1-4aloalkoxy, C1-4haloalkyl, L,
-(Ln-(C1-6alkyl), -(Ln)-(C3-12heterocyclyl), -(Ln)(C6-10aryl), -(Ln)-(5-10
membered heteroaryl), -(Ln)-(C3-10cycloalipahtic), -(Ln)-NO2, -(Ln)-CN,
-(Ln)-OH, -CO2Rb, -CORb, -OC(O)Rb, -NC(O)Rb;
L is C1-10alkyl wherein up to three methylene units are replaced by -NRb-, -O-, -S-, -
CO2-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NRb-, -C(=N-CN), -NRbCO-,
-NRbC(O)O-, -SO2NRb-, -NRbSO2-, -NRbC(O)NR-, -OC(O)NRb-,
-NRbSO2NRb-, -SO-, or -SO2-;
V is C1-10aliphatic wherein up to three methylene units are replaced by Gv, wherein Gv
is selected from -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NR-,
-C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-, -NRC(O)NR-,
-OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
Y is C1-10aliphatic, wherein up to three methylene units are replaced by GY wherein GY
is selected from -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NR-,
-C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-, -NRC(O)NR-,
-OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
Ra is hydrogen or C1-6 aliphatic group optionally substituted with 0-3 JR groups;
Rb is hydrogen or an unsubstituted C1-6aliphatic group;
13

WO 2006/096270 PCT/US2006/004019
n is 0 or l;
provided that:
when R1 and R2 are H, and Z2 and Z3 are H, then Z1 is not methyl;
when R1 is CH3 and R2 is H, then Z1, Z2, and Z3 are not all H;
when R1 and R2 are H, and Z2 and Z3 are H, then Z1 is not unsubstituted phenyl,
4-pyridyl, or one of the structures shown below:

and
when R1 and R2 are H, Z1 and Z2 taken together are not -C≡C-CH2CH2COOH.
[0133] According to one embodiment of this invention, Z1, Z2, and Z3, together
with the carbon atom to which they are attached, form the bicyclic ring shown in
Formula I:

wherein
Q3 is 3-8 membered saturated, unsaturated, or partially saturated monocyclic
ring;
Q and Q3 are each optionally and independently substituted with 0-4 JQ groups.
[ 0134] In one embodiment, Q3 is a cyclopropyl group optionally substituted
with 0-2 JQ groups as shown in formula II:

14

WO 2006/096270 PCT/US2006/004019
[0135] According to another embodiment of this invention, Z1 and Z2, together
with the carbon atom to which they are attached, form a monocyclic, bicyclic, or
tricyclic ring as shown in formula III:

wherein
Z11 is selected from C, N, O, or S;
Z12 is selected from C, N, O, or S;
Q is a 3-8 membered saturated or partially saturated monocyclic ring, optionally fused
to Q1 or Q2;
Q and Q are each independently a 3-8 membered saturated, unsaturated, or partially
saturated monocyclic ring;
Q, Q1 and Q2 each independently contain up to three heteroatoms selected from O, N,
or S;
m is is 0-4; and is independently selected for Q, Q1 and Q2; and
Z3 is H; or if the bond between C and Z11 is a double bond, then Z3 is absent
[0136] In some embodiments, Z1! and Z12 are each independently carbon.
[0137] In one embodiment, Q is C3-7 monocycle and Q1 and Q2 are absent.
[0138] In another embodiment, Q and Q1 together form a fused 6-14 membered
bicyclic ring and Q2 is absent.
[ 0139] In yet another embodiment, Q, Q1, and Q2 together form a fused 8-20
membered tricyclic ring.
[0140] In one embodiment, of the invention Z12 is carbon and the fused ring of
Q, Q1, and optionally Q2 is as shown in Formula IV:
15


WO 2006/096270 PCT/US2006/004019

wherein Q, Q1, and Q2 each independently and optionally contain
a) 0-2 heteroatoms selected from O, N, or S; and
b) 0-4 fQ substituents.
[0141] In one embodiment, the hydrogen atoms at the point of fusion between
ring Q and ring Q1 is in the cis conformation as shown in Formula V:

[ 0142 ] In another embodiment, the hydrogen atoms at the point of fusion
between ring Q and ring Q1 are in the trans conformation.
[0143] In one embodiment, C—Z11 is a single bond.
[0144] In another embodiment, C=Z11 is a double bond.
[ 0145 ] In certain embodiments, ring Q contains up to two heteroatoms. In other
embodiments, ring Q contains one heteroatom; and in yet other embodiments, ring Q
contains zero heteroatoms.
[0146] In one embodiment, Q contains two heteroatoms and each of said
heteroatoms are independently selected from nitrogen, sulfur, or oxygen; preferably
nitrogen and sulfur; more preferably, nitrogen. In some embodiments, both
heteroatoms are nitrogen. In other embodiments, one is nitrogen and the other is sulfur.
In some embodiments, one heteroatom is nitrogen and the other is oxygen. In yet other
embodiments, one heteroatom is nitrogen and the other is sulfur.
[ 0147 ] In another embodiment, Q contains one heteroatom selected from O, N,
or S. In some embodiments, the heteroatom is oxygen; in other embodiments, the

16

WO 2006/096270 PCT/US2006/004019
heteroatom is nitrogen; in yet other embodiments, the heteroatom is sulfur. In some
embodiments, the sulfur is optionally substituted with 0,1, or 2 oxo groups.
[0148] Examples of heterocyclic groups include piperidine, piperazine,
morpholine, thiomorpholine, and pyrrolidine.
[0149] In some embodiments, ring Q is a 5-7 membered cycloaliphatic.
Examples of cycloaliphatic groups include cyclohexane, cyclopentane, cyclohexene,
and cyclopentene.
[0150] In other embodiments, Q1 is a 6-membered aryl or 5-6 membered
heteroaryl ring. Examples of aryl or heteroaryl rings include include phenyl, pyridine,
pyrimidine, thiophene, thiazole, tetrazole, triazole, pyrrole, furan, and pyrazole.
[0151] In some embodiments, Q1 is a 3-7 membered cycloaliphatic ring.
Examples of cycloaliphatic rings include cyclohexane, cyclopentane, cyclohexene,
cyclopentene, cycloheptene, cycloheptane, cyclopropane, cyclobutane, cyclopropene,
and cyclobutene.
[0152] In other embodiment, Q1 is a 3-7 membered heterocyclic ring.
Examples of heterocyclic groups include piperidine, piperazine, morpholine,
thiomorpholine, pyrrolidine, homopiperidine, and homopiperazme.
[0153] In one embodiment,Q or Q-Q1 is represented by the following
structures:

17

WO 2006/096270 PCT/US2006/004019

wherein both R7 and JQ are each independently selected from hydrogen, Y, -(Vn)-CN,
-(Vn)-NO2, -(Vn)-OH, -(Vn)-(C1-6aliphatic), -(Vn)-(C3-12heterocyclyl), -(Vn)-(C6-10aryl),
-(Vn)-(5-10 membered heteroaryl), -(Vn)-(C3-10cycloaliphatic), and
-(C3-10cycloaliphatic)-(C3-12heterocyclyl);
wherein for each Q and Q1, m is independently 0-3; and
each R7 and JQ is optionally and independently substituted with 0-10 JR groups.
[0154] In one embodiment m is 0,1, or 2. In another embodiment, m is 1 or 2.
In some embodiments, m is 0; in other embodiments, m is 1; in yet other embodiments,
m is 2.
[0155] In some embodiments, JQ is Y, -(V1n)-CN, -(V1n)-NO2 -(V1n)-OH,
-(V1n)-(C1-6aliphatic), -(V1n)-(C3-12heterocyclyl), -(V1n)-(C6-10aryl), -(V1n)-(5-l0
membered heteroaryl), -(V1n)-(C3-10cycloaliphatic), or -(C3-10cycloaliphatic)-
(C3-12heterocyclyl); wherein
V1 is -Gv-(X)p, wherein X is a C1-9aliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
p is 0 or l;
n is 0 or l;
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O); and
said JQ is optionally substituted with 0-10 JR groups.
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WO 2006/096270 PCT/US2006/004019
[0156] In one embodiment, X is optionally substituted C1-4aliphatic. In some
embodiments, X is optionally substituted C1-4alkyl. In some embodiments, X is
optionally substituted C1-2alkyl.
[0157] In some embodiments, n is 0. In other embodiments, n is 1. In certain
embodiments, p is 0. In other embodiments, p is 1.
[0158 ] In some embodiments, JQ is optionally substituted with 0-10 JR groups.
In some embodiments, 0-5 JR groups; in other embodiments, 0-3 JR groups; and in yet
other embodiments, 0-2 JR groups; In some embodiments, one JR group, and in certain
embodiments, 0 JR groups.
[0159] In one embodiment,Gv is C=O.
[0160] In another embodiment of this invention, R1 and R2 are each
independently H, halogen, C1-4alkyl, or C1-4alkoxy. In one embodiment,R.1 and R2 are
each independently H.
[0161] In some embodiments, R7 is independently selected from Y, -(V1n)-CN,
-(V1n)-NO2, -(V1n)-OH, -(V1n)-(C1-6aliphatic), -(V1n)-(C3-12heterocyclyl), -(V1n)-
(C6-10aryl). -(V1n)-(5-l0 membered heteroaryl), -(V1n)-(C3-10cycloaliphatic), or
-(C3-10cycloaliphatic)-(C3-12heterocyclyl); wherein
V1 is -Gv-(X)p wherein X is a C1-9aliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
p is 0 or 1;
n is 0 or 1; and
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O).
[0162] Representative examples of compounds of formula I are set forth in
Table 1.
19

20
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WO 2006/096270 PCT/US2006/004019

[0163] In another embodiment of this invention, Z1 and Z2 do not join to form a
ring and Z3 is H or is absent.
[0164] In one embodimentZ1 is H or C1-6aliphatic optionally substituted with 0-
3 JZ groups. In some embodiments, Z1 is H.
[0165] In certain embodiments, C≡Z1 is a triple bond, and Z2 and Z3 are absent.
[0166] In other embodiments, C=Z1 is a double bond and Z3 is absent
[0167] In certain embodiments, Z1 is O; in other embodiments, Z1 is CH2.
[0168] In certain embodiments, Z2 is optionally substituted Y,
-(Vn)-(C1-6aliphalic), -(Vn)(C3-12heterocyclyl), -(Vn)(C6-10aryl), -(Vn)-(5-10 membered
heteroaryl), or -(Vn)-(C3-10cycloaliphatic). In some embodiments, is 0; In other
embodiments, n is 1.
[0169] In other embodiments, Z2 is an optionally substituted 5-7 membered
monocycle selected from heterocyclyl, cycloaliphatic, aryl, or heteroaryl; preferably a
5-7 membered fully or partially saturated monocycle selected from heterocyclyl or
cycloaliphatic; more preferably, a 6-membered monocycle with 0-2 nitrogen atoms. In
one preferred embodiment of this invention, Z2 is piperidine optionally substituted with
0-3 JZ groups.
[0170] In some embodiments, Z2 is optionally substituted
-(Vn)-(C3-10cycloaliphatic) wherein n is 0. In one embodiment, Z2 is a bicyclo-octane
ring. In another embodiment, Z2 is a C5-7cycloaliphatic. In yet another embodiment, Z2
is a C5-7cycloalkyl.
[0171] In one embodiment,J2 is halogen, CF3, optionally substituted C1-
4haloalkyl, -(V1n)-(CN, -(V1n)-NO2, -(V1n)-OH, Y, -(V1n)-(C3-12heterocyclyl),
21

