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Pan P, Ji D, Li Z, Meng X. Design and synthesis of doublecortin-like kinase 1 inhibitors and their bioactivity evaluation. J Enzyme Inhib Med Chem 2024; 39:2287990. [PMID: 38062554 DOI: 10.1080/14756366.2023.2287990] [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: 09/11/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Doublecortin-like kinase 1 (DCLK) is a microtubule-associated serine/threonine kinase that is upregulated in a wide range of cancers and is believed to be related to tumour growth and development. Upregulated DCLK1 has been used to identify patients at high risk of cancer progression and tumours with chemotherapy-resistance. Moreover, DCLK1 has been identified as a cancer stem cell (CSC) biomarker in various cancers, which has received considerable attention recently. Herein, a series of DCLK1 inhibitors were prepared based on the previously reported XMD8-92 structure. Among all the synthesised compounds, D1, D2, D6, D7, D8, D12, D14, and D15 showed higher DCLK1 inhibitory activities (IC50 40-74 nM) than XMD8-92 (IC50 161 nM). Compounds D1 and D2 were selective DCLK1 inhibitors as they showed a rather weak inhibitory effect on LRRK2. The antiproliferative activities of these compounds were also preliminarily evaluated. The structure-activity relationship revealed by our compounds provides useful guidance for the further development of DCLK1 inhibitors.
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Affiliation(s)
- Pengming Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Dengbo Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhongjun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiangbao Meng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
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2
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Bai YR, Yang X, Chen KT, Cuan XD, Zhang YD, Zhou L, Yang L, Liu HM, Yuan S. A comprehensive review of new small molecule drugs approved by the FDA in 2022: Advance and prospect. Eur J Med Chem 2024; 277:116759. [PMID: 39137454 DOI: 10.1016/j.ejmech.2024.116759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
In 2022, the U.S. Food and Drug Administration approved a total of 16 marketing applications for small molecule drugs, which not only provided dominant scaffolds but also introduced novel mechanisms of action and clinical indications. The successful cases provide valuable information for optimizing efficacy and enhancing pharmacokinetic properties through strategies like macrocyclization, bioequivalent group utilization, prodrug synthesis, and conformation restriction. Therefore, gaining an in-depth understanding of the design principles and strategies underlying these drugs will greatly facilitate the development of new therapeutic agents. This review focuses on the research and development process of these newly approved small molecule drugs including drug design, structural modification, and improvement of pharmacokinetic properties to inspire future research in this field.
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Affiliation(s)
- Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Xin Yang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Ke-Tong Chen
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Xiao-Dan Cuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yao-Dong Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Li Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Li Yang
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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3
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Wang D, Wang W, Song M, Xie Y, Kuang W, Yang P. Regulation of protein phosphorylation by PTPN2 and its small-molecule inhibitors/degraders as a potential disease treatment strategy. Eur J Med Chem 2024; 277:116774. [PMID: 39178726 DOI: 10.1016/j.ejmech.2024.116774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
Protein tyrosine phosphatase nonreceptor type 2 (PTPN2) is an enzyme that dephosphorylates proteins with tyrosine residues, thereby modulating relevant signaling pathways in vivo. PTPN2 acts as tumor suppressor or tumor promoter depending on the context. In some cancers, such as colorectal, and lung cancer, PTPN2 defects could impair the protein tyrosine kinase pathway, which is often over-activated in cancer cells, and inhibit tumor development and progression. However, PTPN2 can also suppress tumor immunity by regulating immune cells and cytokines. The structure, functions, and substrates of PTPN2 in various tumor cells were reviewed in this paper. And we summarized the research status of small molecule inhibitors and degraders of PTPN2. It also highlights the potential opportunities and challenges for developing PTPN2 inhibitors as anticancer drugs.
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Affiliation(s)
- Dawei Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenmu Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Mingge Song
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yishi Xie
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China.
