1
|
Fortunati S, Giannetto M, Pedrini F, Nikolaou P, Donofrio G, Bertucci A, Careri M. A novel magnetic ligand-based assay for the electrochemical determination of BRD4. Talanta 2024; 279:126577. [PMID: 39032457 DOI: 10.1016/j.talanta.2024.126577] [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: 06/02/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The first magnetic ligand-based electrochemical assay aimed at the determination of BRD4 was developed and validated. BRD4 is an epigenetic regulator of great interest in oncology in relation to its overexpression observed in the pathogenesis of several cancer diseases. BRD4 also represents a major target for the development of innovative treatments aimed at protein inhibition or degradation. Despite the relevance of BRD4 both for diagnostics and therapeutic purposes, current methodologies for its determination are limited to commercial ELISA kits. We present a novel magnetic ligand-based assay for the electrochemical determination of BRD4. The developed assay is based on the use of a small synthetic fragment of the natural protein ligand for BRD4 as receptor, thus exploiting the intrinsic biological protein-protein recognition mechanism. In addition, the assay features the use of magnetic beads as immobilization platforms and peroxidase-conjugated monoclonal anti-BRD4 antibody for the generation of the electrochemical signal. The ligand-based assay shows outstanding performance in terms of rapidity, with results achievable in less than 20 min, no matrix effect when applied to human plasma or cell lysate samples, and excellent specificity. The proposed method exhibits a limit of detection of 2.66 nM and a response range tunable as a function of the amount of immobilized receptor. The developed ligand-based assay was successfully applied to the accurate determination of BRD4 in untreated cell lysates, as proven by the ELISA reference method. The good performance of the proposed bioassay for determination of BRD4 showed potential application of this strategy in convenient point-of-care testing.
Collapse
Affiliation(s)
- Simone Fortunati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy; Biostructures and Biosystems National Institute (I.N.B.B. Consortium), Viale delle Medaglie d'Oro 305, 00136, Roma, Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy; Biostructures and Biosystems National Institute (I.N.B.B. Consortium), Viale delle Medaglie d'Oro 305, 00136, Roma, Italy
| | - Federica Pedrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Pavlos Nikolaou
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Gaetano Donofrio
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126, Parma, Italy
| | - Alessandro Bertucci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy; Biostructures and Biosystems National Institute (I.N.B.B. Consortium), Viale delle Medaglie d'Oro 305, 00136, Roma, Italy.
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy; Biostructures and Biosystems National Institute (I.N.B.B. Consortium), Viale delle Medaglie d'Oro 305, 00136, Roma, Italy
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Chen L, Qi Q, Jiang X, Wu J, Li Y, Liu Z, Cai Y, Ran H, Zhang S, Zhang C, Wu H, Cao S, Mi L, Xiao D, Huang H, Jiang S, Wu J, Li B, Xie J, Qi J, Li F, Liang P, Han Q, Wu M, Zhou W, Wang C, Zhang W, Jiang X, Zhang K, Li H, Zhang X, Li A, Zhou T, Man J. Phosphocreatine Promotes Epigenetic Reprogramming to Facilitate Glioblastoma Growth Through Stabilizing BRD2. Cancer Discov 2024; 14:1547-1565. [PMID: 38563585 DOI: 10.1158/2159-8290.cd-23-1348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/21/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Glioblastoma (GBM) exhibits profound metabolic plasticity for survival and therapeutic resistance, while the underlying mechanisms remain unclear. Here, we show that GBM stem cells reprogram the epigenetic landscape by producing substantial amounts of phosphocreatine (PCr). This production is attributed to the elevated transcription of brain-type creatine kinase, mediated by Zinc finger E-box binding homeobox 1. PCr inhibits the poly-ubiquitination of the chromatin regulator bromodomain containing protein 2 (BRD2) by outcompeting the E3 ubiquitin ligase SPOP for BRD2 binding. Pharmacological disruption of PCr biosynthesis by cyclocreatine (cCr) leads to BRD2 degradation and a decrease in its targets' transcription, which inhibits chromosome segregation and cell proliferation. Notably, cyclocreatine treatment significantly impedes tumor growth and sensitizes tumors to a BRD2 inhibitor in mouse GBM models without detectable side effects. These findings highlight that high production of PCr is a druggable metabolic feature of GBM and a promising therapeutic target for GBM treatment. Significance: Glioblastoma (GBM) exhibits an adaptable metabolism crucial for survival and therapy resistance. We demonstrate that GBM stem cells modify their epigenetics by producing phosphocreatine (PCr), which prevents bromodomain containing protein 2 (BRD2) degradation and promotes accurate chromosome segregation. Disrupting PCr biosynthesis impedes tumor growth and improves the efficacy of BRD2 inhibitors in mouse GBM models.
Collapse
Affiliation(s)
- Lishu Chen
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Qinghui Qi
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Xiaoqing Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Jin Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yuanyuan Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Zhaodan Liu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Yan Cai
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Haowen Ran
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Songyang Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Cheng Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Huiran Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Shuailiang Cao
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Lanjuan Mi
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Dake Xiao
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Haohao Huang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Shuai Jiang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Jiaqi Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Bohan Li
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Jiong Xie
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Ji Qi
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Fangye Li
- Department of Neurosurgery, First Medical Center of PLA General Hospital, Beijing, China
| | - Panpan Liang
- Intelligent Pathology Institute, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qiuying Han
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Min Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Wenchao Zhou
- Intelligent Pathology Institute, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chenhui Wang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Weina Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Xin Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Kun Zhang
- Department of Ultrasound, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Huiyan Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Xuemin Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Ailing Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Tao Zhou
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Jianghong Man
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| |
Collapse
|
4
|
Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024; 19:2317-2357. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
Collapse
Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| |
Collapse
|
5
|
Lara-Ureña N, Gómez-Marín E, Pozuelo-Sánchez I, Reyes JC, García-Domínguez M. SARS-CoV-2 E protein interacts with BRD2 and BRD4 SEED domains and alters transcription in a different way than BET inhibition. Cell Mol Life Sci 2024; 81:313. [PMID: 39066826 PMCID: PMC11335234 DOI: 10.1007/s00018-024-05343-8] [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: 10/25/2023] [Revised: 05/31/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
Bromodomain and extra-terminal (BET) proteins are relevant chromatin adaptors involved in the transcriptional control of thousands of genes. Two tandem N-terminal bromodomains are essential for chromatin attachment through acetyl-histone recognition. Recently, the BET proteins members BRD2 and BRD4 were found to interact with the SARS-CoV-2 envelope (E) protein, raising the question of whether the interaction constitutes a virus hijacking mechanism for transcription alteration in the host cell. To shed light on this question, we have compared the transcriptome of cells overexpressing E with that of cells treated with the BET inhibitor JQ1. Notably, E overexpression leads to a strong upregulation of natural immunity- and interferon response-related genes. However, BET inhibition results in the downregulation of most of these genes, indicating that these two conditions, far from causing a significant overlap of the altered transcriptomes, course with quite different outputs. Concerning the interaction of E protein with BET members, and differing from previous reports indicating that it occurs through BET bromodomains, we find that it relies on SEED and SEED-like domains, BET regions rich in Ser, Asp, and Glu residues. By taking advantage of this specific interaction, we have been able to direct selective degradation of E protein through a PROTAC system involving a dTAG-SEED fusion, highlighting the possible therapeutic use of this peptide for targeted degradation of a viral essential protein.
Collapse
Affiliation(s)
- Nieves Lara-Ureña
- Department of Cell Dynamics and Signaling, Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, Seville, 41092, Spain
| | - Elena Gómez-Marín
- Department of Genome Biology, Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, Seville, 41092, Spain
| | | | - José C Reyes
- Department of Genome Biology, Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, Seville, 41092, Spain
| | - Mario García-Domínguez
- Department of Cell Dynamics and Signaling, Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, Seville, 41092, Spain.
| |
Collapse
|
6
|
Xu H, Ohoka N, Inoue T, Yokoo H, Demizu Y. Photo-regulated PROTACs: A novel tool for temporal control of targeted protein degradation. Bioorg Med Chem Lett 2024; 107:129778. [PMID: 38702019 DOI: 10.1016/j.bmcl.2024.129778] [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: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
PROTACs (Proteolysis targeting chimeras) are chimeric molecules designed to induce targeted protein degradation via the ubiquitin-proteasome system. These molecules catalytically degrade target proteins and sustainably inhibit their function. Therefore, PROTAC's unique mechanism of action is not only beneficial in medicine but also serves as a valuable tool for molecular biological analysis in fields like chemical biology, biochemistry, and drug discovery. This study presents a novel turn-off (ON-OFF) type PROTAC development strategy utilizing a photocleavable linker. The inclusion of this linker enables temporal control of the degradation activity targeting BRD4 protein upon UV light exposure. PROTAC-2 demonstrated the most potent degradation activity against BRD4 among the other synthesized PROTACs with varying linker lengths. The UV light-induced cleavage of PROTAC-2 was confirmed, leading to a reduction in its BRD4 degradation activity. Notably, this study introduces a novel linker capable of nullifying degradation activity of PROTACs which is activated by light irradiation. These findings offer a promising strategy for the development of turn-off type PROTACs, providing enhanced temporal control over protein degradation. The approach holds significant potential for applications in molecular function studies and drug discovery.
