1
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De S, Sahu R, Palei S, Narayan Nanda L. Synthesis, SAR, and application of JQ1 analogs as PROTACs for cancer therapy. Bioorg Med Chem 2024; 112:117875. [PMID: 39178586 DOI: 10.1016/j.bmc.2024.117875] [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: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
JQ1 is a wonder therapeutic molecule that selectively inhibits the BRD4 signaling pathway and is thus widely used in the anticancer drug discovery program. Due to its unique selective BRD4 binding property, its applications are further extended in the design and synthesis of bi-functional PROTAC molecules. This BRD4 targeting PROTAC molecule selectively degrades the protein by proteolysis. There are several modifications of JQ1 known to date and extensively explored for their applications in PROTAC technology by several research groups in academia as well as industry for targeting oncogenic genes. In this review, we have covered the discovery and synthesis of the JQ1 molecule. The SAR of the JQ1 analogs will help researchers develop potent JQ1 compounds with improved inhibitory properties against malignant cells. Furthermore, we explored the potential application of JQ1 analogs in PROTAC technology. The brief history of the bromodomain family of proteins, as well as the obstacles connected with PROTAC technology, can help comprehend the context of the current research, which has the potential to improve the drug development process. Overall, this review comprehensively appraises JQ1 molecules and their prior implementation in PROTAC technology and cancer therapy.
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Affiliation(s)
- Soumik De
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, An OCC of Homi Bhabha National Institute (HBNI), Khurda, Odisha 752050, India
| | - Raghaba Sahu
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Shubhendu Palei
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Laxmi Narayan Nanda
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Harvard Medical School, Cambridge 02142, United States; P.G. Department of Chemistry, Government Autonomous College, Utkal University, Angul 759143, Odisha, India.
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2
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Ma Z, Zhang C, Bolinger AA, Zhou J. An updated patent review of BRD4 degraders. Expert Opin Ther Pat 2024; 34:929-951. [PMID: 39219068 PMCID: PMC11427152 DOI: 10.1080/13543776.2024.2400166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/17/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Bromodomain-containing protein 4 (BRD4), an important epigenetic reader, is closely associated with the pathogenesis and development of many diseases, including various cancers, inflammation, and infectious diseases. Targeting BRD4 inhibition or protein elimination with small molecules represents a promising therapeutic strategy, particularly for cancer therapy. AREAS COVERED The recent advances of patented BRD4 degraders were summarized. The challenges, opportunities, and future directions for developing novel potent and selective BRD4 degraders are also discussed. The patents of BRD4 degraders were searched using the SciFinder and Cortellis Drug Discovery Intelligence database. EXPERT OPINION BRD4 degraders exhibit superior efficacy and selectivity to BRD4 inhibitors, given their unique mechanism of protein degradation instead of protein inhibition. Excitingly, RNK05047 is now in phase I/II clinical trials, indicating that selective BRD4 protein degradation may offer a viable therapeutic strategy, particularly for cancer. Targeting BRD4 with small-molecule degraders provides a promising approach with the potential to overcome therapeutic resistance for treating various BRD4-associated diseases.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Cun Zhang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
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3
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Horai Y, Suda N, Uchihashi S, Katakuse M, Shigeno T, Hirano T, Takahara J, Fujita T, Mukoyama Y, Haga Y. A novel 7-phenoxy-benzimidazole derivative as a potent and orally available BRD4 inhibitor for the treatment of melanoma. Bioorg Med Chem 2024; 112:117882. [PMID: 39167978 DOI: 10.1016/j.bmc.2024.117882] [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: 07/10/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
The bromodomain-containing protein 4 (BRD4), which is a key epigenetic regulator in cancer, has emerged as an attractive target for the treatment of melanoma. In this study, we investigate 7-phenoxy-benzimidazole derivative 12, which is a novel BRD4 inhibitor for the treatment of melanoma, by performing scaffold hopping on the previously reported benzimidazole derivative 1. Despite their good oral and intravenous exposure, the compounds obtained by modifying derivate 1 exhibit mutagenicity, which was confirmed by the positive Ames test results. Based on our hypothesis that the cause of the Ames test positivity is the metabolic intermediates generated from those chemical series, we implemented a scaffold hopping strategy to avoid the N-benzyl moiety by relocating the substituent groups to preserve the essential interaction. Based on this strategy, we successfully obtained compound 12; the Ames test results of this compound were negative. Notably, compound 12 not only exhibited a favorable pharmacokinetic (PK) profile but also significant tumor growth inhibition in a mouse melanoma xenograft model, indicating its potential as a therapeutic agent for the treatment of melanoma.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yuji Haga
- Maruho Co., Ltd., Kyoto 600-8815, Japan
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4
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Feng B, Yu H, Dong X, Díaz-Holguín A, Antolin AA, Hu H. Combining Data-Driven and Structure-Based Approaches in Designing Dual PARP1-BRD4 Inhibitors for Breast Cancer Treatment. J Chem Inf Model 2024. [PMID: 39292752 DOI: 10.1021/acs.jcim.4c01421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) inhibitors have revolutionized the treatment of many cancers with DNA-repairing deficiencies via synthetic lethality. Advocated by the polypharmacology concept, recent evidence discovered that a significantly synergistic effect in increasing the death of cancer cells was observed by simultaneously perturbating the enzymatic activities of bromodomain-containing protein 4 (BRD4) and PARP1. Here, we developed a novel cheminformatics approach combined with a structure-based method aiming to facilitate the design of dual PARP1-BRD4 inhibitors. Instead of linking pharmacophores, the developed approach first identified merged pharmacophores (a pool of amide-containing ring systems), from which phenanthridin-6(5H)-one was further prioritized. Based on this starting point, several small molecules were rationally designed, among which HF4 exhibited low micromolar inhibitory activity against BRD4 and PARP1, particularly exhibiting strong inhibition of BRD4 BD1 with an IC50 value of 204 nM. Furthermore, it demonstrated potent antiproliferative effects against breast cancer gene-deficient and proficient breast cancer cell lines by arresting cell cycle progression and impeding DNA damage repair. Collectively, our systematic efforts to design lead-like molecules have the potential to open doors for the exploration of dual PARP1-BRD4 inhibitors as a promising avenue for breast cancer treatment. Furthermore, the developed approach can be extended to systematically design inhibitors targeting PARP1 and other related targets.
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Affiliation(s)
- Bo Feng
- Department of Pharmacy, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, P. R. China
| | - Hui Yu
- Information School, University of Sheffield, 211 Portobello, Sheffield, S1 4DP, U.K
| | - Xu Dong
- Department of Pharmacy, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, P. R. China
| | - Alejandro Díaz-Holguín
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24, Uppsala, Sweden
| | - Albert A Antolin
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia 08907, Spain
| | - Huabin Hu
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24, Uppsala, Sweden
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K
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5
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Wei Q, Gan C, Sun M, Xie Y, Liu H, Xue T, Deng C, Mo C, Ye T. BRD4: an effective target for organ fibrosis. Biomark Res 2024; 12:92. [PMID: 39215370 PMCID: PMC11365212 DOI: 10.1186/s40364-024-00641-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Fibrosis is an excessive wound-healing response induced by repeated or chronic external stimuli to tissues, significantly impacting quality of life and primarily contributing to organ failure. Organ fibrosis is reported to cause 45% of all-cause mortality worldwide. Despite extensive efforts to develop new antifibrotic drugs, drug discovery has not kept pace with the clinical demand. Currently, only pirfenidone and nintedanib are approved by the FDA to treat pulmonary fibrotic illness, whereas there are currently no available antifibrotic drugs for hepatic, cardiac or renal fibrosis. The development of fibrosis is closely related to epigenetic alterations. The field of epigenetics primarily studies biological processes, including chromatin modifications, epigenetic readers, DNA transcription and RNA translation. The bromodomain and extra-terminal structural domain (BET) family, a class of epigenetic readers, specifically recognizes acetylated histone lysine residues and promotes the formation of transcriptional complexes. Bromodomain-containing protein 4 (BRD4) is one of the most well-researched proteins in the BET family. BRD4 is implicated in the expression of genes related to inflammation and pro-fibrosis during fibrosis. Inhibition of BRD4 has shown promising anti-fibrotic effects in preclinical studies; however, no BRD4 inhibitor has been approved for clinical use. This review introduces the structure and function of BET proteins, the research progress on BRD4 in organ fibrosis, and the inhibitors of BRD4 utilized in fibrosis. We emphasize the feasibility of targeting BRD4 as an anti-fibrotic strategy and discuss the therapeutic potential and challenges associated with BRD4 inhibitors in treating fibrotic diseases.
