1
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Viviano M, Cipriano A, Fabbrizi E, Feoli A, Castellano S, Sbardella G, Mai A, Milite C, Rotili D. Successes and challenges in the development of BD1-selective BET inhibitors: a patent review. Expert Opin Ther Pat 2024; 34:529-545. [PMID: 38465537 DOI: 10.1080/13543776.2024.2327300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
INTRODUCTION Bromodomain and ExtraTerminal (BET) domain proteins are transcriptional cofactors that, recognizing acetylated lysines of histone and non-histone proteins, can modulate gene expression. The BET family consists of four members, each of which contains two bromodomains (BD1 and BD2) able to recognize the acetylated mark. Pan-BET inhibitors (BETi) have shown a promising anticancer potential in many clinical trials; however, their further development has been in part hampered by the side effects due to their lack of selectivity. Mounting evidence suggests that BD1 is primarily involved in cancer and that its selective inhibition can phenocopy the anticancer effects of pan-BETi with increased tolerability. Therefore, the development of BD1 selective inhibitors is highly pursed in both academia and industry. AREAS COVERED This review aims at giving an overview of the patent literature of BD1-selective BETi between 2014 and 2023. WIPO, USPTO, EPO, and SciFinder® databases were used for the search of patents. EXPERT OPINION The development of BD1-selective BETi, despite challenging, is highly desirable as it could have a great impact on the development of new safer anticancer therapeutics. Several strategies could be applied to discover potent and selective compounds with limited side effects.
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Affiliation(s)
- Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Alessandra Cipriano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Emanuele Fabbrizi
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
| | - Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Antonello Mai
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
| | - Ciro Milite
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Dante Rotili
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
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2
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Shi M, Li Y, Pan W, Fu Z, Wang K, Liu X, Li N, Tang B. A BRD4-Targeting Photothermal Agent for Controlled Protein Degradation. Angew Chem Int Ed Engl 2024:e202403258. [PMID: 38721770 DOI: 10.1002/anie.202403258] [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: 02/15/2024] [Indexed: 06/19/2024]
Abstract
BRD4 protein plays a pivotal role in cell cycle regulation and differentiation. Disrupting the activity of BRD4 has emerged as a promising strategy for inhibiting the growth and proliferation of cancer cells. Herein, we introduced a BRD4-targeting photothermal agent for controlled protein degradation, aiming to enhance low-temperature photothermal therapy (PTT) for cancer treatment. By incorporating a BRD4 protein inhibitor into a cyanine dye scaffold, the photothermal agent specifically bond to the bromodomain of BRD4. Upon low power density laser irradiation, the agent induced protein degradation, directly destroying the BRD4 structure and inhibiting its transcriptional regulatory function. This strategy not only prolonged the retention time of the photothermal agent in cancer cells but also confined the targeted protein degradation process solely to the tumor tissue, minimizing side effects on normal tissues through the aid of exogenous signals. This work established a simple and feasible platform for future PTT agent design in clinical cancer treatment.
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Affiliation(s)
- Mingwan Shi
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Yuanyuan Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Zhongliang Fu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Kaiye Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Xiaohan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, P. R. China
- Laoshan Laboratory, Qingdao, 266237, P. R. China
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3
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Yang J, Yu YC, Wang ZX, Li QQ, Ding N, Leng XJ, Cai J, Zhang MY, Wang JJ, Zhou Y, Wei TH, Xue X, Dai WC, Sun SL, Yang Y, Li NG, Shi ZH. Research strategies of small molecules as chemotherapeutics to overcome multiple myeloma resistance. Eur J Med Chem 2024; 271:116435. [PMID: 38648728 DOI: 10.1016/j.ejmech.2024.116435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Multiple myeloma (MM), a cancer of plasma cells, is the second most common hematological malignancy which is characterized by aberrant plasma cells infiltration in the bone marrow and complex heterogeneous cytogenetic abnormalities. Over the past two decades, novel treatment strategies such as proteasome inhibitors, immunomodulators, and monoclonal antibodies have significantly improved the relative survival rate of MM patients. However, the development of drug resistance results in the majority of MM patients suffering from relapse, limited treatment options and uncontrolled disease progression after relapse. There are urgent needs to develop and explore novel MM treatment strategies to overcome drug resistance and improve efficacy. Here, we review the recent small molecule therapeutic strategies for MM, and introduce potential new targets and corresponding modulators in detail. In addition, this paper also summarizes the progress of multi-target inhibitor therapy and protein degradation technology in the treatment of MM.