Collapse
Affiliation(s)
- Hanqiao Xu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Yosuke Demizu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University, 1-1-1 Tsushimanaka, Kita, Okayama 700-8530, Japan.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Liu S, Dai W, Jin B, Jiang F, Huang H, Hou W, Lan J, Jin Y, Peng W, Pan J. Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets. Mol Cancer 2024; 23:122. [PMID: 38844984 PMCID: PMC11157854 DOI: 10.1186/s12943-024-02033-8] [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: 04/19/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Metastasis remains the principal cause of cancer-related lethality despite advancements in cancer treatment. Dysfunctional epigenetic alterations are crucial in the metastatic cascade. Among these, super-enhancers (SEs), emerging as new epigenetic regulators, consist of large clusters of regulatory elements that drive the high-level expression of genes essential for the oncogenic process, upon which cancer cells develop a profound dependency. These SE-driven oncogenes play an important role in regulating various facets of metastasis, including the promotion of tumor proliferation in primary and distal metastatic organs, facilitating cellular migration and invasion into the vasculature, triggering epithelial-mesenchymal transition, enhancing cancer stem cell-like properties, circumventing immune detection, and adapting to the heterogeneity of metastatic niches. This heavy reliance on SE-mediated transcription delineates a vulnerable target for therapeutic intervention in cancer cells. In this article, we review current insights into the characteristics, identification methodologies, formation, and activation mechanisms of SEs. We also elaborate the oncogenic roles and regulatory functions of SEs in the context of cancer metastasis. Ultimately, we discuss the potential of SEs as novel therapeutic targets and their implications in clinical oncology, offering insights into future directions for innovative cancer treatment strategies.
Collapse
Affiliation(s)
- Shenglan Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wei Dai
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Bei Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Feng Jiang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Hao Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wen Hou
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Jinxia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, China
| | - Yanli Jin
- College of Pharmacy, Jinan University Institute of Tumor Pharmacology, Jinan University, Guangzhou, 510632, China
| | - Weijie Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China.
| | - Jingxuan Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| |
Collapse
|
9
|
Yuan XN, Shao YC, Guan XQ, Liu Q, Chu MF, Yang ZL, Li H, Zhao S, Tian YH, Zhang JW, Wei L. METTL3 orchestrates glycolysis by stabilizing the c-Myc/WDR5 complex in triple-negative breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119716. [PMID: 38547933 DOI: 10.1016/j.bbamcr.2024.119716] [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: 11/17/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The carcinogenic transcription factor c-Myc is the most aggressive oncogene, which drive malignant transformation and dissemination of triple-negative breast cancer (TNBC). Recruitment of many cofactors, especially WDR5, a protein that nucleates H3K4me chromatin modifying complexes, play a pivotal role in regulating c-Myc-dependent gene transcription, a critical process for c-Myc signaling to function in a variety of biological and pathological contexts. For this reason, interrupting the interaction between c-Myc and the transcription cofactor WDR5 may become the most promising new strategy for treating c-Myc driven TNBC. METHODS Immunoprecipitation and mass spectrometry (IP-MS) is used to screen proteins that bind c-Myc/WDR5 interactions. The interaction of METTL3 with c-Myc/WDR5 in breast cancer tissues and TNBC cells was detected by Co-IP and immunofluorescence. Subsequently, we further analyzed the influence of METTL3 expression on c-Myc/WDR5 protein expression and its interaction stability by Western blot and Co-IP. The correlation between METTL3 and c-Myc pathway was analyzed by ChIP-seq sequencing and METTL3 knockdown transcriptome data. The effect of METTL3 expression on c-Myc transcriptional activity was detected by ChIP-qPCR and Dual Luciferase Reporter. At the same time, the overexpression vector METTL3-MUT (m6A) was constructed, which mutated the methyltransferase active site (Aa395-398, DPPW/APPA), and further explored whether the interaction between METTL3 and c-Myc/WDR5 was independent of methyltransferase activity. In addition, we also detected the changes of METTL3 expression on TNBC's sensitivity to small molecule inhibitors such as JQ1 and OICR9429 by CCK8, Transwell and clonal formation assays. Finally, we further verified our conclusions in spontaneous tumor formation mouse MMTV-PyMT and nude mouse orthotopic transplantation tumor models. RESULTS METTL3 was found to bind mainly to c-Myc/WDR5 protein in the nucleus. It enhances the stability of c-Myc/WDR5 interaction through its methyltransferase independent mechanism, thereby enhancing the transcriptional activity of c-Myc on downstream glucose metabolism genes. Notably, the study also confirmed that METTL3 can directly participate in the transcription of glucose metabolism genes as a transcription factor, and knockdown METTL3 enhances the drug sensitivity of breast cancer cells to small molecule inhibitors JQ1 and OICR9429. The study was further confirmed by spontaneous tumor formation mouse MMTV-PyMT and nude mouse orthotopic transplantation tumor models. CONCLUSION METTL3 binds to the c-Myc/WDR5 protein complex and promotes glycolysis, which plays a powerful role in promoting TNBC progression. Our findings further broaden our understanding of the role and mechanism of action of METTL3, and may open up new therapeutic avenues for effective treatment of TNBC with high c-Myc expression.
Collapse
Affiliation(s)
- Xiao-Ning Yuan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - You-Cheng Shao
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Xiao-Qing Guan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Qin Liu
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Meng-Fei Chu
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Ze-Lin Yang
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Hui Li
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Sai Zhao
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Yi-Hao Tian
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China.
| | - Jing-Wei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan, Hubei 430071, PR China.
| | - Lei Wei
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China.
| |
Collapse
|
10
|
Bakiri L, Hasenfuss SC, Guío-Carrión A, Thomsen MK, Hasselblatt P, Wagner EF. Liver cancer development driven by the AP-1/c-Jun~Fra-2 dimer through c-Myc. Proc Natl Acad Sci U S A 2024; 121:e2404188121. [PMID: 38657045 PMCID: PMC11067056 DOI: 10.1073/pnas.2404188121] [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: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. HCC incidence is on the rise, while treatment options remain limited. Thus, a better understanding of the molecular pathways involved in HCC development has become a priority to guide future therapies. While previous studies implicated the Activator Protein-1 (AP-1) (Fos/Jun) transcription factor family members c-Fos and c-Jun in HCC formation, the contribution of Fos-related antigens (Fra-) 1 and 2 is unknown. Here, we show that hepatocyte-restricted expression of a single chain c-Jun~Fra-2 protein, which functionally mimics the c-Jun/Fra-2 AP-1 dimer, results in spontaneous HCC formation in c-Jun~Fra-2hep mice. Several hallmarks of human HCC, such as cell cycle dysregulation and the expression of HCC markers are observed in liver tumors arising in c-Jun~Fra-2hep mice. Tumorigenesis occurs in the context of mild inflammation, low-grade fibrosis, and Pparγ-driven dyslipidemia. Subsequent analyses revealed increased expression of c-Myc, evidently under direct regulation by AP-1 through a conserved distal 3' enhancer. Importantly, c-Jun~Fra-2-induced tumors revert upon switching off transgene expression, suggesting oncogene addiction to the c-Jun~Fra-2 transgene. Tumors escaping reversion maintained c-Myc and c-Myc target gene expression, likely due to increased c-Fos. Interfering with c-Myc in established tumors using the Bromodomain and Extra-Terminal motif inhibitor JQ-1 diminished liver tumor growth in c-Jun~Fra-2 mutant mice. Thus, our data establish c-Jun~Fra-2hep mice as a model to study liver tumorigenesis and identify the c-Jun/Fra-2-Myc interaction as a potential target to improve HCC patient stratification and/or therapy.
