1
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Gazzillo E, Colarusso E, Giordano A, Chini MG, Potenza M, Hofstetter RK, Iorizzi M, Werz O, Lauro G, Bifulco G. Repositioning of Small Molecules through the Inverse Virtual Screening in silico Tool: Case of Benzothiazole-Based Inhibitors of Soluble Epoxide Hydrolase (sEH). Chempluschem 2024:e202400234. [PMID: 38753468 DOI: 10.1002/cplu.202400234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Computational techniques accelerate drug discovery by identifying bioactive compounds for specific targets, optimizing molecules with moderate activity, or facilitating the repositioning of inactive items onto new targets. Among them, the Inverse Virtual Screening (IVS) approach is aimed at the evaluation of one or a small set of molecules against a panel of targets for addressing target identification. In this work, a focused library of benzothiazole-based compounds was re-investigated by IVS. Four items, originally synthesized and tested on bromodomain-containing protein 9 (BRD9) but yielding poor binding, were critically re-analyzed, disclosing only a partial fit with 3D structure-based pharmacophore models, which, in the meanwhile, were developed for this target. Afterwards, these compounds were re-evaluated through IVS on a panel of proteins involved in inflammation and cancer, identifying soluble epoxide hydrolase (sEH) as a putative interacting target. Three items were subsequently confirmed as able to interfere with sEH activity, leading to inhibition percentages spanning from 70 % up to 30 % when tested at 10 μM. Finally, one benzothiazole-based compound emerged as the most promising inhibitor featuring an IC50 in the low micromolar range (IC50=6.62±0.13 μM). Our data confirm IVS as a predictive tool for accelerating the target identification and repositioning processes.
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Affiliation(s)
- Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, Pozzuoli, I-80078, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Marianna Potenza
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Robert Klaus Hofstetter
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Maria Iorizzi
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
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2
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Gazzillo E, Pierri M, Colarusso E, Chini MG, Ferraro MG, Piccolo M, Irace C, Bruno I, Bifulco G, Terracciano S, Lauro G. Exploring the chemical space of functionalized [1,2,4]triazolo[4,3-a]quinoxaline-based compounds targeting the bromodomain of BRD9. Bioorg Chem 2023; 139:106677. [PMID: 37352721 DOI: 10.1016/j.bioorg.2023.106677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/25/2023]
Abstract
Here we report a detailed structure-activity relationship (SAR) study related to [1,2,4]triazolo[4,3-a]quinoxaline-based compounds targeting the reader module of bromodomain containing-protein 9 (BRD9). 3D structure-based pharmacophore models, previously introduced by us, were here employed to evaluate a second generation of compounds, exploring different substitution patterns on the heterocyclic core. Starting from the promising data obtained from our previously identified [1,2,4]triazolo[4,3-a]quinoxaline-based compounds 1-4, the combination of in silico studies, chemical synthesis, biophysical and in vitro assays led to the identification of a new set of derivatives, selected for thoroughly exploring the chemical space of the bromodomain binding site. In more details, the investigation of different linkers at C-4 position highlighted the amine spacer as mandatory for the binding with the protein counterpart and the crucial role of the alkyl substituents at C-1 for increasing the selectivity toward BRD9. Additionally, the importance of a hydrogen bond donor group, critical to anchor the ZA region and required for the interaction with Ile53 residue, was inferred from the analysis of our collected results. Herein we also propose an optimization and an update of our previously reported "pharm-druglike2" 3D structure-based pharmacophore model, introducing it as "pharm-druglike2.1". Compounds 24-26, 32, 34 and 36 were identified as new valuable BRD9 binders featuring IC50 values in the low micromolar range. Among them, 24 and 36 displayed an excellent selectivity towards BRD9 and a good antiproliferative effect on a panel of leukemia models, especially toward CCRF-CEM cell line, with no cytotoxicity on healthy cells. Notably, the interaction of 24 and 36 with the bromodomain and PHD finger-containing protein 1 (BRPF1) also emerged, disclosing them as new and unexplored dual inhibitors for these two proteins highly involved in leukemia. These findings highlight the potential for the identification of new attractive dual epidrugs as well as a promising starting point for the development of chemical degraders endowed with anticancer activities.
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Affiliation(s)
- Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Martina Pierri
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche 86090, Italy
| | - Maria Grazia Ferraro
- BioChem Lab, Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Marialuisa Piccolo
- BioChem Lab, Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Carlo Irace
- BioChem Lab, Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
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3
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Colarusso E, Ceccacci S, Monti MC, Gazzillo E, Giordano A, Chini MG, Ferraro MG, Piccolo M, Ruggiero D, Irace C, Terracciano S, Bruno I, Bifulco G, Lauro G. Identification of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based small molecules as selective BRD9 binders. Eur J Med Chem 2023; 247:115018. [PMID: 36577218 DOI: 10.1016/j.ejmech.2022.115018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Targeting bromodomain-containing protein 9 (BRD9) represents a promising strategy for the development of new agents endowed with anticancer properties. With this aim, a set of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based compounds was investigated following a combined approach that relied on in silico studies, chemical synthesis, biophysical and biological evaluation of the most promising items. The protocol was initially based on molecular docking experiments, accounting a library of 1896 potentially synthesizable items tested in silico against the bromodomain of BRD9. A first set of 21 compounds (1-21) was selected and the binding on BDR9 was assessed through AlphaScreen assays. The obtained results disclosed compounds 17 and 20 able to bind BRD9 in the submicromolar range (IC50 = 0.35 ± 0.18 μM and IC50 = 0.14 ± 0.03 μM, respectively) showing a promising selectivity profile when tested against further nine bromodomains. Taking advantage of 3D structure-based pharmacophore models, additional 10 derivatives were selected in silico for the synthetic step and binding assessment, highlighting seven compounds (22, 23, 25, 26, 28, 29, 31) able to selectively bind BRD9 among different bromodomains. The ability of the identified BRD9 binders to cross artificial membranes in vitro was also assessed, revealing a very good passive permeability profile. Preliminary studies were carried out on a panel of healthy and cancer human cell lines to explore the biological behavior of the selected compounds, disclosing a moderate activity and significant selectivity profile towards leukaemia cells. These results highlighted the applicability of the reported multidisciplinary approach for accelerating the selection of promising items and for driving the chemical synthesis of novel selective BRD9 binders. Moreover, the low molecular weight of the reported 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based BRD9 binders suggests the possibility for further exploring the chemical space in order to obtain new analogues with improved potency.
