Discovery and hit-to-lead optimization of pyrrolopyrimidines as potent, state-dependent Nav1.7 antagonists

Article abstract of DOI:10.1016/j.bmcl.2012.01.015

Herein we describe the discovery, optimization, and structure-activity relationships of novel potent pyrrolopyrimidine Na_v1.7 antagonists. Hit-to-lead SAR studies of the pyrrolopyrimidine core, head, and tail groups of the molecule led to the identification of pyrrolopyrimidine 48 as exceptionally potent Na_v1.7 blocker with good selectivity over hERG and improved microsomal stability relative to our hit molecule and pyrazolopyrimidine 8 as a promising starting point for future optimization efforts.

Full text of DOI:10.1016/j.bmcl.2012.01.015

Bioorganic & Medicinal Chemistry Letters 22 (2012) 2052–2062
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery and hit-to-lead optimization of pyrrolopyrimidines as potent,
state-dependent Nav1.7 antagonists
Nagasree Chakka a, , Howie Bregman a, Bingfan Du a, Hanh Nho Nguyen a, John L. Buchanan a, Elma Feric b,
⇑
Joseph Ligutti c, Dong Liu c, Jeff S. McDermott b, Anruo Zou c, Stefan I. McDonough b, Erin F. DiMauro a
a Department of Chemistry Research and Discovery, Amgen Inc., 360 Binney St., Cambridge, MA 02142, USA
b Neuroscience, Amgen Inc., 360 Binney St., Cambridge, MA 02142, USA
c Department of Neuroscience, Amgen Inc., 360 Binney St., Cambridge, MA 02142, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Herein we describe the discovery, optimization, and structure–activity relationships of novel potent pyr-
rolopyrimidine Nav1.7 antagonists. Hit-to-lead SAR studies of the pyrrolopyrimidine core, head, and tail
groups of the molecule led to the identification of pyrrolopyrimidine 48 as exceptionally potent Nav1.7
blocker with good selectivity over hERG and improved microsomal stability relative to our hit molecule
and pyrazolopyrimidine 8 as a promising starting point for future optimization efforts.
Published by Elsevier Ltd.
Received 16 November 2011
Revised 3 January 2012
Accepted 9 January 2012
Available online 18 January 2012
Keywords:
Nav1.7
Voltage-gated sodium channels
Nav channels
Sodium channel blockers
Sodium channel inhibitors
Sodium channel antagonists
Congenital indifference to pain
Paroxysmal extreme pain disorder
Primary erythromelalgia
Pyrrolopyrimidine
The treatment of chronic pain represents a major unmet medi-
cal need. Current pain treatments suffer from poor efficacy and
dose limiting toxicity. Recent human genetic evidence implicates
the voltage-gated sodium ion channel Nav1.7 (encoded by the
SCN9A gene) as a major regulator of human pain.1 Gain of function
mutations of Nav1.7 cause primary erythromelalgia and paroxys-
mal extreme pain disorder, both characterized by spontaneous
chronic pain.2 In contrast, loss of function mutations in Nav1.7 re-
sult in congenital indifference to pain, characterized by complete
insensitivity to pain.2 Existing sodium channel blockers used clin-
ically are neither very potent, nor selective among the nine mem-
bers of the sodium channel family. Accordingly, Nav1.7 channel is
an attractive target for the development of new and effective pain
therapeutics.3 Herein we describe the discovery and structure–
activity relationships (SAR) around a potent state-dependent pyr-
rolopyrimidine scaffold that could contribute to the development
of Nav1.7 inhibitors.