WO 2006/096270 PCT/US2006/004019
-(V1n)-(C6-10aryl), -(V1n)-(5-10membered heteroaryl), -(V1n)-(C3-10cycloaliphatic), or
-(C3-10cycloaliphatic)-(C3-12heterocyclyl); wherein
V1 is -GV-(X)P wherein X is a C1-paliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2;
p is 0 or l;and
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O).
[0172] In some embodiments, X is C1-5aliphatic. In certain preferred
embodiments, X is C1-5alkyl. In other preferred embodiments, X is C1-2alkyl.
[0173] In some embodiments, Gv is selected from C=O, C(=O)NR, S(O)2 or
S(O). In certain embodiments, Gv is C=O. In omer embodiments, Gv is C(=O)NR. In
yet other embodiments, Gv is S(O)2 or S(O).
[0174] In some embodiments, Jz is halogen, CF3, CN, optionally substituted
C1-6aliphatic, C1-4aloalkyl, -(C1-6alkyl)n-RJ, -(C1-6alkyl)n-C(=O)RJ, -(C1-6alkyl)n-
CON(Rb)Rj, -(C1-6alkyl)n-N(Rb)Rj, -(C1-6alkyl)n-ORJ, -(C1-6alkyl)nOCON(Rb)Rj,
-(C1-6aliphatic)nS(O)N(Rb)Rj, -(C1-6aliphatic)n-S(O)R1, or -(C1-6aliphatic)n-NHC(O)RJ;
wherein
RJ is C1-6aliphatic, C3-12heterocyclyl, C6-10aryl, 5-10 membered heteroaryl,
or C3-10cycloaliphatic; and
n is 0 or 1.
[0175] In other embodiments, Jz is halogen, ORJ, N(Rb)2, CF3, CN, optionally
substituted C1-6alkyl, -(C1-6alkyl)nRj, -C(=O)(C1-6alkyl), -CON(Rb)(C1-6alkyl),
-OCON(Rb)(C1-6alkyl), -S(O)N(Rb)(C1-6alkyl), -S(O)(C1-6alkyl), -NHC(O)C1-6alkyl,
-(C1-6alkyl)-CONH, -(C1-6alky)-N(Rb)2, -(C1-2alkyl)-OCON(Rb)Rj, -(C1-6aliphatic)-
S(O)N(Rb)(C6-10aryl), -N(Rb)C(O)N(Rb)Rj, or -N(Rb)C(O)Rb.
[0176] In other embodiments, Jz is halogen, OR, N(Rb)2, CF3, CN, optionally
substituted C1-6alkyl, -(C1-6alkyl)n-RJ, C(=O)(C1-6alkyl), CONH, -(C1-6alkyl)-CONH,
-(C1-6alkyl)-N(Rb)2, -(C1-6alkyl)-OCON(Rb)Rj, -(C1-6aliphatic)-S(O)N(Rb)(C6-10aryl),
-N(Rb)C(O)N(Rb)2, or N(Rb)C(O)Rb.
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WO 2006/096270 PCT/US2006/004019
[0177] In certain embodiments, RJ is C6-10aryl or 5-10 membered heteroaryl. In
other embodiments, RJ is C1-6aliphatic or C3-10cycloaliphatic. In some embodiments, RJ
is C1-6aliphatic. In other embodiments, RJ is C3-10cycloaliphatic.
[0178] In some embodiments, n is 1. In other embodiments, n is 0.
[0179] In certain embodiments, Jz is optionally substituted -C(=O)(C1-6alkyl),
-C(=O)CH2CN, or C1-6alkyl.
[0180] Representative examples of compounds of formula I are set forth in
Table 2.

23

WO 2006/096270 PCT/US2006/004019

[0181] Representative examples of compounds of Formula I are set forth below
in Table 3:
24

25
WO 2006/096270 PCT/US2006/004019


26
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WO 2006/096270 PCT/US2006/004019

General Synthetic Methodology.
[0182] The compounds of this invention may be prepared in general by
methods known to those skilled in the art for analogous compounds or by those
methods depicted in the Examples below. In general, Example 1 depicts several
methods for the preparation of functionalized quinoxalines.
[0183] Although certain exemplary embodiments are depicted and described
herein, it will be appreciated that a compounds of the invention can be prepared
according to the methods described generally above using appropriate starting materials
by methods generally available to one of ordinary skill in the art.
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WO 2006/096270 PCT/US2006/004019
[0184] All references provided in the synthetic schemes and examples are
herein incorporated by reference. As used herein, all abbreviations, symbols and
conventions are consistent with those used in the contemporary scientific literature.
See, e.g., Janet S. Dodd, ed., The ACS Style Guide: A Manual for Authors and Editors,
2nd Ed., Washington, D.C.: American Chemical Society, 1997, herein incorporated in
its entirety by reference. In addition, the following definitions describe terms and
abbreviations used herein:
Ts-Cl - p-toluenesulfonyl chloride (tosyl chloride)
DMF - dimethylformamide
Tf -triflate
IiHMDS - lithium hexamethyldisilazide
dppf - l,l'-bis(diphenylphosphino)-ferrocene
Ac - acetyl
DME - 1,2-Dimethoxyethane
atm - atmospheres
EDCI - l-Ethyl-3-(3-dimethylaminopropy)carbodiimide
Hydrochloride
DIEA - diisopropylethylamine
LiHMDS - Lithium Hexamethyldisilazane
THF -tetrahydrofuran
HEPES - 4-(2-hydroxyethyl)-l-piperazineethanesulfonic
acid
Glu - glutamate
Tyr - tyrosine
ATP - adenosine triphosphate
Ph - phenyl
Me - methyl
BSA - bovine serum albumin
DTT - dithiothreitol
28

WO 2006/096270 PCT/US2006/004019

Conditions: (a) Ts-Cl, K2CO3, DMF; (b) Tf2O, lutidine or LiHMDS, PhNTf2 -78°C to
r.t.; (c) bispinacolatoborane, Pd(dppf)2Cl2, KOAc then water, (d) Pd(PPh3)4, KOAc,
dioxane or DME, 100-180 °C; (f) LiOH or NaOMe; (g) Pd-C, H2 atm
[0185] Scheme lisa representative scheme for the preparation of compounds
of this invention. Compound 1, which is commercially available, can be protected by a
suitable protecting group (e.g. Tosyl) as described in T.W. Greene & P.G.M Wutz,
"Protective Groups in Organic Synthesis", 3rd Edition, John Wiley & Sons, Inc. (1999))
to form compound 2. Boronic acids/esters (5) can be prepared from the corresponding
vinyl halides (4b) or vinyl triflates (4a) as described in Comins, D. L.; Dehghani, A.
Tetrahedron Lett. 1992,33,6299-6302; McMurry, J. E.; Scott, W. J. Tetrahedron Lett.,
1983,24,979; Stang, P. J.; Fisk, P. J. Synthesis, 1980,283; Stang, P. J.; Fisk, P. J.
Synthesis, 1979,438; Takagi, J.; Takahashi, K.; Ishiyama, T.; Miyaura, N. J. Am.
Chem. Soc, 2002,124,8001 and references therein. The Pd-mediated cross coupling of
the N-protected halide (e.g. chloride) (2) and the boronic acid (3) in the presence of an
appropriate base such as KOAc or Na2CO3 provides compounds of type (6) as
described in A. Suzuki, H. C. Brown "Organic Synthesis Via Boranes; Volume 3:
Suzuki Coupling" Aldrich Chemical Company: Milwaukee, WI, 2003 and references
29

WO 2006/096270 PCT/US2006/004019
therein. Deprotection under basic conditions (e.g. LiOH (aq) or NaOMe) then delivers
(7). Hydrogenation with Pd-C under H2 atmosphere gives (8). Cyclopropanation of
(7), as described in Reiser, Oliver "Cyclopropanation and other reactions of palladium-
carbene (and carbyne) complexes" Handbook of Organopalladium Chemistry for
Organic Synthesis (2002), 11561-1577, gives (9).

Conditions: (a) i: HCl-HNMeOMe, EDCI, DIEA; ii: MeMgBr; (b) LiHMDS, PhNTf2,
THF, -78 °C; (c) bispinacolatoborane, Pd(dppf)2Cl2, KOAc then water; (d) Pd(PPh3)4,
KOAc, dioxane or DME, 100-180 °C; (e) i: LiOH or NaOMe, ii: HC1,; (f) R'COCl,
R'OCOCl, or R'NCO; DIEA or R'OOH; EDCI; and DIEA / wherein R'COCl,
R'OCOCl, and R'NCO refer to suitable acid chlorides, oxalyl chlorides, and
isocyanates which are either commercially available or can be made from commercially
available starting materials.
[0187] Scheme 2 shows additional methods for the preparation of compounds
of this invention. In addition to acid chlorides, isocyanates, and oxalyl chlorides, other
compounds that react with amines can be used to form P1 substitutions. Examples
include, but are not limited to, R'-halogen, R'-tosyl, R'-mesylate, R'S(O)2C1,
30

WO 2006/096270 PCT/US2006/004019
R'NS(O)2C1, R'OH, R'COOH, and R'CH2-halogen. -C=CH2 compounds can
optionally be converted into -C=O compounds with ozonolysis (g).

[0188 ] Scheme III shows an additional method for preparing compounds of this
invention. The aryl bromide or iodide can be coupled with substituted terminal alkynes
in the presence of palladium, base, and Cul under Sonogashira coupling conditions
(Sonogashira, Kenkichi. 'Palladium-catalyzed alkynylation" Editor(s): Negishi, Ei-
ichi. Handbook of Organopalladium Chemistry for Organic Synthesis (2002), 1:493-
529. Publisher: John Wiley & Sons, Inc., Hoboken, N. J.) to form the product as shown.
H=R' refers to suitable terminal alkynes which are either commercially available
or can be made from commercially available starting materials.
[0189] Although certain exemplary embodiments are depicted and described
above and herein, it will be appreciated that a compounds of the invention can be
prepared according to the methods described generally above using appropriate starting
materials by methods generally available to one of ordinary skill in the art.
Uses, Formulations and Administration
[0190] As discussed above, the present invention provides compounds that are
inhibitors of protein kinases, including JAK family, ROCK and PKA kinases,
particularly JAK2 and JAK3 kinases, and thus the present compounds are useful for
the treatment of diseases, disorders, and conditions including, but not limited to,
immunodeficiency disorders, inflammatory diseases, allergic diseases, autoimmune
diseases, proliferative disorders, immunologically-mediated diseases, respiratory
disorders. Accordingly, in another aspect of the present invention, phannaceutically
acceptable compositions are provided, wherein these compositions comprise any of the
compounds as described herein, and optionally comprise a pharmaceuticaUy acceptable
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WO 2006/096270 PCT/US2006/004019
carrier, adjuvant or vehicle. In certain embodiments, these compositions optionally
further comprise one or more additional therapeutic agents.
[ 0191] It will also be appreciated that certain of the compounds of present
invention can exist in free form for treatment, or where appropriate, as a
pharmaceutically acceptable derivative thereof. According to the present invention, a
pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically
acceptable salts, esters, salts of such esters, or any other adduct or derivative which
upon administration to a patient in need is capable of providing, directly or indirectly, a
compound as otherwise described herein, or a metabolite or residue thereof.
[ 0192 ] As used herein, the term "pharmaceutically acceptable salt" refers to
those salts which are, within the scope of sound medical judgment, suitable for use in
contact with the tissues of humans and lower animals without undue toxicity, irritation,
allergic response and the like, and are commensurate with a reasonable benefit/risk
ratio. A "pharmaceutically acceptable salt" means any non-toxic salt of a compound of
this invention.
[0193 ] Pharmaceutically acceptable salts are well known in the art. For
example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in J.
Pharmaceutical Sciences, 1977,66,1-19, incorporated herein by reference.
Pharmaceutically acceptable salts of the compounds of this invention include those
derived from suitable inorganic and organic acids and bases. Examples of
pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group
formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric
acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic
acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using
other methods used in the art such as ion exchange. Other pharmaceutically acceptable
salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate,
bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate,
cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate,
fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate,
hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl
sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate,
nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-
32

