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Journal ArticleDOI: 10.1021/ACS.JMEDCHEM.0C02156

Template-Hopping Approach Leads to Potent, Selective, and Highly Soluble Bromo and Extraterminal Domain (BET) Second Bromodomain (BD2) Inhibitors.

04 Mar 2021-Journal of Medicinal Chemistry (American Chemical Society)-Vol. 64, Iss: 6, pp 3249-3281
Abstract: A number of reports have recently been published describing the discovery and optimization of bromo and extraterminal inhibitors which are selective for the second bromodomain (BD2); these include our own work toward GSK046 (3) and GSK620 (5). This paper describes our approach to mitigating the genotoxicity risk of GSK046 by replacement of the acetamide functionality with a heterocyclic ring. This was followed by a template-hopping and hybridization approach, guided by structure-based drug design, to incorporate learnings from other BD2-selective series, optimize the vector for the amide region, and explore the ZA cleft, leading to the identification of potent, selective, and bioavailable compounds 28 (GSK452), 39 (GSK737), and 36 (GSK217).

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Topics: Bromodomain (52%)

5 results found

Journal ArticleDOI: 10.1021/ACS.JMEDCHEM.1C00592
Adam I. Green1, George M. Burslem1Institutions (1)
Abstract: Epigenetic drug discovery provides a wealth of opportunities for the discovery of new therapeutics but has been hampered by low hit rates, frequent identification of false-positives, and poor synthetic tractability. A key reason for this is that few screening collections consider the unique requirements of epigenetic targets despite significant medicinal chemistry interest. Here we analyze the suitability of some commercially available screening collections in the context of epigenetic drug discovery, with a particular focus on lysine post-translational modifications, and show that even privileged motifs found in U.S. Food and Drug Administration (FDA)-approved drugs are not present in these collections. We propose that the incorporation of epigenetic bioisosteres should become central in the design of new focused screening collections and highlight some opportunities for the development of synthetic methods which may improve the tractability of hit molecules.

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Topics: Drug discovery (51%)

3 Citations

Journal ArticleDOI: 10.1021/ACS.JMEDCHEM.1C00412
Abstract: Second-generation bromodomain and extra terminal (BET) inhibitors, which selectively target one of the two bromodomains in the BET proteins, have begun to emerge in the literature. These inhibitors aim to help determine the roles and functions of each domain and assess whether they can demonstrate an improved safety profile in clinical settings compared to pan-BET inhibitors. Herein, we describe the discovery of a novel BET BD2-selective chemotype using a structure-based drug design from a hit identified by DNA-encoded library technologies, showing a structural differentiation from key previously reported greater than 100-fold BD2-selective chemotypes GSK620, GSK046, and ABBV-744. Following a structure-based hypothesis for the selectivity and optimization of the physicochemical properties of the series, we identified 60 (GSK040), an in vitro ready and in vivo capable BET BD2-inhibitor of unprecedented selectivity (5000-fold) against BET BD1, excellent selectivity against other bromodomains, and good physicochemical properties. This novel chemical probe can be added to the toolbox used in the advancement of epigenetics research.

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Topics: Bromodomain (52%)

2 Citations

Journal ArticleDOI: 10.1021/ACS.JMEDCHEM.1C00708
Li Ding1, Christophe Pannecouque2, Erik De Clercq2, Chunlin Zhuang1  +1 moreInstitutions (2)
Abstract: A series of novel heteroaromatic-difluoro-biphenyl-diarylpyrimidines were designed as non-nucleoside anti-HIV inhibitors targeting reverse transcriptase by a fragment-based replacement strategy with the purpose of improving the druggability. Hopping five- or six-membered heterocycle groups on the biphenyl moiety as bioisosterism for intrinsically cyanophenyl gave 23 derivatives. All of these compounds possessed excellent HIV-1 inhibitory activity in the nanomolar range. Among them, 12g with a 4-pyridine group displayed excellent inhibitory activity toward WT and mutant HIV virus possessing significant selectivity. Moreover, this compound exhibited a decent improvement in druggability than etravirine and rilpivirine: (1) The hydrochloric acid salt of 12g exhibited significantly improved water solubility in different pH conditions. (2) 12g did not show apparent CYP enzymatic inhibitory activity or acute toxicity. (3) Excellent oral bioavailability was also revealed (F = 126%, rats) in 12g. Collectively, these novel heteroaromatic-biphenyl-DAPYs represent promising drug candidates for HIV clinical therapy.