proportion in the hyperexcitable neurons driving chronic pain,
therefore inhibition of inactivated channels should selectively tar-
get sites of aberrant signaling. Pyrrolopyrimidine 13 (Fig. 1) was
identified as a highly potent and state-dependent inhibitor of
hNav1.7 from an electrophysiology-based screening campaign
[IC50 = 0.06 lM (20% inactivated) and 6.4 lM (non-inactivated)
on Nav1.7 channels]. In addition, hit molecule (1) possessed a novel
structure relative to other published Nav inhibitors, had reasonable
physiochemical properties [MW = 434, LogD (pH 7.4) = 4.35,
LipE = 2.65] and a modular structure amenable for rapid SAR explo-
ration at each portion of the molecule. Unfortunately, compound 1
suffered from poor intrinsic stability in liver microsomes (HLM/
RLM intrinsic clearance (lL/min/mg): >399/>399) and though
modestly selective versus hERG (20Â) lacked selectivity over car-
diac hNav1.5 channels. Thus, we initiated a medicinal chemistry ef-
fort towards generating a compound with improved metabolic
stability and selectivity over hERG and hNav1.54 by modulating
LipE (PX IC50-cLogP).
Our initial efforts were focused on modifying or replacing the
pyrrolopyrimidine core (Table 1) with an emphasis on blocking
or removing potential metabolic soft spots and lowering LogD
(pH 7.4) in an attempt to decrease intrinsic clearance and improve
selectivity over hERG. Compounds in which the 2-methyl
It is presumed that sodium channels exist predominantly in
three conformational states: resting, open and inactivated. The
inactivated states of sodium channels are likely to exist in greater
⇑
Corresponding author. Tel.: +1 617 444 5358; fax: +1 617 621 3908.
E-mail addresses: nchakka@amgen.com, nagasree_c@hotmail.com (N. Chakka).
0960-894X/$ - see front matter Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2012.01.015

N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
2053
N
O
N
N
N
N
S
hNav1.7 PX IC50 (µM)
0.15a
0.06 [6.4]a
0.3b
hNav1.7 Manual IC50 (µM)
Binding efficiency (kcal/NHA)
hNav1.5 PX IC50 (µM)
0.12a
hERG dofetilide binding Ki derived (µM) / PX IC50 (µM)
HLM / RLM CLint (µL/min/mg)
2.5 / 0.51
>399 / >399
177 / 65 / >200
4.35 / 56 / 2.65
Symyx solubility - SIF, PBS, 0.01 N HCl (µg/mL)
logD (pH = 7.4) / PSA / LipE
a
Electrophysiology IC50 of partially inactivated channels is shown. Where applicable, bracket indicates IC50 against fully noninactivated channels
determined with manual electrophysiology. Inhibitory activity represents an average of at least two determinations. bBinding efficiency = RT[-
log(hNav1.7 PX IC50)]*(1x10-6)/(number of heavy atoms). LipE = PX IC50-cLogP.
Figure 1. Data for pyrrolopyrimidine hit (1).
substituent was removed (2), and 3-methyl replaced with halogen
(3) or (4) demonstrated a slight increase in potency but no
improvement in intrinsic clearance or hERG selectivity. Deletion
of both methyl groups (5) resulted in retained potency (Nav1.7
role –N– and the head group (R1) (Table 3). More drastic changes,
for example, deleting the methylene (17), homologating (18), or
saturating the phenyl ring [cyclohexyl analog (19)] resulted in
large reductions in potency. Based on this evaluation, further ana-
loging in this space focused on the effect of substitution on the
benzyl head group. In general, compounds resulting from ortho-
substitution provided improved potency regardless of the substitu-
ent. For example, ortho-fluoro analog (20) displayed exceptional
potency of 20 nM on hNav1.7, with retained microsomal stability
and high selectivity over hERG (76Â). Introduction of an ortho-
chloro substituent (23) provided a sixfold improvement in potency
but reduced microsomal stability. Introduction of small and large
hydrophobic groups [Me (26) and CF3 (29)] offered improved po-
tency (6Â and 3Â, respectively), but reduced microsomal stability.
Compounds resulting from meta-substitution [F (21), Cl (24), Me
(27), CF3 (30)] showed improved potency relative to (5), but less
than the ortho-substituted analogs, and afforded no advantage in
terms of microsomal stability or hERG selectivity. All compounds
prepared with para-substitution [F (22), Cl (25), Me (28) or CF3
(31)] suffered 10Â loss in potency. Substitution with polar groups
such as pyridine or thiazole resulted in complete loss in potency
(data not shown). Evaluation of disubstituted analogs (32–35)
showed no major gains.