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4
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Hesham HM, Dokla EME, Elrazaz EZ, Lasheen DS, Abou El Ella DA. FLT3-PROTACs for combating AML resistance: Analytical overview on chimeric agents developed, challenges, and future perspectives. Eur J Med Chem 2024; 277:116717. [PMID: 39094274 DOI: 10.1016/j.ejmech.2024.116717] [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: 05/16/2024] [Revised: 07/13/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
The urgent and unmet medical demand of acute myeloid leukemia (AML) patients has driven the drug discovery process for expansion of the landscape of AML treatment. Despite the several agents developed for treatment of AML, more than 60 % of treated patients undergo relapse again after re-emission, thus, no complete cure for this complex disease has been reached yet. Targeted oncoprotein degradation is a new paradigm that can be employed to solve drug resistance, disease relapse, and treatment failure in complex diseases as AML, the most lethal hematological malignancy. AML is an aggressive blood cancer form and the most common type of acute leukemia, with bad outcomes and a very poor 5-year survival rate. FLT3 mutations occur in about 30 % of AML cases and FLT3-ITD is associated with poor prognosis of this disease. Prevalent FLT3 mutations include internal tandem duplication and point mutations (e.g., D835) in the tyrosine kinase domain, which induce FLT3 kinase activation and result in survival and proliferation of AML cells again. Currently approved FLT3 inhibitors suffer from limited clinical efficacy due to FLT3 reactivation by mutations, therefore, alternative new treatments are highly needed. Proteolysis-targeting chimera (PROTAC) is a bi-functional molecule that consists of a ligand of the protein of interest, FLT3 inhibitor in our case, that is covalently linked to an E3 ubiquitin ligase ligand. Upon FLT3-specific PROTAC binding to FLT3, the PROTAC can recruit E3 for FLT3 ubiquitination, which is subsequently subjected to proteasome-mediated degradation. In this review we tried to address the question if PROTAC technology has succeeded in tackling the disease relapse and treatment failure of AML. Next, we explored the latest FLT3-targeting PROTACs developed in the past few years such as quizartinib-based PROTACs, dovitinib-based PROTACs, gilteritinib-based PROTACs, and others. Then, we followed with a deep analysis of their advantages regarding potency improvement and overcoming AML drug resistance. Finally, we discussed the challenges facing these chimeric molecules with proposed future solutions to circumvent them.
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Affiliation(s)
- Heba M Hesham
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Eman M E Dokla
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
| | - Eman Z Elrazaz
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Deena S Lasheen
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Dalal A Abou El Ella
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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5
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Zhang R, Zheng Y, Xiang F, Zhou J. Inducing or enhancing protein-protein interaction to develop drugs: Molecular glues with various biological activity. Eur J Med Chem 2024; 277:116756. [PMID: 39191033 DOI: 10.1016/j.ejmech.2024.116756] [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: 05/24/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Over the past two decades, molecular glues (MGs) have gradually attracted the attention of the pharmaceutical community with the advent of MG degraders such as IMiDs and indisulam. Such molecules degrade the target protein by promoting the interaction between the target protein and E3 ligase. In addition, as a chemical inducer, MGs promote the dimerization of homologous proteins and heterologous proteins to form ternary complexes, which have great prospects in regulating biological activities. This review focuses on the application of MGs in the field of drug development including protein-protein interaction (PPI) stability and protein degradation. We thoroughly analyze the structure of various MGs and the interactions between MGs and various biologically active molecules, thus providing new perspectives for the development of PPI stabilizers and new degraders.
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Affiliation(s)
- Rongyu Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Yirong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Fengjiao Xiang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China.
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6
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Wang D, Wang Y. Identification of protein partners for small molecules reshapes the understanding of nonalcoholic steatohepatitis and drug discovery. Life Sci 2024; 356:123031. [PMID: 39226989 DOI: 10.1016/j.lfs.2024.123031] [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: 05/31/2024] [Revised: 08/16/2024] [Accepted: 08/30/2024] [Indexed: 09/05/2024]
Abstract
AIMS Nonalcoholic steatohepatitis (NASH) is the severe subtype of nonalcoholic fatty diseases (NAFLD) with few options for treatment. Patients with NASH exhibit partial responses to the current therapeutics and adverse effects. Identification of the binding proteins for the drugs is essential to understanding the mechanism and adverse effects of the drugs and fuels the discovery of potent and safe drugs. This paper aims to critically discuss recent advances in covalent and noncovalent approaches for identifying binding proteins that mediate NASH progression, along with an in-depth analysis of the mechanisms by which these targets regulate NASH. MATERIALS AND METHODS A literature search was conducted to identify the relevant studies in the database of PubMed and the American Chemical Society. The search covered articles published from January 1990 to July 2024, using the search terms with keywords such as NASH, benzophenone, diazirine, photo-affinity labeling, thermal protein profiling, CETSA, target identification. KEY FINDINGS The covalent approaches utilize drugs modified with diazirine and benzophenone to covalently crosslink with the target proteins, which facilitates the purification and identification of target proteins. In addition, they map the binding sites in the target proteins. By contrast, noncovalent approaches identify the binding targets of unmodified drugs in the intact cell proteome. The advantages and limitations of both approaches have been compared, along with a comprehensive analysis of recent innovations that further enhance the efficiency and specificity. SIGNIFICANCE The analyses of the applicability of these approaches provide novel tools to delineate NASH pathogenesis and promote drug discovery.
