4-Amino-5-aryl-6-arylethynylpyrimidines: Structure-activity relationships of non-nucleoside adenosine kinase inhibitors

Article abstract of DOI:10.1016/j.bmc.2006.12.029

A series of non-nucleoside adenosine kinase (AK) inhibitors is reported. These inhibitors originated from the modification of 5-(3-bromophenyl)-7-(6-morpholin-4-ylpyridin-3-yl)pyrido[2,3-d]pyrimidin-4-ylamine (ABT-702). The identification of a linker that would approximate the spatial arrangement found between the pyrimidine ring and the aryl group at C(7) in ABT-702 was a key element in this modification. A search of potential linkers led to the discovery of an acetylene moiety as a suitable scaffold. It was hypothesized that the aryl acetylenes, ABT-702, and adenosine bound to the active site of AK (closed form) in a similar manner with respect to the orientation of the heterocyclic base. Although potent acetylene analogs were discovered based on this assumption, an X-ray crystal structure of 5-(4-dimethylaminophenyl)-6-(6-morpholin-4-ylpyridin-3-ylethynyl)pyrimidin-4-ylamine (16a) revealed a binding orientation contrary to adenosine. In addition, this compound bound tightly to a unique open conformation of AK. The structure-activity relationships and unique ligand orientation and protein conformation are discussed.

Full text of DOI:10.1016/j.bmc.2006.12.029

Bioorganic & Medicinal Chemistry 15 (2007) 1586–1605
4-Amino-5-aryl-6-arylethynylpyrimidines: Structure–activity
relationships of non-nucleoside adenosine kinase inhibitors
Mark A. Matulenko,a,* Ernest S. Paight,a Robin R. Frey,a Arthur Gomtsyan,a
Stanley DiDomenico, Jr.,a Meiqun Jiang,a Chih-Hung Lee,a Andrew O. Stewart,a
Haixia Yu,a Kathy L. Kohlhaas,a Karen M. Alexander,a Steve McGaraughty,a
Joseph Mikusa,a Kennan C. Marsh,b Steven W. Muchmore,c Clarissa L. Jakob,c
Elizabeth A. Kowaluk,a Michael F. Jarvisa and Shripad S. Bhagwata,ꢀ
aNeuroscience Research, Global Pharmaceutical Research Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA
bExploratory Kinetics and Analysis, Global Pharmaceutical Research Abbott Laboratories, 100 Abbott Park Road,
Abbott Park, IL 60064, USA
cStructural Biology, Global Pharmaceutical Research Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA
Received 3 November 2006; accepted 15 December 2006
Available online 20 December 2006
Abstract—A series of non-nucleoside adenosine kinase (AK) inhibitors is reported. These inhibitors originated from the modifica-
tion of 5-(3-bromophenyl)-7-(6-morpholin-4-ylpyridin-3-yl)pyrido[2,3-d]pyrimidin-4-ylamine (ABT-702). The identification of a
linker that would approximate the spatial arrangement found between the pyrimidine ring and the aryl group at C(7) in ABT-
702 was a key element in this modification. A search of potential linkers led to the discovery of an acetylene moiety as a suitable
scaffold. It was hypothesized that the aryl acetylenes, ABT-702, and adenosine bound to the active site of AK (closed form) in a
similar manner with respect to the orientation of the heterocyclic base. Although potent acetylene analogs were discovered based
on this assumption, an X-ray crystal structure of 5-(4-dimethylaminophenyl)-6-(6-morpholin-4-ylpyridin-3-ylethynyl)pyrimidin-4-
ylamine (16a) revealed a binding orientation contrary to adenosine. In addition, this compound bound tightly to a unique open con-
formation of AK. The structure–activity relationships and unique ligand orientation and protein conformation are discussed.
ꢀ 2006 Elsevier Ltd. All rights reserved.
1. Introduction
Strategies to increase local concentrations of ADO have
included inhibition of enzymes responsible for the meta-
bolic transformation of ADO. Specifically, inhibitors of
adenosine deaminase (ADA)7 and adenosine kinase
(AK)7 have received considerable attention in an attempt
to increase concentrations of endogenous ADO. AK is a
ubiquitous intracellular enzyme responsible for the phos-
phorylation of ADO to adenosine monophosphate. Inhi-
bition of AK increases local concentrations of ADO and
displays neuroprotective potential8–10 in such areas as
pain11–13 and inflammation.14,15
During cellular stress,1 local intracellular concentrations
of adenosine (ADO) increase followed by the active
transport of ADO into the extracellular space and sub-
sequent activation of ADO receptor (P1) subtypes.2,3
Upon activation of these receptor subtypes, a variety
of homeostatic inhibitory cellular events contribute
to anti-nociceptive and anti-inflammatory responses
in vivo.4 Attempts to identify selective ADO receptor
agonists5,6 for CNS therapeutic indications have
suffered from cardiovascular side effects such as hypo-
tension and bradycardia.2
Previously, we reported16–24 the identification and struc-
ture–activity relationships of non-nucleoside25 pyrido-
pyrimidine inhibitors of AK. Although the series was
successful, some compounds occasionally suffered toxi-
cological23 and CNS side effects,17 and also lacked
appropriate aqueous solubility19 and oral bioavailabili-
ty.21 This indicated that significant structural changes
Keywords: Adenosine kinase; Inhibitor; Acetylene; Analgesic.
*
Corresponding author. Tel.: +1 847 938 2460; fax: +1 847 937
9195; e-mail: mark.a.matulenko@abbott.com
ꢀ
Present address: Ambit Biosciences, 4215 Sorrento Valley Boulevard,
San Diego, CA 92121, USA.
0968-0896/$ - see front matter ꢀ 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2006.12.029

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1587
to the core were necessary in order to expand on current
achievements. The design of a new class of AK inhibi-
tors based on the pyridopyrimidines required that key
structural elements (for in vitro potency) be identified
and retained. In the pyridopyrimidines, the 4-amino
pyrimidine fragment and the aryl ring occupying the
C(7) position were found to be critical pharmacophoric
elements. Upon removal of the fused pyridine ring and
replacement with an acetylene linker, we discovered that
these pyrimidine analogs were equipotent with the pyri-
dopyrimidines in their ability to inhibit AK in vitro.26
However, an X-ray crystal structure of 16a bound to
the AK active site revealed a binding motif contrary to
adenosine bound to the AK active site.27 In addition,
it was also discovered that the protein adopted a sepa-
rate, active conformation to accommodate the unique li-
gand orientation. Although our overlap hypothesis was
challenged, we were able to discover novel and potent
inhibitors of AK based on the acetylene substitution.
The present paper delineates the general structure–activ-
ity relationships of these novel AK inhibitors as well as a
discussion relating to their unique binding orientation
and accommodating AK protein conformation.
idue on the aryl acetylene. Electron withdrawing groups
on the aryl acetylene were problematic. First, in the
Sonogashira coupling, it was discovered these electron-
poor acetylenes gave largely Glaser-type reaction prod-
ucts with little or no traces of desired chloro acetylene,
4. Second, the attempted aminolysis of 4 resulted in sig-
nificant amounts of hydroamination product. After
aqueous workup, the corresponding ketone was isolated.
Scheme 2 shows two alternative synthetic routes to over-
come these issues. Initially, both routes convert the
dichloropyrimidine, 3, into the diiodo analog, 6, fol-
lowed by aminolysis to provide the amino pyrimidine
7. In method A, the amino pyrimidine is reacted directly
with the desired acetylene to provide 8. In method B, the
iodide is reacted with trimethylsilyl acetylene followed by
removal of the silyl group to give terminal acetylene 10.
This intermediate was more versatile (compared to
2. Results
2.1. Chemistry
The initial strategy to assemble the pyrimidine ring relied
on a formamidine acetate ring cyclization28 (Scheme 1).
Treatment of malonate ester 1 with formamidine acetate
in the presence of an alkoxide base gave dihydroxypyr-
imidine, 2. This intermediate was converted to the
dichloropyrimidine, 3, with POCl3 followed by Sono-
gashira coupling29–34 to provide the C(4) chloro acety-
lene, 4. This particular reaction was found to be low
yielding due to both C(4)/C(6) bis acetylene formation35
and Glaser-type homocoupling36 of the starting acety-
lene. Copper-free variations37–43 to eliminate homocou-
pling were not attempted. Final aminolysis provided
the desired amino pyrimidine, 5, in moderate yields.
Our initial investigation of this synthetic route serendip-
itously utilized an electron-releasing dimethylamino res-
Scheme 2. Reagents and conditions: (a) HI, NaI, acetone, rt; (b)
NH4OH, EtOH, 100 ꢁC, sealed tube; (c) acetylene, PdCl2(PPh3)2,
CH3CN, Et3N, 60 ꢁC; (d) 1 M K2CO3, MeOH; (e) ArI, PdCl2(PPh3)2,
CH3CN, Et3N, 60 ꢁC.
Scheme 1. Reagents and conditions: (a) formamidine acetate, NaOEt,
EtOH, 60 ꢁC; (b) POCl3, reflux; (c) acetylene, PdCl2(PPh3)2, CH3CN,
Et3N, 60 ꢁC; (d) NH4OH, EtOH, 100 ꢁC, sealed tube.

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M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
method A), in that, aryl iodides and bromides could be
reacted directly to provide the desired compound 8,
thereby alleviating the need to synthesize each acetylene
coupling partner. The shortcoming of the strategy out-
lined in Scheme 2 was purification of final product. Mul-
tiple chromatographic purifications were necessary to
remove trace palladium impurities.44
Finally, C(4)-substituted amino analogs (Scheme 4) were
accessed by aminolysis of 4d with an assortment of
amines in ethanol at elevated temperatures.
2.2. Biology
Compounds were evaluated (in vitro) for their ability
to inhibit cytosolic AK (AKcyt) as well as ADO phos-
phorylation in intact cells (AKcell).45 Analgesic activity
(in vivo) was measured utilizing one of the following
methods. Acute thermal nociception (hotplate test)
was performed in mice (n = 6–8 per group) using the
55 ꢁC hotplate test as previously described.45,46 Noci-
ceptive paw flinching (formalin test) in rats (n = 6 per
group) was observed 30 min following an intraplantar
injection of 5% formalin (50 lL) into the right hind-
paw. Compounds were administered intraperitoneally
30 min before nociceptive testing as described earlier.47
Analgesia in a neuropathic pain animal model (Chung
assay) was carried out with male Sprague–Dawley rats
after L5/L6 spinal nerve ligation as described by
Chung et al.48,49
To expand the scope of C(5)-substituted analogs, a more
versatile and expedient route was required (Scheme 3).
Dichloropyrimidine, 11, was converted to the diiodide,
12, with hydroiodic acid and sodium iodide. After ami-
nolysis and treatment with bromine, iodopyrimidine 14
was isolated as a white solid. Palladium coupling with
4-ethynyl-N,N-dimethylaniline provided 15b in good
yield. Bromides 15a or 15b were reacted with various
aryl boronic acids to afford 16a–g. As before, the final
products required multiple chromatographic purifica-
tions to remove palladium impurities. Of the synthetic
routes utilized for the construction of these analogs,
Scheme 1 was preferred for ease of purification but
method B in Scheme 2 was preferred for versatility.
NH2
N
X
NH2
3. Discussion
Z
Br
I
c
d
N
N
N
3.1. General structure–activity relationships
N
Y
N
11 (X=Y=Cl)
14
From initial SAR studies to identify a linker replace-
ment for the pyridopyrimidines (Fig. 1), a two-atom
linker was believed important to represent the approxi-
mate spatial arrangement found in the pyridine ring
and the C(5)-substituted aryl ring of ABT-702. Several
functional groups were evaluated including amides, sul-
fonamides, alkenes, and alkyl chains but all were found
to be inactive. The inactivity of these analogs was attrib-
uted to the linker and its inability to provide proper
overlap between the aromatic ring at C(6) and the aro-
matic ring at C(7) in ABT-702. Based on simple models,
it was concluded that the linearity of an acetylene func-
tionality could provide the required distance to overlap
the C(7) aryl group of ABT-702. Synthesis of acetylene
5d was completed (Table 1) and found to be a potent
AK inhibitor (AKcyt IC50 = 3 nM). Further expansion
of the SAR with the acetylene linker was necessary to
define the scope of this new series of AK inhibitors.
Addition of a methyl group at C(2) (5o) or removal of
a nitrogen from the pyrimidine ring (data not shown)
resulted in loss of AK inhibitory activity. If the aryl ring
at C(5) was replaced by alkyl (cyclohexyl, 5l), the result-
a
15 Z=Br
a NR2=N(CH2CH2)2O
b NR2=NMe2
X
NR2
12 (X=Y=I)
b
e
13 (X=NH2; Y=I)
16a-g (Z=Ar)
R=N(CH2CH2)2O; X=N
Ar=
R=NMe2; X=CH
Ar=
16a 4'-Me2NPh
16b 2'-thienyl
16c 3'-thienyl
16d 2'-benzothienyl
16e 2'-benzofuranyl
16f 3-NO2
16g 3-NH2
Scheme 3. Reagents and conditions: (a) HI, NaI, acetone, rt; (b)
NH4OH, EtOH, 100 ꢁC, sealed tube; (c) Br2, AcOH, rt; (d) alkyne,
Pd(PPh3)4, CH3CN, Et3N, 60 ꢁC; (e) ArB(OH)2, Pd(PPh3)4, 2 M
Na2CO3, DME, reflux.
R1
N
R2
5
Cl
Cl
Cl
N
N
N
a
2
N
4d
17a-h
Br
NMe2
NMe2
NH2
4
N
R1
NH2
R1
R2
R1 R2
Me
4
N
2
17f
17g
17h
CH2CH2OCH2CH2
CH2CH2NHCH2CH2
CH2CH2N(SO2NMe2)CH2CH2
17a
H
N
6
R2
linker
7
2
17b Me Me
N
N
17c
17d
17e
H
H
H
cyclohexyl
N
N
histamine
tryptamine
ABT-702
O
Scheme 4. Reagents and conditions: (a) amine, EtOH, 100 ꢁC, sealed
tube.
Figure 1. Linker strategy for identification of novel non-nucleoside
AK inhibitors.

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
Table 1. General structure–activity relationship of 5d
1589
NHR1
R2
5
N
R3
N
6
2
N
a
Compound
R1
H
R2
Ph
R3
H
AK inhibition (IC50)
5a
20
5d
5i
H
H
H
H
H
H
H
H
H
Bn
H
H
H
H
H
H
H
Me
H
H
H
H
3
Cl
5
NMe2
O
O
5j
9
5l
Cyclohexyl
Bn
300
1000
600
>1000
>1000
>1000
>1000
100
5m
5n
5o
10bb
18
19
20c
CHPh2
Ph
O
O
H
H
NMe2
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM) calculated from at least three determinations (standard error of the mean
(SEM) 6 10%).
b Terminal acetylene at C(6).
c p-Dimethylaminophenyl at C(6).
ing analogs were approximately 100 times less potent.
Placement of a nitrogen between the pyrimidine ring
and the C(5) aryl group provided potent AK inhibitors
(data not shown).26 When the aryl ring was removed
from C(5) or the acetylene at C(6) (18 and 10b, respec-
tively), AK inhibitory potency was lost. An attempt to
fill the space at C(5) of 18 by substitution with an amin-
obenzyl (19) at C(4) was unsuccessful. If the phenyl ring
at C(5) in 5d was replaced with benzyl (5m), a decrease
in activity (AKcyt IC50 = 1000 nM) was observed. If an
aromatic ring was added (benzhydryl 5n, AKcyt
IC50 = 600 nM), some activity returned. This seemed
to indicate that larger groups are tolerated at this posi-
tion. In our previous report,26 it was discovered that
larger alkyl and aromatic groups at C(5) are potent
inhibitors (AKcyt IC50 < 50 nM). Based on these previ-
ous results, an exchange of the C(6) aryl acetylene with
the C(5) aryl group was initiated. Acetylene 20 was com-
pleted (modification of 5i) and found to have an AKcyt
IC50 of 100 nM. This result was intriguing. Clearly,
there is no overlap between the aryl group at C(6) in
20 and the C(7) aryl group in ABT-702, yet AK inhibi-
tory potency was retained. We began to question the
binding orientation (relative to the adenosine heterocy-
clic base) of the acetylenes in the active site of AK. Fur-
thermore, these findings prompted the question as to