IC50 = 0.26
lM), with decreased LogD (pH 7.4) (3.35 vs 4.35) and
improved microsomal stability (130
l
L/min/mg), and selectivity
over hERG (>10Â). Substitution of the 6-position of the pyrrolopyr-
imidine core, with a methyl (6) or trifluoromethyl (7) provided no
improvements in potency or microsomal stability. Introduction of
another nitrogen into the pyrrole ring [pyrazolopyrimidine (8)
and imidazopyrimidine (9)] further decreased LogD and accord-
ingly afforded improved microsomal stability (76 and 60
mg, respectively), but at the expense of potency (0.83 and
7.2 M, respectively). Partial saturation of the core and concomi-
lL/min/
l
tant introduction of gem-dimethyl at the 3-position (10) or further
oxidation of the 2-position (11) afforded no improvement in po-
tency or microsomal stability. SAR studies led to the identification
of (5), which had decreased LogD, retained potency and improved
microsomal stability and selectivity over hERG (hERG PX
IC50 = 0.76 lM, LipE = 3.77, BE = 0.31) relative to 1. Substitution
or modification of the core did not yield any further improvement.
Hence, this core was locked for SAR explorations on the remainder
of the molecule.
Based on the Met ID studies of a similar analog (not reported
here), we directed our efforts towards improving metabolic stabil-
ity by replacing the piperidine ring (Table 2). Contracting the
piperidine ring to pyrrolidine (12) or azetidine (13) or planarizing
the ring to a phenyl (14) resulted in a drastic decrease in potency.
Changing the linker on the 4-position of the piperidine from oxy-
gen to –NH– (15) or –NMe– (16) provided improved microsomal
stability, but these modifications were accompanied by a large
drop in potency. Overall, attempts to replace the alkoxy piperidine
ether resulted in a drastic decrease in potency and therefore the
alkoxy piperidine ether was retained as the optimal linker for fur-
ther SAR.
Concurrent with our head group SAR evaluation replacement or
substitution of the tail group thiazole was investigated (R2, Table 4)
towards improving potency, metabolic stability and/or selectivity
over hERG.
Complete removal of the tail group methylene thiazole (36) re-
sulted in a substantial drop in potency, as did replacement with a
phenyl group (37). Replacement with a benzyl group (38) resulted
in fourfold drop in potency and loss in selectivity over hERG. Intro-
duction of a carbonyl at the methylene junction resulted in amide
(39) which suffered a complete loss of potency.
Replacement of thiazole with alternative five-membered het-
erocyclic rings that afforded lower LogD such as oxazole (40),
imidazole (41), pyrazole (42), its isomer (43), 1-methyl pyrazole
(44), and methyl imidazole (45) and thiazole isomer (47) resulted
in decreased intrinsic clearance and in some cases generally led to
We then separately, but simultaneously, embarked on head
group (R1, Table 3) and tail group (R2, Table 4) SAR evaluations.
We studied the effect of methylene spacer length between the pyr-

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N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
Table 1
SAR: core substitution and modification
CORE
O
N
N
S
hERG Ki
hNav1.7 PX hNav1.5 PX
HLM CLint
LogD
CORE
N
Entry
derived (µM) or
% inh (30 µM)
IC50 (µM)
IC50 (µM)
0.12
(µL/min/mg)
(pH =7.4)
N
1
0.15
>399
>399
2.5
4.35
3.89
N
N
N
N
N
2
3
0.05
0.06
0.05
0.03
1.4
N
236
2.5
1.5
3.49
4.03
N
F
N
N
4
5
6
0.04
0.26
0.31
0.08
0.20
0.35
>399
130
N
Cl
N
N
41%
(PX = 0.76 µM)
3.77
4.15
N
N
N
332
36%
0.99
N
F3C
N
N
N
7
2.29
1.57
>399
5.10
N
N
N
8
9
0.83
7.2
0.93
--
76
60
51%
--
2.18
2.28
N
N
N
N
N
N
N
10
11
0.14
0.10
0.25
0.13
>399
>399
23%
28%
3.94
2.39
N
N
N
O
N

N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
2055
Table 2
SAR: linker group modifications
N
N
N
N
S
HLM CLint
hNav1.7 PX IC50 (µM) or
hNav1.7 % inh (10 µM)
Entry
Linker
(µL/min/mg)
O
O
O
O
5
0.26
6.6
130
125
52
N
N
12
13
>30
N
14
15
16
3.6%
3.51
61
<14
77
NH
N
N
N
7.0%
a significant drop in potency. Introducing a methyl group on
thiazole (46) resulted in decreased microsomal stability.