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Affiliation(s)
- Danyi Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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7
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Wang X, Li N, Liu YH, Wu J, Liu QG, Niu JB, Xu Y, Huang CZ, Zhang SY, Song J. Targeting focal adhesion kinase (FAK) in cancer therapy: A recent update on inhibitors and PROTAC degraders. Eur J Med Chem 2024; 276:116678. [PMID: 39029337 DOI: 10.1016/j.ejmech.2024.116678] [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: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024]
Abstract
Focal adhesion kinase (FAK) is considered as a pivotal intracellular non-receptor tyrosine kinase, and has garnered significant attention as a promising target for anticancer drug development. As of early 2024, a total of 12 drugs targeting FAK have been approved for clinical or preclinical studies worldwide, including three PROTAC degraders. In recent three years (2021-2023), significant progress has been made in designing targeted FAK anticancer agents, including the development of a novel benzenesulfofurazan type NO-releasing FAK inhibitor and the first-in-class dual-target inhibitors simultaneously targeting FAK and HDACs. Given the pivotal role of FAK in the discovery of anticancer drugs, as well as the notable advancements achieved in FAK inhibitors and PROTAC degraders in recent years, this review is underbaked to present a comprehensive overview of the function and structure of FAK. Additionally, the latest findings on the inhibitors and PROTAC degraders of FAK from the past three years, along with their optimization strategies and anticancer activities, were summarized, which might help to provide novel insights for the development of novel targeted FAK agents with promising anticancer potential and favorable pharmacological profiles.
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Affiliation(s)
- Xiao Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Na Li
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yun-He Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ji Wu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Qiu-Ge Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jin-Bo Niu
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yan Xu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chen-Zheng Huang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Sai-Yang Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention &Treatment, Zhengzhou, 450001, China.
| | - Jian Song
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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Zheng S, Chen R, Zhang L, Tan L, Li L, Long F, Wang T. Unraveling the future: Innovative design strategies and emerging challenges in HER2-targeted tyrosine kinase inhibitors for cancer therapy. Eur J Med Chem 2024; 276:116702. [PMID: 39059182 DOI: 10.1016/j.ejmech.2024.116702] [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: 06/14/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024]
Abstract
Human epidermal growth factor receptor 2 (HER2) is a transmembrane receptor-like protein with tyrosine kinase activity that plays a vital role in processes such as cell proliferation, differentiation, and angiogenesis. The degree of malignancy of different cancers, notably breast cancer, is strongly associated with HER2 amplification, overexpression, and mutation. Currently, widely used clinical HER2 tyrosine kinase inhibitors (TKIs), such as lapatinib and neratinib, have several drawbacks, including susceptibility to drug resistance caused by HER2 mutations and adverse effects from insufficient HER2 selectivity. To address these issues, it is essential to create innovative HER2 TKIs with enhanced safety, effectiveness against mutations, and high selectivity. Typically, SPH5030 has advanced to phase I clinical trials for its strong suppression of four HER2 mutations. This review discusses the latest research progress in HER2 TKIs, with a focus on the structural optimization process and structure-activity relationship analysis. In particular, this study highlights promising design strategies to address these challenges, providing insightful information and inspiration for future development in this field.
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Affiliation(s)
- Sixiang Zheng
- Department of Clinical Research, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Ruixian Chen
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lele Zhang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lun Tan
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lintao Li
- Department of Radiotherapy, Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
| | - Fangyi Long
- Laboratory Medicine Center, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610032, China.
| | - Ting Wang
- Department of Clinical Research, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
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9
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De S, Sahu R, Palei S, Narayan Nanda L. Synthesis, SAR, and application of JQ1 analogs as PROTACs for cancer therapy. Bioorg Med Chem 2024; 112:117875. [PMID: 39178586 DOI: 10.1016/j.bmc.2024.117875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
JQ1 is a wonder therapeutic molecule that selectively inhibits the BRD4 signaling pathway and is thus widely used in the anticancer drug discovery program. Due to its unique selective BRD4 binding property, its applications are further extended in the design and synthesis of bi-functional PROTAC molecules. This BRD4 targeting PROTAC molecule selectively degrades the protein by proteolysis. There are several modifications of JQ1 known to date and extensively explored for their applications in PROTAC technology by several research groups in academia as well as industry for targeting oncogenic genes. In this review, we have covered the discovery and synthesis of the JQ1 molecule. The SAR of the JQ1 analogs will help researchers develop potent JQ1 compounds with improved inhibitory properties against malignant cells. Furthermore, we explored the potential application of JQ1 analogs in PROTAC technology. The brief history of the bromodomain family of proteins, as well as the obstacles connected with PROTAC technology, can help comprehend the context of the current research, which has the potential to improve the drug development process. Overall, this review comprehensively appraises JQ1 molecules and their prior implementation in PROTAC technology and cancer therapy.
