51
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Duan Y, Guan Y, Qin W, Zhai X, Yu B, Liu H. Targeting Brd4 for cancer therapy: inhibitors and degraders. MEDCHEMCOMM 2018; 9:1779-1802. [PMID: 30542529 PMCID: PMC6238758 DOI: 10.1039/c8md00198g] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022]
Abstract
Bromodomain-containing protein 4 (Brd4) plays an important role in mediating the expression of genes involved in cancers and non-cancer diseases such as inflammatory diseases and acute heart failure. Inactivating Brd4 or downregulating its expression inhibits cancer development, leading to the current interest in Brd4 as a promising anticancer drug target. Numerous Brd4 inhibitors have been studied in recent years and some of them are currently in various phases of clinical trials. Recently, selective degradation of target proteins by small bifunctional molecules (PROTACs) has emerged as an attractive drug discovery approach owing to the advantages it could offer over traditional small-molecule inhibitors. A number of Brd4 degraders have been reported and showed more efficient anticancer activities than just protein inhibition. In this review, we will discuss recent findings in the discovery and development of small-molecule inhibitors and degraders that target Brd4 as a potential anticancer agent.
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Affiliation(s)
- Yingchao Duan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Yuanyuan Guan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Wenping Qin
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Xiaoyu Zhai
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Bin Yu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
| | - Hongmin Liu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
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52
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Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. Insight into selective mechanism of class of I-BRD9 inhibitors toward BRD9 based on molecular dynamics simulations. Chem Biol Drug Des 2018; 93:163-176. [PMID: 30225973 DOI: 10.1111/cbdd.13398] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/10/2018] [Accepted: 09/02/2018] [Indexed: 02/06/2023]
Abstract
Recently, bromodomain-containing protein 9 (BRD9), 7 (BRD7), and 4 (BRD4) have been potential targets of anticancer drug design. Molecular dynamic simulations followed by molecular mechanics Poisson-Boltzmann surface area calculation were performed to study the selective mechanism of I-BRD9 inhibitor H1B and its derivatives N1D, TVU, and 5V2 toward BRD9 and BRD4. The rank of our calculated binding free energies agrees with that of the experimental data. The results show that binding free energy of H1B to BRD7 is slightly lower than that of H1B to BRD9, and all four inhibitors bind more tightly to BRD9 than to BRD4. Decomposition of binding free energies into individual residues implies that Ile164 and Asn211 in BRD7 and Ile53 and Asn100 in BRD9 play a significant role in the selectivity of H1B toward BRD7 and BRD9. Besides, several key residues Phe44, Ile53, Asn100, Thr104 in BRD9 and Pro82, Lys91, Asn140, Asp144 in BRD4 that are located in the ZA-loop and BC-loop provide significant contributions to binding selectivity of inhibitors to BRD9 and BRD4. This study is expected to provide important theoretical guidance for rational designs of highly selective inhibitors targeting BRD9 and BRD4.
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Affiliation(s)
- Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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53
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Hoffer L, Muller C, Roche P, Morelli X. Chemistry-driven Hit-to-lead Optimization Guided by Structure-based Approaches. Mol Inform 2018; 37:e1800059. [PMID: 30051601 DOI: 10.1002/minf.201800059] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/24/2018] [Indexed: 12/17/2022]
Abstract
For several decades, hit identification for drug discovery has been facilitated by developments in both fragment-based and high-throughput screening technologies. However, a major bottleneck in drug discovery projects continues to be the optimization of primary hits from screening campaigns in order to derive lead compounds. Computational chemistry or molecular modeling can play an important role during this hit-to-lead (H2L) stage by both suggesting putative optimizations and decreasing the number of compounds to be experimentally synthesized and evaluated. However, it is also crucial to consider the feasibility of organically synthesizing these virtually designed compounds. Furthermore, the generated molecules should have reasonable physicochemical properties and be medicinally relevant. This review focuses on chemistry-driven and structure-based computational methods that can be used to tackle the difficult problem of H2L optimization, with emphasis being placed on the strategy developed in our laboratory.
