Discovery of a novel azaindole class of antibacterial agents targeting the ATPase domains of DNA gyrase and Topoisomerase IV

Article abstract of DOI:10.1016/j.bmcl.2012.05.128

We present the discovery and optimization of a novel series of bacterial topoisomerase inhibitors. Starting from a virtual screening hit, activity was optimized through a combination of structure-based design and physical property optimization. Synthesis

Full text of DOI:10.1016/j.bmcl.2012.05.128

Bioorganic & Medicinal Chemistry Letters 22 (2012) 5150–5156
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery of a novel azaindole class of antibacterial agents targeting
the ATPase domains of DNA gyrase and Topoisomerase IV
⇑
John I. Manchester , Daemian D. Dussault, Jonathan A. Rose, P. Ann Boriack-Sjodin, Maria Uria-Nickelsen,
Georgine Ioannidis, Shanta Bist, Paul Fleming, Kenneth G. Hull
Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
We present the discovery and optimization of a novel series of bacterial topoisomerase inhibitors. Start-
ing from a virtual screening hit, activity was optimized through a combination of structure-based design
and physical property optimization. Synthesis of fewer than a dozen compounds was required to achieve
inhibition of the growth of methicillin-resistant Staphyloccus aureus (MRSA) at compound concentrations
Received 11 April 2012
Revised 18 May 2012
Accepted 29 May 2012
Available online 19 June 2012
of 1.56 lM. These compounds simultaneously inhibit DNA gyrase and Topoisomerase IV at similar nano-
molar concentrations, reducing the likelihood of the spontaneous occurrence of target-based mutations
resulting in antibiotic resistance, an increasing threat in the treatment of serious infections.
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
Antibacterial
DNA gyrase
Azaindole
Structure-based design
Bacterial resistance to antibiotics results in higher costs to treat
infections and in higher mortality rates.1 Despite the development
of new antibiotics in the decades since resistance was first recog-
nized, the incidence of resistant infections continues to rise.2,3
Resistance can result from acquisition or activation of genes which
encode proteins that modify the compound, potentially changing
its properties, or which exclude or actively remove the antibiotic
from the cell. Additionally, resistance can result from mutations
in the gene for the drug target, as well as enzymatic modification
of the target itself. Drugs that act upon more than one essential tar-
get in bacteria are thus less susceptible to target-based resistance
since independent genetic mutations for each target are required
in order to neutralize their pharmacologic effects. Topoisomerases
are interesting in this regard since bacteria express two isoforms,
DNA gyrase and Topoisomerase IV, which are both required for
maintenance of proper DNA topology during transcription and rep-
lication. The ATPase subunits of these isozymes exhibit high
homology among pathogenic bacteria, but low homology with
eukaryotes, offering the potential to develop broad-spectrum anti-
bacterial agents with improved safety profiles relative to other
classes of antibiotics. So-called ‘dual targeting’ topoisomerase
inhibitors have been previously reported.4–7 Here we describe
the design of a novel class of dual-targeting azaindole-carboxam-
ide topoisomerase inhibitors.
ring of ATP is involved in both donor and acceptor hydrogen bond
interaction between the ligand and the protein, with a conserved
Asp (residue 78 in Streptococcus pneumoniae ParE) accepting a
hydrogen bond and a water molecule acting as the hydrogen bond
donor. This is similar to the donor/acceptor motif that has been
successfully exploited in kinase drug design for multiple inhibi-
tors.11 Indeed, both the pyrrolamide12 and the arylurea4 series ex-
ploit this donor/acceptor motif in their interactions with the
protein (Fig. 1). Efforts by others have demonstrated that virtual
screening is a viable approach for identifying such fragments
which bind DNA gyrase.13–15 Therefore, a small library of molecular
fragments extracted from kinase inhibitors displaying hinge-bind-
ing motifs was assembled for use in lead generation efforts for the
ATPase domain of topoisomerases. The virtual library, abstracted
from proprietary series pursued within discovery programs at
AstraZeneca, contained 57 molecular fragments, with a mean
molecular weight of 215 Daltons.