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Affiliation(s)
- Soumik De
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, An OCC of Homi Bhabha National Institute (HBNI), Khurda, Odisha 752050, India
| | - Raghaba Sahu
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Shubhendu Palei
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Laxmi Narayan Nanda
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Harvard Medical School, Cambridge 02142, United States; P.G. Department of Chemistry, Government Autonomous College, Utkal University, Angul 759143, Odisha, India.
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10
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Liao Y, Zhang W, Liu Y, Zhu C, Zou Z. The role of ubiquitination in health and disease. MedComm (Beijing) 2024; 5:e736. [PMID: 39329019 PMCID: PMC11424685 DOI: 10.1002/mco2.736] [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: 02/11/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Ubiquitination is an enzymatic process characterized by the covalent attachment of ubiquitin to target proteins, thereby modulating their degradation, transportation, and signal transduction. By precisely regulating protein quality and quantity, ubiquitination is essential for maintaining protein homeostasis, DNA repair, cell cycle regulation, and immune responses. Nevertheless, the diversity of ubiquitin enzymes and their extensive involvement in numerous biological processes contribute to the complexity and variety of diseases resulting from their dysregulation. The ubiquitination process relies on a sophisticated enzymatic system, ubiquitin domains, and ubiquitin receptors, which collectively impart versatility to the ubiquitination pathway. The widespread presence of ubiquitin highlights its potential to induce pathological conditions. Ubiquitinated proteins are predominantly degraded through the proteasomal system, which also plays a key role in regulating protein localization and transport, as well as involvement in inflammatory pathways. This review systematically delineates the roles of ubiquitination in maintaining protein homeostasis, DNA repair, genomic stability, cell cycle regulation, cellular proliferation, and immune and inflammatory responses. Furthermore, the mechanisms by which ubiquitination is implicated in various pathologies, alongside current modulators of ubiquitination are discussed. Enhancing our comprehension of ubiquitination aims to provide novel insights into diseases involving ubiquitination and to propose innovative therapeutic strategies for clinical conditions.
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Affiliation(s)
- Yan Liao
- Faculty of AnesthesiologyChanghai HospitalNaval Medical UniversityShanghaiChina
- School of AnesthesiologyNaval Medical UniversityShanghaiChina
| | - Wangzheqi Zhang
- Faculty of AnesthesiologyChanghai HospitalNaval Medical UniversityShanghaiChina
- School of AnesthesiologyNaval Medical UniversityShanghaiChina
| | - Yang Liu
- Faculty of AnesthesiologyChanghai HospitalNaval Medical UniversityShanghaiChina
- School of AnesthesiologyNaval Medical UniversityShanghaiChina
| | - Chenglong Zhu
- Faculty of AnesthesiologyChanghai HospitalNaval Medical UniversityShanghaiChina
- School of AnesthesiologyNaval Medical UniversityShanghaiChina
| | - Zui Zou
- Faculty of AnesthesiologyChanghai HospitalNaval Medical UniversityShanghaiChina
- School of AnesthesiologyNaval Medical UniversityShanghaiChina
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11
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Cai Y, Lv Z, Chen X, Jin K, Mou X. Recent advances in biomaterials based near-infrared mild photothermal therapy for biomedical application: A review. Int J Biol Macromol 2024; 278:134746. [PMID: 39147342 DOI: 10.1016/j.ijbiomac.2024.134746] [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: 05/23/2024] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
Mild photothermal therapy (MPTT) generates heat therapeutic effect at the temperature below 45 °C under near-infrared (NIR) irradiation, which has the advantages of controllable treatment efficacy, lower hyperthermia temperatures, reduced dosage, and minimized damage to surrounding tissues. Despite significant progress has been achieved in MPTT, it remains primarily in the stage of basic and clinical research and has not yet seen widespread clinical adoption. Herein, a comprehensive overview of the recent NIR MPTT development was provided, aiming to emphasize the mechanism and obstacles, summarize the used photothermal agents, and introduce various biomedical applications such as anti-tumor, wound healing, and vascular disease treatment. The challenges of MPTT were proposed with potential solutions, and the future development direction in MPTT was outlooked to enhance the prospects for clinical translation.
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Affiliation(s)
- Yu Cai
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China; Clinical Research Institute, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
| | - Zhenye Lv
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, China
| | - Xiaoyi Chen
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China; Clinical Research Institute, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Ketao Jin
- Department of Gastrointestinal, Colorectal and Anal Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang 310006, China.
| | - Xiaozhou Mou
- Clinical Research Institute, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
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12
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Abbas A, Ye F. Computational methods and key considerations for in silico design of proteolysis targeting chimera (PROTACs). Int J Biol Macromol 2024; 277:134293. [PMID: 39084437 DOI: 10.1016/j.ijbiomac.2024.134293] [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: 05/29/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs), as heterobifunctional molecules, have garnered significant attention for their ability to target previously undruggable proteins. Due to the challenges in obtaining crystal structures of PROTAC molecules in the ternary complex, a plethora of computational tools have been developed to aid in PROTAC design. These computational tools can be broadly classified into artificial intelligence (AI)-based or non-AI-based methods. This review aims to provide a comprehensive overview of the latest computational methods for the PROTAC design process, covering both AI and non-AI approaches, from protein selection to ternary complex modeling and prediction. Key considerations for in silico PROTAC design are discussed, along with additional considerations for deploying AI-based models. These considerations are intended to guide subsequent model development in the PROTAC design process. Finally, future directions and recommendations are provided.
