15 research outputs found
Human Cbx3 chromodomain binds to methylated histone H1K26 and G9aK185.
<p>ITC data for Cbx3 chromodomain binding to (A) H1K26 peptides (residues 18–29) and (B) G9aK185 peptides (residues 179–190). Lower panel show fit to a one-site binding model to the binding isotherms.</p
Comparison of three structures of Cbx3 chromodomain binding to methylated histone H3, H1 and G9a peptides.
<p>(A) Superposition of human Cbx3 chromodomain in complex with methylated histone H1 peptide (yellow), histone H3 peptide (orange), G9a peptide (cyan), Cbx3 chromodomains are colored as magenta, gray and green, respectively. (B) Superposition of histone H1 peptide (yellow), histone H3 peptide (orange). (C) Structure of Cbx3-H3K9me3 complex (magenta) was superposed to one protomer of the tetramer of Cbx3-G9aK185me3 complex (green) formed in one asymmetric unit. (D) The α helix (residues 70 to 79) of the chromodomain in the structure of Cbx3-G9aK185me3 complex (green) shifts 4.9 Å away from its counterpart in the structures of Cbx3-H3K9me3 (magenta).</p
X-ray Data collection and refinement statistics.
a<p>The values in parentheses refer to statistics in the highest shell.</p>b<p>Rmerge = |Ii−<i>|/|Ii| where Ii is the intensity of the ith measurement, and <i>is the mean intensity for that reflection.</i></i></p><i><i>c<p>Rwork = Σh|Fo(h)−Fc(h)|/ΣhFo(h), where Fo and Fc are the observed and calculated structure factor amplitudes, respectively.</p>d<p>Rfree was calculated with 10% of the reflections in the test set.</p>e<p>Categories were defined by MolProbity.</p></i></i
Structure basis for Cbx3 binding to methylated histone H1K26 and G9aK185 peptide.
<p>(A and C) Electrostatic surface depiction of human Cbx3-histone H1K26me2, and Cbx3-G9aK185me3 complex. Peptide substrates are shown in a stick mode. Surfaces with positive electrostatic potential are blue, and negative potential are red. The side chain of residue H1A24 (G9aA183) inserts into the small hydrophobic pocket formed by Phe48 and Leu49 of human Cbx3. The size of the pocket is only sufficient to accommodate a methyl group but not other residue side chains. (B and D) Binding of histone H1 peptide and G9a peptide in the binding groove of Cbx3 chromodomain, respectively. Hydrogen-bonds are shown as dashed lines. Yellow: histone H1 peptide; Gray: Cbx3 chromodomain in Cbx3-histone H1K26me2 complex. Cyan: G9a peptide; Green: Cbx3 chromodomain in Cbx3-G9aK185me3 complex.</p
Identification and Structure–Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors
HDAC6
plays a central role in the recruitment of protein aggregates
for lysosomal degradation and is a promising target for combination
therapy with proteasome inhibitors in multiple myeloma. Pharmacologically
displacing ubiquitin from the zinc-finger ubiquitin-binding domain
(ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition.
Here, we present the discovery of an HDAC6 ZnF-UBD-focused chemical
series and its progression from virtual screening hits to low micromolar
inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin,
and an extended aromatic system stacking with W1182 and R1155, are
necessary for activity. One of the compounds induced a conformational
remodeling of the binding site where the primary binding pocket opens
up onto a ligand-able secondary pocket that may be exploited to increase
potency. The preliminary structure–activity relationship accompanied
by nine crystal structures should enable further optimization into
a chemical probe to investigate the merit of targeting the ZnF-UBD
of HDAC6 in multiple myeloma and other diseases
Identification and Structure–Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors
HDAC6
plays a central role in the recruitment of protein aggregates
for lysosomal degradation and is a promising target for combination
therapy with proteasome inhibitors in multiple myeloma. Pharmacologically
displacing ubiquitin from the zinc-finger ubiquitin-binding domain
(ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition.
Here, we present the discovery of an HDAC6 ZnF-UBD-focused chemical
series and its progression from virtual screening hits to low micromolar
inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin,
and an extended aromatic system stacking with W1182 and R1155, are
necessary for activity. One of the compounds induced a conformational
remodeling of the binding site where the primary binding pocket opens
up onto a ligand-able secondary pocket that may be exploited to increase
potency. The preliminary structure–activity relationship accompanied
by nine crystal structures should enable further optimization into
a chemical probe to investigate the merit of targeting the ZnF-UBD
of HDAC6 in multiple myeloma and other diseases
Identification and Structure–Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors
HDAC6
plays a central role in the recruitment of protein aggregates
for lysosomal degradation and is a promising target for combination
therapy with proteasome inhibitors in multiple myeloma. Pharmacologically
displacing ubiquitin from the zinc-finger ubiquitin-binding domain
(ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition.
Here, we present the discovery of an HDAC6 ZnF-UBD-focused chemical
series and its progression from virtual screening hits to low micromolar
inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin,
and an extended aromatic system stacking with W1182 and R1155, are
necessary for activity. One of the compounds induced a conformational
remodeling of the binding site where the primary binding pocket opens
up onto a ligand-able secondary pocket that may be exploited to increase
potency. The preliminary structure–activity relationship accompanied
by nine crystal structures should enable further optimization into
a chemical probe to investigate the merit of targeting the ZnF-UBD
of HDAC6 in multiple myeloma and other diseases
Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin
Inhibitors of HDAC6 have attractive
potential in numerous cancers.
HDAC6 inhibitors to date target the catalytic domains, but targeting
the unique zinc-finger ubiquitin-binding domain (Zf-UBD) of HDAC6
may be an attractive alternative strategy. We developed X-ray crystallography
and biophysical assays to identify and characterize small molecules
capable of binding to the Zf-UBD and competing with ubiquitin binding.
Our results revealed two adjacent ligand-able pockets of HDAC6 Zf-UBD
and the first functional ligands for this domain
Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin
Inhibitors of HDAC6 have attractive
potential in numerous cancers.
HDAC6 inhibitors to date target the catalytic domains, but targeting
the unique zinc-finger ubiquitin-binding domain (Zf-UBD) of HDAC6
may be an attractive alternative strategy. We developed X-ray crystallography
and biophysical assays to identify and characterize small molecules
capable of binding to the Zf-UBD and competing with ubiquitin binding.
Our results revealed two adjacent ligand-able pockets of HDAC6 Zf-UBD
and the first functional ligands for this domain