Collapse
Affiliation(s)
- Latifa Bakiri
- Laboratory Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Genes, Development and Disease Group, National Cancer Research Centre, 28029, Madrid, Spain
| | - Sebastian C. Hasenfuss
- Genes, Development and Disease Group, National Cancer Research Centre, 28029, Madrid, Spain
| | - Ana Guío-Carrión
- Genes, Development and Disease Group, National Cancer Research Centre, 28029, Madrid, Spain
| | - Martin K. Thomsen
- Department of Biomedicine, University of Aarhus, 8000, Aarhus, Denmark
| | - Peter Hasselblatt
- Department of Medicine II, University Hospital and Faculty of Medicine, 79106, Freiburg, Germany
| | - Erwin F. Wagner
- Laboratory Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Laboratory Genes and Disease, Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| |
Collapse
|
11
|
Liu N, Wang A, Xue M, Zhu X, Liu Y, Chen M. FOXA1 and FOXA2: the regulatory mechanisms and therapeutic implications in cancer. Cell Death Discov 2024; 10:172. [PMID: 38605023 PMCID: PMC11009302 DOI: 10.1038/s41420-024-01936-1] [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: 01/14/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
FOXA1 (Forkhead Box A1) and FOXA2 (Forkhead Box A2) serve as pioneering transcription factors that build gene expression capacity and play a central role in biological processes, including organogenesis and differentiation, glycolipid metabolism, proliferation, migration and invasion, and drug resistance. Notably, FOXA1 and FOXA2 may exert antagonistic, synergistic, or complementary effects in the aforementioned biological processes. This article focuses on the molecular mechanisms and clinical relevance of FOXA1 and FOXA2 in steroid hormone-induced malignancies and highlights potential strategies for targeting FOXA1 and FOXA2 for cancer therapy. Furthermore, the article describes the prospect of targeting upstream regulators of FOXA1/FOXA2 to regulate its expression for cancer therapy because of the drug untargetability of FOXA1/FOXA2.
Collapse
Affiliation(s)
- Na Liu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China.
| | - Anran Wang
- Department of Radiotherapy and Oncology, Gusu School, Nanjing Medical University, The First People's Hospital of Kunshan, Suzhou, 215300, Jiangsu Province, China
| | - Mengen Xue
- Department of Radiotherapy and Oncology, Gusu School, Nanjing Medical University, The First People's Hospital of Kunshan, Suzhou, 215300, Jiangsu Province, China
| | - Xiaoren Zhu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Yang Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minbin Chen
- Department of Radiotherapy and Oncology, Gusu School, Nanjing Medical University, The First People's Hospital of Kunshan, Suzhou, 215300, Jiangsu Province, China.
| |
Collapse
|
12
|
Suo Y, Du D, Chen C, Zhu H, Wang X, Song N, Lu D, Yang Y, Li J, Wang J, Luo Z, Zhou B, Luo C, Zhou H. Uncovering PROTAC Sensitivity and Efficacy by Multidimensional Proteome Profiling: A Case for STAT3. J Med Chem 2024. [PMID: 38466231 DOI: 10.1021/acs.jmedchem.3c02371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Proteolysis-targeting chimera (PROTAC) is a powerful technology that can effectively trigger the degradation of target proteins. The intricate interplay among various factors leads to a heterogeneous drug response, bringing about significant challenges in comprehending drug mechanisms. Our study applied data-independent acquisition-based mass spectrometry to multidimensional proteome profiling of PROTAC (DIA-MPP) to uncover the efficacy and sensitivity of the PROTAC compound. We profiled the signal transducer and activator of transcription 3 (STAT3) PROTAC degrader in six leukemia and lymphoma cell lines under multiple conditions, demonstrating the pharmacodynamic properties and downstream biological responses. Through comparison between sensitive and insensitive cell lines, we revealed that STAT1 can be regarded as a biomarker for STAT3 PROTAC degrader, which was validated in cells, patient-derived organoids, and mouse models. These results set an example for a comprehensive description of the multidimensional PROTAC pharmacodynamic response and PROTAC drug sensitivity biomarker exploration.
Collapse
Affiliation(s)
- Yuying Suo
- University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Daohai Du
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Chao Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongwen Zhu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiongjun Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Nixue Song
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Dayun Lu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Yaxi Yang
- University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiacheng Li
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jun Wang
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhongyuan Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bing Zhou
- University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
13
|
Chen M, Guo X, Guo J, Shi C, Wu Y, Chen L, Mao R, Fan Y. Cytoplasmic Accumulation of Histones Induced by BET Inhibition Protects Cells from C9orf72 Poly(PR)-Induced Cell Death. Adv Biol (Weinh) 2024; 8:e2300334. [PMID: 38213020 DOI: 10.1002/adbi.202300334] [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: 07/14/2023] [Revised: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Repeat dipeptides such as poly(proline-arginine) (polyPR) are generated from the hexanucleotide GGGGCC repeat expansions in the C9orf72 gene. These dipeptides are often considered as the genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In the study, fluorescein isothiocyanate (FITC) labeled PR20 is used to investigate PR20-induced cell death. The findings reveal that the cell death induced by PR20 is dependent on its nuclear distribution and can be blocked by a nuclear import inhibitor called importazole. Further investigation reveals that BRD4 inhibitors, such as JQ-1 and I-BET762, restrict cytoplasmic localization of PR20, thereby reducing its cytotoxic effect. Mechanistically, the inhibition of BRD4 leads to an increase in the expression of numerous histones, resulting in the accumulation of histones in the cytoplasm. These cytoplasmic histones associate with PR20 and limit its distribution within the nucleus. Notably, the ectopic expression of histones alone is enough to confer protection to cells treated with PR20. In addition, phenylephrine (PE) induces cellular hypertrophy and cytoplasmic distribution of histone, which also helps protect cells from PR20-induced cell death. The research suggests that temporarily inducing the presence of cytoplasmic histones may alleviate the neurotoxic effects of dipeptide repeat proteins.
Collapse
Affiliation(s)
- Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xiaohong Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Jinjing Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Conglin Shi
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yuanyuan Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
| | - Liuting Chen
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| |
Collapse
|
14
|
Bauer N, Balourdas DI, Schneider JR, Zhang X, Berger LM, Berger BT, Schwalm MP, Klopp NA, Siveke JT, Knapp S, Joerger AC. Development of Potent Dual BET/HDAC Inhibitors via Pharmacophore Merging and Structure-Guided Optimization. ACS Chem Biol 2024; 19:266-279. [PMID: 38291964 PMCID: PMC10878397 DOI: 10.1021/acschembio.3c00427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024]
Abstract
Bromodomain and extra-terminal domain (BET) proteins and histone deacetylases (HDACs) are prime targets in cancer therapy. Recent research has particularly focused on the development of dual BET/HDAC inhibitors for hard-to-treat tumors, such as pancreatic cancer. Here, we developed a new series of potent dual BET/HDAC inhibitors by choosing starting scaffolds that enabled us to optimally merge the two functionalities into a single compound. Systematic structure-guided modification of both warheads then led to optimized binders that were superior in potency to both parent compounds, with the best molecules of this series binding to both BRD4 bromodomains as well as HDAC1/2 with EC50 values in the 100 nM range in cellular NanoBRET target engagement assays. For one of our lead molecules, we could also show the selective inhibition of HDAC1/2 over all other zinc-dependent HDACs. Importantly, this on-target activity translated into promising efficacy in pancreatic cancer and NUT midline carcinoma cells. Our lead molecules effectively blocked histone H3 deacetylation in pancreatic cancer cells and upregulated the tumor suppressor HEXIM1 and proapoptotic p57, both markers of BET inhibition. In addition, they have the potential to downregulate the oncogenic drivers of NUT midline carcinoma, as demonstrated for MYC and TP63 mRNA levels. Overall, this study expands the portfolio of available dual BET/class I HDAC inhibitors for future translational studies in different cancer models.
Collapse
Affiliation(s)
- Nicolas Bauer
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
| | - Joel R. Schneider
- Bridge
Institute of Experimental Tumor Therapy, West German Cancer Center,
University Hospital Essen, University of
Duisburg-Essen, 45147 Essen, Germany
- Division
of Solid Tumor Translational Oncology, German
Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research
Center, DKFZ, 69120 Heidelberg, Germany
| | - Xin Zhang
- Bridge
Institute of Experimental Tumor Therapy, West German Cancer Center,
University Hospital Essen, University of
Duisburg-Essen, 45147 Essen, Germany
- Division
of Solid Tumor Translational Oncology, German
Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research
Center, DKFZ, 69120 Heidelberg, Germany
| | - Lena M. Berger
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
| | - Benedict-Tilman Berger
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
| | - Martin P. Schwalm
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
- German
Translational Cancer Network (DKTK) Site Frankfurt/Mainz, Frankfurt am Main 60438, Germany
| | - Nick A. Klopp
- Bridge
Institute of Experimental Tumor Therapy, West German Cancer Center,
University Hospital Essen, University of
Duisburg-Essen, 45147 Essen, Germany
- Division
of Solid Tumor Translational Oncology, German
Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research
Center, DKFZ, 69120 Heidelberg, Germany
| | - Jens T. Siveke
- Bridge
Institute of Experimental Tumor Therapy, West German Cancer Center,
University Hospital Essen, University of
Duisburg-Essen, 45147 Essen, Germany
- Division
of Solid Tumor Translational Oncology, German
Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research
Center, DKFZ, 69120 Heidelberg, Germany
| | - Stefan Knapp
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
- German
Translational Cancer Network (DKTK) Site Frankfurt/Mainz, Frankfurt am Main 60438, Germany
| | - Andreas C. Joerger
- Institute
of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural
Genomics Consortium (SGC), Buchmann Institute
for Life Sciences, Max-von-Laue-Str.