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Affiliation(s)
- Qun Wei
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Cailing Gan
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Sun
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuting Xie
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongyao Liu
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Taixiong Xue
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Conghui Deng
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tinghong Ye
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Ningxia Medical University, Yin Chuan, 640100, China.
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6
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Ma Y, Liu N, Shi Y, Ma S, Wang Y, Zheng W, Sun R, Song Y, Chen M, Qu L, Mao R, Fan Y. BRD4L cooperates with MYC to block local tumor invasion via suppression of S100A10. Cell Signal 2024; 119:111173. [PMID: 38604343 DOI: 10.1016/j.cellsig.2024.111173] [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: 01/07/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Targeted therapy based on BRD4 and MYC shows promise due to their well-researched oncogenic functions in cancer, but their tumor-suppressive roles are less understood. In this study, we employ a systematic approach to delete exons that encode the low-complexity domain (LCD) of BRD4L in cells by using CRISPR-Cas9. In particular, the deletion of exon 14 (BRD4-E14) results in cellular morphological changes towards spindle-shaped and loosely packed. BRD4-E14 deficient cells show increased cell migration and reduced cell adhesion. The expression of S100A10 was significantly increased in cells lacking E14. BRD4L binds with MYC via the E14-encoded region of the LCD to inhibit the expression of S100A10. In cancer tissues, there is a positive correlation between BRD4 and MYC, while both of these proteins are negatively associated with S100A10 expression. Finally, knocking out the BRD4-E14 region or MYC promotes tumor growth in vivo. Together, these data support a tumor-suppressive role of BRD4L and MYC in some contexts. This discovery emphasizes the significance of a discreetly design and precise patient recruitment in clinical trials that testing cancer therapy based BRD4 and MYC.
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Affiliation(s)
- Yongyi Ma
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Nan Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yu Shi
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Shuyan Ma
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Yingjun Wang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China
| | - Wen Zheng
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Rong Sun
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yihua Song
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Lishuai Qu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China.
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China.
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7
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Zhang Y, Ming A, Wang J, Chen W, Fang Z. PROTACs targeting androgen receptor signaling: Potential therapeutic agents for castration-resistant prostate cancer. Pharmacol Res 2024; 205:107234. [PMID: 38815882 DOI: 10.1016/j.phrs.2024.107234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
After the initial androgen deprivation therapy (ADT), part of the prostate cancer may continuously deteriorate into castration-resistant prostate cancer (CRPC). The majority of patients suffer from the localized illness at primary diagnosis that could rapidly assault other organs. This disease stage is referred as metastatic castration-resistant prostate cancer (mCRPC). Surgery and radiation are still the treatment of CRPC, but have some adverse effects such as urinary symptoms and sexual dysfunction. Hormonal castration therapy interfering androgen receptor (AR) signaling pathway is indispensable for most advanced prostate cancer patients, and the first- and second-generation of novel AR inhibitors could effectively cure hormone sensitive prostate cancer (HSPC). However, the resistance to these chemical agents is inevitable, so many of patients may experience relapses. The resistance to AR inhibitor mainly involves AR mutation, splice variant formation and amplification, which indicates the important role in CRPC. Proteolysis-targeting chimera (PROTAC), a potent technique to degrade targeted protein, has recently undergone extensive development as a biological tool and therapeutic drug. This technique has the potential to become the next generation of antitumor therapeutics as it could overcome the shortcomings of conventional small molecule inhibitors. In this review, we summarize the molecular mechanisms on PROTACs targeting AR signaling for CRPC, hoping to provide insights into drug development and clinical medication.
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Affiliation(s)
- Yulu Zhang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China; Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, China
| | - Annan Ming
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China; Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, China
| | - Junyan Wang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
| | | | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China.
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8
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Qiao XP, Wang XT, Wang S, Mu HX, Wang QS, Chen SW. Discovery of indole-2-one derivatives as BRD4 (BD1) selective inhibitors. Bioorg Med Chem 2024; 106:117752. [PMID: 38749341 DOI: 10.1016/j.bmc.2024.117752] [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: 03/10/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
Bromodomain protein 4 (BRD4) is a member of the BET family, and its overexpression is closely associated with the development of many tumors. Inhibition of BRD4 shows great therapeutic potential in anti-tumor, and pan-BRD4 inhibitors show adverse effects of dose limiting toxicity and thrombocytopenia in clinical trials. To improve clinical effects and reduce side effects, more efforts have focused on seeking selective inhibitors of BD1 or BD2. Herein, a series of indole-2-one derivatives were designed and synthesized through docking-guided optimization to find BRD4-BD1 selective inhibitors, and their BRD4 inhibitory and antiproliferation activities were evaluated. Among them, compound 21r had potent BRD4 inhibitory activity (the IC50 values of 41 nM and 313 nM in BD1 and BD2 domain), excellent anti-proliferation (the IC50 values of 4.64 ± 0.30 µM, 0.78 ± 0.03 µM, 5.57 ± 1.03 µM against HL-60, MV-4-11 and HT-29 cells), and displayed low toxicity against normal cell GES-1 cells. Further studies revealed that 21r inhibited proliferation by decreasing the expression of proto-oncogene c-Myc, blocking cell cycle in G0/G1 phase, and inducing apoptosis in MV-4-11 cells in a dose-dependent manner. All the results showed that compound 21r was a potent BRD4 inhibitor with BD1 selectivity, which had potential in treatment of leukemia.
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Affiliation(s)
- Xue-Peng Qiao
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Xue-Ting Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Hong-Xia Mu
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Qing-Shan Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Shi-Wu Chen
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
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Yin C, Jia S, Yang X, Wu L. Discovery of potent and novel dual NAMPT/BRD4 inhibitors for efficient treatment of hepatocellular carcinoma. Eur J Med Chem 2024; 271:116444. [PMID: 38691889 DOI: 10.1016/j.ejmech.2024.116444] [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: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
The NAPRT-induced increase in NAD+ levels was proposed as a mechanism contributing to hepatocellular carcinoma (HCC) resistance to NAMPT inhibitors. Thus, concurrently targeting NAMPT and NAPRT could be considered to overcome drug resistance. A BRD4 inhibitor downregulates the expression of NAPRT in HCC, and the combination of NAMPT inhibitors with BRD4 inhibitors simultaneously blocks NAD+ generation via salvage and the PH synthesis pathway. Moreover, the combination of the two agents significantly downregulated the expression of tumor-promoting genes and strongly promoted apoptosis. The present work identified various NAMPT/BRD4 dual inhibitors based on the multitargeted drug rationale. Among them, compound A2, which demonstrated the strongest effect, exhibited potent inhibition of NAMPT and BRD4 (IC50 = 35 and 58 nM, respectively). It significantly suppressed the growth and migration of HCC cells and facilitated their apoptosis. Furthermore, compound A2 also manifested a robust anticancer effect in HCCLM3 xenograft mouse models, with no apparent toxic effects. Our findings in this study provide an effective approach to target NAD+ metabolism for HCC treatment.
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Affiliation(s)
- Chunjia Yin
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Shuting Jia
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Jincheng People's Hospital, Jincheng 048026, China
| | - Xiaojuan Yang
- School of Pharmacy, Xinxiang University, Xinxiang 453003, China
| | - Liqiang Wu
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China.
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Liu Z, Xie Q, Zhao X, Tan Y, Wang W, Cao Y, Wei X, Mu G, Zhang H, Zhou S, Wang X, Cao Y, Li X, Chen S, Cao D, Cui Y, Xiang Q. The Pharmacogenetic Variability Associated with the Pharmacokinetics and Pharmacodynamics of Rivaroxaban in Healthy Chinese Subjects: A National Multicenter Exploratory Study. Clin Ther 2024; 46:313-321. [PMID: 38553322 DOI: 10.1016/j.clinthera.2024.02.009] [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: 10/20/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE This study aimed to explore the pharmacogenetic variability associated with the pharmacokinetics (PK) and pharmacodynamics (PD) of rivaroxaban in healthy Chinese subjects. METHODS This was a multicenter study that included 304 healthy adults aged 18 to 45 years with unknown genotypes. All participants were administered a single dose of rivaroxaban at 10 mg, 15 mg, or 20 mg. PK and PD parameters were measured, and exome-wide association analysis was conducted. FINDINGS Sixteen SNPs located on 11 genes influenced the AUC0-t. Among these, the 3 most influential genes were MiR516A2, PARP14, and MIR618. Thirty-six SNPs from 28 genes were associated with the PD of rivaroxaban. The 3 most influential genes were PKNOX2, BRD3, and APOL4 for anti-Xa activity, and GRIP2, PLCE1, and MLX for diluted prothrombin time (dPT). Among them, BRD3 played an important role in both the PK and PD of rivaroxaban. Anti-Xa activity (ng/mL) differed significantly among subjects with BRD3 rs467387: 145.1 ± 55.5 versus 139.9 ± 65.1 versus 164.0 ± 68.6 for GG, GA, and AA carriers, respectively (P = 0.0002). IMPLICATIONS This study found that that the regulation of the BRD3 gene might affect the PK and PD of rivaroxaban, suggesting that it should be studied as a new pharmacologic target. The correlation between this gene locus and clinical outcomes has yet to be verified in patients undergoing clinical treatment.
