Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors

Article abstract of DOI:10.1021/acs.jmedchem.5b00961

The emergence and spread of multidrug resistant bacteria are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the discovery of azaindole ureas as a novel class of bacterial gyrase B inhibitors and detail the story of their evolution from a de novo design hit based on structure-based drug design. These inhibitors show potent minimum inhibitory concentrations against fluoroquinolone resistant MRSA and other Gram-positive bacteria.

Full text of DOI:10.1021/acs.jmedchem.5b00961

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Article
The Discovery of Azaindole Ureas as a
Novel Class of Bacterial Gyrase B Inhibitors
Jing Zhang, Qingyi Yang, Jason B Cross, Jan A Romero, Katherine M Poutsiaka, Felix
Epie, Douglas Bevan, Bin Wang, Yanzhi Zhang, Xin Zhang, Anu Daniel, Moy Terence,
Kien Nguyen, Brian P Chamberlain, Nicole Carter, Ajit Chavan, Joseph Shotwell, Jared
a Silverman, Chester A Metcalf, Dominic M Ryan, Blaise Lippa, and Roland E Dolle
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.5b00961 • Publication Date (Web): 13 Oct 2015
Downloaded from http://pubs.acs.org on October 19, 2015
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The Discovery of Azaindole Ureas as a Novel
Class of Bacterial Gyrase B Inhibitors
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Jing Zhang , Qingyi Yang, Jason Cross, Jan Antoinette C. Romero, Katherine M. Poutsiaka,
Felix Epie, Douglas Bevan, Bin Wang, Yanzhi Zhang, Ajit Chavan, Xin Zhang, Terence Moy,
Anu Daniel, Kien Nguyen, Brian Chamberlain, Nicole Carter, Joseph Shotwell, Jared Silverman,
Chester A. Metcalf, III, Dominic Ryan, Blaise Lippa, Roland E. Dolle
Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, USA
ABSTRACT: The emergence and spread of multidrugꢀresistant bacteria are widely believed to
endanger human health. New drug targets and lead compounds exempt from crossꢀresistance
with existing drugs are urgently needed. We report on the discovery of azaindole ureas as a novel
class of bacterial gyrase B inhibitors and detail the story of their evolution from a de novo design
hit based on structure based drug design. These inhibitors show potent MICs against
fluoroquinolone resistant MRSA and other Gramꢀpositive bacteria.
INTRODUCTION
Due to the increasing prevalence of bacterial antibiotic resistance, the current available
antibiotics continue to lose their efficacy. Therefore, the investigation and development of new
antibacterials that avoid the existing mechanisms of resistance offer a solution to this growing
unmet medical need. Bacterial DNA type II topoisomerases are wellꢀestablished targets for both
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Gramꢀpositive and Gramꢀnegative bacteria. The GyrA subunit of the DNA Gyrase complex is
the target for fluoroquinolones. The GyrB subunit, the target of Novobiocin, offers an
opportunity for overcoming the widespread crossꢀresistance to fluoroquinolones. Due to the
clinical success of the fluoroquinolone class of antibacterials, GyrB has attracted a great deal of
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interest from both industrial and academic institutions . Some representative GyrB inhibitors
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are depicted in Figure 1: the tricyclic pyrimidines 1a from Trius , aminobenzimidazoles 1b from
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Vertex , cyclothialidines 1c pyrrolamides 1d from AstraꢀZeneca
and imidazolopyridine
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1e from Pfizer . Herein we wish to report the evolution of azaindole ureas as a novel class of
GyrB inhibitors from our de novo design starting point 1f.
RESULTS AND DISCUSSION
Chemistry. The de novo design starting point aminothiazole 1f was synthesized from
commercially available 1Hꢀpyrroleꢀ2ꢀcarbaldehyde 2 (Scheme 1). After the indole NH
protection as its tosylate 3, condensation with methyl N,Nꢀdimethylaminoacetate gave αꢀ
ketoester 4 in an unoptimized 15% yield, which upon cyclization with thiourea provided the key
intermediate 5 in 28% yield. Urea formation with ethylisocyanate yielded 6 in 67% yield, which
was converted into 1f via LiAlH mediated ester reduction and tosylate deprotection in one pot in
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8% overall yield
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The synthesis of azaindole derivatives is quite straightforward starting from the commercial 6ꢀ
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bromoꢀ3ꢀnitroꢀ4ꢀazaindole 8 (Scheme 2) . Iron powder mediated nitro reduction, followed by
treating with ethylisocyanate gave 10 in 75% overall yield. Suzuki coupling provided the NH
unsubstituted parent azaindole 11 in 66% isolated yield. Alternatively, SN reaction of 10 with
Ar
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ꢀfluoropyridine and the subsequent Suzuki coupling provided analog 12 in 43% and 63% yields,
respectively. The syntheses of all the azaindole analogs follow this general synthetic route.
Discussion. Compound 1f was discovered as a promising medicinal chemistry starting point
using structure based de novo virtual design and the subsequent preliminary analoging efforts. It
has an IC of 2.5 uM against Staphylococcus GyrB with high ligand efficiency. In addition, it
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also demonstrates weak antibacterial activity with an MIC of 128 ug/mL and 16 ug/mL vs MSSA
and Streptococcus pneumoniae. We were able to resolve the Xꢀray structure of compound 1f
bound in the ATPase pocket of a 24kDa portion of the Staphylococcus GyrB protein (Figure 2,
PDB code 5D6P). The coꢀcrystal structure revealed the following binding features: 1) a hydrogen
bond donorꢀacceptor interaction network between the thiazole urea (thiazole ring N, two urea
NH), catalytic Asp81 and a conserved water molecule, which is stabilized by the hydrogen bond
interactions with Asp81, Gly85 and Thr173; 2) the ethyl fits snugly in the small lipophilic
pocket; 3) the hydroxyl has a HB with Glu58 while also forming an intramolecular HB with
pyrrole NH, helping to restrict the pyrrole conformation; 4) the pyrrole sits in the open binding
pocket surrounded by lipophilic residues such as Ile86 and Pro87; 5) there is no contact with
Arg84 and Arg144. It has been well known that engaging these two Args could dramatically
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improve the enzymatic activity of an inhibitor . From the Xꢀray structure, it is clear that the C4ꢀ
thiazole substituent projects toward the two arginines, and the C5ꢀsubstituent is near the
lipophilic pocket while also offering opportunities to engage the two arginines.
With compound 1f as our medicinal chemistry starting point, we undertook extensive SAR
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studies around the thiazole ring . Surprisingly, the SAR around the C2, C4 and C5 positions
were very flat (data not shown). For C2 substitution, the ethylurea is the best group to occupy the
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small lipophilic pocket (Figure 2). For C5 substitution, small substituents lead to a decrease of
binding potency while larger groups such as aryls or biaryls are preferred, however with rather
flat SAR. Due to the spatial arrangement of the C5 substitution in the protein pocket, we were
never able to engage any meaningful interactions with Arg84 and Arg144 residues. Therefore,
any apparent 2ꢀ3X increases in binding potency was neutralized by the increase in molecular
weight and overall clogP.
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Significant medicinal and computational chemistry efforts were then directed toward the C4
position to try to engage the two Arg redidues. Although a rather flat SAR was developed here
again, compound 7 caught our attention as its GyrB cocrystal structure showed the pyridine
indeed engaged the two Arg residues via a hydrogen bond and a ꢀꢀcation stacking interaction
(Figure 3, PDB code 5D6Q). The C5 pyrrole was again positioned in the lipophilic pocket. The
thiazole nitrogen together with the two urea NHs formed the characteristic hydrogen bond
network with Asp81 via the conserved water molecule. We realized that there was a nonꢀ
conserved water molecule forming a hydrogen bond to the thiazole nitrogen in the open binding
pocket adjacent to the Asp81 hydrogen bond network. It was envisaged that if we could fuse a
heterocycle to the thiazole with an appropriately placed heteroatom to displace the nonꢀ
conserved water molecule, we should be able to improve the binding affinity significantly
(Figure 4). Based on molecular modeling and synthetic feasibility, we chose azaindole as the
core scaffold to test this hypothesis.