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Affiliation(s)
- Laurent Hoffer
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France
| | | | - Philippe Roche
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France
| | - Xavier Morelli
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France.,Institut Paoli-Calmettes, IPC Drug Discovery, Marseille, France
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54
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Hoffer L, Voitovich YV, Raux B, Carrasco K, Muller C, Fedorov AY, Derviaux C, Amouric A, Betzi S, Horvath D, Varnek A, Collette Y, Combes S, Roche P, Morelli X. Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach. J Med Chem 2018; 61:5719-5732. [PMID: 29883107 DOI: 10.1021/acs.jmedchem.8b00653] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few decades, hit identification has been greatly facilitated by advances in high-throughput and fragment-based screenings. One major hurdle remaining in drug discovery is process automation of hit-to-lead (H2L) optimization. Here, we report a time- and cost-efficient integrated strategy for H2L optimization as well as a partially automated design of potent chemical probes consisting of a focused-chemical-library design and virtual screening coupled with robotic diversity-oriented de novo synthesis and automated in vitro evaluation. The virtual library is generated by combining an activated fragment, corresponding to the substructure binding to the target, with a collection of functionalized building blocks using in silico encoded chemical reactions carefully chosen from a list of one-step organic transformations relevant in medicinal chemistry. The proof of concept was demonstrated using the optimization of bromodomain inhibitors as a test case, leading to the validation of several compounds with improved affinity by several orders of magnitude.
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Affiliation(s)
- Laurent Hoffer
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Yuliia V Voitovich
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia
| | - Brigitt Raux
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Kendall Carrasco
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Christophe Muller
- IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Aleksey Y Fedorov
- Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia
| | - Carine Derviaux
- IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Agnès Amouric
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Stéphane Betzi
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Dragos Horvath
- Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Alexandre Varnek
- Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Yves Collette
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Sébastien Combes
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Philippe Roche
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Xavier Morelli
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
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55
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Kim YH, Kim M, Yoo M, Kim JE, Lee HK, Heo JN, Lee CO, Yoo M, Jung KY, Yun CS, Moon SW, Chang HK, Chung CW, Pyo S, Choi SU, Park CH. A natural compound, aristoyagonine, is identified as a potent bromodomain inhibitor by mid-throughput screening. Biochem Biophys Res Commun 2018; 503:882-887. [PMID: 29928885 DOI: 10.1016/j.bbrc.2018.06.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
Abstract
Bromodomain-containing protein 4 (Brd4) is known to play a key role in tumorigenesis. It binds acetylated histones to regulate the expression of numerous genes. Because of the importance of brd4 in tumorigenesis, much research has been undertaken to develop brd4 inhibitors with therapeutic potential. As a result, various scaffolds for bromodomain inhibitors have been identified. To discover new scaffolds, we performed mid-throughput screening using two different enzyme assays, alpha-screen and ELISA. We found a novel bromodomain inhibitor with a unique scaffold, aristoyagonine. This natural compound showed inhibitory activity in vitro and tumor growth inhibition in a Ty82-xenograft mouse model. In addition, we tested Brd4 inhibitors in gastric cancer cell lines, and found that aristoyagonine exerted cytotoxicity not only in I-BET-762-sensitive cancer cells, but also in I-BET-762-resistant cancer cells. This is the first paper to describe a natural compound as a Brd4 bromodomain inhibitor.
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Affiliation(s)
- Young Hun Kim
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Minsung Kim
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon City, Kyunggi-do, 16419, Republic of Korea
| | - Miyoun Yoo
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Ji Eun Kim
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Heung Kyoung Lee
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Jung-Nyoung Heo
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Chong Ock Lee
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Minjin Yoo
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Kwan-Young Jung
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chang-Soo Yun
- Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea; Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Sung Woong Moon
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Hye Kyung Chang
- LegoChem Biosciences, Inc, 8-26 Munoyeongseo-ro, Daedeok-gu, Daejeon, 34302, Republic of Korea
| | - Chul-Woong Chung
- LegoChem Biosciences, Inc, 8-26 Munoyeongseo-ro, Daedeok-gu, Daejeon, 34302, Republic of Korea
| | - Suhkneung Pyo
- School of Pharmacy, Sungkyunkwan University, Suwon City, Kyunggi-do, 16419, Republic of Korea
| | - Sang Un Choi
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
| | - Chi Hoon Park
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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56
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Xie F, Huang M, Lin X, Liu C, Liu Z, Meng F, Wang C, Huang Q. The BET inhibitor I-BET762 inhibits pancreatic ductal adenocarcinoma cell proliferation and enhances the therapeutic effect of gemcitabine. Sci Rep 2018; 8:8102. [PMID: 29802402 PMCID: PMC5970200 DOI: 10.1038/s41598-018-26496-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/10/2018] [Indexed: 02/06/2023] Open
Abstract
As one of the most fatal malignancies, pancreatic ductal adenocarcinoma (PDAC) has significant resistance to the currently available treatment approaches. Gemcitabine, the standard chemotherapeutic agent for locally advanced and metastatic PDAC, has limited efficacy, which is attributed to innate/acquired resistance and the activation of prosurvival pathways. Here, we investigated the in vitro efficacy of I-BET762, an inhibitor of the bromodomain and extraterminal (BET) family of proteins, in treating PDAC cell lines alone and in combination with gemcitabine (GEM). The effect of these two agents was also examined in xenograft PDAC tumors in mice. We found that I-BET762 induced cell cycle arrest in the G0/G1 phase and cell death and suppressed cell proliferation and metastatic stem cell factors in PDAC cells. In addition, the BH3-only protein Bim, which is related to chemotherapy resistance, was upregulated by I-BET762, which increased the cell death triggered by GEM in PDAC cells. Moreover, GEM and I-BET762 exerted a synergistic effect on cytotoxicity both in vitro and in vivo. Furthermore, Bim is necessary for I-BET762 activity and modulates the synergistic effect of GEM and I-BET762 in PDAC. In conclusion, we investigated the effect of I-BET762 on PDAC and suggest an innovative strategy for PDAC treatment.