15, 60438 Frankfurt
am Main, Germany
| |
Collapse
|
15
|
Ren J. Bromodomain-containing protein 4 inhibition improves the efficacy of cisplatin and radiotherapy in oral squamous cell carcinoma by suppressing programmed cell death-ligand 1 expression. Basic Clin Pharmacol Toxicol 2024; 134:272-283. [PMID: 38014458 DOI: 10.1111/bcpt.13962] [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: 04/12/2023] [Revised: 09/01/2023] [Accepted: 09/16/2023] [Indexed: 11/29/2023]
Abstract
The bromodomain-containing protein 4 (BRD4) is highly expressed in oral squamous cell carcinoma (OSCC) and plays a crucial role in tumour progression. However, the impact of BRD4 on the efficacy of chemotherapy and radiotherapy by regulating the expression of programmed cell death-ligand 1 (PD-L1) in OSCC remains unclear. In this study, we found that the BRD4 inhibitor JQ1 effectively enhanced the inhibitory effects of cisplatin and radiotherapy on cell proliferation and promoted the apoptosis of OSCC cells by cisplatin and radiotherapy. Furthermore, treatment with JQ1 reversed the increase of the expression of PD-L1 by cisplatin and radiotherapy, whereas the overexpression of PD-L1 partially countered the beneficial effects of JQ1 on the anticancer efficacy of cisplatin and radiotherapy. These results demonstrate that the inhibition of BRD4 improves the anticancer effect of chemotherapy and radiotherapy by suppressing the expression of PD-L1 in OSCC, suggesting that targeting BRD4 could be a promising therapeutic approach for chemo/radioresistant OSCC.
Collapse
Affiliation(s)
- Jiajie Ren
- Department of Stomatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Vadak N, Borkar MR, Bhatt LK. Deciphering neuroprotective mechanism of nitroxoline in cerebral ischemia: network pharmacology and molecular modeling-based investigations. Mol Divers 2024:10.1007/s11030-023-10791-8. [PMID: 38233690 DOI: 10.1007/s11030-023-10791-8] [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: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024]
Abstract
Cerebral ischemia is one of the major causes of death and disability worldwide. Currently, existing approved therapies are based on reperfusion and there is an unmet need to search for drugs with neuroprotective effects. The present study aims to investigate the neuroprotective mechanisms of nitroxoline, a nitro derivative of 8-Hydroxyquinoline, against cerebral ischemia using integrated network pharmacology and molecular docking approaches. Critical analytical tools used were SwissTarget, PharmMapper, BindingDB, DisGeNet, Cytoscape, GeneMANIA, ShinyGo, Metascape, GeneCodis, and Schrodinger GLIDE. Thirty-six overlapping drug and disease targets were identified and used for further analysis. Gene Ontology results showed that nitroxoline enriched the genes involved in biological processes of oxidative stress and apoptotic cell death that are highly implicated in hypoxic injury. KEGG enrichment analysis showed nitroxoline influenced a total of 159 biological pathways, out of which, top pathways involved in cerebral ischemia included longevity regulating pathway, VEGF signaling, EGFR tyrosine kinase inhibitor resistance, IL-17 and HIF-1 pathways, FoxO signaling, and AGE-RAGE pathway. Protein-protein interaction analysis using string database showed PARP1, EGFR, PTEN, BRD4, RAC1, NOS2, MTOR, MAPK3, BCL2, MAPK1, APP, METAP2, MAPK14, SIRT1, PRKAA1, and MCL1 as highly interactive proteins involved in pathogenesis of ischemic stroke regulated by nitroxoline. The highly interactive protein targets were validated by molecular docking studies and molecular dynamic simulations. Amongst all these targets, nitroxoline showed the highest binding affinity towards BRD4 followed by PARP1 and PTEN. Nitroxoline, through network pharmacology analysis, showed a role in regulating proteins, biological processes, and pathways crucial in cerebral ischemia. The current study thus provides a preliminary insight that nitroxoline might be used as a neuroprotectant against cerebral ischemia via modulating the epigenetic reader BRD4 and transcription factors such as RELA, NF-κβ1, and SP1. However, further in-vitro and preclinical studies need to be performed for concrete evidence.
Collapse
Affiliation(s)
- Namrata Vadak
- Department of Pharmacology, SVKM's Dr Bhanuben, Nanavati College of Pharmacy, Vile Parle (W), Mumbai, India
| | - Maheshkumar R Borkar
- Department of Pharmaceutical Chemistry, SVKM's Dr, Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr Bhanuben, Nanavati College of Pharmacy, Vile Parle (W), Mumbai, India.
| |
Collapse
|
18
|
Rios F, Uriostegui-Arcos M, Zurita M. Transcriptional Stress Induces the Generation of DoGs in Cancer Cells. Noncoding RNA 2024; 10:5. [PMID: 38250805 PMCID: PMC10801504 DOI: 10.3390/ncrna10010005] [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: 11/21/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
A characteristic of the cellular response to stress is the production of RNAs generated from a readthrough transcription of genes, called downstream-of-gene-(DoG)-containing transcripts. Additionally, transcription inhibitor drugs are candidates for fighting cancer. In this work, we report the results of a bioinformatic analysis showing that one of the responses to transcription inhibition is the generation of DoGs in cancer cells. Although some genes that form DoGs were shared between the two cancer lines, there did not appear to be a functional correlation between them. However, our findings show that DoGs are generated as part of the cellular response to transcription inhibition like other types of cellular stress, suggesting that they may be part of the defense against transcriptional stress.
Collapse
Affiliation(s)
| | | | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca Morelos 62250, Mexico (M.U.-A.)
| |
Collapse
|
19
|
Li M, Ni QY, Yu SY. Integration of single-cell transcriptomics and epigenetic analysis reveals enhancer-controlled TIMP1 as a regulator of ferroptosis in colorectal cancer. Genes Genomics 2024; 46:121-133. [PMID: 38032469 DOI: 10.1007/s13258-023-01474-7] [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: 06/25/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Ferroptosis is an iron-dependent non-apoptotic programmed cell death. However, the regulatory mechanism of ferroptosis in colorectal cancer (CRC) is still unclear. OBJECTIVE The aim of this study was to investigate the role and mechanism of enhancer-controlled genes in ferroptosis in CRC. METHODS Dimensionality reduction and differentially expressed genes (DEGs) identification were conducted using Seurat algorithm based on single-cell RNA sequencing (scRNA-seq) data from the GSE200997 dataset. Ferroptosis-related pathway enrichment analysis was performed using the FerrDb V2 database. Enhancers were identified using HOMER algorithm based on H3K27ac ChIP-seq data from the GSE166254 dataset. Kaplan-Meier Plotter online tool was used to analyze prognosis and gene expression correlation. Transcription factors were predicted using the transcription factor affinity prediction web tool. The binding of enhancer to transcription factor and H3K27ac enrichment were detected by ChIP-qPCR. RSL3 was used to induce ferroptosis in CRC cells. Gene transcription was detected by qRT-PCR. Cell proliferation was detected by CCK8 assay. RESULTS Nine cell clusters including T cells, natural killer cells, macrophages, mast cells, epithelial cells, fibroblasts, goblet cells, B cells and dendritic cells were identified in CRC and normal colonic tissue samples. Compared to normal colonic tissue-derived epithelial cells, 1075 DEGs were screened in CRC tissue-derived epithelial cells. Ferroptosis-related pathway enrichment suggested that DEGs were associated with the regulation of ferroptosis. DPEP1, ETV4, CEBPG, TIMP1, DUOX2 and LCN2 were identified as the significantly upregulated genes enriched in the "ferroptosis regulator" term, and their H3K27ac signals were significantly higher in CRC tissues than in normal colonic tissues. Of these, only the expression of TIMP1 predicted a poor prognosis of CRC patients. Transcription factor SPI1 drove TIMP1 transcription by binding to its enhancer. Overexpression of TIMP1 significantly promoted the resistance to ferroptosis induced by RSL3 in CRC cells, which was partially restored by SPI1 knockdown. CONCLUSION Transcription of TIMP1 was driven by transcription factor SPI1 in combination with its enhancer, consequently promoting CRC cells against ferroptosis. The SPI1/TIMP1 axis confers ferroptosis resistance in CRC, and thus has the potential to be the molecular targets for CRC treatment.