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Affiliation(s)
- Zhiyan Liu
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China; Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Qiufen Xie
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China; Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Xia Zhao
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Yunlong Tan
- Psychiatry Research Center, Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - Wenping Wang
- Department of GCP Center, Affiliated Hospital of Liaoning University of TCM, Shenyang City, Liaoning Province, China
| | - Yu Cao
- Office of Drug Clinical Trial Management, Affiliated Hospital of Qingdao University, Qingdao City, Shandong Province, China
| | - Xiaohua Wei
- Clinical Trial Research Center, Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, China
| | - Guangyan Mu
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Hanxu Zhang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Shuang Zhou
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Ying Cao
- Department of GCP Center, Affiliated Hospital of Liaoning University of TCM, Shenyang City, Liaoning Province, China
| | - Xin Li
- Office of Drug Clinical Trial Management, Affiliated Hospital of Qingdao University, Qingdao City, Shandong Province, China
| | - Song Chen
- Psychiatry Research Center, Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - Duanwen Cao
- Clinical Trial Research Center, Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, China
| | - Yimin Cui
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
| | - Qian Xiang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
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11
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Wu T, Chen Y, You Q, Jiang Z, Chen X. Targeting bromodomian-containing protein 8 (BRD8): An advanced tool to interrogate BRD8. Eur J Med Chem 2024; 268:116271. [PMID: 38401187 DOI: 10.1016/j.ejmech.2024.116271] [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: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Epigenetic modifications play crucial roles in physiological processes, including cell differentiation, proliferation, and death. Bromodomain/Brd-containing proteins (BCPs) regulate abnormal gene expression in various diseases by recognizing the lysine-ε-N-acetylated residues (KAc) or by acting as transcriptional co-activators. Small molecule inhibitors targeting BCPs offer an attractive strategy for modulating aberrant gene expression. Besides the extensive research on the bromodomain and extra-terminal (BET) domain family proteins, the non-BET proteins have gained increasing attention. Bromodomain containing protein 8 (BRD8), a reader of KAc and co-activator of nuclear receptors (NRs), plays a key role in various cancers. This review provides a comprehensive analysis of the structure, disease-related functions, and inhibitor development of BRD8. Opportunities and challenges for future studies targeting BRD8 in disease treatment are discussed.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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.
| | - 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.
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12
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Li Y, Shen Z, Ratia K, Zhao J, Huang F, Dubrovyskyii O, Indukuri D, Fu J, Lozano Ramos O, Thatcher GRJ, Xiong R. Structure-Guided Design and Synthesis of Pyridinone-Based Selective Bromodomain and Extra-Terminal Domain (BET)-First Bromodomain (BD1) Inhibitors. J Med Chem 2024; 67:2712-2731. [PMID: 38295759 DOI: 10.1021/acs.jmedchem.3c01837] [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] [Indexed: 02/02/2024]
Abstract
The bromodomain and extra-terminal domain (BET) proteins are epigenetic readers, regulating transcription via two highly homologous tandem bromodomains, BD1 and BD2. Clinical development of nonselective pan-BD BET inhibitors has been challenging, partly due to dose-limiting side effects such as thrombocytopenia. This has prompted the push for domain-selective BET inhibitors to achieve a more favorable therapeutic window. We report a structure-guided drug design campaign that led to the development of a potent BD1-selective BET inhibitor, 33 (XL-126), with a Kd of 8.9 nM and 185-fold BD1/BD2 selectivity. The high selectivity was first assayed by SPR, validated by a secondary time-resolved fluorescence energy transfer assay, and further corroborated by BROMOscan (∼57-373 fold selectivity). The cocrystal of 33 with BRD4 BD1 and BD2 demonstrates the source of selectivity: repulsion with His437 and lost binding with the leucine clamp. Notably, the BD1 selectivity of BET inhibitor 33 leads to both the preservation of platelets and potent anti-inflammatory efficacy.
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Affiliation(s)
- Yangfeng Li
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Zhengnan Shen
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Kiira Ratia
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jiong Zhao
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Fei Huang
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Oleksii Dubrovyskyii
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Divakar Indukuri
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jiqiang Fu
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Omar Lozano Ramos
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Gregory R J Thatcher
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Rui Xiong
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
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13
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Liu Y, Liang J, Zhu R, Yang Y, Wang Y, Wei W, Li H, Chen L. Application of PROTACs in Target Identification and Target Validation. ACTA MATERIA MEDICA 2024; 3:72-87. [PMID: 39373008 PMCID: PMC11452161 DOI: 10.15212/amm-2024-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
PROTAC, as a novel therapeutic drug model, has received widespread attention from the academic and pharmaceutical industries. At the same time, PROTAC technology has led many researchers to focus on developing chemical biology tool properties due to its unique operating mechanism and protein dynamic regulatory properties. In recent years, the rapid development of PROTAC technology has gradually made it an essential tool for target identification and target validation. To further promote the application of PROTAC tools in drug discovery and basic medical sciences research, this review distinguished between target identification and target validation concepts. It summarized the research progress of PROTAC technology in these aspects.
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Affiliation(s)
- Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Rui Zhu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yueying Yang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yali Wang
- Fujian Key Laboratory of Chinese Materia Medica, Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Fujian Key Laboratory of Chinese Materia Medica, Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
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14
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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: 1] [Impact Index Per Article: 1.0] [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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15
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Zhu R, Li J, Dong R, Hu Q, Chen Z, Chen X, Zhong Z, Xiang Q, Huang C, Lin B, Wu X, Zhang Y, Zhao L, Xu Y. Optimization of the synthesis of BET BD2 selective inhibitor XY153. Chem Biodivers 2024; 21:e202301584. [PMID: 38163253 DOI: 10.1002/cbdv.202301584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
XY153 is a promising BET BD2 inhibitor with an IC50 value of 0.79 nM against BRD4 BD2. It shows 354-fold selectivity over BRD4-BD1 and 6-fold selectivity over other BET BD2 domains. However, the reported synthesis route of XY153 and its derivatives are extremely poor-yielding. After the synthesis of three key fragments, XY153 can only be obtained with a yield of 1.3 % in the original four-step reaction. In this study, we reported a three-step alternative route in the synthesis process of XY153. The reaction conditions for this route were thoroughly investigated and optimized, resulting in a significantly improved yield of 61.5 %. This efficient synthesis route establishes a robust chemical foundation for the rapid synthesis of XY153 derivatives as BET BD2 inhibitors in the near future.
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Affiliation(s)
- Run Zhu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - 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
| | - 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, Changchun, Jilin, 130021, China
| | - Qingqing Hu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Zhiming 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, Beijing, 100049, 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, Beijing, 100049, China
| | - Zhixin Zhong
- 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, Beijing, 100049, China
| | - Qiuping Xiang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Cen Huang
- Jiangsu S&T Exchange Center with Foreign Countries, No. 175 Longpan Road, Nanjing, 210042, China
| | - Bin Lin
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. 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
| | - 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
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yong Xu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, 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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16
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Wu SY, Lai HT, Sanjib Banerjee N, Ma Z, Santana JF, Wei S, Liu X, Zhang M, Zhan J, Chen H, Posner B, Chen Y, Price DH, Chow LT, Zhou J, Chiang CM. IDR-targeting compounds suppress HPV genome replication via disruption of phospho-BRD4 association with DNA damage response factors. Mol Cell 2024; 84:202-220.e15. [PMID: 38103559 PMCID: PMC10843765 DOI: 10.1016/j.molcel.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Compounds binding to the bromodomains of bromodomain and extra-terminal (BET) family proteins, particularly BRD4, are promising anticancer agents. Nevertheless, side effects and drug resistance pose significant obstacles in BET-based therapeutics development. Using high-throughput screening of a 200,000-compound library, we identified small molecules targeting a phosphorylated intrinsically disordered region (IDR) of BRD4 that inhibit phospho-BRD4 (pBRD4)-dependent human papillomavirus (HPV) genome replication in HPV-containing keratinocytes. Proteomic profiling identified two DNA damage response factors-53BP1 and BARD1-crucial for differentiation-associated HPV genome amplification. pBRD4-mediated recruitment of 53BP1 and BARD1 to the HPV origin of replication occurs in a spatiotemporal and BRD4 long (BRD4-L) and short (BRD4-S) isoform-specific manner. This recruitment is disrupted by phospho-IDR-targeting compounds with little perturbation of the global transcriptome and BRD4 chromatin landscape. The discovery of these protein-protein interaction inhibitors (PPIi) not only demonstrates the feasibility of developing PPIi against phospho-IDRs but also uncovers antiviral agents targeting an epigenetic regulator essential for virus-host interaction and cancer development.