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Topics: Druggability (53%)

1 Citations

Journal ArticleDOI: 10.1016/J.PHRS.2021.105702
Yi Wang1, Qiang Xie1, Huidan Tan2, Minru Liao1  +4 moreInstitutions (4)
Abstract: Epigenetics mainly refers to covalent modifications to DNA or histones without affecting genomes, which ultimately lead to phenotypic changes in cells or organisms. Given the abundance of regulatory targets in epigenetic pathways and their pivotal roles in tumorigenesis and drug resistance, the development of epigenetic drugs holds a great promise for the current cancer therapy. However, lack of potent, selective, and clinically tractable small-molecule compounds makes the strategy to target cancer epigenetic pathways still challenging. Therefore, this review focuses on epigenetic pathways, small molecule inhibitors targeting DNA methyltransferase (DNMT) and small molecule inhibitors targeting histone modification (the main regulatory targets are histone acetyltransferases (HAT), histone deacetylases (HDACs) and histone methyltransferases (HMTS)), as well as the combination strategies of the existing epigenetic therapeutic drugs and more new therapies to improve the efficacy, which will shed light on a new clue on discovery of more small-molecule drugs targeting cancer epigenetic pathways as promising strategies in the future.

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Topics: Histone methyltransferase (60%), Epigenetics (56%), Carcinogenesis (51%) ... read more

Journal ArticleDOI: 10.1016/J.EJMECH.2021.113853
Yuantao Fu1, Yanzhi Zhang1, Haiying Sun1Institutions (1)
Abstract: Dysfunction of the bromo and extra terminal domain (BET) family proteins is associated with many human diseases, therefore the BET family proteins have been considered as promising targets for drug development. Numerous small molecular compounds targeting the N-terminal two tandem bromodomains BD1 and BD2 of the BET family proteins have been reported, and a number of them have been advanced into clinical trials. Most of the BET inhibitors entered clinical trials are pan-BET inhibitors which show poor selectivity among BET members and bind to the BD1 and BD2 of the BET family proteins with comparable binding affinities. In order to elucidate the distinct functions of BD1s and BD2s, many BD1 and BD2 selective BET inhibitors have also been developed. In this review, we summarized the recent progress in the development of BD1 and BD2 selective BET inhibitors, and provided the perspectives for future studies of BET inhibitors.

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Topics: Bromodomain (50%)

74 results found

Open accessJournal ArticleDOI: 10.1038/NATURE09504
Panagis Filippakopoulos1, Jun Qi2, Sarah Picaud1, Yao Shen3  +22 moreInstitutions (5)
23 Dec 2010-Nature
Abstract: Epigenetic proteins are intently pursued targets in ligand discovery. So far, successful efforts have been limited to chromatin modifying enzymes, or so-called epigenetic 'writers' and 'erasers'. Potent inhibitors of histone binding modules have not yet been described. Here we report a cell-permeable small molecule (JQ1) that binds competitively to acetyl-lysine recognition motifs, or bromodomains. High potency and specificity towards a subset of human bromodomains is explained by co-crystal structures with bromodomain and extra-terminal (BET) family member BRD4, revealing excellent shape complementarity with the acetyl-lysine binding cavity. Recurrent translocation of BRD4 is observed in a genetically-defined, incurable subtype of human squamous carcinoma. Competitive binding by JQ1 displaces the BRD4 fusion oncoprotein from chromatin, prompting squamous differentiation and specific antiproliferative effects in BRD4-dependent cell lines and patient-derived xenograft models. These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chemical scaffold for the development of chemical probes more broadly throughout the bromodomain family.