Collapse
Affiliation(s)
- Meng Li
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China
| | - Qian-Yang Ni
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China
| | - Su-Yang Yu
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China.
| |
Collapse
|
20
|
Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
Collapse
Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
21
|
Huang Y, Durall RT, Luong NM, Hertzler HJ, Huang J, Gokhale PC, Leeper BA, Persky NS, Root DE, Anekal PV, Montero Llopis PD, David CN, Kutok JL, Raimondi A, Saluja K, Luo J, Zahnow CA, Adane B, Stegmaier K, Hawkins CE, Ponne C, Le Q, Shapiro GI, Lemieux ME, Eagen KP, French CA. EZH2 Cooperates with BRD4-NUT to Drive NUT Carcinoma Growth by Silencing Key Tumor Suppressor Genes. Cancer Res 2023; 83:3956-3973. [PMID: 37747726 PMCID: PMC10843040 DOI: 10.1158/0008-5472.can-23-1475] [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: 05/17/2023] [Revised: 07/31/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
NUT carcinoma is an aggressive carcinoma driven by the BRD4-NUT fusion oncoprotein, which activates chromatin to promote expression of progrowth genes. BET bromodomain inhibitors (BETi) are a promising treatment for NUT carcinoma that can impede BRD4-NUT's ability to activate genes, but the efficacy of BETi as monotherapy is limited. Here, we demonstrated that enhancer of zeste homolog 2 (EZH2), which silences genes through establishment of repressive chromatin, is a dependency in NUT carcinoma. Inhibition of EZH2 with the clinical compound tazemetostat potently blocked growth of NUT carcinoma cells. Epigenetic and transcriptomic analysis revealed that tazemetostat reversed the EZH2-specific H3K27me3 silencing mark and restored expression of multiple tumor suppressor genes while having no effect on key oncogenic BRD4-NUT-regulated genes. Indeed, H3K27me3 and H3K27ac domains were found to be mutually exclusive in NUT carcinoma cells. CDKN2A was identified as the only gene among all tazemetostat-derepressed genes to confer resistance to tazemetostat in a CRISPR-Cas9 screen. Combined inhibition of EZH2 and BET synergized to downregulate cell proliferation genes, resulting in more pronounced growth arrest and differentiation than either inhibitor alone. In preclinical models, combined tazemetostat and BETi synergistically blocked tumor growth and prolonged survival of NUT carcinoma-xenografted mice, with complete remission without relapse in one cohort. Identification of EZH2 as a dependency in NUT carcinoma substantiates the reliance of NUT carcinoma tumor cells on epigenetic dysregulation of functionally opposite, yet highly complementary, chromatin regulatory pathways to maintain NUT carcinoma growth. SIGNIFICANCE Repression of tumor suppressor genes, including CDKN2A, by EZH2 provides a mechanistic rationale for combining EZH2 and BET inhibitors for the clinical treatment of NUT carcinoma. See related commentary by Kazansky and Kentsis, p. 3827.
Collapse
Affiliation(s)
- Yeying Huang
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - R. Taylor Durall
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nhi M. Luong
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hans J. Hertzler
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Julianna Huang
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brittaney A. Leeper
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Praju V. Anekal
- MicRoN, Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Karan Saluja
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, TX, USA
| | - Jia Luo
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cynthia A. Zahnow
- Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
| | - Catherine E. Hawkins
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher Ponne
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Quan Le
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kyle P. Eagen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher A. French
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
22
|
Nevi L, Pöllänen N, Penna F, Caretti G. Targeting Epigenetic Regulators with HDAC and BET Inhibitors to Modulate Muscle Wasting. Int J Mol Sci 2023; 24:16404. [PMID: 38003594 PMCID: PMC10671811 DOI: 10.3390/ijms242216404] [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: 10/13/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Epigenetic changes contribute to the profound alteration in the transcriptional program associated with the onset and progression of muscle wasting in several pathological conditions. Although HDACs and their inhibitors have been extensively studied in the field of muscular dystrophies, the potential of epigenetic inhibitors has only been marginally explored in other disorders associated with muscle atrophy, such as in cancer cachexia and sarcopenia. BET inhibitors represent a novel class of recently developed epigenetic drugs that display beneficial effects in a variety of diseases beyond malignancies. Based on the preliminary in vitro and preclinical data, HDACs and BET proteins contribute to the pathogenesis of cancer cachexia and sarcopenia, modulating processes related to skeletal muscle mass maintenance and/or metabolism. Thus, epigenetic drugs targeting HDACs and BET proteins may emerge as promising strategies to reverse the catabolic phenotype associated with cachexia and sarcopenia. Further preclinical studies are warranted to delve deeper into the molecular mechanisms associated with the functions of HDACs and BET proteins in muscle atrophy and to establish whether their epigenetic inhibitors represent a prospective therapeutic avenue to alleviate muscle wasting.
Collapse
Affiliation(s)
- Lorenzo Nevi
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Noora Pöllänen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Fabio Penna
- Department of Clinical and Biological Sciences, University of Torino, 10125 Torino, Italy
| | | |
Collapse
|
23
|
Mohammed A, Waddell MB, Sutkeviciute I, Danda A, Philips SJ, Lang W, Slavish PJ, Kietlinska SJ, Kaulage M, Sourav D, Ansari AZ. Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions. J Am Chem Soc 2023. [PMID: 37923569 DOI: 10.1021/jacs.3c06297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
SynTEF1, a prototype synthetic genome reader/regulator (SynGR), was designed to target GAA triplet repeats and restore the expression of frataxin (FXN) in Friedreich's ataxia patients. It achieves this complex task by recruiting BRD4, via a pan-BET ligand (JQ1), to the GAA repeats by using a sequence-selective DNA-binding polyamide. When bound to specific genomic loci in this way, JQ1 functions as a chemical prosthetic for acetyl-lysine residues that are natural targets of the two tandem bromodomains (BD1 and BD2) in bromo- and extra-terminal domain (BET) proteins. As next-generation BET ligands were disclosed, we tested a select set with improved physicochemical, pharmacological, and bromodomain-selective properties as substitutes for JQ1 in the SynGR design. Here, we report two unexpected findings: (1) SynGRs bearing pan-BET or BD2-selective ligands license transcription at the FXN locus, whereas those bearing BD1-selective ligands do not, and (2) rather than being neutral or inhibitory, an untethered BD1-selective ligand (GSK778) substantively enhances the activity of all active SynGRs. The failure of BD1-selective SynGRs to recruit BRD4/BET proteins suggests that rather than functioning as "epigenetic/chromatin mimics," active SynGRs mimic the functions of natural transcription factors in engaging BET proteins through BD2 binding. Moreover, the enhanced activity of SynGRs upon cotreatment with the BD1-selective ligand suggests that natural transcription factors compete for a limited pool of nonchromatin-bound BET proteins, and blocking BD1 directs pan-BET ligands to more effectively engage BD2. Taken together, SynGRs as chemical probes provide unique insights into the molecular recognition principles utilized by natural factors to precisely regulate gene expression, and they guide the design of more sophisticated synthetic gene regulators with greater therapeutic potential.
Collapse
Affiliation(s)
- Ashraf Mohammed
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ieva Sutkeviciute
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Adithi Danda
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Steven J Philips
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Walter Lang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sandra J Kietlinska
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Mangesh Kaulage
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Das Sourav
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554211. [PMID: 37662262 PMCID: PMC10473607 DOI: 10.1101/2023.08.21.554211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules provide advantages over target-focused approaches, including the ability to detect previously unknown targets, and the inclusion of chemical off-compete controls leading to high-confidence identifications. We describe the BioTAC system, a small-molecule guided proximity labelling platform, to rapidly identify both direct and complexed small molecule binding proteins. The BioTAC system overcomes a limitation of current approaches, and supports identification of both inhibitor bound and molecular glue bound complexes.