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Affiliation(s)
- Fang Xie
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, China
| | - Mei Huang
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, China
| | - Xiansheng Lin
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China
| | - Chenhai Liu
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China
| | - Zhen Liu
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China
| | - Futao Meng
- Anhui Medical University Affiliated Provincial Hospital, No. 9, Lujiang Road, Hefei, Anhui province, China
| | - Chao Wang
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China
| | - Qiang Huang
- Department of General Surgery, Anhui Provincial Hospital, No. 17, Lujiang Road, Hefei, Anhui province, China.
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57
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Liu Z, Tian B, Chen H, Wang P, Brasier AR, Zhou J. Discovery of potent and selective BRD4 inhibitors capable of blocking TLR3-induced acute airway inflammation. Eur J Med Chem 2018; 151:450-461. [PMID: 29649741 PMCID: PMC5924617 DOI: 10.1016/j.ejmech.2018.04.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 01/01/2023]
Abstract
A series of diverse small molecules have been designed and synthesized through structure-based drug design by taking advantage of fragment merging and elaboration approaches. Compounds ZL0420 (28) and ZL0454 (35) were identified as potent and selective BRD4 inhibitors with nanomolar binding affinities to bromodomains (BDs) of BRD4. Both of them can be well docked into the acetyl-lysine (KAc) binding pocket of BRD4, forming key interactions including the critical hydrogen bonds with Asn140 directly and Tyr97 indirectly via a H2O molecule. Both compounds 28 and 35 exhibited submicromolar potency of inhibiting the TLR3-dependent innate immune gene program, including ISG54, ISG56, IL-8, and Groβ genes in cultured human small airway epithelial cells (hSAECs). More importantly, they also demonstrated potent efficacy reducing airway inflammation in a mouse model with low toxicity, indicating a proof of concept that BRD4 inhibitors may offer the therapeutic potential to block the viral-induced airway inflammation.
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Affiliation(s)
- Zhiqing Liu
- Chemical Biology Program, Department of Pharmacology and Toxicology, Galveston, TX, 77555, USA
| | - Bing Tian
- Department of Internal Medicine, Galveston, TX, 77555, USA; Sealy Center for Molecular Medicine, Galveston, TX, 77555, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, Galveston, TX, 77555, USA
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, Galveston, TX, 77555, USA
| | - Allan R Brasier
- Department of Internal Medicine, Galveston, TX, 77555, USA; Sealy Center for Molecular Medicine, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, Galveston, TX, 77555, USA; Sealy Center for Molecular Medicine, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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58
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Law RP, Atkinson SJ, Bamborough P, Chung CW, Demont EH, Gordon LJ, Lindon M, Prinjha RK, Watson AJB, Hirst DJ. Discovery of Tetrahydroquinoxalines as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the Second Bromodomain. J Med Chem 2018; 61:4317-4334. [DOI: 10.1021/acs.jmedchem.7b01666] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Robert P. Law
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K
| | | | | | | | | | | | | | | | - Allan J. B. Watson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K
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59
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Runcie AC, Zengerle M, Chan KH, Testa A, van Beurden L, Baud MGJ, Epemolu O, Ellis LCJ, Read KD, Coulthard V, Brien A, Ciulli A. Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition. Chem Sci 2018; 9:2452-2468. [PMID: 29732121 PMCID: PMC5909127 DOI: 10.1039/c7sc02536j] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/23/2018] [Indexed: 12/27/2022] Open
Abstract
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins.