Although the parent azaindole analog 11 only showed similar GyrB IC to thiazole analog 7,
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possibly due to the loss of pyrrole lipophilic interactions, it was gratifying to find out that the
novel analog 12 showed ~40X IC50 improvement over 7 with improved ligand efficiency.
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Moreover, 12 showed an MIC of 16 ug/mL vs a MRSA strain. We were then able to resolve the
Xꢀray coꢀcrystal structure of 12 complexed with GyrB (Figure 5, PDB code 5D7C). The
pyridine nitrogen indeed displaces the nonꢀconserved water molecule as designed. In addition,
the pyridine nitrogen along with one of the urea NHs form a water mediated hydrogen bond
network with Asp81. We realized that the other urea NH sits a bit further from the Asp81
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carbonyl and could not form a bifurcated hydrogen bond as in Vertex’s urea analog . This nonꢀ
optimized hydrogen bonding could offer an opportunity for further potency improvement if both
NHs could be engaged. As predicted, the C6ꢀpyridine forms a hydrogen bond and ꢀꢀcation
stacking interaction with the two Arg residues. The para position of the pyridine ring projects
toward the solvent exposed area, offering an opportunity to incorporate polar functional groups
to improve the overall physiochemical properties. The N1ꢀpyridine adopts a small dihedral angle
with respect to the parent azaindole core, and sits in the upper lipophilic pocket.
With Azaindole urea 12 identified as a novel GyrB inhibitor, we carried out detailed SAR studies
around the azaindole scaffold. The azaindole N1 aryl SAR is detailed in Table 1. Realizing that
the 2ꢀpyridyl adopts a small dihedral angle in regards to the azaindole bicycle, we anticipate that
the 2ꢀpyrimidyl substitution would partially relieve the torsional strain between the aryl and
azaindole, potentially improving the potency due to substrate preorganization. Analog 13 is
indeed ~2X more potent in both IC50 and MIC than 12. Analog 14, with increased torsional
strain, is 10X less potent than 12, further substantiating the torsional strain hypothesis. Further
SAR studies were thus based on 2ꢀpyrimidyl substitution. While 4ꢀsubstituted pyrimidine
analogs 15ꢀ19 show potent GyrB inhibition, they all show poor MICs except 19. 5ꢀPyrimidine
substitution shows intriguing SARs with regard to electronic properties of the substituents. Small
electronꢀdonating substituents are all tolerated. 5ꢀMethylpyrimidine analog 20 improves the IC50
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and MIC by 2X over 13. The corresponding ethyl and methoxy analogs 21 and 22 have similar
profiles to 13. 5ꢀHalopyrimidines 23ꢀ25 all display a similar GyrB IC . Though 5ꢀ
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fluoropyrimidine 23 gives disappointing MICs, the corresponding chloroꢀ and bromoꢀ
derivatives 24 and 25 display a very impressive level of MICs across the Gram+ MIC panel
including a fluoroquinolone resistant MRSA strain. The improved MIC profile of these haloꢀ
analogs is probably due to enhanced bacterial cell penetration. 5ꢀSubstituents with electronꢀ
withdrawing properties such as 26 and 27 in general show poor MICs. Though 26 with a small 5ꢀ
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CN shows 18 nM GyrB potency, slightly larger 5ꢀCF analog 27 is totally inactive, consistent
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with a small tight binding pocket around the 5ꢀpyrimidine position as shown in the Xꢀray
cocrystal structure.
In order to further improve the physiochemical properties of the azaindole analogs, we also
explored the nonaryl substitutions as shown in Table 2. In the 12ꢀGyrB cocrystal structure
(Figure 5), the coplanar arrangement of the 2ꢀpyridine and azaindole bicycle is the preferred
binding conformation. It is therefore not surprising that steep SAR was observed (Table 1). Most
of the analogs show GyrB binding potency in the micromolar range with a few exceptions such
as those carrying unsaturation in 31, 33 and 38. Nꢀcyclohexyl analog 34 is also worth noting due
to the marginal potency loss from 2ꢀpyridyl analog 12. Interestingly, moderately active acrylate
analog 38 could serve as a tool compound to explore covalent GyrB inhibitors due to the reactive
acrylate warhead.
With N1 substituents optimized, we next turned our attention to the C6 aryl region (Table 3).
The goal was to optimize the interactions of the aryl with the two Arg residues and improve the
overall physiochemical properties for better ADME profile. Cyanopyrimidine analog 39 gave
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potent GyrB inhibition with rather poor MICs. 2ꢀFluoropyridyl derivative 40 lost enzymatic
activity dramatically, possibly due to the perturbation of the dihedral angle induced by the
fluorine. Compound 41 adopted from Vertex’s Gyrase program showed great enzymatic activity
and 2X MIC improvements over 12. Nꢀmethylpyridone derivative 42 gave substantially
improved IC and 4X MIC improvements over 12, clearly demonstrating the superiority of the
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pyridone moiety over pyridine to interact with the two Arginine residues and improve the overall
cell penetration properties. Our strategy to combine Nꢀmethylpyridone with the best azaindole
Nꢀsubstitutions resulted in the discovery of 44ꢀ46 with excellent MIC profile across the Gram+
MIC panel including a fluoroquinolone resistant MRSA strain, a Streptococcus pneumoniae
strain, and two Enterococcus strains. Surprisingly, Nꢀhydroxyethylpyridone analog 47 gave
much poorer MIC profile relative to Nꢀmethyl analog 46.
CONCLUSION
In summary, using structure based drug design, we were able to quickly analyze the SAR around
our de novo starting compound 1f and design a series of more potent and novel azaindoleꢀbased
gyrase B inhibitors. Our strategy evolved to displace a nonꢀconserved water molecule identified
in the coꢀcrystal structure of 7. Further SAR studies around the azaindole core resulted in the
discovery of a number of potent gyrase B inhibitors with excellent Gram+ MIC profiles. There is
virtually no MIC shift between quinolone susceptible and resistant MRSA strains for all our GyrB
inhibitors. These molecules could provide great utility in the fight against fluoroquinolone
resistance. Further in vitro and in vivo characterization of a few select azaindoles will be reported
in a future publication.
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Figure 1. Structures of some representative GyrB inhibitors
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Figure 2. Xꢀray crystal structure of 1f bound to the 24 kDa Sa GyrB ATPase active site (1.6 Å,
PDB code 5D6P)
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Figure 3. Structure of 7 and its Xꢀray structure with 24 kDa Sa GyrB ATPase (PDB code 5D6Q)
Figure 4. Working hypothesis leading to the azaindole scaffold
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N
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Sa GyrB IC50 = 5.8 uM
LE = 0.31 LipE = 2.4
Sa GyrB IC50 = 6.5 uM
LE = 0.35 LipE = 4.0
Sa GyrB IC50 = 0.14 uM
LE = 0.36 LipE = 4.4
MIC: Sa 16 ug/mL
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Figure 5. The evolution of azaindole 12 and its Xꢀray structure with 24 kDa Sa GyrB ATPase
PDB code 5D7C)
(
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Scheme 1. The synthesis of aminothiazole 1f
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Scheme 2. Representative synthesis of azaindole urea analogs
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1
2
3
4
5
6
7
8
9
0
HN
HN
N
HN
O
a
b
NH2
N
N
H
NO2
Br
Br
Br
N
H
N
8
9
10
d, e
N
HN
N
O
N
O
c
N
H
N
H
N
N
H
H
N
N
11
N
12
a
Reaction conditons: a) Fe, NH Cl, EtOH, H O; b) ethyl isocyanate, THF, 75% over 2 steps, ; c)
4
2
pyridinꢀ3ꢀylboronic acid, Pd(dppf)Cl , Na CO aq, 1,4ꢀdioxane, 66%; d) 2ꢀfluoropyridine,
2
2
3
Cs CO , NMP, 43%; e) pyridinꢀ3ꢀylboronic acid, Pd(dppf)Cl , Na CO aq, 1,4ꢀdioxane, 63%.
