modeling using the 3D structure of the PDZ domain of interest.
The new derivatives were again evaluated using an NMR-based
approach. The best compound, a mixture of diastereoisomers,
exhibited a 5 μM affinity for AF6-PDZ. Molecular docking using
the MOE package (http://www.chemcomp.com) was performed
to identify the most likely active stereoisomer from the diastereoisomer mixture.
Dishevelled (Dvl) is an essential protein in the Wnt signaling
pathway that relies on its PDZ domain for transduction of downstream signals [11]. Interestingly, a known sulindac drug was
shown to inhibit the canonical Wnt signaling pathway by binding
to the PDZ domain of Dvl [40]. NMR experiments enabled the
determination of the “sulindac / PDZ domain” complex and concluded that sulindac is located within the peptide binding pocket of
the PDZ domain. Finally, a K i value of 10 μM was measured for
sulindac in a competitive assay with a reference peptide. Additional
chemical compounds, which bind to the Dvl-PDZ domain in the
low micromolar range affinity, were discovered using a protocol
involving both molecular modeling and NMR spectroscopy
[11]. In silico experiments employed a structure-based pharmacophore search using the Unity module from Sybyl [41] to identify
small organic compounds that could mimic the binding mode of
the Dapper protein partner within the PDZ domain. Then, the
FlexX docking tool [42] was used to confirm the ability of selected
compounds to act as potential PDZ domain binders. NMR spectroscopy was used as an experimental method to validate (or not)
the selected compounds. A benzoic acid molecule, which displayed
the most significant chemical shift perturbations, exhibited a 10 μM
K d value. Finally, in vivo studies confirmed its ability to reduce the
growth rate of prostate cancer cell lines. A similar strategy was used
in another study to target the PSD95-PDZ domain [43]. The
binding of the best identified fragment (quinoline-2,7-dicarboxylic
acid) was confirmed using NMR experiments.
Another study focused on the Dvl protein identified small
molecules that perturb the Dvl-PDZ/CXXC5 PPI [44]. Inhibition
of this interaction may have potential interest in bone anabolic
osteoporosis therapy by enhancing osteoblast differentiation
[44]. More than 50 analogs were synthesized to explore the chemical space around the hit while also trying to increase the microsomal
stability and optimize the physicochemical properties. Binding
modes of representative compounds from the series were predicted
using molecular docking with DOCKER from the Discovery Studio package [45]. The best compound, which exhibited a Dvl-PDZ
binding affinity of 8 μM, successfully rescued bone loss in an
ovariectomized mouse model. These authors also reported additional studies that focused on the same Dvl protein and employed
various computational approaches to identify other PDZ inhibitors
[46, 47]. For example, in the work reported by Ma et al. [47], X-ray
Rational Design of PDZ Domain Inhibitors
283
The new derivatives were again evaluated using an NMR-based
approach. The best compound, a mixture of diastereoisomers,
exhibited a 5 μM affinity for AF6-PDZ. Molecular docking using
the MOE package (http://www.chemcomp.com) was performed
to identify the most likely active stereoisomer from the diastereoisomer mixture.
Dishevelled (Dvl) is an essential protein in the Wnt signaling
pathway that relies on its PDZ domain for transduction of downstream signals [11]. Interestingly, a known sulindac drug was
shown to inhibit the canonical Wnt signaling pathway by binding
to the PDZ domain of Dvl [40]. NMR experiments enabled the
determination of the “sulindac / PDZ domain” complex and concluded that sulindac is located within the peptide binding pocket of
the PDZ domain. Finally, a K i value of 10 μM was measured for
sulindac in a competitive assay with a reference peptide. Additional
chemical compounds, which bind to the Dvl-PDZ domain in the
low micromolar range affinity, were discovered using a protocol
involving both molecular modeling and NMR spectroscopy
[11]. In silico experiments employed a structure-based pharmacophore search using the Unity module from Sybyl [41] to identify
small organic compounds that could mimic the binding mode of
the Dapper protein partner within the PDZ domain. Then, the
FlexX docking tool [42] was used to confirm the ability of selected
compounds to act as potential PDZ domain binders. NMR spectroscopy was used as an experimental method to validate (or not)
the selected compounds. A benzoic acid molecule, which displayed
the most significant chemical shift perturbations, exhibited a 10 μM
K d value. Finally, in vivo studies confirmed its ability to reduce the
growth rate of prostate cancer cell lines. A similar strategy was used
in another study to target the PSD95-PDZ domain [43]. The
binding of the best identified fragment (quinoline-2,7-dicarboxylic
acid) was confirmed using NMR experiments.
Another study focused on the Dvl protein identified small
molecules that perturb the Dvl-PDZ/CXXC5 PPI [44]. Inhibition
of this interaction may have potential interest in bone anabolic
osteoporosis therapy by enhancing osteoblast differentiation
[44]. More than 50 analogs were synthesized to explore the chemical space around the hit while also trying to increase the microsomal
stability and optimize the physicochemical properties. Binding
modes of representative compounds from the series were predicted
using molecular docking with DOCKER from the Discovery Studio package [45]. The best compound, which exhibited a Dvl-PDZ
binding affinity of 8 μM, successfully rescued bone loss in an
ovariectomized mouse model. These authors also reported additional studies that focused on the same Dvl protein and employed
various computational approaches to identify other PDZ inhibitors
[46, 47]. For example, in the work reported by Ma et al. [47], X-ray
Rational Design of PDZ Domain Inhibitors
283