These fragments were docked into an in-house structure of S.
pneumoniae ParE using GOLD (v3.0.1).16,17 5-phenyl azaindole (1)
ranked within the top 5 hits in the virtual screen (fig. 2). Both het-
eroatoms of 1 were predicted to participate in a hydrogen-bonding
network with Asp 78 and the bound water molecule, with the aza-
indole core oriented so that the 5-substituent pointed toward Arg
140, which was previously demonstrated as important for potent
inhibition of the target.4,12 Therefore, to expedite evaluation of
the series, the trans-cinnamic acid 2 was designed, which was pre-
dicted to form a salt bridge with Arg 140, and which was accessible
readily available starting materials in a single step.18 Compound 2
The structure of the ATPase domain of topoisomerases has been
previously described.8–10 When substrate is bound, the adenine
⇑
Corresponding author. Tel.: +1 781 839 4844.
E-mail address: john.manchester@astrazeneca.com (J.I. Manchester).
exhibited an IC50 of 7.7 lM in S. pneumoniae ParE (IC50s deter-
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.05.128

J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
Asp78
5151
Asp78
Asp78
O
O
O
H
O
H
N
H
O
H
O
H
O
H
O
O
O
H
N
H
N
H
N
H
N
H
N
R
N
H
N
O
HN
R
N
Cl
Cl
N
R
R'
Adenine
Pyrrolamides
Arylureas
Figure 1. The donor/acceptor binding motif through which diverse ATPase domain binders interact with Asp78 and a bound water molecule. Left: Adenine interactions as
observed in Escherichia coli ParE (1S16)10; Center: pyrrolamide interactions observed in S. aureus GyrB (3TTZ)12; Right: Arylurea interactions postulated in models10 and
observed in 3FV5 (no reference given in PDB).
Further modeling studies predicted that an amide substitution
at the azaindole 2-position would provide an additional interaction
to the hydrogen-bond network between the ligand, Asp 78 and the
bound water molecule. This type of network has been previously
noted among substituted aryl ureas.4 Ab initio molecular orbital
calculations at the B3LYP/6-31+g(d,p) level, employing the IEFPCM
polarizable continuum solvent model in GAUSSIAN09,20 were used to
assess the energy penalty associated with achieving the cis confor-
mation of the urea desired for optimal activity. Whereas the cis
configuration was estimated to be disfavored relative to trans by
approximately 3 kcals/mol in aqueous solution, a simple binding
pocket model employing a hydroxide anion to mimic Asp 78 indi-
cated the cis conformation would actually be favored by as much as
6 kcal/mol upon binding the enzyme (Fig. 4).
H
H
N
N
N
N
O
OH
1
2
Figure 2. Chemical structures of the virtual screening hit (1) and the initial
compound designed for synthesis (2) based up on it.
mined as in Ref. 19). A structure of 2 bound to S. pneumoniae ParE
was obtained using X-ray crystallographic methods (Boriack-Sjo-
din et al, in preparation) and, as shown in Fig. 3, the donor/acceptor
hydrogen bond network and the salt bridge predicted by modeling
were confirmed by the experimental data. This structure has been
deposited in the Protein Data Bank (http://www.rcsb.org/pdb) with
PDB ID 4EM7.
The synthesis of the azaindole core scaffold is depicted in
Scheme 1 starting from the previously described 7-azaindole
derivative (3).21 The TIPS protecting group was removed using sul-
furic acid followed by conversion to the sulfone (4) using NaH and
phenylsulfonyl chloride in good overall yield. Selective deprotona-
Asp78
Arg81
Arg140
Figure 3. X-ray crystal structure of 2 in S. pneumonia ParE. H-bond network between Asp 78, a water molecule and the azaindole core on the left are complemented by the
salt bridge between the trans-cinnamic acid and Arg 140, and a pi-stacking interaction with Arg 81. 2 exhibited an IC50 of 7.7 M. Arg140.
l

5152
J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
tion at C-2 was effected using LDA at ꢀ78 °C and subsequent cap-
H
H
N
H
N
N
N
O
N
ture of the anion with carbon dioxide gas provided the carboxylic
acid (5) in 70% yield. The carboxamide (6) was prepared from this
acid using alkylamines and standard HATU coupling conditions.