2
3
2
2
3
Table 1. Enzymatic and in vitro Antibacterial Activities of Azaindole Analogs: N1 Aryl
SAR (MICs; µg/mL)
MIC (ug/mL)
Sa GyrB
Cmpd
R
ATPase
IC50(uM)
Sa1721
Sa42
MSSA
Sa1118
MRSA
S.
E.
E.
MRSA
R
Pneum. Faecium Faecalis
Cipro
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1
1
1
2
H
6.50
0.14
>32
16
>32
16
>32
ND
>32
8
>32
8
>32
8
13
<0.079
1.9
8
8
16
>32
>32
32
4
>32
4
8
>32
2
2
>32
1
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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29
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31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
1
4
>32
>32
32
>32
>32
32
15
0.14
a
1
1
6
7
0.009
0.042
8
16
4
ND
32
32
32
4
0.5
1
1
8
9
0.048
0.015
>32
8
>32
8
>32
8
1
>32
8
ND
ND
0.5
2
2
2
0
1
2
0.064
0.046
0.143
4
16
4
4
16
8
4
16
8
4
16
4
4
16
8
1
8
1
2
2
2
3
4
5
0.127
0.092
0.128
32
2
32
4
>32
4
32
2
32
2
32
0.5
1
2
2
1
2
0.25
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7
8
9
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
2
6
0.018
>100
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
27
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
a
ND = Not Determined.
Table 2. Enzymatic Activities of Azaindole Analogs: Nꢀnonaryl Substitutions
Sa GyrB
ATPase
IC50(uM)
Sa GyrB
ATPase
IC50(uM)
Cmpd
R
Cmpd
33
R
1
2
2
1
8
9
H
6.5
1.8
3.2
0.24
0.35
6.42
Me
Bn
34
35
3
3
0
1
2.4
36
5.29
0.43
1.22
37
38
1.13
0.28
32
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Table 3. Enzymatic and in vitro Antibacterial Activities of Azaindole Analogs: C6 Aryl
SAR (MICs; µg/mL)
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
MIC (ug/mL)
Sa GyrB
ATPase
IC50(uM)
1
2
Cmpd
R
R
Sa1721
Sa42
MSSA
Sa1118
MRSA
S.
Pneum.
E.
E.
MRSA
R
Faecium Faecalis
Cipro
1
3
2
9
3-Pyridyl
H
<0.079
0.025
8
8
16
4
8
2
Cl
Cl
>32
>32
>32
>32
>32
>32
4
4
4
0
1
2
6.06
>32
4
>32
4
>32
4
>32
2
>32
8
>32
a
H
0.010
ND
H
Me
Cl
0.012
0.013
0.262
0.071
2
>32
1
2
>32
1
4
>32
2
2
4
4
>32
2
ND
0.5
ND
ND
43
4
4
1
45
Et
1
1
1
0.25
0.25
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7
8
9
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
4
4
6
7
Br
Br
0.094
0.008
1
8
1
8
1
8
1
8
1
8
ND
ND
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
a
ND = Not Determined.
AUTHOR INFORMATION
Corresponding Author
*Email: jackzhang49@yahoo.com. Phone: (781)640ꢀ2333
ACKNOWLEDGMENT
We would like to thank Dr. Ole Andersen and Dr. John Barker at Evotec AG for the
crystallographic work, and Dr. Hongwu Gao’s team in Chempartner for analog synthesis.
ABBREVIATIONS
GyrA, gyrase A; GyrB, gyrase B; SAR, structure activity relationship; MIC, minimum inhibitory
concentration; ADME, absorption, distribution, metabolism and excretion; MRSA, methicillinꢀ
resistant staphylococcus aureus; MSSA, methicillinꢀsusceptible staphylococcus aureus; Sa,
staphylococcus aureus; S. Pneum., Streptococcus pneumonia; E. faecalis, Enterococcus faecalis;
E. faecium, Enterococcus faecium.
REFERENCES
(
1) Bisacchi, G. S.; Manchester, J. I. A newꢀclass antibacterial ꢀ almost. Lessons in drug
discovery and development: a critical analysis of more than 50 years of effort toward ATPase
inhibitors of DNA gyrase and topoisomerase IV. ACS Infect. Dis. 2015, 1, 4ꢀ41.
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5
6
7
8
9
(
2) Tomašić, T.; Mašič, L. P. Prospects for developing new antibacterials targeting bacterial
type IIA topoisomerases. Curr. Top. Med. Chem. 2014, 14, 130–51.
3) Oblak, M.; Kotnik, M.; Solmajer, T. Discovery and development of ATPase inhibitors of
(
10
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12
13
14
15
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19
20
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22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
DNA gyrase as antibacterial agents. Curr. Med. Chem. 2007, 14(19), 2033ꢀ47.
(4) Collin, F.; Karkare, S.; Maxwell, A. Exploiting bacterial DNA gyrase as a drug target:
current state and perspectives. Appl. Microbiol. Biotechnol. 2011, 92(3), 479–497.
(5) Tari, L. W.; Li, X.; Trzoss, M.; Bensen, D. C.; Chen, Z.; Lam, T.; Zhang, J.; Lee, S. J.;
Hough, G.; Phillipson, D.; AkersꢀRodriguez, S.; Cunningham, M. L.; Kwan, B. P.; Nelson, K. J.;
Castellano, A.; Locke, J. B.; BrownꢀDriver, V.; Murphy, T. M.; Ong, V. S.; Pillar, C. M.;
Shinabarger, D. L.; Nix, J.; Lightstone, F. C.; Wong, S. E.; Nguyen, T. B.; Shaw, K. J.; Finn, J.
Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broadꢀspectrum dualꢀtargeting
antibacterial agents. PLoS One 2013, 8(12), 1–13.
(6) Ronkin, S. M.; Badia, M.; Bellon, S.; Grillot, A. L.; Gross, C. H.; Grossman, T. H.; Mani, N.;
Parsons, J. D.; Stamos, D.; Trudeau, M.; Wei, Y.; Charifson, P. S. Discovery of pyrazolthiazoles
as novel and potent inhibitors of bacterial gyrase. Bioorganic Med. Chem. Lett. 2010, 20, 2828–
2831.
(7) Charifson, P. S.; Grillot, A.ꢀL.; Grossman, T. H.; Parsons, J. D.; Badia, M.; Bellon, S.;
Deininger, D. D.; Drumm, J. E.; Gross, C. H.; LeTiran, A.; Liao, Y.; Mani, N.; Nicolau, D. P.;
Perola, E.; Ronkin, S.; Shannon, D.; Swenson, L. L.; Tang, Q.; Tessier, P. R.; Tian, S.ꢀK.;
Trudeau, M.; Wang, T.; Wei, Y.; Zhang, H.; Stamos, D. Novel dualꢀtargeting benzimidazole
urea inhibitors of DNA gyrase and topoisomerase IV possessing potent antibacterial activity:
intelligent design and evolution through the judicious use of structureꢀguided design and
structureꢀactivity relationships. J. Med. Chem. 2008, 51(17), 5243ꢀ5263.
