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Figure 3.
Figure 3. Pyrazole scaffold bound to PDE4B and PDE4D and the
discovery of potent pyrazole inhibitors for PDE4 in three steps.
Superposition of six different pyrazoles (nos. 2, 8, 17, 19,
20 and 21) in seven cocrystal structures with PDE4B and/or PDE4D
revealed the consistent binding mode of the scaffold moiety
(panels a -c). For clarity, only several side chains for one
PDE4B cocrystal structure are shown. The three pockets in the
active site are highlighted on the solvent accessible surface:
the metal binding pocket (M) in blue, purine-selective glutamine
and hydrophobic clamp pocket (Q) in red (which is further
divided into Q[1], Q[2] sub-pockets) and solvent-filled side
pocket (S) in green. The discovery of potent pyrazole inhibitors
for PDE4 in three steps is illustrated in panels d -f. (a) A
view looking down into the active site. The pyrazole carboxylate
scaffold fits into the narrow passage formed by the hydrophobic
clamp. (b) A view looking away from the S pocket. The pyrazole
carboxylate scaffold forms an H-bond with the invariant Q443^4B.
(c) A view looking towards the S pocket. The ethoxy group
occupies the Q[1]-pocket. The scaffold that the six different
pyrazoles share is marked by a dashed oval. (d) Scaffold
discovery. The scaffold candidate,
3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester (pyrazole
no. 2), is a weak PDE4D inhibitor with IC[50] of 82  M.
(e) Scaffold validation. The derivative of the scaffold,
3,5-dimethyl-1-phenyl-1H-pyrazole-4-carboxylic acid ethyl ester
(pyrazole no. 8) has significantly increased potency towards
PDE4D with IC[50] of 0.27 M.
(f) Chemical optimization. The validated scaffold was optimized
into a potent PDE4D inhibitor,
3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid
ethyl ester (pyrazole no. 21), with IC[50] of 0.021 M.
A 4,000-fold increase in potency was achieved in two rounds of
chemical synthesis. Compounds are represented by solid surface
colored by atomic types. The active site is represented by the
blue mesh. The PDE4D is represented by cartoons where helices
are shown as cylinders and loops are shown as tubes.
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