Prior experience with the aminopyrimidine series6 suggested
incorporation of a trifluoromethylpyrazole at the 4-position. Intro-
duction of the N-linked pyrazole at C-4 of the azaindole was
achieved by displacement of the chloride using either 3-(trifluoro-
methyl)pyrazole or 3-methyl-5-(trifluoromethyl)pyrazole in NMP/
K2CO3 at 150 °C. During the pyrazole coupling reaction, the sulfon-
amide was also cleaved to give the 5-bromo-4-pyrazole-7-azain-
dole (7). Finally, heteroaromatic groups were introduced at C-5
via a Suzuki–Miyaura22 reaction using Pd(dppf)Cl2 and the corre-
sponding aromatic boronic acid/ester to provide the core scaffold
(8) in 50–85% yield.
(a)
N
H
O
trans favored by ~3 kcal/mol
H
O
H
O
H
N
H
N
H
N
O
N
N
(b)
N
H
O
Table 1 summarizes the results of efforts to optimize the
biochemical and antibacterial activity of lead compounds in the
azaindole series. At the 2-position, ethylaminocarboxamide substi-
tution provided the best biochemical and antibacterial activity.
Compound 10 yielded equivalent IC50s of 5 nM in the S. pneumo-
niae topo IV homolog ParE and the Staphyloccus aureus DNA gyrase
homolog GyrB, and a minimum inhibitory concentration23 (MIC) of
6.25 lM in S. pneumoniae (ARC548 in the AstraZeneca bacterial
culture collection). An X-ray crystal structure of 10 in complex
with S. pneumoniae ParE (PDB ID 4EMV) showed that the predicted
cis favored by ~6 kcal/mol
Figure 4. Ab initio molecular orbital calculations were used to assess the energetics
associated with attaining the cis of the urea required for optimal interaction with
Asp73. (a) Isolated from the enzyme in aqueous solution, the trans configuration of
the urea is predicted to be more stable by approximately 3 kcals/mol. (b) In the
binding pocket, however, interaction with the carboxy anion (modeled here using
hydroxide anion) is predicted to reverse that preference, favoring the cis config-
uration by ꢁ6 kcal/mol. B3LYP/6-31+g(d,p) calculations were performed with
Gaussian09 and the IEFPCM solvation model.20
Cl
N
Cl
Cl
Br
Br
Br
O
a
c
b
N
N
N
OH
N
N
SO2Ph
SO2Ph
Si(i-Pr)3
3
4
5
F
F
F
F
F
F
Cl
N
N
N
Br
R2
R2
O
N
N
N
d
e
Br
Het/Ar
O
O
N
N
H
R1
SO2Ph
N
H
N
H
R1
N
H
N
H
R1
N
6
7
R2 = H, Me
R2 = H, Me
8
Scheme 1. Reagents and conditions: (a) (1) H2SO4, IPA; (2) NaH, THF; (3) PhSO2Cl (75%); (b) (1) LDA, THF,ꢀ78 °C; (2) CO2 (gas), then warm to room temperature and quench
with aq NH4Cl, 70%; (c) HATU, DIEA, DMF, alkylamine; 60–80%; (d) 3-Methyl-5-(trifluoromethyl)pyrazole or 3-(trifluoromethyl)pyrazole, K2CO3, NMP, 150 °C, R2 = H (70%),
R
2 = Me (25%); (e) Het/ArB(OR)2, Pd(dppf)Cl2, Na2CO3, water/dioxane; 50–85%.