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Affiliation(s)
- Jin Yang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Zi-Xuan Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xue-Jiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jiao Cai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Meng-Yuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jing-Jing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yun Zhou
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Tian-Hua Wei
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Wei-Chen Dai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Zhi-Hao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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4
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Chen X, Wu T, Du Z, Kang W, Xu R, Meng F, Liu C, Chen Y, Bao Q, Shen J, You Q, Cao D, Jiang Z, Guo X. Discovery of a brain-permeable bromodomain and extra terminal domain (BET) inhibitor with selectivity for BD1 for the treatment of multiple sclerosis. Eur J Med Chem 2024; 265:116080. [PMID: 38142510 DOI: 10.1016/j.ejmech.2023.116080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory autoimmune disease and lacks effective therapeutic agents. Dysregulation of transcription mediated by bromodomain and extra-terminal domain (BET) proteins containing two different bromodomains (BD1 and BD2) is an important factor in multiple diseases, including MS. Herein, we identified a series of BD1-biased inhibitors, in which compound 16 showed nanomolar potency for BD1 (Kd = 230 nM) and a 60-fold selectivity for BRD4 BD1 over BD2. The co-crystal structure of BRD4 BD1 with 16 indicated that the hydrogen bond interaction of 16 with BD1-specific Asp145 is important for BD1 selectivity. 16 showed favorable brain distribution in mice and PK properties in rats. 16 was able to inhibit microglia activation and had significant therapeutic effects on EAE mice including improvement of spinal cord inflammatory conditions and demyelination protection. Overall, these results suggest that brain-permeable BD1 inhibitors have the potential to be further investigated as therapeutic agents for MS.
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Affiliation(s)
- Xuetao Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Tingting Wu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhiyan Du
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Wenjing Kang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Rujun Xu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fanying Meng
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Chihong Liu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yali Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qichao Bao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Jingkang Shen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Danyan Cao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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5
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Jiang W, Hou Q, Xu H, Yang K, Wang X, Zhang K, Zeng Y, Li W, Wang B, Luo G, Zhao X, Shen H, Xu Y, Wu X. Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia. J Med Chem 2024; 67:1513-1532. [PMID: 38175809 DOI: 10.1021/acs.jmedchem.3c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Bromodomain-selective BET inhibition has emerged as a promising strategy to improve the safety profiles of pan-BET inhibitors. Herein, we report the discovery of potent phenoxyaryl pyridones as highly BD2-selective BET inhibitors. Compound 23 (IC50 = 2.9 nM) exhibited a comparable BRD4 BD2 inhibitory activity relative to 10 (IC50 = 1.0 nM) and remarkably improved selectivity over BRD4 BD1 (23: 2583-fold; 10: 344-fold). This lead compound significantly inhibited the proliferation of acute myeloid leukemia (AML) cell lines through induction of G0/G1 arrest and apoptosis in vitro. Excellent in vivo antitumor efficacy with 23 was achieved in an MV;411 mouse xenograft model. Pleasingly, compound 23 (hERG IC50 > 30 μM) mitigated the inhibition of the human ether-à-go-go-related gene (hERG) ion channel compared with 10 (hERG IC50 = 2.8 μM). This work provides a promising BD2-selective lead for the development of more effective and safe BET inhibitors as anticancer agents.
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Affiliation(s)
- Wenhua Jiang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Kexin Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaohui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Kuojun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Zeng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Wenqiang Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaofan Zhao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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6
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Bradley E, Fusani L, Chung CW, Craggs PD, Demont EH, Humphreys PG, Mitchell DJ, Phillipou A, Rioja I, Shah RR, Wellaway CR, Prinjha RK, Palmer DS, Kerr WJ, Reid M, Wall ID, Cookson R. Structure-Guided Design of a Domain-Selective Bromodomain and Extra Terminal N-Terminal Bromodomain Chemical Probe. J Med Chem 2023; 66:15728-15749. [PMID: 37967462 PMCID: PMC10726358 DOI: 10.1021/acs.jmedchem.3c00906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/11/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023]
Abstract
Small-molecule-mediated disruption of the protein-protein interactions between acetylated histone tails and the tandem bromodomains of the bromodomain and extra-terminal (BET) family of proteins is an important mechanism of action for the potential modulation of immuno-inflammatory and oncology disease. High-quality chemical probes have proven invaluable in elucidating profound BET bromodomain biology, with seminal publications of both pan- and domain-selective BET family bromodomain inhibitors enabling academic and industrial research. To enrich the toolbox of structurally differentiated N-terminal bromodomain (BD1) BET family chemical probes, this work describes an analysis of the GSK BRD4 bromodomain data set through a lipophilic efficiency lens, which enabled identification of a BD1 domain-biased benzimidazole series. Structure-guided growth targeting a key Asp/His BD1/BD2 switch enabled delivery of GSK023, a high-quality chemical probe with 300-1000-fold BET BD1 domain selectivity and a phenotypic cellular fingerprint consistent with BET bromodomain inhibition.