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Affiliation(s)
- Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hsien-Tsung Lai
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - N Sanjib Banerjee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Shuguang Wei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xisheng Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meirong Zhang
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Jian Zhan
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yadong Chen
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Louise T Chow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Zhu Z, Tang W, Qiu X, Xin X, Zhang J. Advances in targeting Phosphodiesterase 1: From mechanisms to potential therapeutics. Eur J Med Chem 2024; 263:115967. [PMID: 38000211 DOI: 10.1016/j.ejmech.2023.115967] [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: 10/04/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023]
Abstract
Phosphodiesterase 1 (PDE1) is an enzyme entrusted with the hydrolysis of the second messengers cAMP and cGMP, thereby governing a plethora of metabolic processes, encompassing ion channel modulation and cellular apoptosis. Recent advancements in the realm of small molecule structural variations have greatly facilitated the exploration of innovative applications for PDE1. Remarkably, a recent series of PDE1 inhibitors (PDE1i) have been meticulously formulated and devised, showcasing enhanced selectivity and potency. Among them, ITI-214 has entered Phase II clinical trials, holding promise for the treatment of Parkinson's disease and heart failure. Nevertheless, the majority of current PDE1 inhibitors have encountered substantial side effects in clinical trials attributable to their limited selectivity, this predicament presents a formidable obstacle in the development of specific small molecule inhibitors targeting PDE1. This Perspective endeavors to illuminate the potential design approaches, structure-activity relationships, and biological activities of current PDE1i, aiming to offer support and insights for clinical practice and the development of novel PDE1i.
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Affiliation(s)
- Ziyu Zhu
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Wentao Tang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xuemei Qiu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xin Xin
- State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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18
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Chen L, Wang K, Wang L, Wang W, Wang L, Wang W, Li J, Liu X, Wang M, Ruan B. Design and synthesis of pterostilbene derivatives bearing triazole moiety that might treat DSS-induced colitis in mice through modulation of NF-κB/MAPK signaling pathways. Eur J Med Chem 2024; 263:115949. [PMID: 37989058 DOI: 10.1016/j.ejmech.2023.115949] [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: 07/27/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
In this study, a series of novel anti-inflammatory compounds with high activity and low toxicity were designed and synthesized based on the natural product pterostilbene skeleton. According to the strategy of pharmacophore combination, we introduced thiazole moiety into pterostilbene skeleton to design and synthesize a novel series of pterostilbene derivatives (a total of 41 compounds), and lipopolysaccharide (LPS)-treated RAW 264.7 cells were screened for anti-inflammatory activity and cytotoxicity. Among them, compound 8 was found to be the most active (against NO: IC50 = 0.6 μM) compared with pterostilbene and indomethacin. Anti-inflammatory mechanism studies revealed that compound 8 inhibited pro-inflammatory cytokines by blocking the NF-κB/MAPK signaling pathway in LPS-treated RAW 264.7 cells. In vivo experiments showed that compound 8 had a good relieving effect on DSS-induced acute colitis in mice, and also demonstrated a good safety in acute toxicity experiments. In conclusion, compound 8 may be a promising anti-inflammatory lead compound in the treatment of acute colitis.
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Affiliation(s)
- Liuzeng Chen
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China; School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases Anhui Medical University, Hefei, 230032, PR China
| | - Ke Wang
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Lingyun Wang
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Wei Wang
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Lifan Wang
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Wei Wang
- Hefei Food and Drug Inspection Center, Hefei, 230071, PR China
| | - Jia Li
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Xiaohan Liu
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Mengya Wang
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China
| | - Banfeng Ruan
- School of Biology, Food and Environment, Hefei University, Hefei, 230601, PR China.
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19
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Wahi A, Manchanda N, Jain P, Jadhav HR. Targeting the epigenetic reader "BET" as a therapeutic strategy for cancer. Bioorg Chem 2023; 140:106833. [PMID: 37683545 DOI: 10.1016/j.bioorg.2023.106833] [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: 07/04/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Bromodomain and extraterminal (BET) proteins have the ability to bind to acetylated lysine residues present in both histones and non-histone proteins. This binding is facilitated by the presence of tandem bromodomains. The regulatory role of BET proteins extends to chromatin dynamics, cellular processes, and disease progression. The BET family comprises of BRD 2, 3, 4 and BRDT. The BET proteins are a class of epigenetic readers that regulate the transcriptional activity of a multitude of genes that are involved in the pathogenesis of cancer. Thus, targeting BET proteins has been identified as a potentially efficacious approach for the treatment of cancer. BET inhibitors (BETis) are known to interfere with the binding of BET proteins to acetylated lysine residues of chromatin, thereby leading to the suppression of transcription of several genes, including oncogenic transcription factors. Here in this review, we focus on role of Bromodomain and extra C-terminal (BET) proteins in cancer progression. Furthermore, numerous small-molecule inhibitors with pan-BET activity have been documented, with certain compounds currently undergoing clinical assessment. However, it is apparent that the clinical effectiveness of the present BET inhibitors is restricted, prompting the exploration of novel technologies to enhance their clinical outcomes and mitigate undesired adverse effects. Thus, strategies like development of selective BET-BD1, & BD2 inhibitors, dual and acting BET are also presented in this review and attempts to cover the chemistry needed for proper establishment of designed molecules into BRD have been made. Moreover, the review attempts to summarize the details of research till date and proposes a space for future development of BET inhibitor with diminished side effects. It can be concluded that discovery of isoform selective BET inhibitors can be a way forward in order to develop BET inhibitors with negligible side effects.
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Affiliation(s)
- Abhishek Wahi
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India
| | - Namish Manchanda
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India.
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani-Pilani Campus, Vidya Vihar Pilani, Rajasthan 333031, India
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20
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Li XY, Yu JT, Dong YH, Shen XY, Hou R, Xie MM, Wei J, Hu XW, Dong ZH, Shan RR, Jin J, Shao W, Meng XM. Protein acetylation and related potential therapeutic strategies in kidney disease. Pharmacol Res 2023; 197:106950. [PMID: 37820854 DOI: 10.1016/j.phrs.2023.106950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Kidney disease can be caused by various internal and external factors that have led to a continual increase in global deaths. Current treatment methods can alleviate but do not markedly prevent disease development. Further research on kidney disease has revealed the crucial function of epigenetics, especially acetylation, in the pathology and physiology of the kidney. Histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyllysine readers jointly regulate acetylation, thus affecting kidney physiological homoeostasis. Recent studies have shown that acetylation improves mechanisms and pathways involved in various types of nephropathy. The discovery and application of novel inhibitors and activators have further confirmed the important role of acetylation. In this review, we provide insights into the physiological process of acetylation and summarise its specific mechanisms and potential therapeutic effects on renal pathology.
