range. The AutoDock tool [31–33] was employed to predict the
binding mode of the compound within the PDZ binding site.
Molecular dynamics simulations were performed with the
AMBER package [34] to refine the predicted binding mode. During subsequent SAR studies around FSC231, Bach et al. managed
to slightly improve the K i value by replacing chlorine atom in the
meta position with a trifluoromethyl group [35].
More potent chemical inhibitors targeting the PDZ domain
from PICK1 were recently published [36]. These inhibitors were
able to modulate the amyloid beta-mediated synaptic dysfunction
by interfering with the PICK1-PDZ/GluA2 PPI. Such potent
compounds in the submicromolar range are interesting for the
biological study of memory mechanisms and may be used as potential treatments for neurodegenerative disorders. An integrated
strategy involving high-throughput screening, structure-based
drug design, and biochemical and cellular assays was used to discover potent small molecule PICK1-PDZ inhibitors. This
structure-based strategy relied on determining the protein–ligand
structure using X-ray crystallography, followed by intensive SAR
studies to increase the potency of the series. The X-ray crystallography experiments were more difficult than expected because conventional methods and conditions failed to produce any cocrystal
structures. A new approach called the “lock and chop” method was
developed to tackle this issue [37]. Analysis of the X-ray crystal
structure of the complex (PDB ID: 6AR4) revealed that the chemical compound was located in the expected binding pocket and was
able to tightly interact with a phenylalanine sidechain that was not
targeted by the endogenous peptide. The most potent compound
from the series exhibited an approximately 200-fold better potency
than that from the C-terminal of the GluA2 partner. Selectivities
with respect to other reference PDZ domains were also measured
for this series of compounds. This remarkable integrated study
reported the highest affinity for small molecule inhibitors of the
PDZ domain known to date, with an IC 50 value of 70 nM. The
X-ray crystal structure, deposited in the protein databank (PDB ID:
6AR4), corresponds to a compound from the series with an IC 50
value of 600 nM. Unfortunately, these compounds were unable to
cross the blood brain barrier, preventing any potential use as drug
candidates. However, they can still be used as chemical probes in
biology studies due to their high potency.
NMR spectroscopy-based screening allowed the detection of
weakly binding inhibitors for the PDZ domain from AF6, which is
an essential component of cell junctions [38]. A dissociation constant (K d ) value of 100 μM, which is in the same range as last
residues from the endogenous EphB2 partner, was obtained with
one analog designed around the rhodanine core. More intensive
SAR studies around the same core were published several years later
[39]. The design of new compounds was guided by molecular
282
Laurent Hoffer et al.
binding mode of the compound within the PDZ binding site.
Molecular dynamics simulations were performed with the
AMBER package [34] to refine the predicted binding mode. During subsequent SAR studies around FSC231, Bach et al. managed
to slightly improve the K i value by replacing chlorine atom in the
meta position with a trifluoromethyl group [35].
More potent chemical inhibitors targeting the PDZ domain
from PICK1 were recently published [36]. These inhibitors were
able to modulate the amyloid beta-mediated synaptic dysfunction
by interfering with the PICK1-PDZ/GluA2 PPI. Such potent
compounds in the submicromolar range are interesting for the
biological study of memory mechanisms and may be used as potential treatments for neurodegenerative disorders. An integrated
strategy involving high-throughput screening, structure-based
drug design, and biochemical and cellular assays was used to discover potent small molecule PICK1-PDZ inhibitors. This
structure-based strategy relied on determining the protein–ligand
structure using X-ray crystallography, followed by intensive SAR
studies to increase the potency of the series. The X-ray crystallography experiments were more difficult than expected because conventional methods and conditions failed to produce any cocrystal
structures. A new approach called the “lock and chop” method was
developed to tackle this issue [37]. Analysis of the X-ray crystal
structure of the complex (PDB ID: 6AR4) revealed that the chemical compound was located in the expected binding pocket and was
able to tightly interact with a phenylalanine sidechain that was not
targeted by the endogenous peptide. The most potent compound
from the series exhibited an approximately 200-fold better potency
than that from the C-terminal of the GluA2 partner. Selectivities
with respect to other reference PDZ domains were also measured
for this series of compounds. This remarkable integrated study
reported the highest affinity for small molecule inhibitors of the
PDZ domain known to date, with an IC 50 value of 70 nM. The
X-ray crystal structure, deposited in the protein databank (PDB ID:
6AR4), corresponds to a compound from the series with an IC 50
value of 600 nM. Unfortunately, these compounds were unable to
cross the blood brain barrier, preventing any potential use as drug
candidates. However, they can still be used as chemical probes in
biology studies due to their high potency.
NMR spectroscopy-based screening allowed the detection of
weakly binding inhibitors for the PDZ domain from AF6, which is
an essential component of cell junctions [38]. A dissociation constant (K d ) value of 100 μM, which is in the same range as last
residues from the endogenous EphB2 partner, was obtained with
one analog designed around the rhodanine core. More intensive
SAR studies around the same core were published several years later
[39]. The design of new compounds was guided by molecular
282
Laurent Hoffer et al.