Table 1
Structure–activity relationship of azaindole analogues
IC50
(
l
M)
MIC (lM)
H
N
N
S.pneumoniae
S.aureus
GyrB
S.pneumoniae S.aureus S.aureus
logD
R1
ParE
MRQRa
R1
R2
R3
R2
R3
1
2
H
H
H
H
—
—
—
—
—
—
—
COOH
7.7
200
>200
>200
0.58

J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
5153
Table 1 (continued)
IC50
(
l
M)
MIC (lM)
H
N
N
S.pneumoniae
S.aureus
GyrB
S.pneumoniae S.aureus S.aureus
logD
R1
ParE
MRQRa
R1
R2
R3
R2
R3
COOH
COOH
COOH
COOH
COOH
NH
o
N
N
10
11
12
13
14
15
16
17
0.005
0.045
0.044
0.006
0.065
0.009
0.016
0.010
0.005
0.058
0.147
0.039
0.133
0.009
0.011
0.023
6.25
>25
>25
25
>25
>25
>25
>25
>25
25
>25
>25
>25
>25
>25
>25
12.5
1.56
ꢀ0.99
ꢀ0.79
ꢀ0.62
ꢀ0.98
ꢀ0.88
1.81
N
N
N
N
N
CF3
NH
o
N
N
N
N
CF3
NH
o
N
CF3
NH
N
o
CF3
NH
o
N
N
12.5
0.2
CF3
O
NH
o
N
N
N
N
N
NH2
N
CF3
O
NH
o
N
N
H
0.098
0.2
6.25
3.13
2.21
N
N
CF3
CN
NH
o
N
2.62
CF3
O
O
NH
o
N
NH
18
19
0.003
0.003
<0.001
<0.03
<0.03
0.40
0.78
1.10
1.56
1.65
2.32
N
CF3
N
N
O
NH
o
N
N
O
O
N
NH
0.004
N
CF3
O
NH
o
O
N
NH
20
0.003
0.002
<0.02
0.098
0.2
2.91
N
CF3
O
N
Novobiocin
Levofloxacin
—
—
—
—
—
—
—
—
—
—
0.78
3.13
0.39
0.78
0.39
>25
—
—
a
Methicillin-resistant, quinolone-resistant S. aureus.

5154
J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
(a)
Asp78
Arg81
Asn51
Arg140
Pro84
Ile98
Thr94
(b)
Arg81
Arg140
Pro84
Ile98
Thr94
Figure 5. X-ray crystal structure of compound 10 in S. pneumoniae ParE. (a) The ethylcarboxamide participates in a bifurcated hydrogen bond (shown as dotted lines) with
Asp78 as predicted, as well as an unexpected hydrogen bond with Asn 51 due to an alternate rotomer of that residue observed in this structure. Additionally, the nicotinic acid
forms a salt bridge with Arg140 while p-stacking with Arg81. This interaction as well as the overall steric complementarity between 10 and the binding site can be seen more
clearly in (b) which shows molecular surface of the enzyme. Of particular note is the interaction between the trifluoromethyl group and the hydrophobic sub-pocket formed
by Met83, Pro84, Thr 94 and Ile98 (Met83, which lies behind the ligand, has been omitted for clarity). 10 exhibited an IC50 of 5 nM in S. pneumoniae ParE.
hydrogen bonding network between the 2-aminocarboxamido
azaindole, Asp 78 and a bound water molecule were all made. In
addition, a new electrostatic interaction with Asn 51 was observed,
gion. The trifluoromethyl pyrazole makes extensive hydrophobic
interactions, in particular with a small pocket formed by Met 83,
Pro 84, Thr 94 and Ile 98. These interactions are summarized inFig-
ure 5.