From the SAR that we have evaluated we can conclude that
methylene-2-pyridyl moiety (48) was the optimal tail group in
terms of Nav 1.7 inhibitory activity, binding efficiency (0.32), met-
abolic stability and selectivity over hERG.
In an attempt to realize a cumulative effect, we combined our
optimal head groups and tail group into our next series of ana-
logs (Table 5). Accordingly, ortho fluoro analog (59) and ortho,
meta-disubstituted derivatives (60–62) were prepared, demon-
strating modestly improved potencies but comparable or de-
creased stability in HLM and reduced selectivity over hERG
relative to lead 48.
The syntheses of target molecules 2, 5–8, 18–35 was accom-
plished as outlined in Scheme 1. The general procedure involved
alkylation of the pyrrole nitrogen of 4-chloro-pyrrolopyrimidine
(63) with a suitably substituted R1CH2X to obtain 64.5 Subsequent
nucleophilic aromatic substitution (SNAr) reaction6 with alcohol
65, which was obtained by reductive amination7 of thiazole-4-
carbaldehyde with piperidin-4-ol, afforded desired compounds 2,
5–8, 18–35.
Replacement of the thiazole with a six membered heterocycle
led to the discovery of 2-pyridyl analog (48), with similar potency
and moderate intrinsic clearance with good selectivity over hERG
(>100Â). The 3-substituted pyridyl (49) and 4-substituted pyridyl
(50) analogs were much less potent.
Once the 2-pyridyl group was identified as a good replacement
of the thiazole moiety, further optimization of (48) was conducted.
Initial efforts were geared towards gauging the influence of intro-
ducing small substituents around the pyridine ring. Accordingly,
methyl substitution at the 2-, 3-, 4- or 5-positions (51–54) main-
tained potency, but with a significant increase in intrinsic clear-
ance. The 2-fluoro substituted 2-pyridyl analog (55) displayed a
10-fold loss in potency and reduction in microsomal stability while
3-fluoro substituted analog (56) had similar potency and micro-
somal stability as compared to the lead (48) but suffered a reduc-
tion in hERG selectivity. The 5-fluoro substituted analog (57)
showed about a fivefold loss in potency and significant loss in
microsomal stability. Replacing the pyridine with other heterocy-
cles such as pyrazine (58), to decrease LogD, resulted in a signifi-
cant drop in potency and an increase in intrinsic clearance.
