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M. Kozíšek et al. / Bioorg. Med. Chem. Lett. xxx (2016) xxx–xxx
2
Table 1
O
Structure–activity relationship of the pyridine-4-yl derivatives
COOEt
R2
HN
N
HN
N
NH
N
N
N
R1
N
N
N
N
Figure 1. 4-Aminophenylquinazoline derivatives that bind to the C-terminal
Compound
R2
IC50
28
(lM)
domain of the HIV-1 capsid protein.7
11*
3
COOEt
COOEt
O
Cl
12*
>100
(i)
(ii)
NH2.HCl
NH
N
R1
N
HN
R1
N
13*
14*
>100
>100
C(=O)NH(CH2)2F
Ac
Y
Y
Y
X
X
X
1
3-6
7-10
: X=CH, Y=N
2: X=N, Y=CH
F
R2
15*
81
36
8
NH
COOH
F
HN
N
(iii-iv)
(vi,iv)
(v)
N
16**
17**
18**
3
COOEt
N
R1
N
R1
Y
X
>100
C(=O)NH(CH2)2F
Ac
Y
11-21
: X=CH, Y=N
22-45: X=N, Y=CH
X
54
5
Scheme 1. Synthesis of pyrimidines 11–45. R1 = H, CH3. The following reagents and
conditions were used: (i) ethyl formylacetate sodium salt, ethanol, reflux or methyl
acetoacetate, NaHCO3, ethanol, reflux; (ii) neat POCl3, 100 °C; (iii) aniline, HCl,
dioxane, reflux or HCl, ethanol, water, reflux; (iv) HCl in dioxane; (v) aminobenzoic
acid, HCl, ethanol, water, reflux; (vi) amine, TBTU, Et3N, DMF.
Ac
F
19**
20**
21**
>100
>100
C(=O)NH(CH2)2F
F
Ac
utilizes an amplified luminescent proximity assay system
(AlphaScreen). Briefly, interaction of CAI linked to donor beads
with CA CTD on acceptor beads results in a strong luminescent sig-
nal originating from energy transfer from excited donor to acceptor
beads. The presence of an effective assembly inhibitor causes the
beads to separate, resulting in decreased luminescence.
We previously identified a set of unique capsid assembly inhibi-
tors binding to CA CTD from a high throughput screen.7 Because
the inhibitors compete with CAI, we proposed that they bind into
a conserved hydrophobic groove in CA CTD.20 We further opti-
mized the identified hits to improve the inhibitory activity, result-
ing in the compounds shown in Figure 1. These compounds exhibit
moderate affinity to the binding site in vitro, as determined by
AlphaScreen assay and ITC.7
To improve the pharmacokinetics and binding of those quinazo-
line compounds, we searched for derivatives with superior solubil-
ity. From previous work,7 it was obvious that the 4-N-phenyl and
2-pyridinyl moieties are crucial for binding. Therefore, we decided
to replace the parent quinazoline scaffold with a smaller, and less
hydrophobic, heterocyclic pyrimidine.
Here, we report evaluation of two series of N-4-phenyl-2-
pyridinylpyrimidines that are substituted at the N-phenyl moiety.
Pyridine-4-ylpyrimidines (compounds 11–21) and pyridine-3-
ylpyrimidines (compounds 22–45), shown in Scheme 1, are
bioisosteres that act as new classes of capsid assembly inhibitors
binding to CA CTD.
83
7
The IC50 value was determined as the compound concentration sufficient for
decreasing the AlphaScreen signal by 50%. For experimental details, see Supple-
mentary materials.
2,4-Disubstituted pyrimidine derivative (R1 = H).
2,4,6-Trisubstituted pyrimidine derivative (R1 = Me).
*
**
The compounds reported here were synthesized according to
the general route outlined in Scheme 1. The commercially available
3-/4-cyanopyridines were first converted to corresponding amidi-
nes 1 and 2 by treatment with sodium methoxide and later with
ammonium chloride.21 The resulting amidines were either com-
bined with the sodium salt of ethyl formylacetate, which was pre-
pared by aldol condensation of ethyl acetate with ethyl formate, or
with methyl acetoacetate to yield pyrimidinones 3–6.21,22
Subsequent treatment23 with phosphorus oxychloride yielded
4-chloropyrimidines 7–10, which were subjected to nucleophilic
displacement of the chlorine atom by variously substituted ani-
lines.7,24 To prepare the carboxamide series (13, 17, 20, 28–31,
39–44), a different synthetic approach was used. An appropriate
chloropyrimidine was first treated with aminobenzoic acid, and
when TLC indicated its disappearance, the entire reaction mixture
was evaporated to dryness and subjected to standard amidation
using TBTU as a coupling agent. We found that this stepwise
approach was superior to the nucleophilic aromatic substitution
carried out with corresponding N-alkyl aminobenzamides in terms
of yield and versatility. Finally, all prepared compounds were con-
verted into the corresponding hydrochloride salts.
We explored the structure–activity relationship (SAR) of these
compounds with regard to substitution of the N-phenyl moieties.
From previous work,7 we concluded that the attachment of
electron-withdrawing groups lead to the decrease of in vitro IC50
values determined by AlphaScreen assay. In particular, carbonyl
and carboxyl functionalities were superior to sulfonamides and
carboxamides, except for N-2-fluoroethylcarboxamide.
We started with preparation of pyridine-4-ylpyrimidines,
which are congeners of the compounds shown in Figure 1. The first
round of SAR studies revealed that ablation of the annulated ben-
zene ring from the parent quinazoline led to a significant decrease
ˇ