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1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
(
8) Lewis, R. J.; Singh, O. M.; Smith, C. V; Skarzynski, T.; Maxwell, a; Wonacott, a J.; Wigley,
D. B. The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed
by Xꢀray crystallography. EMBO J. 1996, 15, 1412–1420.
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
(9) Angehrn, P.; Goetschi, E.; Gmuender, H.; Hebeisen, P.; Hennig, M.; Kuhn, B.; Luebbers, T.;
Reindl, P.; Ricklin, F.; SchmittꢀHoffmann, A. A new DNA gyrase inhibitor subclass of the
cyclothialidine family based on a bicyclic dilactamꢀlactone scaffold: synthesis and antibacterial
properties. J. Med. Chem. 2011, 54(7), 2207–2224.
(10) Dumas, J.; Sherer, B. (2ꢀpyridinꢀ3ꢀylimidazo[1,2ꢀb]pyridazinꢀ6ꢀyl) urea derivatives as
antibacterial agents. Int. Pat. Appl. WO2009027733 A1.
(
11) Basarab, G.; Hill, P.; Zhou, F. Piperidine compounds and uses thereof. Int. Pat. Appl.
WO2008152418 A1.
12) Illingworth, R.N.; UriaꢀNickelsen, M.; Bryant, J.; Eakin, A.E. Presented at the 48th
Interscience Conference on Antimicrobial Agents, Washington D.C., 2008, Poster F1ꢀ2028.
13) Starr, J. T., Sciotti, R. J.; Hanna, D. L., Huband, M. D., Mullins, L. M., Cai, H., Gage, J. W.,
(
(
Lockard, M., Rauckhorst, M. R., Owen, R. M., Lall, M. S., Tomilo, M., Chen, H., McCurdy, S.
P., Barbachyn, M. R. 5ꢀ(2ꢀPyrimidinyl)ꢀimidazo[1,2ꢀa]pyridines are antibacterial agents
targeting the ATPase domains of DNA gyrase and topoisomerase IV. Bioorg. Med. Chem. Lett.,
2
009, 19(18), 5302ꢀ5306.
(14) 6ꢀBromoꢀ3ꢀnitroꢀ1Hꢀpyrrolo[3,2ꢀb]pyridine was purchased from Sinova Product List.
15) The detailed SAR studies will be reported in a future publication.
(
EXPERIMENTAL SECTION
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General Procedures. All common solvents and chemicals were used as purchased without
further purification. 6ꢀBromoꢀ3ꢀnitroꢀ1Hꢀpyrrolo[3,2ꢀb]pyridine 8 was purchased from Sinova
Product List. The progress of all reactions was monitored on Aldrich precoated silica gel plates
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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29
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31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
(
with fluorescence indicator UV254) using ethyl acetate/nꢀhexane or methanol/dichloromethane
as solvent system, and by a Waters UPLCꢀMS with model number C10UPB090A. Column
chromatography was performed with Aldrich silica gel 60 (230−400 mesh ASTM) with the
solvent mixtures specified in the corresponding experiment. Purity of all final compounds was
95% or higher. Spots were visualized by irradiation with ultraviolet light (254 nm). Proton (1H)
NMR spectra were recorded on Bruker Avance 500 or 300 MHz using solvents as indicated in
the experimental section. Chemical shifts are given in parts per million (ppm) (δ relative to
1
residual solvent peak for H).
1ꢀTosylꢀ1Hꢀpyrroleꢀ2ꢀcarbaldehyde (3) To a solution of 1Hꢀpyrroleꢀ2ꢀcarbaldehyde 2 (5.0 g,
o
5
2.6 mmol) in THF (80 mL) was added NaH (2.31 g, 57.8 mmol) at 0 C. After stirring at this
temperature for 30 minutes, tosyl chloride (10.52 g, 55.2 mmol) in 20 mL THF was added drop
o
wise. The reaction mixture was stirred at 0 C for 2 hours, then diluted with ethyl acetate (200
mL). The organic phase was washed with water (100 mL), brine (50 mL), dried over Na SO and
2
4
evaporated in vacuo. The residue was purified by silica gel column chromatography eluting with
5
% ethyl acetate in petroleum ether to give the title compound 3 (11 g, 82%) as a white solid.
1
HꢀNMR (400 MHz, CDCl ): δ 2.42 (s, 3H), 6.40 (t, J=3.6 Hz, 1H), 7.16 (m, 1H), 7.32 (d, J=8.0
3
Hz, 2H), 7.62 (m, 1H), 7.82 (d, J=8.0 Hz, 2H) 9.97 (s, 1H).
o
(E)ꢀMethyl 2ꢀhydroxyꢀ3ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)acrylate (4) To a 0 C solution of NaH
(2.88g, 72 mmol) in THF (60 mL) was added a solution of 1ꢀtosylꢀ1Hꢀpyrroleꢀ2ꢀcarbaldehyde 3
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1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
(
8.98g, 36 mmol) and methyl 2ꢀ(N, Nꢀdimethylamino)acetate (12.66 g, 108 mmol) in THF (60
mL). The mixture was then warmed up and stirred at room temperature for 4 hours. It was then
diluted with ethyl acetate and water. The organic phase was washed with 1 N HCl (100mL),
brine (50 mL), dried over Na SO , filtered and concentrated in vacuo. The residue was purified
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
2
4
by silica gel column chromatography eluting with 10% ethyl acetate in petroleum ether to give
1
6
the title compound 4 (2 g, 15%) as a white solid. HꢀNMR (400MHz, DMSOꢀd ): δ 2.36 (s, 3H),
.82 (s, 3H), 6.44 (t, J=3.2 Hz, 1H), 6.93 (m, 1H), 7.03 (s, 1H), 7.44(d, J=8.0Hz, 2H), 7.49(m,
3
1H), 7.71 (d, J=8.0 Hz, 2H), 9.79 (s, 1H).
Methyl 2ꢀaminoꢀ5ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)thiazoleꢀ4ꢀcarboxylate (5) A mixture of (E)ꢀ
methyl 2ꢀhydroxyꢀ3ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)acrylate 4 (1.8 g, 5.6 mmol), thiourea (0.85 g, 11.2
mmol) and iodine (1.42 g, 5.6 mmol) in 150 mL 1, 4ꢀdioxane was refluxed for 24 hours. The
mixture was cooled down and diluted with ethyl acetate, washed with water, and brine. The
organic phase was dried over Na SO , filtered and concentrated in vacuo. The residue was
2
4
purified by silica gel column chromatography eluting with 1% methanol in dichloromethane to
1
give the title compound 5 (0.6 g, 28%) HꢀNMR (400MHz, CDCl ): δ 2.39 (s, 3H), 3.44 (s, 3H),
3
5
.46 (s, 2H), 6.32 (m, 2H), 7.22(d, J=8.0Hz, 2H), 7.50(m, 1H), 7.51 (d, J=8.0 Hz, 2H).