and the nicotinic acid at the 5-position forms p-stacking and elec-
trostatic interactions with Arg 81 and Arg 140, respectively,
although these are less optimal than those of the longer trans-cin-
namic acid in 2 which extends further into the arginine binding re-
Despite the low-nanomolar potency of 10, its MICs in S. aureus
were assessed at >25
lM. Modification of the ethylcarboxamide
did not improve potency. Addition of a single methyl group to form

J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
5155
slightly diminished activity in S. aureus. Moving the methoxyl sub-
stituent to the 2-position of the pyridine (20) further increased
logD to 2.9 and produced the best overall antibacterial activity,
with MICs of <0.02 lM in S. pneumoniae and 0.098 and 0.2 lM in
the two strains of S. aureus. The relationships among antibacterial
activity, biochemical potency and hydrophobicity for these com-
pounds are summarized in Fig. 6, which shows strong correlations
between logD and the MIC/IC50 ratios for S. pneumoniae and par-
ticularly S. aureus. Because there is essentially no relationship be-
tween IC50 and logD in Table 1 for either strain, this analysis
suggests that the improvements in antibacterial activity observed
are a result of optimization of physical properties rather than
changes in potency.
The MICs of the optimized azaindoles are low compared to the
topoisomerase inhibitors novobiocin and levofloxacin, and do not
show cross-resistance with the quinolone-resistant strain of S. aur-
eus, further demonstrating that these compounds act through inhi-
bition of GyrB/ParE. Moreover, a representative azaindole did not
show an elevated MIC in a novobiocin-resistant strain of S. aureus,
in which a single mutation (T175A) was mapped to GyrB, suggest-
ing antibacterial activity through ParE, in addition to GyrB. Resis-
tance rates among the azaindoles were 610ꢀ9 at fourfold the MIC
in both S. pneumonia and S. aureus. These rates are low and similar
to those for the fluoroquinolones, known dual-targeting agents.24
Figure 6. The ratio of MIC to IC50 for S. aureus (squares) and S. pneumoniae (circles)
plotted against logD for the azaindoles in Table 1 (excluding indeterminate values).
The ratios for both species show strong correlations with logD, with S. pneumoniae
more tolerant of polarity among these compounds.
the propyl- (11) or isopropylaminocarboxamide (12) resulted in
approximately a 10-fold drop in potency. Cyclopropylaminocarb-
oxamide (13) was equivalent in S. pneumoniae but significantly
worse in S. aureus. In fact it is the only compound that showed
greater than a threefold difference in IC50 between the two iso-
zymes. This is likely due to a single amino acid difference, Ala 52
in S. pneumoniae ParE versus Ser 55 in S. aureus GyrB, which results
in a narrowing of the pocket around the amide substituent unfa-
vorable to the cyclopropyl group. Similarly, addition of a methyl
group to trifluoromethylpyrazole at the azaindole 4-position (14)
resulted in more than a 10-fold loss in potency. Antibacterial activ-
ity (MIC) also declined with increasing substitution at these
positions.
These observations, coupled with the effectively equivalent IC50s
in GyrB and ParE in Table 1, support the dual-targeting nature of
the azaindoles.
We have described the discovery of a novel scaffold for dual
inhibition of bacterial DNA gyrase and Topoisomerase IV through
virtual screening. Using structure-based design inspired by careful
analysis of the SAR of other series which bind the same pocket of
these enzymes, low-nanomolar enzymatic inhibition was rapidly
achieved. Further optimization of physical properties produced po-
tent, broad-spectrum antibacterial compounds. The dual-targeting
nature of these novel and potent compounds is expected to result
in decreased development of antibacterial resistance due to target
mutations.
At the azaindole 5-position, conversion of the nicotinic acid (10)
to nicotinamide (15) maintained biochemical potency and resulted
in a 30-fold improvement in antibacterial activity against S. pneu-
moniae. Alkylation of 15 to the acetamide 16 resulted in a further
twofold drop in MIC against S. pneumoniae, and activities of 6.25
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2012.05.