WO 2006/096270 PCT/US2006/004019
phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate,
tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts
derived from appropriate bases include alkali metal, alkaline earth metal, ammonium
and N+(C1-4alkyl)4 salts. This invention also envisions the quaternization of any basic
nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or
dispersible products may be obtained by such quaternization. Representative alkali or
alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and
the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic
ammonium, quaternary ammonium, and amine cations formed using counterfoils such
as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and
aryl sulfonate.
[0194] As described above, the pharmaceutically acceptable compositions of
the present invention additionally comprise a pharmaceutically acceptable carrier,
adjuvant, or vehicle, which, as used herein, includes any and all solvents, diluents, or
other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic
agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the
like, as suited to the particular dosage form desired. Remington's Pharmaceutical
Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980)
discloses various carriers used in formulating pharmaceutically acceptable
compositions and known techniques for the preparation thereof. Except insofar as any
conventional carrier medium is incompatible with the compounds of the invention, such
as by producing any undesirable biological effect or otherwise interacting in a
deleterious manner with any other component(s) of the pharmaceutically acceptable
composition, its use is contemplated to be within the scope of this invention. Some
examples of materials which can serve as pharmaceutically acceptable carriers include,
but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum
proteins, such as human serum albumin, buffer substances such as phosphates, glycine,
sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty
acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen
phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica,
magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylene-
polyoxypropylene-block polymers, wool fat, sugars such as lactose, glucose and
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sucrose; starches such as corn starch and potato starch; cellulose and its derivatives
such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate;
powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and
suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil;
olive oil; corn oil and soybean oil; glycols; such a propylene glycol or polyethylene
glycol; esters such as ethyl oleate and ethyl laurate; agar, buffering agents such as
magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water;
isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well
as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium
stearate, as well as coloring agents, releasing agents, coating agents, sweetening,
flavoring and perfuming agents, preservatives and antioxidants can also be present in
the composition, according to the judgment of the formulator.
[0195] In yet another aspect, a method for the treatment or lessening the
severity of a proliferative disorder, a cardiac disorder, a neurodegenerative disorder, an
autoimmune disorder, a condition associated with organ transplant, an inflammatory
disorder, or an immunologically mediated disorder is provided comprising
administering an effective amount of a compound, or a pharmaceutically acceptable
composition comprising a compound to a subject in need thereof. In certain
embodiments of the present invention an "effective amount" of the compound or
pharmaceutically acceptable composition is that amount effective for treating or
lessening the severity of a proliferative disorder, a cardiac disorder, a
neurodegenerative disorder, an autoimmune disorder, a condition associated with organ
transplant, an inflammatory disorder, a psychotic disorder, a viral disease, a bone
disorder or an immunologically mediated disorder. The compounds and compositions,
according to the method of the present invention, may be administered using any
amount and any route of administration effective for treating or lessening the severity
of a proliferative disorder, a cardiac disorder, a neurodegenerative disorder, an
autoimmune disorder, a condition associated with organ transplant, an inflammatory
disorder, a psychotic disorder, a viral disease, a bone disorder or an immunologically
mediated disorder. The exact amount required will vary from subject to subject,
depending on the species, age, and general condition of the subject, the severity of the
infection, the particular agent, its mode of administration, and the like. The compounds
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WO 2006/096270 PCT/US2006/004019
of the invention are preferably formulated in dosage unit form for ease of
administration and uniformity of dosage. The expression "dosage unit form" as used
herein refers to a physically discrete unit of agent appropriate for the patient to be
treated. It will be understood, however, that the total daily usage of the compounds and
compositions of the present invention will be decided by the attending physician within
the scope of sound medical judgment The specific effective dose level for any
particular patient or organism will depend upon a variety of factors including the
disorder being treated and the severity of the disorder; the activity of the specific
compound employed; the specific composition employed; the age, body weight, general
health, sex and diet of the patient; the time of administration, route of administration,
and rate of excretion of the specific compound employed; the duration of the treatment;
drugs used in combination or coincidental with the specific compound employed, and
like factors well known in the medical arts. The term "patient", as used herein, means
an animal, preferably a mammal, and most preferably a human.
[ 0196] The pharmaceutically acceptable compositions of this invention can be
administered to humans and other animals orally, rectally, parenterally, intracisternally,
intravaginally, intraperitoneally, topically (as by powders, ointments, or drops),
bucally, as an oral or nasal spray, or the like, depending on the severity of the infection
being treated. In certain embodiments, the compounds of the invention may be
administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50
mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight
per day, one or more times a day, to obtain the desired therapeutic effect.
[0197] liquid dosage forms for oral administration include, but are not limited
to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions,
syrups and elixirs. In addition to the active compounds, the liquid dosage forms may
contain inert diluents commonly used in the art such as, for example, water or other
solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol,
ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-
butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn,
germ, olives, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene
glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents,
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the oral compositions can also include adjuvants such as wetting agents, emulsifying
and suspending agents, sweetening, flavoring, and perfuming agents.
[0198] Injectable preparations, for example, sterile injectable aqueous or
oleaginous suspensions may be formulated according to the known art using suitable
dispersing or wetting agents and suspending agents. The sterile injectable preparation
may also be a sterile injectable solution, suspension or emulsion in a nontoxic
parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
Among the acceptable vehicles and solvents that may be employed are water, Ringer's
solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are
conventionally employed as a solvent or suspending medium. For this purpose any
bland fixed oil can be employed including synthetic mono- or diglycerides. In addition,
fatty acids such as oleic acid are used in the preparation of injectables.
[0199] The injectable formulations can be sterilized, for example, by filtration
through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of
sterile solid compositions which can be dissolved or dispersed in sterile water or other
sterile injectable medium prior to use.
[0200] In order to prolong the effect of a compound of the present invention, it
is often desirable to slow the absorption of the compound from subcutaneous or
intramuscular injection. This may be accomplished by the use of a liquid suspension of
crystalline or amorphous material with poor water solubility. The rate of absorption of
the compound then depends upon its rate of dissolution that, in turn, may depend upon
crystal size and crystalline form. Alternatively, delayed absorption of a parenterally
administered compound form is accomplished by dissolving or suspending the
compound in an oil vehicle. Injectable depot forms are made by forming
microencapsule matrices of the compound in biodegradable polymers such as
polylactide-polyglycolide. Depending upon the ratio of compound to polymer and the
nature of the particular polymer employed, the rate of compound release can be
controlled. Examples of other biodegradable polymers include poly(orthoesters) and
poly(anhydrides). Depot injectable formulations are also prepared by entrapping the
compound in liposomes or microemulsions that are compatible with body tissues.
[0201] Compositions for rectal or vaginal administration are preferably
suppositories which can be prepared by mixing the compounds of this invention with
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suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or
a suppository wax which are solid at ambient temperature but liquid at body
temperature and therefore melt in the rectum or vaginal cavity and release the active
compound.
[0202] Solid dosage forms for oral administration include capsules, tablets,
pills, powders, and granules. In such solid dosage forms, the active compound is mixed
with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium
citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose,
sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example,
carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia,
c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium
carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate,
e) solution retarding agents such as paraffin, f) absorption accelerators such as
quaternary ammonium compounds, g) wetting agents such as, for example, cetyl
alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and
i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene
glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and
pills, the dosage form may also comprise buffering agents.
[0203] Solid compositions of a similar type may also be employed as fillers in
soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as
well as high molecular weight polyethylene glycols and the like. The solid dosage
forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings
and shells such as enteric coatings and other coatings well known in the pharmaceutical
formulating art. They may optionally contain opacifying agents and can also be of a
composition that they release the active ingredient(s) only, or preferentially, in a certain
part of the intestinal tract, optionally, in a delayed manner. Examples of embedding
compositions that can be used include polymeric substances and waxes. Solid
compositions of a similar type may also be employed as fillers in soft and hard-filled
gelatin capsules using such excipients as lactose or milk sugar as well as high
molecular weight polethylene glycols and the like.
[0204] The active compounds can also be in micro-encapsulated form with one
or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules,
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pills, and granules can be prepared with coatings and shells such as enteric coatings,
release controlling coatings and other coatings well known in the pharmaceutical
formulating art. In such solid dosage forms the active compound may be admixed with
at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also
comprise, as is normal practice, additional substances other than inert diluents, e.g.,
tableting lubricants and other tableting aids such a magnesium stearate and
microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms
may also comprise buffering agents. They may optionally contain opacifying agents
and can also be of a composition that they release the active ingredient(s) only, or
preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
Examples of embedding compositions that can be used include polymeric substances
and waxes.
[0205] Dosage forms for topical or transdermal administration of a compound
of this invention include ointments, pastes, creams, lotions, gels, powders, solutions,
sprays, inhalants or patches. The active component is admixed under sterile conditions
with a pharmaceutically acceptable carrier and any needed preservatives or buffers as
may be required. Ophthalmic formulation, ear drops, and eye drops are also
contemplated as being within the scope of this invention. Additionally, the present
invention contemplates the use of transdermal patches, which have the added advantage
of providing controlled delivery of a compound to the body. Such dosage forms can be
made by dissolving or dispensing the compound in the proper medium. Absorption
enhancers can also be used to increase the flux of the compound across the skin. The
rate can be controlled by either providing a rate controlling membrane or by dispersing
the compound in a polymer matrix or gel.
[0206] As described generally above, the compounds of the invention are useful
as inhibitors of protein kinases, particularly for the JAK family kinases, ROCK and
PKA. In a specific embodiment, the compounds and compositions of the invention are
inhibitors of JAK2 and JAK3. The compounds and compositions are useful for treating
or lessening the severity of a disease, condition, or disorder where activation of a JAK
family kinase, ROCK and/or PKA is implicated in the disease, condition, or disorder.
In a particular embodiment, the compounds and compositions are useful for treating or
lessening the severity of a disease, condition, or disorder where activation of JAK2 or
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WO 2006/096270 PCT/US2006/004019
JAK3 is implicated in the disease, condition, or disorder. When activation of JAK2,
JAK3, ROCK or PKA is implicated in a particular disease, condition, or disorder, the
disease, condition, or disorder may also be referred to as "JAK2-mediated disease",
"JAK3-mediated disease", "ROCK-mediated disease" or "PKA-mediated disease",
respectively. Accordingly, in another aspect, the present invention provides a method
for treating or lessening the severity of a disease, condition, or disorder where
activation of a JAK family kinase, ROCK or PKA, particularly JAK2 or JAK3, is
implicated in the disease state.
[0207] The activity of a compound utilized in this invention as an inhibitor of a
JAK family kinase, ROCK or PKA, particularly JAK2 or JAK3, may be assayed in
vitro, in vivo or in a cell line. In vitro assays include assays that determine inhibition of
either the phosphorylation activity or ATPase activity of activated JAK2, JAK3, ROCK
or PKA. Alternate in vitro assays quantitate the ability of the inhibitor to bind to JAK2,
JAK3, ROCK or PKA. Inhibitor binding may be measured by radiolabelling the
inhibitor prior to binding, isolating the inhibitor/kinase complex and determining the
amount of radiolabel bound Alternatively, inhibitor binding may be determined by
running a competition experiment where new inhibitors are incubated with the kinase
of interest bound to known radioligands.
[0208] The term "detectably inhibit", as used herein means a detectable
change in JAK2, JAK3, ROCK or PKA activity between a sample comprising said
composition and JAK2, JAK3, ROCK or PKA and an equivalent sample comprising
JAK2, JAK3, ROCK or PKA, respectively, in the absence of said composition.
[0209] The term "JAK3-mediated disease" or "JAK3-mediated condition",
as used herein means any disease or other deleterious condition in which JAK3 is
known to play a role. A JAK3-mediated condition or disease also means those diseases
or conditions that are alleviated by treatment with a JAK3 inhibitor. Such conditions
include, without limitation, immune responses such as allergic or type I
hypersensitivity reactions, asthma, autoimmune diseases such as transplant rejection,
graft versus host disease, rheumatoid arthritis, amyotrophic lateral sclerosis, and
multiple sclerosis, neurodegenerative disorders such as Familial amyotrophic lateral
sclerosis (FALS), as well as in solid and hematologic malignancies such as leukemias
and lymphomas.
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[0210] The term "JAK2-mediated disease" or "JAK2-mediated condition", as
used herein means any disease or other deleterious condition in which JAK2 is known
to play a role. A JAK2-mediated condition or disease also means those diseases or
conditions that are alleviated by treatment with a JAK2 inhibitor. Such conditions
include, without limitation, myeloproliferative disorders, including polycythemia vera,
essential thrombocythemia, chronic idiopathic myelofibrosis, myeloid metaplasia with
myelofibrosis, chronic myeloid leukemia, chronic myelomonocytic leukemia, chronic
eosinophilic leukemia, hypereosinophilic syndrome and systematic mast cell disease.
[0211] The term "ROCK-mediated disease" or "ROCK-mediated condition", as
used herein, means any disease or other deleterious condition in which ROCK is known
to play a role. A ROCK-mediated condition or disease also means those diseases or
conditions that are alleviated by treatment with a ROCK inhibitor. Such conditions
include, without limitation, hypertension, angina, angina pectoris, cerebrovascular
contraction, asthma, peripheral circulation disorder, premature birth, cancer, erectile
dysfunction, arteriosclerosis, spasm (cerebral vasospasm and coronary vasospasm),
retinopathy (e.g., glaucoma), inflammatory disorders, autoimmune disorders, AIDS,
osteoporosis, myocardial hypertrophy, ischemia/reperfusion-induced injury, endothelial
dysfunction, Alzheimer's disease, or benign prostatic hyperplasia. In other
embodiments, such conditions in which ROCK is known to play a role include, without
limitation, hypertension, cerebral vasospasm, coronary vasospasm, bronchial asthma,
preterm labor, erectile dysfunction, glaucoma, vascular smooth muscle cell
proliferation, myocardial hypertrophy, malignoma, ischemia/reperfusion-induced
injury, endothelial dysfunction, Crohn's Disease and colitis, neurite outgrowth,
Raynaud's Disease, angina, Alzheimer's disease, benign prostatic hyperplasia, or
atherosclerosis.
[0212] The term 'TKA-mediated disease" or "PKA-mediated condition", as
used herein, means any disease or other deleterious condition in which PKA is known
to play a role. The term PKA-mediated condition or disease also means those diseases
or conditions that are alleviated by treatment with a PKA inhibitor. PKA-mediated
diseases or conditions include, but are not limited to, proliferative disorders and cancer.
[ 0213 ] It will also be appreciated that the compounds and pharmaceutically
acceptable compositions of the present invention can be employed in combination
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therapies, that is, the compounds and phannaceutically acceptable compositions can be
administered concurrently with, prior to, or subsequent to, one or more other desired
therapeutics or medical procedures. The particular combination of therapies
(therapeutics or procedures) to employ in a combination regimen will take into account
compatibility of the desired therapeutics and/or procedures and the desired therapeutic
effect to be achieved. It will also be appreciated that the therapies employed may
achieve a desired effect for the same disorder (for example, an inventive compound
may be administered concurrently with another agent used to treat the same disorder),
or they may achieve different effects (e.g., control of any adverse effects). As used
herein, additional therapeutic agents that are normally administered to treat or prevent a
particular disease, or condition, are known as "appropriate for the disease, or condition,
being treated".
[0214] The amount of additional therapeutic agent present in the compositions
of this invention will be no more than the amount that would normally be administered
in a composition comprising that therapeutic agent as the only active agent. Preferably
the amount of additional therapeutic agent in the presently disclosed compositions will
range from about 50% to 100% of the amount normally present in a composition
comprising that agent as the only therapeutically active agent.
[0215] The compounds of this invention or phannaceutically acceptable
compositions thereof may also be incorporated into compositions for coating
implantable medical devices, such as prostheses, artificial valves, vascular grafts, stents
and catheters. Accordingly, the present invention, in another aspect, includes a
composition for coating an implantable device comprising a compound of the present
invention as described generally above, and in classes and subclasses herein, and a
carrier suitable for coating said implantable device. In still another aspect, the present
invention includes an implantable device coated with a composition comprising a
compound of the present invention as described generally above, and in classes and
subclasses herein, and a carrier suitable for coating said implantable device.
[0216] Vascular stents, for example, have been used to overcome restenosis (re-
narrowing of the vessel wall after injury). However, patients using stents or other
implantable devices risk clot formation or platelet activation. These unwanted effects
may be prevented or mitigated by pre-coating the device with a phannaceutically
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WO 2006/096270 PCT/US2006/004019
acceptable composition comprising a kinase inhibitor. Suitable coatings and the
general preparation of coated implantable devices are described in US Patents
6,099,562; 5,886,026; and 5,304,121. The coatings are typically biocompatible
polymeric materials such as a hydrogel polymer, polymethyldisiloxane,
polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and
mixtures thereof. The coatings may optionally be further covered by a suitable topcoat
of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations
thereof to impart controlled release characteristics in the composition.
[ 0217 ] Another aspect of the invention relates to inhibiting JAK2, JAK3,
ROCK or PKA activity in a biological sample, which method comprises contacting said
biological sample with a compound of formula I or a composition comprising said
compound. The term "biological sample", as used herein, is an ex vivo or in vitro
sample, and includes, without limitation, cell cultures or extracts thereof; biopsied
material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces,
semen, tears, or other body fluids or extracts thereof.
[0218] Inhibition of JAK2, JAK3, ROCK or PKA kinase activity in a biological
sample is useful for a variety of purposes that are known to one of skill in the art.
Examples of such purposes include, but are not limited to, blood transfusion, organ-
transplantation, biological specimen storage, and biological assays.
EXAMPLES
[ 0219 ] For Examples 1-7,1H-NMR spectra were recorded at 500 MHz using a
Bruker AMX 500 instrument. Mass spectrometry samples were analyzed on a
MicroMass ZQ or Quattro II mass spectrometer operated in single MS mode with
electrospray ionization. Samples were introduced into the mass spectrometer using
flow injection (HA) or chromatography. Mobile phase for all mass spectrometric
analyses consisted of acetonitrile-water mixtures with 0.2% formic acid as a modifier.
As used herein, the term "Rtt" refers to the HPLC retention time, in minutes, associated
with the compound.
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4-chloro-7-tosyI-7H-pyrrolo[2,3-d]pyrimidine
[0220] A slurry of 1 (307 mg, 2.00 mmol), Tosyl-chloride (418 mg, 2.20 mmol)
and freshly ground K2CO3 (1.1 g, 8.0 mmol) in DMF (5.0 mL) was stirred at R.T. for 2
h. The mixture was partitioned between water and EtOAc and the organic phase was
washed with brine (2x), dried (Na2SO4), filtered, and concentrated to provide the title
compound (583 mg, 1.89 mmol, 95% yield) as a white solid.