Collapse
Affiliation(s)
- Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Bridget T. Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J. Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| |
Collapse
|
26
|
Huang Y, Durall RT, Luong NM, Hertzler HJ, Huang J, Gokhale PC, Leeper BA, Persky NS, Root DE, Anekal PV, Montero Llopis PD, David CN, Kutok JL, Raimondi A, Saluja K, Luo J, Zahnow CA, Adane B, Stegmaier K, Hawkins CE, Ponne C, Le Q, Shapiro GI, Lemieux ME, Eagen KP, French CA. EZH2 synergizes with BRD4-NUT to drive NUT carcinoma growth through silencing of key tumor suppressor genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553204. [PMID: 37645799 PMCID: PMC10461970 DOI: 10.1101/2023.08.15.553204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
NUT carcinoma (NC) is an aggressive carcinoma driven by the BRD4-NUT fusion oncoprotein, which activates chromatin to promote expression of pro-growth genes. BET bromodomain inhibitors (BETi) impede BRD4-NUT's ability to activate genes and are thus a promising treatment but limited as monotherapy. The role of gene repression in NC is unknown. Here, we demonstrate that EZH2, which silences genes through establishment of repressive chromatin, is a dependency in NC. Inhibition of EZH2 with the clinical compound tazemetostat (taz) potently blocked growth of NC cells. Epigenetic and transcriptomic analysis revealed that taz reversed the EZH2-specific H3K27me3 silencing mark, and restored expression of multiple tumor suppressor genes while having no effect on key oncogenic BRD4- NUT-regulated genes. CDKN2A was identified as the only gene amongst all taz-derepressed genes to confer resistance to taz in a CRISPR-Cas9 screen. Combined EZH2 inhibition and BET inhibition synergized to downregulate cell proliferation genes resulting in more pronounced growth arrest and differentiation than either inhibitor alone. In pre-clinical models, combined taz and BETi synergistically blocked growth and prolonged survival of NC-xenografted mice, with all mice cured in one cohort. STATEMENT OF SIGNIFICANCE Identification of EZH2 as a dependency in NC substantiates the reliance of NC tumor cells on epigenetic dysregulation of functionally opposite, yet highly complementary chromatin regulatory pathways to maintain NC growth. In particular, repression of CDKN2A expression by EZH2 provides a mechanistic rationale for combining EZH2i with BETi for the clinical treatment of NC.
Collapse
Affiliation(s)
- Yeying Huang
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - R. Taylor Durall
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nhi M. Luong
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hans J. Hertzler
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Julianna Huang
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brittaney A. Leeper
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Praju V. Anekal
- MicRoN, Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Karan Saluja
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, TX, USA
| | - Jia Luo
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cynthia A. Zahnow
- Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
| | - Catherine E. Hawkins
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher Ponne
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Quan Le
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kyle P. Eagen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher A. French
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
27
|
Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
Collapse
Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
| |
Collapse
|
28
|
Vilca S, Wahlestedt C, Izenwasser S, Gainetdinov RR, Pardo M. Dopamine Transporter Knockout Rats Display Epigenetic Alterations in Response to Cocaine Exposure. Biomolecules 2023; 13:1107. [PMID: 37509143 PMCID: PMC10377455 DOI: 10.3390/biom13071107] [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: 06/05/2023] [Revised: 06/22/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: There is an urgent need for effective treatments for cocaine use disorder (CUD), and new pharmacological approaches targeting epigenetic mechanisms appear to be promising options for the treatment of this disease. Dopamine Transporter (DAT) transgenic rats recently have been proposed as a new animal model for studying susceptibility to CUD. (2) Methods: DAT transgenic rats were treated chronically with cocaine (10 mg/kg) for 8 days, and the expression of epigenetic modulators, Lysine Demethylase 6B (KDM6B) and Bromodomain-containing protein 4 (BRD4), was examined in the prefrontal cortex (PFC). (3) Results: We show that only full knockout (KO) of DAT impacts basal levels of KDM6B in females. Additionally, cocaine altered the expression of both epigenetic markers in a sex- and genotype-dependent manner. In response to chronic cocaine, KDM6B expression was decreased in male rats with partial DAT mutation (HET), while no changes were observed in wild-type (WT) or KO rats. Indeed, while HET male rats have reduced KDM6B and BRD4 expression, HET female rats showed increased KDM6B and BRD4 expression levels, highlighting the impact of sex on epigenetic mechanisms in response to cocaine. Finally, both male and female KO rats showed increased expression of BRD4, but only KO females exhibited significantly increased KDM6B expression in response to cocaine. Additionally, the magnitude of these effects was bigger in females when compared to males for both epigenetic enzymes. (4) Conclusions: This preliminary study provides additional support that targeting KDM6B and/or BRD4 may potentially be therapeutic in treating addiction-related behaviors in a sex-dependent manner.
Collapse
Affiliation(s)
- Samara Vilca
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (S.V.); (C.W.); (S.I.)
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (S.V.); (C.W.); (S.I.)
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sari Izenwasser
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (S.V.); (C.W.); (S.I.)
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034 St. Petersburg, Russia;
| | - Marta Pardo
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| |
Collapse
|
29
|
Hu J, Hu B, Xu F, Wang M, Qin C, McEachern D, Stuckey J, Wang S. Precise Conformational Control Yielding Highly Potent and Exceptionally Selective BRD4 Degraders with Strong Antitumor Activity. J Med Chem 2023; 66:8222-8237. [PMID: 37289649 PMCID: PMC10436693 DOI: 10.1021/acs.jmedchem.3c00520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Starting from a nonselective bromodomain and extraterminal (BET) inhibitor and a cereblon ligand, we have used precise conformational control for the development of two potent and highly selective BRD4 degraders, BD-7148 and BD-9136. These compounds induce rapid degradation of BRD4 protein in cells at concentrations as low as 1 nM and demonstrate ≥1000-fold degradation selectivity over BRD2 or BRD3 protein. Proteomic analysis of >5700 proteins confirmed their highly selective BRD4 degradation. A single dose of BD-9136 selectively and effectively depletes BRD4 protein in tumor tissues for >48 h. BD-9136 effectively inhibits tumor growth without adverse effects on mice and is more efficacious than the corresponding pan BET inhibitor. This study suggests selective degradation of BRD4 as a strategy for the treatment of human cancers and demonstrates a strategy for the design of highly selective PROTAC degraders.
Collapse
Affiliation(s)
- Jiantao Hu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Biao Hu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fuming Xu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mi Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chong Qin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donna McEachern
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
30
|
Schwalm MP, Krämer A, Dölle A, Weckesser J, Yu X, Jin J, Saxena K, Knapp S. Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Cell Chem Biol 2023:S2451-9456(23)00157-5. [PMID: 37354907 DOI: 10.1016/j.chembiol.2023.06.002] [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: 01/02/2023] [Revised: 04/03/2023] [Accepted: 06/01/2023] [Indexed: 06/26/2023]
Abstract
The multi-step degradation process of PROteolysis TArgeting Chimeras (PROTACs) poses a challenge for their rational development, as the rate-limiting steps that determine PROTACs efficiency remain largely unknown. Moreover, the slow throughput of currently used endpoint assays does not allow the comprehensive analysis of larger series of PROTACs. Here, we developed cell-based assays using the NanoLuciferase and HaloTag that allow measuring PROTAC-induced degradation and ternary complex formation kinetics and stability in cells. Using PROTACs developed for the degradation of WD40 repeat domain protein 5 (WDR5), the characterization of the mode of action of these PROTACs in the early degradation cascade revealed a key role of ternary complex formation and stability. Comparing a series of ternary complex crystal structures highlighted the importance of an efficient E3-target interface for ternary complex stability. The developed assays outline a strategy for the rational optimization of PROTACs using a series of live cell assays monitoring key steps of the early PROTAC-induced degradation pathway.
Collapse
Affiliation(s)
- Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Dölle
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Janik Weckesser
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Krishna Saxena
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany.
| |
Collapse
|
31
|
Yellapu NK, Pei D, Nissen E, Thompson JA, Koestler DC. Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches. Comput Struct Biotechnol J 2023; 21:3224-3233. [PMID: 38213901 PMCID: PMC10781883 DOI: 10.1016/j.csbj.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 01/13/2024] Open
Abstract
JQ1 and GSK2801 are bromo domain inhibitors (BDI) known to exhibit enhanced anti-cancer activity when combined with other agents. However, the underlying molecular mechanisms behind such enhanced activity remain unclear. We used network-pharmacology approaches to understand the shared molecular mechanisms behind the enhanced activity of JQ1 and GSK2801 when used together to treat breast cancer (BC). The gene targets of JQ1 and GSK2801 were intersected with known BC-targets and their putative targets against BC were derived. The key genes were explored through gene-ontology-enrichment, Protein-Protein-Interaction (PPI) networking, survival analysis, and molecular modeling simulations. The genes, CTSB, MAPK14, MET, PSEN2 and STAT3, were found to be common targets for both drugs. In total, 49 biological processes, five molecular functions and 61 metabolic pathways were similarly enriched for JQ1 and GSK2801 BC targets among which several terms are related to cancer: IL-17, TNF and JAK-STAT signaling pathways. Survival analyses revealed that all five putative synergistic targets are significantly associated with survival in BC (log-rank p < 0.05). Molecular modeling studies showed stable binding of JQ1 and GSK2801 against their targets. In conclusion, this study explored and illuminated the possible molecular mechanisms behind the enhanced activity of JQ1 and GSK2801 against BC and suggests synergistic action through their similar BC-targets and gene-ontologies.