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Affiliation(s)
- Erin Bradley
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Thomas
Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Lucia Fusani
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Thomas
Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Chun-wa Chung
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | - Peter D. Craggs
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | | | | | | | - Alex Phillipou
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | - Inmaculada Rioja
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | - Rishi R. Shah
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | | | - Rab K. Prinjha
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | - David S. Palmer
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Thomas
Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - William J. Kerr
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Thomas
Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Marc Reid
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Thomas
Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Ian D. Wall
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
| | - Rosa Cookson
- GSK,
Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.
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7
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Shi M, Zheng X, Zhou Y, Yin Y, Lu Z, Zou Z, Hu Y, Liang Y, Chen T, Yang Y, Jing M, Lei D, Yang P, Li X. Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:33658-33674. [PMID: 37744850 PMCID: PMC10515184 DOI: 10.1021/acsomega.3c03935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Bromodomain and extra-terminal domain (BET) proteins play an important role in epigenetic regulation and are linked to several diseases; therefore, they are interesting targets. BET has two bromodomains: bromodomain 1 (BD1) and BD2. Selective targeting of BD1 or BD2 may produce different activities and greater effects than pan-BD inhibitors. However, the selective mechanism of the specific core must be studied at the atomic level. This study determined the effectiveness of pyrrolopyridone analogues to selectively inhibit BD2 using a pan-BD inhibitor (ABBV-075) and a selective-BD2 inhibitor (ABBV-744). Molecular dynamics simulations and calculations of binding free energies were used to systematically study the selectivity of BD2 inhibition by the pyrrolopyridone analogues. Overall, the pyrrolopyridone analogue inhibitors targeting BD2 interacted mainly with the following amino acid pairs between bromodomain-containing protein 4 (BRD4)-BD1 and BRD4-BD2 complexes: I146/V439, N140/N433, D144/H437, P82/P375, V87/V380, D88/D381, and Y139/Y432. The pyrrolopyridone analogues targeting BRD4-BD2 were divided into five regions based on selectivity mechanism. These results suggest that the R3 and R5 regions of pyrrolopyridone analogues can be modified to improve the selectivity between BRD4-BD1 and BRD4-BD2. The selectivity of BD2 inhibition by pyrrolopyridone analogues can be used to design novel BD2 inhibitors based on a pyrrolopyridone core.
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Affiliation(s)
- Mingsong Shi
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
- Innovation
Center of Nursing Research, Nursing Key Laboratory of Sichuan Province,
West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xueting Zheng
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Zhou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuan Yin
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhou Lu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhiyan Zou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Hu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuanyuan Liang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Tingting Chen
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuhan Yang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Meng Jing
- Department
of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Dan Lei
- School
of Life Science and Engineering, Southwest
University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Pei Yang
- Department
of Hepatobiliary Surgery, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Xiaoan Li
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
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8
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Cooper SA, Kostallari E, Shah VH. Angiocrine Signaling in Sinusoidal Health and Disease. Semin Liver Dis 2023; 43:245-257. [PMID: 37442155 PMCID: PMC10798369 DOI: 10.1055/a-2128-5907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Liver sinusoidal endothelial cells (LSECs) are key players in maintaining hepatic homeostasis. They also play crucial roles during liver injury by communicating with liver cell types as well as immune cells and promoting portal hypertension, fibrosis, and inflammation. Cutting-edge technology, such as single cell and spatial transcriptomics, have revealed the existence of distinct LSEC subpopulations with a clear zonation in the liver. The signals released by LSECs are commonly called "angiocrine signaling." In this review, we summarize the role of angiocrine signaling in health and disease, including zonation in healthy liver, regeneration, fibrosis, portal hypertension, nonalcoholic fatty liver disease, alcohol-associated liver disease, aging, drug-induced liver injury, and ischemia/reperfusion, as well as potential therapeutic advances. In conclusion, sinusoidal endotheliopathy is recognized in liver disease and promising preclinical studies are paving the path toward LSEC-specific pharmacotherapies.