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Topics: BET inhibitor (59%), Bromodomain (59%), Squamous carcinoma (57%) ... read more

2,991 Citations

Open accessJournal ArticleDOI: 10.1038/NATURE10334
Johannes Zuber1, Junwei Shi2, Junwei Shi1, Eric Wang1  +20 moreInstitutions (9)
27 Oct 2011-Nature
Abstract: Epigenetic pathways can regulate gene expression by controlling and interpreting chromatin modifications. Cancer cells are characterized by altered epigenetic landscapes, and commonly exploit the chromatin regulatory machinery to enforce oncogenic gene expression programs. Although chromatin alterations are, in principle, reversible and often amenable to drug intervention, the promise of targeting such pathways therapeutically has been limited by an incomplete understanding of cancer-specific dependencies on epigenetic regulators. Here we describe a non-biased approach to probe epigenetic vulnerabilities in acute myeloid leukaemia (AML), an aggressive haematopoietic malignancy that is often associated with aberrant chromatin states. By screening a custom library of small hairpin RNAs (shRNAs) targeting known chromatin regulators in a genetically defined AML mouse model, we identify the protein bromodomain-containing 4 (Brd4) as being critically required for disease maintenance. Suppression of Brd4 using shRNAs or the small-molecule inhibitor JQ1 led to robust antileukaemic effects in vitro and in vivo, accompanied by terminal myeloid differentiation and elimination of leukaemia stem cells. Similar sensitivities were observed in a variety of human AML cell lines and primary patient samples, revealing that JQ1 has broad activity in diverse AML subtypes. The effects of Brd4 suppression are, at least in part, due to its role in sustaining Myc expression to promote aberrant self-renewal, which implicates JQ1 as a pharmacological means to suppress MYC in cancer. Our results establish small-molecule inhibition of Brd4 as a promising therapeutic strategy in AML and, potentially, other cancers, and highlight the utility of RNA interference (RNAi) screening for revealing epigenetic vulnerabilities that can be exploited for direct pharmacological intervention.

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Topics: Chromatin remodeling (60%), Chromatin (57%), Epigenetics (53%) ... read more

1,591 Citations

Open accessJournal ArticleDOI: 10.1038/NATURE09589
Edwige Nicodeme, Kate L. Jeffrey1, Uwe Schaefer1, Soren Beinke2  +13 moreInstitutions (2)
23 Dec 2010-Nature
Abstract: Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defence, is frequently deleterious to the host due to the exaggerated production of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signalling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a critical step in the regulation of gene expression. Here we present a novel pharmacological approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compound (I-BET) that by 'mimicking' acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compounds specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.

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Topics: Bromodomain (60%), Chromatin (58%), Regulation of gene expression (56%) ... read more

1,272 Citations

Open accessJournal ArticleDOI: 10.1016/J.CELL.2012.02.013
Panagis Filippakopoulos1, Sarah Picaud1, Maria M. Mangos1, T. Keates1  +12 moreInstitutions (6)
30 Mar 2012-Cell
Abstract: Bromodomains (BRDs) are protein interaction modules that specifically recognize e-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.

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Topics: Bromodomain (54%)

1,120 Citations

Journal ArticleDOI: 10.1021/AC961242D
Abstract: A new chromatographic hydrophobicity index (CHI) is described which can be used as part of a protocol for high-throughput (50−100 compounds/day) physicochemical property profiling for rational drug design. The index is derived from retention times (tR) observed in a fast gradient reversed-phase HPLC method. The isocratic retention factors (log k‘) were measured for a series of 76 structurally unrelated compounds by using various concentrations of acetonitrile in the mobile phase. By plotting the log k‘ as a function of the acetonitrile concentration, the slope (S) and the intercept (log k‘w) values were calculated. The previously validated index of hydrophobicity φ0 was calculated as −log k‘w/S. A good linear correlation was obtained between the gradient retention time values, tR and the isocratically determined φ0 values for the 76 compounds. The constants of this linear correlation can be used to calculate CHI. For most compounds, CHI is between 0 and 100 and in this range it approximates to the percent...

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363 Citations