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M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
Table 2. In vitro characterization at C(4) of AK inhibitors 17a–h in
cytosolic and intact cell assays
whether all the acetylene analogs of this series were
bound in the same orientation or was there a possibility
of multiple binding motifs within this series (e.g., 5d vs
20). In addition to ligand orientation within the active
site, we had to consider the possibility of different pro-
tein conformations. The ability of structurally unique
inhibitors to bind tightly to different protein conforma-
tions50 of a single enzyme is not without precedence. The
concept of either a lock and key51 or induced fit52 mech-
anism has evolved to the idea of receptor conformation-
al ensembles.53 In essence, this concept states that
several distinctive enzyme conformations (different than
the native substrate–protein interactions) exist of which
any one could bind tightly to structurally different sub-
strates.54–56 Recent examples include both aspartic pep-
tidase inhibitors57 as well as HIV protease inhibitors.58
The possibility of this particular series of acetylene
inhibitors binding to different AK conformational
ensembles had to be considered. Therefore, if the poten-
cy of 5d validated an SAR expansion of the acetylene
series, then the potency of 20 stressed the importance
of obtaining an X-ray structure of an acetylene inhibitor
in the active site of AK to probe such a question.
Although our initial assumptions relating to ligand
overlap with adenosine were unclear, the acetylene series
was a potent class of non-nucleoside AK inhibitors.
With the general scope of the acetylene series defined,
research focus was turned to the C(4) amino group.
Cl
R
N
N
NMe2
a
Compound
R
AK inhibition (IC50)
Cytosolic
3
Intact cells
700
5d
NH2
17a
17b
17c
17d
NHMe
NMe2
14
300
350
>1000
>1000
>1000
NHcyclohexyl
>1000
80
N
NH
HN
HN
17e
38
>1000
NH
3.2. C(4) Structure–activity relationships
Table 2 shows the effect of amino substitution at C(4).
The observed activity, by successive methyl substitution,
decreased from amino (AKcyt IC50 = 3 nM), to mono
methyl amino, 17a (AKcyt IC50 = 14 nM) to dimethyl
amino, 17b (AKcyt IC50 = 300 nM). Larger amino alkyl
residues, such as cyclohexyl (17c), were inactive. If, how-
ever, an alkyl linker was placed between amine at C(4)
and the ‘large’ group (17d, 17e) or the dialkyl amine
O
17f
6
8
970
N
H
N
N
17g
>1000
was tied up as
a morpholine ring (17f, AKcyt
IC50 = 6 nM) or piperizine ring (17g, AKcyt IC50 = 8 nM)
activity returned. Even substituted piperazine 17h re-
tained activity (AKcyt IC50 = 20 nM). In general, C(4)
substitution retained AKcyt inhibition (compared to 5d)
and, in some cases (17a, 17h), improved the AKcell inhi-
bition.59 However, the AK inhibitory activity in intact
cells (AKcell) of these analogs was too weak to be consid-
ered for any further in vivo studies in animal models of
pain.24 Therefore, subsequent investigation of C(4)-
substituted analogs was suspended and the expansion
of C(5) and C(6) substitution was pursued to improve
biochemical potency.
N
O
S
N
O
17h
13
330
N
ABT-702
1.7b
50.7b
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
b Jarvis et al.45
used to modulate physiochemical properties without det-
rimental effects on AK inhibition.
3.3. C(5) structure–activity relationships
Table 3 shows the effect of aromatic substitution at C(5).
Evaluation of mono chloro substituted phenyl analogs
revealed that potency decreased from the para substitut-
ed analog (5d; AKcyt IC50 = 3 nM) to the meta position
(5c; AKcyt IC50 = 10 nM) to the ortho position (5b; AKcyt
IC50 = 75 nM). It is interesting to note that the 3,4-dime-
thoxy analog, 5h (IC50 = 20 nM), had comparable poten-
cy to 5g. This suggests that the meta position could be
The electronic nature of the substituents on the aromatic
ring appears to be important and favors electron-with-
drawing groups. Compounds 5e, 5d, and16f were more
potent than 5f, 5g, and 16g. The notable exceptions were
5i (AKcyt IC50 = 5 nM; AKcell IC50 = 240 nM) and 5j
(AKcyt IC50 = 9 nM; AKcell IC50 = 250 nM). In addi-
tion, these analogs showed significant inhibition in

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1591
Table 3. In vitro characterization of selected C(5)-substituted AK
inhibitors 5a–k and 16f,g in cytosolic and intact cell assays
Table 4. In vitro characterization of selected C(6) aryl and heteroaryl
acetylene AK inhibitors 5p–r and 8a–f in cytosolic and intact cell
assays
4'
NH2
R
Cl
NH2
N
2'
N
N
N
R
NMe2
a
a
Compound
R
AK inhibition (IC50)
Compound
R
AK inhibition (IC50)
Cytosolic
Intact cells
Cytosolic
Intact cells
5p
5q
5r
8a
8b
8c
8d
8e
8f
Ph
40-MePh
60
25
>1000
830
5a
5b
5c
5d
5e
5f
H
20
75
10
3
>1000
700
550
20-Cl
40-i-PrPh
50
>1000
>1000
>1000
>1000
>1000
230
30-Cl
40-Cl
40-BrPh
40-Me
40-OMe
30,40-DiOMe
40-NMe2
30,40-OCH2O
40-i-Pr
30-NO2
30-NH2
50-pyrmidinyl
20-pyridyl
20-thienyl
40-NO2Ph
40-NH2Ph
40-morpholinePh
216
500
43
700
600
3
13
18
20
5
330
730
43
10
5g
5h
5i
500
240
17
275
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
5j
9
250
5k
16f
16g
22
16
90
>1000
>1000
1000
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
calculated logP values between 3 and 4 appeared to be
the most potent. For example, 5d (AKcell IC50
700 nM, clogP = 5.09) and 5r (AKcell IC50 > 1000 nM,
clogP = 6.35) were less potent than 8e (AKcell IC50
=
=
intact cell AK; believed to more closely resemble the
physiological environment. Factors that influence the
IC50 AKcell were studied with both more lipophilic ana-
logs, such as 40-isopropyl, 5k, as well as more polar com-
pounds like 30-amino phenyl, 16g. These polarity
extremes showed comparable cytosolic potency to 5i
but were inactive in the intact cell assay. These findings
suggest a ‘U-shaped’ correlation between lipophilicity
and cell permeability. Calculations related to logP
(clogP)60 for 5i (clogP = 4.68), 5k (clogP = 5.79), and
16g (clogP = 3.38) suggested that values between 4
and 5 provided optimal AK inhibition in intact cells.
230 nM, clogP = 3.70) and 8f (AKcell IC50 = 275,
clogP = 4.38). The most potent inhibitors from this
group were screened in a mouse hotplate model of anal-
gesia. None displayed significant activity, due most
likely to relatively poor potency in inhibiting AK in in-
tact cells. Previous observations from the pyridopyrimi-
dines (like ABT-702) suggested that an acetylene at C(6)
with a substituted heterocycle such as pyridine would in-
crease cell penetration (and AK inhibition) and, per-
haps, lead to activity in an animal model of pain.
Table 5 shows the C(6) 2-aminopyridyl replacements.
Generally, this replacement (vs substituted aryl) had a
positive effect on the AKcell inhibition. The potent ana-
logs have a clogP of 3.5–4.5. The most potent com-
pound from this initial screen was the morpholine
analog, 8l (AKcell IC50 = 58 nM; clogP = 3.43). More
polar analogs (like 8j and others not shown) with
clogP < 3.5 and more lipophilic analogs 8o and 8q
(clogP > 4.5) were less potent (AKcell) than those ana-
logs with a clogP between 3.5 and 4.5. There are nota-
ble exceptions, however. Pyrimidine 8g (AKcell
IC50 = 200 nM, clogP = 2.67) and acetyl piperazine 8p
(AKcell IC50 = 39 nM, clogP = 3.01) both showed better
AKcell inhibition than predicted, while the pyridazine, 8h
(AKcell IC50 = 700 nM, clogP = 2.40), and morpholine
regioisomer, 8i (AKcell IC50 = 110 nM, clogP = 3.43),
behaved as predicted. The physiochemical properties
and their relationship to cell penetration are not well
understood. These examples illustrate the care that must
be taken in attempted correlations between predicted
Although 5i and 5j were potent inhibitors of AKcell
,
both were inactive in a mouse hotplate model of analge-
sia.46 Attempts to further optimize AKcell inhibition at
C(5) with dimethylaminophenyl acetylene were unsuc-
cessful. Consequently, focus was turned to optimization
of the aryl acetylene at C(6).
3.4. C(6) structure–activity relationships
Table 4 shows the optimization of substituted phenyl
acetylene at C(6). In general, AKcyt inhibition seems to
show a substituent effect opposite that in the C(5)
SAR. Electron-donating substituted phenyl analogs
seemed to be more potent than those containing elec-
tron-withdrawing groups. For example, 8e was more po-
tent (AKcyt
) than 8d. Additionally, unsubstituted
heterocyclic replacements (pyrimidine 8a, pyridine 8b)
seem to show less activity than phenyl, 5p. The thio-
phene bioisostere, 8c, displayed similar potency to 5p.
None showed activity in inhibiting intact cell AK.
lipophilicity (clogP) and expected potency in AKcell
.
Examination of AKcell inhibition showed a polarity-de-
pendent trend similar to the C(5) SAR. Analogs with
The most potent analogs 8g, 8i, 8k, 8l, and 8m were
evaluated in animal models of pain. Mouse hotplate

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M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
Table 5. In vitro characterization of selected C(6) pyridyl acetylene
AK inhibitors 8g–q in cytosolic and intact cell assays
Table 6. In vivo characterization of selected AK inhibitors
Compound Hotplate analgesia,a % MPEb Formalin,c % RFNd
Cl
8f
8g
67
20
36
49
20
29
48
47
44
44
49
NH2
100
nde
73
N
N
8i
8k
8l
100
nd
8m
8r
N
R
nd
16a
16b
16d
16e
ABT-702
100
nd
a
Compound
R
AK inhibition (IC50)
nd
nd
36
g
Cytosolic
8
Intact cells
200
f
8gb
a Values represent compounds administered by ip injection at 30 lmol/
kg dose.
N
N
N
O
O
O
b % MPE = % maximal protective effect ([postdrug latency] ꢀ [vehicle
latency])/([maximum latency] ꢀ [vehicle latency]) · 100%, where
maximum (cutoff) latency was 180 s. Values represent means within
8% and p < 0.05 to vehicle treated mice.46
8hc
8id
8j
45
8
700
110
333
83
c Values represent compounds administered by ip injection at 10 lmol/
kg dose.
d % RFN = % reduction in formalin-induced nociception ([vehicle
flinches] ꢀ [postdrug flinches])/[vehicle flinches] · 100%. Values rep-
resent means within 5% and p < 0.05 to vehicle treated rats.
e nd, not determined.
NH2
14
6
f ED50 = 8 lmol/kg from Jarvis et al.45
g ED50 = 15 lmol/kg from Kowaluk et al.47
8k
8l
NMe2
N
3
58
acetylene SAR was that the 2-morpholino pyridine acet-
ylene at C(6) was adequate for modest in vivo activity
but reoptimization of C(5) was required to further in-
crease the AKcell potency.
O
NMe
N
8m
8n
8o
8p
8q
1
80
OMe
3.5. Analog reoptimization and in vivo evaluation
6
131
>1000
39
NSO2NMe2
NBoc
Although the in vivo efficacy of 8l was encouraging,
our expectation was to discover a more efficacious acet-
ylene analog that displayed activity in several different
animal models of pain including neuropathic pain. De-
spite the anomaly between clogP and AKcell with 8g
and 8p, we decided to target analogs with a clogP be-
tween 3 and 4.5. Substitution (Table 7) in the para po-
sition produced compounds that were less potent
(AKcell) than 8l (data not shown). The one exception
was 16a (AKcell IC50 = 68 nM) that was nearly equipo-
tent to 8l. Heterocyclic replacements at C(5) included
thienyl analogs (16b, 16c) and bicyclic heterocycles
(16d, 16e). These replacements showed good AK inhib-
itory potency in intact cells, however, these did not sur-
pass the parent compound 8l. Compounds 16a–e all
showed good efficacy in the formalin assay but, like
in earlier analogs, were inactive in the Chung model
of neuropathic pain.
N
62
1
N
NC(O)Me
N
9
733
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
b C(6) pyridine replacement: C(6)-[20-morpholin-40-ylpyrimidin-50-yl].
c C(6) pyridine replacement: C(6)-[60-morpholin-40-ylpyridazin-30-yl].
d C(6) pyridine replacement: C(6)-[50-morpholin-40-ylpyridin-30-yl].
experiments using 8g, 8k, and 8l at doses of 30 lmol/kg
showed significant efficacy (% MPE61 > 70). All of these
compounds were assessed further in the formalin assay
(Table 6). Although these analogs displayed lower dose
activity in a formalin assay, none showed efficacy in a
neuropathic animal model of pain (Chung assay).49 Pyr-
idopyrimidines, however, substituted with 2-aminopyr-
idyl at C(7) were efficacious in several animal models
of pain.8,45,48,62 The conclusion from the heteroaryl
It was previously reported63 that the active site of AK
possesses a hydrophilic binding pocket that accommo-
dates a phosphate group needed for the conversion of
ADO to AMP. To investigate this secondary binding
site, a series of C(6) trisubstituted pyridyl acetylene ana-
logs were synthesized and tested. Table 8 shows polar
examples at both C(5)0 and C(6)0 of pyridyl acetylene
analogs.64 As indicated in Table 8, these trisubstituted

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
Table 7. Reoptimization of C(5) aryl acetylene AK inhibitors 8l, 8r
and 16a–e in cytosolic and intact cell assays
1593
3.6. ADME considerations
The pharmacokinetic (PK) analysis of 16a (Table 9)
indicated that both the half-life and volume of distribu-
tion were slightly less than ABT-702; plasma clearance
was slightly greater for 16a. In vitro metabolism studies
in both rat hepatocyte and human microsomes of 16a
indicated a significant decrease in parent after 24 h in
rat and 1 h in human microsomes (compared to ABT-
702). Although identification of metabolic products
was not performed on 16a, several possible sites include
the morpholine ring,65 the dimethyl amino group at
C(5), and the acetylene itself. The increases in both
clearance and in rat metabolism of 16a (compared to
ABT-702) may be a part of several factors contributing
to lack of efficacy in animal models. Later reoptimiza-
tion of C(5) to address some of these issues led to acet-
ylene analogs that displayed good efficacy in both
formalin and neuropathic pain animal models.26 Key
to the in vivo efficacy of these latter compounds was
the placement of a nitrogen atom at C(5) and extending
the alkyl chain several carbon atoms.
NH2
R
N
N
N
N
O
a
Compound
R
AK inhibition (IC50)
Cytosolic
Intact cells
8l
40-ClPh
3
10
2
58
120
68
8r
30,40-OCH2OPh
40-Me2NPh
20-Thienyl
16a
16b
16c
16d
16e
13
38
0.4
1
167
212
100
123
30-Thienyl
20-Benzothienyl
20-Benzofuranyl
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
3.7. X-ray crystal structure analysis
Table 8. In vitro characterization of selected C(6) trisubstituted
pyridylacetylene AK inhibitors 8s–v in cytosolic and intact cell assays
As the biological evaluation of 8s–v was concluding, an
X-ray crystal structure27 of 16a bound to the AK active
site was determined. Surprisingly, 16a was not observed
to bind in the same manner as adenosine (Fig. 2). A pre-
viously determined crystal structure reported66 that two
key hydrogen bonds and a p–p interaction with F170
were important for adenosine binding to the AK pro-
tein. First, the N(6) amino group forms a hydrogen
bond with T173 through a water bridge. Second, the side
chain of N14 donates a hydrogen bond to N(1) of aden-
osine. In addition, a ‘flap’ region closes down over the
native substrate and the catalytic process occurs. Model-
ing this same binding motif to the acetylene series
(Fig. 1) predicts a hydrogen bond between the C(4) ami-
no group (presumably through a water bridge) and T173
as well as a hydrogen bond between N14 and N(3) of the
pyrimidine ring. However, the crystal structure of 16a
shows hydrogen bonds between the C(4) amino group
and D18 as well as between the N(3) pyrimidine and
the S65 amide nitrogen. This orients the C(6) aryl
acetylene group through a groove in the enzyme, formed
by a hinge opening rearrangement of the protein, and
out into solvent space thus stabilizing an open form of
the enzyme.27 In short, the binding orientation for the
O
NH2
O
R2
N
N
1
6'
R
2'
N
N
O
a
Compound R1
R2
AK inhibition (IC50)
Cytosolic Intact cells
8r
8s
8t
8u
8v
H
H
10
26
120
161
215
88
NMe2
H
H
NMe2
H
72
H
O
N
18
NH
OMe
H
101
198
N
a Assay with cytosolic AK. Mean values for inhibitors (IC50 in nM)
calculated from at least three determinations (standard error of the
mean (SEM) 6 10%).
Table 9. Pharmacokinetic data and metabolism for ABT-702 and 16a
Compound
Pharmacokineticsa
t1/2 Vb CLp Cmax
0.9 1.0 0.8
0.5 0.7 1.0
Metabolismb
F
Ratc Humand
ABT-702
16a
0.55
0.08
23 61
21
78
74
9
analogs did not offer any potency advantage in vitro.
Furthermore, in vivo evaluation of 8s in an animal mod-
el (formalin) showed no efficacy up to 30 lmol/kg (ip).
Because of the continued lack of in vivo efficacy in these
analogs, the physiochemical properties of selected acety-
lene compounds were evaluated.
a iv dose in rat at 5 lmol/kg for t1/2, Vb, and CLp. po dose in rat at
5 lmol/kg for Cmax and F. Units: t1/2 in h; Vb in L/kg; CLp in L/hkg;
Cmax in lg/mL; F as %.
b % parent.
c Assay run in hepatocytes. Analyzed after 24 h.
d Assay run in microsomes. Analyzed after 1 h.