Methyl 2ꢀ(3ꢀethylureido)ꢀ5ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)thiazoleꢀ4ꢀcarboxylate (6) To a solution
of methyl 2ꢀaminoꢀ5ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)thiazoleꢀ4ꢀcarboxylate 5 (0.51 g, 1.35 mmol) in
THF (100 mL) was added ethyl isocyanate (1.92 g, 27 mmol) at room temperature. The mixture
was then refluxed for 3 days. The mixture was concentrated in vacuo and purified by silica gel
column chromatography eluting with 2% methanol in dichloromethane to give the title
6
compound 6 (0.4 g, 67%). HꢀNMR (400MHz, DMSOꢀd ): δ 1.07 (t, J=7.2Hz, 3H), 2.35 (s, 3H),
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.16 (m, 2H), 3.41(s, 3H) 6.37 (m, 1H), 6.41 (m, 1H), 6.83(br, 1H), 7.33(d, J=8.4 Hz, 2H),
+
+
7.42(d, J=8.4 Hz, 2H), 7.58(m, 1H), 11.08(br, 1H). MS (EI , m/z): 449 [M+H] .
1
ꢀEthylꢀ3ꢀ(4ꢀ(hydroxymethyl)ꢀ5ꢀ(1Hꢀpyrrolꢀ2ꢀyl)thiazolꢀ2ꢀyl)urea (1f) To a solution of
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
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59
60
methyl 2ꢀ(3ꢀethylureido)ꢀ5ꢀ(1ꢀtosylꢀ1Hꢀpyrrolꢀ2ꢀyl)thiazoleꢀ4ꢀcarboxylate 6 (3.0 g, 6.7 mmol) in
o
THF (450 mL) was added LiAlH (1.27 g, 33.4 mmol) at 0 C. The mixture was slowly warmed
4
up to room temperature and stirred overnight. The mixture was carefully quenched by
Na SO ·10H O (5 g), filtered and concentrated in vacuo. The residue was purified by silica gel
2
4
2
chromatography eluting with 3% methanol in dichloromethane to give the title compound 1f
1
6
(0.15 g, 8%). HꢀNMR (400MHz, DMSOꢀd ): δ 1.06 (t, J = 7.2Hz, 3H), 3.15ꢀ3.16 (m, 2H),
4.39(s, 2H), 5.23ꢀ5.25 (br, 1H), 6.10ꢀ6.12 (m, 1H), 6.20ꢀ6.22 (m, 1H), 6.53ꢀ6.55 (br, 1H), 6.82ꢀ
+
+
6
.84 (m, 1H), 10.29ꢀ10.30 (br, 1H), 10.96 (s, 1H). MS (EI , m/z): 267 [M+H] .
1ꢀ(6ꢀBromoꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (10) To a solution of 6ꢀbromoꢀ3ꢀ
nitroꢀ1Hꢀpyrrolo[3,2ꢀb]pyridine 8 (1.21 g, 5.0 mmol) in water (20 mL) and ethanol (300 mL)
was added NH Cl (1.34 g, 25.0 mmol) and iron powder (1.40 g, 25.0 mmol) in two portions. The
4
o
mixture was heated to 80 C for 2 h and cooled to room temperature, filtered through celite. The
filtrate was concentrated to give the crude product 9 (1.06 g, 100%) as a dark solid, which was
+
+
taken to the next step without further purification. MS (EI , m/z): 213 [M+H] .
To a suspension of the 6ꢀbromoꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀamine 9 (1.06 g, 5 mmol) in THF
o
(
60 mL) was added ethyl isocyanate (1.8 g, 25.0 mmol). The reaction mixture was heated at 70 C
for 1.5 hours and then concentrated. The residue was purified by silica gel column
chromatography eluting with 33% ethyl acetate in hexane to afford the title compound 10 (1.06
1
6
g, 75% over 2 steps) as an offꢀwhite solid. HꢀNMR (500 MHz, DMSOꢀd ): δ 10.92 (s, 1H), 8.37
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(
s, 1H), 8.33 (s, 1H), 7.95 (s, 1H), 7.75 (s, 1H), 6.42ꢀ6.44 (m, 1H), 3.12ꢀ3.16 (m, 2H), 1.05 (t, J
+
+
=
6.0 Hz, 3H). MS (EI , m/z): 283 [M+H] .
1
ꢀEthylꢀ3ꢀ(6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (11) A mixture of 1ꢀ(6ꢀ
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8
9
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bromoꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea 10 (120 mg, 0.426 mmol), pyridinꢀ3ꢀyl
boronic acid (105 mg, 0.85 mmol), Pd(dppf)Cl (13 mg, 0.002 mmol) and aqeous Na CO (0.6
2
2
3
o
mL, 1.21 mmol, 2 M) in 1,4ꢀdioxane (5.0 mL) was heated at 130 C for 30 minutes in the
microwave reactor under N atmosphere. The reaction mixture was purified by reverse phase
2
1
HPLC directly to give the title compound 11 (77 mg, 66%) as an offꢀwhite solid. HꢀNMR (500
6
MHz, DMSOꢀd ): δ 11.83 (s, 1H), 9.12 (s, 1H), 8.82 (s, 1H), 8.72 (s, 1H), 8.54 (s, 1H), 8.43 (s,
1
H), 7.97 (d, J = 2.0 Hz, 1H), 7.72ꢀ7.75 (m, 1H), 6.58ꢀ6.59 (m, 1H), 3.16ꢀ3.18 (m, 2H), 1.06ꢀ
+
+
1
.08 (m, 3H). MS (EI , m/z): 282.1[M+H] .
1
ꢀethylꢀ3ꢀ(1ꢀ(pyridinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (12) To a
mixture of 1ꢀ(6ꢀbromoꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea 10 (200 mg, 0.71 mmol) in Nꢀ
methylpyrrolidinone (7.5 mL) was added Cs CO (1.16 g, 3.55 mmol) and 2ꢀfluoropyridine (138
2
3
o
mg, 1.42 mmol). The mixture was heated at 150 C for 30 minutes in a microwave reactor and
cooled to room temperature and treated with water (40 mL). The resulting precipitates were
collected and dried in vacuo to give the crude 1ꢀ(6ꢀbromoꢀ1ꢀ(pyridinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀ
b]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (190 mg, 43%) as an offꢀwhite solid, which was taken to the next
+
+
step without further purification. MS (EI , m/z): 360.1[M+H] .
A mixture of 1ꢀ(6ꢀbromoꢀ1ꢀ(pyridinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (160 mg,
0
.446 mmol), pyridinꢀ3ꢀyl boronic acid (110 mg, 0.89 mmol), Pd(dppf)Cl (13 mg, 0.002 mmol)
2
o
and aqueous Na CO (0.7 mL, 1.34 mmol, 2 M) in 1,4ꢀdioxane (2.0 mL) was heated at 130 C
2
3
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for 30 minutes in a microwave reactor under N atmosphere. The reaction mixture was purified
2
by reverse phase HPLC directly to give the title compound 12 (120 mg, 63%) as an offꢀwhite
1
6
solid. HꢀNMR (500 MHz, DMSOꢀd ): δ 9.06ꢀ9.28 (m, 2H), 8.52ꢀ8.92 (m, 6H), 7.78ꢀ8.05 (m,
10
11
12
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15
16
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+
3
H), 7.30ꢀ7.36 (m, 1H), 6.70ꢀ6.72 (m, 1H), 3.20ꢀ3.22 (m, 2H), 1.12 (t, J = 7.0 Hz, 3H). MS (EI ,
+
m/z): 329.1[M+H] .