128.
and 12.5 lM against methicillin-sensitive and multidrug-resistant
strains of S. aureus, respectively. The improvements in antibacterial
activity among these compounds were not correlated with
improvements in potency, but rather appeared to track with
changes in their hydrophobicity as assessed by logD. Compound
10 exhibited a logD of ꢀ1.0, whereas 15 and 16 exhibited logDs
of 1.8 and 2.2, respectively. It was therefore hypothesized that
excessive polarity led to poor permeability across the cellular
envelope, limiting the antibacterial activity despite the excellent
potency of these compounds. 3-cyanopyridine was introduced at
the 5-position (17) which increased logD to 2.6. Although inhibi-
tion of enzyme activity was slightly reduced, improved MICs of
References and notes
1. Giske, C. G.; Monnet, D. L.; Cars, O.; Carmeli, Y. ReAct-Action on Antibiotic
Resistance Antimicrob Agents Chemother. 2008, 52, 813.
2. Boucher, H. W.; Talbot, G. H.; Bradley, J. S.; Edwards, J. E.; Gilbert, D.; Rice, L. B.;
Scheld, M.; Spellberg, B.; Bartlett, J. Clin. Infect. Dis. 2009, 48, 1.
3. Spellberg, B.; Guidos, R.; Gilbert, D.; Bradley, J.; Boucher, H. W.; Scheld, W. M.;
Bartlett, J. G.; Edwards, J., Jr Clin. Infect. Dis. 2008, 46, 155.
4. 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. J.
Med. Chem. 2008, 51, 5243.
5. Basarab, G. S.; Bist, S.; Manchester, J. I.; Sherer, B. 2008, U.S. Patent Appl. Publ.
US20080132546A1.
6. Boriack-Sjodin, A.; Carcanague, D. R.; Dussault, D. D.; Hatoum-Mokdad, H.;
Hull, K. G.; Ioannidis, G.; Manchester, J. I.; McGuire, H. M.; McKinney, D. C.;
Stokes, S. 2010, PCT Int. Appl. WO2010038081A2.
7. East, S. P.; White, C. B.; Barker, O.; Barker, S.; Bennett, J.; Brown, D.; Boyd, E. A.;
Brennan, C.; Chowdhury, C.; Collins, I.; Convers-Reignier, E.; Dymock, B. W.;
Fletcher, R.; Haydon, D. J.; Gardiner, M.; Hatcher, S.; Ingram, P.; Lancett, P.;
Mortenson, P.; Papadopoulos, K.; Smee, C.; Thomaides-Brears, H. B.; Tye, H.;
Workman, J.; Czaplewski, L. G. Bioorg. Med. Chem. Lett. 2009, 19, 894.
8. Wigley, D. B.; Davies, G. J.; Dodson, E. J.; Maxwell, A.; Dodson, G. Nature 1991,
351, 624.
3.13 and 1.56 lM against the methicillin-sensitive and multi-
drug-resistant strains of S. aureus were seen. Replacement of the
nitrile with the weakly acidic oxadiazolone hetereocycle in 18
lowered logD to 1.7, but restored biochemical potency in
S. pneumoniae ParE and improved it to <1 nM in S. aureus GyrB. This
boost in potency is likely due to improved interactions with Arg 81
and Arg 140, as the oxadiazolone extends further into the arginine
binding region. In that compound, MICs were further improved to
<0.03 lM in S. pneumoniae, and 0.4 and 1.10 lM in the sensitive
and multi-drug resistant strains of S. aureus. Incorporation of
3-oxadiazolo,4-methoxypyridine (19) restored logD to 2.3 and pre-
served biochemical and antibacterial activity in S. pneumoniae, but
9. Lafitte, D.; Lamour, V.; Tsvetkov, P. O.; Makarov, A. A.; Klich, M.; Deprez, P.;
Moras, D.; Briand, C.; Gilli, R. Biochemistry (N.Y.) 2002, 41, 7217.

5156
J. I. Manchester et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5150–5156
10. Bellon, S.; Parsons, J. D.; Wei, Y.; Hayakawa, K.; Swenson, L. L.; Charifson, P. S.;
Lippke, J. A.; Aldape, R.; Gross, C. H. Antimicrob. Agents Chemother. 1856, 2004,
48.