4-cyclopentenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine
[0221] A mixture of 4-chloro-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (62 mg,
0.20 mmol), cyclopenteneboronic acid (27 mg, 0.24 mmol), KOAc (78 mg, 0.80
mmol), and Pd(PPh3)4 (11 mg, 0.010 mmol), in dioxane (0.6 mL) was heated to 150
°C (MW, 600s) in a sealed tube. The reaction mixture was subjected to flash
chromatography (SiO2,0-50% EtOAc—hexanes, gradient elution) to provide the title
compound (55 mg, 0.16 mmol, 81 % yield) as a white solid.

4-cycIopentenyl-7H-pyrroIo[2,3-d]pyrimidine (Compound 1)
[0222] A mixture of 4-cyclopentenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (55
mg, 0.16 mmol) in methanol (0.5 mL) was treated with NaOMe (0.5 N, 0.25 mL) and
warmed to 60 °C for 25 min. the reaction was diluted, quenched with TFA,
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WO 2006/096270 PCT/US2006/004019
concentrated and subjected to flash chromatography to provide the title compound (19
mg) as a white solid.
LC-MS Rtt = 1.57 min, (M+H+) 186.00
1H NMR (500 MHz, CDC13) 9.30 (br s, 1H), 8.86 (s, 1H), 7.33 (dd, 1H), 6.98 (dd, 1H),
6.79 (dd, 1H), 3.06 (m, 2H), 2.70 (m, 2H), 2.13 (q, 2H)

4-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidine (Compound 3)
[0223] A mixture of 4-cyclopentenyl-7H-pyrrolo[2,3-d]pyrirnidine (11 mg,
0.060 mmol) and Pd-C (10% on carbon, 22 mg) in EtOAc (1 mL) was stirred under H2
atmosphere (balloon) for 5 h.. The mixture was filtered and concentrated to provide the
title compound (10 mg) as a white solid.
LC-MS Rtt= 1.37 min, (M+H+) 188.10
1H NMR (500 MHz, CDC13) 9.00 (br s, 1H), 8.80 (s, 1H), 7.24 (buried dd, 1H), 6.63
(dd, 1H), 3.56 (q, 2H), 2.13 (m, 2H), 2.05 (m, 2H), 1.92 (m, 2H), 1.75 (m, 2H)
[0224 ] The compounds in Examples 3-7 were made according to Scheme II.

4-(1-phenylvinyl)-7H-pyrrolo[2,3-d]pyrimidine (Compound 8)
LC-MS Rtt = 2 min, (M+H+) 221
1HNMR 500MHz; DMSO-d6:12.6(br m,lH), 8.85(s,l), 7.53(m,lH), 7.4(m,5H),
6.03(m,3H)
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WO 2006/096270 PCT/US2006/004019

4-(4-fluorostyryl)-7H-pyrrolo[2,3-d]pyrimidine (Compound 5)
LC-MS Rtt = 2 min, (M+H+) 239
1HNMR: 500MHZ; DMSO-d6:13.8(br m,lH), 8.93(s,l), 8.14(d,lH), 7.92(dd,2H),
7.83(m,lH), 7.71(d,lH), 7,35(dd,2H), 7.27(m,lH)

4-(4-chlorostyryl)-7H-pyrrolo[2,3-d]pyrimidine (Compound 6)
LC-MS Rtt = 2.3 min, (M+H+) 255
lH NMR: 500MHz; DMSO-d6:12.7(br m,lH), 8.90(s,l), 8.10(d,lH), 7.90(d,2H),
7.79(m,2H), 7.54(d,2H), 7.22(m,lH)

4-(4-(trifluoromethyl)styryl)-7H-pyrrolo[2,3-d]pyrimidine (Compound 7)
LC-MS Rtt = 2.7 min, (M+H+) 289
1HNMR: 500MHZ; DMSO-d6:12.5(brm,lH), 8.88(s,l), 8.15(d,lH), 8.07(d,2H),
7.90(d,lH), 7.85(d,2H), 7.75(m,lH), 7.45(m,lH), 7.17(m,lH)

4-styryl-7H-pyrrolo[2,3-d]pyrimidine (Compound 4)
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WO 2006/096270 PCT/US2006/004019
LC-MS Rtt = 2 min, (M+H+) 221
1HNMR: 500MHz;DMSO-d6:12.8(brm,lH),8.93(s,l),8.14(d,2H),7.85(d,2H),
7.83(m,lH), 7.75(d,lH), 7.51(d,2H), 7.47(m,lH), 7.28(m,lH)

[0225] Step 1: Compound A (l-(tert Butoxycarbonyl)-3-piperidine carboxylic
acid) (4.60g, 20.0 mMol) was suspended in 40 ml of CH2C12. Added was EDCI (4.60 g,
24.0 mMol), followed by N.O-Dimethylamine (HC1) (2.34 g (24.0 mMol) and catalytic
DMAP. The resulting mixture was allowed to stir at room temperature overnight. All
volatiles were removed at reduced pressure. The residue was dissolved in saturated
aqueous NaHCO3 solution and EtOAc. The layers were separated and the organic was
washed with brine, dried over MgSO4, filtered and evaporated to dryness. No further
purification, material used as is. Yield: 4.7 g, approximately 86%. HNMR (500 MHz,
CDC13) 3.73 (s, 3H), 3.18 (s, 3H), 2.87 - 2.81 (m, 4H), 1.94 (s, H), 1.73 - 1.65 (m, 4H),
1.49 - 1.46 (m, 9H).
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[0226] Step 2: To a solution of compound B (4.7 g, 17.2 mMol) in 70 ml of
THF at 0°C (under N2) was added a 3.0 M (11.5 ml, 34.5 mMol) solution of Methyl
Magnesium Bromide in THF. After the addition was complete, the cooling bath was
removed and the resulting mixture was allowed to rise to room temperature where it
was allowed to stir overnight. The resulting mixture was quenched with a saturated
aqueous KHSO4 solution and diluted with EtOAc. The organic phase was washed with
brine, dried over MgSO4, filtered and evaporated to dryness. The crude residue was
passed through a plug of silica gel and eluted with 5-20% EtOAc/Hexane. Yield:
2.37g, approximately 60%. HNMR (500 MHz, CDC13) 4.10 (d, J = 12.0 Hz, H), 3.92
(s, H), 2.94 (dd, J = 10.3,13.3 Hz, H), 2.82 - 2.77 (m, H), 2.52 - 2.48 (m, H), 2.18 (s,
3H), 1.98 (dd, J = 3.6,12.9 Hz, H), 1.73 -1.69 (m, H), 1.56 -1.44 (m, 11H).
[0227] Step 3: Compound C (2.37 g, 10.4 mMol) was dissolved in 5.0 ml of
THF and added (under N2) to a solution of LiHMDS (13.0 ml, 13.0 mMol) at -78°C
(IPA-dry ice bath). After 30 min., added was 2-[N,N-bis(trifluoromethylsulfonyl)
amino]pyridine (4.11g, 11.5mMol) and after 10 min. the cooling bath was removed.
The resulting mixture gradually rose to room temperature where it was allowed to stir
overnight. The resulting mixture was quenched with saturated aqueous KHSO4 solution
and diluted with EtOAc. The layers were separated and the organic was washed with
brine, dried over MgSO4, filtered and evaporated to dryness. The crude was passed
through a plug of silica gel and eluted with 10% EtOAc / Hexane. Yield: 2.93 g,
approximately 79%. HNMR (500 MHz, CDC13) 5.19 (d, J = 4.1 Hz, H), 5.01 (dd, J =
1.0,4.1 Hz, H), 4.14 - 4.11 (m, H), 2.84 (dd, J = 9.7,13.2 Hz, 3H), 2.41 (s, H), 2.04 -
2.00 (m, H), 1.72 (t, J = 3.4 Hz, H), 1.52 -1.46 (m, 11H).
[0228] Step 4: Compound D (2.93 g, 8.2 mMol) was dissolved in 30 ml of
toluene. Added was Bis(Pinacoloto)diboron (2.07 g, 8.2 mMol) followed by Triphenyl
phosphine (117.3 mg, 0.44mMol) and Potassium phenoxide (1.48 g, 11.2 mMol). The
RM was degassed with Ar for 5 min. Added was trans-Dichlorobis
(triphenylphosphine)palladium (II) (157.0 mg, 0.22 mMol) and the resulting mixture
was allowed stir at 55°C for 3 hours. The resulting mixture was allowed to cool to room
temperature where it was stirred overnight. The resulting mixture was diluted with
saturated aqueous NaHCO3 solution and EtOAc. The layers were separated and the
organic was washed with brine, dried over MgSO4, filtered and evaporated to dryness.
47

WO 2006/096270 PCT/US2006/004019
The crude was passed through a plug of silica gel eluting with 5-15 % EtOAc/Hexane.
Phenol was still present, so material was dissolved in Et2O and washed with 1N NaOH
solution. The organic phase was dried over MgSO4, filtered and evaporated to dryness.
Yield: 2.01 g, approximately 73%. HNMR (500 MHz, CDC13) 5.83 (d, J = 2.6 Hz, H),
5.65 (s, H), 4.07 (dd, J = 1.6,12.8 Hz, 2H), 2.64 - 2.58 (m, 2H), 2.26 (t, J = 11.2 Hz,
H), 1.82 - 1.79 (m, H), 1.67 -1.64 (m, H), 1.50 (t, J = 3.7 Hz, 11H), 1.29 - 1.19 (m,
12H).
48
[0229] Step 5: Compound E (45.7 mg, 0.14 mMol) was dissolved in 1.0 ml of
DME. Added was 4-Chloro-7H-pyrrolo[2,3-d]pyrimidine (20.8 mg, 0.14 mMol)
followed by a 2.0 M solution of Na2CO3 (200uL, 0.4 mMol). The resulting mixture was
degassed with Ar for 5 minutes and added was catalytic tetrakis triphenylphosphine
palladium (0). The resulting mixture was warmed to 160°C via microwave irradiation.
After 10 minutes, the resulting mixture was cooled to room temperature. The resulting
mixture was diluted with H2O and EtOAc. The layers were separated and the organic
washed with brine, dried over MgSO4, filtered and evaporated to dryness. The crude
residue was chromatographed on a plug of silica gel and eluted with 10 - 30% EtOAc /
Hexane. Yield: 7.1 mg of Compound 22.