The synthesis of pyrrolopyrimidines 9, 38, 40–58 was accom-
plished in three steps starting from compound 66 (a or b). Substi-
tution of the chloride was performed with tert-butyl 4-

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N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
Table 3
SAR: head group substitution
R1
N
N
O
N
N
N
S
Entry No. R1
hNav1.7 PX IC50
(l
M) hNav1.5 PX IC50
(l
M) HLM CLint
(l
L/min/mg) hERG Ki derived (
lM) or % inh (30
l
M) LogD (pH 7.4)
5
17
18
19
0.26
>30
0.2
—
130
71
41%
—
3.44
3.30
3.87
4.32
25.2
3.26
—
>399
306
—
—
—
F
20
0.02
0.02
188
1.5
3.49
F
21
0.12
7.62
0.05
—
89
1.1
—
3.49
3.49
4.03
22
—
143
280
F
Cl
23
0.11
32%
Cl
24
0.07
0.3
304
1.2
4.03
25
26
3.81
0.04
—
204
264
—
4.03
3.90
Cl
0.14
3.2
27
28
0.07
2.9
0.06
2.2
237
156
0.93
2.75
3.90
3.90
F3C
29
0.08
0.12
249
2.46
4.01
CF3
30
31
32
0.13
3.49
0.02
0.19
—
246
178
197
0.6
—
4.01
4.01
3.45
CF3
F
F
0.07
2.3
F
Cl
33
34
0.02
0.03
0.05
0.04
277
179
0.95
0.3
4.19
4.08
F
F
CF3
35
0.16
0.04
192
2.3
3.58
F

N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
2057
hydroxypiperidine-1-carboxylate using potassium tert-butoxide as
a base to obtain 67 (a or b).6 Subsequent tert-butyloxy-carbonyl
(Boc) cleavage under standard conditions (TFA, DCM) provided
amine 68 (a or b) as its TFA salt. In the final step, reductive amina-
tion with the appropriate aldehyde in the presence of sodium cya-
noborohydride afforded desired compounds 9, 38, 40–58. The
coupling of 68a with thiazole-4-carboxylic acid in presence of
HATU provided compound 39 and reaction of 68a with bromoben-
zene in presence of a base (potassium tert-butoxide) provided
compound 37.
Table 4
SAR: tail group modification
N
N
N
O
N
R2
hERG Ki
hNav1.7 PX IC50
(µM) or hNav1.7 %
inh (10 µM)
hNav1.5
PX IC50
(µM)
Entry
No
HLM CLint
LogD
R2
derived (µM) or
% inh (30 µM)
(µL/min/mg)
(pH =7.4)
5
0.26
0.2
--
130
<14
41%
--
3.44
1.24
N
S
36
H
8.4%
37
38
1.5%
1.1
--
102
177
--
5.31
4.96
0.74
1.2
O
N
39
40
2.6%
4.7
--
--
61
57
--
--
3.07
3.10
S
O
N
41
2.7
2.7
23
36%
2.35
N
HN
42
43
1.4
14
0.58
--
61
33
45%
--
3.02
3.16
NH
N
N
N
H
44
45
1.7
4.6
0.44
--
65
46%
--
3.01
2.93
N
N
N
184
N
(continued on next page)

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N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
Table 4. (continued)
hERG Ki
hNav1.7 PX IC50
(µM) or hNav1.7 %
inh (10 µM)
hNav1.5
PX IC50
(µM)
Entry
No
HLM CLint
LogD
R2
derived (µM) or
% inh (30 µM)
(µL/min/mg)
(pH =7.4)
46
47
48
0.27
6.5
0.08
--
294
62
32%
--
4.10
4.81
3.70
N
S
S
N
N
2
0.11
0.16
130
37%
5
3
4
49
50
51
52
9.7
9.6
--
121
152
--
--
3.67
3.69
4.08
4.15
N
--
N
N
0.33
0.30
0.09
0.06
>399
306
2.4
0.98
N
N
N
53
0.95
0.04
>399
2.2
4.15
54
55
0.19
1.13
0.15
0.55
399
227
0.73
2.9
4.15
3.83
N
F
N
56
0.18
0.11
156
1.1
3.76
F
N
N
57
58
0.51
5.15
0.09
--
355
115
44%
--
3.77
2.71
F
N
The synthesis of pyrrolopyrimidines 3 and 4 was accomplished
in three steps (Scheme 2). Halogenation of 4-chloro-pyrrolopyrim-
idine (63) afforded 3-fluoro8 or 3-chloro9 analog 69 (a or b) in the
presence of selectfluor or N-chloro-succinimide (NCS), respec-
tively. Subsequent alkylation5 of the pyrrole nitrogen and SNAr
reaction6 with the alkoxide of 65 provided compounds 3 and 4.
Compound 17 was prepared by coupling of pyrrole nitrogen 63
with phenyl boronic acid in presence of copper acetate followed
by SNAr reaction6 with 66a.
of thiazole-4-carbaldehyde with cyclic amino alcohol 71 (a or b)
gave compound 72 (a or b), followed by SNAr reaction6 with 66a
afforded desired compounds 12 and 13.