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Affiliation(s)
- Amr Abbas
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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13
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Ma Z, Zhang C, Bolinger AA, Zhou J. An updated patent review of BRD4 degraders. Expert Opin Ther Pat 2024; 34:929-951. [PMID: 39219068 DOI: 10.1080/13543776.2024.2400166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/17/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Bromodomain-containing protein 4 (BRD4), an important epigenetic reader, is closely associated with the pathogenesis and development of many diseases, including various cancers, inflammation, and infectious diseases. Targeting BRD4 inhibition or protein elimination with small molecules represents a promising therapeutic strategy, particularly for cancer therapy. AREAS COVERED The recent advances of patented BRD4 degraders were summarized. The challenges, opportunities, and future directions for developing novel potent and selective BRD4 degraders are also discussed. The patents of BRD4 degraders were searched using the SciFinder and Cortellis Drug Discovery Intelligence database. EXPERT OPINION BRD4 degraders exhibit superior efficacy and selectivity to BRD4 inhibitors, given their unique mechanism of protein degradation instead of protein inhibition. Excitingly, RNK05047 is now in phase I/II clinical trials, indicating that selective BRD4 protein degradation may offer a viable therapeutic strategy, particularly for cancer. Targeting BRD4 with small-molecule degraders provides a promising approach with the potential to overcome therapeutic resistance for treating various BRD4-associated diseases.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Cun Zhang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
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14
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Chen S, Chen K, Lin Y, Wang S, Yu H, Chang C, Cheng T, Hsieh C, Li J, Lai H, Chen D, Huang C. Ganoderic acid T, a Ganoderma triterpenoid, modulates the tumor microenvironment and enhances the chemotherapy and immunotherapy efficacy through downregulating galectin-1 levels. Toxicol Appl Pharmacol 2024; 491:117069. [PMID: 39142358 DOI: 10.1016/j.taap.2024.117069] [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: 05/14/2024] [Revised: 07/29/2024] [Accepted: 08/10/2024] [Indexed: 08/16/2024]
Abstract
Ganoderic acid T (GAT), a triterpenoid molecule of Ganoderma lucidum, exhibits anti-cancer activity; however, the underlying mechanisms remain unclear. Therefore, in this study, we aimed to investigate the anti-cancer molecular mechanisms of GAT and explore its therapeutic applications for cancer treatment. GAT exhibited potent anti-cancer activity in an ES-2 orthotopic ovarian cancer model in a humanized mouse model, leading to significant alterations in the tumor microenvironment (TME). Specifically, GAT reduced the proportion of α-SMA+ cells and enhanced the infiltration of tumor-infiltrating lymphocytes (TILs) in tumor tissues. After conducting proteomic analysis, it was revealed that GAT downregulates galectin-1 (Gal-1), a key molecule in the TME. This downregulation has been confirmed in multiple cancer cell lines and xenograft tumors. Molecular docking suggested a theoretical direct interaction between GAT and Gal-1. Further research revealed that GAT induces ubiquitination of Gal-1. Moreover, GAT significantly augmented the anti-cancer effects of paclitaxel, thereby increasing intratumoral drug concentrations and reducing tumor size. Combined with immunotherapy, GAT enhanced the tumor-suppressive effects of the anti-programmed death-ligand 1 antibody and increased the proportion of CD8+ cells in the EMT6 syngeneic mammary cancer model. In conclusion, GAT inhibited tumor growth, downregulated Gal-1, modulated the TME, and promoted chemotherapy and immunotherapy efficacy. Our findings highlight the potential of GAT as an effective therapeutic agent for cancer.
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Affiliation(s)
- Suyu Chen
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Kuangdee Chen
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Yihsiu Lin
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Ssuchia Wang
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Huichuan Yu
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Chaohsuan Chang
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Tingchun Cheng
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Chiaoyun Hsieh
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Jiayi Li
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Hsiaohsuan Lai
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan
| | - Denghai Chen
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan.
| | - Chengpo Huang
- Trineo Biotechnology Co., Ltd, 20F, No.81, Sec.1, Xintai 5th Rd, Xizhi Dist., New Taipei City 221, Taiwan.