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Affiliation(s)
- Xiang-Yu Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ju-Tao Yu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yu-Hang Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Xiao-Yu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Rui Hou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Man-Man Xie
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Jie Wei
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei 230601, Anhui, China
| | - Xiao-Wei Hu
- Department of Clinical Pharmacy, Anhui Provincial Children's Hospital, Hefei 230051, China
| | - Ze-Hui Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Run-Run Shan
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Juan Jin
- Research Center for Translational Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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21
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Horai Y, Suda N, Uchihashi S, Katakuse M, Shigeno T, Hirano T, Takahara J, Fujita T, Mukoyama Y, Haga Y. Discovery of a potent, orally available tricyclic derivative as a novel BRD4 inhibitor for melanoma. Bioorg Med Chem 2023; 93:117461. [PMID: 37659219 DOI: 10.1016/j.bmc.2023.117461] [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: 07/27/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023]
Abstract
The epigenetic regulation of the protein bromodomain-containing protein 4 (BRD4) has emerged as a compelling target for cancer treatment. In this study, we outline the discovery of a novel BRD4 inhibitor for melanoma therapy. Our initial finding was that benzimidazole derivative 1, sourced from our library, was a powerful BRD4 inhibitor. However, it exhibited a poor pharmacokinetic (PK) profile. To address this, we conducted a scaffold-hopping procedure with derivative 1, which resulted in the creation of benzimidazolinone derivative 5. This new derivative displayed an improved PK profile. To further enhance the BRD4 inhibitory activity, we attempted to introduce hydrogen bond acceptors. This indeed improved the activity, but at the cost of decreased membrane permeability. Our search for a potent inhibitor with desirable permeability led to the development of tricyclic 18. This compound demonstrated powerful inhibitory activity and a favorable PK profile. More significantly, tricyclic 18 showed antitumor efficacy in a mouse melanoma xenograft model, suggesting that it holds potential as a therapeutic agent for melanoma treatment.
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Affiliation(s)
- Yuhei Horai
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan.
| | - Naoki Suda
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
| | | | - Mayako Katakuse
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
| | - Tomomi Shigeno
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
| | | | | | - Tomoyuki Fujita
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
| | - Yohei Mukoyama
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
| | - Yuji Haga
- Research Department, Maruho Co., Ltd., Kyoto 600-8815, Japan
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22
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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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23
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Oh DH, Ma X, Hogg SJ, He J, Kearney C, Brasacchio D, Susanto O, Maher B, Jennings IG, Newbold A, Fraser P, Gruber E, Kats LM, Gregory GP, Johnstone RW, Thompson PE, Shortt J. Rationally designed chimeric PI3K-BET bromodomain inhibitors elicit curative responses in MYC-driven lymphoma. Proc Natl Acad Sci U S A 2023; 120:e2306414120. [PMID: 37643213 PMCID: PMC10483632 DOI: 10.1073/pnas.2306414120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
Targeted inhibitors of bromodomain and extraterminal (BET)-bromodomains and phosphatidylinositol-3-kinase (PI3K) signaling demonstrate potent but self-limited antilymphoma activity as single agents in the context of cellular Myelocytomatosis (cMYC) oncogene-dysregulation. However, combined PI3K and BET inhibition imparts synergistic anticancer activity with the potential for more sustained disease responses due to the mutual antagonism of compensatory epigenetic and signaling networks. Here, we describe the mechanistic and therapeutic validation of rationally designed dual PI3K/BET bromodomain inhibitors, built by linkage of established PI3K and BET inhibitor pharmacophores. The lead candidate demonstrates high selectivity, nanomolar range cellular potency, and compelling in vivo efficacy, including curative responses in the aggressive Eµ-Myc lymphoma model. These studies further support the therapeutic strategy of combined PI3K and BET inhibition and provide a potential step-change in approach to orthogonal MYC antagonism using optimized chimeric small-molecule technology.
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Affiliation(s)
- Danielle H. Oh
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
- Monash Haematology, Monash Health, MelbourneVIC3168, Australia
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
| | - Xiao Ma
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, ParkvilleVIC3052, Australia
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA02115
| | - Simon J. Hogg
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Oncology Discovery Research, Abbvie, South San Francisco, CA94080
| | - Jackson He
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, ParkvilleVIC3052, Australia
| | - Conor Kearney
- Olivia Newton-John Cancer Research Institute, HeidelbergVIC3084, Australia
- School of Cancer Medicine, La Trobe University, HeidelbergVIC3084, Australia
| | - Daniella Brasacchio
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
| | - Olivia Susanto
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
| | - Belinda Maher
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
| | - Ian G. Jennings
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, ParkvilleVIC3052, Australia
| | - Andrea Newbold
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
| | - Peter Fraser
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
| | - Emily Gruber
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
| | - Lev M. Kats
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
| | - Gareth P. Gregory
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
- Monash Haematology, Monash Health, MelbourneVIC3168, Australia
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
| | - Ricky W. Johnstone
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
| | - Philip E. Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, ParkvilleVIC3052, Australia
| | - Jake Shortt
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, MelbourneVIC3168, Australia
- Monash Haematology, Monash Health, MelbourneVIC3168, Australia
- Cancer Biology Therapeutics Program, Peter MacCallum Cancer Centre, MelbourneVIC3000, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, MelbourneVIC3000, Australia
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24
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Liu YJ, Zhong HJ, Wang H, Chong CM, Yang GJ. Editorial: Community series in epigenetics of the immune component of inflammation-volume II. Front Immunol 2023; 14:1266133. [PMID: 37654499 PMCID: PMC10465791 DOI: 10.3389/fimmu.2023.1266133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Affiliation(s)
- Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hai-Jing Zhong
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - Haitao Wang
- Center for Cancer Research, National Cancer Institute (NIH), Bethesda, MD, United States
| | - Cheong-Meng Chong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, Macao SAR, China
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
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25
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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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26
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Vadla R, Miki S, Taylor B, Kawauchi D, Jones BM, Nathwani N, Pham P, Tsang J, Nathanson DA, Furnari FB. Glioblastoma Mesenchymal Transition and Invasion are Dependent on a NF-κB/BRD2 Chromatin Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.546613. [PMID: 37461511 PMCID: PMC10349949 DOI: 10.1101/2023.07.03.546613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Glioblastoma (GBM) represents the most aggressive subtype of glioma, noted for its profound invasiveness and molecular heterogeneity. The mesenchymal (MES) transcriptomic subtype is frequently associated with therapy resistance, rapid recurrence, and increased tumor-associated macrophages. Notably, activation of the NF-κB pathway and alterations in the PTEN gene are both associated with this malignant transition. Although PTEN aberrations have been shown to be associated with enhanced NF-κB signaling, the relationships between PTEN, NF-κB and MES transition are poorly understood in GBM. Here, we show that PTEN regulates the chromatin binding of bromodomain and extraterminal (BET) family proteins, BRD2 and BRD4, mediated by p65/RelA localization to the chromatin. By utilizing patient-derived glioblastoma stem cells and CRISPR gene editing of the RELA gene, we demonstrate a crucial role for RelA lysine 310 acetylation in recruiting BET proteins to chromatin for MES gene expression and GBM cell invasion upon PTEN loss. Remarkably, we found that BRD2 is dependent on chromatin associated acetylated RelA for its recruitment to MES gene promoters and their expression. Furthermore, loss of BRD2 results in the loss of MES signature, accompanied by an enrichment of proneural signature and enhanced therapy responsiveness. Finally, we demonstrate that disrupting the NFκB/BRD2 interaction with a brain penetrant BET-BD2 inhibitor reduces mesenchymal gene expression, GBM invasion, and therapy resistance in GBM models. This study uncovers the role of hitherto unexplored PTEN-NF-κB-BRD2 pathway in promoting MES transition and suggests inhibiting this complex with BET-BD2 specific inhibitors as a therapeutic approach to target the MES phenotype in GBM.
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Affiliation(s)
- Raghavendra Vadla
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shunichiro Miki
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brett Taylor
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Daisuke Kawauchi
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brandon M Jones
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nidhi Nathwani
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Philip Pham
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonathan Tsang
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - David A Nathanson
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - Frank B Furnari
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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27
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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: 10] [Impact Index Per Article: 10.0] [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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28
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Yang X, Gao Y, Cao F, Wang S. Molecular Dynamics Simulations Combined with Markov Model to Explore the Effect of Allosteric Inhibitor Binding on Bromodomain-Containing Protein 4. Int J Mol Sci 2023; 24:10831. [PMID: 37446009 DOI: 10.3390/ijms241310831] [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: 05/23/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Bromodomain-Containing Protein 4 (BRD4) can play an important role in gene transcriptional regulation of tumor development and survival by participating in histone modification epigenetic mechanism. Although it has been reported that novel allosteric inhibitors such as ZL0590 have a high affinity with target protein BRD4 and good efficacy, their inhibitory mechanism has not been studied further. The aim of this study was to reveal the inhibition mechanism of allosteric inhibitor ZL0590 on Free-BRD4 and BRD4 binding MS436 (orthosteric inhibitor) by molecular dynamics simulation combined with a Markov model. Our results showed that BRD4-ZL0590 led to α-helices formation of 100-105 compared with Free-BRD4; the combination of MS436 caused residues 30-40 and 95-105 to form α-helices, while the combination of allosteric inhibitors untangled the α-helices formed by the MS436. The results of Markov flux analysis showed that the binding process of inhibitors mainly involved changes in the degree of α-helices at ZA loop. The binding of ZL0590 reduced the distance between ZA loop and BC loop, blocked the conformation at the active site, and inhibited the binding of MS436. After the allosteric inhibitor binding, the MS436 that could normally penetrate into the interior of the pocket was floating on the edge of the active pocket and did not continue to penetrate into the active pocket as expected. In summary, we provide a theoretical basis for the inhibition mechanism of ZL0590 against BRD4, which can be used as a reference for improving the development of drug targets for cancer therapy.