1
1
ꢀEthylꢀ3ꢀ(6ꢀ(pyridinꢀ3ꢀyl)ꢀ1ꢀ(pyrimidinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (13) Hꢀ
6
NMR (500 MHz, DMSOꢀd ): δ 9.28 (s, 1H), 9.20 (s, 1H), 8.78ꢀ8.88 (m, 6H), 8.57 (d, J = 8.0 Hz,
H), 7.87 (t, J = 5.5 Hz, 1H), 7.34 (t, J = 4.5 Hz, 1H), 6.70 (s, 1H), 3.18 (m, 2H), 1.10 (t, J = 7.0
1
+
+
Hz, 3H). MS (EI , m/z): 360.2 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(3ꢀmethylpyridinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
1
6
(
14) HꢀNMR (500 MHz, DMSOꢀd ): δ 8.95 (s, 1H), 8.77 (s, 1H), 8.69 (s, 1H), 8.58 (s, 1H), 8.45
s, 1H), 8.15 (s, 1H), 8.07 (s, 1H), 8.01 (s, 1H), 7.95 (d, J = 7.5 Hz, 1H), 7.42ꢀ7.50 (m, 2H), 6.59
(
+
+
(t, J = 5.5 Hz, 1H), 3.16ꢀ3.18 (m, 2H), 1.09 (t, J = 7.5 Hz, 3H). MS (EI , m/z): 373.2 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(4ꢀmethylpyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
1
6
(
15) HꢀNMR (400 MHz, DMSOꢀd ): δ 9.19 (dd, J = 9.6 Hz, J = 1.6Hz, 2H), 8.70ꢀ8.86 (m, 6H),
.56 (d, J = 2.0 Hz, 1H), 7.86 (dd, J = 8.0, J = 5.2Hz), 6.70 (s, 1H), 3.18 (m, 2H), 2.30 (s, 3H),
8
+
+
1.10 (t, J = 6.8 Hz, 3H). MS (EI , m/z): 373.1 [M+H] .
1
3
1
ꢀEthylꢀ3ꢀ(1ꢀ(4ꢀ(2ꢀhydroxyethyl)pyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ
1
6
ꢀyl)urea (16) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.28 (d, J = 2.0 Hz, 2H), 9.01 (d, J = 2.0 Hz,
H), 8.64ꢀ8.84 (m, 5H), 8.21 (t, J = 7.0 Hz, 1H), 7.56ꢀ7.59 (m, 1H), 7.23 (s, 1H), 6.71 (s, 1H),
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.91 (t, J = 6.0 Hz, 2H), 3.17ꢀ3.19 (m, 2H), 2.99 (t, J = 6.0 Hz, 2H), 1.10(t, J = 7.0 Hz, 3H). MS
+
+
(EI , m/z): 404.1 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(4ꢀ(3ꢀhydroxypropyl)pyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀ
0
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3
4
5
6
7
8
9
0
1
6
b]pyridinꢀ3ꢀyl)urea (17) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.31 (d, J = 2.0 Hz, 1H), 9.12 (d, J
2.0 Hz, 1H), 8.71ꢀ8.87 (m, 5H), 8.42 (d, J = 7.0 Hz, 1H), 7.73 (t, J = 5.5 Hz, 1H), 7.23 (d, J =
.0 Hz, 1H), 6.70 (s, 1H), 3.52 (t, J = 6.5 Hz, 2H), 3.17ꢀ3.19 (m, 2H), 2.88 (t, J = 8.0 Hz, 2H),
=
5
1
+
+
.94ꢀ2.00 (m, 2H), 1.10(t, J = 7.5 Hz, 3H). MS (EI , m/z): 418.2 [M+H] .
3ꢀ(2ꢀ(3ꢀ(3ꢀEthylureido)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ1ꢀyl)pyrimidinꢀ4ꢀ
1
6
yl)propanoic acid (18) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.24 (s, 1H), 9.05 (s, 1H), 8.76ꢀ8.82
m, 3H), 8.73 (s, 1H), 8.63 (d, J = 4.0 Hz, 1H), 8.53 (s, 1H), 8.26 (d, J = 9.0 Hz, 1H), 7.55 (dd, J
7.5 Hz, J = 5.0 Hz, 1H), 6.69 (d, J = 5.5 Hz, 1H), 3.15ꢀ3.20 (m, 2H), 3.03ꢀ3.07 (m, 2H), 2.88
(
=
+
+
(m, 2H), 2.28 (s, 3H), 1.09 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 445.2 [M+H] .
4ꢀ(2ꢀ(3ꢀ(3ꢀethylureido)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ1ꢀyl)pyrimidinꢀ4ꢀ
1
6
yl)butanoic acid (19) HꢀNMR (400 MHz, DMSOꢀd ): δ 9.15 (s, 1H), 8.97 (s, 1H), 8.60ꢀ8.77
m, 4H), 8.43 (s, 1H), 8.14 (d, J = 8.0 Hz, 1H), 7.54 (dd, J = 8.0 Hz, J = 5.2 Hz, 1H), 6.67 (t, J =
.2 Hz, 1H), 3.13ꢀ3.23 (m, 2H), 2.78 (t, J = 7.2 Hz, 2H), 2.35 (t, J = 7.2 Hz, 2H), 2.19 (s, 3H),
(
5
+
+
2.03 (t, J = 7.2 Hz, 2H), 1.09 (t, J = 7.2 Hz, 3H). MS (EI , m/z): 459.2 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(5ꢀmethylpyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
1
6
(20) HꢀNMR (400 MHz, DMSOꢀd ): δ 9.29 (d, J = 2.0 Hz, 1H), 9.20 (d, J = 2.0 Hz, 1H), 8.87
(d, J = 2.0 Hz, 1H), 8.77ꢀ8.81 (m, 3H), 8.70 (d, J = 2.8 Hz, 1H), 8.58 (d, J = 8.4 Hz, 1H), 7.88
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(
dd, J = 8.0 Hz, 5.6 Hz, 1H), 7.22 (d, J = 9.2 Hz, 1H), 6.70 (s, 1H), 3.18 (d, J = 6.0 Hz, 2H), 2.58
+
+
(s, 3H), 1.10 (t, J = 7.2 Hz, 3H). MS (EI , m/z): 373.1 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(5ꢀethylpyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
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35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
1
6
(21) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.20 (d, J = 1.0 Hz, 1H), 9.00 (d, J = 2.5 Hz, 1H), 8.73ꢀ
8
.82 (m, 5H), 8.64 (t, J = 4.0 Hz, 1H), 7.56ꢀ7.58 (m, 1H), 6.68 (t, J = 5.0 Hz, 1H), 3.17ꢀ3.21 (m,
+
2
H), 2.63ꢀ2.68 (m, 2H), 1.25(t, J = 7.5 Hz, 3H), 1.10(t, J = 7.0 Hz, 3H). MS (EI , m/z): 388.2
+
[
M+H] .
1ꢀEthylꢀ3ꢀ(1ꢀ(5ꢀmethoxypyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀ
1
6
yl)urea (22) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.19 (d, J = 1.5 Hz, 1H), 9.11 (s, 1H), 8.84 (d, J
2.0 Hz, 1H), 8.78 (s, 1H), 8.72ꢀ8.74 (m, 2H), 8.67 (s, 2H), 8.42 (s, 1H), 7.75 (s, 1H), 6.68 (s,
=
+
+
1
H), 3.98 (s, 3H), 3.17 (m, 2H), 1.09 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 390.2 [M+H] .
1ꢀEthylꢀ3ꢀ(1ꢀ(5ꢀfluoropyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
1
6
(
23) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.15ꢀ9.17 (m, 2H), 8.97 (s, 2H), 8.87 (d, J = 2.0 Hz, 1H),
8
.82 (s, 1H), 8.77 (s, 2H), 8.71 (s, 1H), 8.49 (d, J = 7.5 Hz, 1H), 7.80 (s, 1H), 6.70 (s, 1H), 3.17
+
+
(
m, 2H), 1.09(t, J = 7.0 Hz, 3H). MS (EI , m/z): 378.2 [M+H] .