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Affiliation(s)
- Shawna A. Cooper
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota
| | - Enis Kostallari
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Vijay H. Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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9
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Gajjela BK, Zhou MM. Bromodomain inhibitors and therapeutic applications. Curr Opin Chem Biol 2023; 75:102323. [PMID: 37207401 PMCID: PMC10524616 DOI: 10.1016/j.cbpa.2023.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
The bromodomain acts to recognize acetylated lysine in histones and transcription proteins and plays a fundamental role in chromatin-based cellular processes including gene transcription and chromatin remodeling. Many bromodomain proteins, particularly the bromodomain and extra terminal domain (BET) protein BRD4 have been implicated in cancers and inflammatory disorders and recognized as attractive drug targets. Although clinical studies of many BET bromodomain inhibitors have made substantial progress toward harnessing the therapeutic potential of targeting the bromodomain proteins, the development of this new class of epigenetic drugs is met with challenges, especially on-target dose-limiting toxicity. In this review, we highlight the current development of new-generation small molecule inhibitors for the BET and non-BET bromodomain proteins and discuss the research strategies used to target different bromodomain proteins for a wide array of human diseases including cancers and inflammatory disorders.
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Affiliation(s)
- Bharath Kumar Gajjela
- 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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10
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Divakaran A, Harki DA, Pomerantz WC. Recent progress and structural analyses of domain-selective BET inhibitors. Med Res Rev 2023; 43:972-1018. [PMID: 36971240 PMCID: PMC10520981 DOI: 10.1002/med.21942] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 12/21/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
Epigenetic mechanisms for controlling gene expression through heritable modifications to DNA, RNA, and proteins, are essential processes in maintaining cellular homeostasis. As a result of their central role in human diseases, the proteins responsible for adding, removing, or recognizing epigenetic modifications have emerged as viable drug targets. In the case of lysine-ε-N-acetylation (Kac ), bromodomains serve as recognition modules ("readers") of this activating epigenetic mark and competition of the bromodomain-Kac interaction with small-molecule inhibitors is an attractive strategy to control aberrant bromodomain-mediated gene expression. The bromodomain and extra-terminal (BET) family proteins contain eight similar bromodomains. These BET bromodomains are among the more commonly studied bromodomain classes with numerous pan-BET inhibitors showing promising anticancer and anti-inflammatory efficacy. However, these results have yet to translate into Food and Drug Administration-approved drugs, in part due to a high degree of on-target toxicities associated with pan-BET inhibition. Improved selectivity within the BET-family has been proposed to alleviate these concerns. In this review, we analyze the reported BET-domain selective inhibitors from a structural perspective. We highlight three essential characteristics of the reported molecules in generating domain selectivity, binding affinity, and mimicking Kac molecular recognition. In several cases, we provide insight into the design of molecules with improved specificity for individual BET-bromodomains. This review provides a perspective on the current state of the field as this exciting class of inhibitors continue to be evaluated in the clinic.
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Affiliation(s)
- Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
| | - William C.K. Pomerantz
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
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11
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Pan Z, Zhao Y, Wang X, Xie X, Liu M, Zhang K, Wang L, Bai D, Foster LJ, Shu R, He G. Targeting bromodomain-containing proteins: research advances of drug discovery. MOLECULAR BIOMEDICINE 2023; 4:13. [PMID: 37142850 PMCID: PMC10159834 DOI: 10.1186/s43556-023-00127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Bromodomain (BD) is an evolutionarily conserved protein module found in 46 different BD-containing proteins (BCPs). BD acts as a specific reader for acetylated lysine residues (KAc) and serves an essential role in transcriptional regulation, chromatin remodeling, DNA damage repair, and cell proliferation. On the other hand, BCPs have been shown to be involved in the pathogenesis of a variety of diseases, including cancers, inflammation, cardiovascular diseases, and viral infections. Over the past decade, researchers have brought new therapeutic strategies to relevant diseases by inhibiting the activity or downregulating the expression of BCPs to interfere with the transcription of pathogenic genes. An increasing number of potent inhibitors and degraders of BCPs have been developed, some of which are already in clinical trials. In this paper, we provide a comprehensive review of recent advances in the study of drugs that inhibit or down-regulate BCPs, focusing on the development history, molecular structure, biological activity, interaction with BCPs and therapeutic potentials of these drugs. In addition, we discuss current challenges, issues to be addressed and future research directions for the development of BCPs inhibitors. Lessons learned from the successful or unsuccessful development experiences of these inhibitors or degraders will facilitate the further development of efficient, selective and less toxic inhibitors of BCPs and eventually achieve drug application in the clinic.