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins. The four BET (bromodomain & extra-terminal domain) proteins – BRD2, BRD3, BRD4 and BRDT bind acetylated chromatin via their bromodomains and regulate processes such as cell proliferation and inflammation. BET bromodomains are of particular interest, as they are attractive therapeutic targets but existing inhibitors are pan-selective. We previously established a bump-&-hole system for the BET bromodomains, pairing a leucine/alanine mutation with an ethyl-derived analogue of an established benzodiazepine scaffold. Here we optimize upon this system with the introduction of a more conservative and less disruptive leucine/valine mutation. Extensive structure–activity-relationships of diverse benzodiazepine analogues guided the development of potent, mutant-selective inhibitors with desirable physiochemical properties. The active enantiomer of our best compound – 9-ME-1 – shows ∼200 nM potency, >100-fold selectivity for the L/V mutant over wild-type and excellent DMPK properties. Through a variety of in vitro and cellular assays we validate the capabilities of our optimized system, and then utilize it to compare the relative importance of the first and second bromodomains to chromatin binding. These experiments confirm the primacy of the first bromodomain in all BET proteins, but also significant variation in the importance of the second bromodomain. We also show that, despite having a minor role in chromatin recognition, BRD4 BD2 is still essential for gene expression, likely through the recruitment of non-histone proteins. The disclosed inhibitor:mutant pair provides a powerful tool for future cellular and in vivo target validation studies.
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Affiliation(s)
- A C Runcie
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M Zengerle
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K-H Chan
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - A Testa
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L van Beurden
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M G J Baud
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - O Epemolu
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L C J Ellis
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K D Read
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - V Coulthard
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Brien
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Ciulli
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
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60
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Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. A theoretical insight into selectivity of inhibitors toward two domains of bromodomain-containing protein 4 using molecular dynamics simulations. Chem Biol Drug Des 2017; 91:828-840. [DOI: 10.1111/cbdd.13148] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/22/2017] [Accepted: 11/01/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jing Su
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Xinguo Liu
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Shaolong Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Fangfang Yan
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Qinggang Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Jianzhong Chen
- School of Science; Shandong Jiaotong University; Jinan China
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61
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Yan G, Hou M, Luo J, Pu C, Hou X, Lan S, Li R. Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and biological evaluation for the discovery of novel BRD4 inhibitors. Chem Biol Drug Des 2017; 91:478-490. [PMID: 28901664 DOI: 10.1111/cbdd.13109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023]
Abstract
Bromodomain is a recognition module in the signal transduction of acetylated histone. BRD4, one of the bromodomain members, is emerging as an attractive therapeutic target for several types of cancer. Therefore, in this study, an attempt has been made to screen compounds from an integrated database containing 5.5 million compounds for BRD4 inhibitors using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations. As a result, two molecules of twelve hits were found to be active in bioactivity tests. Among the molecules, compound 5 exhibited potent anticancer activity, and the IC50 values against human cancer cell lines MV4-11, A375, and HeLa were 4.2, 7.1, and 11.6 μm, respectively. After that, colony formation assay, cell cycle, apoptosis analysis, wound-healing migration assay, and Western blotting were carried out to learn the bioactivity of compound 5.
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Affiliation(s)
- Guoyi Yan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Manzhou Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Jiang Luo
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Chunlan Pu
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Xueyan Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Suke Lan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Rui Li
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
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Ayoub AM, Hawk LML, Herzig RJ, Jiang J, Wisniewski AJ, Gee CT, Zhao P, Zhu JY, Berndt N, Offei-Addo NK, Scott TG, Qi J, Bradner JE, Ward TR, Schönbrunn E, Georg GI, Pomerantz WC. BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen. J Med Chem 2017; 60:4805-4817. [PMID: 28535045 PMCID: PMC5558211 DOI: 10.1021/acs.jmedchem.6b01336] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemical inhibition of epigenetic regulatory proteins BrdT and Brd4 is emerging as a promising therapeutic strategy in contraception, cancer, and heart disease. We report an easily synthesized dihydropyridopyrimidine pan-BET inhibitor scaffold, which was uncovered via a virtual screen followed by testing in a fluorescence anisotropy assay. Dihydropyridopyimidine 3 was subjected to further characterization and is highly selective for the BET family of bromodomains. Structure-activity relationship data and ligand deconstruction highlight the importance of the substitution of the uracil moiety for potency and selectivity. Compound 3 was also cocrystallized with Brd4 for determining the ligand binding pose and rationalizing subsequent structure-activity data. An additional series of dihydropyridopyrimidines was synthesized to exploit the proximity of a channel near the ZA loop of Brd4, leading to compounds with submicromolar affinity and cellular target engagement. Given these findings, novel and easily synthesized inhibitors are being introduced to the growing field of bromodomain inhibitor development.