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M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
T 173
F 170
O
T 173
H
O
H
O
H
N
O
hydrophobic
groove out
to solvent
H
pocket
Me
N
N
H
H
O
H
H
F 170
Me
N
N
N 68
Me
H
N
N
O
HN
O
N
H
N
N
Me
O
O
H
N
H
N 14
H
N
H
N
N
N 14
N
H
O
O
S 65
H
O
D 18
S 65
H
H
O
N
O
N
O
N
OH
HO
G 64
actual (type II)
G 64
predicted (type I)
Figure 2. Predicted (type I) and actual (type II) binding of 16a in the active site of adenosine kinase.
acetylene series (type II) is flipped approximately 180 de-
grees through the C(5) aryl group (compared to adeno-
sine type I) in the active site of AK. In addition, the
protein itself exists in an open state with 16a compared
to a closed state in the case of adenosine binding.
aryl acetylene projected into solvent space? Additional
X-ray structures of C(6) acetylene analogs would be nec-
essary to answer these questions.
4. Conclusion
The type II binding observed in the 16a crystal structure
can now explain the SAR of other analogs in this series.
For example, when a type I binding mode was assumed
for the trisubstituted analogs, 8s–v, one would predict
increased potency by reaching into the hydrophilic
pocket. No such increase in potency was observed.
However, this result is consistent with the type II bind-
ing mode. The aryl acetylene fragment projects through
a groove in the active site and out into solvent space. As
a result, the earlier hypothesis of reaching a secondary
phosphate binding site by using a trisubstituted aryl ring
at C(6) proved false. To reach the phosphate binding
site, placement of more polar side chains should origi-
nate from C(4). However, no further attempts were ini-
tiated at C(4) to confirm this redirected hypothesis.
In conclusion, we identified novel non-nucleoside inhib-
itors of AK with an acetylene functional group. The
in vitro potency of these acetylene analogs compared
favorably to ABT-702. The efficacy in animal models
of pain, however, was diminished compared to ABT-
702. This lack of in vivo efficacy is thought to result
from lower plasma levels after systemic dosing of these
aryl acetylene analogs relative to the pyridopyrimidines
like ABT-702. During the course of this investigation, an
X-ray structure was obtained of 16a bound in the active
site of AK.27 This result showed that binding orientation
of the acetylene series (type II binding) was flipped 180
degrees through the C(5) aryl group compared to aden-
osine (type I binding). The aryl acetylene portion pro-
jects through a groove in the enzyme out into solvent
space thus stabilizing an open form of the enzyme.
The anomalous SAR exhibited by some analogs, like
20, may be explained if type II binding is considered.
What is unclear, however, is the possibility of other aryl
acetylenes adopting other binding orientations or addi-
tional AK enzyme conformations that could be stabi-
lized similar to type II binding. These questions will
require considerable SAR and X-ray crystallographic
expansion of the current series.
Acetylene analog, 20, showed moderate (AKcyt
IC50 = 100 nM) AK inhibition, which could not be
rationalized using a type I binding orientation. Type II
binding predicts that the C(5) aryl acetylene projects
though the enzyme groove thus providing a potent ana-
log. Several interesting questions concerning 20 can,
therefore, be posed. How is the rest of this analog ori-
ented in the active site? Does the C(6) aryl group reside
near F170 (p–p interaction as in adenosine) or does the
C(4) amino group form a hydrogen bond with T173?
Even if acetylene 20 adopts one orientation, perhaps
other analogs within the C(5) acetylene series prefer
other orientations depending on specific substitutions.
No further expansion of C(5) aryl acetylenes was ex-
plored. This same question may be posed to the C(6)
acetylene analogs as well. Although 16a was shown to
prefer the orientation shown in Figure 1, could other
orientations within the series be possible as long as the
5. Experimental
5.1. General procedures
General experimental procedures and techniques are
reported in the supplemental section of this report. Prep-
aration of ABT-702 is reported22 elsewhere.

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1595
5.2. Chemical procedures
5.2.5. 5-(3-Chlorophenyl)-6-(4-dimethylaminophenylethy-
nyl)pyrimidin-4-ylamine (5c). Starting with 4c, the title
compound was prepared according to the general pro-
cedure described for the aminolysis reaction (method
A). Aqueous work up and triturating with Et2O pro-
vided 176 mg (65%) of 5c: yellow solid. 1H NMR
(300 MHz, DMSO-d6) d 8.31 (s, 1H, @N–CH@N),
7.53 (m, 2H, 40- and 60-ArH), 7.47 (m, 1H, 20-ArH),
7.36 (m, 1H, 50-ArH), 6.99 (AA0BB0, 2H, J = 8.8,
ArH), 6.65 (AA0BB0, 2H, J = 9.2, ArH), 6.60 (br s,
2H, NH2), 2.93 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 160.8 (s), 157.2 (d), 150.7 (s),
146.7 (s), 136.3 (s), 133.1 (s), 132.7 (d), 130.5 (d),
129.8 (d), 128.7 (d), 128.0 (d), 117.6 (s), 111.7 (d),
106.6 (s), 96.3 (s), 86.1 (s), 39.5 (q). MS (DCI/NH3)
m/z 349 (M+H)+. Anal. Calcd for C20H17ClN4Æ0.2H2O:
C, 68.16; H, 4.98; N, 15.90. Found: C, 68.21; H, 4.67;
N, 15.72.
5.2.1. General procedure for the formation of 4-amino-5-
aryl-6-arylethynylpyrimidines (aminolysis-method A). To
a slurry of 4 in EtOH (0.1 M) was added concentrated
NH4OH (0.2 M), the reaction mixure was sealed in a
tube and heated to 100 ꢁC until judged complete by
TLC (typically 30–60 h). The mixture was cooled, the
product filtered, and washed with EtOH. The solid
was dried in a vacuum oven at 50 ꢁC overnight. In an
alternative work up (aqueous), the mixture was concen-
trated, the residue taken up in CH2Cl2, washed with sat-
urated NaHCO3, brine, and concentrated. The residue
was purified by chromatography with the indicated
solvent.
5.2.2. General procedure for the formation of 4-alkyl-
amino-5-aryl-6-arylethynylpyrimidines (aminolysis-method
B). A solution of 4d (1.0 equiv) in EtOH (0.1 M) was
treated with 2.2 equiv of the amine (or excess as indicat-
ed) sealed in a tube and heated to 100 ꢁC overnight. The
reaction mixture was cooled, concentrated, and the res-
idue purified by chromatography (elution with the indi-
cated solvent) to provide the desired amine addition
product.
5.2.6. 5-(4-Chlorophenyl)-6-(4-dimethylaminophenylethy-
nyl)pyrimidin-4-ylamine (5d). Starting with 4d, the title
compound was prepared according to the general proce-
dure described for the aminolysis reaction (method A).
Aqueous work up and purification by chromatography
(elution with 50% EtOAc–hexane then 5% MeOH–
CHCl3) gave 75 mg (59%) of 5d: yellow solid; Rf 0.29
1
5.2.3. 6-(4-Dimethylaminophenylethynyl)-5-phenylpyrim-
idin-4-ylamine (5a). Starting with 4a, the title compound
was prepared according to the general procedure de-
scribed for the aminolysis reaction (method A). Aque-
ous work up and purification by chromatography
(elution with 50% EtOAc–hexane then 10% MeOH–
(50% EtOAc–hexane). H NMR (300 MHz, CDCl3) d
8.50 (s, 1H, @N–CH@N), 7.51 (AA0BB0, 2H, J = 8.8,
ArH), 7.44 (AA0BB0, 2H, J = 8.4, ArH), 7.11 (AA0BB0,
2H, J = 9.2, ArH), 6.56 (AA0BB0, 2H, J = 9.2, ArH),
5.01 (br s, 2H, NH2), 2.97 (s, 6H, N(CH3)2). 13C
NMR (75 MHz, CDCl3) d 160.6 (s), 157.5 (d), 150.9
(s), 148.4 (s), 134.6 (s), 133.5 (d), 132.4 (s), 131.4 (d),
129.3 (d), 118.1 (s), 111.6 (d), 107.8 (s), 98.2 (s), 85.7
(s), 40.0 (q). MS (DCI/NH3) m/z 349 (M+H)+. IR
(KBr) 3291, 2951, 2206, 1608, 817 cmꢀ1. Anal. Calcd
for C20H17ClN4: C, 68.86; H, 4.91; N, 16.06. Found:
C, 68.61; H, 4.85; N, 15.88.
1
CH2Cl2) provided 70 mg (79%) of 5a: yellow solid. H
NMR (300 MHz, CDCl3) d 8.52 (s, 1H, @N–CH@N),
7.50 (m, 5H, ArH), 7.08 (AA0BB0, 2H, J = 7.5, ArH),
6.53 (AA0BB0, 2H, J = 7.5, ArH), 4.88 (br s, 2H,
NH2), 2.97 (s, 6H, N(CH3)2). 13C NMR (100 MHz,
DMSO-d6) d 160.9 (s), 156.9 (d), 150.6 (s), 146.6 (s),
134.0 (s), 132.6 (d), 129.8 (d), 128.6 (d), 128.0 (d),
118.9 (s), 111.6 (d), 106.8 (s), 95.7 (s), 86.3 (s), 39.5
(q). MS (ESI) m/z 315 (M+H)+. Anal. Calcd for
C20H18N4Æ0.2H2O: C, 75.54; H, 5.83; N, 17.62. Found:
C, 75.38; H, 5.75; N, 17.33.
5.2.7. 5-(4-Bromophenyl)-6-(4-dimethylaminophenylethy-
nyl)pyrimidin-4-ylamine (5e). Starting with 4e, the title
compound was prepared according to the general proce-
dure described for the aminolysis reaction (method A).
Aqueous work up and purification by chromatography
(50% EtOAc–hexane then EtOAc) afforded 130 mg
(45%) of 5e: light yellow solid. 1H NMR (300 MHz,
DMSO-d6) d 8.30 (s, 1H, @N–CH@N), 7.71 (AA0BB0,
2H, J = 8.5, ArH), 7.37 (AA0BB0, 2H, J = 8.5, ArH),
6.99 (AA0BB0, 2H, J = 8.8, ArH), 6.65 (AA0BB0, 2H,
J = 9.2, ArH), 6.58 (br s, 2H, NH2), 2.93 (s, 6H,
N(CH3)2). 13C NMR (100 MHz, DMSO-d6) d 160.8
(s), 157.1 (d), 150.6 (s), 146.5 (s), 133.3 (s), 132.6 (d),
132.1 (d), 131.5 (d), 121.3 (s), 117.7 (s), 111.7 (d),
106.6 (s), 96.0 (s), 86.1 (s), 39.5 (q). MS (DCI/NH3) m/
z 393/395 (M+H)+. Anal. Calcd for C20H17BrN4Æ0.2
EtOAc: C, 60.80; H, 4.56; N, 13.63. Found: C, 60.95;
H, 4.45; N, 13.72.
5.2.4. 5-(2-Chlorophenyl)-6-(4-dimethylaminophenylethy-
nyl)pyrimidin-4-ylamine (5b). Starting with 4b, the title
compound was prepared according to the general proce-
dure described for the aminolysis reaction (method A).
Aqueous work up and purification by chromatography
(elution with 5% MeOH–CH2Cl2 (300 mL) then 10%
MeOH–CH2Cl2) provided 287 mg (71%) of 5b: yellow
1
solid. H NMR (300 MHz, DMSO-d6) d 8.33 (s, 1H,
@N–CH@N), 7.63 (m, 1H, ArH), 7.54-7.45 (m, 2H,
ArH), 7.38 (m, 1H, ArH), 6.85 (AA0BB0, 2H, J = 8.8,
ArH), 6.61 (AA0BB0, 2H, J = 9.2, ArH), 6.56 (br s,
2H, NH2), 2.91 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 160.7 (s), 157.5 (d), 150.6 (s),
147.4 (s), 133.7 (s), 133.2 (s), 132.7 (d), 132.3 (d), 130.0
(d), 129.5 (d), 127.5 (d), 116.9 (s), 111.6 (d), 106.6 (s),
96.4 (s), 85.7 (s), 39.5 (q). MS (DCI/NH3) m/z 349
(M+H)+. Anal. Calcd for C20H17ClN4Æ0.2H2O: C,
68.16; H, 4.98; N, 15.90. Found: C, 68.05; H, 4.78; N,
16.27.
5.2.8. 6-(4-Dimethylaminophenylethynyl)-5-p-tolylpyrimi-
din-4-ylamine (5f). Starting with 4f, the title compound
was prepared according to the general procedure de-
scribed for the aminolysis reaction (method A). Aqueous
work up and purification by chromatography (5%