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Affiliation(s)
- Zhaoping Pan
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Xie
- College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mingxia Liu
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyao Zhang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lian Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Gu He
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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12
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Barros EP, Ries B, Champion C, Rieder SR, Riniker S. Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. J Chem Inf Model 2023; 63:1794-1805. [PMID: 36917685 PMCID: PMC10052353 DOI: 10.1021/acs.jcim.2c01610] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by affecting the thermodynamics and thus the outcome of the binding process. As individual water contributions are impossible to measure experimentally, a range of computational methods have emerged to identify hydration sites in protein pockets and characterize their energetic contributions for drug discovery applications. Even though several methods model solvation effects explicitly, they focus on determining the stability of specific water sites independently and neglect solvation correlation effects upon replacement of clusters of water molecules, which typically happens in hit-to-lead optimization. In this work, we rigorously determine the conjoint effects of replacing all combinations of water molecules in protein binding pockets through the use of the RE-EDS multistate free-energy method, which combines Hamiltonian replica exchange (RE) and enveloping distribution sampling (EDS). Applications on the small bovine pancreatic trypsin inhibitor and four proteins of the bromodomain family illustrate the extent of solvation correlation effects on water thermodynamics, with the favorability of replacement of the water sites by pharmacophore probes highly dependent on the composition of the water network and the pocket environment. Given the ubiquity of water networks in biologically relevant protein targets, we believe our approach can be helpful for computer-aided drug discovery by providing a pocket-specific and a priori systematic consideration of solvation effects on ligand binding and selectivity.
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Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Candide Champion
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Salomé R Rieder
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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13
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Divakaran A, Scholtz CR, Zahid H, Lin W, Griffith EC, Lee RE, Chen T, Harki DA, Pomerantz WCK. Development of an N-Terminal BRD4 Bromodomain-Targeted Degrader. ACS Med Chem Lett 2022; 13:1621-1627. [PMID: 36262390 PMCID: PMC9575167 DOI: 10.1021/acsmedchemlett.2c00300] [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: 06/29/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Targeted protein degradation is a powerful induced-proximity tool to control cellular protein concentrations using small molecules. However, the design of selective degraders remains empirical. Among bromodomain and extra-terminal (BET) family proteins, BRD4 is the primary therapeutic target over family members BRD2/3/T. Existing strategies for selective BRD4 degradation use pan-BET inhibitors optimized for BRD4:E3 ubiquitin ligase (E3) ternary complex formation, but these result in residual inhibition of undegraded BET-bromodomains by the pan-BET ligand, obscuring BRD4-degradation phenotypes. Using our selective inhibitor of the first BRD4 bromodomain, iBRD4-BD1 (IC50 = 12 nM, 23- to 6200-fold intra-BET selectivity), we developed dBRD4-BD1 to selectively degrade BRD4 (DC50 = 280 nM). Notably, dBRD4-BD1 upregulates BRD2/3, a result not observed with degraders using pan-BET ligands. Designing BRD4 selectivity up front enables analysis of BRD4 biology without wider BET-inhibition and simplifies designing BRD4-selective heterobifunctional molecules, such as degraders with new E3 recruiting ligands or for additional probes beyond degraders.
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Affiliation(s)
- Anand Divakaran
- Department
of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Cole R. Scholtz
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Wenwei Lin
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Elizabeth C. Griffith
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C. K. Pomerantz
- Department
of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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14
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Li J, Zhang C, Xu H, Wang C, Dong R, Shen H, Zhuang X, Chen X, Li Q, Lu J, Zhang M, Wu X, Loomes KM, Zhou Y, Zhang Y, Liu J, Xu Y. Structure-Based Discovery and Optimization of Furo[3,2- c]pyridin-4(5 H)-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors. J Med Chem 2022; 65:5760-5799. [PMID: 35333526 DOI: 10.1021/acs.jmedchem.2c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pan-bromodomain and extra terminal (Pan-BET) inhibitors show profound efficacy but exhibit pharmacology-driven toxicities in clinical trials. The development of domain-selective BET inhibitors to separate efficacy and toxicity is urgently needed. Herein, we report a series of furo[3,2-c]pyridin-4(5H)-one derivatives as novel BD2-selective BET inhibitors. The representative compound 8l (XY153) potently bound to BRD4 BD2 with an half-maximum inhibitory concentration (IC50) value of 0.79 nM and displayed 354-fold selectivity over BRD4 BD1. Besides, 8l exhibited 6-fold BRD4 BD2 domain selectivity over other BET BD2 domains. Compound 8l displayed potent antiproliferative activity against multiple tumor cell lines, especially MV4-11 (IC50 = 0.55 nM), while showing weak cytotoxicity against the normal lung fibroblast cell line. It highlights the safety profile of this series of BD2 inhibitors. 8l also demonstrated good metabolic stability in vitro. These data indicate that 8l may serve as a new and valuable lead compound for the development of potential therapeutics against acute myeloid leukemia (AML).