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Affiliation(s)
- Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Sara Ceccacci
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale Delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Dafne Ruggiero
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy.
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4
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Hill MD, Fang H, Norris D, Delucca GV, Huang H, DeBenedetto M, Quesnelle C, Schmitz WD, Tokarski JS, Sheriff S, Yan C, Fanslau C, Haarhoff Z, Huang C, Kramer M, Madari S, Menard K, Monereau L, Morrison J, Raghavan N, Shields EE, Simmermacher-Mayer J, Sinz M, Tye CK, Westhouse R, Xie C, Zhang H, Zhang L, Zvyaga T, Lee F, Gavai AV, Degnan AP. Development of BET Inhibitors as Potential Treatments for Cancer: Optimization of Pharmacokinetic Properties. ACS Med Chem Lett 2022; 13:1165-1171. [DOI: 10.1021/acsmedchemlett.2c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Matthew D. Hill
- Research & Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Haiquan Fang
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Derek Norris
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - George V. Delucca
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Hong Huang
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Mikkel DeBenedetto
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Claude Quesnelle
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - William D. Schmitz
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - John S. Tokarski
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Steven Sheriff
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Chunhong Yan
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Caroline Fanslau
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Zuzana Haarhoff
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Christine Huang
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Melissa Kramer
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Shilpa Madari
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Krista Menard
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Laura Monereau
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - John Morrison
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Nirmala Raghavan
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Eric E. Shields
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Jean Simmermacher-Mayer
- Research & Development, Bristol Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Michael Sinz
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Ching Kim Tye
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Richard Westhouse
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Chunshan Xie
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Haiying Zhang
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Lisa Zhang
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Tatyana Zvyaga
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Francis Lee
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Ashvinikumar V. Gavai
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Andrew P. Degnan
- Research & Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States
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5
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Pierri M, Gazzillo E, Chini MG, Ferraro MG, Piccolo M, Maione F, Irace C, Bifulco G, Bruno I, Terracciano S, Lauro G. Introducing structure-based three-dimensional pharmacophore models for accelerating the discovery of selective BRD9 binders. Bioorg Chem 2021; 118:105480. [PMID: 34823196 DOI: 10.1016/j.bioorg.2021.105480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 01/18/2023]
Abstract
A well-structured in silico workflow is here reported for disclosing structure-based pharmacophore models against bromodomain-containing protein 9 (BRD9), accelerating virtual screening campaigns and facilitating the identification of novel binders. Specifically, starting from 23 known ligands co-crystallized with BRD9, three-dimensional pharmacophore models, namely placed in a reference protein structure, were developed. Specifically, we here introduce a fragment-related pharmacophore model, useful for the identification of new promising small chemical probes targeting the protein region responsible of the acetyllysine recognition, and two further pharmacophore models useful for the selection of compounds featuring drug-like properties. A pharmacophore-driven virtual screening campaign was then performed to facilitate the selection of new selective BRD9 ligands, starting from a large library of commercially available molecules. The identification of a promising BRD9 binder (7) prompted us to re-iterate this computational workflow on a second focused in-house built library of synthesizable compounds and, eventually, three further novel BRD9 binders were disclosed (8-10). Moreover, all these compounds were tested among a panel comprising other nine bromodomains, showing a high selectivity for BRD9. Preclinical bioscreens for potential anticancer activity highlighted compound 7 as that showing the most promising biological effects, proving the reliability of this in silico pipeline and confirming the applicability of the here introduced structure-based three-dimensional (3D) pharmacophore models as straightforward tools for the selection of new BRD9 ligands.
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Affiliation(s)
- Martina Pierri
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche 86090, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Francesco Maione
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
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6
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Hill MD, Quesnelle C, Tokarski J, Fang H, Fanslau C, Haarhoff Z, Kramer M, Madari S, Wiebesiek A, Morrison J, Simmermacher-Mayer J, Sinz M, Westhouse R, Xie C, Zhao J, Huang L, Sheriff S, Yan C, Marsilio F, Everlof G, Zvyaga T, Lee F, Gavai AV, Degnan AP. Development of BET inhibitors as potential treatments for cancer: A new carboline chemotype. Bioorg Med Chem Lett 2021; 51:128376. [PMID: 34560263 DOI: 10.1016/j.bmcl.2021.128376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/05/2021] [Accepted: 09/15/2021] [Indexed: 11/27/2022]
Abstract
We describe our efforts to introduce structural diversity to a previously described triazole-containing N1-carboline series of bromodomain and extra-terminal (BET) inhibitors. N9 carbolines were designed to retain favorable binding interactions that the N1-carbolines possess. A convergent synthetic route enabled modifications to reduce clearance, enhance physicochemical properties, and improve the overall in vitro profile. This work led to the identification of a potent BET inhibitor, (S)-2-{8-fluoro-5-[(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-7-[4-(2H3)methyl-1-methyl-1H-1,2,3-triazol-5-yl]-5H-pyrido[3,2-b]indol-3-yl}propan-2-ol (10), a compound with enhanced oral exposure in mice. Subsequent evaluation in a mouse triple-negative breast cancer tumor model revealed efficacy at 4 mg/kg of N9-carboline 10.
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Affiliation(s)
- Matthew D Hill
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA.
| | - Claude Quesnelle
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - John Tokarski
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Haiquan Fang
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Carolynn Fanslau
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Zuzana Haarhoff
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Melissa Kramer
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Shilpa Madari
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Amy Wiebesiek
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - John Morrison
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | | | - Michael Sinz
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Richard Westhouse
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Chunshan Xie
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Jiuqiao Zhao
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Lisa Huang
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Steven Sheriff
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Chunhong Yan
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Frank Marsilio
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Gerry Everlof
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Tatyana Zvyaga
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Francis Lee
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Ashvinikumar V Gavai
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
| | - Andrew P Degnan
- Bristol Myers Squibb Research and Development, 100 Binney St, Cambridge, MA 02142-1096, USA
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7
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Kiely-Collins H, Winter GE, Bernardes GJL. The role of reversible and irreversible covalent chemistry in targeted protein degradation. Cell Chem Biol 2021; 28:952-968. [PMID: 33789091 DOI: 10.1016/j.chembiol.2021.03.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/30/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) that degrade disease-causing proteins by hijacking the endogenous ubiquitin-proteasome system have emerged as an exciting and transformative technology in both chemical biology and drug discovery. Currently, the majority of PROTACs use reversible non-covalent ligands for both the target protein of interest (POI) and E3 ligase. In this review, we explore the burgeoning role of reversible and irreversible covalent chemistry in targeted protein degradation. We highlight the key advantages of targeted covalent inhibitors, whether as the target POI or E3 ligase ligand, such as their ability to enhance the selectivity of PROTACs, enable access to more of the "undruggable" proteome and expand the repertoire of recruited E3 ligases.