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15
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Wang H, Jin W, Li Z, Guo C, Zhang L, Fu L. Targeting eukaryotic elongation factor 2 kinase (eEF2K) with small-molecule inhibitors for cancer therapy. Drug Discov Today 2024; 29:104155. [PMID: 39214495 DOI: 10.1016/j.drudis.2024.104155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/15/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024]
Abstract
Eukaryotic elongation factor 2 kinase (eEF2K) is a member of the α-kinase family that is activated by calcium/calmodulin. Of note, eEF2K is crucial for regulating translation and is often highly overexpressed in malignant cells. Therefore in this review, we summarize the molecular structure of eEF2K and its oncogenic roles in cancer. Moreover, we further discuss the inhibition of eEF2K with small-molecule inhibitors and other new emerging therapeutic strategies in cancer therapy. Taken together, these inspiring findings provide new insights into a promising strategy for inhibiting eEF2K to greatly improve future cancer therapy.
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Affiliation(s)
- Huiping Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Wenke Jin
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Zixiang Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Chuanxin Guo
- Nucleic Acid Division, Shanghai Cell Therapy Group, Shanghai 201805, China.
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
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16
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Hashemi M, Mohandesi Khosroshahi E, Tanha M, Khoushab S, Bizhanpour A, Azizi F, Mohammadzadeh M, Matinahmadi A, Khazaei Koohpar Z, Asadi S, Taheri H, Khorrami R, Ramezani Farani M, Rashidi M, Rezaei M, Fattah E, Taheriazam A, Entezari M. Targeting autophagy can synergize the efficacy of immune checkpoint inhibitors against therapeutic resistance: New promising strategy to reinvigorate cancer therapy. Heliyon 2024; 10:e37376. [PMID: 39309904 PMCID: PMC11415696 DOI: 10.1016/j.heliyon.2024.e37376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/29/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Immune checkpoints are a set of inhibitory and stimulatory molecules/mechanisms that affect the activity of immune cells to maintain the existing balance between pro- and anti-inflammatory signaling pathways and avoid the progression of autoimmune disorders. Tumor cells can employ these checkpoints to evade immune system. The discovery and development of immune checkpoint inhibitors (ICIs) was thereby a milestone in the area of immuno-oncology. ICIs stimulate anti-tumor immune responses primarily by disrupting co-inhibitory signaling mechanisms and accelerate immune-mediated killing of tumor cells. Despite the beneficial effects of ICIs, they sometimes encounter some degrees of therapeutic resistance, and thereby do not effectively act against tumors. Among multiple combination therapies have been introduced to date, targeting autophagy, as a cellular degradative process to remove expired organelles and subcellular constituents, has represented with potential capacities to overcome ICI-related therapy resistance. It has experimentally been illuminated that autophagy induction blocks the immune checkpoint molecules when administered in conjugation with ICIs, suggesting that autophagy activation may restrict therapeutic challenges that ICIs have encountered with. However, the autophagy flux can also provoke the immune escape of tumors, which must be considered. Since the conventional FDA-approved ICIs have designed and developed to target programmed cell death receptor/ligand 1 (PD-1/PD-L1) as well as cytotoxic T lymphocyte-associated molecule 4 (CTLA-4) immune checkpoint molecules, we aim to review the effects of autophagy targeting in combination with anti-PD-1/PD-L1- and anti-CTLA-4-based ICIs on cancer therapeutic resistance and tumor immune evasion.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Elaheh Mohandesi Khosroshahi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahsa Tanha
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Saloomeh Khoushab
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Anahita Bizhanpour
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Farnaz Azizi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahsa Mohammadzadeh
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Arash Matinahmadi
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun, Poland
| | - Zeinab Khazaei Koohpar
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - Saba Asadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hengameh Taheri
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Rezaei
- Health Research Center, Chamran Hospital, Tehran, Iran
| | - Eisa Fattah
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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17
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Chen H, Gridnev A, Schlamowitz N, Hu W, Dey K, Zheng G, Misra JR. Targeted degradation of specific TEAD paralogs by small molecule degraders. Heliyon 2024; 10:e37829. [PMID: 39328531 PMCID: PMC11425103 DOI: 10.1016/j.heliyon.2024.e37829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
The transcription factors, TEAD1-4 together with their co-activator YAP/TAZ function as key downstream effectors of the Hippo pathway. Hyperactivation of TEAD-YAP/TAZ activity is observed in many human cancers. TEAD1-4 possess distinct physiological and pathological functions, with conserved sequences and structures. Targeting specific isoforms within TEAD1-4 can serve as valuable chemical probes for investigating TEAD-related functions in both development and diseases. We report the TEAD-targeting proteolysis targeting chimera (PROTAC), HC278, which achieves effective and specific targeting of TEAD1 and TEAD3 at low nanomolar doses while weakly degrading TEAD2 and TEAD4 at higher doses. Proteomic analysis of >6000 proteins confirmed their highly selective TEAD1 and TEAD3 degradation. Consistently, HC278 can suppress the proliferation of YAP-dependent NCI-H226 mesothelioma cells. Mechanistic exploration revealed that both CRBN and proteasome systems are involved in the TEAD degradation induced by HC278. Moreover, RNA-seq and Gene Set Enrichment Analysis (GSEA) revealed that the YAP signature genes such as CTGF, CYR61, and ANKRD1 are significantly downregulated by HC278 treatment. Overall, HC278 serves as a valuable chemical tool for unraveling the intricate biological roles of TEAD1 and TEAD3 and holds the potential as a lead compound for developing targeted therapy for TEAD1/3-driven pathologies.