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Affiliation(s)
- Junhua Li
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Cheng Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chao Wang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Ruibo Dong
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xiaoxi Zhuang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xiaoshan Chen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Qiu Li
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Jibu Lu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Maofeng Zhang
- College of Pharmacy, Taizhou Polytechnic College, Taizhou 225300, China
| | - Xishan Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Kerry M Loomes
- School of Biological Sciences & Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand
| | - Yulai Zhou
- School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Jinsong Liu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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15
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Chen J, Tang P, Wang Y, Wang J, Yang C, Li Y, Yang G, Wu F, Zhang J, Ouyang L. Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and Development. J Med Chem 2022; 65:5184-5211. [PMID: 35324195 DOI: 10.1021/acs.jmedchem.1c01835] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Blocking the interactions between bromodomain and extraterminal (BET) proteins and acetylated lysines of histones by small molecules has important implications for the treatment of cancers and other diseases. Many pan-BET inhibitors have shown satisfactory results in clinical trials, but their potential for poor tolerability and toxicity persist. However, recently reported studies illustrate that some BET bromodomain (BET-BD1 or BET-BD2)-selective inhibitors have advantage over pan-inhibitors, including reduced toxicity concerns. Furthermore, some selective BET inhibitors have similar or even better therapeutic efficacy in inflammatory diseases or cancers. Therefore, the development of selective BET inhibitors has become a hot spot for medicinal chemists. Here, we summarize the known selective BET-BD1 and BET-BD2 inhibitors and review the methods for enhancing the selectivity and potency of these inhibitors based on their different modes of interactions with BET-BD1 or BET-BD2. Finally, we discuss prospective strategies that selectively target the bromodomains of BET proteins.
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Affiliation(s)
- Juncheng Chen
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chengcan Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yang Li
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Gaoxia Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fengbo Wu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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16
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Cai M, Dong J, Li H, Qin JJ. Recent Developments in Targeting Bromodomain and Extra Terminal Domain Proteins for Cancer Therapeutics. Curr Med Chem 2022; 29:4391-4409. [PMID: 35152859 DOI: 10.2174/0929867329666220211091806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Bromodomain and extra-terminal domain (BET) proteins are a well-studied family of proteins associated with a variety of diseases including malignancy and chronic inflammation. Currently, numerous pan BET inhibitors have exhibited potent efficacy in several in vivo preclinical models and entered clinical trials, but have largely stalled due to their adverse events. Therefore, the development of new selective inhibitors and PROTACs (Proteolysis Targeting Chimeras) targeting BET is urgently needed. In the present review, we summarize the BET protein structure, the recent development of BET inhibitors, focusing mainly on BRD4-selective inhibitors and PROTAC degraders.
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Affiliation(s)
- Maohua Cai
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jinyun Dong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Haobin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jiang-Jiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
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17
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Cui H, Divakaran A, Hoell ZJ, Ellingson MO, Scholtz CR, Zahid H, Johnson JA, Griffith EC, Gee CT, Lee AL, Khanal S, Shi K, Aihara H, Shah VH, Lee RE, Harki DA, Pomerantz WCK. A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J Med Chem 2022; 65:2342-2360. [PMID: 35007061 DOI: 10.1021/acs.jmedchem.1c01779] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.
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Affiliation(s)
- Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Zachariah J Hoell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Mikael O Ellingson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Cole R Scholtz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Elizabeth C Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Amani L Lee
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Shalil Khanal
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Vijay H Shah
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
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18
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Progress in the development of domain selective inhibitors of the bromo and extra terminal domain family (BET) proteins. Eur J Med Chem 2021; 226:113853. [PMID: 34547507 DOI: 10.1016/j.ejmech.2021.113853] [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: 07/02/2021] [Revised: 09/04/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022]
Abstract
Dysfunction of the bromo and extra terminal domain (BET) family proteins is associated with many human diseases, therefore the BET family proteins have been considered as promising targets for drug development. Numerous small molecular compounds targeting the N-terminal two tandem bromodomains BD1 and BD2 of the BET family proteins have been reported, and a number of them have been advanced into clinical trials. Most of the BET inhibitors entered clinical trials are pan-BET inhibitors which show poor selectivity among BET members and bind to the BD1 and BD2 of the BET family proteins with comparable binding affinities. In order to elucidate the distinct functions of BD1s and BD2s, many BD1 and BD2 selective BET inhibitors have also been developed. In this review, we summarized the recent progress in the development of BD1 and BD2 selective BET inhibitors, and provided the perspectives for future studies of BET inhibitors.
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19
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Buchholz CR, Pomerantz WCK. 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery. RSC Chem Biol 2021; 2:1312-1330. [PMID: 34704040 PMCID: PMC8496043 DOI: 10.1039/d1cb00085c] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.