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Affiliation(s)
- Hannah Kiely-Collins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Instituto de Medicina Molecular, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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8
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Gazizov DA, Gorbunov EB, Rusinov GL, Ulomsky EN, Charushin VN. A New Family of Fused Azolo[1,5- a]pteridines and Azolo[5,1- b]purines. ACS OMEGA 2020; 5:18226-18233. [PMID: 32743198 PMCID: PMC7391858 DOI: 10.1021/acsomega.0c01849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/26/2020] [Indexed: 05/02/2023]
Abstract
The nitration of azolo[1,5-a]pyrimidin-7-amines with several nitration agents (such as acetic nitric anhydride, nitronium tetrafluoroborate, and a mixture of concentrated nitric acid and sulfuric acid) has been investigated. It has been shown that, depending on the conditions, the nitration of pyrazolopyrimidin-7-amines bearing electron-withdrawing groups in the pyrazole ring leads to nitration products in the pyrimidine and/or pyrazole ring. The nitration of triazolo[1,5-a]pyrimidin-7-amines with "nitrating mixture" has been optimized, thus allowing us to obtain a series of 6-nitro[1,2,4]triazolo[1,5-a]pyrimidin-7-amines, followed by their reduction into the corresponding [1,2,4]triazolo[1,5-a]pyrimidin-6,7-diamines (yields 86-89%). The latter have been subjected to heterocyclization by a variety of electrophilic compounds (such as CS2, glyoxal, triethyl orthoformate) with the formation of five- or six-membered annulated cycles.
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Affiliation(s)
- Denis A. Gazizov
- Postovsky
Institute of Organic Synthesis of Ural Branch of Russian Academy of
Sciences, Sofia Kovalevskoy St. 22/20, Ekaterinburg 620108, Russia
| | - Evgeny B. Gorbunov
- Postovsky
Institute of Organic Synthesis of Ural Branch of Russian Academy of
Sciences, Sofia Kovalevskoy St. 22/20, Ekaterinburg 620108, Russia
| | - Gennady L. Rusinov
- Postovsky
Institute of Organic Synthesis of Ural Branch of Russian Academy of
Sciences, Sofia Kovalevskoy St. 22/20, Ekaterinburg 620108, Russia
- Department
of Organic and Biomolecular Chemistry, Ural
Federal University, Mira St. 19, Ekaterinburg 620002, Russia
| | - Evgeny N. Ulomsky
- Postovsky
Institute of Organic Synthesis of Ural Branch of Russian Academy of
Sciences, Sofia Kovalevskoy St. 22/20, Ekaterinburg 620108, Russia
- Department
of Organic and Biomolecular Chemistry, Ural
Federal University, Mira St. 19, Ekaterinburg 620002, Russia
| | - Valery N. Charushin
- Postovsky
Institute of Organic Synthesis of Ural Branch of Russian Academy of
Sciences, Sofia Kovalevskoy St. 22/20, Ekaterinburg 620108, Russia
- Department
of Organic and Biomolecular Chemistry, Ural
Federal University, Mira St. 19, Ekaterinburg 620002, Russia
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9
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Alimova I, Pierce A, Danis E, Donson A, Birks DK, Griesinger A, Foreman NK, Santi M, Soucek L, Venkataraman S, Vibhakar R. Inhibition of MYC attenuates tumor cell self-renewal and promotes senescence in SMARCB1-deficient Group 2 atypical teratoid rhabdoid tumors to suppress tumor growth in vivo. Int J Cancer 2019; 144:1983-1995. [PMID: 30230537 DOI: 10.1002/ijc.31873] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 12/31/2022]
Abstract
Loss of SMARCB1 is the hallmark genetic event that characterizes rhabdoid tumors in children. Rhabdoid tumors of the brain (ATRT) occur in young children and are particularly challenging with poor long-term survival. SMARCB1 is a member of the SWI/SNF chromatin remodeling complex that is responsible for determining cellular pluripotency and lineage commitment. The mechanisms by which SMARCB1 deletion results in tumorigenesis remain unclear. Recent studies demonstrate that ATRT consists of 3 genomic subgroups with a subset of poor outcome tumors expressing high BMP and MYC pathway activation. Here we show that MYC occupies distinct promoter loci in ATRT compared to embryonic stem (ES) cells. Furthermore, using human ATRT cell lines, patient-derived cell culture, ex vivo patient-derived tumor, and orthotopic xenograft models, we show that MYC inhibition is a molecular vulnerability in SMARCB1-deleted tumors and that such inhibition effectively suppresses BMP and pluripotency-associated genomic programs, attenuates tumor cell self-renewal, promotes senescence, and inhibits ATRT tumor growth in vivo. Transgenic expression of Omomyc (a bona-fide MYC dominant negative) or chemical inhibition of MYC transcriptomic programs with the BET inhibitor JQ1 phenocopy genetic depletion of MYC, effectively restricting ATRT tumor growth and opening a promising therapeutic avenue for rhabdoid tumors in children.
