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with functionalized 4-amino-5-formyl-pyrimidine A to give the
desired product D.
An alternate route to compounds bearing a second amide (D3)
is shown in Scheme 3. These were prepared by hydrolysis with
methanolic hydroxide of the corresponding ester (D1) to the acid
D2 followed by amide formation to give D3.
Exploration of modification at C2 was achieved by starting with
the methylsulfanyl substituted analogue D4. These were oxidized
with Oxone to form the sulfonyl derivative D5. Heating D5 with
an appropriate amine provided the desired modification at C2.
The original hit 1 from a focused screen showed modest activity
The geminally disubstituted analog (24) and the 3,4-dihydro-
1H-isoquinoline-2-yl analog (25) were prepared in an effort to
reduce the flexibility of the amino-alkyl chain. This reduced the
potency against DYRK1B considerably. Also, methylation of the ter-
minal amine resulted in lower activity (26).
Table 3 summarized results around the exploration of substitu-
tion on C2 and C4 of the pyrimidine ring. X-ray structure indicated
that substitution at C2 should be pointing out towards solvent, and
thus should be able to accommodate a variety of groups. This was
used in an effort to increase aqueous solubility of this class of com-
pounds.20 All the compounds studied showed very good potency in
the biochemical and cellular assay. Compound 30 showed the best
potency with a cellular activity of SW620 EC50 of 27 nM and
DYRK1B IC50 of 8 nM. The methylation at C4 of the pyrimidine ring
(compound 32) resulted in a significant loss in the enzymatic po-
tency (compared with 16).
in inhibiting DYRK1B with an IC50 of 0.57 lM in the kinase enzy-
matic assay. Through hit-to-lead efforts, we identified the pyr-
ido[2,3-d]pyrimidine series which was further optimized towards
the discovery of potent inhibitors of DYRK1B. Tables 1–3 summa-
rize the preliminary SAR observed for this series.
Changing from the quinolone 1 to the analogous pyrido[2,3-
The DYRK1B program was supported by X-ray crystallography
using DYRK1A, which crystallizes more readily than DYRK1B, and
differs from DYRK1B in the ATP site by only one residue; Met240
is a leucine in 1B, but the side chain does not point towards the
ATP site. The co-crystal structure of DYRK1A with compound 3
(PDB code 4MQ1) bound showed that the pyridone moiety of the
core makes a pair of hydrogen bonds to the hinge of the kinase,
although the geometry of the ligand NH-Leu241 C@O hydrogen
d]pyrimidine
2 improved the potency against DYRK1B to
0.25 M. The replacement of the methyl group in 2 on the benzene
l
ring by different halogens (e.g. 3) suggested that a chlorine was a
good substituent which provided up to 30 fold increase in the cel-
lular potency against the human colon tumor cell line SW 620 with
an EC50 of 3.3 lM. Interestingly, reversing the amide functionality
as in 4 resulted in complete loss of activity. (see discussion of X-ray
crystallographic structure below). The methyl ester moiety of 3 is
unstable metabolically. Converting the ester moiety of 3 to an
amide showed minimal improvement on the DYRK1B potency
(compounds 5 and 6), however, based on the available X-ray crys-
tallographic structure of compound 3 complexed with DYRK1A
(Fig. 1) we were interested in probing more deeply this region of
the protein. (see X-ray structure comment below).
As shown in Table 2, preliminary SAR exploration (7–11) indi-
cated that the 3-chloro-benzyl benzamide moiety showed in-
creased potency relative to 3. Lengthening the carbon chain from
benzyl (9) to phenethyl (10) or introduction of N-methyl group
to the amide nitrogen (11) resulted in lower potency. It was also
observed that the phenyl group of benzyl amide moiety could be
replaced by heteroaryl rings such as 2-thiophenyl and 3-thio-
phenyl groups while maintaining potency (12 and 13). However,
replacing the amide functionality by a tetrazole ring (14) resulted
in a significant loss in potency, demonstrating the importance of
this amide group for efficient binding. Molecular modeling indi-
cated that there could be room to extend off the benzylic position
of 8. Different lengths of amino-alkyl chains (1–4 carbon) were
synthesized and tested (compounds 15–18). It was gratifying to
observe that the first compound (15) with sub-micromolar potency
in the cellular assay was obtained. The amino-alkyl chains contain-
ing one to three carbon atoms showed comparable potency
whereas the four-carbon amino-alkyl chain (18) had a significant
drop in potency. Compound 19 with the phenyl group missing
and saturation of the terminal phenyl ring to a cyclohexyl group
(20) resulted in reduction in potency, pointing to the importance
of the contribution of the aromatic group to binding.
The chiral resolution of racemic [3-(1,3-dioxo-1,3-dihydro-iso-
indol-2-yl)-3-phenyl-propyl]-carbamic acid tert-butyl ester using
super critical fluid chromatography (SFC) provided the intermedi-
ates needed for the synthesis of the two pure enantiomers of 16
by the process of Scheme 3. The R-enantiomer (21, stereo-chemical
assignment was based on observation that only R-enantiomer was
observed in crystal structure, see Fig. 2B) for the 2-carbon chain
was identified as the active compound showing very potent activ-
ity of 9 and 450 nM in the enzymatic and cellular assay respec-
tively. The corresponding S-enantiomer (22) was considerably
less active. Combining the amino ethyl chain at the benzylic posi-
tion and the 3-chloro phenyl group gave a very active compound
(23) in the cellular assay with a value of 240 nM.
Figure 2. (A) Upper, PDB code 4MQ1 X-ray crystallographic structure of compound
3 bound to DYRK1A; (B) Lower, PDB code 4MQ2 X-ray crystallographic structure of
compound 23 (racemic mixture used in crystallization, only R-isomer observed in
crystal) bound to DYRK1A.