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M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
MeOH–CH2Cl2) provided 152 mg (69%) of 5f: orange
solid. H NMR (300 MHz, DMSO-d6) d 8.28 (s, 1H,
130.3 (d), 120.8 (s), 119.2 (s), 112.2 (d), 111.7 (d),
107.1 (s), 95.0 (s), 86.8 (s), 40.0 (q), 39.6 (q). MS
(DCI/NH3) m/z 358 (M+H)+. Anal. Calcd for
C22H23N5Æ0.2H2O: C, 73.18; H, 6.53; N, 19.40. Found:
C, 73.15; H, 6.37; N, 19.10.
1
@N–CH@N), 7.34 (AA0BB0, 2H, J = 8.5, ArH), 7.30
(AA0BB0, 2H, J = 7.8, ArH), 6.98 (AA0BB0, 2H, J = 8.8,
ArH), 6.64 (AA0BB0, 2H, J = 8.8, ArH), 6.40 (br s, 2H,
NH2), 2.93 (s, 6H, N(CH3)2), 2.40 (s, 3H, ArCH3). 13C
NMR (75 MHz, DMSO-d6) d 161.1 (s), 156.7 (d), 150.5
(s), 146.5 (s), 137.2 (s), 132.6 (d), 130.9 (s), 129.6 (d),
129.1 (d), 118.8 (s), 111.6 (d), 106.9 (s), 95.5 (s), 86.3 (s),
39.5 (q), 20.9 (q). MS (DCI/NH3) m/z 329 (M+H)+. Anal.
Calcd for C21H20N4Æ0.6H2OÆ0.1CH2Cl2: C, 72.88; H,
6.20; N, 16.11. Found: C, 73.15; H, 5.81; N, 15.78.
5.2.12. 5-Benzo[1,3]dioxol-5-yl-6-(4-dimethylaminophen-
ylethynyl)pyrimidin-4-ylamine (5j). Starting with 4j, the
title compound was prepared according to the general
procedure described for the aminolysis reaction (method
A). Aqueous work up and purification by chromatogra-
phy (elution with 50% EtOAc–hexane then 10% MeOH–
CH2Cl2) provided 112 mg (51%) of 5j: yellow solid; Rf
0.12 (50% EtOAc–hexane). 1H NMR (300 MHz,
CDCl3) d 8.49 (s, 1H, @N–CH@N), 7.19 (AA0BB0,
2H, J = 8.8, ArH), 6.96 (m, 3H, ArH), 6.57 (AA0BB0,
2H, J = 9.2, ArH), 6.06 (s, 2H, OCH2O), 5.06 (br s,
2H, NH2), 2.98 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 161.3 (s), 156.7 (d), 150.6 (s),
147.4 (s), 146.9 (s), 146.6 (s), 132.7 (d), 127.4 (s), 123.5
(d), 118.7 (s), 111.7 (d), 110.2 (d), 108.6 (d), 106.9 (s),
101.0 (t), 95.7 (s), 86.3 (s), 39.5 (q). MS (DCI/NH3) m/
z 359 (M+H)+. Anal. Calcd for C21H18N4O2Æ0.20H2Oꢁ
0.30EtOAc: C, 68.65; H, 5.40; N, 14.42. Found: C,
68.74; H, 5.21; N, 14.48.
5.2.9. 6-(4-Dimethylaminophenylethynyl)-5-(4-methoxy-
phenyl)pyrimidin-4-ylamine (5g). Starting with 4g, the ti-
tle compound was prepared according to the general
procedure described for the aminolysis reaction (meth-
od A). Aqueous work up and purification by chroma-
tography (5% MeOH–CH2Cl2) gave 243 mg (70%) of
5g: yellow solid. 1H NMR (300 MHz, DMSO-d6) d
8.27 (s, 1H, @N–CH@N), 7.34 (AA0BB0, 2H, J = 8.8,
ArH), 7.08 (AA0BB0, 2H, J = 8.8, ArH), 7.01 (AA0BB0,
2H, J = 9.2, ArH), 6.65 (AA0BB0, 2H, J = 9.2, ArH),
6.42 (br s, 2H, NH2), 3.83 (s, 3H, OCH3), 2.93 (s,
6H, N(CH3)2). 13C NMR (75 MHz, DMSO-d6) d
161.3 (s), 159.0 (s), 156.6 (d), 150.6 (s), 146.6 (s),
132.6 (d), 131.1 (d), 125.9 (s), 118.7 (s), 114.1 (d),
111.7 (d), 106.9 (s), 95.5 (s), 86.4 (s), 55.2 (q), 39.5
(q). MS (DCI/NH3) m/z 345 (M+H)+. Anal. Calcd
for C21H20N4O: C, 73.23; H, 5.85; N, 16.27. Found:
C, 72.88; H, 5.81; N, 15.89.
5.2.13. 6-(4-Dimethylaminophenylethynyl)-5-(4-isopro-
pylphenyl)pyrimidin-4-ylamine (5k). Starting with 4k,
the title compound was prepared according to the gener-
al procedure described for the aminolysis reaction
(method A) followed by filtration to afford 225 mg
(60%) of 5k: orange solid. 1H NMR (300 MHz,
DMSO-d6) d 8.29 (s, 1H, @N–CH@N), 7.40 (AA0BB0,
2H, J = 8.1, ArH), 7.32 (AA0BB0, 2H, J = 8.1, ArH),
6.92 (AA0BB0, 2H, J = 8.8, ArH), 6.59 (AA0BB0, 2H,
J = 9.1, ArH), 6.43 (br s, 2H, NH2), 2.99 (m, 1H,
CH(CH3)2), 2.92 (s, 6H, N(CH3)2), 1.29 (d, 6H,
J = 6.8, CH(CH3)2). 13C NMR (100 MHz, DMSO-d6)
d 161.0 (s), 156.7 (d), 150.5 (s), 148.1 (s), 146.8 (s),
132.6 (d), 131.4 (s), 129.8 (d), 126.5 (d), 119.0 (s),
111.5 (d), 106.9 (s), 95.8 (s), 86.5 (s), 39.5 (q), 33.3 (d),
23.8 (q). MS (DCI/NH3) m/z 357 (M+H)+. Anal. Calcd
for C23H24N4Æ0.4H2O: C, 75.96; H, 6.87; N, 15.41.
Found: C, 76.16; H, 6.82; N, 15.55.
5.2.10.
5-(3,4-Dimethoxyphenyl)-6-(4-dimethylamino-
phenylethynyl)pyrimidin-4-ylamine (5h). Starting with
4h, the title compound was prepared according to the
general procedure described for the aminolysis reaction
(method A) followed by filtration to provide 210 mg
(62%) of 5h: light yellow solid. 1H NMR (300 MHz,
CDCl3) d 8.50 (s, 1H, @N–CH@N), 7.15 (AA0BB0,
2H, J = 9.2, ArH), 7.04 (m, 3H, ArH), 6.56 (AA0BB0,
2H, J = 9.2, ArH), 5.04 (br s, 2H, NH2), 3.97 (s, 3H,
OCH3), 3.88 (s, 3H, OCH3), 2.97 (s, 6H, N(CH3)2).
13C NMR (75 MHz, DMSO-d6) d 161.2 (s), 156.6 (d),
150.5 (s), 148.7 (s), 148.5 (s), 146.5 (s), 132.6 (d), 126.1
(s), 122.1 (d), 118.8 (s), 113.4 (d), 112.0 (d), 111.7 (d),
106.9 (s), 95.4 (s), 86.5 (s), 55.5 (q), 55.4 (q), 39.5 (q).
MS (DCI/NH3) m/z 375 (M+H)+. Anal. Calcd for
C22H22N4O2: C, 70.47; H, 6.03; N, 14.87. Found: C,
70.60; H, 5.92; N, 14.96.
5.2.14. 5-Cyclohexyl-6-(4-dimethylaminophenylethynyl)-
pyrimidin-4-ylamine (5l). Starting with 4l, the title
compound was prepared according to the general proce-
dure described for the aminolysis reaction (method A)
followed by filtration to afford 500 mg (59%) of 5l:
yellow solid. 1H NMR (400 MHz, DMSO-d6) d 8.14
(s, 1H, @N–CH@N), 7.39 (AA0BB0, 2H, J = 8.9,
ArH), 6.77 (AA0BB0, 2H, J = 8.9, ArH), 6.75 (br s,
2H, NH2), 2.97 (s, 6H, N(CH3)2), 2.94 (m, 1H, cyclohex-
yl-H), 2.25 (m, 2H, cyclohexyl-H), 1.83–1.71 (m, 3H,
cyclohexyl-H), 1.56 (m, 2H, cyclohexyl-H), 1.45–1.32
(m, 3H, cyclohexyl-H). 13C NMR (100 MHz, DMSO-
d6) d 161.6 (s), 155.2 (d), 150.7 (s), 145.6 (s), 132.2 (d),
121.5 (s), 112.0 (d), 107.3 (s), 95.7 (s), 87.0 (s), 39.6
(q), 36.4 (br d), 28.6 (t), 26.4 (t), 25.4 (t). MS (DCI/
NH3) m/z 321 (M+H)+. Anal. Calcd for C20H24N4Æ0.6-
H2OÆ0.5 EtOH: C, 71.20; H, 8.02; N, 15.81. Found: C,
71.14; H, 7.66; N, 15.74.
5.2.11. 5-(4-Dimethylaminophenyl)-6-(4-dimethylamino-
phenylethynyl)pyrimidin-4-ylamine (5i). Starting with 4i,
the title compound was prepared according to the gener-
al procedure described for the aminolysis reaction
(method A) followed by aqueous work up and triturat-
ing with Et2O to provide 150 mg (50%) of 5i: yellow sol-
1
id. H NMR (300 MHz, DMSO-d6) d 8.24 (s, 1H, @N–
CH@N), 7.25 (AA0BB0, 2H, J = 8.5, ArH), 7.05
(AA0BB0, 2H, J = 8.9, ArH), 6.86 (AA0BB0, 2H,
J = 8.8, ArH), 6.64 (AA0BB0, 2H, J = 9.2, ArH), 6.39
(br s, 2H, NH2), 2.97 (s, 6H, N(CH3)2), 2.93 (s, 6H,
N(CH3)2). 13C NMR (100 MHz, DMSO-d6) d 161.4
(s), 156.2 (d), 150.5 (s), 150.0 (s), 146.3 (s), 132.7 (d),

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1597
5.2.15. 5-Benzyl-6-(4-dimethylaminophenylethynyl)pyri-
midin-4-ylamine (5m). Starting with 4m, the title com-
pound was prepared according to the general
procedure described for the aminolysis reaction (method
A) followed by filtration to provide 101 mg (69%) of 5m:
7.23–7.19 (m, 2H, ArH), 6.72 (br s, 2H, NH2). 13C
NMR (100 MHz, DMSO-d6) d 161.2 (s), 157.3 (d),
145.7 (s), 132.9 (s), 132.6 (s), 131.8 (d), 131.3 (d), 129.6
(d), 128.8 (d), 120.9 (s), 119.0 (s), 93.1 (s), 87.3 (s), one
methine overlapped. MS (DCI/NH3) m/z 306 (M+H)+.
Anal. Calcd for C18H12ClN3: C, 70.71; H, 3.96; N,
13.74. Found: C, 70.59; H, 3.79; N, 13.76.
1
yellow solid. H NMR (300 MHz, DMSO-d6) d 8.21 (s,
1H, @N–CH@N), 7.35–7.15 (m, 5H, ArH), 7.32
(AA0BB0, 2H, J = 8.8, ArH), 6.87 (br s, 2H, NH2),
6.71 (AA0BB0, 2H, J = 9.2, ArH), 4.06 (s, 2H, CH2Ph),
2.96 (s, 6H, N(CH3)2). 13C NMR (100 MHz, DMSO-
d6) d 162.0 (s), 156.2 (d), 154.7 (s), 147.6 (s), 138.8 (s),
132.9 (d), 128.2 (d), 128.0 (d), 126.1 (d), 116.6 (s),
111.8 (d), 106.8 (s), 95.8 (s), 85.7 (s), 39.5 (q), 32.1 (t).
MS (DCI/NH3) m/z 329 (M+H)+. Anal. Calcd for
C21H20N4Æ0.3H2O: C, 75.56; H, 6.22; N, 16.78. Found:
C, 75.59; H, 5.91; N, 16.85.
5.2.19. 5-(4-Chlorophenyl)-6-p-tolylethynylpyrimidin-4-
ylamine (5q). Starting with 4q, the title compound was
prepared according to the general procedure described
for the aminolysis reaction (method A). Aqueous work
up and purification by chromatography (elution with
50% EtOAc–hexane the 10% MeOH–CH2Cl2) gave
1
71 mg (76%) of 5q: white solid. H NMR (300 MHz,
DMSO-d6) d 8.55 (s, 1H, @N–CH@N), 7.52 (AA0BB0,
2H, J = 8.8, ArH), 7.44 (AA0BB0, 2H, J = 8.8, ArH),
7.16 (AA0BB0, 2H, J = 8.5, ArH), 7.10 (AA0BB0, 2H,
J = 7.8, ArH), 4.96 (br s, 2H, NH2), 2.33 (s, 3H,
ArCH3).
5.2.16. 5-Benzhydryl-6-(4-dimethylaminophenylethynyl)-
pyrimidin-4-ylamine (5n). Starting with 4n, the title com-
pound was prepared according to the general procedure
described for the aminolysis reaction (method A). Aque-
ous work up and purification by chromatography (elu-
tion with 20% EtOAc–hexane then 5% MeOH–
CH2Cl2) provided 95 mg (14%) of 5n: 1H NMR
(400 MHz, DMSO-d6) d 8.27 (s, 1H, @N–CH@N),
7.37–7.22 (m, 10H, ArH), 7.11 (AA0BB0, 2H, J = 8.9,
ArH), 6.64 (AA0BB0, 2H, J = 8.9, ArH), 6.34 (br s,
2H, NH2), 6.02 (s, 1H, CHPh2), 2.92 (s, 6H,
N(CH3)2). 13C NMR (100 MHz, DMSO-d6) d 161.9
(s), 156.2 (d), 150.6 (s), 148.2 (s), 140.5 (s), 132.9 (d),
128.5 (d), 126.6 (d), 118.8 (s), 111.6 (d), 106.7 (s), 97.4
(s), 86.6 (s), 48.2 (d), 39.5 (q), one quaternary carbon
overlapped. MS (DCI/NH3) m/z 405 (M+H)+. Anal.
Calcd for C27H24N4Æ1.2EtOH: C, 76.80; H, 6.80; N,
12.19. Found: C, 76.80; H, 6.62; N, 12.33.
This material was converted to the HCl salt for final bio-
1
logical testing: H NMR (300 MHz, DMSO-d6) d 8.56
(s, 1H, @N–CH@N), 7.63 (AA0BB0, 2H, J = 8.5,
ArH), 7.49 (AA0BB0, 2H, J = 8.5, ArH), 7.24 (AA0BB0,
2H, J = 8.1, ArH), 7.15 (AA0BB0, 2H, J = 7.8, ArH),
2.32 (s, 3H, ArCH3). 13C NMR (100 MHz, DMSO-d6)
d 162.6 (s), 151.8 (d), 141.3 (s), 136.0 (s), 134.1 (s),
131.72 (d), 131.69 (d), 129.7 (s), 129.6 (d), 129.1 (d),
118.9 (s), 116.2 (s), 100.8 (s), 80.9 (s), 21.1 (q). MS
(DCI/NH3) m/z 320 (M+H)+. Anal. Calcd for
C19H14ClN3Æ1.5HClÆ0.5H2O: C, 59.51; H, 4.34; N,
10.96. Found: C, 59.72; H, 4.71; N, 10.63.
5.2.20. 5-(4-Chlorophenyl)-6-(4-isopropylphenylethynyl)-
pyrimidin-4-ylamine (5r). Starting with 7a, the title com-
pound was prepared according to the general procedure
described for 8b substituting 1-ethynyl-4-isopropylben-
zene (S12) for 2-ethynylpyridine. Residue was purified
by chromatography (1% gradient elution from 0% to
2% MeOH–CH2Cl2) to provide 430 mg (41%) of 5r:
light yellow solid; Rf 0.58 (5% MeOH–CH2Cl2). 1H
NMR (300 MHz, DMSO-d6) d 8.35 (s, 1H, @N–
CH@N), 7.58 (AA0BB0, 2H, J = 8.5, ArH), 7.44
(AA0BB0, 2H, J = 8.5, ArH), 7.26 (AA0BB0, 2H,
J = 8.1, ArH), 7.13 (AA0BB0, 2H, J = 8.5, ArH), 6.69
(br s, 2H, NH2), 2.88 (sept, 1H, J = 6.5, CH(CH3)2),
1.17 (d, 6H, J = 6.8, CH(CH3)2). 13C NMR (100 MHz,
DMSO-d6) d 161.1 (s), 157.3 (d), 150.4 (s), 145.9 (s),
132.9 (s), 132.7 (s), 131.8 (d), 131.4 (d), 128.7 (d),
126.8 (d), 118.8 (s), 118.3 (s), 93.5 (s), 86.8 (s), 33.3
(d), 23.4 (q). MS (DCI/NH3) m/z 348 (M+H)+. Anal.
Calcd for C21H18ClN3Æ0.5H2O: C, 70.68; H, 5.37; N,
11.78. Found: C, 70.74; H, 5.04; N, 12.01.
5.2.17. 6-(4-Dimethylaminophenylethynyl)-2-methyl-5-phe-
nylpyrimidin-4-ylamine (5o). Starting with 4o, the title
compound was prepared according to the general proce-
dure described for the aminolysis reaction (method A).
Aqueous work up and purification by chromatography
(elution with 50% EtOAc–hexane then 5% MeOH–
CH2Cl2) provided 440 mg (63%) of 5o: yellow solid.
1H NMR (300 MHz, DMSO-d6) d 7.55–7.35 (m, 5H,
ArH), 6.95 (AA0BB0, 2H, J = 8.8, ArH), 6.62 (AA0BB0,
2H, J = 9.2, ArH), 6.38 (br s, 2H, NH2), 2.92 (s, 6H,
N(CH3)2), 2.34 (s, 3H, ArCH3). 13C NMR (100 MHz,
DMSO-d6) d 165.3 (s), 161.0 (s), 150.5 (s), 146.8 (s),
134.2 (s), 132.6 (d), 130.0 (d), 128.5 (d), 127.8 (d),
116.3 (s), 111.6 (d), 107.0 (s), 95.1 (s), 86.5 (s), 39.5
(q), 25.1 (q). MS (DCI/NH3) m/z 329 (M+H)+. Anal.
Calcd for C21H20N4Æ0.2H2O: C, 75.97; H, 6.19; N,
16.87. Found: C, 76.00; H, 6.08; N, 16.94.
5.2.18. 5-(4-Chlorophenyl)-6-phenylethynylpyrimidin-4-
ylamine (5p). Starting with 4p, the title compound was
prepared according to the general procedure described
for the aminolysis reaction (method A). Aqueous work
up and purification by chromatography (elution with
3% MeOH–CH2Cl2) gave 204 mg (62%) of 5p: 1H
NMR (300 MHz, DMSO-d6) d 8.35 (s, 1H, @N–
CH@N), 7.59 (AA0BB0, 2H, J = 8.8, ArH), 7.45
(AA0BB0, 2H, J = 8.5, ArH), 7.43–7.35 (m, 3H, ArH),
5.2.21. 5-(4-Chlorophenyl)-6-pyrimidin-5-ylethynylpyrim-
idin-4-ylamine (8a).
A solution of 10a (200 mg,
0.873 mmol) in CH3CN (5 mL) and Et3N (5 mL) was
treated with 5-bromopyrimidine [4595-59-9] (277 mg,
1.74 mmol), Pd(PPh3)2Cl2 (31 mg, 0.044 mmol), and
CuI (7 mg, 0.037 mmol), and the reaction mixture heat-
ed to 60 ꢁC for 2 h. The mixture was cooled, concentrat-
ed, and purified by chromatography (elution with 2%