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Affiliation(s)
- Irina Alimova
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Angela Pierce
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Etienne Danis
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Andrew Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Diane K Birks
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Andrea Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA.,Department of Neurosurgery, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Mariarita Santi
- The Children's Hospital of Philadelphia and University of Pennsylvania Perelman, School of Medicine, Philadelphia, PA, 19104, USA
| | - Laura Soucek
- Vall d'Hebron Institute of Oncology (VHIO), Cellex Centre, Barcelona, 08035, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Sujatha Venkataraman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA.,Department of Neurosurgery, University of Colorado Denver, Aurora, CO, 80045, USA
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10
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Liu S, Yosief HO, Dai L, Huang H, Dhawan G, Zhang X, Muthengi AM, Roberts J, Buckley DL, Perry JA, Wu L, Bradner JE, Qi J, Zhang W. Structure-Guided Design and Development of Potent and Selective Dual Bromodomain 4 (BRD4)/Polo-like Kinase 1 (PLK1) Inhibitors. J Med Chem 2018; 61:7785-7795. [PMID: 30125504 PMCID: PMC6309379 DOI: 10.1021/acs.jmedchem.8b00765] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The simultaneous inhibition of polo-like kinase 1 (PLK1) and BRD4 bromodomain by a single molecule could lead to the development of an effective therapeutic strategy for a variety of diseases in which PLK1 and BRD4 are implicated. Compound 23 has been found to be a potent dual kinase-bromodomain inhibitor (BRD4-BD1 IC50 = 28 nM, PLK1 IC50 = 40 nM). Compound 6 was found to be the most selective PLK1 inhibitor over BRD4 in our series (BRD4-BD1 IC50 = 2579 nM, PLK1 IC50 = 9.9 nM). Molecular docking studies with 23 and BRD4-BD1/PLK1 as well as with 6 corroborate the biochemical assay results.
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Affiliation(s)
- Shuai Liu
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Hailemichael O Yosief
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Lingling Dai
- Phase I Clinical Trial Center & Department of Clinical Pharmacology, Xiangya Hospital , Central South University , Changsha , Hunan 410008 , P.R. China
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Gagan Dhawan
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
- Department of Biomedical Science, Acharya Narendra Dev College , University of Delhi , New Delhi 110019 , India
| | - Xiaofeng Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Alex M Muthengi
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | | | | | | | | | - James E Bradner
- Novartis Institutes for Biomedical Research , Cambridge , Massachusetts 02139 , United States
| | - Jun Qi
- Department of Medicine , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Wei Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
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11
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Design and Synthesis of Proteolysis Targeting Chimeras for Inducing BRD4 Protein Degradation. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7299-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Wang S, Song Y, Wang Y, Gao Y, Yu S, Zhao Q, Jin X, Lu H. Design and synthesis of novel bispecific molecules for inducing BRD4 protein degradation. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7272-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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13
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Krämer KF, Moreno N, Frühwald MC, Kerl K. BRD9 Inhibition, Alone or in Combination with Cytostatic Compounds as a Therapeutic Approach in Rhabdoid Tumors. Int J Mol Sci 2017; 18:ijms18071537. [PMID: 28714904 PMCID: PMC5536025 DOI: 10.3390/ijms18071537] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 01/07/2023] Open
Abstract
Rhabdoid tumors (RT) are malignant neoplasms of early childhood. Despite intensive therapy, survival is poor and new treatment approaches are required. The only recurrent mutations in these tumors affect SMARCB1 and less commonly SMARCA4, both subunits of the chromatin remodeling complex SWItch/Sucrose Non-Fermentable (SWI/SNF). Loss of these two core subunits alters the function of the SWI/SNF complex, resulting in tumor development. We hypothesized that inhibition of aberrant SWI/SNF function by selective blockade of the BRD9 subunit of the SWI/SNF complex would reduce tumor cell proliferation. The cytotoxic and anti-proliferative effects of two specific chemical probes (I-BRD9 and BI-9564) which target the bromodomain of SWI/SNF protein BRD9 were evaluated in 5 RT cell lines. Combinatorial effects of I-BRD9 and cytotoxic drugs on cell proliferation were evaluated by cytotoxicity assays. Single compound treatment of RT cells with I-BRD9 and BI-9564 resulted in decreased cell proliferation, G1-arrest and apoptosis. Combined treatment of doxorubicin or carboplatin with I-BRD9 resulted in additive to synergistic inhibitory effects on cell proliferation. In contrast, the combination of I-BRD9 with vincristine demonstrated the antagonistic effects of these two compounds. We conclude that the BRD9 bromodomain is an attractive target for novel therapies in this cancer.
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Affiliation(s)
- Katja F Krämer
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology, 48149 Münster, Germany.
| | - Natalia Moreno
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology, 48149 Münster, Germany.
| | - Michael C Frühwald
- Children's Hospital and Swabian Children's Cancer Center, 86156 Augsburg, Germany.
| | - Kornelius Kerl
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology, 48149 Münster, Germany.
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14
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Heinzelmann G, Henriksen NM, Gilson MK. Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain. J Chem Theory Comput 2017; 13:3260-3275. [PMID: 28564537 PMCID: PMC5541932 DOI: 10.1021/acs.jctc.7b00275] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bromodomains, protein domains involved in epigenetic regulation, are able to bind small molecules with high affinity. In the present study, we report free energy calculations for the binding of seven ligands to the first BRD4 bromodomain, using the attach-pull-release (APR) method to compute the reversible work of removing the ligands from the binding site and then allowing the protein to relax conformationally. We test three different water models, TIP3P, TIP4PEw, and SPC/E, as well as the GAFF and GAFF2 parameter sets for the ligands. Our simulations show that the apo crystal structure of BRD4 is only metastable, with a structural transition happening in the absence of the ligand typically after 20 ns of simulation. We compute the free energy change for this transition with a separate APR calculation on the free protein and include its contribution to the ligand binding free energies, which generally causes an underestimation of the affinities. By testing different water models and ligand parameters, we are also able to assess their influence in our results and determine which one produces the best agreement with the experimental data. Both free energies associated with the conformational change and ligand binding are affected by the choice of water model, with the two sets of ligand parameters affecting their binding free energies to a lesser degree. Across all six combinations of water model and ligand potential function, the Pearson correlation coefficients between calculated and experimental binding free energies range from 0.55 to 0.83, and the root-mean-square errors range from 1.4-3.2 kcal/mol. The current protocol also yields encouraging preliminary results when used to assess the relative stability of ligand poses generated by docking or other methods, as illustrated for two different ligands. Our method takes advantage of the high performance provided by graphics processing units and can readily be applied to other ligands as well as other protein systems.