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Affiliation(s)
- Xiaotang Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yilin Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Song Wang
- The Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2 Liutiao Road, Changchun 130012, China
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29
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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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30
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Yang X, Xu L, Yang L. Recent advances in EZH2-based dual inhibitors in the treatment of cancers. Eur J Med Chem 2023; 256:115461. [PMID: 37156182 DOI: 10.1016/j.ejmech.2023.115461] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
The enhancer of zeste homolog 2 (EZH2) protein is the catalytic subunit of one of the histone methyltransferases. EZH2 catalyzes the trimethylation of lysine 27 of histone H3 (H3K27me3) and further alters downstream target levels. EZH2 is upregulated in cancer tissues, wherein its levels correlate strongly with cancer genesis, progression, metastasis, and invasion. Consequently, it has emerged as a novel anticancer therapeutic target. Nonetheless, developing EZH2 inhibitors (EZH2i) has encountered numerous difficulties, such as pre-clinical drug resistance and poor therapeutic effect. The EZH2i synergistically suppresses cancers when used in combination with additional antitumor drugs, such as PARP inhibitors, HDAC inhibitors, BRD4 inhibitors, EZH1 inhibitors, and EHMT2 inhibitors. Typically, the use of dual inhibitors of two different targets mediated by one individual molecule has been recognized as the preferred approach for overcoming the limitations of EZH2 monotherapy. The present review discusses the theoretical basis for designing EZH2-based dual-target inhibitors, and also describes some in vitro and in vivo analysis results.
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Affiliation(s)
- Xiaojuan Yang
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China.
| | - Lu Xu
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China
| | - Li Yang
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China
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31
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Yan Z, Lyu X, Lin D, Wu G, Gong Y, Ren X, Xiao J, Lou J, Huang H, Chen Y, Zhao Y. Selective degradation of cellular BRD3 and BRD4-L promoted by PROTAC molecules in six cancer cell lines. Eur J Med Chem 2023; 254:115381. [PMID: 37084596 DOI: 10.1016/j.ejmech.2023.115381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Targeted degradation of BET family proteins BRD2/3/4 or only BRD4 with PROTAC molecules has been a promising strategy for the treatment of human cancer. Meanwhile, selective degradation of cellular BRD3 and BRD4-L remains a challenging task. We report herein a novel PROTAC molecule 24 that promoted selective degradation of cellular BRD3 and BRD4-L, but not BRD2 or BRD4-S, in a panel of six cancer cell lines. The observed target selectivity was partially attributed to differences in protein degradation kinetics and in types of cell lines. In a MM.1S mouse xenograft model, an optimized lead compound 28 promoted selective degradation of BRD3 and BRD4-L in vivo and exhibited robust antitumor activity. In summary, we have demonstrated that selective degradation of BRD3 and BRD4-L over BRD2 and BRD4-S is a feasible and robust approach in multiple cancer cell lines and an animal model, which could be helpful for further investigations on BRD3 and BRD4-L that ultimately benefitting cancer research and therapeutics.
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Affiliation(s)
- Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Dongze Lin
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Gaoxing Wu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yang Gong
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jian Xiao
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jianfeng Lou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - He Huang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Yi Chen
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China.
| | - Yujun Zhao
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China.
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32
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Zhang M, Li J, Wang Q, Urabe G, Tang R, Huang Y, Mosquera JV, Kent KC, Wang B, Miller CL, Guo LW. Gene-repressing epigenetic reader EED unexpectedly enhances cyclinD1 gene activation. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:717-729. [PMID: 36923952 PMCID: PMC10009644 DOI: 10.1016/j.omtn.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Epigenetically switched, proliferative vascular smooth muscle cells (SMCs) form neointima, engendering stenotic diseases. Histone-3 lysine-27 trimethylation (H3K27me3) and acetylation (H3K27ac) marks are associated with gene repression and activation, respectively. The polycomb protein embryonic ectoderm development (EED) reads H3K27me3 and also enhances its deposition, hence is a canonical gene repressor. However, herein we found an unexpected role for EED in activating the bona fide pro-proliferative gene Ccnd1 (cyclinD1). EED overexpression in SMCs increased Ccnd1 mRNA, seemingly contradicting its gene-repressing function. However, consistently, EED co-immunoprecipitated with gene-activating H3K27ac reader BRD4, and they co-occupied at both mitogen-activated Ccnd1 and mitogen-repressed P57 (bona fide anti-proliferative gene), as indicated by chromatin immunoprecipitation qPCR. These results were abolished by an inhibitor of either the EED/H3K27me3 or BRD4/H3K27ac reader function. In accordance, elevating BRD4 increased H3K27me3. In vivo, while EED was upregulated in rat and human neointimal lesions, selective EED inhibition abated angioplasty-induced neointima and reduced cyclinD1 in rat carotid arteries. Thus, results uncover a previously unknown role for EED in Ccnd1 activation, likely via its cooperativity with BRD4 that enhances each other's reader function; i.e., activating pro-proliferative Ccnd1 while repressing anti-proliferative P57. As such, this study confers mechanistic implications for the epigenetic intervention of neointimal pathology.
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Affiliation(s)
- Mengxue Zhang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Qingwei Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Go Urabe
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Runze Tang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yitao Huang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - K. Craig Kent
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Bowen Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Clint L. Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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33
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Yu X, Long Q, Shen S, Liu Z, Chandran J, Zhang J, Ding H, Zhang H, Cai D, Kim ES, Huang Y, Guo H. Screening of an epigenetic compound library identifies BRD4 as a potential antiviral target for hepatitis B virus covalently closed circular DNA transcription. Antiviral Res 2023; 211:105552. [PMID: 36737008 PMCID: PMC10036215 DOI: 10.1016/j.antiviral.2023.105552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
HBV cccDNA is the persistent form of viral genome, which exists in host cell nucleus as an episomal minichromosome decorated with histone and non-histone proteins. cccDNA is the authentic viral transcription template and resistant to current antivirals. Growing evidence shows that the transcriptional activity of cccDNA minichromosome undergoes epigenetic regulations, suggesting a new perspective for anti-cccDNA drug development through targeting histone modifications. In this study, we screened an epigenetic compound library in the cccDNA reporter cell line HepBHAe82, which produces the HA-tagged HBeAg in a cccDNA-dependent manner. Among the obtained hits, a bromodomain-containing protein 4 (BRD4) inhibitor MS436 exhibited marked inhibition of cccDNA transcription in both HBV stable cell line HepAD38 and HepG2-NTCP or primary human hepatocyte infection system under noncytotoxic concentrations. Chromatin immunoprecipitation (ChIP) assay demonstrated that MS436 dramatically reduced the enrichment of H3K27ac, an activating histone modification pattern, on cccDNA minichromosome. RNAseq differential analysis showed that MS436 does not drastically change host transcriptome or induce any known anti-HBV factors/pathways, indicating a direct antiviral effect of MS436 on cccDNA minichromosome. Interestingly, the MS436-mediated inhibition of cccDNA transcription is accompanied by cccDNA destabilization in HBV infection and a recombinant cccDNA system, indicating that BRD4 activity may also play a role in cccDNA maintenance. Furthermore, depletion of BRD4 by siRNA knockdown or PROTAC degrader resulted in cccDNA inhibition in HBV-infected HepG2-NTCP cells, further validating BRD4 as an antiviral target. Taken together, our study has demonstrated the practicability of HepBHAe82-based anti-HBV drug screening system and provided a proof-of-concept for targeting HBV cccDNA with epigenetic compounds.
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Affiliation(s)
- Xiaoyang Yu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Quanxin Long
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Shen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhentao Liu
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Electrical and Computer Engineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jithin Chandran
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Junjie Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hao Ding
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hu Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dawei Cai
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elena S Kim
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Electrical and Computer Engineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.