1598
M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
MeOH–CH2Cl2) to provide 86 mg (32%) of 8a: light tan
solid. H NMR (300 MHz, DMSO-d6) d 9.19 (s, 1H,
8.23 (AA0BB0, 2H, J = 9.2, ArH), 7.59 (AA0BB0, 2H,
J = 8.5, ArH), 7.49 (AA0BB0, 2H, J = 8.8, ArH), 7.48
(AA0BB0, 2H, J = 8.5, ArH), 6.82 (br s, 2H, NH2). 13C
NMR (100 MHz, DMSO-d6) d 161.3 (s), 157.4 (d),
147.4 (s), 144.9 (s), 133.1 (s), 132.6 (d), 132.2 (s), 131.7
(d), 128.9 (d), 127.5 (s), 123.9 (d), 119.6 (s), 91.4 (s),
90.6 (s). MS (DCI/NH3) m/z 351 (M+H)+. Anal. Calcd
for C18H11ClN4O2Æ1.2H2O: C, 58.06; H, 3.63; N,
15.05. Found: C, 57.89; H, 3.36; N, 14.86.
1
@N–CH@N), 8.67 (s, 2H, 40- and 60-pyrimidine-H),
8.39 (s, 1H, @N–CH@N), 7.60 (AA0BB0, 2H, J = 8.5,
ArH), 7.48 (AA0BB0, 2H, J = 8.8, ArH), 6.83 (br s,
2H, NH2). 13C NMR (100 MHz, DMSO-d6) d 161.2
(s), 158.6 (d), 157.4 (d), 144.8 (s), 133.1 (s), 132.2 (s),
131.7 (d), 128.9 (d), 119.6 (s), 117.6 (s), 93.2 (s), 86.2
(s), one methine overlapped. MS (DCI/NH3) m/z 308
(M+H)+. Anal. Calcd for C16H10ClN5Æ0.9H2OÆ0.05
PPh3: C, 60.06; H, 3.77; N, 20.72. Found: C, 60.37; H,
3.53; N, 20.73.
5.2.25. 6-(4-Aminophenylethynyl)-5-(4-chlorophenyl)pyr-
imidin-4-ylamine (8e). Starting with 7a, the title com-
pound was prepared according to the procedure
described for 8b substituting 4-aminophenylacetylene67
[14235-81-5] for 2-ethynylpyridine to provide 410 mg
(42%) of 8e. light yellow solid; Rf 0.14 (5% MeOH–
CH2Cl2). 1H NMR (300 MHz, DMSO-d6) d 8.29 (s,
1H, @N–CH@N), 7.57 (AA0BB0, 2H, J = 8.5, ArH),
7.41 (AA0BB0, 2H, J = 8.8, ArH), 6.83 (AA0BB0, 2H,
J = 8.5, ArH), 6.54 (br s, 2H, NH2), 6.48 (AA0BB0,
2H, J = 8.8, ArH), 5.70 (br s, 2H, NH2). 13C NMR
(100 MHz, DMSO-d6) d 161.0 (s), 157.1 (d), 150.4 (s),
146.8 (s), 133.1 (s), 132.9 (d), 132.7 (s), 131.9 (d), 128.7
(d), 117.7 (br s), 113.5 (d), 106.4 (s), 96.6 (s), 85.6 (br
s). MS (DCI/NH3) m/z 321 (M+H)+. Anal. Calcd for
C18H13ClN4Æ0.5H2O: C, 65.56; H, 4.28; N, 16.99.
Found: C, 65.80; H, 3.95; N, 16.96.
5.2.22. 5-(4-Chlorophenyl)-6-pyridin-2-ylethynylpyrimidin-
4-ylamine (8b). To a solution of 7a (250 mg, 0.755 mmol)
in CH3CN (3 mL) and Et3N (3 mL) were added 2-ethynyl-
pyridine [1945-84-2] (187 mg, 1.81 mmol), Pd(PPh3)2Cl2
(26 mg, 0.037 mmol), CuI (6 mg, 0.03 mmol), and the reac-
tion mixture was heated to 50 ꢁC for 1 h. The mixture was
cooled, concentrated, and purified by chromatography
(elution with 3% MeOH–CH2Cl2) to give 48 mg (21%) of
8b: tan solid. 1H NMR (300 MHz, DMSO-d6) d 8.57
(ddd, 1H, J = 4.8, 1.8, 0.7, 30-pyridine-H), 8.38 (s, 1H,
@N–CH@N), 7.81 (ddd, 1H, J = 7.8, 7.8, 1.7, 50-pyri-
dine-H), 7.57 (AA0BB0, 2H, J = 8.5, ArH), 7.46 (AA0BB0,
2H, J = 8.1, ArH), 7.41 (ddd, 1H, J = 7.8, 5.8, 1.0, 40-pyri-
dine-H), 7.25 (ddd, 1H, J = 7.8. 0.7, 0.7, 60-pyridine-H),
6.75 (br s, 2H, NH2). 13C NMR (75 MHz, DMSO-d6) d
161.3 (s), 157.4 (d), 150.3 (d), 145.0 (s), 141.1 (s), 136.8
(d), 133.1 (s), 132.2 (s), 131.7 (d), 128.9 (d), 127.6 (d),
124.2 (d), 119.5 (s), 91.9 (s), 85.8 (s). MS (DCI/NH3) m/z
307 (M+H)+. Anal. Calcd for C17H11ClN4Æ0.1H2O: C,
66.18; H, 3.66; N, 18.16. Found: C, 65.86; H, 3.43; N, 18.08.
5.2.26. 5-(4-Chlorophenyl)-6-(4-morpholin-4-ylphenyleth-
ynyl)pyrimidin-4-ylamine (8f). Starting with 10a, the title
compound was prepared according to the procedure de-
scribed for 8a substituting 4-(4-iodophenyl)morpho-
line68 [87350-77-4] for 5-bromopyrimidine. Residue
was purified by chromatography (elution with 5%
MeOH–CH2Cl2) to provide 182 mg (43%) of 8f: 1H
NMR (300 MHz, DMSO-d6) d 8.32 (s, 1H, @N–
CH@N), 7.57 (AA0BB0, 2H, J = 8.8, ArH), 7.43
(AA0BB0, 2H, J = 8.5, ArH), 7.04 (AA0BB0, 2H,
J = 8.8, ArH), 6.90 (AA0BB0, 2H, J = 9.2, ArH), 6.61
(br s, 2H, NH2), 3.70 (app t, 4H, J = 4.7, NCH2CH2O),
3.17 (app t, 4H, J = 4.7, NCH2CH2O). 13C NMR
(100 MHz, DMSO-d6) d 161.0 (s), 157.1 (d), 151.4 (s),
146.3 (s), 132.85 (s), 132.78 (s), 132.6 (d), 131.8 (d),
128.7 (d), 118.1 (s), 114.2 (d), 109.8 (s), 95.1 (s), 86.2
(s), 65.8 (t), 47.1 (t). MS (DCI/NH3) m/z 391 (M+H)+.
Anal. Calcd for C22H19ClN4O: C, 67.60; H, 4.90; N,
14.33. Found: C, 67.38; H, 5.04; N, 14.26.
5.2.23. 5-(4-Chlorophenyl)-6-thiophen-2-ylethynylpyrimi-
din-4-ylamine (8c). Starting with 10a, the title compound
was prepared according to the procedure described for
8a substituting 2-iodothiophene [3437-95-4] for 5-
bromopyrimidine. Residue was purified by chromatog-
raphy (elution with 3% MeOH–CH2Cl2) to afford
110 mg (40%) of 8c: light tan solid. 1H NMR
(300 MHz, DMSO-d6) d 8.35 (s, 1H, @N–CH@N),
7.70 (dd, 1H, J = 5.1, 1.4, 30-thienyl-H), 7.57 (AA0BB0,
2H, J = 8.5, ArH), 7.43 (AA0BB0, 2H, J = 8.5, ArH),
7.22 (dd, 1H, J = 3.7, 1.0, 50-thienyl-H), 7.09 (dd, 1H,
J = 5.1, 3.7, 40-thienyl-H), 6.72 (br s, 2H, NH2). 13C
NMR (75 MHz, DMSO-d6) d 161.1 (s), 157.3 (d),
145.6 (s), 133.7 (d), 133.0 (s), 132.4 (s), 131.7 (d), 130.6
(d), 128.8 (d), 127.8 (d), 120.3 (s), 118.9 (br s), 91.3
(br s), 86.9 (s). MS (DCI/NH3) m/z 312 (M+H)+.
Anal. Calcd for C16H10ClN3SÆ0.5H2OÆ0.4CH2Cl2: C,
55.52; H, 3.35; N, 11.84. Found: C, 55.41; H, 3.19; N,
11.44.
5.2.27. 5-(4-Chlorophenyl)-6-(2-morpholin-4-ylpyrimidin-
5-ylethynyl)pyrimidin-4-ylamine (8g). A slurry of 4-{5-[5-
(4-chlorophenyl)-6-iodopyrimidin-4-ylethynyl]pyrimi-
din-2- yl}morpholine (S17; 255 mg, 0.506 mmol) in
EtOH (3 mL) and concentrated NH4OH (1 mL) was
sealed in a tube and heated to 100 ꢁC for 28 h. The reac-
tion mixure was concentrated and the residue purified
by chromatography (elution with 50% EtOAc–hexane
to remove non-polar impurities then 10% MeOH–
5.2.24. 5-(4-Chlorophenyl)-6-(4-nitrophenylethynyl)pyr-
imidin-4-ylamine (8d). Starting with 10a, the title com-
pound was prepared according to the procedure
described for 8a substituting 1-iodo-4-nitrobenzene
[636-98-6] for 5-bromopyrimidine. Upon completion of
the reaction, the solution was cooled, filtered, and
washed with cold CH3CN. Solid was dried to give
201 mg (66%) of 8d: light green solid. 1H NMR
(300 MHz, DMSO-d6) d 8.39 (s, 1H, @N–CH@N),
1
CH2Cl2) to give 56 mg (28%) of 8g: yellow solid. H
NMR (300 MHz, DMSO-d6) d 8.33 (s, 1H, @N–
CH@N), 8.19 (s, 2H, pyrimidinyl-H), 7.58 (AA0BB0,
2H, J = 8.5, ArH), 7.44 (AA0BB0, 2H, J = 8.5, ArH),
6.71 (br s, 2H, NH2), 3.74 (app t, 4H, J = 5.1,
OCH2CH2N), 3.63 (app t, 4H, J = 5.1, OCH2CH2N).

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1599
13C NMR (100 MHz, DMSO-d6) d 161.1 (s), 160.1 (d),
159.2 (s), 157.2(d), 145.7 (s), 132.9 (s), 132.6 (s), 131.8
(d), 128.8 (d), 118.4 (s), 104.5 (s), 90.5 (s), 89.4 (s),
65.8 (t), 43.8 (t). MS (DCI/NH3) m/z 393 (M+H)+. Anal.
Calcd for C20H17ClN6OÆ0.8H2O: C, 58.98; H, 4.60; N,
20.64. Found: C, 58.96; H, 4.30; N, 20.36.
J = 8.4), 7.44 (AA0BB0, 2H, J = 8.4), 7.43 (m, 1H),
6.37 (br s, 2H). 13C NMR (125 MHz, DMSO-d6) at
90 ꢁC d 160.8 (s), 156.8 (d), 151.0 (s), 150.3 (d), 145.4
(s), 140.3 (d), 132.7 (s), 132.2 (s), 131.2 (d), 128.4 (d),
118.6 (s), 112.8 (s), 111.6 (br d), 90.0 (s), 89.1 (s), one
methine broad or overlapped. MS (DCI/NH3) m/z 350
(M+H)+. Anal. Calcd for C17H12ClN50.3H2O0.8
MeOH: C, 59.30; H, 4.18; N, 18.39. Found: C, 59.39;
H, 4.08; N, 18.22. The light tan solid was dissolved in
MeOH (10 mL) and treated with 1 M NaOH (2 mL).
The mixture was heated to reflux for 10 min, cooled,
concentrated, and the residue purified by chromatogra-
phy (elution with 3% MeOH–CH2Cl2) to afford 74 mg
(64%) of 8j: light tan solid. 1H NMR (300 MHz,
DMSO-d6) d 8.33 (s, 1H, @N–CH@N), 7.72 (dd, 1H,
J = 2.2, 0.7, 20-pyridyl-H), 7.58 (AA0BB0, 2H, J = 8.1,
ArH), 7.44 (AA0BB0, 2H, J = 8.5, ArH), 7.17 (dd, 1H,
J = 8.5, 2.2, 40-pyridyl-H), 6.42 (dd, 1H, J = 8.5,
0.7, 50-pyridyl-H). 13C NMR (75 MHz, DMSO-d6) d
161.0 (s), 159.7 (s), 157.2 (d), 151.9 (d), 146.4 (s), 139.2
(d), 132.9 (s), 132.8 (s), 131.9 (d), 128.7 (d), 118.0 (s),
107.7 (d), 104.6 (s), 93.4 (s), 87.8 (s). MS (DCI/NH3)
m/z 322 (M+H)+. Anal. Calcd for C17H12ClN5Æ0.2H2O:
C, 62.75; H, 3.84; N, 21.52. Found: C, 62.73; H, 3.88; N,
21.43.
5.2.28. 5-(4-Chlorophenyl)-6-(6-morpholin-4-ylpyridazin-
3-ylethynyl)pyrimidin-4-ylamine (8h). Starting with 7a,
the title compound was prepared according to the proce-
dure described for 8b substituting 4-(6-ethynylpyridazin-
3-yl)morpholine (S20) for 2-ethynylpyridine to provide
1
38 mg (11%) of 8h: H NMR (300 MHz, DMSO-d6) d
8.38 (s, 1H, @N–CH@N), 7.56 (AA0BB0, 2H, J = 8.5,
ArH), 7.46 (AA0BB0, 2H, J = 8.5, ArH), 7.22 (d, 1H,
J = 9.8, pyridazinyl-H), 7.16 (d, 1H, J = 9.5, pyridazi-
nyl-H), 6.78 (br s, 2H, NH2), 3.70 (app t, 4H, J = 4.4,
OCH2CH2N), 3.61 (app t, 4H, J = 4.5, OCH2CH2N).
MS (DCI/NH3) m/z 393 (M+H)+. Anal. Calcd for
C20H17ClN6OÆ1.6H2O: C, 56.97; H, 4.83; N, 19.93.
Found: C, 56.90; H, 4.38; N, 19.53.
5.2.29. 5-(4-Chlorophenyl)-6-(5-morpholin-4-ylpyridin-3-
ylethynyl)pyrimidin-4-ylamine (8i). The silyl group of 4-
(5-trimethylsilanylethynylpyridin-3-yl)morpholine (S22;
1.33 mmol) was removed as previously described for 4-
(5-ethynylpyrimidin-2-yl)morpholine (S16) to provide
4-(5-ethynyl-pyridin-3-yl)-morpholine (S23): light yel-
5.2.31. 5-(4-Chlorophenyl)-6-(6-dimethylaminopyridin-3-
ylethynyl)pyrimidin-4-ylamine (8k). Starting with 7a,
the title compound was prepared according to the proce-
dure described for 8b substituting (5-ethynylpyridin-2-
yl)dimethylamine (S29) for 2-ethynylpyridine to provide
112 mg (47%) of 8k: tan solid. 1H NMR (300 MHz,
DMSO-d6) d 8.32 (s, 1H, @N–CH@N), 7.88 (d, 1H,
J = 2.0, 20-pyridine-H), 7.58 (AA0BB0, 2H, J = 8.1,
ArH), 7.43 (AA0BB0, 2H, J = 8.5, ArH), 7.25 (dd, 1H,
J = 8.8, 2.4, 40-pyridine-H), 6.62 (d, 1H, J = 8.8, 50-pyr-
idine-H), 6.62 (br s, 2H, NH2), 3.04 (s, 6H, N(CH3)2).
13C NMR (100 MHz, DMSO-d6) d 161.3 (s), 158.4 (s),
157.5 (d), 151.5 (d), 146.7 (s), 139.5 (d), 133.15 (s),
133.10 (s), 132.2 (d), 129.0 (d), 118.3 (s), 105.8 (d),
104.3 (s), 93.4 (s), 88.5 (s), 37.7 (q). MS (DCI/NH3) m/
z 350 (M+H)+. Anal. Calcd for C19H16ClN5: C, 65.24;
H, 4.61; N, 20.02. Found: C, 64.98; H, 4.47; N, 20.04.
1
low solid. H NMR (300 MHz, DMSO-d6) d 8.32 (d,
1H, J = 3.1), 8.09 (d, 1H, J = 1.4), 7.38 (dd, 1H,
J = 3.1, 1.7), 4.34 (s, 1H), 3.73 (app t, 4H, J = 4.7),
3.19 (app t, 4H, J = 4.8). 13C NMR (100 MHz,
DMSO-d6) d 146.0 (s), 141.9 (d), 137.3 (d), 123.4 (d),
118.4 (s), 83.1 (d), 80.9 (s), 65.8 (t), 47.2 (t). MS (DCI/
NH3) m/z 189 (M+H)+.
Starting with 7a, the title compound was prepared
according to the procedure described for 8b substituting
S23 for 2-ethynylpyridine to provide 60 mg (16%) of 8i:
1
yellow solid. H NMR (300 MHz, DMSO-d6) d 8.37 (s,
1H, @N–CH@N), 8.34 (d, 1H, J = 2.7, 20- or 60-pyridyl-
H), 7.80 (d, 1H, J = 1.7, 20- or 60-pyridyl-H), 7.61
(AA0BB0, 2H, J = 8.5, ArH), 7.45 (AA0BB0, 2H,
J = 8.5, ArH), 6.93 (dd, 1H, J = 2.7, 1.7, 40-pyridyl-H),
6.75 (br s, 2H, NH2), 3.74 (app t, 4H, J = 4.8,
OCH2CH2N), 3.15 (app t, 4H, J = 4.7, OCH2CH2N).
13C NMR (100 MHz, DMSO-d6) d 161.1 (s), 157.4 (d),
146.0 (s), 145.6 (s), 141.2 (d), 138.0 (d), 133.0 (s), 132.7
(s), 131.9 (d), 128.8 (d), 122.7 (d), 119.5 (s), 117.7 (s),
90.9 (s), 89.5 (s), 65.7 (t), 47.1 (t). MS (DCI/NH3) m/z
392 (M+H)+. Anal. Calcd for C21H18ClN5OÆ0.6H2O:
C, 62.64; H, 4.81; N, 17.39. Found: C, 62.86; H, 4.84;
N, 17.02.
5.2.32. 5-(4-Chlorophenyl)-6-(6-morpholin-4-ylpyridin-3-
ylethynyl)pyrimidin-4-ylamine (8l). Starting with 7a, the
title compound was prepared according to the procedure
described for 8b substituting 4-(5-ethynylpyridin-2-
yl)morpholine (S32) for 2-ethynylpyridine to provide
220 mg (61%) of 8l: light tan solid, Rf 0.34 (5%
MeOH–CH2Cl2). 1H NMR (300 MHz, DMSO-d6) d
8.33 (br s, 1H, @N–CH@N), 7.92 (d, 1H, J = 2.4, 50-pyr-
idyl-H), 7.58 (AA0BB0, 2H, J = 8.5, ArH), 7.44
(AA0BB0, 2H, J = 8.5, ArH), 7.31 (dd, 1H, J = 8.8, 2.4,
40-pyridyl-H), 6.82 (d, 1H, J = 9.2, 30-pyridyl-H), 6.63
(br s, 2H, NH2), 3.66 (app t, 4H, J = 4.4, OCH2CH2N),
3.51 (app t, 4H, J = 4.4, OCH2CH2N). 13C NMR
(75 MHz, DMSO-d6) d 161.0 (s), 158.0 (s), 157.1 (br
s), 151.0 (d), 146.1 (br s), 139.6 (d), 132.8 (s), 131.8
(d), 128.7 (d), 106.4 (d), 105.8 (s), 92.5 (s), 65.7 (t),
44.5 (t), 2 quaternary carbons and one methine carbon
overlapped or broad. MS (DCI/NH3) m/z 392
(M+H)+. Anal. Calcd for C21H18ClN5OÆ0.4H2O: C,
5.2.30. 6-(6-Aminopyridin-3-ylethynyl)-5-(4-chlorophen-
yl)pyrimidin-4-ylamine (8j). The N-formyl compound
was prepared according to 8b substituting N-(5-ethynyl-
pyridin-2-yl)formamide (S26) for 2-ethynylpyridine to
provide 125 mg (17%) of N-{5-[6-amino-5-(4-chlorophe-
nyl)pyrimidin-4-ylethynyl]pyridin-2-yl}formamide: light
1
yellow solid. H NMR (500 MHz, DMSO-d6) at 90 ꢁC
d 10.51 (br s, 1H), 8.86 (br s, 1H), 8.38 (s, 1H), 8.07
(d, 1H, J = 2.3), 7.57 (m, 1H), 7.56 (AA0BB0, 2H,