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Affiliation(s)
- Germano Heinzelmann
- Departamento de Fı́sica, Universidade Federal de Santa Catarina , Florianópolis, Santa Catarina 88040-900, Brazil
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
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15
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Prolyl isomerase PIN1 regulates the stability, transcriptional activity and oncogenic potential of BRD4. Oncogene 2017; 36:5177-5188. [PMID: 28481868 PMCID: PMC5589477 DOI: 10.1038/onc.2017.137] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
BRD4 has emerged as an important factor in tumorigenesis by promoting the transcription of genes involved in cancer development. However, how BRD4 is regulated in cancer cells remains largely unknown. Here, we report that the stability and functions of BRD4 are positively regulated by prolyl-isomerase PIN1 in gastric cancer cells. PIN1 directly binds to phosphorylated threonine (T) 204 of BRD4 as revealed by peptide binding and crystallographic studies and enhances BRD4’s stability by inhibiting its ubiquitination. PIN1 also catalyses the isomerization of proline 205 of BRD4 and induces its conformational change, which promotes its interaction with CDK9 and increases BRD4’s transcriptional activity. Substitution of BRD4 with PIN1 binding-defective BRD4-T204A mutant in gastric cancer cells reduces BRD4’s stability, attenuates BRD4-mediated gene expression by impairing its interaction with CDK9, and suppresses gastric cancer cell proliferation, migration and invasion, and tumor formation. Our results identify BRD4 as a new target of PIN1 and suggest that interfering with their interaction could be a potential therapeutic approach for cancer treatment.
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16
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Zhou B, Hu J, Xu F, Chen Z, Bai L, Fernandez-Salas E, Lin M, Liu L, Yang CY, Zhao Y, McEachern D, Przybranowski S, Wen B, Sun D, Wang S. Discovery of a Small-Molecule Degrader of Bromodomain and Extra-Terminal (BET) Proteins with Picomolar Cellular Potencies and Capable of Achieving Tumor Regression. J Med Chem 2017; 61:462-481. [PMID: 28339196 PMCID: PMC5788414 DOI: 10.1021/acs.jmedchem.6b01816] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
bromodomain and extra-terminal (BET) family proteins, consisting
of BRD2, BRD3, BRD4, and testis-specific BRDT members, are epigenetic
“readers” and play a key role in the regulation of gene
transcription. BET proteins are considered to be attractive therapeutic
targets for cancer and other human diseases. Recently, heterobifunctional
small-molecule BET degraders have been designed based upon the proteolysis
targeting chimera (PROTAC) concept to induce BET protein degradation.
Herein, we present our design, synthesis, and evaluation of a new
class of PROTAC BET degraders. One of the most promising compounds, 23, effectively degrades BRD4 protein at concentrations as
low as 30 pM in the RS4;11 leukemia cell line, achieves an IC50 value of 51 pM in inhibition of RS4;11 cell growth and induces
rapid tumor regression in vivo against RS4;11 xenograft tumors. These
data establish that compound 23 (BETd-260/ZBC260) is
a highly potent and efficacious BET
degrader.
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Affiliation(s)
- Bing Zhou
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jiantao Hu
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Fuming Xu
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Zhuo Chen
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ester Fernandez-Salas
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Mei Lin
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yujun Zhao
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Sally Przybranowski
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- University of Michigan Comprehensive Cancer Center, and Departments of ‡Internal Medicine, §Pathology, ∥Pharmaceutical Sciences, ⊥Medicinal Chemistry, and #Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
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17
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Humphreys PG, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon AM, Renaux JF, Suckling CJ, Tough DF, Prinjha RK. Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem 2017; 60:695-709. [DOI: 10.1021/acs.jmedchem.6b01566] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Paola Grandi
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | - Anne-Marie Michon
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Colin J. Suckling
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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18
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19
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Spiliotopoulos D, Caflisch A. Fragment-based in silico screening of bromodomain ligands. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:81-90. [PMID: 27769362 DOI: 10.1016/j.ddtec.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 01/31/2023]
Abstract
We review the results of fragment-based high-throughput docking to the N-terminal bromodomain of BRD4 and the CREBBP bromodomain. In both docking campaigns the ALTA (anchor-based library tailoring) procedure was used to reduce the size of the initial library by selecting for flexible docking only the molecules that contain a fragment with favorable predicted binding energy. Ranking by a force field-based energy with solvation has resulted in small-molecule hits with low-micromolar affinity and favorable ligand efficiency. Importantly, the binding modes predicted by docking have been validated by X-ray crystallography. One of the hits for the CREBBP bromodomain has been optimized by medicinal chemistry into a series of potent and selective ligands.
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Affiliation(s)
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
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20
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Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O'Mahony A, Berg E, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR. Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit. J Med Chem 2016; 59:4800-11. [PMID: 27115555 DOI: 10.1021/acs.jmedchem.6b00012] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.
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Affiliation(s)
- Brian S Gerstenberger
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - John D Trzupek
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Panagis Filippakopoulos
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Paul E Brennan
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Vita Fedele
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Martin
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Picaud
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Catherine Rogers
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Mihir Parikh
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alexandria Taylor
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian Samas
- Pfizer Worldwide Medicinal Chemistry , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alison O'Mahony
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Ellen Berg
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Gabriel Pallares
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Adam D Torrey
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Daniel K Treiber
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Ivan J Samardjiev
- Eurofins Lancaster PPS , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian T Nasipak
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Teresita Padilla-Benavides
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Mark E Bunnage
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Susanne Müller
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.,Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Dafydd R Owen
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
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21
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Chen J, Wang Z, Hu X, Chen R, Romero-Gallo J, Peek RM, Chen LF. BET Inhibition Attenuates Helicobacter pylori-Induced Inflammatory Response by Suppressing Inflammatory Gene Transcription and Enhancer Activation. THE JOURNAL OF IMMUNOLOGY 2016; 196:4132-42. [PMID: 27084101 DOI: 10.4049/jimmunol.1502261] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022]
Abstract
Helicobacter pylori infection causes chronic gastritis and peptic ulceration. H. pylori-initiated chronic gastritis is characterized by enhanced expression of many NF-κB-regulated inflammatory cytokines. Brd4 has emerged as an important NF-κB regulator and regulates the expression of many NF-κB-dependent inflammatory genes. In this study, we demonstrated that Brd4 was not only actively involved in H. pylori-induced inflammatory gene mRNA transcription but also H. pylori-induced inflammatory gene enhancer RNA (eRNA) synthesis. Suppression of H. pylori-induced eRNA synthesis impaired H. pylori-induced mRNA synthesis. Furthermore, H. pylori stimulated NF-κB-dependent recruitment of Brd4 to the promoters and enhancers of inflammatory genes to facilitate the RNA polymerase II-mediated eRNA and mRNA synthesis. Inhibition of Brd4 by JQ1 attenuated H. pylori-induced eRNA and mRNA synthesis for a subset of NF-κB-dependent inflammatory genes. JQ1 also inhibited H. pylori-induced interaction between Brd4 and RelA and the recruitment of Brd4 and RNA polymerase II to the promoters and enhancers of inflammatory genes. Finally, we demonstrated that JQ1 suppressed inflammatory gene expression, inflammation, and cell proliferation in H. pylori-infected mice. These studies highlight the importance of Brd4 in H. pylori-induced inflammatory gene expression and suggest that Brd4 could be a potential therapeutic target for the treatment of H. pylori-triggered inflammatory diseases and cancer.