WO 2006/096270 PCT/US2006/004019
(a) tri-n-butyl(l-ethoxyvinyl) tin, Pd(PPh3)2Cl2, toluene, 90°C (b) 6N HC1, MeOH,
THF (c) HBr, HOAc (d) HNR1R2) Et3N (e) NaOR or HOR, Et3N (f) LiOH, or NaOMe

[0230] 4-Iodo-7-(toluene-4-sulfonyl)-7H-pyrroIo[2,3-d]pyrimidine: [5g.
16.2mmol] of -Chloro-7-(toluene-4-sulfonyl)-7H-pyrrolo[2,3-d]pyrimidine (as
described in Example 1) was added in small portions, to l00mL of cold stirring 47%
stabilized hydriodic acid at 0°C and stirred for one hour cold; the temperature was then
allowed to warm to ambient temperature and stirred an additional 5 hrs. The reaction
mixture was diluted with water and the solid was isolated via suction filtration, the
solid being washed with additional water. The crude solid was dissolved in
dichloromethane and washed with saturated sodium hydrogen carbonate solution twice,
brined, dried (Na2SO4) and the solvent was removed under reduced pressure and
triturated with a 2:1 mixture of hexanes/ MTBE to yield 5.7g of a white material (88%).
1HNMR: 500Mhz in CDCL3 8.61(s,lH), 8.06(d,2H J=8.5Hz), 7.75(d,lH J= 4.1Hz),
7.32(d,2H J=8.5Hz), 6.45(d,lH J= 4.1Hz), 2.4(s,3H).

[0231] Step a: 4-(1-Ethoxy-vinyl)-7-(toluene-4-sulfonyl)-7H-pyrrolo[2,3-
d]pyrimidine: [l0g, 25mmol] of 4-Iodo-7-(toluene-4-sulfonyl)-7H-pyrrolo[2,3-
d]pyrimidine (as described above) was dissolved/suspended in 200mL of dry toluene
along with [2.0g, 2.85mmol] of palladium (II) bis-triphenylphosphine dichloride. The
mixture was purged with nitrogen gas for ~5 minutes before mixture was heated to
90°C in an oil bath under an atmosphere of nitrogen gas. Added slowly dropwise over
2 hours, was [12.66mL, 13.54g, 37.5mmol] of tri-n-butyl( 1-ethoxyvinyl) tin in l00mL
49

WO 2006/096270 PCT/US2006/004019
of dry toluene. After completing the addition, the mixture was heated for an additional
6 hours under nitrogen. The reaction was cooled to ambient temperature and the
solvent was removed under reduced pressure until the remaining volume was 1/5 the
original. Added to this slurry was 160mL of petroleum ether and the mixture was
stirred for 1 hour, the solid being isolated via suction filtration and washed with
petroleum ether. The damp solid was slurried in acetonitrile, stirred for one hour and
the solid re-isolated via suction filtration and airdried. The resulting pale yellow solid,
7.2g representing an 82% yield was utilized without further treatment. 1HNMR:
500Mhz in CDCL3 8.9(s,lH), 8.07(d, 2H, J=8.5Hz), 7.7(d, 1H, J=4.1Hz), 7.28(d,2H,
J=8.5Hz), 7.04(d,lH, J=4.1Hz), 5.7(d,lH, J=2Hz), 4.58(d,lH,J=2Hz), 4.0(quart,2H),
2.4(s,3H), 1.5(t,3H).

[0232] Step b: l-[7-(Toluene-4-sulfonyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-
ethanone: [7.25g,21.12mmol] of 4-(l-Ethoxy-vinyl)-7-(toluene-4-sulfonyl)-7H-
pyrrolo[2,3-d]pyrimidine was dissolved in 50mL each of methanol and THF and stirred
with l0mL of 6N HCL for 4.0 hours at ambient temperature. The solvents were
removed under reduced pressure and the residue was partitioned between
dichloromethane and saturated sodium hydrogen carbonate solution. The organic
fraction was brined and dried with anhydrous sodium sulphate and the solvent was
removed under reduced pressure. The crude material was triturated with a mixture of
MTBE and petroleum ether (1:4) for several hours and the solid finally isolated via
suction filtration and air dried. The 5.95g of pale yellow material, representing a 89%
yield was used without further purification. 1HNMR:500Mhz CDCL3 9.0(s,lH),
8.08(d,2H, J=8.4Hz), 7.87(d,, 1H, J=4.1Hz), 7.3(m,3H), 2.8(s,3H), 2.4(s,3H).
50

WO 2006/096270 PCT/US2006/004019

[0233] Step c: 2-Bromo-1-[7-(toluene-4-sulfonyl)-7H-pyrrolo[2,3-

(a) Alkylzinc halide, THF, r.t-100 C (b) LiOH/THF or NaOMe/MeOH
51
d]pyrimidin-4-yl]-ethanone: [5.95g, 18.88mmol] of l-[7-(Toluene-4-sulfonyl)-7H-
pyrrolo[2,3-d]pyrimidin-4-yl]-ethanone was dissolved/suspended in 90mL of glacial
acetic acid and [7.53mL, 10.197g, 37.76mmol] of 30% hydrogen bromide in acetic
acid. Added dropwise to this stirring mixture at ambient temperature, was [0.970mL,
3.02g, 18.88mmol] of bromine in l0mL of glacial acetic acid over 1.0 hour. The
reaction was stirred an additional 4.0 hours at ambient temperature during which time a
yellow precipitate forms. The solvent was removed under reduced pressure and the
residue was partitioned between dichloromethane and sat'ed sodium hydrogen
carbonate solution. The organic phase was washed with water, brine, and dried with
anhydrous sodium sulphate and the solvent was removed under reduce pressure. The
crude solid was triturated /stirred with MTBE overnight and the solid isolated via
suction filtration and airdried to yield 4.2g of pale yellow solid, a 56.6% yield. 1H
NMR: 500Mhz in CDCL3 9.1(s,lH), 8.09(d,2H, J=8.5Hz), 7.93(d,lH, J=4.0Hz),
7.33(d,2H, J=8.5Hz). 7.29(d,lH, J=4.0Hz), 4.83(s,2H), 2.4(s,3H).
[ 0234 ] Steps d, e: Conversion of the bromide may be accomplished upon
nucleophilic displacement with primary or secondary amines (i.e., step d) or upon
treatment with an alcohol (i.e., step e) under basic conditions.
[ 0235] Step f: The compound is deprotected as described for Compound 1.

WO 2006/096270 PCT/US2006/004019

(a) Alkylzinc halide, THF, r.t.- 80 C (b) NaOMe/MeOH
[0236] Steps a,b: 4-Bicyclo[2.2.1]hept-2-yl-7H-pyrrolo[2,3-d]pyrimidine:
To a solution of N-tosyl-4-chlorodeazapurine (40 mg, 0.13 mmol) in anhydrous THF
(0.5 mL) was added an appropriate alkylzinc halide (e.g., exo-2-norbornylzinc bromide
[0.40 mL, 0.5 M]) and the mixture is stirred overnight at room temperature. Then the
mixture is heated to 80°C for an additional 1.5h and cooled to room temperature. The
reaction mixture is treated with NaOMe (200 uL, 0.5 M) in MeOH at 50°C for 1.5 h
before work up. Rochelle's salt is added and the mixture is extracted repeatedly with
EtOAc. The organic layer is filtered and concentrated. The crude residue is purified by
HPLC to provide the Compound 26. LC-MS: RT = 1.86, (M+H) = 214.2; 1H NMR
(DMSO) 12.42 (m, 2H), 8.78 (s, 1H), 8.74 (s, 1H), 7.62 (br s, 2H), 6.82 (s, 1H), 6.77 (s,
1H),3.76 (m, 1H), 3.31 (s, 1H), 2.75 (m, 1H), 2.46 (m, 1H), 2.37 (m, 2H), 2.14 (m,
2H), 1.90 (m, 1H), 1.72 (m, 1H), 1.67 (d, 2H), 1.59 (m, 2H), 1.55-1.42 (complex m,
3H), 1.33 (m, 2H), 1.23 (m, 1H), 1.17 (d, 1H), 0.99 (m, 1H).
[0237] Compounds 23,24,25,27,28,29,30 and 31 were prepared by the
method described above.
[0238] . Table 4 below depicts exemplary 1H-NMR data (NMR) and liquid
chromatographic mass spectral data, reported as mass plus proton (M+H), as
determined by electrospray, and retention time (RT) for certain compounds of the
present invention, wherein compound numbers in Table 4 correspond to the compounds
depicted in Table 3 (empty cells indicate that the test was not performed):
52


WO 2006/096270 PCT/US2006/004019
Table 4

Cmpd# M+H+ LC-MS Rt 1HNMR
Lot 1: (500 MHz, CDC13) 8.92 (br s, 1H), 8.81 (s,
2 Lot l:
200.00 Lot 1:1.93 1H), 7.26 (burned dd, 1H), 6.86 (m, 1H), 6.72
(dd, 1H), 2.70 (m, 2H), 2.34 (m, 2H), 1.84 (m,
2H), 1.76 (m, 2H)
(CDC13) 10.07 (br s, 1H), 8.86 (s, 1H), 7.35 (d,
9 301.00 2.05 1H), 6.83 (d, 1H), 6.73 (br s, 1H), 4.24 (br s, 2H),
3.71 (br s, 2H), 2.86 (br s, 2H), 1.52 (s, 9H)
(d4-methanol) 8.71 (s, 1H), 7.52 (d, 1H), 6.86
10 (m, 1H), 6.84 (d, 1H), 4.01 (br s, 2H), 3.54 (dd,
2H),3.08(brs,2H)
(500 MHz, CDC13) 9.24 (s, 1H), 7.7 (brs, 1H),
11 213.80 2.40 7.56 (s, 1H), 7.02 (d, 1H), 6.93 (br s, 1H), 3.68
(m, 2H), 2.62 (m, 2H), 2.28 (m, 1H), 2.16 (m,
1H), 2.03 (m, 1H), 1.94 (m, 1H), 1.29 (d, 3H)
(500 MHz, CD30D) 8.90 (s, 1H), 7.81 (d, 1H),
12 228.19 2.17 6.95 (d, 1H), 5.83 (br s, 2H), 2.79 (m, 1H), 1.85
(complex m, 4H), 1.75 (br d, 1H), 1.47-1.24
[complex m, 5H)
500Mhz;DMSO-d6: 12.1(brs,lH), 8.7(s,lH),
13 218.00 1.50 7.5(s,lH),7.0(s,lH),6.73
[s,lH), 3.45(s,2H), 2.9(s,4H)
(CDC13) 10.70 (br s, 1H), 8.89 (s, 1H), 7.39 (d,
14 146.00 0.60 1H), 7.15 (dd, 1H), 6.73 (d, 1H), 6.66 (dd, 1H),
5.82(dd,lH)
15 242.90 0.52
16 310.90 1.61
(d4-methanol) 8.76 (s, 1H), 7.61 (d, 1), 6.93 (d,
17 268.20 0.60 1H), 6.90 and 6.86 (2m, 1H), 4.40 and 4.34 (2m,
2H), 4.01 and 3.97 (2s, 2H), 3.90 and 3.78 (2t,
2H), 2.94 (m, 2H)
(500MHz, CD30D) 8.81 (s, 1H), 7.66 (d, 1H),
18 214.23 1.97 6.85 (d, 1H), 5.78 and 5.77 (two s, 2H), 1.94 (m,
2H), 1.78 (m, 2H), 1.70 (m, 2H), 1.50 (m, 2H)
ppm.
(500MHz, CD30D) 8.86 (s, 1H), 7.83 (d, 1H),
19 214.21 1.75 7.08 (d, 1H), 7.05 (m, 1H), 3.16 (m, 1H), 2.99 (m,
1H), 2.33 (m, 1H), 2.20 (m, 1H), 1.23 (d, 3H),
1.18 (d,3H) ppm.
1H NMR (500 MHz, CD30D) 8.86 (s, 1H), 7.84
20 214.20 2.60 (m, 1H), 7.00 (m, 2H), 2.88 (m, 2H), 2.58 (m,
2H), 1.97 (m, 2H), 1.81 (m, 2H), 1.72 (m, 2H).
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WO 2006/096270 PCT/US2006/004019