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Affiliation(s)
- Hui Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Artem Gridnev
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
- Graduate School of Biomedical Sciences, Oregon Health & Sciences University, Portland, OR, USA
| | - Netanya Schlamowitz
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
- Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Kuntala Dey
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Jyoti R Misra
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
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18
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Sun D, Macedonia C, Chen Z, Chandrasekaran S, Najarian K, Zhou S, Cernak T, Ellingrod VL, Jagadish HV, Marini B, Pai M, Violi A, Rech JC, Wang S, Li Y, Athey B, Omenn GS. Can Machine Learning Overcome the 95% Failure Rate and Reality that Only 30% of Approved Cancer Drugs Meaningfully Extend Patient Survival? J Med Chem 2024; 67:16035-16055. [PMID: 39253942 DOI: 10.1021/acs.jmedchem.4c01684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Despite implementing hundreds of strategies, cancer drug development suffers from a 95% failure rate over 30 years, with only 30% of approved cancer drugs extending patient survival beyond 2.5 months. Adding more criteria without eliminating nonessential ones is impractical and may fall into the "survivorship bias" trap. Machine learning (ML) models may enhance efficiency by saving time and cost. Yet, they may not improve success rate without identifying the root causes of failure. We propose a "STAR-guided ML system" (structure-tissue/cell selectivity-activity relationship) to enhance success rate and efficiency by addressing three overlooked interdependent factors: potency/specificity to the on/off-targets determining efficacy in tumors at clinical doses, on/off-target-driven tissue/cell selectivity influencing adverse effects in the normal organs at clinical doses, and optimal clinical doses balancing efficacy/safety as determined by potency/specificity and tissue/cell selectivity. STAR-guided ML models can directly predict clinical dose/efficacy/safety from five features to design/select the best drugs, enhancing success and efficiency of cancer drug development.
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Affiliation(s)
| | | | - Zhigang Chen
- LabBotics.ai, Palo Alto, California 94303, United States
| | | | | | - Simon Zhou
- Aurinia Pharmaceuticals Inc., Rockville, Maryland 20850, United States
| | | | | | | | | | | | | | | | | | - Yan Li
- Translational Medicine and Clinical Pharmacology, Bristol Myers Squibb, Summit, New Jersey 07901, United States
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19
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Poudel YB, Thakore RR, Chekler EP. The New Frontier: Merging Molecular Glue Degrader and Antibody-Drug Conjugate Modalities To Overcome Strategic Challenges. J Med Chem 2024; 67:15996-16001. [PMID: 39231796 DOI: 10.1021/acs.jmedchem.4c01289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Herein, we discuss advancements in the field of a unique class of antibody-drug conjugates (ADCs) named molecular glue-antibody conjugate (MAC). ADCs traditionally employ cytotoxic agents as payloads, and this approach has been used in all approved ADCs to treat cancer. Complementary to this approach, proteolysis targeting chimera (PROTAC) degrader antibody conjugates (DACs) provide a unique opportunity to deliver these bifunctional agents to tumors by using antibodies as a delivery mechanism to overcome the bioavailability issues encountered by PROTAC payloads. Recently, a cereblon binding monovalent degrader called molecular glues has been used in new ADCs that we have coined the term molecular-glue antibody conjugates (MACs). In this article, we intend to review advancements made in the field of targeted delivery of cereblon-based molecular glue degraders.