1
ꢀ(1ꢀ(5ꢀChloropyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea
1
6
(
24) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.12ꢀ9.16 (m, 2H), 8.96 (s, 2H), 8.87 (d, J = 2.0 Hz, 1H),
8
.84 (s, 1H), 8.75ꢀ8.76 (m, 2H), 8.68 (s, 1H), 8.44ꢀ8.46 (m, 1H), 7.77ꢀ7.79 (m, 1H), 6.70 (s, 1H),
+
+
3
.17 (m, 2H), 1.09(t, J = 7.0 Hz, 3H). MS (EI , m/z): 394.1 [M+H] .
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ꢀ(1ꢀ(5ꢀBromopyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea
1
6
(
25) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.09 (s, 1H), 8.99 (s, 3H), 8.80ꢀ8.81 (m, 2H), 8.63ꢀ8.65
m, 2H), 8.18 (d, J = 7.5 Hz, 1H), 7.51 (s, 1H), 6.70 (s, 1H), 3.18ꢀ3.19 (m, 2H), 1.09(t, J = 7.0
(
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
+
+
Hz, 3H). MS (EI , m/z): 438.0 [M+H] .
1
ꢀ(1ꢀ(5ꢀCyanopyrimidinꢀ2ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea
1
6
(
(
(
26) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.29 (s, 2H), 9.15 (d, J = 2.0 Hz, 1H), 9.00 (s, 1H), 8.92
s, 1H), 8.88 (d, J = 2.0 Hz, 1H), 8.67 (s, 2H), 8.20 (d, J = 8.0 Hz, 1H), 7.57ꢀ7.60 (m, 1H), 6.75
+
+
t, J = 5.5 Hz, 1H), 3.17ꢀ3.19 (m, 2H), 1.09 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 385.1 [M+H] .
1
3
1
ꢀEthylꢀ3ꢀ(6ꢀ(pyridinꢀ3ꢀyl)ꢀ1ꢀ(5ꢀ(trifluoromethyl)pyrimidinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ
1
6
ꢀyl)urea (27) H NMR (300 MHz, DMSOꢀd ) δ 9.24 (s, 2H), 9.19 (d, J = 2.0 Hz, 1H), 8.97 (s,
H), 8.88 – 8.82 (m, 2H), 8.68 (s, 1H), 8.61 (d, J = 3.4 Hz, 1H), 8.17 (d, J = 8.4 Hz, 1H), 7.53
(dd, J = 8.1, 4.9 Hz, 1H), 6.70 (s, 1H), 3.19 – 3.09 (m, 2H), 1.04 (t, J = 7.2 Hz, 3H).
1
1ꢀEthylꢀ3ꢀ(1ꢀmethylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (28) HꢀNMR (500
6
MHz, DMSOꢀd ): δ 9.29 (s, 1H), 9.05 (s, 1H), 8.94 (s, 1H), 8.88 (d, J = 5.0 Hz, 1H), 8.82 (d, J =
8.5 Hz, 1H), 8.02ꢀ8.06 (m, 2H), 4.10 (s, 3H), 3.32ꢀ3.34 (m, 4H), 1.21 (t, J = 7.0 Hz, 3H). MS
+
+
(EI , m/z): 296.1 [M+H] .
1
1
ꢀ(1ꢀBenzylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (29) HꢀNMR (500
6
MHz, DMSOꢀd ): δ 9.24 (s, 1H), 8.86 (s, 1H), 8.80 (d, J = 4.5 Hz, 1H), 8.75 (s, 1H), 8.64ꢀ8.66
(m, 2H), 8.05 (s, 1H), 7.88ꢀ7.90 (m, 1H), 7.30ꢀ7.31 (m, 5H), 6.60 (s, 1H), 5.55 (s, 2H), 3.31ꢀ3.34
+
+
(m, 2H), 1.07 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 372.2 [M+H] .
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ꢀEthylꢀ3ꢀ(1ꢀ(2ꢀmethoxyethyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (30) Hꢀ
6
NMR (500 MHz, DMSOꢀd ): δ 9.02 (d, J = 1.0 Hz, 1H), 8.65 (s, 1H), 8.58 (d, J = 5.0 Hz, 1H),
8
.47 (s, 1H), 8.26 (s, 1H), 8.19 (d, J = 8.0 Hz, 1H), 7.85 (s, 1H), 7.51ꢀ7.54 (m, 1H), 6.50 (s, 1H),
.37(t, J = 4.5 Hz, 2H), 3.65 (t, J = 4.5 Hz, 2H), 3.22 (s, 3H), 3.14 (t, J = 6.5 Hz, 3H), 1.07(t, J =
10
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15
16
17
18
19
20
21
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26
27
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29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
4
+
+
7.0 Hz, 3H). MS (EI , m/z): 340.2 [M+H] .
1
1
ꢀ(1ꢀAllylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (31) HꢀNMR (500
6
MHz, DMSOꢀd ): δ 9.00 (s, 1H), 8.66 (d, J = 2.0 Hz, 1H), 8.58ꢀ8.59 (m, 1H), 8.50 (s, 1H), 8.23
d, J = 2.0 Hz, 1H), 8.18 (d, J = 8.0 Hz, 1H), 7.82(s, 1H), 7.51ꢀ7.53 (m, 1H), 6.49 (s, 1H), 5.98ꢀ
6.01 (m, 1H), 5.10ꢀ5.18 (m, 2H), 4.86 (d, J = 5.5 Hz, 2H), 3.12ꢀ3.15 (m, 2H), 1.06 (t, J = 6.0 Hz,
(
+
+
3
H). MS (EI , m/z): 322.0 [M+H] .
1
ꢀ(1ꢀ(2,3ꢀDihydroxypropyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea
1
6
(
32) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.00 (d, J = 2.0 Hz, 1H), 8.63 (d, J = 2.0 Hz, 1H), 8.58
(d, J = 4.5 Hz, 1H), 8.17ꢀ8.20 (m, 2H), 7.85 (s, 1H), 7.51ꢀ7.54 (m, 1H), 6.48 (t, J = 6.0 Hz, 1H),
.99 (d, J = 5.0 Hz, 1H), 4.79 (t, J = 5.0 Hz, 1H), 4.28ꢀ4.32 (m, 1H), 4.10ꢀ4.15 (m, 1H), 3.78 (d,
J = 4.5 Hz, 1H), 3.37 (s, 1H), 3.27ꢀ3.30 (m, 1H), 3.11ꢀ3.17 (m, 2H), 1.07 (t, J = 7.0 Hz, 3H). MS
4
+
+
(EI , m/z): 356.1 [M+H] .
1ꢀ(1ꢀ(Cyclohexꢀ2ꢀenꢀ1ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (33)
1
6
HꢀNMR (500 MHz, DMSOꢀd ): δ 9.14 (s, 1H), 8.76 (s, 1H), 8.69 (d, J = 3.0 Hz, 1H), 8.51ꢀ8.53
(
m, 2H), 8.45 (d, J = 7.5 Hz, 1H), 7.88 (s, 1H), 7.71 (s, 1H), 6.53 (s, 1H), 6.16ꢀ6.18 (m, 1H),
5.78ꢀ5.80 (m, 1H), 5.35 (s, 1H), 3.22ꢀ3.30 (m, 2H), 2.07ꢀ2.20 (m, 2H), 1.71ꢀ1.73 (m, 3H), 1.06
+
+
(
t, J = 7.0 Hz, 3H). MS (EI , m/z): 362.2 [M+H] .