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Affiliation(s)
- Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
| | - William C K Pomerantz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
- Department of Chemistry, University of Minnesota 207 Pleasant St. SE Minneapolis Minnesota 55455 USA
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20
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Zahid H, Buchholz CR, Singh M, Ciccone MF, Chan A, Nithianantham S, Shi K, Aihara H, Fischer M, Schönbrunn E, Dos Santos CO, Landry JW, Pomerantz WCK. New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. J Med Chem 2021; 64:13902-13917. [PMID: 34515477 DOI: 10.1021/acs.jmedchem.1c01294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (Kd = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.
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Affiliation(s)
- Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Manjulata Singh
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Michael F Ciccone
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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21
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Wang Q, Shao X, Leung ELH, Chen Y, Yao X. Selectively targeting individual bromodomain: Drug discovery and molecular mechanisms. Pharmacol Res 2021; 172:105804. [PMID: 34450309 DOI: 10.1016/j.phrs.2021.105804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins include bromodomain and extra-terminal (BET) and non-BET families. Due to the conserved bromodomain (BD) module between BD-containing proteins, and especially BETs with each member having two BDs (BD1 and BD2), the high degree of structural similarity makes BD-selective inhibitors much difficult to be designed. However, increasing evidences emphasized that individual BDs had distinct functions and different cellular phenotypes after pharmacological inhibition, and selectively targeting one of the BDs could result in a different efficacy and tolerability profile. This review is to summarize the pioneering progress of BD-selective inhibitors targeting BET and non-BET proteins, focusing on their structural features, biological activity, therapeutic application and experimental/theoretical mechanisms. The present proteolysis targeting chimeras (PROTAC) degraders targeting BDs, and clinical status of BD-selective inhibitors were also analyzed, providing a new insight into future direction of bromodomain-selective drug discovery.
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Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China
| | - Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China.
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22
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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23
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Liu M, Cao S, He L, Gao J, Arab JP, Cui H, Xuan W, Gao Y, Sehrawat TS, Hamdan FH, Ventura-Cots M, Argemi J, Pomerantz WCK, Johnsen SA, Lee JH, Gao F, Ordog T, Mathurin P, Revzin A, Bataller R, Yan H, Shah VH. Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis. Nat Commun 2021; 12:4560. [PMID: 34315876 PMCID: PMC8316465 DOI: 10.1038/s41467-021-24843-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
Alcoholic hepatitis (AH) is associated with liver neutrophil infiltration through activated cytokine pathways leading to elevated chemokine expression. Super-enhancers are expansive regulatory elements driving augmented gene expression. Here, we explore the mechanistic role of super-enhancers linking cytokine TNFα with chemokine amplification in AH. RNA-seq and histone modification ChIP-seq of human liver explants show upregulation of multiple CXCL chemokines in AH. Liver sinusoidal endothelial cells (LSEC) are identified as an important source of CXCL expression in human liver, regulated by TNFα/NF-κB signaling. A super-enhancer is identified for multiple CXCL genes by multiple approaches. dCas9-KRAB-mediated epigenome editing or pharmacologic inhibition of Bromodomain and Extraterminal (BET) proteins, transcriptional regulators vital to super-enhancer function, decreases chemokine expression in vitro and decreases neutrophil infiltration in murine models of AH. Our findings highlight the role of super-enhancer in propagating inflammatory signaling by inducing chemokine expression and the therapeutic potential of BET inhibition in AH treatment.
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Affiliation(s)
- Mengfei Liu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Li He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhang Gao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
| | - Juan P Arab
- Department of Gastroenterology and Hepatology, School of Medicine of the Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Weixia Xuan
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, China
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yandong Gao
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tejasav S Sehrawat
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Meritxell Ventura-Cots
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josepmaria Argemi
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Steven A Johnsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fei Gao
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Ramon Bataller
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Huihuang Yan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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24
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Cui H, Carlson AS, Schleiff MA, Divakaran A, Johnson JA, Buchholz CR, Zahid H, Vail NR, Shi K, Aihara H, Harki DA, Miller GP, Topczewski JJ, Pomerantz WCK. 4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. J Med Chem 2021; 64:10497-10511. [PMID: 34236185 DOI: 10.1021/acs.jmedchem.1c00933] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The bromodomain and extra terminal (BET) protein family recognizes acetylated lysines within histones and transcription factors using two N-terminal bromodomains, D1 and D2. The protein-protein interactions between BET bromodomains, acetylated histones, and transcription factors are therapeutic targets for BET-related diseases, including inflammatory disease and cancer. Prior work demonstrated that methylated-1,2,3-triazoles are suitable N-acetyl lysine mimetics for BET inhibition. Here we describe a structure-activity relationship study of triazole-based inhibitors that improve affinity, D1 selectivity, and microsomal stability. These outcomes were accomplished by targeting a nonconserved residue, Asp144 and a conserved residue, Met149, on BRD4 D1. The lead inhibitors DW34 and 26 have a BRD4 D1 Kd of 12 and 6.4 nM, respectively. Cellular activity was demonstrated through suppression of c-Myc expression in MM.1S cells and downregulation of IL-8 in TNF-α-stimulated A549 cells. These data indicate that DW34 and 26 are new leads to investigate the anticancer and anti-inflammatory activity of BET proteins.
