13 research outputs found
Research data supporting '2,3-dihydropyrrolo[1,2-a]quinazolin-5(1H)-one inhibitors targeting bromodomains within the Switch/Sucrose Non-Fermenting complex'.
Data in support of the characterisation of compounds and their biological binding to proteins in the above manuscript. For synthesised compounds infra-red characterisation traces, HPLC traces where performed, and processed NMR files are provided. Raw files for the interaction of key compounds with PB1(5) and SMARCA2 and SMARCA4 proteins as measured by isothermal calorimetry are included. X-ray crystallography files are available through the Protein Data Bank.This work was supported by the EPSRC [grant numbers EP/K099494/1 EP/K039520/1], Wellcome Trust [grant number 092809/Z/10/Z] and the Cambridge PhD Training Programme in Molecular Medicine
An Activity-based Probe Targeting Non-catalytic, Highly Conserved Amino Acid Residues Within Bromodomains
Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from physiological recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag, via copper-catalyzed alkyne azide coupling, to an alkyne handle on the probe allowed in-gel visualization and selective pull-down of the desired bromodomains using both recombinant and endogenous proteins.</b
Identification and Development of 2,3-Dihydropyrrolo[1,2â<i>a</i>]quinazolin-5(1<i>H</i>)âone Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex
Bromodomain containing proteins PB1,
SMARCA4, and SMARCA2 are important
components of SWI/SNF chromatin remodeling complexes. We identified
bromodomain inhibitors that target these proteins and display unusual
binding modes involving water displacement from the KAc binding site.
The best compound binds the fifth bromodomain of PB1 with a <i>K</i><sub>D</sub> of 124 nM, SMARCA2B and SMARCA4 with <i>K</i><sub>D</sub> values of 262 and 417 nM, respectively, and
displays excellent selectivity over bromodomains other than PB1, SMARCA2,
and SMARCA4
Discovery of an MLLT1/3 YEATS Domain Chemical Probe
YEATS domain (YD) containing proteins are an emerging
class of epigenetic targets in drug discovery. Dysregulation of these modified lysine binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small molecule chemical probe, SGC-iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is a potent and selective inhibitor of MLLT1/3 -histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small molecule X-ray co-crystal structures with the MLLT1 YD are also reported. This first in class probe molecule can be used to understand MLLT1/3 associated biology and the therapeutic potential of small molecule YD inhibitors.</p
[1,2,4]Triazolo[4,3â<i>a</i>]phthalazines: Inhibitors of Diverse Bromodomains
Bromodomains
are gaining increasing interest as drug targets. Commercially
sourced and de novo synthesized substituted [1,2,4]ÂtriazoloÂ[4,3-<i>a</i>]Âphthalazines are potent inhibitors of both the BET bromodomains
such as BRD4 as well as bromodomains outside the BET family such as
BRD9, CECR2, and CREBBP. This new series of compounds is the first
example of submicromolar inhibitors of bromodomains outside the BET
subfamily. Representative compounds are active in cells exhibiting
potent cellular inhibition activity in a FRAP model of CREBBP and
chromatin association. The compounds described are valuable starting
points for discovery of selective bromodomain inhibitors and inhibitors
with mixed bromodomain pharmacology
Discovery and Optimization of Small-Molecule Ligands for the CBP/p300 Bromodomains
Small-molecule inhibitors that target
bromoÂdomains outside
of the bromoÂdomain and extra-terminal (BET) sub-family are lacking.
Here, we describe highly potent and selective ligands for the bromoÂdomain
module of the human lysine acetyl transferase CBP/p300, developed
from a series of 5-isoxazolyl-benzÂimidÂazoles. Our starting
point was a fragment hit, which was optimized into a more potent and
selective lead using parallel synthesis employing Suzuki couplings,
benzÂimidÂazole-forming reactions, and reductive aminations.
The selectivity of the lead compound against other bromoÂdomain
family members was investigated using a thermal stability assay, which
revealed some inhibition of the structurally related BET family members.
To address the BET selectivity issue, X-ray crystal structures of
the lead compound bound to the CREB binding protein (CBP) and the
first bromoÂdomain of BRD4 (BRD4(1)) were used to guide the design
of more selective compounds. The crystal structures obtained revealed
two distinct binding modes. By varying the aryl substitution pattern
and developing conformationally constrained analogues, selectivity
for CBP over BRD4(1) was increased. The optimized compound is highly
potent (<i>K</i><sub>d</sub> = 21 nM) and selective, displaying
40-fold selectivity over BRD4(1). Cellular activity was demonstrated
using fluorescence recovery after photo-bleaching (FRAP) and a p53
reporter assay. The optimized compounds are cell-active and have nanoÂmolar
affinity for CBP/p300; therefore, they should be useful in studies
investigating the biological roles of CBP and p300 and to validate
the CBP and p300 bromoÂdomains as therapeutic targets
A Chemical Probe For Tudor Domain Protein Spindlin1 to Investigate Chromatin Functions
Modifications of histone tails, including
lysine/arginine methylation, provide the basis of a \u27chromatin or histone
code\u27. Proteins that contain \u27reader\u27 domains can bind to these modifications
and form specific effector complexes, which ultimately mediate chromatin
function. The spindlin1 (SPIN1) protein contains three Tudor
methyllysine/arginine reader domains and was identified as a putative oncogene
and transcriptional co-activator. Here we report a SPIN1 chemical probe
inhibitor with low nanomolar in vitro activity, exquisite selectivity on a
panel of methyl reader and writer proteins, and with submicromolar cellular
activity. X-ray crystallography showed that this Tudor domain chemical probe
simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode.
Small molecule inhibition and siRNA knockdown of SPIN1, as well as
chemoproteomic studies, identified genes which are transcriptionally regulated
by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a roll in
cancer related inflammation and/or cancer metastasis.<br /