Cmpd# M+H+ LC-MS Rt HNMR
21 211.90 1.60 500MHz, CDC13: 12.3.0(brm,lH), 9.0(s,lH),
7.63(s,lH), 7.58(s,lH), 6.93
(s,lH), 3.75(s,lH), 3.30(s,lH), 1.97(m,2H),
1.74(d,lH), 1.45(d,lH), 1.33
(m,lH), 1.22(m,lH)
22 328.90 2.46 500 Mhz, CDC13 10.16 (s, br, 1H), 8.87 (s, 1H),
7.34 (s, 1H), 6.67 (s, 1H), 5.59 (s, 1H), 4.11 (d,
br, 2H), 3.18 (m, 1H), 2.79 (t, 2H), 2.00 (m, 1H),
1.71 (m, 2H), 1.64 -1.48 (m, 2H), 1.43 (s, 9H).
23 224.20 1.91
24 220.20 1.52 12.47 (br s, 1H), 8.79 (s, 1H), 7.65 (s, 1H), 6.81
(s, 1H), 3.55 (s, 3H), 3.39 (q, 1H), 3.16 (m, 2H),
1.15 (d, 3H)
25 176.20 1.65
27 216.20 2.04
28 201.20 1.48
29 234.20 1.52
30 243.20 1.91
31 190.20 1.91
Example 11: JAK3 Inhibition Assay
[0239] Compounds were screened for their ability to inhibit JAK using the
assay shown below. Reactions were carried out in a kinase buffer containing 100 mM
HEPES (pH 7.4), 1 mM DTT, 10 mM MgCl2, 25 mM NaCl, and 0.01% BSA.
[0240] Substrate concentrations in the assay were 5 M ATP (200 uCi/mole
ATP) and 1 M poly(Glu)4Tyr. Reactions were carried out at 25 °C and 1 nM JAK3.
[0241] To each well of a 96 well polycarbonate plate was added 1.5 1 of a
candidate JAK3 inhibitor along with 50 l of kinase buffer containing 2 M
poly(Glu)4Tyr and 10 M ATP. This was then mixed and 50l of kinase buffer
containing 2 nM JAK3 enzyme was added to start the reaction. After 20 minutes at
room temperature (25C), the reaction was stopped with 50l of 20% trichloroacetic
acid (TCA) that also contained 0.4 mM ATP. The entire contents of each well were
then transferred to a 96 well glass fiber filter plate using a TomTek Cell Harvester.
After washing, 60 l of scintillation fluid was added and 33P incorporation detected on
a Perkin Elmer TopCount
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WO 2006/096270 PCT/US2006/004019
Example 12: JAK2 Inhibition Assay
[ 0242 ] As described above in Example 11 except that JAK-2 enzyme is used,
the final poly(Glu)4Tyr concentration is 15 M, and final ATP concentration is 12 M.
Example 13: ROCK Inhibition Assays
[0243] Compounds are screened for their ability to inhibit ROCK I (AA 6-553)
activity using a standard coupled enzyme system (Fox et al. Protein Sci. 7:2249,1998).
Reactions are carried out in a solution containing 100 mM HEPES (pH 7.5), 10 mM
MgCl2,25 mM NaCl, 2 mMDTT and 1.5% DMSO. Final substrate concentrations in
the assay are 45 M ATP (Sigma Chemicals, St Louis, MO) and 200 M peptide
(American Peptide, Sunnyvale, CA). Reactions are carried out at 30 °C and 45 nM
ROCK I. Final concentrations of the components of the coupled enzyme system are 2.5
mM phosphoenolpyruvate, 350 M NADH, 30 g/ml pyruvate kinase and 10 g/ml
lactate dehydrogenase.
[0244 ] Compounds are screened for their ability to inhibit ROCK using a
standard radioactive enzyme assay. Assays are carried out in a solution containing 100
mM HEPES (pH 7.5), 10 mM MgCl2,25 mM NaCl, 2 mM DTT and 1.5% DMSO.
Final substrate concentrations in the assay are 13 M [-33P] ATP (25mCi 33P
ATP/mmol ATP, Perkin Elmer, Cambridge, MA /Sigma Chemicals, St Louis, MO) and
27 M Myelin Basic Protein (MBP). Final enzyme concentration in the assay is 5 nM
ROCK. Assays are carried out at room temperature. 1.5l of DMSO stock containing
serial dilutions of the compound of the present invention (concentrations ranging from
10 M to 2.6nM) is placed in a 96 well plate. 50 l of Solution 1 (100 mM HEPES (pH
7.5), 10 mM MgCl2,26 mM [-33P] ATP) is added to the plate. The reaction is initiated
by addition of 50 l of Solution 2 (100 mM HEPES (pH 7.5), 10 mM MgCl2,4 mM
DTT, 54 mM MBP and 10 nM ROCK). After 2 hours the reaction is quenched with 50
L of 30% trichloroacetic acid (TCA, Fisher) containing 9mM ATP. Transfer of 140
L of the quenched reaction to a glass fiber filter plate (Corning, Cat. No.3511) is
followed by washing 3 times with 5% TCA. 50 L of Optima Gold scintillation fluid
(Perkin Elmer) is added and the plates are counted on a Top Count (Perkin Elmer).
55

WO 2006/096270 PCT/US2006/004019
After removing mean background values for all of the data points the data is fit using
Prism software to obtain a Ki(app).
Example 14: PKA Inhibition Assay
[0245] Compounds were screened for their ability to inhibit PKA using a
standard coupled enzyme assay (Fox et aL, Protein Sci, 1998,7,2249). Assays were
carried out in a mixture of 100 mM HEPES (pH 7.5), 10 mM MgCl2,25 mM NaCl, 1
mM DTT and 3% DMSO. Final substrate concentrations in the assay were 50 M ATP
(Sigma Chemicals) and 80 M peptide (Kemptide, American Peptide, Sunnyvale, CA).
Assays were carried out at 30 °C and 18 nM PKA. Final concentrations of the
components of the coupled enzyme system were 2.5 mM phosphoenolpyruvate, 300
M NADH, 30 g/ml pyruvate kinase and 10 g/ml lactate dehydrogenase.
[0246] An assay stock buffer solution was prepared containing all of the
reagents listed above, with the exception of ATP, and the test compound of the present
invention. 55 I of the stock solution was placed in a 96 well plate followed by
addition of 2 l of DMSO stock containing serial dilutions of the test compound of the
present invention (typically starting from a final concentration of 5fiM). The plate was
preincubated for 10 minutes at 30°C and the reaction initiated by addition of 5 I of
ATP (final concentration 50 M). Initial reaction rates were determined with a
Molecular Devices SpectraMax Plus plate reader over a 15 minute time course. IC50
and Ki data were calculated from non-linear regression analysis using the Prism
software package (GraphPad Prism version 3.0a for Macintosh, GraphPad Software,
San Diego California, USA).
[0247] Table 5 depicts enzyme inhibition data (Ki) for certain exemplary
compounds. Compound numbers in Table 5 correspond to those compounds depicted
in Table 3. In Table 5, "A" represents a Ki of less than 0.5 M, "B" represents a Ki of
between 0.5 and 5.0 M, and "C" represents a Ki, of greater than 5.0 M.
56

WO 2006/096270 PCT/US2006/004019
Table 5

Cmpd# JAK2 JAK3 PKA ROCK
1 A A B B
2 A A B B
3 B B B B
4 A A B B
5 A A B B
6 A A B B
7 A A B B
8 C B B B
9 A A B B
10 C C B B
11 B A B B
12 B B B B
13 A A B B
14 B B B B
15 C C B B
16 B C B B
17 A B B B
18 A A B B
19 A A B B
20 A A B B
21 A A B B
22 B B B B
23 B B B B
24 C C B B
25 B B B B
26 A A B B
27 A A B B
28 B B B B
29 B B B B
30 B B B B
31 A A B B
57

WO 2006/096270 PCT/US2006/004019
CLAIMS
We claim:
1. A compound of formula (I):

or a pharmaceutically acceptable salt thereof, wherein:
wherein
R1 is H, -NO2, -CN, -OCF3, halogen, or amino; or C1-6aliphatic, C3-7cycloaliphatic,
C1-6alkoxy, or C1-4aloalkyl optionally substituted with 0-10 JR groups;
R2 is H, -NO2, -CN, -OCF3, halogen, or amino; or Ci1-6aliphatic, C3-7cycloaliphatic,
C1-6alkoxy, or C1-4aloalkyl optionally substituted with 0-10 JR groups;
Z1 is C1-6aliphatic or C3-10cycloaliphatic optionally substituted with 0-10 Jz groups; if
the bond between Z1 and C is a double bond, then Z1 may also be =O, =NR, or
=C(R)2;
Z2 is H or halogen; or C1-10haloalkyl, C1-4haloalkoxy, Y, -(Vn)-CN, -(Vn)-NO2,
-(Vn)-OH, -(Vn)-(C1-6aliphatic), -(Vn)-(C3-12heterocyclyl), -(Vn)-(C6-10aryl),
-(Vn)-(5-10 membered heteroaryl), or -(Vn)-(C3-10cycloaliphatic) optionally
substituted with 0-10 Jz groups; or
Z1 and Z2, together with the carbon atom to which they are attached, form ring Q;
Z3 is H or C1-6alkyl optionally substituted with 0-3 Jz groups; or
Z1, Z2, and Z3, together with the carbon atom to which they are attached, form an 6-14
membered saturated, partially saturated, or unsaturated bicyclic ring having 0-3
heteroatoms;
if the bond between Z1 and C is a triple bond, then Z2 is absent;
58

WO 2006/096270 PCT/US2006/004019
if the bond between Z1 and C is a double bond or a triple bond, then Z3 is absent;
Q is a 3-8 membered saturated or partially saturated monocyclic ring having 0-3
heteroatoms selected from nitrogen, oxygen, or sulfur, wherein said Q is
optionally and independently fused to Q1 or Q2; or to both Q1 and Q2; wherein
said Q is optionally substituted with 0-4 JQ groups;
Q1 is a 3-8 membered saturated, partially saturated, or unsaturated monocyclic ring
having 0-3 heteroatoms selected from nitrogen, oxygen, or sulfur, wherein said
Q1 group is optionally substituted with 0-4 JQ groups;
Q2 is a 3-8 membered saturated, partially saturated, or unsaturated monocyclic ring
having 0-3 heteroatoms selected from nitrogen, oxygen, or sulfur wherein said
Q2 group is optionally substituted with 0-4 JQ groups;
R is H, optionally substituted C1-6 aliphatic, C3-10 cycloaliphatic, C6-10 aryl, 5-14
membered heteroaryl, or 5-14 membered heterocyclyl; or two R groups, on the
same substituent or different substituents, together with the atom(s) to which
each R group is bound, form an optionally substituted 3-14 membered saturated,
partially unsaturated, or fully unsaturated monocyclic, bicyclic, ortricyclic ring
having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur
wherein each R is optionally substituted with 0-10 JR groups;
each JQ and Jz substituent on an unsaturated carbon atom is independently selected
from hydrogen, -OCF3, C1-6haloalkyl, N(R)2, OR, halogen, Y, -(Vn)-CN,
-(Vn)-NO2, -(Vn)-OH, -(Vn)-(C1-6aliphatic), -(C3-10cycloaliphatic)-C(O)R,
-(C3-10cycloaliphatic)-(C3-12heterocyclyl); -(Vn)-(C3-12heterocyclyl), -(Vn)-
(C6-10aryl), -(Vn)-(5-10 membered heteroaryl), -(Vn)-(C3-10cycloaliphatic);
wherein eachJQ and Jz is optionally substituted with up to 10 JR groups;
each JQ and Jz substituent on a saturated carbon atom is selected from those listed
above for an unsaturated carbon and also the following: =0, =NN(Ra)2,
=NNHC(O)Ra, =NNHCO2(C1-4alkyl), =NNHSO2(C1-4alkyl), and =NRa wherein
each JQ and Jz is optionally substituted with up to 10 JR groups;
each JQ and Jz substituent on a nitrogen atom is independently selected from hydrogen,
Y, -(Vn)-CN, -(Vn)-NO2, -(Vn)-OH, -(Vn)-(C1-6aliphatic), -(C3-10cycloaliphatic)-
C(O)R, -(C3-10cycloaliphatic)-(C3-12heterocyclyl), -(Vn)-(C3-12heterocyclyl),
-(Vn)-(C6-10aryl), -(Vn)-(5-10 membered heteroaryl), -(Vn)-(C3-10cycloaliphatic);
59