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Affiliation(s)
- Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Angela S Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Nora R Vail
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Joseph J Topczewski
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
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25
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Bai P, Lan Y, Wang H, Liu Y, Striar R, Yuan G, Afshar S, Zagaroli JS, Tocci DR, Langan AG, Wang C. Synthesis and Characterization of a Positron Emission Tomography Imaging Probe Selectively Targeting the Second Bromodomain of Bromodomain Protein BRD4. Bioconjug Chem 2021; 32:1711-1718. [PMID: 34139120 DOI: 10.1021/acs.bioconjchem.1c00245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Two tandem bromodomains (BD1 and BD2) of bromodomain and extraterminal domain (BET) family proteins have shown distinct roles in mediating gene transcription and expression. Inhibitors that interact with a specific bromodomain may contribute to a specific therapeutic potential with fewer side effects. However, little is known about this disease-related target. Positron emission tomography (PET) imaging could allow us to achieve in-depth knowledge of the BD2 bromodomain. Herein we describe the radiosynthesis and evaluation of [11C]1 as a BRD4 BD2 bromodomain PET imaging radioligand. Our preliminary PET imaging results in rodents demonstrated that [11C]1 had suitable biodistribution in peripheral organs and tissues. Further blocking studies indicated that [11C]1 had good binding specificity toward the BD2 bromodomain. This study may pave the way for the development of a PET radioligand specifically targeting BD1/2 bromodomains as well as for the biological mechanism investigation of BD1/2 bromodomains.
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26
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Tang P, Zhang J, Liu J, Chiang CM, Ouyang L. Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development. J Med Chem 2021; 64:2419-2435. [PMID: 33616410 DOI: 10.1021/acs.jmedchem.0c01487] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomain and extraterminal (BET) proteins bind acetylated lysine residues in histones and nonhistone proteins via tandem bromodomains and regulate chromatin dynamics, cellular processes, and disease procession. Thus targeting BET proteins is a promising strategy for treating various diseases, especially malignant tumors and chronic inflammation. Many pan-BET small-molecule inhibitors have been described, and some of them are in clinical evaluation. Nevertheless, the limited clinical efficacy of the current BET inhibitors is also evident and has inspired the development of new technologies to improve their clinical outcomes and minimize unwanted side effects. In this Review, we summarize the latest protein characteristics and biological functions of BRD4 as an example of BET proteins, analyze the clinical development status and preclinical resistance mechanisms, and discuss recent advances in BRD4-selective inhibitors, dual-target BET inhibitors, proteolysis targeting chimera degraders, and protein-protein interaction inhibitors.
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Affiliation(s)
- Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Pharmacology, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
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27
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Kalra P, McGraw L, Kimbrough JR, Pandey AK, Solberg J, Cui H, Divakaran A, John K, Hawkinson JE, Pomerantz WCK. Quantifying the Selectivity of Protein-Protein and Small Molecule Interactions with Fluorinated Tandem Bromodomain Reader Proteins. ACS Chem Biol 2020; 15:3038-3049. [PMID: 33138352 PMCID: PMC8185897 DOI: 10.1021/acschembio.0c00720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multidomain bromodomain-containing proteins regulate gene expression via chromatin binding, interactions with the transcriptional machinery, and by recruiting enzymatic activity. Selective inhibition of members of the bromodomain and extra-terminal (BET) family is important to understand their role in disease and gene regulation, although due to the similar binding sites of BET bromodomains, selective inhibitor discovery has been challenging. To support the bromodomain inhibitor discovery process, here we report the first application of protein-observed fluorine (PrOF) NMR to the tandem bromodomains of BRD4 and BRDT to quantify the selectivity of their interactions with acetylated histones as well as small molecules. We further determine the selectivity profile of a new class of ligands, 1,4-acylthiazepanes, and find them to have ≥3-10-fold selectivity for the C-terminal bromodomain of both BRD4 and BRDT. Given the speed and lower protein concentration required over traditional protein-observed NMR methods, we envision that these fluorinated tandem proteins may find use in fragment screening and evaluating nucleosome and transcription factor interactions.
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Affiliation(s)
- Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Logan McGraw
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jennifer R Kimbrough
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Anil K Pandey
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jonathan Solberg
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
| | - Kristen John
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Jon E Hawkinson
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
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