1600
M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
63.21; H, 4.75; N, 17.55. Found: C, 63.21; H, 4.65; N,
17.55.
J = 4.7, NCH2CH2NBoc), 1.42 (s, 9H, C(CH3)3). 13C
NMR (100 MHz, DMSO-d6) d 161.0 (s), 157.7 (s),
157.2 (d), 153.8 (s), 151.0 (d), 146.1 (s), 139.1 (d),
132.8 (s), 132.7 (s), 131.8 (d), 128.7 (d), 118.2 (s), 106.6
(d), 105.6 (s), 92.5 (s), 88.3 (s), 79.1 (s), 43.8 (t), 42.9
(br t), 28.0 (q). MS (DCI/NH3) m/z 491 (M+H)+. Anal.
Calcd for C26H27ClN6O2Æ0.8H2OÆ0.6MeOH: C, 60.90;
H, 5.96; N, 16.02. Found: C, 60.62; H, 5.68; N, 15.81.
5.2.33. 5-(4-Chlorophenyl)-6-{6-[(2-methoxyethyl)methyl-
amino]pyridin-3-ylethynyl}pyrimidin-4-ylamine (8m). Start-
ing with 7a, the title compound was prepared according to
the procedure described for 8b substituting (5-ethynyl-
pyridin-2-yl)-(2-methoxyethyl)methylamine (S35) for
2-ethynylpyridine. Residue was purified by chromatogra-
phy (1% gradient elution from 0% to 4% MeOH–CH2Cl2)
to provide 72 mg (24%) of 8m: light yellow solid. 1H
NMR (300 MHz, DMSO-d6) d 8.32 (s, 1H, @N–CH@N),
7.88 (d, 1H, J = 2.2, 20-pyridine-H), 7.59 (AA0BB0, 2H,
J = 8.8, ArH), 7.43 (AA0BB0, 2H, J = 8.9, ArH), 7.25
(dd, 1H, J = 8.8, 2.2, 40-pyridine-H), 6.63 (d, 1H,
J = 8.8, 50-pyridine-H), 6.63 (br s, 2H, NH2), 3.69 (app
t, 2H, J = 5.5, NCH2CH2OMe), 3.47 (app t, 2H, J =
5.5, NCH2CH2OMe), 3.23 (s, 3H, OCH3), 3.03 (s, 3H,
NCH3). IR (KBr) 3409, 2207. MS (DCI/NH3) m/z 394
(M+H)+. HRMS calcd for C21H20ClN5O (M+H)+
394.1435. Found 394.1428. Anal. Calcd for
C21H20ClN5OÆ0.35H2O: C, 63.03; H, 5.21; N, 17.50.
Found: C, 63.07; H, 5.42; N, 17.23.
5.2.36.
1-(4-{5-[6-Amino-5-(4-chlorophenyl)pyrimidin-4-
ylethynyl]pyridin-2-yl}piperazin-1-yl)ethanone (8p). Start-
ing with 7a, the title compound was prepared according
to the procedure described for 8b substituting 1-[4-(5-ethy-
nylpyridin-2-yl)piperazin-1-yl]ethanone (S41) for 2-ethy-
nylpyridine to provide 16 mg (3%) of 8p: off-white solid.
1H NMR (300 MHz, DMSO-d6) d 8.32 (s, 1H, @N–
CH@N), 7.91 (d, 1H, J = 2.4, 20-pyridyl-H), 7.58
(AA0BB0, 2H, J = 8.5, ArH), 7.44 (AA0BB0, 2H, J = 8.5,
ArH), 7.31 (dd, 1H, J = 8.8, 2.4, 40-pyridyl-H), 6.84 (d,
1H, J = 8.5, 50-pyridyl-H), 6.65 (br s, 2H, NH2), 3.64-
3.50 (m, 8H, NCH2CH2N x 2), 2.03 (s, 3H, C(O)CH3).
13C NMR (75 MHz, DMSO-d6) d 168.4 (s), 161.0 (s),
157.6 (s), 157.2 (d), 151.0 (d), 146.2 (s), 139.7 (d), 132.81
(s), 132.77 (s), 131.8 (d), 128.7 (d), 118.2 (s), 106.5 (d),
105.6 (s), 92.4 (s), 88.3 (s), 45.0 (t), 44.1 (t), 43.8 (t), 40.3
(t), 21.1 (q). MS (DCI/NH3) m/z 433 (M+H)+. Anal.
Calcd for C23H21ClN6O: C, 63.81; H, 4.89; N, 19.41.
Found: C, 63.55; H, 5.10; N, 19.19.
5.2.34. 4-{5-[6-Amino-5-(4-chlorophenyl)pyrimidin-4-yl-
ethynyl]pyridin-2-yl}piperazine-1-sulfonic acid dimethyl-
amide (8n). Starting with 10a, the title compound was
prepared according to the procedure described for 8a
substituting 4-(5-iodopyridin-2-yl)piperazine-1-sulfonic
acid dimethylamide (S38) for 5-bromopyrimidine. The
residue was purified by chromatography (elution with
5% MeOH–CH2Cl2) to provide 285 mg (49%) of 8n:
5.2.37. 5-(4-Chlorophenyl)-6-(3,4,5,6-tetrahydro-2H-[1,20]bi-
pyridinyl-50-ylethynyl)pyrimidin-4-ylamine (8q). Starting
with 7a, the title compound was prepared according to
the procedure described for 8b substituting 50-ethynyl-
3,4,5,6-tetrahydro-2H-[1,20]bipyridinyl (S44) for 2-ethy-
nylpyridine. This material was converted to the HCl salt
1
light yellow solid. H NMR (300 MHz, DMSO-d6) d
8.83 (s, 1H, @N–CH@N), 7.92 (d, 1H, J = 1.7, 60-pyri-
dine-H), 7.58 (AA0BB0, 2H, J = 8.5, ArH), 7.44
(AA0BB0, 2H, J = 8.5, ArH), 7.33 (dd, 1H, J = 8.8, 2.4,
40-pyridine-H), 6.86 (d, 1H, J = 9.2, 30-pyridine-H),
6.64 (br s, 2H, NH2), 3.64 (app t, 4H, J = 4.7,
NCH2CH2NSO2), 3.22 (app t, 4H, J = 5.1,
NCH2CH2NSO2), 2.78 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 161.0 (s), 157.5 (s), 157.2 (d),
151.0 (d), 146.1 (s), 139.8 (d), 132.82 (s), 132.77 (s),
131.8 (d), 128.7 (d), 118.2 (br s), 106.7 (d), 106.0 (s),
92.2 (s), 88.4 (br s), 45.6 (t), 43.9 (t), 37.8 (q). MS
(DCI/NH3) m/z 498 (M+H)+. Anal. Calcd for
C23H24ClN7O2S: C, 55.47; H, 4.86; N, 19.69. Found:
C, 55.27; H, 4.73; N, 19.49.
1
to provide 135 mg (27%) of 8q: orange solid. H NMR
(300 MHz, DMSO-d6) d 8.31 (s, 1H, @N–CH@N),
7.87 (d, 1H, J = 2.4, 50-pyridyl-H), 7.58 (AA0BB0, 2H,
J = 8.1, ArH), 7.43 (AA0BB0, 2H, J = 8.5, ArH), 7.24
(dd, 1H, J = 9.2, 2.4, 40-pyridyl-H), 6.79 (d, 1H,
J = 9.2, 20-pyridyl-H), 6.65 (br s, 2H, NH2), 3.57 (app
t, 4H, J = 5.1, piperidinyl-H), 1.60 (m, 2H, piperidinyl-
H), 1.49 (m, 4H, piperidinyl-H). 13C NMR (100 MHz,
DMSO-d6) d 162.8 (s), 154.8 (s), 150.8 (d), 148.0 (d),
141.2 (d), 134.5 (s), 134.3 (s), 131.8 (d), 129.3 (d),
118.1 (s), 109.3 (d), 102.6 (s), 100.3 (s), 82.1 (s), 46.4
(t), 25.1 (t), 23.7 (t), one quaternary carbon overlapped.
MS (DCI/NH3) m/z 390 (M+H)+. Anal. Calcd for
C22H20ClN5Æ3.0HClÆ1.0H2O: C, 51.08; H, 4.87; N,
13.54. Found: C, 50.96; H, 4.60; N, 13.50.
5.2.35. 4-{5-[6-Amino-5-(4-chlorophenyl)pyrimidin-4-yl-
ethynyl]pyridin-2-yl}piperazine-1-carboxylic acid tert-
butyl ester (8o). Starting with 10a, the title compound
was prepared according to the procedure described for
8a substituting 4-(5-iodopyridin-2-yl)piperazine-1-car-
boxylic acid tert-butyl ester (S36) for 5-bromopyrimi-
dine. The residue was purified by chromatography (1%
gradient elution from 1% to 5% MeOH–CH2Cl2) to af-
ford 117 mg (29%) of 8o: yellow solid. 1H NMR
(300 MHz, DMSO-d6) d 8.32 (s, 1H, @N–CH@N),
7.91 (d, 1H, J = 2.4, 60-pyridine-H), 7.58 (AA0BB0, 2H,
J = 8.5, ArH), 7.43 (AA0BB0, 2H, J = 8.5, ArH), 7.31
(dd, 1H, J = 8.8, 2.4, 40-pyridine-H), 6.82 (dd, 1H,
J = 9.2, 30-pyridine-H), 6.64 (br s, 2H, NH2), 3.56 (app
t, 4H, J = 4.7, NCH2CH2NBoc), 3.39 (app t, 4H,
5.2.38. 5-Benzo[1,3]dioxol-5-yl-6-(6-morpholin-4-ylpyri-
din-3-ylethynyl)pyrimidin-4-ylamine (8r). Starting with
7b, the title compound was prepared according to the
procedure described for 8b substituting 4-(5-ethynylpyri-
din-2-yl)morpholine (S32) for 2-ethynylpyridine to give
121 mg (33%) of 8r: yellow solid; Rf 0.38 (5% MeOH–
CH2Cl2). 1H NMR (300 MHz, DMSO-d6) d 8.29 (s,
1H, @N–CH@N), 7.97 (d, 1H, J = 2.2, 20-pyridyl-H),
7.35 (dd, 1H, J = 8.8, 2.2, 40-pyridyl-H), 7.07 (d, 1H,
J = 8.1, 30-ArH), 6.95 (d, 1H, J = 1.8, 60-ArH), 6.87
(dd, 1H, J = 8.1, 1.8, 40-ArH), 6.84 (d, 1H, J = 8.8, 30-
pyridyl-H), 6.09 (br s, 2H, NH2), 3.66 (app t, 4H,