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Journal of Medicinal Chemistry
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ꢀ(1ꢀCyclohexylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (34) HꢀNMR
6
(
500 MHz, DMSOꢀd ): δ 9.03 (d, J = 2.0 Hz, 1H), 8.64 (d, J = 1.5 Hz, 1H), 8.58ꢀ8.59 (m, 1H),
8
6
.46 (s, 1H), 8.33 (d, J = 1.5 Hz, 1H), 8.22 (d, J = 8.0 Hz, 1H), 7.91 (s, 1H),7.51ꢀ7.53 (m, 1H),
0
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2
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8
9
0
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9
0
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8
9
0
1
2
3
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7
8
9
0
1
2
3
4
5
6
7
8
9
0
.48 (s, 1H), 4.50 (s, 1H), 3.12ꢀ3.14 (m, 2H), 1.94ꢀ1.95 (m, 2H), 1.84ꢀ1.85 (m, 2H), 1.71ꢀ1.72
+
(m, 2H), 1.50ꢀ1.51 (m, 2H), 1.32ꢀ1.35 (m, 1H), 1.07 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 364.3
+
[
M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(1ꢀmethylpiperidinꢀ4ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea
+
+
(35) MS (EI , m/z): 379.2 [M+H] .
1
ꢀEthylꢀ3ꢀ(1ꢀ(1ꢀmethylꢀ2ꢀoxopyrrolidinꢀ3ꢀyl)ꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀ
1
6
yl)urea (36) HꢀNMR (500 MHz, DMSOꢀd ): δ 9.00 (d, J = 2.0 Hz, 1H), 8.68 (d, J = 2.0 Hz,
1
H), 8.59ꢀ8.60 (m, 1H), 8.55 (s, 1H), 8.18ꢀ8.22 (m, 2H), 7.72(s, 1H), 7.52ꢀ7.55 (m, 1H), 6.50ꢀ
.51 (m, 1H), 5.50ꢀ5.51 (m, 1H), 3.52ꢀ3.54 (m, 2H), 3.12ꢀ3.14 (m, 2H), 2.88 (s, 3H), 2.60ꢀ2.62
6
+
+
(m, 1H), 2.20ꢀ2.24 (m, 1H), 1.06 (t, J = 6.0 Hz, 3H). MS (EI , m/z): 379.3 [M+H] .
1
1
ꢀEthylꢀ3ꢀ(1ꢀpicolinoylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)urea (37) HꢀNMR
6
(
500 MHz, DMSOꢀd ): δ 9.00 (s, 1H), 8.95 (s,1H), 8.82ꢀ8.85 (m, 2H), 8.65 (d, J = 1.5 Hz, 1H),
8
.36 (s, 1H), 8.21 (d, J = 3.0 Hz, 1H), 8.14ꢀ8.17 (m, 1H), 8.07(s, 1H), 7.74ꢀ7.77 (m, 1H), 7.56ꢀ
+
7.59 (m, 1H), 6.72ꢀ6.73 (m, 1H), 3.22ꢀ3.24 (m, 2H), 1.05 (t, J = 7.5 Hz, 3H). MS (EI , m/z):
+
387.1 [M+H] .
1
1ꢀ(1ꢀAcryloylꢀ6ꢀ(pyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀethylurea (38)
HꢀNMR
6
(
500 MHz, DMSOꢀd ): δ 8.99 (d, J = 2.0 Hz, 1H), 8.86ꢀ8.91 (m, 3H), 8.64ꢀ8.66 (m, 1H), 8.30 (s,
1H), 8.20 (t, J = 6.0 Hz, 1H), 7.55ꢀ7.58 (m, 1H), 7.24ꢀ7.30 (m, 1H), 6.73 (s, 1H), 6.54ꢀ6.58 (m,
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+
1
H), 6.14ꢀ6.16 (m, 1H), 3.16ꢀ3.19 (m, 2H), 1.10 (t, J = 7.0 Hz, 3H). MS (EI , m/z): 336.1
+
[
M+H] .
1
ꢀ(1ꢀ(5ꢀChloropyrimidinꢀ2ꢀyl)ꢀ6ꢀ(2ꢀcyanopyrimidinꢀ5ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀ
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48
49
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58
59
60
1
6
ethylurea (39) H NMR (300 MHz, DMSOꢀd ) δ 9.44 (s, 2H), 9.23 (d, J = 1.9 Hz, 1H), 8.94 (d,
J = 2.0 Hz, 1H), 8.91 (s, 2H), 8.82 (s, 1H), 8.68 (s, 1H), 8.41 (s, 2H), 6.67 (s, 1H), 3.12 (m, 2H),
+
+
1
.03 (t, J = 7.2 Hz, 3H). MS (EI , m/z): 420.6 [M+H] .
1
ꢀ(1ꢀ(5ꢀChloropyrimidinꢀ2ꢀyl)ꢀ6ꢀ(2ꢀfluoropyridinꢀ3ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ3ꢀyl)ꢀ3ꢀ
1
6
ethylurea (40) H NMR (300 MHz, DMSOꢀd ) δ 9.10 (t, J = 1.7 Hz, 1H), 8.95 (s, 2H), 8.84 (s,
1
H), 8.73 – 8.68 (m, 2H), 8.35 – 8.30 (m, 1H), 8.26 (dd, J = 9.9, 2.2 Hz, 1H), 7.56 (ddd, J = 7.1,
.8, 1.8 Hz, 1H), 6.70 (t, J = 5.5 Hz, 1H), 3.17 (dt, J = 12.6, 7.0 Hz, 2H), 1.09 (t, J = 7.2 Hz, 3H).
4
+
+
MS (EI , m/z): 412.6 [M+H] .
NꢀCyclopropylꢀ1ꢀ(3ꢀ(3ꢀethylureido)ꢀ1ꢀ(pyrimidinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀb]pyridinꢀ6ꢀyl)ꢀ1Hꢀ
1
6
imidazoleꢀ4ꢀcarboxamide (41) HNMR (500 MHz, DMSOꢀd ) δ 9.16 ꢀ 9.15 (m, 1H), 8.89 (d, J
4.8 Hz, 2H), 8.86 ꢀ 8.84 (m, 2H), 8.77 (s, 1H), 8.40 (s, 1H), 8.30 (s, 1H), 8.15 ꢀ 8.14 (m, 1H),
.36 (t, J = 4.8 Hz, 1H), 6.69ꢀ6.67 (m, 1H), 3.19 ꢀ 3.16 (m, 2H), 2.88 ꢀ 2.82 (m, 1H), 1.09 (t, J =
=
7
7
+
+
.2 Hz, 3H), 0.71 ꢀ 0.61 (m, 4H). MS (EI , m/z): 432.2 [M+H] .
1
ꢀEthylꢀ3ꢀ(6ꢀ(1ꢀmethylꢀ2ꢀoxoꢀ1,2ꢀdihydropyridinꢀ4ꢀyl)ꢀ1ꢀ(pyrimidinꢀ2ꢀyl)ꢀ1Hꢀpyrrolo[3,2ꢀ
1
6
b]pyridinꢀ3ꢀyl)urea (42) HNMR (500 MHz, DMSOꢀd ) δ 9.21 ꢀ 9.20 (m, 1H), 8.89 (d, J = 4.8
Hz, 2H), 8.84 ꢀ 8.80 (m, 2H), 8.78 (s, 1H), 7.87 ꢀ 7.85 (m, 1H), 7.34 (t, J = 4.8 Hz, 1H), 6.82 ꢀ
6
.78 (m, 1H), 6.73 ꢀ 6.67 (m, 2H), 3.49 (s, 3H), 3.19 ꢀ 3.16 (m, 2H), 1.09 (t, J = 7.2 Hz, 3H). MS
+
+
(EI , m/z): 390.0 [M+H] .
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