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Affiliation(s)
- Jinjing Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Zhen Wang
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiangming Hu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China
| | - Judith Romero-Gallo
- Division of Gastroenterology, Department of Medicine and Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232; and
| | - Richard M Peek
- Division of Gastroenterology, Department of Medicine and Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232; and
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Medical Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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22
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Progress in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2016; 11:477-87. [PMID: 26749027 DOI: 10.1002/cmdc.201500540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/09/2015] [Indexed: 12/19/2022]
Abstract
The bromodomain and extra terminal (BET) family of bromodomains have been the focus of extensive research, leading to the development of many potent, selective chemical probes and recent clinical assets. The profound biology associated with BET bromodomain inhibition has provided a convincing rationale for targeting bromodomains for the treatment of disease. However, the BET family represents just eight of the at least 56 human bromodomains identified to date. Until recently, there has been significantly less interest in non-BET bromodomains, leaving a vast area of research and the majority of this new target class yet to be thoroughly investigated. It has been widely reported that several non-BET bromodomain containing proteins are associated with various diseases including cancer and HIV. Therefore, the development of chemical probes for non-BET bromodomains will facilitate elucidation of their precise biological roles and potentially lead to the development of new medicines. This review summarises the progress made towards the development of non-BET bromodomain chemical probes to date. In addition, we highlight the potential for future work in this new and exciting area.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.
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23
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Abstract
BACKGROUND High attrition rates in drug discovery call for new approaches to improve target validation. Academia is filling gaps, but often lacks the experience and resources of the pharmaceutical industry resulting in poorly characterized tool compounds. DISCUSSION The SGC has established an open access chemical probe consortium, currently encompassing ten pharmaceutical companies. One of its mandates is to create well-characterized inhibitors (chemical probes) for epigenetic targets to enable new biology and target validation for drug development. CONCLUSION Epigenetic probe compounds have proven to be very valuable and have not only spurred a plethora of novel biological findings, but also provided starting points for clinical trials. These probes have proven to be critical complementation to traditional genetic targeting strategies and provided sometimes surprising results.
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Affiliation(s)
- Peter J Brown
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
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24
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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25
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Theodoulou NH, Bamborough P, Bannister AJ, Becher I, Bit RA, Che KH, Chung CW, Dittmann A, Drewes G, Drewry DH, Gordon L, Grandi P, Leveridge M, Lindon M, Michon AM, Molnar J, Robson SC, Tomkinson NCO, Kouzarides T, Prinjha RK, Humphreys PG. Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. J Med Chem 2015; 59:1425-39. [PMID: 25856009 DOI: 10.1021/acs.jmedchem.5b00256] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acetylation of histone lysine residues is one of the most well-studied post-translational modifications of chromatin, selectively recognized by bromodomain "reader" modules. Inhibitors of the bromodomain and extra terminal domain (BET) family of bromodomains have shown profound anticancer and anti-inflammatory properties, generating much interest in targeting other bromodomain-containing proteins for disease treatment. Herein, we report the discovery of I-BRD9, the first selective cellular chemical probe for bromodomain-containing protein 9 (BRD9). I-BRD9 was identified through structure-based design, leading to greater than 700-fold selectivity over the BET family and 200-fold over the highly homologous bromodomain-containing protein 7 (BRD7). I-BRD9 was used to identify genes regulated by BRD9 in Kasumi-1 cells involved in oncology and immune response pathways and to the best of our knowledge, represents the first selective tool compound available to elucidate the cellular phenotype of BRD9 bromodomain inhibition.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Paul Bamborough
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew J Bannister
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rino A Bit
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ka Hing Che
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Chun-wa Chung
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Antje Dittmann
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David H Drewry
- Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, North Carolina 27709, United States
| | - Laurie Gordon
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Melanie Leveridge
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew Lindon
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anne-Marie Michon
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Judit Molnar
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Samuel C Robson
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Tony Kouzarides
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Rab K Prinjha
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Philip G Humphreys
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
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26
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Venkataraman S, Alimova I, Balakrishnan I, Harris P, Birks DK, Griesinger A, Amani V, Cristiano B, Remke M, Taylor MD, Handler M, Foreman NK, Vibhakar R. Inhibition of BRD4 attenuates tumor cell self-renewal and suppresses stem cell signaling in MYC driven medulloblastoma. Oncotarget 2015; 5:2355-71. [PMID: 24796395 PMCID: PMC4058011 DOI: 10.18632/oncotarget.1659] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Medulloblastoma is a pediatric brain tumor with a variable prognosis due to clinical and genomic heterogeneity. Among the 4 major genomic sub-groups, patients with MYC amplified tumors have a particularly poor prognosis despite therapy with surgery, radiation and chemotherapy. Targeting the MYC oncogene has traditionally been problematic. Here we report that MYC driven medulloblastoma can be targeted by inhibition of the bromodomain protein BRD4. We show that bromodomain inhibition with JQ1 restricts c-MYC driven transcriptional programs in medulloblastoma, suppresses medulloblastoma cell growth and induces a cell cycle arrest. Importantly JQ1 suppresses stem cell associated signaling in medulloblastoma cells and inhibits medulloblastoma tumor cell self-renewal. Additionally JQ1 also promotes senescence in medulloblastoma cells by activating cell cycle kinase inhibitors and inhibiting activity of E2F1. Furthermore BRD4 inhibition displayed an anti-proliferative, pro-senescence effect in a medulloblastoma model in vivo. In clinical samples we found that transcriptional programs suppressed by JQ1 are associated with adverse risk in medulloblastoma patients. Our work indicates that BRD4 inhibition attenuates stem cell signaling in MYC driven medulloblastoma and demonstrates the feasibility BET domain inhibition as a therapeutic approach in vivo.