The synthesis of target molecules 10 and 11 was accomplished
as outlined in Scheme 4. Oxidation of 66a in the presence of oxone
gave compound 73 which was bis-alkylated using methyl iodide to
provide 74. Subsequent SNAr reaction6 of 74 with tert-butyl 4-
hydroxypiperidine-1-carboxylate under basic conditions followed
by Boc cleavage and reductive amination with thiazole-4-carbalde-
hyde afforded compound 10. The lactam moiety of 10 was reduced
to alcohol 75 in the presence of lithium aluminum hydride. Com-
The synthesis of pyrrolopyrimidines 12 and 13 was accom-
plished in two steps as described in scheme 3. Reductive amination

N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
2059
Table 5
SAR: optimal tail and head group combinations
R1
N
N
O
N
N
N
Entry No.
R1
hNav1.7 PX IC50
0.11
(
lM)
hNav1.5 PX IC50
0.16
(
lM)
HLM CLint
130
(l
L/min/mg)
hERG Ki derived (
lM) or % inh (30
l
M)
LogD (pH 7.4)
48
37%
3.70
3.75
F
F
F
F
59
60
61
62
0.04
0.04
0.03
0.06
0.03
0.02
0.08
0.19
145
209
248
153
1.8
F
1.0
3.71
4.46
4.35
Cl
0.68
0.32
CF3
R1
2, Z = C-H, Y = C-CH3, R3 = H
5, Z = Y = C-H, R3 = H
R3
N
N
Y
Z
N
OH
N
R1
6, Z = Y = C-H, R3 = CH3
7, Z = Y = C-H, R3 = CF3
8, Z = N, Y = C-H, R3 = H
18-35, Z = Y = C-H, R3 = H
H
R3
N
N
S
O
R3
N
N
N
Z
Y
65
Z
a
N
N
N
N
b
Y
Cl
63
Cl
64
S
Z = C-H
R
a
3 = H
N
N
N
N
O
N
Y
N
N
N
Y
9, Y = N
e
N
N
N
c
N
d
Y
Y
38, 40-58, Y = C-H
O
Cl
O
66a Y = C-H
66b Y = N
BocN
N
TFA
f
HN
67a Y = C-H
67b Y = N
68a Y = C-H
68b Y = N
R2
g
39, Y = C-H
37, Y = C-H
Scheme 1. Reagents and conditions: (a) R1CH2X, K2CO3, ACN, rt, 2–18 h (23–99%); (b) NaH, DMSO, 0 °C to rt, 16 h (10–41%); (c) tert-butyl 4-hydroxypiperidine-1-carboxylate,
KOtBu, ACN, rt, 2 h (56%); (d) TFA, DCM, rt, 2 h (Y = C–H, N, 99%); (e) R2CHO, NaBH3(CN) (35–60%); (f) thiazole-4-carboxylic acid, HATU, diea, DMF, rt, 20 h (48%); (g)
bromobenzene, KOtBu, toluene, 135 °C, 4 days (7%).
pound 11 was then obtained by reducing alcohol (75) in presence
of TFA and triethyl silane.
quent SNAr10 reaction with compound 66a provided target
compounds 15 and 16 (scheme 5).
Reductive amination of thiazole-4-carbaldehyde with piperi-
dine 76 followed by Boc cleavage yielded compound 77. Subse-
The Grignard reagent generated from phenyl bromide 78 was
added to thiazole-4-carbaldehyde to provide alcohol 79. Reductive

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N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
H
N
dehydroxylation in the presence of TFA and triethyl silane and sub-
H
N
N
N
sequent demethylation using BBr3 afforded compound (80). Finally
3 or 4
SNAr reaction11 with 66a yielded 14 (scheme 6).