Collapse
Affiliation(s)
- Nanda Kumar Yellapu
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, Kansas City, KS, USA
| | - Dong Pei
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, Kansas City, KS, USA
| | - Emily Nissen
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, Kansas City, KS, USA
| | - Jeffrey A. Thompson
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, Kansas City, KS, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, Kansas City, KS, USA
| |
Collapse
|
32
|
Pietrobono S, Stecca B. Combined targeting of HEDGEHOG signaling and BRD4 as a novel therapeutic option against melanoma. Oncotarget 2023; 14:526-527. [PMID: 37235835 DOI: 10.18632/oncotarget.28441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
|
33
|
Rayego-Mateos S, Basantes P, Morgado-Pascual JL, Brazal Prieto B, Suarez-Alvarez B, Ortiz A, Lopez-Larrea C, Ruiz-Ortega M. BET Protein Inhibitor JQ1 Modulates Mitochondrial Dysfunction and Oxidative Stress Induced by Chronic Kidney Disease. Antioxidants (Basel) 2023; 12:antiox12051130. [PMID: 37237996 DOI: 10.3390/antiox12051130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Among the mechanisms involved in the progression of kidney disease, mitochondrial dysfunction has special relevance. Epigenetic drugs such as inhibitors of extra-terminal domain proteins (iBET) have shown beneficial effects in experimental kidney disease, mainly by inhibiting proliferative and inflammatory responses. The impact of iBET on mitochondrial damage was explored in in vitro studies in renal cells stimulated with TGF-β1 and in vivo in murine unilateral ureteral obstruction (UUO) model of progressive kidney damage. In vitro, JQ1 pretreatment prevented the TGF-β1-induced downregulation of components of the oxidative phosphorylation chain (OXPHOS), such as cytochrome C and CV-ATP5a in human proximal tubular cells. In addition, JQ1 also prevented the altered mitochondrial dynamics by avoiding the increase in the DRP-1 fission factor. In UUO model, renal gene expression levels of cytochrome C and CV-ATP5a as well as protein levels of cytochrome C were reduced These changes were prevented by JQ1 administration. In addition, JQ1 decreased protein levels of the DRP1 fission protein and increased the OPA-1 fusion protein, restoring mitochondrial dynamics. Mitochondria also participate in the maintenance of redox balance. JQ1 restored the gene expression of antioxidant proteins, such as Catalase and Heme oxygenase 1 in TGF-β1-stimulated human proximal tubular cells and in murine obstructed kidneys. Indeed, in tubular cells, JQ1 decreased ROS production induced by stimulation with TGF-β1, as evaluated by MitoSOXTM. iBETs, such as JQ1, improve mitochondrial dynamics, functionality, and oxidative stress in kidney disease.
Collapse
Affiliation(s)
- Sandra Rayego-Mateos
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
- Ricors2040, 28029 Madrid, Spain
| | - Pamela Basantes
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
- Ricors2040, 28029 Madrid, Spain
| | - José Luis Morgado-Pascual
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University of Cordoba, 14004 Cordoba, Spain
| | - Beatriz Brazal Prieto
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
- Ricors2040, 28029 Madrid, Spain
| | - Beatriz Suarez-Alvarez
- Ricors2040, 28029 Madrid, Spain
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Alberto Ortiz
- Ricors2040, 28029 Madrid, Spain
- Division of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
| | - Carlos Lopez-Larrea
- Ricors2040, 28029 Madrid, Spain
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Marta Ruiz-Ortega
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, 28040 Madrid, Spain
- Ricors2040, 28029 Madrid, Spain
| |
Collapse
|
34
|
Koravovic M, Mayasundari A, Tasic G, Keramatnia F, Stachowski TR, Cui H, Chai SC, Jonchere B, Yang L, Li Y, Fu X, Hiltenbrand R, Paul L, Mishra V, Klco JM, Roussel MF, Pomerantz WC, Fischer M, Rankovic Z, Savic V. From PROTAC to inhibitor: Structure-guided discovery of potent and orally bioavailable BET inhibitors. Eur J Med Chem 2023; 251:115246. [PMID: 36898329 PMCID: PMC10165889 DOI: 10.1016/j.ejmech.2023.115246] [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: 12/05/2022] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
An X-ray structure of a CLICK chemistry-based BET PROTAC bound to BRD2(BD2) inspired synthesis of JQ1 derived heterocyclic amides. This effort led to the discovery of potent BET inhibitors displaying overall improved profiles when compared to JQ1 and birabresib. A thiadiazole derived 1q (SJ1461) displayed excellent BRD4 and BRD2 affinity and high potency in the panel of acute leukaemia and medulloblastoma cell lines. A structure of 1q co-crystalised with BRD4-BD1 revealed polar interactions with the AZ/BC loops, in particular with Asn140 and Tyr139, rationalising the observed affinity improvements. In addition, exploration of pharmacokinetic properties of this class of compounds suggest that the heterocyclic amide moiety improves drug-like features. Our study led to the discovery of potent and orally bioavailable BET inhibitor 1q (SJ1461) as a promising candidate for further development.
Collapse
Affiliation(s)
- Mladen Koravovic
- University of Belgrade, Faculty of Pharmacy, Department of Organic Chemistry, Vojvode Stepe 450, 11221, Belgrade, Serbia
| | - Anand Mayasundari
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Gordana Tasic
- University of Belgrade, Faculty of Pharmacy, Department of Organic Chemistry, Vojvode Stepe 450, 11221, Belgrade, Serbia
| | - Fatemeh Keramatnia
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Timothy R Stachowski
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN, 55455, United States
| | - Sergio C Chai
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Barbara Jonchere
- Department of Tumour Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Li
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiang Fu
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Leena Paul
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Martine F Roussel
- Department of Tumour Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - William Ck Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN, 55455, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Vladimir Savic
- University of Belgrade, Faculty of Pharmacy, Department of Organic Chemistry, Vojvode Stepe 450, 11221, Belgrade, Serbia.
| |
Collapse
|
35
|
To KKW, Xing E, Larue RC, Li PK. BET Bromodomain Inhibitors: Novel Design Strategies and Therapeutic Applications. Molecules 2023; 28:molecules28073043. [PMID: 37049806 PMCID: PMC10096006 DOI: 10.3390/molecules28073043] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
The mammalian bromodomain and extra-terminal domain (BET) family of proteins consists of four conserved members (Brd2, Brd3, Brd4, and Brdt) that regulate numerous cancer-related and immunity-associated genes. They are epigenetic readers of histone acetylation with broad specificity. BET proteins are linked to cancer progression due to their interaction with numerous cellular proteins including chromatin-modifying factors, transcription factors, and histone modification enzymes. The spectacular growth in the clinical development of small-molecule BET inhibitors underscores the interest and importance of this protein family as an anticancer target. Current approaches targeting BET proteins for cancer therapy rely on acetylation mimics to block the bromodomains from binding chromatin. However, bromodomain-targeted agents are suffering from dose-limiting toxicities because of their effects on other bromodomain-containing proteins. In this review, we provided an updated summary about the evolution of small-molecule BET inhibitors. The design of bivalent BET inhibitors, kinase and BET dual inhibitors, BET protein proteolysis-targeting chimeras (PROTACs), and Brd4-selective inhibitors are discussed. The novel strategy of targeting the unique C-terminal extra-terminal (ET) domain of BET proteins and its therapeutic significance will also be highlighted. Apart from single agent treatment alone, BET inhibitors have also been combined with other chemotherapeutic modalities for cancer treatment demonstrating favorable clinical outcomes. The investigation of specific biomarkers for predicting the efficacy and resistance of BET inhibitors is needed to fully realize their therapeutic potential in the clinical setting.
Collapse
|
36
|
Mandl A, Markowski MC, Carducci MA, Antonarakis ES. Role of bromodomain and extraterminal (BET) proteins in prostate cancer. Expert Opin Investig Drugs 2023; 32:213-228. [PMID: 36857796 DOI: 10.1080/13543784.2023.2186851] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
INTRODUCTION The bromodomain and extraterminal (BET) family of proteins are epigenetic readers of acetylated histones and are critical activators of oncogenic networks across many cancers. Therapeutic targeting of BET proteins has been an attractive area of clinical development for metastatic castration-resistant prostate cancer. In recent years, many structurally diverse BET inhibitors have been discovered and tested. Preclinical studies have demonstrated significant antiproliferative activity of BET inhibitors against prostate cancer. However, their clinical success as monotherapies has been limited by treatment-associated toxicities, primary and acquired drug resistance, and a lack of predictive biomarkers of benefit. AREAS COVERED This review provides an overview of advancements in BET inhibitor design, preclinical research, and conclusions from clinical trials in prostate cancer. We speculate on incorporating BET inhibitors into combination regimens with other agents to improve the therapeutic index of BET inhibition in treating prostate cancer. EXPERT OPINION The therapeutic potential of BET inhibitors for prostate cancer has been demonstrated in preclinical studies. However, further research is needed to identify biomarkers that can predict sensitivity to BET inhibitors and to develop novel, highly selective inhibitors to reduce toxicities. Finally, BET inhibitors are likely to hold the most clinical potential in combination with other agents.