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34
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Xu KY, Wang XT, Cheng L, Cui QH, Shi JT, Zhang LW, Chen SW. Design, synthesis, and biological evaluation of quinoxalinone derivatives as potent BRD4 inhibitors. Bioorg Med Chem 2023; 78:117152. [PMID: 36599264 DOI: 10.1016/j.bmc.2022.117152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
The bromodomain-containing protein 4 (BRD4) has gained growing interest as an effective drug target for the treatment of hepatocellular carcinoma (HCC). Herein, we designed and synthesized a series of quinoxalinone derivatives as BRD4 inhibitors via scaffold hopping. The representative compound X9 showed potent BRD4 inhibitory activity (with IC50 = 82.3 nM), and preferable antiproliferative activity against HepG2 cells (with IC50 = 1.13 ± 0.07 μM), as well as less toxicity against GES-1 cells (with IC50 = 57.24 ± 5.46 μM). Furthermore, compound X9 dose-dependently inhibited colony formation and blocked the migration of HepG2 cells by down-regulating the expression of Snail and MMP-9 while up-regulating the E-cadherin and Occludin. Besides, compound X9 efficiently down-regulated the expression of c-Myc in HepG2 cells, induced apoptosis, and arrested at G0/G1 phase. In total, quinoxalinone was a potential core as BRD4 inhibitor and compound X9 might be effective for liver cancer therapy.
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Affiliation(s)
- Kai-Yan Xu
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Xue-Ting Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Lei Cheng
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Qi-Hang Cui
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Jian-Tao Shi
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Li-Wen Zhang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Shi-Wu Chen
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
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35
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Design, synthesis and anti-ovarian cancer activities of thieno[2,3-d]pyrimidine based chimeric BRD4 inhibitor/nitric oxide-donator. Eur J Med Chem 2023; 246:114970. [PMID: 36470106 DOI: 10.1016/j.ejmech.2022.114970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Bromodomain protein 4 (BRD4) is an attractive epigenetic target that regulating diverse cellular processes, and the discovery of dual-target inhibitors including BRD4 is an effective approach in cancer treatment to increase potency and reduce drug resistance. Based on the multifunctional drug development strategy, a series of new derivatives of nitrooxy (ONO2) or furoxan (1,2,5-oxadiazole 2-oxide) with BRD4 inhibitor capable of inhibiting BRD4 and simultaneously releasing NO were designed and synthesized. When NO concentrations were measured with Griess reagent under physiological conditions, all compounds released NO at micromolar levels, reaching effective antitumor concentrations. Biological studies showed that the most potent BRD4/NO hybrid 11a exhibited good BRD4 inhibitory activity and selectivity. Further mechanistic studies revealed that 11a significantly decreased the expression of BRD4 and c-Myc, as well as induced cellular apoptosis and autophagic cell death both in vitro and in vivo. In summary, we optimized the chimeric BRD4-inhibitor/NO-donor based on our previous studies, and it should be a lead compound for targeted therapy of OC (ovarian cancer) in the future. This interesting strategy could expand the usage of BRDi in human malignancies and endogenous gastro-transmitters.
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36
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Zerio CJ, Sivinski J, Wijeratne EMK, Xu YM, Ngo DT, Ambrose AJ, Villa-Celis L, Ghadirian N, Clarkson MW, Zhang DD, Horton NC, Gunatilaka AAL, Fromme R, Chapman E. Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem 2023; 66:913-933. [PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.
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Affiliation(s)
- Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - E M Kithsiri Wijeratne
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Ya-Ming Xu
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Duc T Ngo
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Luis Villa-Celis
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85719, United States
| | - Donna D Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - A A Leslie Gunatilaka
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Raimund Fromme
- School of Molecular Sciences, Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, Arizona 85287, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
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Medicinal Chemistry of Anti-HIV-1 Latency Chemotherapeutics: Biotargets, Binding Modes and Structure-Activity Relationship Investigation. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010003. [PMID: 36615199 PMCID: PMC9822059 DOI: 10.3390/molecules28010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The existence of latent viral reservoirs (LVRs), also called latent cells, has long been an acknowledged stubborn hurdle for effective treatment of HIV-1/AIDS. This stable and heterogeneous reservoir, which mainly exists in resting memory CD4+ T cells, is not only resistant to highly active antiretroviral therapy (HAART) but cannot be detected by the immune system, leading to rapid drug resistance and viral rebound once antiviral treatment is interrupted. Accordingly, various functional cure strategies have been proposed to combat this barrier, among which one of the widely accepted and utilized protocols is the so-called 'shock-and-kill' regimen. The protocol begins with latency-reversing agents (LRAs), either alone or in combination, to reactivate the latent HIV-1 proviruses, then eliminates them by viral cytopathic mechanisms (e.g., currently available antiviral drugs) or by the immune killing function of the immune system (e.g., NK and CD8+ T cells). In this review, we focuse on the currently explored small molecular LRAs, with emphasis on their mechanism-directed drug targets, binding modes and structure-relationship activity (SAR) profiles, aiming to provide safer and more effective remedies for treating HIV-1 infection.
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38
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Regulation of programmed cell death by Brd4. Cell Death Dis 2022; 13:1059. [PMID: 36539410 PMCID: PMC9767942 DOI: 10.1038/s41419-022-05505-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Epigenetic factor Brd4 has emerged as a key regulator of cancer cell proliferation. Targeted inhibition of Brd4 suppresses growth and induces apoptosis of various cancer cells. In addition to apoptosis, Brd4 has also been shown to regulate several other forms of programmed cell death (PCD), including autophagy, necroptosis, pyroptosis, and ferroptosis, with different biological outcomes. PCD plays key roles in development and tissue homeostasis by eliminating unnecessary or detrimental cells. Dysregulation of PCD is associated with various human diseases, including cancer, neurodegenerative and infectious diseases. In this review, we discussed some recent findings on how Brd4 actively regulates different forms of PCD and the therapeutic potentials of targeting Brd4 in PCD-related human diseases. A better understanding of PCD regulation would provide not only new insights into pathophysiological functions of PCD but also provide new avenues for therapy by targeting Brd4-regulated PCD.
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39
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Li D, Yu D, Li Y, Yang R. A bibliometric analysis of PROTAC from 2001 to 2021. Eur J Med Chem 2022; 244:114838. [DOI: 10.1016/j.ejmech.2022.114838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022]
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40
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Fu S, Zheng Q, Zhang D, Lin C, Ouyang L, Zhang J, Chen L. Medicinal chemistry strategies targeting PRMT5 for cancer therapy. Eur J Med Chem 2022; 244:114842. [DOI: 10.1016/j.ejmech.2022.114842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022]
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41
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Cipriano A, Milite C, Feoli A, Viviano M, Pepe G, Campiglia P, Sarno G, Picaud S, Imaide S, Makukhin N, Filippakopoulos P, Ciulli A, Castellano S, Sbardella G. Discovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022; 17:e202200343. [PMID: 36040095 PMCID: PMC9826262 DOI: 10.1002/cmdc.202200343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/29/2022] [Indexed: 01/11/2023]
Abstract
The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each containing two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biological role(s), with potential clinical applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compounds MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compound (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compounds.
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Affiliation(s)
- Alessandra Cipriano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Ciro Milite
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Alessandra Feoli
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Monica Viviano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giacomo Pepe
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Pietro Campiglia
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giuliana Sarno
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Sarah Picaud
- Nuffield Department of MedicineOxford UniversityOX3 7DQOxfordUK
| | - Satomi Imaide
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Discovery Technology Research LaboratoriesOno Pharmaceutical Co., Ltd.618-8585OsakaJapan
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Oncology R&DTumour Targeted DeliveryAstraZenecaQMB Innovation Centre42 New RoadLondonE1 2AXUK
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK
| | - Sabrina Castellano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Gianluca Sbardella
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
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42
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Chen IP, Ott M. Viral Hijacking of BET Proteins. Viruses 2022; 14:v14102274. [PMID: 36298829 PMCID: PMC9609653 DOI: 10.3390/v14102274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
Proteins of the bromodomain and exterminal domain (BET) family mediate critical host functions such as cell proliferation, transcriptional regulation, and the innate immune response, which makes them preferred targets for viruses. These multidomain proteins are best known as transcriptional effectors able to read acetylated histone and non-histone proteins through their tandem bromodomains. They also contain other short motif-binding domains such as the extraterminal domain, which recognizes transcriptional regulatory proteins. Here, we describe how different viruses have evolved to hijack or disrupt host BET protein function through direct interactions with BET family members to support their own propagation. The network of virus-BET interactions emerges as highly intricate, which may complicate the use of small-molecule BET inhibitors-currently in clinical development for the treatment of cancer and cardiovascular diseases-to treat viral infections.