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Affiliation(s)
- Alex M. Ayoub
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Laura M. L. Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Ryan J. Herzig
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Jiewei Jiang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Andrea J. Wisniewski
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Clifford T. Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Peiliang Zhao
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Jin-Yi Zhu
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Norbert Berndt
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Nana K. Offei-Addo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Thomas G. Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Timothy R. Ward
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Gunda I. Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - William C.K. Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
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63
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Liu Z, Wang P, Chen H, Wold EA, Tian B, Brasier AR, Zhou J. Drug Discovery Targeting Bromodomain-Containing Protein 4. J Med Chem 2017; 60:4533-4558. [PMID: 28195723 PMCID: PMC5464988 DOI: 10.1021/acs.jmedchem.6b01761] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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BRD4,
the most extensively studied member of the BET family, is
an epigenetic regulator that localizes to DNA via binding to acetylated
histones and controls the expression of therapeutically important
gene regulatory networks through the recruitment of transcription
factors to form mediator complexes, phosphorylating RNA polymerase
II, and by its intrinsic histone acetyltransferase activity. Disrupting
the protein–protein interactions between BRD4 and acetyl-lysine
has been shown to effectively block cell proliferation in cancer,
cytokine production in acute inflammation, and so forth. To date,
significant efforts have been devoted to the development of BRD4 inhibitors,
and consequently, a dozen have progressed to human clinical trials.
Herein, we summarize the advances in drug discovery and development
of BRD4 inhibitors by focusing on their chemotypes, in vitro and in
vivo activity, selectivity, relevant mechanisms of action, and therapeutic
potential. Opportunities and challenges to achieve selective and efficacious
BRD4 inhibitors as a viable therapeutic strategy for human diseases
are also highlighted.
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Affiliation(s)
- Zhiqing Liu
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Bing Tian
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
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64
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Zeng Z, Jin H, Xie J, Tian B, Rudolph M, Rominger F, Hashmi ASK. α-Imino Gold Carbenes from 1,2,4-Oxadiazoles: Atom-Economical Access to Fully Substituted 4-Aminoimidazoles. Org Lett 2017; 19:1020-1023. [PMID: 28218539 DOI: 10.1021/acs.orglett.7b00001] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A novel and atom-economical synthesis of fully substituted 4-aminoimidazoles via gold-catalyzed selective [3 + 2] annulation of 1,2,4-oxadiazoles with ynamides is reported. This protocol represents a new strategy to access α-imino gold carbenes, which corresponds to an unprecedented intermolecular transfer of N-acylimino nitrenes to ynamides. Moreover, the reaction proceeds with 100% atom economy, exhibits good functional group tolerance, and can be conducted in gram scale.
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Affiliation(s)
- Zhongyi Zeng
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hongming Jin
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jin Xie
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Bing Tian
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Matthias Rudolph
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - A Stephen K Hashmi
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.,Chemistry Department, Faculty of Science, King Abdulaziz University (KAU) , 21589 Jeddah, Saudi Arabia
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65
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Cheng C, Diao H, Zhang F, Wang Y, Wang K, Wu R. Deciphering the mechanisms of selective inhibition for the tandem BD1/BD2 in the BET-bromodomain family. Phys Chem Chem Phys 2017; 19:23934-23941. [DOI: 10.1039/c7cp04608a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bromodomain and extra terminal domain (BET) family of bromodomains (BRDs) are well-known drug targets for many human diseases.
