Small-molecule inhibitors that target
bromodomains outside
of the bromodomain and extra-terminal (BET) sub-family are lacking.
Here, we describe highly potent and selective ligands for the bromodomain
module of the human lysine acetyl transferase CBP/p300, developed
from a series of 5-isoxazolyl-benzimidazoles. Our starting
point was a fragment hit, which was optimized into a more potent and
selective lead using parallel synthesis employing Suzuki couplings,
benzimidazole-forming reactions, and reductive aminations.
The selectivity of the lead compound against other bromodomain
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 bromodomain 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 (Kd = 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 nanomolar
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 bromodomains as therapeutic targets.
The histone acetyltransferases CBP/p300 are involved in recurrent leukemia-associated chromosomal translocations and are key regulators of cell growth. Therefore, efforts to generate inhibitors of CBP/p300 are of clinical value. We developed a specific and potent acetyl-lysine competitive protein-protein interaction inhibitor, I-CBP112, that targets the CBP/p300 bromodomains. Exposure of human and mouse leukemic cell lines to I-CBP112 resulted in substantially impaired colony formation and induced cellular differentiation without significant cytotoxicity. I-CBP112 significantly reduced the leukemia-initiating potential of MLL-AF9 þ acute myeloid leukemia cells in a dose-dependent manner in vitro and in vivo. Interestingly, I-CBP112 increased the cytotoxic activity of BET bromodomain inhibitor JQ1 as well as doxorubicin. Collectively, we report the development and preclinical evaluation of a novel, potent inhibitor targeting CBP/p300 bromodomains that impairs aberrant self-renewal of leukemic cells. The synergistic effects of I-CBP112 and current standard therapy (doxorubicin) as well as emerging treatment strategies (BET inhibition) provide new opportunities for combinatorial treatment of leukemia and potentially other cancers. Cancer Res; 75(23); 5106-19. Ó2015 AACR.
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 KD of 124 nM, SMARCA2B and SMARCA4 with KD values of 262 and 417 nM, respectively, and
displays excellent selectivity over bromodomains other than PB1, SMARCA2,
and SMARCA4.
TRIM24 is a transcriptional regulator
as well as an E3 ubiquitin
ligase. It is overexpressed in diverse tumors, and high expression
levels have been linked to poor prognosis in breast cancer patients.
TRIM24 contains a PHD/bromodomain offering the opportunity to develop
protein interaction inhibitors that target this protein interaction
module. Here we identified potent acetyl-lysine mimetic benzimidazolones
TRIM24 bromodomain inhibitors. The best compound of this series is
a selective BRPF1B/TRIM24 dual inhibitor that bound with a KD of 137 and 222 nM, respectively, but exerted
good selectivity over other bromodomains. Cellular activity of the
inhibitor was demonstrated using FRAP assays as well as cell viability
data.
The bromodomain containing proteins
BAZ2A/B play essential roles
in chromatin remodeling and regulation of noncoding RNAs. We present
the structure based discovery of a potent, selective, and cell active
inhibitor 13 (BAZ2-ICR) of the BAZ2A/B bromodomains through
rapid optimization of a weakly potent starting point. A key feature
of the presented inhibitors is an intramolecular aromatic stacking
interaction that efficiently occupies the shallow bromodomain pockets. 13 represents an excellent chemical probe for functional studies
of the BAZ2 bromodomains in vitro and in vivo.
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