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Affiliation(s)
- Irene P. Chen
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Correspondence:
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43
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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: 5] [Impact Index Per Article: 2.5] [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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44
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Rezaie H, Asadollahi-Baboli M, Hassaninejad-Darzi SK. Hybrid consensus and k-nearest neighbours (kNN) strategies to classify dual BRD4/PLK1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:779-792. [PMID: 36330747 DOI: 10.1080/1062936x.2022.2139292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
A novel decision-making procedure is proposed here for the first time to identify active/inactive and selective/non-selective dual inhibitors using consensus approaches and pools of k-nearest neighbours (kNN) classifications instead of individual models. Dual BRD4/PLK1 inhibition with adequate selectivity is a potential therapeutic strategy for targeting tumour cells in high-risk patients. We report the unique way to identify both active and selective dual BRD4/PLK1 inhibitors using consensus and kNN strategies together with two sources of receptor-based and ligand-based information which are the ranked binding energies of residues and important molecular features, respectively. The results of consensus approaches were compared with the results of individual kNN models. The chemical space similarity was measured using three different distance functions to increase the reliability. All activity and selectivity classification models were validated using cross-validation and y-randomization tests. The outcomes show that consensus approaches can increase the reliability and accuracy of active/inactive or selective/non-selective detections up to 90%. Consensus approaches also reached more balanced values of sensitivity and specificity compared to the individual kNN models because of the compensation in the integration of diverse sources of information.
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Affiliation(s)
- H Rezaie
- Department of Chemistry, Faculty of Science, Babol Noshirvani University of Technology, Babol, Iran
| | - M Asadollahi-Baboli
- Department of Chemistry, Faculty of Science, Babol Noshirvani University of Technology, Babol, Iran
| | - S K Hassaninejad-Darzi
- Department of Chemistry, Faculty of Science, Babol Noshirvani University of Technology, Babol, Iran
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45
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Poongavanam V, Atilaw Y, Siegel S, Giese A, Lehmann L, Meibom D, Erdelyi M, Kihlberg J. Linker-Dependent Folding Rationalizes PROTAC Cell Permeability. J Med Chem 2022; 65:13029-13040. [PMID: 36170570 PMCID: PMC9574858 DOI: 10.1021/acs.jmedchem.2c00877] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and molecular dynamics (MD) simulations independently to gain insights into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with a low solvent-accessible 3D polar surface area in an apolar environment is correlated to high cell permeability. The chemical nature and the flexibility of the linker were essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, π-π interactions, and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stephan Siegel
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Anja Giese
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Lutz Lehmann
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Daniel Meibom
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Mate Erdelyi
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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46
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Shi X, Wang Y, Zhang L, Zhao W, Dai X, Yang YG, Zhang X. Targeting bromodomain and extra-terminal proteins to inhibit neuroblastoma tumorigenesis through regulating MYCN. Front Cell Dev Biol 2022; 10:1021820. [PMID: 36187481 PMCID: PMC9523081 DOI: 10.3389/fcell.2022.1021820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bromodomain and extra-terminal domain (BET) family proteins play important roles in regulating the expression of multiple proto-oncogenes by recognizing acetylation of histones and non-histone proteins including transcription factors, which subsequently promote tumor cell proliferation, survival, metastasis and immune escape. Therefore, BET family proteins are considered attractive therapeutic targets in various cancers. Currently, blocking of the BET proteins is a widely used therapeutic strategy for MYCN amplified high-risk neuroblastoma. Here, we summarized and reviewed the recent research progresses for the critical function of BET proteins, as an epigenetic reader, on tumorigenesis and the therapeutic potential of the BET/BRD4 inhibitors on MYCN amplified neuroblastoma. We also discussed the combined therapeutic strategies for BET inhibitor-resistant neuroblastoma.
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47
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Lespinasse M, Wei K, Perrin J, Winkler M, Hamaidia S, Leroy A, Macek Jilkova Z, Philouze C, Marche PN, Petosa C, Govin J, Emadali A, Wong Y. Enantioselective Approach for Expanding the Three‐Dimensional Space of Tetrahydroquinoline to Develop BET Bromodomain Inhibitors**. Chemistry 2022; 28:e202202293. [DOI: 10.1002/chem.202202293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
| | - Kaiyao Wei
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
- Univ. Grenoble Alpes CEA CNRS 5075 IBS 38000 Grenoble France
| | - Justine Perrin
- Univ. Grenoble Alpes CNRS 5063 DPM 38000 Grenoble France
| | | | - Sieme Hamaidia
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
| | - Alexis Leroy
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
| | - Zuzana Macek Jilkova
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
- Univ. Grenoble Alpes CHU Grenoble Alpes 38000 Grenoble France
| | | | - Patrice N. Marche
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
| | - Carlo Petosa
- Univ. Grenoble Alpes CEA CNRS 5075 IBS 38000 Grenoble France
| | - Jérôme Govin
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
| | - Anouk Emadali
- Univ. Grenoble Alpes Inserm U1209 CNRS 5309 IAB 38000 Grenoble France
- Univ. Grenoble Alpes CHU Grenoble Alpes 38000 Grenoble France
| | - Yung‐Sing Wong
- Univ. Grenoble Alpes CNRS 5063 DPM 38000 Grenoble France
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48
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Liu YJ, Wang H, Zhong HJ, Chong CM, Yang GJ. Editorial: Epigenetics of the immune component of inflammation. Front Immunol 2022; 13:1000836. [PMID: 36072580 PMCID: PMC9443511 DOI: 10.3389/fimmu.2022.1000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultral Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Haitao Wang
- Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, MA, United States
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Hai-Jing Zhong
- College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Cheong-Meng Chong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, Macao SAR, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultral Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Haitao Wang, ; Cheong-Meng Chong, ; Hai-Jing Zhong,
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49
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Chen H, Liu Z, Zheng L, Wang R, Shi L. BET inhibitors: an updated patent review (2018-2021). Expert Opin Ther Pat 2022; 32:953-968. [PMID: 35982031 DOI: 10.1080/13543776.2022.2115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Bromodomain and extraterminal (BET) proteins are epigenetic readers that regulate gene transcription and cell growth by binding to acetylated lysine resides on histones. They are involved in many physiological processes and pathological conditions such as cancer, inflammation, and metabolic diseases. Blockade of BET proteins has become an encouraging approach for the treatment of these human diseases, especially cancer. To date, a number of potent and specific BET inhibitors have been discovered and many of them have entered clinical trials. AREAS COVERED This review aims at providing an overview of molecular mechanisms of BET inhibitors and highlighting the research advancements published in recent patent literatures between 2018 and 2021. Web of Science, PubMed, SciFinder, WIPO, EPO, USPTO and CNIPA databases were used for searching the literature and patents for BET inhibitors. EXPERT OPINION In recent years, an increasing number of structurally diverse BET inhibitors have been identified, including pan BET inhibitors, BD1 or BD2 selective BET inhibitors, bivalent BET inhibitors, kinase and BET dual inhibitors and BET-PROTACs. Despite of many challenges, BET inhibitors have high potential in the treatment of cancer and other diseases and the development of next-generation BET inhibitors could be promising.
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Affiliation(s)
- Huanhuan Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhenling Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Lili Zheng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Rongrong Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Lei Shi
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
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50
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Guan X, Cheryala N, Karim RM, Chan A, Berndt N, Qi J, Georg GI, Schönbrunn E. Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity. J Med Chem 2022; 65:10441-10458. [PMID: 35867655 DOI: 10.1021/acs.jmedchem.2c00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bromodomain and extraterminal domain (BET) proteins are important regulators of gene transcription and chromatin remodeling. BET family members BRD4 and BRDT are validated targets for cancer and male contraceptive drug development, respectively. Due to the high structural similarity of the acetyl-lysine binding sites, most reported inhibitors lack intra-BET selectivity. We surmised that protein-protein interactions induced by bivalent inhibitors may differ between BRD4 and BRDT, conferring an altered selectivity profile. Starting from nonselective monovalent inhibitors, we developed cell-active bivalent BET inhibitors with increased activity and selectivity for BRDT. X-ray crystallographic and solution studies revealed unique structural states of BRDT and BRD4 upon interaction with bivalent inhibitors. Varying spacer lengths and symmetric vs unsymmetric connections resulted in the same dimeric states, whereas different chemotypes induced different dimers. The findings indicate that the increased intra-BET selectivity of bivalent inhibitors is due to the differential plasticity of BET bromodomains upon inhibitor-induced dimerization.
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Affiliation(s)
- Xianghong Guan
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Narsihmulu Cheryala
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Rezaul Md Karim
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Alice Chan
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Norbert Berndt
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Ernst Schönbrunn
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
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