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1601
J = 5.2, OCH2CH2N), 3.51 (app t, 4H, J = 5.2,
OCH2CH2N). MS (DCI/NH3) m/z 402 (M+H)+. Anal.
Calcd for C22H19N5O3Æ0.15H2O: C, 65.39; H, 4.81; N,
17.33. Found: C, 65.21; H, 4.78; N, 17.00.
was concentrated and the residue purified by chroma-
tography (1% gradient elution from 0% to 4% (5%
NH4OH–EtOH)–CHCl3) to provide 315 mg (43%) of
1
8u: light tan solid. H NMR (300 MHz, DMSO-d6) d
8.31 (s, 1H, @N–CH@N), 8.18 (d, 1H, J = 2.0, pyri-
dine-H), 7.77 (d, 1H, J = 2.0, pyridine-H), 7.54 (br s,
1H, NH), 7.06 (d, 1H, J = 8.1, 30-ArH), 7.02 (m, 1H),
6.94 (d, 1H, J = 1.4, 60-ArH), 6.86 (dd, 1H, J = 7.8,
1.7, 40-ArH), 6.63 (br s, 2H, NH2), 6.11 (s, 2H, OCH2O),
3.79 (app t, 4H, J = 5.1, NCH2CH2O), 3.75 (m, 1H,
CH(CH3)2), 2.99 (app t, 4H, J = 4.8, NCH2CH2O),
1.12 (d, 6H, J = 6.4, CH(CH3)2). 13C NMR (100 MHz,
DMSO-d6) d 161.4 (s), 156.9 (d), 154.1 (s), 152.1 (s),
147.5 (s), 147.2 (s), 145.7 (s), 142.4 (d), 128.1 (d), 128.0
(s), 126.9 (s), 123.4 (d), 119.8 (s), 112.8 (s), 109.9 (d),
108.7 (d), 101.1 (t), 90.7 (s), 89.0 (s), 65.7 (t), 49.3 (t),
41.2 (d), 22.8 (q). MS (DCI/NH3) m/z 502 (M+H)+,
443 (MꢀNPr-i)+. Anal. Calcd for C26H27N7O4Æ0.3H2O:
C, 61.60; H, 5.49; N, 19.34. Found: C, 61.39; H, 5.53; N,
19.13.
5.2.39. 5-Benzo[1,3]dioxol-5-yl-6-(5-dimethylamino-6-mor-
pholin-4-ylpyridin-3-ylethynyl)pyrimidin-4-ylamine (8s). To
a solution of (5-iodo-2-morpholin-4-ylpyridin-3-yl)dim-
ethylamine (S48; 478 mg, 1.43 mmol) in DMF (5 mL)
and Et3N (5 mL) were added Pd(PPh3)2Cl2 (49 mg,
0.070 mmol) and CuI (27 mg, 0.14 mmol). To this mixture
was added 10b (690 mg, 2.88 mmol) in DMF (3 mL) and
Et3N (3 mL). After 15 min, the reaction mixture was con-
centrated and the residue purified by chromatography
(1% gradient elution from 0% to 4% (5% NH4OH–
EtOH)–CHCl3) to provide 636 mg (64%) of 8s: yellow sol-
id. 1H NMR (300 MHz, DMSO-d6) d 8.30 (br s, 1H, @N–
CH@N), 7.72 (d, 1H, J = 1.7, 60-ArH or pyridyl-H), 7.08
(d, 1H, J = 7.8, 30-ArH), 6.96 (d, 1H, J = 1.7, 60-ArH or
pyridyl-H), 6.88 (dd, 1H, J = 7.8, 1.7, 40-ArH), 6.82 (d,
1H, J = 1.7, 60-ArH or pyridyl-H), 6.60 (br s, 2H, NH2),
6.07 (s, 2H, OCH2O), 3.72 (app t, 4H, J = 4.8,
NCH2CH2O), 3.37 (app t, 4H, J = 4.4, NCH2CH2O),
2.67 (s, 6H, N(CH3)2). 13C NMR (100 MHz, DMSO-d6)
d 161.3 (s), 156.8 (br d), 152.5 (s), 147.4 (s), 147.1 (s),
146.0 (br s), 142.0 (d), 137.7 (s), 127.2 (s), 126.2 (d),
123.7 (d), 110.3 (s), 110.1 (d), 108.6 (d), 101.1 (t), 91.9
(s), 89.1 (br s), 66.1 (t), 46.7 (t), 39.9 (q), one quaternary
carbon too broad or overlapped. MS (DCI/NH3) m/z
445 (M+H)+. Anal. Calcd for C24H24N6O3Æ0.2H2O: C,
64.33; H, 5.49; N, 18.75. Found: C, 64.01; H, 5.68; N,
18.45.
5.2.42. 5-Benzo[1,3]dioxol-5-yl-6-{4-[(2-methoxyethyl)-
methylamino]-6-morpholin-4-ylpyridin-3-ylethynyl}pyrimi-
din-4-ylamine (8v). Starting with 10b, the title compound
was prepared according to the procedure described for
8a substituting (5-iodo-2-morpholin-4-ylpyridin-4-yl)-
(2-methoxyethyl)methylamine (S57) for 5-bromopyrimi-
dine to afford 113 mg (11%) of 8v: brown solid. 1H
NMR (300 MHz, DMSO-d6) d 8.27 (s, 1H, @N–
CH@N), 7.59 (s, 1H, pyridine-H), 7.05 (d, 1H, J = 7.8,
30-ArH), 6.91 (d, 1H, J = 1.4, 60-ArH), 6.83 (dd, 1H,
J = 8.1, 1.7, 50-ArH), 6.50 (br s, 2H, NH2), 6.07 (s,
2H, OCH2O), 5.84 (s, 1H, pyridine-H), 3.65–3.59 (m,
6H, OCH2CH2N), 3.44–3.40 (m, 6H, OCH2CH2N),
3.19 (s, 3H, OCH3), 2.90 (s, 3H, NCH3). 13C NMR
(100 MHz, DMSO-d6) d 161.4 (s), 159.6 (s), 156.8 (d),
156.6 (s), 154.9 (d), 147.5 (s), 147.0 (s), 146.7 (s), 127.4
(s), 123.5 (d), 118.0 (s), 110.1 (d), 108.8 (d), 101.1 (t),
95.6 (s), 93.5 (s), 92.1 (s), 90.0 (d), 70.4 (t), 65.9 (t),
58.0 (q), 51.9 (t), 44.8 (t), 39.3 (q). MS (ESI) m/z 489
(M+H)+. Anal. Calcd for C26H28N6O4Æ0.5H2O: C,
62.76; H, 5.87; N, 16.89. Found: C, 62.55; H, 5.78; N,
16.69.
5.2.40. 5-Benzo[1,3]dioxol-5-yl-6-(4-dimethylamino-6-mor-
pholin-4-ylpyridin-3-ylethynyl)pyrimidin-4-ylamine (8t).
Starting with 10b, the title compound was prepared
according to the procedure described for 8a substitut-
ing
(5-iodo-2-morpholin-4-ylpyridin-4-yl)dimethyl-
amine (S54) for 5-bromopyrimidine to afford 144 mg
(15%) of 8t: yellow solid. 1H NMR (300 MHz,
DMSO-d6) d 8.27 (s, 1H, @N–CH@N), 7.65 (s, 1H, pyr-
idyl-H), 7.03 (d, 1H, J = 7.8, 30-ArH), 6.91 (d, 1H,
J = 1.7, 60-ArH), 6.82 (dd, 1H, J = 8.1, 1.7, 40-ArH),
6.45 (br s, 2H, NH2), 6.07 (s, 2H, OCH2O), 5.83 (s,
1H, pyridyl-H), 3.65 (app t, 4H, J = 4.4, NCH2CH2O),
3.44 (app t, 4H, J = 4.4, NCH2CH2O), 2.86 (s, 6H,
N(CH3)2). 13C NMR (75 MHz, DMSO-d6) d 161.4 (s),
159.5 (s), 157.9 (s), 156.8 (d), 154.6 (d), 147.5 (s), 147.0
(s), 146.7 (s), 127.4 (s), 123.5 (d), 118.0 (s), 110.1 (d),
108.7 (d), 101.1 (t), 96.2 (s), 93.4 (s), 92.2 (s), 89.9 (d),
65.8 (t), 44.8 (t), 41.0 (q). MS (DCI/NH3) m/z 445
(M+H)+. Anal. Calcd for C24H24N6O3Æ0.1H2O: C,
64.59; H, 5.47; N, 18.83. Found: C, 64.65; H, 5.54; N,
18.48.
5.2.43. 5-(4-Dimethylaminophenyl)-6-(6-morpholin-4-yl-
pyridin-3-ylethynyl)pyrimidin-4-ylamine (16a). To a solu-
tion of 15a (611 mg, 1.70 mmol) in DME (30 mL) and
2 M Na2CO3 (5 mL) at rt were added 4-dim-
ethylaminophenylboronic acid [586-77-6] (1.16 g,
5.80 mmol) and Pd(PPh3)4 (308 mg, 0.267 mmol), and
the mixture heated to 80 ꢁC for 28 h. The mixture was
partitioned between H2O and CH2Cl2, the organic phase
dried (Na2SO4), concentrated, and the residue purified
by chromatography (elution with 2% then 5% MeOH–
CH2Cl2) to afford 275 mg (41%) of 16a: Rf 0.13 (5%
MeOH–CH2Cl2). Material was converted to the HCl
salt for biological evaluation. light yellow solid. 1H
NMR (300 MHz, DMSO-d6) d 8.25 (s, 1H, @N–
CH@N), 7.98 (d, 1H, J = 2.1, 20-pyridyl-H), 7.36 (dd,
1H, J = 9.1, 2.4, 40-pyridyl-H), 7.25 (AA0BB0, 2H,
J = 8.8, ArH), 6.85 (AA0BB0, 2H, J = 8.9, ArH), 6.83
(d, 1H, J = 8.9, 50-pyridyl-H), 3.66 (app t, 4H, J = 4.4,
OCH2CH2N), 3.50 (app t, 4H, J = 4.4, OCH2CH2N),
5.2.41. 1-[5-(6-Amino-5-benzo[1,3]dioxol-5-ylpyrimidin-4-yl-
ethynyl)-2-morpholin-4-ylpyridin-3-yl]-3-isopropylurea (8u).
To a solution of 1-(5-iodo-2-morpholin-4-ylpyridin-3-
yl)-3-isopropylurea (S49; 565 mg, 1.45 mmol) in DMF
(5 mL) and Et3N (5 mL) were added Pd(PPh3)2Cl2
(50 mg, 0.071 mmol) and CuI (26 mg, 0.14 mmol). To
this mixture was added 10b (695 mg, 2.91 mmol) in
DMF (3 mL) and Et3N (3 mL). After 2 h, the reaction

1602
M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
2.96 (s, 6H, N(CH3)2). 13C NMR (100 MHz, C6D5N) d
163.2 (s), 158.6 (s), 157.8 (d), 152.2 (d), 150.8 (s), 147.7
(s), 140.4 (d), 131.2 (d), 122.0 (s), 121.1 (s), 112.9 (d),
107.9 (s), 106.4 (d), 92.8 (s), 90.4 (s), 66.5 (t), 45.2 (t),
40.2 (q). MS (DCI/NH3) m/z 401 (M+H)+. Anal. Calcd
for C23H24N6OÆ3.0HCl: C, 54.35; H, 5.62; N, 16.28.
Found: C, 54.18; H, 5.34; N, 16.48.
DMSO-d6) d 8.38 (s, 1H, @N–CH@N), 8.10 (d, 1H,
J = 2.2, 20-pyridyl-H), 7.75 (dd, 1H, J = 7.3, 0.7, 40 or
70-ArH), 7.66 (dd, 1H, J = 7.7, 0.7, 40 or 70-ArH), 7.48
(dd, 1H, J = 9.2, 2.6, 40-pyridyl-H), 7.35 (d, 1H,
J = 0.8, 30-furanyl-H), 7.34 (m, 2H, ArH), 7.34 (br s,
2H, NH2), 6.84 (d, 1H, J = 8.8, 50-pyridyl-H), 3.66
(app t, 4H, J = 4.4, OCH2CH2N), 3.52 (app t, 4H,
J = 4.4, OCH2CH2N). MS (DCI/NH3) m/z 398
(M+H)+. Anal. Calcd for C23H19N5O2Æ0.4H2O: C,
68.27; H, 4.93; N, 17.31. Found: C, 68.20; H, 4.74; N,
17.23.
5.2.44. 6-(6-Morpholin-4-ylpyridin-3-ylethynyl)-5-thio-
phen-2-ylpyrimidin-4-ylamine (16b). Starting with 15a,
the title compound was prepared according to the proce-
dure described for 16a substituting thiophene-2-boronic
acid [6165-68-0] for 4-dimethylaminophenylboronic acid
to give 61 mg (20%) of 16b: 1H NMR (300 MHz,
DMSO-d6) d 8.32 (s, 1H, @N–CH@N), 7.98 (d, 1H,
J = 2.0, 20-pyridyl-H), 7.78 (dd, 1H, J = 3.0, 3.0, 40-thie-
nyl-H), 7.39 (dd, 1H, J = 8.8, 2.4, 40-pyridyl-H), 7.23 (m,
2H, 30- and 50-thienyl-H), 6.83 (d, 1H, J = 8.8, 50-pyr-
idyl-H), 6.82 (br s, 2H, NH2), 3.66 (app t, 4H, J = 4.4,
OCH2CH2N), 3.52 (app t, 4H, J = 4.4, OCH2CH2N).
MS (DCI/NH3) m/z 364 (M+H)+. Anal. Calcd for
C19H17N5OSÆ0.6H2OÆ0.05PPh3: C, 61.70; H, 4.93; N,
18.08. Found: C, 61.44; H, 4.55; N, 17.95.
5.2.48. 6-(4-Dimethylaminophenylethynyl)-5-(3-nitroph-
enyl)pyrimidin-4-ylamine (16f). To a solution of 15b
(515 mg, 1.62 mmol) and 3-nitrophenyl boronic acid
([13331-27-6]; 1.37 g, 8.21 mmol) in DME (5 mL) and
2 M Na2CO3 (5 mL) was added Pd(PPh3)4 (100 mg,
0.0087 mmol) and the mixture heated to reflux for
12 h. The reaction mixture was cooled, partitioned be-
tween H2O and CH2Cl2. The organic layer was dried
(Na2SO4) and concentrated. The residue was purified
by chromatography (elution with CHCl3 then 10%
MeOH–CHCl3). The appropriate fractions were collect-
ed and concentrated. The resulting solid was triturated
with Et2O, sonicated (to eliminate trapped triphenyl-
phosphine), filtered, and dried to give 67 mg (11%) of
16f: yellow solid. 1H NMR (300 MHz, DMSO-d6) d
8.37 (s, 1H, @N–CH@N), 8.33 (ddd, 1H, J = 8.3, 2.5,
1.2, 40-ArH), 8.26 (dd, 1H, J = 1.8, 1.8, 20-ArH), 7.92
(ddd, 1H, J = 7.8, 1.2, 1.2, 60-ArH), 7.82 (dd, 1H,
J = 8.0, 8.0, 50-ArH), 6.96 (AA0BB0, 2H, J = 8.9,
ArH), 6.77 (br s, 2H, NH2), 6.61 (AA0BB0, 2H,
J = 8.9, ArH), 2.92 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 160.9 (s), 157.6 (d), 150.7 (s),
148.1 (s), 146.9 (s), 137.2 (d), 135.9 (s), 132.7 (d), 130.2
(d), 125.0 (d), 122.9 (d), 116.7 (s), 111.7 (d), 106.3 (s),
96.6 (s), 85.9 (s), 39.5 (q). MS (DCI/NH3) m/z 360
(M+H)+. Anal. Calcd for C20H17N5O2Æ0.4H2OÆ0.2
Et2O: C, 65.50; H, 5.23; N, 18.36. Found: C, 65.41; H,
4.93; N, 18.58.
5.2.45. 6-(6-Morpholin-4-ylpyridin-3-ylethynyl)-5-thio-
phen-3-ylpyrimidin-4-ylamine (16c). Starting with 15a,
the title compound was prepared according to the proce-
dure described for 16a substituting thiophene-3-boronic
acid [6165-69-1] for 4-dimethylaminophenylboronic acid
to give 58 mg (30%) of 16c: white solid. 1H NMR
(300 MHz, DMSO-d6) d 8.30 (s, 1H, @N–CH@N),
8.01 (dd, 1H, J = 2.2, 20-pyridyl-H), 7.73 (m, 2H, thie-
nyl-H), 7.41 (dd, 1H, J = 8.9, 2.3, 40-pyridyl-H), 7.25
(m, 1H, thienyl-H), 6.84 (d, 1H, J = 8.8, 50-pyridyl-H),
6.65 (br s, 2H, NH2), 3.67 (app t, 4H, J = 4.4,
OCH2CH2N), 3.52 (app t, 4H, J = 4.0, OCH2CH2N).
MS (DCI/NH3) m/z 364 (M+H)+. Anal. Calcd for
C19H17N5OSÆ0.6H2OÆ0.1PPh3: C, 62.38; H, 4.96; N,
17.49. Found: C, 62.23; H, 4.92; N, 17.66.
5.2.46. 5-Benzo[b]thiophen-2-yl-6-(6-morpholin-4-ylpyri-
din-3-ylethynyl)pyrimidin-4-ylamine (16d). Starting with
15a, the title compound was prepared according to the
procedure described for 16a substituting benzo[b]thio-
phene-2-boronic acid [98437-23-1] for 4-dim-
ethylaminophenylboronic acid to give 254 mg (35%) of
16d: 1H NMR (300 MHz, DMSO-d6) d 8.36 (s, 1H,
@N–CH@N), 8.05 (m, 1H, ArH), 7.93 (m, 1H, ArH),
7.88 (d, 1H, J = 2.4, 20-pyridyl-H), 7.58 (s, 1H, 30-thie-
nyl-H), 7.42 (m, 2H, ArH), 7.28 (dd, 1H, J = 9.2, 2.4,
40-pyridyl-H), 7.01 (br s, 2H, NH2), 6.76 (d, 1H,
J = 9.2, 50-pyridyl-H), 3.63 (app t, 4H, J = 4.4,
OCH2CH2N), 3.47 (app t, 4H, J = 4.1, OCH2CH2N).
MS (DCI/NH3) m/z 414 (M+H)+. Anal. Calcd for
C23H19N5OSÆ0.2H2OÆ0.2MeOH: C, 65.80; H, 4.81; N,
16.54. Found: C, 66.11; H, 4.59; N, 16.27.
5.2.49. 5-(3-Aminophenyl)-6-(4-dimethylaminophenyleth-
ynyl)pyrimidin-4-ylamine (16g). Starting with 15b, the
title compound was prepared according to the procedure
described for 16f substituting 3-aminophenylboronic
acid [206658-89-1] for 3-nitrophenyl boronic acid. After
aqueous workup, the residue was purified by chroma-
tography (elution with 5% MeOH–CH2Cl2). The appro-
priate fractions were collected and concentrated. The
resulting solid was triturated with Et2O, sonicated (to
eliminate trapped triphenylphosphine), filtered, and
1
dried to afford 708 mg (68%) of 16g: yellow solid. H
NMR (300 MHz, DMSO-d6) d 8.27 (s, 1H, @N–
CH@N), 7.15 (dd, 1H, J = 7.8, 7.8, 50-ArH), 7.05
(AA0BB0, 2H, J = 9.2, ArH), 6.64 (AA0BB0, 2H,
J = 9.2, ArH), 6.62 (m, 2H, 20-and 40-ArH), 6.51 (ddd,
1H, J = 7.5, 1.7, 1.0, 60-ArH), 6.34 (br s, 2H, NH2),
5.20 (br s, 2H, NH2), 2.93 (s, 6H, N(CH3)2). 13C
NMR (100 MHz, DMSO-d6) d 160.9 (s), 156.6 (d),
150.5 (s), 148.9 (s), 146.2 (s), 134.3 (s), 132.8 (d), 129.1
(d), 119.7 (s), 116.8 (d), 114.9 (d), 113.6 (d), 111.6 (d),
107.1 (s), 95.5 (s), 86.5 (s), 39.3 (q). MS (DCI/NH3) m/
z 330 (M+H)+. Anal. Calcd for C20H19N5Æ0.5H2OÆ0.15
5.2.47. 5-Benzofuran-2-yl-6-(6-morpholin-4-ylpyridin-3-
ylethynyl)pyrimidin-4-ylamine (16e). Starting with 15a,
the title compound was prepared according to the proce-
dure described for 16a substituting 2-benzofuranboronic
acid [100124-06-9] for 4-dimethylaminophenylboronic
1
acid to give 75 mg (18%) of 16e: H NMR (300 MHz,