WO 2006/096270 PCT/US2006/004019
wherein two Jz groups, on the same substituent or different substituents,
together with the atom(s) to which each Jz group is bound, can optionally form
an optionally substituted 3-14 membered saturated, partially unsaturated, or
fully unsaturated monocyclic, bicyclic, or tricyclic ring having 0-4 heteroatoms
independently selected from nitrogen, oxygen, or sulfur; wherein each JQ and Jz
is optionally substituted with up to 10 JR groups;
JR is selected from halogen, -N(Rb)2, SRb, ORb, oxo, C1-4aloalkoxy, C1-4haloalkyl, L,
-(Ln)-(C1-6alkyl), -(Ln)-(C3-12heterocyclyl), -(Ln)-(C6-10aryl), -(Ln)-(5-10
membered heteroaryl), -(Ln)-(C3-10cycloalipahtic), -(Ln)-NO2 -(Ln)-CN,
-(Ln)-OH, -CO2Rb, -CORb, -OC(O)Rb, -NC(O)Rb;
L is C1-10alkyl wherein up to three methylene units are replaced by -NRb-, -O-, -S-, -
CO2-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NRb-, -C(=N-CN), -NRbCO-,
-NRbC(O)O-, -SO2NRb-, -NRbSO2-, -NRbC(O)NR-, -OC(O)NRb-,
-NRbSO2NRb-, -SO-, or -SO2-;
V is C1-10aliphatic wherein up to three methylene units are replaced by Gv, wherein Gv
is selected from -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NR-,
-C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-, -NRC(O)NR-,
-OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
Y is C1-10aliphatic, wherein up to three methylene units are replaced by GY wherein GY
is selected from -NR-, -O-, -S-, -CO2*-, -OC(O)-, -C(O)CO-, -C(O)-, -C(O)NR-,
-C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-, -NRC(O)NR-,
-OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
Ra is hydrogen or C1-6aliphatic group optionally substituted with 0-3 JR groups;
Rb is hydrogen or an unsubstituted C1-6 aliphatic group;
n is 0 or 1;
provided that:
when R1 and R2 are H, and Z2 and Z3 are H, then Z1 is not methyl;
when R1 is CH3 and R2 is H, then Z1, Z2, and Z3 are not all H;
when R1 and R2 are H, and Z2 and Z3 are H, then Z1 is not unsubstituted phenyl,
4-pyridyl, or one of the structures shown below:
60

WO 2006/096270 PCT/US2006/004019

and
when R1 and R2 are H, Z1 and Z2 taken together are not -CC-CH2CH2COOH.
2. The compound according to claim 1 wherein Z1, Z2, and Z3, together with the carbon
atom to which they are attached, form the bicyclic ring shown in Formula II:

wherein
Q3 is 3-8 membered saturated, unsaturated, or partially saturated monocyclic
ring;
Q and Q3 are each optionally and independently substituted with 0-4 J^ groups.
3. The compound according claim 2 wherein Q3 is a cyclopropyl group and both Q and
Q3 are each optionally substituted with 0-2 J^ groups as shown in formula HI:

4. The compound according to claim 1, wherein Z1 and Z2, together with the carbon
atom to which they are attached, form a compound as shown in Formula IV:
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WO 2006/096270 PCT/US2006/004019

wherein
Z11 is selected from C, N, O, or S;
Z12 is selected from C, N, O, or S;
Q is a 3-8 membered saturated or partially saturated monocyclic ring, optionally fused
toQ1orQ2;
Q1 and Q2 are each independently a 3-8 membered saturated, unsaturated, or partially
saturated monocyclic ring;
Q, Q1 and Q2 each independently contain up to three heteroatoms selected from O, N,
orS;
m is is 0-4; and is independently selected for Q, Q1 and Q2; and
Z3 is H; or if the bond between C and Z11 is a double bond, then Z3 is absent
5. The compound according to claim 4, wherein Z11 and Z12 are each independently
carbon.
6. The compound according to claim 4 or claim 5, wherein Q is C3-7 monocycle and Q1
and Q2 are absent.
7. The compound according to claim 4 or claim 5, wherein Q and Q1 together form a
fused 6-14 membered bicyclic ring and Q2 is absent.
8. The compound according to claim 4 or claim 5, wherein Q, Q1, and Q2 together
form a fused 8-20 membered tricyclic ring.
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9. The compound according to claim 7 or claim 8, wherein Z12 is carbon and the fused
ring of Q, Q1, and optionally Q2 is as shown in Formula V:

wherein Q, Q1, and Q2 each independently and optionally contain
c) 0-2 heteroatoms selected from O, N, or S; and
d) 0-4 JQ substituents.
10. The compound according to claim 9, wherein the hydrogen atoms at the point of
fusion between ring Q and ring Q1 is in the cis conformation as shown in Formula VI:

11. The compound according to any one of claims 6-10, wherein C-Z11 is a single
bond.
12. The compound according to any one of claims 6-10, wherein C=Z11 is a double
bond.
13. The compound according to any one of claims 2-12, wherein ring Q contains two
heteroatoms.
14. The compound according to any one of claims 2-12, wherein ring Q contains one
heteroatom.
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15. Hie compound according any one of claims 2-12, wherein ring Q contains zero
heteroatoms.
16. The compound according to claim 13, wherein each of said heteroatoms are
independently selected from nitrogen or sulfur.
17. The compound according to claim 13, wherein both heteroatoms are nitrogen.
18. The compound according to claim 14, wherein the heteroatom is nitrogen.
19. The compound according to any one of claims 13,14 and 16, wherein the sulfur is
optionally substituted with 0,1, or 2 oxo groups.
20. The compound according to claim 15, wherein ring Q is a 5-7 membered
cycloaliphatic.
21. The compound according to any one of claims 7-20, wherein Q1 is a 6-membered
aryl or 5-6 membered heteroaryl ring.
22. The compound according to any one of claims 7-20, wherein Q1 is a 5-8 membered
cycloaliphatic ring.
23. The compound according to any one of claims 7-20, wherein Q1 is a 5-8 membered
heterocyclic ring.
24. The compound according to claim 1, wherein Q or Q-Q1 is represented is selected
from
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WO 2006/096270 PCT/US2006/004019

wherein
both R7 and JQ are each independently selected from hydrogen, Y, -(Vn)-CN,
-(Vn)-NO2, -(Vn)OH, -(Vn)-(C1-6aliphatic), -(Vn)-(C3-12heterocyclyl),
-(Vn)-(C6-10aryl), -(Vn)-(5-10 membered heteroaryl),
-(Vn)-(C3-10cycloaliphatic), and -(C3-10cycloaliphatic)-
(C3-12heterocyclyl);
each Q and Q1, m is independently 0-3; and
each R7 and JQ is optionally and independently substituted with 0-10 JR groups.
25. The compound according any one of claims 21-24, wherein m is 0.
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26.1116 compound according to any one of claims 21-24, wherein m is 1 or 2.
27. The compound according claim 25 or claim 26, wherein JQ2 is Y, -(V1n)-CN,
-(V1n)-NO2-,-(V1n)-OH, -(V1n)-(C1-6aliphatic), -(V1n)C3-12eterocyclyl), -(V1n)
(C6-10aryl), -(V1n)-(5-l0 membered heteroaryl), -(V1n)-(C3-10cycloaliphatic), or
-(C3-10cycloaliphatic)-(C3-12heterocyclyl); wherein
V1 is -GV-(X)P, wherein X is a C1-9aliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
p is 0 or 1;
n is 0 or 1;
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O); and
said JQ is optionally substituted with 0-10 JR groups.
28. The compound according to claim 27, wherein X is C1-4aliphatic and JQ is
optionally substituted with 0-3 JR groups.
29. The compound according to claim 27, wherein n is 0.
30.The compound according to claim 27 or 28, wherein n is 1.
31.The compound according to claim 29 or claim 30, wherein p is 0.
32. The compound according to any one of claims 27-31, wherein Gv is C=O.
33. The compound according to any one of claims 1-32, wherein R1 and R2 are each
independently H, halogen, C1-4alkyl, or C1-4alkoxy.
34. The compound according to any one of claims 1-32, wherein R1 and R2 are each
independently H.
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35. The compound according to any one of claims 24-34, wherein R7 is independently
selected from Y, -(V1n)-CN, -(V1n)-NO2, -(V1n)-OH, -(Vn)-(C1-6aliphatic), -(V1n)-
(C3-12heterocyclyl), -(V1n)-(C6-10aryl), -(V1n)-(5-10 membered heteroaryl), -(V1n)-
(C3-10cycloaliphatic), or -(C3-10cycloaliphatic)-(C3-12heterocyclyl); wherein
V1 is -GV-(X)P wherein X is a C1-9aliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2-;
p is 0 or 1;
n is 0 or 1; and
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O).
36. A compound of formula VH:

67
wherein A is selected from:


WO 2006/096270 PCT/US2006/004019

37. The compound according to claim 1, wherein Z1 and Z2 do not join to form a ring
and Z3 is H or is absent.
38. The compound according to claim 37, wherein Z1 is H or C1-6aliphatic optionally
substituted with 0-3 Jz groups.
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39. The compound according to claim 37, wherein Z1 is H.
40. The compound according to claim 37, wherein CZ1 is a triple bond, and Z2 and
Z3 are absent.
41. The compound according to claim 37, wherein C=Z1 is a double bond and Z3 is
absent
42.The compound according to claim 41, wherein Z1 is O.
43. The compound according to claim 41, wherein Z1 is CH2.
44. The compound according to any one of claims 37-43, wherein Z2is optionally
substituted Y, -(Vn)-(C1-6aliphatic), -(Vn)-(C3-12heterocyclyl), -(Vn)-(C6-10aryl),
-(Vn)-(5-10 membered heteroaryl), or -(Vn)-(C3-10cycloaliphatic); wherein n is 0.
45. The compound according to claim 44, wherein Z2 is an optionally substituted 5-7
membered monocycle selected from heterocyclyl, cycloaliphatic, aryl, or heteroaryl.
46. The compound according to claim 45, wherein Z2 is an optionally substituted 5-7
membered fully or partially saturated monocycle selected from heterocyclyl or
cycloaliphatic.
47. The compound according to claim 45 or 46, wherein Z2 is an optionally substituted
6-membered monocycle with 0-2 nitrogen atoms.
48. The compound according to claim 47, wherein Z2 is piperidine optionally
substituted with 0-3 Jz groups.
49. The compound according to claim 44, wherein Z2 is optionally substituted
C3-10cycloalipharic.
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50. The compound according to claim 49, wherein Z2 is a bicyclo-octane ring.
51. The compound according to any one of claims 37-50, wherein Jz is halogen, CF3,
optionally substituted C1-4haloalkyl, -(V1n)-CN, -(V1n)-NO2, -(V1n)-OH, Y, -(VV1n)-
(C3-12heterocyclyl), -(V1n)- (C6-10aryl), -(V1n)- (5-10 membered heteroaryl), -(V1n)-
(C3-10cycloaliphatic), or -(C3-10cycloaliphatic)-(C3-12heterocyclyl); wherein
V1 is -Gv-(X)p wherein X is a C1-9aliphatic wherein up to two methylene units
are replaced by -NR-, -O-, -S-, -CO2-, -OC(O)-, -C(O)CO-, -C(O)-,
-C(O)NR-, -C(=N-CN), -NRCO-, -NRC(O)O-, -SO2NR-, -NRSO2-,
-NRC(O)NR-, -OC(O)NR-, -NRSO2NR-, -SO-, or -SO2;
p is 0 or 1; and
Gv is selected from C=O, C(=O)NR, S(O)2 or S(O).
52. The compound according to claim 51, wherein X is C1-2alkyl and Gv is selected
from C=O, C(=O)NR, S(O)2 or S(O).
53. The compound according to claim 51, wherein Jz is halogen, CF3, CN,
optionally substituted C1-6aliphatic, -(C1-6alkyl)n-RJ, C1-4haloalkyl,
-(C1-6alkyl)n-C(=O)RJ, -(C1-6alkyl)n-CON(Rb)RJ, -(C1-6alkyl)n-N(Rb)RJ,
-(C1-6alkyl)n-ORJ, -(C1-6alkyl)n-OCON(Rb)RJ, -(C1-6aliphatic)n-S(O)N(Rb)RJ,
-(C3-12aliphatic)n-S(O)RJ, or -(C1-6aliphatic)n-NHC(O)RJ wherein RJ is C1-6aliphatic,
C3-12heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, or C3-10cycloaliphatic; and n is
O or l.
54. The compound according claim 53 wherein Jz is halogen, ORJ, N(Rb)2, CF3,
CN, optionally substituted C1-6alkyl, -(C1-6aIkyl)RJ, -C(=O)(C1-6alkyl), -
CON(Rb)(C1-6alkyl), -OCON(Rb)(C1-6alkyl), -S(O)NC(Rb)(C1-6alkyl), -S(O)(C1-6alkyl),
-NHC(O)C1-6alkyl, -(C1-6alkyl)-CONH, -(C1-6alkyl-N(Rb)2, -(C1-6alkyl)-OCON(Rb)RJ,
-(C1-6aliphatic)-S(O)N(Rb)(C6-10aryl), -N(Rb)2C(O)N(Rb)2, or -N(Rb)C(O)Rb.
55. The compound according claim 54 wherein Jz is halogen, OR, N(Rb)2 CF3, CN,
optionally substituted C1-6alkyl, -(C1-6alkyl)n-RJ, C(=O)(C1-6alkyl), CONH,
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WO 2006/096270 PCT/US2006/004019
-(C1-6alkyl)-CONH, -(C1-6alkyl)-N(Rb)2, -(C1-6alkyl)-OCON(Rb)R, -(C1-6aliphatic)-
S(O)N(Rb)(C6-10aryl), -N(Rb)C(O)N(Rb)2, or -N(Rb)C(O)Rb.
56. The compound according to any one of claims 53-55 wherein RJ is C1-6aliphatic
or C3-10cycloaliphatic.
57. The compound according to any one of claims 53-55 wherein Rj is C6-10aryl or
5-10 membered heteroaryl.
58. The compound according to any one of claims 53-55 wherein n is 1.
59. The compound according to claim 55 wherein Jz is selected from
-C(=O)(C1-6alkyl), -C(=O)CH2CN, orC1-6alkyl.
60. A compound of formula VIII:

