merge them. Ultimately, a combination of molecular docking studies using GOLD software [50, 51] and SAR studies produced a
fused compound that exhibited a dissociation constant (K d ) of
21 μM for Synt-PDZ1. From a biological point of view, glioblastoma multiform (GBM) is one of the most aggressive cancers and is
associated with short survival times and poor response to radiotherapy because of its invasive properties. It has been shown that
syntenin is overexpressed in this kind of cancer. Both genetic and
pharmacological strategies to modulate syntenin reduced invasion
gains in GBM cells following radiation. Finally, intraperitoneal
administration of the developed inhibitor improved the survival of
brain tumor-bearing mice.
Finally, we also reported an integrated study by combining
proteomic and genetic techniques with structural biochemistry
and molecular modeling, providing a detailed discovery of small
compounds targeting the PDZ domain from GRASP55 [52]. The
impacts on germ cell Golgi remodeling and spermatogenesis after
administration of the compound were also studied. First, X-ray
crystal structures of GRASP55 in complex with JAM-C or JAM-B
were obtained and revealed that GRASP55 underwent conformational changes with respect to its free conformation, with the latter
being more open. An in silico protocol involving high-throughput
docking and pharmacophore filtering was performed to identify
potential GRASP55-PDZ inhibitors. A library of 200,000 compounds dedicated to PPIs was used, and these compounds were
docked into the binding site of the closed GRASP55-PDZ conformation using the Surflex docking tool [53], thereby producing
millions of poses. Pharmacophore filtering, using Unity package
from Sybyl [41], was then used to extract compounds that could
mimic the canonical binding mode of the JAM peptides. Approximately 50 molecules were purchased and tested experimentally
using homogeneous time-resolved fluorescence (HTRF), leading
to the identification of a chemical compound that inhibited the
GRASP55-PDZ–JAM interaction with an IC 50 of 8 μM. Unfortunately, despite intensive efforts, an X-ray crystal structure for this
compound in complex with GRASP55-PDZ was not obtained. In
the end, the biological relevance of the GRASP55-PDZ–JAM-C
interaction in spermatogenesis was validated using both genetic
ablation of the encoding GRASP55 gene and disruption of this
PPI using a small organic compound. Treatment of mice with the
inhibitor induced premature release of spermatids and germ cell
loss; thus, this inhibitor has potential to be used as male
contraception.
Rational Design of PDZ Domain Inhibitors
285
fused compound that exhibited a dissociation constant (K d ) of
21 μM for Synt-PDZ1. From a biological point of view, glioblastoma multiform (GBM) is one of the most aggressive cancers and is
associated with short survival times and poor response to radiotherapy because of its invasive properties. It has been shown that
syntenin is overexpressed in this kind of cancer. Both genetic and
pharmacological strategies to modulate syntenin reduced invasion
gains in GBM cells following radiation. Finally, intraperitoneal
administration of the developed inhibitor improved the survival of
brain tumor-bearing mice.
Finally, we also reported an integrated study by combining
proteomic and genetic techniques with structural biochemistry
and molecular modeling, providing a detailed discovery of small
compounds targeting the PDZ domain from GRASP55 [52]. The
impacts on germ cell Golgi remodeling and spermatogenesis after
administration of the compound were also studied. First, X-ray
crystal structures of GRASP55 in complex with JAM-C or JAM-B
were obtained and revealed that GRASP55 underwent conformational changes with respect to its free conformation, with the latter
being more open. An in silico protocol involving high-throughput
docking and pharmacophore filtering was performed to identify
potential GRASP55-PDZ inhibitors. A library of 200,000 compounds dedicated to PPIs was used, and these compounds were
docked into the binding site of the closed GRASP55-PDZ conformation using the Surflex docking tool [53], thereby producing
millions of poses. Pharmacophore filtering, using Unity package
from Sybyl [41], was then used to extract compounds that could
mimic the canonical binding mode of the JAM peptides. Approximately 50 molecules were purchased and tested experimentally
using homogeneous time-resolved fluorescence (HTRF), leading
to the identification of a chemical compound that inhibited the
GRASP55-PDZ–JAM interaction with an IC 50 of 8 μM. Unfortunately, despite intensive efforts, an X-ray crystal structure for this
compound in complex with GRASP55-PDZ was not obtained. In
the end, the biological relevance of the GRASP55-PDZ–JAM-C
interaction in spermatogenesis was validated using both genetic
ablation of the encoding GRASP55 gene and disruption of this
PPI using a small organic compound. Treatment of mice with the
inhibitor induced premature release of spermatids and germ cell
loss; thus, this inhibitor has potential to be used as male
contraception.
Rational Design of PDZ Domain Inhibitors
285