N
N
c, d
a or b
R1
In conclusion, we have described the discovery, synthesis and
hit-to-lead optimization of a novel class of potent pyrrolopyrimi-
dines as Nav1.7 antagonists. Removal of two methyl groups from
the pyrrolopyrimidine core of hit molecule 1 resulted in lead mol-
ecule 5 with reduced LogD, improved microsomal stability and
hERG selectivity. Exceptional Nav1.7 potency was realized by
replacing the benzyl head group of 5 with an ortho fluoro-benzyl
(20) and ortho, meta difluoro-benzyl (32). Replacement of the thi-
azole tail group of 5 with an ortho pyridine (48) afforded a modest
improvement in potency. Combining the optimized head and tail
groups (59–62) yielded slightly improved potency, but reduced
hERG selectivity and provided no improvements in microsomal
stability. Inhibitory potency on hNav1.5 was routinely monitored
for all potent compounds throughout this SAR exploration and gen-
erally tracked with hNav1.7 potency such that no gains in selectiv-
ity over Nav1.5 were realized.
Cl
Cl
63
e
69a R1 = F
69b R1 = Cl
N
N
N
N
f, g
N
O
N
Cl
70
N
N
17
S
Analysis of the visualization of described analogs (Fig. 2) reveals
that the lipophilic compounds [LogD (pH 7.4) >3.5] generally had
good potency (<10 nM) but poor microsomal stability (HLM >150
Scheme 2. Reagents and conditions: (a) selectfluor, AcOH, ACN, 70 °C, 12 h (50%);
(b) NCS, THF, rt, 1 h (79%); (c) benzyl bromide, NaH, DMF, 0 °C to rt, 16 h (R1 = F,
50%, R1 = Cl, 63%); (d) 65, NaH, DMSO, 0 °C to rt, 16 h (R1 = F, 18%, R1 = Cl, 16%); (e)
Cu(OAc)2, pyridine, phenyl boronic acid, DCM, rt, 16 h (13%); (f) 65, KOtBu, ACN, rt,
16 h (13%); (g) 65, KOtBu, ACN, rt, 16 h (43%).
(
l
L/min/mg)). Less lipophilic compounds [LogD (pH 7.4) <3.5] gen-
erally exhibited weak potency (>1 M) and moderate to good
microsomal stability (HLM <150 L/min/mg). In light of these
l
l
trends, the identification of highly potent compounds which were
also highly stable in human liver microsomes was challenging. One
promising lead was pyrazolopyrimidine 8, which had moderate po-
N
O
N
tency (Nav1.7 IC50 = 0.83
(76 L/min/mg).
lM) and good microsomal stability
N
n
l
n
The visualization in Fig. 3 compares LogD (pH 7.4) with Nav1.7
potency with compounds sized by microsomal stability and further
breakdown by lipophilic efficiency (LipE). In addition to the previ-
ously described potency and microsomal stability properties, com-
pound 8 possesses high lipophilic efficiency. As a moderately
potent, lipophilically efficient and intrinsically stable lead with
good selectivity over hERG, pyrazolopyrimidine 8 is a promising
lead for further exploration.
n
N
OH
HN
OH
a
N
N
b
N
71a n = 2
71b n = 1
72a n = 2
72b n = 1
S
12 : n = 2
13 : n = 1
S
Scheme 3. Reagents and conditions: (a) thiazole-4-carbaldehyde, NaBH3(CN), 1,2
dichloroethane (n = 1, 92%; n = 2, 46%); (b) 66a, NaH, DMSO, 0 °C to rt, 16 h (n = 1, 2,
10%).
N
O
N
N
O
N
O
N
N
N
N
N
N
N
N
O
OH
O
O
N
a
N
c,d,e
N
N
g
N
N
N
b
f
Cl
Cl
Cl
66a
73
74
10
75
N
11
N
N
N
N
S
S
S
Scheme 4. Reagents and conditions: (a) oxone, ACN/H2O (1:1), 50 °C, 3 h (56%); (b) NaH, DMSO, MeI, 0 °C to rt, 1 h (68%); (c) tert-butyl 4-hydroxypiperidine-1-carboxylate,
KOtBu, ACN, rt, 2 h (34%); (d) TFA, DCM, rt, 2 h (64%) (e) thiazole-4-carbaldehyde, NaBH3(CN), 1,2 dichloroethane (39%); (f) LAH, THF, 0 °C to rt, 2 h (66%); (g) DCM, TFA,
triethyl silane, 0 °C to rt, 2 h (31%).
