K. E. Murphy-Benenato et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
3
As can be seen in Table 2, compound 4a indicates substitution
at R1 is required for activity. As the size increased (4b, 4c) so did
the activity, with compound 4c showing moderate cellular activity
and excellent solubility. Cyclic derivatives 4d–4g show comparable
biochemical activity to 4c. Extending the alkyl substituent, as in 4h
and 4i caused a marked decrease in biochemical activity. Aryl
derivatives 4j and 4k were also less potent in biochemical assays
when compared to the alkyl derivatives. As seen with other
series,15 tert-butyl derivative 4l demonstrated the best biochemical
and cellular activity as compared to the other substituents. How-
ever, when comparing the matched pair to 4l, compound 2, there
is an overall loss in all biochemical activity with the pyridopyrim-
idine core in contrast to the napthyridine.
Based on this data, we planned to move forward to explore the
R2 position with a tert-butyl group at R1. We chose a substrate with
a chloro substituent at the R2 position to enable access to a diverse
set of compounds. Condensation of diethyl malonate and amidine
10 (Scheme 3), followed by Vilsmeier reaction, provided
dichloroaldehyde 13. Oxime formation, elimination to the nitrile,
followed by mono displacement with ammonia, provided aminon-
itrile 14. Due to concern about the stability of chloride 14 to the
basic cyclization conditions, we performed a Stille cross-coupling
at this point to provide 15. Direct cyclization with malononitrile,
analogous to the previous highlighted routes, did not afford any
desired product so a two-step conversion was explored. However,
after formation of amide 16, no cyclization conditions could be
found to form the desired product (see Scheme 4).
With the inability of the chloride to survive the cyclization con-
ditions and our inability to cyclize with the R2 substituent in place,
we required a more inert cross-coupling partner. Thioethers offer a
similar reactivity profile in cross-coupling reactions as aryl chlo-
rides and should be more chemically stable.16,17 Recent reports
have demonstrated that thioethers undergo efficient transition
metal catalyzed cross-coupling reactions with a variety of nucle-
ophiles. Therefore, we sought an efficient synthesis of a thioether
cross coupling partner. Beginning with dinitrile 17, cyclization pro-
vided thiomethyl substituted pyrimidine 18. Alkylation with
cyanoacetate, followed by cyclization afforded 19. Chlorination
and two-step introduction of the amine provided the key substrate
for diversification, 21. The antibacterial activity of compound 21
(Table 3) was improved as compared to the unsubstituted deriva-
tive 4l. The biochemical and cellular activity was comparable to the
original naphthyridine 2, indicating substitution at this position is
favorable.
Intermediate 21 enables the exploration of
a variety of
cross-coupling reactions to access C-linked derivatives. Initial
Table 2
SAR of R1 substituted pyridopyrimidines
H2N
NC
N
N
R1
N
NH2
#
R1
Ligase IC50
(l
M)a
MIC (
lM)
Soln (
lM)
AZ logD
Spn
Sau
Hin
Spn ARC 548
Sau ARC 516
Hin ARC 158
4a
4b
4c
4d
4e
4f
4g
4h
4i
H
Me
iso-Pr
Cyclopropyl
Cyclobutyl
Cyclopentyl
Cyclohexyl
CH2-cyclohexyl
iso-Bu
44
13
1.5
>200
>10
>10
>10
13
>10
>10
>10
>10
>10
>10
>200
NT
NT
25
100
50
50
200
NT
NT
>200
NT
NT
NT
NT
NT
25
6
783
>1000
23
217
89
81
8
268
NT
13
0.1
0.3
1.3
1
1.5
2
2.5
2.9
1.7
2.1
1.7
1.9
>10
0.34
0.53
0.46
0.52
0.59
5
0.41
0.67
0.69
0.47
0.81
3.7
>200
200
200
200
>200
NT
NT
>200
NT
200
>200
200
>200
NT
NT
>200
NT
1.8
1.1
4j
4k
4l
Ph
Bn
tert-Butyl
0.72
>10
0.12
0.97
>10
0.22
12.5
25
200
37.2
a
Spn = Streptococcus pneumoniae, Sau = Staphylococcus aureus, Hin = Haemophilus influenzae, NT = not tested. Pathogens; Streptococcus pneumoniae ARC548, Staphylococcus
aureus ARC516 (CLSI QC MRSA reference strain), Haemophilus influenzae ARM158 (acrB gene deletion based on ARC446). Soln is aqueous solubility measured at pH 7.4 from
dried DMSO stock as determined in a 0.1 M phosphate buffer at 20 °C after 18 h.
H2N
NC
N
Cl
N
O
O
a, b
c, d, e
O
N
N
EtO
OEt
Cl
Cl
12
14
13
H
N
H2N
NC
N
N
NC
g
f
N
S
O
N
S
NC
N
N
16
15
Scheme 3. Attempts at synthesis of R2 substituted analogues. Reagents and conditions: (a) 10, Na, EtOH, 90 °C, 79%; (b) POCl3, DMF, 110 °C, 12 h, 48%; (c) HONH2ÁHCl, H2O,
AcOH, 30 min, 64%; (d) SOCl2, 3 h, 97%; (e) NH3, EtOH, 75 °C, 30 min, 31%; (f) 2-tributylstannylthiazole, Pd(PPh3)2Cl2, Ag2O, DMF, 100 °C, 24 h, 53%; (g) 2-cyanoacetic acid,
Ac2O, 80 °C, 30 min, 39%.