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Affiliation(s)
- Sujatha Venkataraman
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, Denver, CO, USA
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27
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Tough DF, Lewis HD, Rioja I, Lindon MJ, Prinjha RK. Epigenetic pathway targets for the treatment of disease: accelerating progress in the development of pharmacological tools: IUPHAR Review 11. Br J Pharmacol 2014; 171:4981-5010. [PMID: 25060293 PMCID: PMC4253452 DOI: 10.1111/bph.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
The properties of a cell are determined both genetically by the DNA sequence of its genes and epigenetically through processes that regulate the pattern, timing and magnitude of expression of its genes. While the genetic basis of disease has been a topic of intense study for decades, recent years have seen a dramatic increase in the understanding of epigenetic regulatory mechanisms and a growing appreciation that epigenetic misregulation makes a significant contribution to human disease. Several large protein families have been identified that act in different ways to control the expression of genes through epigenetic mechanisms. Many of these protein families are finally proving tractable for the development of small molecules that modulate their function and represent new target classes for drug discovery. Here, we provide an overview of some of the key epigenetic regulatory proteins and discuss progress towards the development of pharmacological tools for use in research and therapy.
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Affiliation(s)
- David F Tough
- Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Epinova DPU, Stevenage, UK
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28
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Gosmini R, Nguyen VL, Toum J, Simon C, Brusq JMG, Krysa G, Mirguet O, Riou-Eymard AM, Boursier EV, Trottet L, Bamborough P, Clark H, Chung CW, Cutler L, Demont EH, Kaur R, Lewis AJ, Schilling MB, Soden PE, Taylor S, Walker AL, Walker MD, Prinjha RK, Nicodème E. The discovery of I-BET726 (GSK1324726A), a potent tetrahydroquinoline ApoA1 up-regulator and selective BET bromodomain inhibitor. J Med Chem 2014; 57:8111-31. [PMID: 25249180 DOI: 10.1021/jm5010539] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Through their function as epigenetic readers of the histone code, the BET family of bromodomain-containing proteins regulate expression of multiple genes of therapeutic relevance, including those involved in tumor cell growth and inflammation. BET bromodomain inhibitors have profound antiproliferative and anti-inflammatory effects which translate into efficacy in oncology and inflammation models, and the first compounds have now progressed into clinical trials. The exciting biology of the BETs has led to great interest in the discovery of novel inhibitor classes. Here we describe the identification of a novel tetrahydroquinoline series through up-regulation of apolipoprotein A1 and the optimization into potent compounds active in murine models of septic shock and neuroblastoma. At the molecular level, these effects are produced by inhibition of BET bromodomains. X-ray crystallography reveals the interactions explaining the structure-activity relationships of binding. The resulting lead molecule, I-BET726, represents a new, potent, and selective class of tetrahydroquinoline-based BET inhibitors.
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Affiliation(s)
- Romain Gosmini
- Candidate Discovery, ‡Discovery Biology, §DMPK, GlaxoSmithKline Les Ulis, Centre de Recherches François Hyafil, GlaxoSmithKline R&D , 25 Avenue du Québec, 91140 Villebon-sur-Yvette, France
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29
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Phenotypic screening and fragment-based approaches to the discovery of small-molecule bromodomain ligands. Future Med Chem 2014; 6:179-204. [PMID: 24467243 DOI: 10.4155/fmc.13.197] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues and hence facilitate protein-protein interactions. These bromodomain-mediated interactions often play key roles in transcriptional regulation and their dysfunction is implicated in a large number of diseases. The discovery of potent and selective small-molecule bromodomain and extra C-terminal domain bromodomain ligands, which show promising results for the treatment of cancers and atherosclerosis, has promoted intense interest in this area. Here we describe the progress that has been made to date in the discovery of small-molecule bromodomain ligands, with particular emphasis on the roles played by phenotypic screening and fragment-based approaches. In considering the future of the field we discuss the prospects for development of molecular probes and drugs for the non-bromodomain and extra C-terminal domain bromodomains.
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30
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Smith SG, Sanchez R, Zhou MM. Privileged diazepine compounds and their emergence as bromodomain inhibitors. ACTA ACUST UNITED AC 2014; 21:573-83. [PMID: 24746559 DOI: 10.1016/j.chembiol.2014.03.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/02/2014] [Accepted: 03/15/2014] [Indexed: 12/23/2022]
Abstract
Chemical compounds built on a diazepine scaffold have recently emerged as potent inhibitors of the acetyl-lysine binding activity of bromodomain-containing proteins, which is required for gene transcriptional activation in cancer and inflammation. Not only have these chemical compounds validated bromodomains as attractive epigenetic drug targets, but they have also brought to the forefront another application of the diazepine, which had already been regarded as a versatile chemical scaffold in rational drug design. This article reviews the success of diazepine compounds as therapeutic agents and examines the unique chemical and geometric features of this privileged scaffold that make it an excellent template for developing potent and selective molecules that control bromodomain-related gene expression in human diseases.
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Affiliation(s)
- Steven G Smith
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Roberto Sanchez
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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31
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Wu X, Qi J, Bradner JE, Xiao G, Chen LF. Bromodomain and extraterminal (BET) protein inhibition suppresses human T cell leukemia virus 1 (HTLV-1) Tax protein-mediated tumorigenesis by inhibiting nuclear factor κB (NF-κB) signaling. J Biol Chem 2013; 288:36094-105. [PMID: 24189064 DOI: 10.1074/jbc.m113.485029] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The etiology of human T cell leukemia virus 1 (HTLV-1)-mediated adult T cell leukemia is associated with the ability of viral oncoprotein Tax to induce sustained NF-κB activation and the expression of many NF-κB target genes. Acetylation of the RelA subunit of NF-κB and the subsequent recruitment of bromodomain-containing factor Brd4 are important for the expression of NF-κB target genes in response to various stimuli. However, their contributions to Tax-mediated NF-κB target gene expression and tumorigenesis remain unclear. Here we report that Tax induced the acetylation of lysine 310 of RelA and the binding of Brd4 to acetylated RelA to facilitate Tax-mediated transcriptional activation of NF-κB. Depletion of Brd4 down-regulated Tax-mediated NF-κB target gene expression and cell proliferation. Inhibiting the interaction of Brd4 and acetylated RelA with the bromodomain extraterminal protein inhibitor JQ1 suppressed the proliferation of Tax-expressing rat fibroblasts and Tax-positive HTLV-1-infected cells and Tax-mediated cell transformation and tumorigenesis. Moreover, JQ1 attenuated the Tax-mediated transcriptional activation of NF-κB, triggering the polyubiquitination and proteasome-mediated degradation of constitutively active nuclear RelA. Our results identify Brd4 as a key regulator for Tax-mediated NF-κB gene expression and suggest that targeting epigenetic regulators such as Brd4 with the bromodomain extraterminal protein inhibitor might be a potential therapeutic strategy for cancers and other diseases associated with HTLV-1 infection.