M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
1603
Et2O: C, 70.79; H, 6.20; N, 20.02. Found: C, 70.71; H,
5.82; N, 19.87.
Calcd for C26H27ClN4Æ0.5H2O: C, 70.98; H, 6.41; N,
12.73. Found: C, 70.78; H, 6.17; N, 12.63.
5.2.50. [5-(4-Chlorophenyl)-6-(4-dimethylaminophenyl-
ethynyl)pyrimidin-4-yl]methylamine (17a). Starting with
4d, the title compound was prepared according to the
general procedure described for the aminolysis reaction
(method B) with excess methylamine (40% in H2O). Res-
idue was purified by chromatography (elution with 2.5%
MeOH–CH2Cl2) to give 232 mg (47%) of 17a: yellow
5.2.53. [5-(4-Chlorophenyl)-6-(4-dimethylaminophenyle-
thynyl)pyrimidin-4-yl]-[2-(1H-imidazol-4-yl)ethyl]amine
(17d). Starting with 4d, the title compound was prepared
according to the general procedure described for the
aminolysis reaction (method B) using histamine ([56-
92-8]; 2.1 equiv). Residue was purified by chromatogra-
phy (elution with 5% MeOH–CH2Cl2) to provide
180 mg (30%) of 17d: yellow solid. 1H NMR
(300 MHz, DMSO-d6) d 11.89 (br s, 1H, NH), 8.40
(s, 1H, @N–CH@N), 7.58 (AA0BB0, 2H, J = 8.5,
ArH), 7.49 (d, 1H, J = 1.0, imidazoyl-H), 7.38
(AA0BB0, 2H, J = 8.5, ArH), 6.98 (AA0BB0, 2H,
J = 8.8, ArH), 6.78 (br s, 1H, imidazoyl-H), 6.65
(AA0BB0, 2H, J = 8.8, ArH), 3.52 (m, 2H,
NHCH2CH2), 2.93 (s, 6H, N(CH3)2), 2.71 (m, 2H,
NHCH2CH2). 13C NMR (100 MHz, DMSO-d6) d
159.2 (s), 157.1 (d), 150.6 (s), 145.6 (s), 134.9 (s),
134.5 (d), 132.9 (s), 132.6 (d), 132.5 (s), 132.0 (d),
128.7 (d), 118.9 (s), 116.1 (d), 111.7 (d), 106.7 (s),
96.0 (s), 86.0 (s), 40.6 (t), 39.5 (q), 26.1 (t). MS (DCI/
NH3) m/z 443 (M+H)+. Anal. Calcd for
C25H23ClN6Æ0.1EtOH: C, 67.02; H, 5.62; N, 18.03.
Found: C, 67.12; H, 5.54; N, 17.78.
1
solid. H NMR (300 MHz, DMSO-d6) d 8.41 (s, 1H,
@N–CH@N), 7.59 (AA0BB0, 2H, J = 8.8, ArH), 7.41
(AA0BB0, 2H, J = 8.8, ArH), 6.97 (AA0BB0, 2H,
J = 9.2, ArH), 6.64 (AA0BB0, 2H, J = 9.2, ArH), 6.47
(q, 1H, J = 4.1, NHCH3), 2.93 (s, 6H, N(CH3)2), 2.78
(d, 3H, J = 4.7, NHCH3). 13C NMR (100 MHz,
DMSO-d6) d 159.7 (s), 157.1 (d), 150.6 (s), 145.3 (s),
132.8 (s), 132.6 (s), 132.5 (d), 132.1 (d), 128.7 (d),
118.9 (s), 111.7 (d), 106.7 (s), 95.8 (s), 86.0 (s), 39.5
(q), 27.8 (q). MS (DCI/NH3) m/z 363 (M+H)+. Anal.
Calcd for C21H19ClN4: C, 69.51; H, 5.28; N, 15.44.
Found: C, 69.20; H, 5.04; N, 15.20.
5.2.51. [5-(4-Chlorophenyl)-6-(4-dimethylaminophenyl-
ethynyl)pyrimidin-4-yl]dimethylamine (17b). Starting
with 4d, the title compound was prepared according to
the general procedure described for the aminolysis reac-
tion (method B) with excess dimethylmethylamine (40%
in H2O). Residue was purified by chromatography (elu-
tion with 2.5% MeOH–CH2Cl2) to provide 277 mg
(54%) of 17b: yellow solid. 1H NMR (300 MHz,
DMSO-d6) d 8.45 (s, 1H, @N–CH@N), 7.56 (AA0BB0,
2H, J = 8.1, ArH), 7.45 (AA0BB0, 2H, J = 8.5, ArH),
7.02 (AA0BB0, 2H, J = 8.8, ArH), 6.65 (AA0BB0, 2H,
J = 9.2, ArH), 2.94 (s, 6H, ArN(CH3)2), 2.75 (s, 6H,
C(4)-N(CH3)2). 13C NMR (100 MHz, DMSO-d6) d
161.5 (s), 156.0 (d), 150.7 (s), 149.2 (s), 136.0 (s), 133.3
(d), 131.6 (d), 128.2 (d), 118.8 (s), 111.5 (d), 108.0 (s),
97.9 (s), 86.2 (s), 40.5 (q), 39.9 (q), one quaternary car-
bon overlapped. MS (DCI/NH3) m/z 377 (M+H)+.
Anal. Calcd for C22H21ClN4Æ0.25H2O: C, 69.28; H,
5.68; N, 14.69. Found: C, 69.05; H, 5.68; N, 14.64.
5.2.54. [5-(4-Chlorophenyl)-6-(4-dimethylaminophenyl-
ethynyl)pyrimidin-4-yl]-[2-(1H-indol-3-yl)ethyl]amine (17e).
Starting with 4d, the title compound was prepared accord-
ing to the general procedure described for the aminolysis
reaction (method B) using tryptamine ([61-54-1];
2.1 equiv). Residue was purified by chromatography (elu-
tion with 2.5% MeOH–CH2Cl2) to provide 252 mg (38%)
1
of 17e: yellow solid. H NMR (300 MHz, DMSO-d6) d
10.78 (br s, 1H, NH), 8.44 (s, 1H, @N–CH@N), 7.55
(AA0BB0, 2H, J = 8.5, ArH), 7.54 (m, 1H, ArH), 7.35
(AA0BB0, 2H, J = 8.5, ArH), 7.33 (m, 1H, ArH), 7.13
(d, 1H, J = 2.0, C=CH-NH), 7.06 (ddd, 1H, J = 7.1, 7.1,
1.4, ArH), 6.98 (AA0BB0, 2H, J = 9.2, ArH), 6.97 (m,
1H, ArH), 6.65 (AA0BB0, 2H, J = 9.2, ArH), 6.50 (br t,
1H, J = 5.8, NH), 3.59 (m, 2H, NHCH2CH2), 2.93 (s,
6H, N(CH3)2), 2.91 (m, 2H, NHCH2CH2). 13C NMR
(100 MHz, DMSO-d6) d 159.2 (s), 157.1 (d), 150.6 (s),
145.6 (s), 136.2 (s), 132.8 (s), 132.6 (d), 132.5 (s), 132.0
(d), 128.7 (d), 127.2 (s), 122.6 (d), 120.8 (d), 118.8 (s),
118.3 (d), 118.1 (d), 111.71 (s), 111.67 (d), 111.2 (d),
106.7 (s), 95.9 (s), 86.0 (s), 41.3 (t), 39.5 (q), 24.6 (t). MS
(DCI/NH3) m/z 492 (M+H)+. Anal. Calcd for
C30H26ClN5Æ0.4CH2Cl2: C, 69.42; H, 5.14; N, 13.31.
Found: C, 69.58; H, 5.04; N, 13.49.
5.2.52. [5-(4-Chlorophenyl)-6-(4-dimethylaminophenyl-
ethynyl)pyrimidin-4-yl]cyclohexylamine (17c). Starting
with 4d, the title compound was prepared according to
the general procedure described for the aminolysis reac-
tion (method B) using cyclohexylamine ([108-91-8];
2.0 equiv). Residue was purified by chromatography
(elution with 5% MeOH–CH2Cl2) to provide 134 mg
(23%) of 17c: yellow solid. 1H NMR (400 MHz, CDCl3)
d 8.52 (s, 1H, @N–CH@N), 7.50 (AA0BB0, 2H, J = 8.6,
ArH), 7.38 (AA0BB0, 2H, J = 8.6, ArH), 7.09 (AA0BB0,
2H, J = 9.2, ArH), 6.55 (AA0BB0, 2H, J = 8.9, ArH),
4.59 (d, 1H, J = 8.0, NHCH(CH2)2), 4.00 (m, 1H,
NHCH(CH2)2), 2.95 (s, 6H, N(CH3)2), 1.97 (m, 2H,
cyclohexyl-H), 1.70-1.59 (m, 3H, cyclohexyl-H), 1.46-
1.36 (m, 2H, cyclohexyl-H), 1.18-1.05 (m, 3H, cyclohex-
yl-H). 13C NMR (100 MHz, CDCl3) d 159.0 (s), 157.4
(d), 150.7 (s), 146.4 (s), 134.4 (s), 133.3 (d), 132.3 (s),
131.5 (d), 129.4 (d), 118.5 (s), 111.5 (d), 108.0 (s), 97.5
(s), 85.7 (s), 49.4 (d), 40.0 (q), 32.9 (br t), 25.5 (br t),
24.8 (br t). MS (DCI/NH3) m/z 431 (M+H)+. Anal.
5.2.55. {4-[5-(4-Chlorophenyl)-6-morpholin-4-ylpyrimidin-
4-ylethynyl]phenyl}dimethylamine (17f). Starting with 4d,
the title compound was prepared according to the general
procedure described for the aminolysis reaction (method
B) with excess morpholine (11 equiv). Residue was purified
by chromatography (elution with 30% EtOAc–hexane) to
afford 79 mg (60%) of 17f: light yellow solid; Rf 0.16 (50%
1
EtOAc–hexane). H NMR (300 MHz, DMSO-d6) d 8.55
(s, 1H, @N–CH@N), 7.60 (AA0BB0, 2H, J = 8.5, ArH),
7.53 (AA0BB0, 2H, J = 8.5, ArH), 7.07 (AA0BB0, 2H,
J = 8.8, ArH), 6.67 (AA0BB0, 2H, J = 8.8, ArH), 3.47

1604
M. A. Matulenko et al. / Bioorg. Med. Chem. 15 (2007) 1586–1605
(app t, 4H, J = 4.4, OCH2CH2N), 3.20 (app t, 4H, J = 4.7,
OCH2CH2N), 2.94 (s, 6H, N(CH3)2). 13C NMR
(100 MHz, DMSO-d6) d 161.4 (s), 156.3 (d), 150.8 (s),
149.0 (s), 135.2 (s), 132.8 (d), 132.6 (s), 131.4 (d), 128.5
(d), 120.1 (s), 111.7 (d), 106.3 (s), 97.1 (s), 86.3 (s), 65.5
(t), 47.3 (t), 39.5 (q). MS (DCI/NH3) m/z 419 (M+H)+.
Anal. Calcd for C24H23ClN4OÆ0.24EtOAc: C, 68.12; H,
5.71; N, 12.73. Found: C, 68.31; H, 5.74; N, 12.41.
2.95 (s, 6H, N(CH3)2). 13C NMR (75 MHz, DMSO-
d6) d 163.8 (s), 155.3 (d), 151.2 (s), 150.1 (s), 132.1
(d), 129.9 (d), 124.8 (s), 111.7 (d), 110.7 (d), 110.5
(s), 108.9 (s), 100.7 (s), 81.7 (s), 81.3 (s), 39.7 (q), one
methyl overlapped.
Acknowledgments
5.2.56. {4-[5-(4-Chlorophenyl)-6-piperazin-1-ylpyrimidin-
4-ylethynyl]phenyl}dimethylamine (17g). Starting with 4d,
the title compound was prepared according to the general
procedure described for the aminolysis reaction (method
B) with excess piperazine (5 equiv). Residue was purified
by chromatography (elution with 5% MeOH–CH2Cl2) to
The authors would like to thank members of the Abbott
Structural Chemistry group (Dr. Tom Pagano, Dave
Whittern, Jan Waters, and Carmina Presto) for helpful
NMR and mass spec characterization.
1
provide 174 mg (38%) of 17g: yellow solid. H NMR
Supplementary data
(300 MHz, DMSO-d6) d 8.50 (s, 1H, @N–CH@N), 7.59
(AA0BB0, 2H, J = 8.5, ArH), 7.51 (AA0BB0, 2H,
J = 8.5, ArH), 7.06 (AA0BB0, 2H, J = 8.8, ArH), 6.67
(AA0BB0, 2H, J = 9.2, ArH), 3.14 (app t, 4H, J = 5.1,
HNCH2CH2N), 2.94 (s, 6H, N(CH3)2), 2.55 (app t, 4H,
J = 5.1, HNCH2CH2N). 13C NMR (100 MHz, DMSO-
d6) d 161.5 (s), 156.2 (d), 150.7 (s), 148.8 (s), 135.5 (s),
132.7 (d), 132.4 (s), 131.4 (d), 128.4 (d), 120.0 (s), 111.7
(d), 106.4 (s), 96.8 (s), 86.4 (s), 47.9 (t), 44.8 (t), 39.5
(q). MS (DCI/NH3) m/z 418 (M+H)+. Anal. Calcd for
C24H24ClN5Æ0.3H2O: C, 68.09; H, 5.86; N, 16.54. Found:
C, 68.47; H, 5.79; N, 16.18.
Experimental details and characterization for all inter-
mediates can be found in the supplementary section of
this report. Supplementary data associated with this
article can be found, in the online version, at
doi:10.1016/j.bmc.2006.12.029.
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