2
D. J. Burdick et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Tos
N
purine
7- azaindole
H
N
5H-pyrrolo[3,2-b]pyrazine (3)
H
N
N
N
H
N
N
N
N
a
b, c
d, e
e
e
e
g
Back
Pocket
g
g
n
HN
n
R1
X
n
i
HN
HN
i
i
N
R1
H
R1
H
N
N
H
Br
N
R2
I
N
N
N
N
4
7 - 21
40, 41
22 - 39
Minimal
pharmacophores
Structural
diversity
NHBn
N
X
Scheme 1. (a) [PdCl2(dppf)]CH2Cl2, aryl-B(OH)2 or pinacol ester, 1 M Na2CO3, CH3-
CN; (b) NIS, acetone; (c) NaH, TosCl, DMF; (d) [PdCl2(dppf)]CH2Cl2, appropriate aryl-
B(OH)2 or pinacol ester, 1 M Na2CO3, CH3CN; (e) 1 M NaOH, MeOH, THF.
Imidazole
region
Figure 2. Proposed core hopping strategy: replacement of the purine with the
minimal pharmacophore 7-azaindole would provide the needed hinge hydrogen
bonding interactions as well as providing new vectors to probe the imidazole region
and the back pocket.
ingly, the imidazole is within hydrogen-bond distance to the side
chains of Asp111 and Lys114, indicative of the potential for engag-
ing additional hydrogen bonds to the protein by linking the frag-
ments (Fig. 1).
We then investigated whether fragment expansion into the imi-
dazole-binding site can enhance the potency. Analysis of crystal
structures (Fig. 1) indicated that although both compounds 1 and
2 form the hydrogen bond interactions with the hinge, the purine
core of compound 1 is more co-planar with the imidazole ring. This
co-planarity may allow substitutions at positions 2 and 6 of the
purine core to reach the imidazole binding site. Compound 2 was
deemed less interesting because it sits well above the plane of
the imidazole ring and it was not obvious how to engage the imi-
dazole binding pocket; thus we focused our attention on 1.
Initial modification of the purine along the accessible vectors at
C2 and C6 did not lead to a significant improvement in potency and
ligand efficiency rapidly decreased (data not shown). It quickly
became clear that an alternate ring system that provided access
to different vectors was needed.
ment hit 1 (Table 1); however, it is approximately twice as ligand
efficient. We determined the crystal structure of 3 bound to ERK2
to confirm the binding mode. As shown in Figure 3, compound 3
engages the hinge through both classical and C–H type hydrogen
bonds with Asp106 and Met108, and again indicated that substitu-
tion at C2 and C7 can potentially generate additional interactions
with Asp111, Lys114 and Gln105. Encouraged by these results,
we tested a small series of commercially available 5H-pyrrolo
[3,2-b]pyrazines in the SPR assay. A bromine at C2 of the 5H-pyr-
rolo[3,2-b]pyrazine core was tolerated (4) while halide substitu-
tion at C7 (5 and 6) improved potency and preserved good ligand
efficiency. These initial results gave us confidence that we could
expand SAR along these vectors and we embarked on a medicinal
chemistry campaign to further improve the 5H-pyrrolo[3,2-b]pyr-
azine series.
Alternative cores were considered that would maintain a two or
three point hinge interactions like the initial fragment 1; reach the
back pocket to form additional hydrogen bond interactions; and
make an additional contact in the imidazole fragment region. An
additional consideration to move away from the heavily explored
purine scaffold, is that purines are the basis of many drug discov-
ery campaigns and finding novel inhibitors may prove to be
difficult.7
After determining the key pharmacophore features and consid-
ering a number of different cores, we proposed changing the purine
core of the screening hit to 5H-pyrrolo[3,2-b]pyrazine (3, Fig. 2).
This core is less represented in the literature relative to the purine.8
Furthermore this scaffold retains the same hydrogen bonding
donor/acceptor pair available for interacting with the hinge of
the protein and it has the proper pKa range at N7 to ensure that
it acts as a hydrogen bond acceptor. In addition, this core has car-
bon atoms at the proper positions to furnish vectors that point
toward the back side of ATP binding pocket as well as the region
where the imidazole was observed in the crystal structure.
The un-substituted 5H-pyrrolo[3,2-b]pyrazine core 3 was eval-
uated by SPR and was found to be slightly less active than the frag-
We then explored different groups at the 2 position of pyrrolo
[3,2-b]pyrazine (Table 2). Addition of a phenyl group (7) increased
the activity by more than 4 fold (Table 2), whereas a bromo group
(4) at this position showed no appreciable change in binding affin-
ity (Table 2).
These results suggested aryl substitutions would be productive
at the C2 position. To further explore the C2 position, we made a
series of analogues substituted with aryl and small heteroaryl rings
to mimic the imidazole that we observed in the initial crystal
structures. Analysis of the aryl analogues tested revealed that meta
substitutions (8 and 9) were not tolerated most likely due to steric
clashes with Glu109 and Asp111. para substitutions (10 and 11)
showed marginal improvement over the phenyl analogue regard-
less of the electronic nature of the functional group. The 4-fluoro
(12) and 4-hydroxy compounds (13) were the most potent of this
set of phenyl analogues, which indicated that a small hydrogen
bond accepting group may be advantageous and would interact
with Lys114. The pyridyl analogues, which contain a hydrogen
bond acceptor in the ring, were also active. The para-pyridyl (14)
and 2-fluoropyridin-4-yl (15) analogues were more active and
had higher ligand efficiencies than the meta analogue (16) possibly
NH2
B.
C.
A. HN
Q105
Q105
N
N
O
E106
2.7
3.0
E106
2.8
3.1
N
L107
L107
M108
NH
N
K54
K54
Cl
M108
3.2
3.2
1
2
Compound SPR KD ( M)
LE
µ
D111
K114
1
2
247
940
0.29
0.38
D111
K114
Figure 1. (A) Structure and activity of two potent and ligand efficient fragments found in both the NMR STD and SPR screens. (B) Crystal structure of N-benzyl-9H-purin-6-
amine (1) (PDB ID: 4QP1) and (C) 5-chlorobenzo[d]oxazol-2-amine (2) (PDB ID: 4QP2) in complex with ERK2. Both fragments form multiple hydrogen bonds (including non-
classical C–H type) with the kinase hinge as shown by green dashed lines (distances are in angstroms). The crystallographic imidazole fragments are colored in magenta.