N
N
N
N
H
N
Boc
N
R1
R1
R1
a,b
c
N
N
N
N
HN
HCl
15 = R1 = H
16 = R1= Me
76
77
S
S
Scheme 5. Reagents and conditions: (a) thiazole-4-carbaldehyde, NaBH(OAc)3, 1,2 dichloroethane rt, 16 h (R1 = H, 34%; R1 = Me, 42%); (b) dioxane, HCl, rt, 0 °C to rt, 16 h,
(R1 = H, 24%; R1 = Me, 57%); (c) 66a, Cs2CO3, DMF, 0–80 °C, 16 h, (R1 = H, 8%; R1 = Me, 10%).

N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
2061
O
O
OH
N
N
N
a
b,c
d
O
Br
78
S
S
HO
N
N
14
79
80
N
S
Scheme 6. Reagents and conditions: (a) Mg/THF, thiazole-4-carbaldehyde (42%); (b) DCM, TFA, triethyl silane, 0 °C to rt, 2 h (80%); (c) BBr3, DCM (28%); (d) 66a, Cs2CO3, DMF,
0–80 °C, 16 h, (45%).
Figure 2. Visualization of LogD (pH 7.4) versus HLM (lL/min/mg) for described compounds colored by hNav1.7 potency (PX, lM).
Figure 3. Visualization of LogD (pH 7.4) versus potency for described compounds sized by microsomal stability with lines representing lipophilic efficiencies (LipE), colored
by hNav1.7 IC50 (PX, M).
l

2062
N. Chakka et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2052–2062
J.; O’Donnell, D.; Raynoschek, C.; Salter, H.; Rouleau, G. A.; Krupp, J. J. Hum. Mol.
Acknowledgments
Genet. 2007, 16, 2114.
3. Compound 1 was commercially obtained.
The authors would like to thank Grace Bi for purification sup-
port and Dr. Margaret Y. Chu-Moyer for proofreading the
manuscript.
4. Bregman, H.; Berry, L.; Buchanan, J. L.; Chen, A.; Du, B.; Feric, E.; Hierl, M.;
Huang, L.; Immke, D.; Janosky, B.; Johnson, D.; Li, X.; Ligutti, J.; Liu, D.;
Malmberg, A.; Matson, D.; McDermott, J.; Miu, P.; Nguyen, H. N.; Patel, V. F.;
Waldon, D.; Wilenkin, B.; Zheng, X.-M.; Zou, A.; McDonough, S. I.; DiMauro, E. F.
J. Med. Chem. 2011, 54, 4427.
5. Kelley, J. L.; Davis, R. G.; McLean, E. W.; Glen, R. C.; Soroko, F. E.; Cooper, B. R. J.
Med. Chem. 1995, 38, 3884.
6. Ibrahim, P. N.; Spevak, W.; Cho, H.; Shi, S. U.S. Pat. Appl. Publ. 20090286783,
2009.
7. Conditions: Thiazole 4-carboxyaldehyde, piperidine-4-ol, NaBH(OAc)3, acetic
acid, DCE, yield 62%.
8. Eldrup, A. B.; Prhavc, M.; Brooks, J.; Bhat, B.; Prakash, T. P.; Song, Q.; Bera, S.;
Bhat, N.; Dande, P.; Cook, P. D.; Bennett, C. F.; Carroll, S. S.; Ball, R. G.;
Bosserman, M.; Burlein, C.; Colwell, L. F.; Fay, J. F.; Flores, O. A.; Getty, K.;
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Langen, D.; Wolanski, B.; Olsen, D. J. Med. Chem. 2004, 47, 5284.
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Mabon, R.; Gardyan, M.; Hamman, B. D.; Allen, J.; Gopinathan, S.; McKnight, B.;
Crist, M.; Zhang, Y.; Liu, Y.; Courtney, L. F.; Key, B.; Zhou, J.; Patel, N.; Yates, P.
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