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Affiliation(s)
- Chunyan Cheng
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Hongjuan Diao
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Yongheng Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Kai Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
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66
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Nicholas DA, Andrieu G, Strissel KJ, Nikolajczyk BS, Denis GV. BET bromodomain proteins and epigenetic regulation of inflammation: implications for type 2 diabetes and breast cancer. Cell Mol Life Sci 2017; 74:231-243. [PMID: 27491296 PMCID: PMC5222701 DOI: 10.1007/s00018-016-2320-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 12/18/2022]
Abstract
Chronic inflammation drives pathologies associated with type 2 diabetes (T2D) and breast cancer. Obesity-driven inflammation may explain increased risk and mortality of breast cancer with T2D reported in the epidemiology literature. Therapeutic approaches to target inflammation in both T2D and cancer have so far fallen short of the expected improvements in disease pathogenesis or outcomes. The targeting of epigenetic regulators of cytokine transcription and cytokine signaling offers one promising, untapped approach to treating diseases driven by inflammation. Recent work has deeply implicated the Bromodomain and Extra-Terminal domain (BET) proteins, which are acetylated histone "readers", in epigenetic regulation of inflammation. This review focuses on inflammation associated with T2D and breast cancer, and the possibility of targeting BET proteins as an approach to regulating inflammation in the clinic. Understanding inflammation in the context of BET protein regulation may provide a basis for designing promising therapeutics for T2D and breast cancer.
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Affiliation(s)
- Dequina A Nicholas
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Guillaume Andrieu
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Katherine J Strissel
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Barbara S Nikolajczyk
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Gerald V Denis
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA.
- Section of Hematology/Oncology, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, K520, Boston, MA, 02118, USA.
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67
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Yang Y, Zhao L, Xu B, Yang L, Zhang J, Zhang H, Zhou J. Design, synthesis and biological evaluation of dihydroquinoxalinone derivatives as BRD4 inhibitors. Bioorg Chem 2016; 68:236-44. [DOI: 10.1016/j.bioorg.2016.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 12/01/2022]
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68
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Meslamani J, Smith SG, Sanchez R, Zhou MM. Structural features and inhibitors of bromodomains. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:3-15. [PMID: 27769355 DOI: 10.1016/j.ddtec.2016.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/12/2016] [Accepted: 09/06/2016] [Indexed: 01/02/2023]
Abstract
Bromodomains are conserved structural modules responsible for recognizing acetylated-lysine residues on histone tails and other transcription-associated proteins, such as transcription factors and co-factors. Owing to their important functions in the regulation of ordered gene transcription in chromatin, bromodomains of the BET family proteins have recently been shown as druggable targets for a wide array of human diseases, including cancer and inflammation. Here we review the structural and functional features of the bromodomains and their small-molecule inhibitors. Additional new insights provided herein highlight the landscape of the ligand binding sites in the bromodomains that will hopefully facilitate further development of new inhibitors with optimal affinity and selectivity.
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Affiliation(s)
- Jamel Meslamani
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States.
| | - Steven G Smith
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States
| | - Roberto Sanchez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States
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69
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Carlino L, Rastelli G. Dual Kinase-Bromodomain Inhibitors in Anticancer Drug Discovery: A Structural and Pharmacological Perspective. J Med Chem 2016; 59:9305-9320. [DOI: 10.1021/acs.jmedchem.6b00438] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Carlino
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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70
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Galdeano C, Ciulli A. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology. Future Med Chem 2016; 8:1655-80. [PMID: 27193077 PMCID: PMC5321501 DOI: 10.4155/fmc-2016-0059] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.
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Affiliation(s)
- Carles Galdeano
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) & Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Alessio Ciulli
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
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71
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Andrieu G, Belkina AC, Denis GV. Clinical trials for BET inhibitors run ahead of the science. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:45-50. [PMID: 27769357 DOI: 10.1016/j.ddtec.2016.06.004] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/21/2016] [Accepted: 06/02/2016] [Indexed: 12/16/2022]
Abstract
Several cancer clinical trials for small molecule inhibitors of BET bromodomain proteins have been initiated. There is enthusiasm for the anti-proliferative effect of inhibiting BRD4, one of the targets of these inhibitors, which is thought to cooperate with MYC, a long-desired target for cancer therapeutics. However, no current inhibitor is selective for BRD4 among the three somatic BET proteins, which include BRD2 and BRD3; their respective functions are partially overlapping and none are functionally redundant with BRD4. Each BET protein controls distinct transcriptional pathways that are important for functions beyond cancer cell proliferation, including insulin production, cytokine gene transcription, T cell differentiation, adipogenesis and most seriously, active repression of dangerous latent viruses like HIV. BET inhibitors have been shown to reactivate HIV in human cells. Failure to appreciate that at concentrations used, no available BET inhibitor is member-selective, or to develop a sound biological basis to understand the diverse functions of BET proteins before undertaking for these clinical trials is reckless and likely to lead to adverse events. More mechanistic information from new basic science studies should enable proper focus on the most relevant cancers and define the expected side effect profiles.