11. Chuaqui, C.; Deng, Z.; Singh, J. J. Med. Chem. 2005, 48, 121.
12. Sherer, B. A.; Hull, K.; Green, O.; Basarab, G.; Hauck, S.; Hill, P.; Loch, J. T., 3rd;
Mullen, G.; Bist, S.; Bryant, J.; Boriack-Sjodin, A.; Read, J.; DeGrace, N.; Uria-
Nickelsen, M.; Illingworth, R. N.; Eakin, A. E. Bioorg. Med. Chem. Lett. 2011, 21,
7416.
13. Boehm, H. J.; Boehringer, M.; Bur, D.; Gmuender, H.; Huber, W.; Klaus, W.;
Kostrewa, D.; Kuehne, H.; Luebbers, T.; Meunier-Keller, N.; Mueller, F. J. Med.
Chem. 2000, 43, 2664.
14. Firth-Clark, S.; Todorov, N. P.; Alberts, I. L.; Williams, A.; James, T.; Dean, P. M. J.
Chem. Inf. Model. 2006, 46, 1168.
chromatography (water, acetonitrile, formic acid additive) was used for
purification, and it was characterized by HPLC (UV, 254 nm) and proton NMR).
19. Eakin, A. E.; Green, O.; Hales, N.; Walkup, G. K.; Bist, S.; Singh, A.; Mullen, G.;
Bryant, J.; Embrey, K.; Gao, N.; Breeze, A.; Timms, D.; Andrews, B.; Uria-
Nickelsen, M.; Demeritt, J.; Loch, J. T., 3rd; Hull, K.; Blodgett, A.; Illingworth, R.
N.; Prince, B.; Boriack-Sjodin, P. A.; Hauck, S.; MacPherson, L. J.; Ni, H.; Sherer,
B. Antimicrob. Agents Chemother. 2012, 56, 1240.
20. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;
Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.;
Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.;
Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.;
Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven,
T.; Montgomery, J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.;
Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.;
Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.;
Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.;
Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.;
Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.;
Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas
Foresman. J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. GAUSSIAN 09, Revision B.01,
GAUSSIAN, Inc., Wallingford CT 2009.
15. Oblak, M.; Grdadolnik, S. G.; Kotnik, M.; Jerala, R.; Filipic, M.; Solmajer, T.
Bioorg. Med. Chem. Lett. 2005, 15, 5207.
16. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J. Mol. Biol. 1997, 267,
727.
17. Jones, G.; Willett, P.; Glen, R. C. J. Mol. Biol. 1995, 245, 43.
18.
A
stirred suspension of 5-bromo-1H-pyrrolo[2,3-b]pyridine (150 mg,
0.76 mmoles),
2-(Dicyclohexylphosphino)-20,40,60-tri-i-propyl-1,10-biphenyl
(109 mg, 0.23 mmoles), Tris(dibenzylideneacetone)dipalladium (0) (70 mg,
0.08 mmoles), Sodium carbonate (121 mg, 1.14 mmoles), and 3-(2-
carboxyvinyl)benzeneboronic acid (219 mg, 1.14 mmoles) in acetonitrile
(4 mL) and water (1 mL). This was placed under an atmosphere of nitrogen
and warmed to 90 °C for about 90 min. Aqueous workup was performed using
methylene chloride. The organic phases were combined, washed with brine,
dried over sodium sulfate, and concentrated in vacuo. Reverse-phase
21. L’Heureux, A.; Thibault, C.; Ruel, R. Tetrahedron Lett. 2004, 45, 2317.
22. Miyaura, N.; Yamada, K.; Suzuki, A. Tetrahedron Lett. 1979, 20, 3437.
23. Clinical and Laboratory Standards Institute Methods for Dilution Antimicrobial
Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard, 9th
Ed. M07–A8; Clinical and Laboratory Standards Institute: Wayne, PA., 2009.
24. Fukuda, H.; Hiramatsu, K. Antimicrob. Agents Chemother. 1999, 43, 410.