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Affiliation(s)
- Xuewei Wu
- From the Department of Biochemistry and
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32
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33
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Zou Z, Huang B, Wu X, Zhang H, Qi J, Bradner J, Nair S, Chen LF. Brd4 maintains constitutively active NF-κB in cancer cells by binding to acetylated RelA. Oncogene 2013; 33:2395-404. [PMID: 23686307 DOI: 10.1038/onc.2013.179] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 04/01/2013] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
Acetylation of the RelA subunit of NF-κB at lysine-310 regulates the transcriptional activation of NF-κB target genes and contributes to maintaining constitutively active NF-κB in tumors. Bromodomain-containing factor Brd4 has been shown to bind to acetylated lysine-310 (AcLys310) and to regulate the transcriptional activity of NF-κB, but the role of this binding in maintaining constitutively active NF-κB in tumors remains elusive. In this study, we demonstrate the structural basis for the binding of bromodomains (BDs) of bromodomain-containing protein 4 (Brd4) to AcLys310 and identify the BD inhibitor JQ1 as an effective small molecule to block this interaction. JQ1 suppresses TNF-α-mediated NF-κB activation and NF-κB-dependent target gene expression. In addition, JQ1 inhibits the proliferation and transformation potential of A549 lung cancer cells and suppresses the tumorigenicity of A549 cells in severe combined immunodeficiency mice. Furthermore, we demonstrate that depletion of Brd4 or treatment of cells with JQ1 induces the ubiquitination and degradation of the constitutively active nuclear form of RelA. Our results identify a novel function of Brd4 in maintaining the persistently active form of NF-κB found in tumors, and they suggest that interference with the interaction between acetylated RelA and Brd4 could be a potential therapeutic approach for the treatment of NF-κB-driven cancer.
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Affiliation(s)
- Z Zou
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - B Huang
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - X Wu
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - H Zhang
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - J Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - S Nair
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - L-F Chen
- 1] Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA [2] College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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34
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Gu B, Watanabe K, Sun P, Fallahi M, Dai X. Chromatin effector Pygo2 mediates Wnt-notch crosstalk to suppress luminal/alveolar potential of mammary stem and basal cells. Cell Stem Cell 2013; 13:48-61. [PMID: 23684539 DOI: 10.1016/j.stem.2013.04.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 03/13/2013] [Accepted: 04/16/2013] [Indexed: 02/04/2023]
Abstract
Epigenetic mechanisms regulating lineage differentiation of mammary stem cells (MaSCs) remain poorly understood. Pygopus 2 (Pygo2) is a histone methylation reader and a context-dependent Wnt/β-catenin coactivator. Here we provide evidence for Pygo2's function in suppressing luminal/alveolar differentiation of MaSC-enriched basal cells. We show that Pygo2-deficient MaSC/basal cells exhibit partial molecular resemblance to luminal cells, such as elevated Notch signaling and reduced mammary repopulating capability upon transplantation. Inhibition of Notch signaling suppresses basal-level and Pygo2-deficiency-induced luminal/alveolar differentiation of MaSC/basal cells, whereas activation of Wnt/β-catenin signaling suppresses luminal/alveolar differentiation and Notch3 expression in a Pygo2-dependent manner. We show that Notch3 is a direct target of Pygo2 and that Pygo2 is required for β-catenin binding and maintenance of a poised/repressed chromatin state at the Notch3 locus in MaSC/basal cells. Together, our data support a model where Pygo2-mediated chromatin regulation connects Wnt signaling and Notch signaling to restrict the luminal/alveolar differentiation competence of MaSC/basal cells.
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Affiliation(s)
- Bingnan Gu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
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35
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Hewings D, Fedorov O, Filippakopoulos P, Martin S, Picaud S, Tumber A, Wells C, Olcina MM, Freeman K, Gill A, Ritchie AJ, Sheppard DW, Russell AJ, Hammond EM, Knapp S, Brennan PE, Conway SJ. Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands. J Med Chem 2013; 56:3217-27. [PMID: 23517011 PMCID: PMC3640414 DOI: 10.1021/jm301588r] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Indexed: 12/14/2022]
Abstract
The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.
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Affiliation(s)
- David
S. Hewings
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Martin
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Anthony Tumber
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Christopher Wells
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Monica M. Olcina
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Katherine Freeman
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Andrew Gill
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Alison J. Ritchie
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - David W. Sheppard
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Angela J. Russell
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ester M. Hammond
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Stefan Knapp
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Paul E. Brennan
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Stuart J. Conway
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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36
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Hewings DS, Rooney TPC, Jennings LE, Hay DA, Schofield CJ, Brennan PE, Knapp S, Conway SJ. Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. J Med Chem 2012; 55:9393-413. [PMID: 22924434 DOI: 10.1021/jm300915b] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains, protein modules that recognize and bind to acetylated lysine, are emerging as important components of cellular machinery. These acetyl-lysine (KAc) "reader" domains are part of the write-read-erase concept that has been linked with the transfer of epigenetic information. By reading KAc marks on histones, bromodomains mediate protein-protein interactions between a diverse array of partners. There has been intense activity in developing potent and selective small molecule probes that disrupt the interaction between a given bromodomain and KAc. Rapid success has been achieved with the BET family of bromodomains, and a number of potent and selective probes have been reported. These compounds have enabled linking of the BET bromodomains with diseases, including cancer and inflammation, suggesting that bromodomains are druggable targets. Herein, we review the biology of the bromodomains and discuss the SAR for the existing small molecule probes. The biology that has been enabled by these compounds is summarized.
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Affiliation(s)
- David S Hewings
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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