Collapse
Affiliation(s)
- Adel Mandl
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, MD, USA
| | - Mark C Markowski
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, MD, USA
| | - Michael A Carducci
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, MD, USA
| | - Emmanuel S Antonarakis
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| |
Collapse
|
37
|
Chauhan J, Yoshioka M, Pogash S, Strovel JW, Fletcher S. Discovery and anti-tumor activity of 4-(benzylamino)-6-(3,5-dimethylisoxazol-4-yl)quinoline-2(1H)-one (CG13250), a potent, selective and orally bioavailable BET bromodomain inhibitor. Bioorg Med Chem Lett 2023; 86:129220. [PMID: 36905966 DOI: 10.1016/j.bmcl.2023.129220] [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: 01/14/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
The bromodomain and extra-terminal domain (BET) proteins are epigenetic readers involved in the regulation of gene transcription. Inhibitors of the BET proteins, in particular BRD4, have demonstrated anti-tumour activities and efficacies in clinical trials. Herein, we describe the discovery of potent and selective inhibitors of BRD4, and demonstrate that the lead compound CG13250 is orally bioavailable and efficacious in a mouse xenograft model of leukemia.
Collapse
Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Makoto Yoshioka
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Sarah Pogash
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Jeffrey W Strovel
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA.
| |
Collapse
|
38
|
Martella N, Pensabene D, Varone M, Colardo M, Petraroia M, Sergio W, La Rosa P, Moreno S, Segatto M. Bromodomain and Extra-Terminal Proteins in Brain Physiology and Pathology: BET-ing on Epigenetic Regulation. Biomedicines 2023; 11:biomedicines11030750. [PMID: 36979729 PMCID: PMC10045827 DOI: 10.3390/biomedicines11030750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer’s disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and pathology, as well as their pharmacological potential as targets for therapeutic purposes.
Collapse
Affiliation(s)
- Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Michela Varone
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Michele Petraroia
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - William Sergio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, via dei Marsi 78, 00185 Rome, Italy
| | - Sandra Moreno
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Correspondence:
| |
Collapse
|
39
|
When Just One Phosphate Is One Too Many: The Multifaceted Interplay between Myc and Kinases. Int J Mol Sci 2023; 24:ijms24054746. [PMID: 36902175 PMCID: PMC10003727 DOI: 10.3390/ijms24054746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Myc transcription factors are key regulators of many cellular processes, with Myc target genes crucially implicated in the management of cell proliferation and stem pluripotency, energy metabolism, protein synthesis, angiogenesis, DNA damage response, and apoptosis. Given the wide involvement of Myc in cellular dynamics, it is not surprising that its overexpression is frequently associated with cancer. Noteworthy, in cancer cells where high Myc levels are maintained, the overexpression of Myc-associated kinases is often observed and required to foster tumour cells' proliferation. A mutual interplay exists between Myc and kinases: the latter, which are Myc transcriptional targets, phosphorylate Myc, allowing its transcriptional activity, highlighting a clear regulatory loop. At the protein level, Myc activity and turnover is also tightly regulated by kinases, with a finely tuned balance between translation and rapid protein degradation. In this perspective, we focus on the cross-regulation of Myc and its associated protein kinases underlying similar and redundant mechanisms of regulation at different levels, from transcriptional to post-translational events. Furthermore, a review of the indirect effects of known kinase inhibitors on Myc provides an opportunity to identify alternative and combined therapeutic approaches for cancer treatment.
Collapse
|
40
|
Wang C, Chan DW, Hendrickson EA. Kinome-wide screening uncovers a role for Bromodomain Protein 3 in DNA double-stranded break repair. DNA Repair (Amst) 2023; 122:103445. [PMID: 36608404 PMCID: PMC10353298 DOI: 10.1016/j.dnarep.2022.103445] [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: 07/12/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Double-stranded breaks (DSBs) are toxic DNA damage and a serious threat to genomic integrity. Thus, all living organisms have evolved multiple mechanisms of DNA DSB repair, the two principal ones being classical-non homologous end joining (C-NHEJ), and homology dependent recombination (HDR). In mammals, C-NHEJ is the predominate DSB repair pathway, but how a cell chooses to repair a particular DSB by a certain pathway is still not mechanistically clear. To uncover novel regulators of DSB repair pathway choice, we performed a kinome-wide screen in a human cell line engineered to express a dominant-negative C-NHEJ factor. The intellectual basis for such a screen was our hypothesis that a C-NHEJ-crippled cell line might need to upregulate other DSB repair pathways, including HDR, in order to survive. This screen identified Bromodomain-containing Protein 3 (BRD3) as a protein whose expression was almost completely ablated specifically in a C-NHEJ-defective cell line. Subsequent experimentation demonstrated that BRD3 is a negative regulator of HDR as BRD3-null cell lines proved to be hyper-recombinogenic for gene conversion, sister chromatid exchanges and gene targeting. Mechanistically, BRD3 appears to be working at the level of Radiation Sensitive 51 (RAD51) recruitment. Overall, our results demonstrate that BRD3 is a novel regulator of human DSB repair pathway choice.
Collapse
Affiliation(s)
- Chen Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Doug W Chan
- Department of Systems Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| |
Collapse
|
41
|
Bhela I, Ranza A, Balestrero FC, Serafini M, Aprile S, Di Martino RMC, Condorelli F, Pirali T. A Versatile and Sustainable Multicomponent Platform for the Synthesis of Protein Degraders: Proof-of-Concept Application to BRD4-Degrading PROTACs. J Med Chem 2022; 65:15282-15299. [PMID: 36323630 PMCID: PMC9706574 DOI: 10.1021/acs.jmedchem.2c01218] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 11/06/2022]
Abstract
The use of small molecules to induce targeted protein degradation is increasingly growing in the drug discovery landscape, and protein degraders have progressed rapidly through the pipelines. Despite the advances made so far, their synthesis still represents a significant burden and new approaches are highly demanded. Herein we report an unprecedented platform that leverages the modular nature of both multicomponent reactions and degraders to enable the preparation of highly decorated PROTACs. As a proof of principle, our platform has been applied to the preparation of potential BRD4-degrading PROTACs, resulting in the discovery of a set of degraders endowed with high degradation efficiency. Compared to the existing methods, our approach offers a versatile and cost-effective means to access libraries of protein degraders and increase the chance of identifying successful candidates.
Collapse
Affiliation(s)
- Irene
Preet Bhela
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Alice Ranza
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Federica Carolina Balestrero
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | | | - Silvio Aprile
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Rita Maria Concetta Di Martino
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Fabrizio Condorelli
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Tracey Pirali
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| |
Collapse
|
42
|
Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
Collapse
Affiliation(s)
- Václav Němec
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
| |
Collapse
|
43
|
High-Throughput Identification of Epigenetic Compounds to Enhance Chicken Host Defense Peptide Gene Expression. Antibiotics (Basel) 2022; 11:antibiotics11070933. [PMID: 35884187 PMCID: PMC9311565 DOI: 10.3390/antibiotics11070933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 01/02/2023] Open
Abstract
Enhancing the synthesis of endogenous host defense peptides (HDPs) has emerged as a novel antibiotic-free approach to infectious disease control and prevention. A number of epigenetic compounds have been identified as HDP inducers and several have proved beneficial in antimicrobial therapy. However, species-specific regulation of HDP synthesis is evident. In attempt to identify epigenetic compounds with potent HDP-inducing activity for poultry-specific application, we developed a stable luciferase reporter cell line, known as HTC/AvBD10-luc, following our earlier construction of HTC/AvBD9-luc. HTC/AvBD10-luc was developed through permanent integration of a chicken macrophage cell line, HTC, with a lentiviral luciferase reporter vector driven by a 4-Kb AvBD10 gene promoter. Using a high throughput screening assay based on the two stable cell lines, we identified 33 hits, mostly being histone deacetylase (HDAC) inhibitors, from a library of 148 epigenetic compounds. Among them, entinostat and its structural analog, tucidinostat, were particularly effective in promoting multiple HDP gene expression in chicken macrophages and jejunal explants. Desirably, neither compounds triggered an inflammatory response. Moreover, oral gavage of entinostat significantly enhanced HDP gene expression in the chicken intestinal tract. Collectively, the high throughput assay proves to be effective in identifying HDP inducers, and both entinostat and tucidinostat could be potentially useful as alternatives to antibiotics to enhance intestinal immunity and disease resistance.
Collapse
|