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Affiliation(s)
- Guillaume Andrieu
- Department of Medicine, Cancer Research Center, Boston University School of Medicine, Boston, MA 02118, United States
| | - Anna C Belkina
- Flow Cytometry Core Facility, Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, United States
| | - Gerald V Denis
- Department of Medicine, Cancer Research Center, Boston University School of Medicine, Boston, MA 02118, United States; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, United States.
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72
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NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds. Acta Pharmacol Sin 2016; 37:984-93. [PMID: 27238211 DOI: 10.1038/aps.2016.19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/04/2016] [Indexed: 12/13/2022] Open
Abstract
AIM Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. METHODS 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. RESULTS An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8-10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100-260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. CONCLUSION An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors.
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73
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Kharenko OA, Gesner EM, Patel RG, Norek K, White A, Fontano E, Suto RK, Young PR, McLure KG, Hansen HC. RVX-297- a novel BD2 selective inhibitor of BET bromodomains. Biochem Biophys Res Commun 2016; 477:62-67. [PMID: 27282480 DOI: 10.1016/j.bbrc.2016.06.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/05/2016] [Indexed: 11/26/2022]
Abstract
Bromodomains are epigenetic readers that specifically bind to the acetyl lysine residues of histones and transcription factors. Small molecule BET bromodomain inhibitors can disrupt this interaction which leads to potential modulation of several disease states. Here we describe the binding properties of a novel BET inhibitor RVX-297 that is structurally related to the clinical compound RVX-208, currently undergoing phase III clinical trials for the treatment of cardiovascular diseases, but is distinctly different in its biological and pharmacokinetic profiles. We report that RVX-297 preferentially binds to the BD2 domains of the BET bromodomain and Extra Terminal (BET) family of protein. We demonstrate the differential binding modes of RVX-297 in BD1 and BD2 domains of BRD4 and BRD2 using X-ray crystallography, and describe the structural differences driving the BD2 selective binding of RVX-297. The isothermal titration calorimetry (ITC) data illustrate the related differential thermodynamics of binding of RVX-297 to single as well as dual BET bromodomains.
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Affiliation(s)
- Olesya A Kharenko
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada.
| | - Emily M Gesner
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Reena G Patel
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Karen Norek
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Andre White
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Eric Fontano
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Robert K Suto
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Peter R Young
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Kevin G McLure
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Henrik C Hansen
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
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74
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Ghoshal A, Yugandhar D, Srivastava AK. BET inhibitors in cancer therapeutics: a patent review. Expert Opin Ther Pat 2016; 26:505-22. [PMID: 26924192 DOI: 10.1517/13543776.2016.1159299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Inhibition of Bromodomain and Extra Terminal (BET) proteins is an emerging approach for developing advanced cancer therapeutics. In 2015, at least thirty patents have been published for developing cancer chemotherapeutics by targeting BET. Currently there are seven small molecule BET inhibitors in various stages of clinical trials for the development of anti-cancer drugs. AREAS COVERED Important patents focusing on development of BET inhibitors as potential cancer therapeutics published in 2015 have been covered. The reports are presented together with a review of the related structural chemical space. This review mainly focuses on the therapeutic applications, chemical class and structural modifications along with the molecules currently in clinical trials. EXPERT OPINION BET sub-family proteins are one of the emerging targets to develop anti-cancer agents. Although many research groups have demonstrated the rationality of BET inhibition to combat cancer, a detailed molecular study needs to be performed to investigate the affected biological pathways. Selectivity among BET proteins should be kept in mind while developing BET inhibitors. In-silico molecular modelling studies can also provide valuable information for designing selective BET inhibitors towards anti-cancer drug discovery and development.
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Affiliation(s)
- Anirban Ghoshal
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India
| | - D Yugandhar
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India.,b Chemical Science Division, Academy of Scientific & Innovative Research (AcSIR) , New Delhi , India
| | - Ajay Kumar Srivastava
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India.,b Chemical Science Division, Academy of Scientific & Innovative Research (AcSIR) , New Delhi , India
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