71
wherein A is selected:


WO 2006/096270 PCT/US2006/004019

61. A compound selected from Table 3.
62. A composition comprising an effective amount of compound of claim 1 or claim
61, and a pharmaceutically acceptable carrier, adjuvant, or vehicle.

61. The composition of claim 62, additionally comprising a therapeutic agent selected
from a chemotherapeutic or anti-proliferative agent, an anti-inflammatory agent, an
immunomodulatory or immunosuppressive agent, a neurotrophic factor, an agent for
treating cardiovascular disease, an agent for treating diabetes, or an agent for treating
immunodeficiency disorders.
62. The composition of claim 61 wherein said therapeutic agent is an
immunomodulatory or immunosuppressive agent.
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63. A method of inhibiting JAK3 kinase activity in a patient comprising administering
to said patient a compound according to claim 1 or a composition comprising said
compound.
64. A method of inhibiting JAK3 kinase activity in a biological sample comprising
administering to contacting said biological sample with a compound according to claim
1 or a composition comprising said compound.
65. A method of treating or lessening the severity of a disease of condition selected
from a proliferative disorder, a cardiac disorder, a neurodegenerative disorder, an
autoimmune disorder, a condition associated with organ transplant, an inflammatory
disorder, or an immunologically mediated disorder, comprising the step of
administering to said patient a compound of claim 1 or a composition comprising said
compound.
66. The method of claim 65, comprising the additional step of administering to said
patient an additional therapeutic agent selected from a chemotherapeutic or anti-
proliferative agent, an anti-inflammatory agent, an immunomodulatory or
immunosuppressive agent, a neurotrophic factor, an agent for treating cardiovascular
disease, an agent for treating diabetes, or an agent for treating immunodeficiency
disorders, wherein:
said additional therapeutic agent is appropriate for the disease being treated; and
said additional therapeutic agent is administered together with said composition.
67. The method of claim 65 or claim 68 wherein the disease or disorder is allergic
or type I hypersensitivity reactions, asthma, diabetes, Alzheimer's disease,
Huntington's disease, Parkinson's disease, AIDS-associated dementia, amyotrophic
lateral sclerosis (AML, Lou Gehrig's disease), multiple sclerosis (MS), schizophrenia,
cardiomyocyte hypertrophy, reperfusion/ischemia, stroke, baldness, transplant
rejection, graft versus host disease, rheumatoid arthritis, amyotrophic lateral sclerosis,
and multiple sclerosis, and solid and hematologic malignancies such as leukemias and
lymphomas.
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WO 2006/096270 PCT/US2006/004019
68. The method of claim 67, wherein said disease or disorder is asthma.
69. The method of claim 67, wherein said disease or disorder is transplant rejection.

72. A method of inhibiting JAK2 kinase activity in a patient comprising administering
to said patient a compound according to claim 1 or a composition comprising said
compound.
73. A method of inhibiting JAK2 kinase activity in a biological sample comprising
administering to contacting said biological sample with a compound according to claim
1 or a composition comprising said compound.
74. A method of treating or lessening the severity of a myeloprolif erative disorder in a
patient in need thereof, comprising the step of administering to said patient a compound
according to claim 1 or a composition comprising said compound.
75. The method according to claim 74, wherein said myeloprolif erative disorder is
polycythemia vera, essential thrombocythemia, chronic idiopathic myelofibrosis,
myeloid metaplasia with myelofibrosis, chronic myeloid leukemia, chronic
myelomonocytic leukemia, chronic eosinophilic leukemia, hypereosinophilic syndrome
or systematic mast cell disease.
76. The method of either of claims 74 or 75, comprising the additional step of
administering to said patient an additional therapeutic agent selected from a
chemotherapeutic or anti-proliferative agent, wherein:
said additional therapeutic agent is appropriate for the disease being treated; and
said additional therapeutic agent is administered together with said composition.
77. A method of inhibiting ROCK kinase activity in a patient comprising administering
to said patient a compound according to claim 1 or a composition comprising said
compound.
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WO 2006/096270 PCT/US2006/004019
78. A method of inhibiting ROCK kinase activity in a biological sample comprising
administering to contacting said biological sample with a compound according to claim
1 or a composition comprising said compound.
79. A method of treating or lessening the severity of a disease condition or disorder
selected from a proliferative disorder, a cardiac disorder, a neurodegenerative disorder,
a psychotic disorder, an autoimmune disorder, a condition associated with organ
transplant, an inflammatory disorder, an immunologically mediated disorder, a viral
disease, or a bone disorder, comprising the step of administering to said patient a
compound according to claim 1 or a composition comprising said compound.
80. The method of claim 79, comprising the additional step of administering to said
patient an additional therapeutic agent selected from a chemotherapeutic or anti-
proliferative agent, an anti-inflammatory agent, an immunomodulatory or
immunosuppressive agent, a neurotrophic factor, an anti-psychotic agent, an agent for
treating cardiovascular disease, an agent for treating destructive bone disorders, an
agent for treating liver disease, an anti-viral agent, an agent for treating blood disorders,
an agent for treating diabetes, or an agent for treating immunodeficiency disorders,
wherein:
said additional therapeutic agent is appropriate for the disease being treated; and
said additional therapeutic agent is administered together with said composition
as a single dosage form or separately from said composition as part of a
multiple dosage form.
81. The method of either of claims 79 or 80, wherein said disease, condition, or
disorder is hypertension, angina, angina pectoris, cerebrovascular contraction, allergy,
asthma, peripheral circulation disorder, preterm labor, cancer, erectile dysfunction,
atherosclerosis, cerebral vasospasm, coronary vasospasm, retinopathy, glaucoma,
inflammatory disorders, autoimmune disorders, AIDS, osteoporosis, myocardial
hypertrophy, ischemia/reperfusion-induced injury, endothelial dysfunction,
Alzheimer's disease, benign prostatic hyperplasia, vascular smooth muscle cell
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WO 2006/096270 PCT/US2006/004019
proliferation, myocardial hypertrophy, malignoma, endothelial dysfunction, Crohn's
Disease, colitis, neurite outgrowth, Raynaud's Disease or benign prostatic hyperplasia.
82. A method of inhibiting PKA kinase activity in a patient comprising administering
to said patient a compound according to claim 1 or a composition comprising said
compound.
83. A method of inhibiting PKA kinase activity in a biological sample comprising
administering to contacting said biological sample with a compound according to claim
1 or a composition comprising said compound.
84. A method of treating or lessening the severity of a proliferative disorder in a
patient in need thereof, comprising the step of administering to said patient a compound
according to claim 1 or a composition comprising said compound.
85. The method according to claim 84, wherein said proliferative disorder is cancer.
86. The method of either of claims 84 or 85, comprising the additional step of
administering to said patient an additional therapeutic agent selected from a
chemotherapeutic or anti-proliferative agent, wherein:
said additional therapeutic agent is appropriate for the disease being treated; and
said additional therapeutic agent is administered together with said composition.
76

The present invention relates to compounds of formula (I) useful as inhibitors of protein kinases. The invention also provides pharmaceutically acceptable compositions comprising said compounds and methods of using the compositions in the treatment of various disease, conditions, or disorders.

Documents:

02988-kolnp-2007-abstract.pdf

02988-kolnp-2007-claims.pdf

02988-kolnp-2007-correspondence others.pdf

02988-kolnp-2007-description complete.pdf

02988-kolnp-2007-form 1.pdf

02988-kolnp-2007-form 3.pdf

02988-kolnp-2007-form 5.pdf

02988-kolnp-2007-gpa.pdf

02988-kolnp-2007-international publication.pdf

02988-kolnp-2007-international search report.pdf

02988-kolnp-2007-pct request form.pdf

02988-kolnp-2007-priority document.pdf

2988-KOLNP-2007-(22-08-2012-)-ABSTRACT.pdf

2988-KOLNP-2007-(22-08-2012-)-AMANDED CLAIMS.pdf

2988-KOLNP-2007-(22-08-2012-)-AMANDED PAGES OF SPECIFICATION.pdf

2988-KOLNP-2007-(22-08-2012-)-ANNEXURE TO FORM 3.pdf

2988-KOLNP-2007-(22-08-2012-)-CORRESPONDENCE.pdf

2988-KOLNP-2007-(22-08-2012-)-DESCRIPTION (COMPLETE).pdf

2988-KOLNP-2007-(22-08-2012-)-FORM-1.pdf

2988-KOLNP-2007-(22-08-2012-)-FORM-13.pdf

2988-KOLNP-2007-(22-08-2012-)-FORM-2.pdf

2988-KOLNP-2007-(22-08-2012-)-FORM-3.pdf

2988-KOLNP-2007-(22-08-2012-)-FORM-5.pdf

2988-KOLNP-2007-(22-08-2012-)-OTHERS.pdf

2988-KOLNP-2007-(22-08-2012-)-PETITION UNDER RULE 137.pdf

2988-kolnp-2007-form 18.pdf

abstract-02988-kolnp-2007.jpg


Patent Number 257125
Indian Patent Application Number 2988/KOLNP/2007
PG Journal Number 36/2013
Publication Date 06-Sep-2013
Grant Date 04-Sep-2013
Date of Filing 14-Aug-2007
Name of Patentee VERTEX PHARMACEUTICALS INCORPORATED
Applicant Address 130 WAVERLY STREET, CAMBRIDGE MA
Inventors:
# Inventor's Name Inventor's Address
1 LEDEBOER, MARK, W. 36 FAULKNER HILL ROAD, ACTON, MA 01720
2 BEMIS, GUY, W. 256 APPLETON STREET, ARLINGTON, MA 02476
3 FARMER, LUC, J. 19 HOWE LANE, FOXBORO, MA 02035
4 WANG, TIANSHENG 2 DUNBAR WAY, CONCORD, MA 01742
5 MESSERSMITH, DAVID 16 HERBERT STREET, SOMERVILLE, MASSACHUSETTS 02144
6 DUFFY, JOHN, P. 175 CARRIAGE HILL ROAD, NORTHBOROUGH, MA 01532
7 WANG, JIAN 15 ELLIOT STREET, NEWTON, MA 02461
8 SALITURO, FRANCESCO, G. 25 BAKER DRIVE, MARLBORO, MA 01752
9 PIERCE, ALBERT, C. 27 FAINWOOD CIRCLE, #1, CAMBRIDGE, MA 02139
PCT International Classification Number C07D 487/04
PCT International Application Number PCT/US2006/004019
PCT International Filing date 2006-02-02
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/649,781 2005-02-03 U.S.A.