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Affiliation(s)
- Yam B Poudel
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Ruchita R Thakore
- Bristol Myers Squibb, 10300 Campus Point Drive, San Diego, California 92121, United States
| | - Eugene P Chekler
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
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20
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Zhang Y, Tan Y, Zhang Z, Cheng X, Duan J, Li Y. Targeting Thyroid-Stimulating Hormone Receptor: A Perspective on Small-Molecule Modulators and Their Therapeutic Potential. J Med Chem 2024; 67:16018-16034. [PMID: 39269788 DOI: 10.1021/acs.jmedchem.4c01525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
TSHR is a member of the glycoprotein hormone receptors, a subfamily of class A G-protein-coupled receptors and plays pivotal roles in various physiological and pathological processes, particularly in thyroid growth and hormone production. The aberrant TSHR function has been implicated in several human diseases including Graves' disease and orbitopathy, nonautoimmune hyperthyroidism, hypothyroidism, cancer, neurological disorders, and osteoporosis. Consequently, TSHR is recognized as an attractive therapeutic target, and targeting TSHR with small-molecule modulators including agonists, antagonists, and inverse agonists offers great potential for drug discovery. In this perspective, we summarize the structures and biological functions of TSHR as well as the recent advances in the development of small-molecule TSHR modulators, highlighting their chemotypes, mode of actions, structure-activity relationships, characterizations, in vitro/in vivo activities, and therapeutic potential. The challenges, new opportunities, and future directions in this area are also discussed.
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Affiliation(s)
- Yu Zhang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Ye Tan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Zian Zhang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Jia Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- Center for Structure & Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Venturi A, Di Bona S, Desantis J, Eleuteri M, Bartalucci M, Baroni M, Benedetti P, Goracci L, Cruciani G. Between Theory and Practice: Computational/Experimental Integrated Approaches to Understand the Solubility and Lipophilicity of PROTACs. J Med Chem 2024; 67:16355-16380. [PMID: 39271471 DOI: 10.1021/acs.jmedchem.4c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Emerging drug candidates more often fall in the beyond-rule-of-five chemical space. Among them, proteolysis targeting chimeras (PROTACs) have gained great attention in the past decade. Although physicochemical properties of small molecules accomplishing Lipinski's rule-of-five can now be easily predicted through models generated by large data collections, for PROTACs the knowledge is still limited and heterogeneous, hampering their prediction. Here, the kinetic solubility and the coefficient of distribution at pH 7.4 (LogD7.4) of 44 PROTACs, designed and synthesized to cover a wide chemical space, were measured. Their generally low solubility and high lipophilicity required an optimization of the experimental methods. Concerning the LogD7.4, several in silico prediction tools were tested, which were quite accurate for classical small molecules but provided dissimilar outcomes for PROTACs. Finally, in silico models for the prediction of PROTACs' kinetic solubility and LogD7.4 were proposed by combining in-house generated experimental data with 3D description of PROTACs' structures.
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Affiliation(s)
- Andrea Venturi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Stefano Di Bona
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Matteo Bartalucci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Paolo Benedetti
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
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22
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Krygier K, Wijetunge AN, Srayeddin A, Mccann H, Rullo AF. Leveraging Covalency to Stabilize Ternary Complex Formation For Cell-Cell "Induced Proximity". ACS Chem Biol 2024. [PMID: 39325690 DOI: 10.1021/acschembio.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Recent advances in the field of translational chemical biology use diverse "proximity-inducing" synthetic modalities to elicit new modes of "event driven" pharmacology. These include mechanisms of targeted protein degradation and immune clearance of pathogenic cells. Heterobifunctional "chimeric" compounds like Proteolysis TArgeting Chimeras (PROTACs) and Antibody Recruiting Molecules (ARMs) leverage these mechanisms, respectively. Both systems function through the formation of reversible "ternary" or higher-order biomolecular complexes. Critical to function are key parameters, such as bifunctional molecule affinity for endogenous proteins, target residence time, and turnover. To probe the mechanism and enhance function, covalent chemical approaches have been developed to kinetically stabilize ternary complexes. These include electrophilic PROTACs and Covalent Immune Recruiters (CIRs), the latter designed to uniquely enforce cell-cell induced proximity. Inducing cell-cell proximity is associated with key challenges arising from a combination of steric and/or mechanical based destabilizing forces on the ternary complex. These factors can attenuate the formation of ternary complexes driven by high affinity bifunctional/proximity inducing molecules. This Account describes initial efforts in our lab to address these challenges using the CIR strategy in antibody recruitment or receptor engineered T cell model systems of cell-cell induced proximity. ARMs form ternary complexes with serum antibodies and surface protein antigens on tumor cells that subsequently engage immune cells via Fc receptors. Binding and clustering of Fc receptors trigger immune cell killing of the tumor cell. We applied the CIR strategy to convert ARMs to covalent chimeras, which "irreversibly" recruit serum antibodies to tumor cells. These covalent chimeras leverage electrophile preorganization and kinetic effective molarity to achieve fast and selective covalent engagement of the target ternary complex protein, e.g., serum antibody. Importantly, covalent engagement can proceed via diverse binding site amino acids beyond cysteine. Covalent chimeras demonstrated striking functional enhancements compared to noncovalent ARM analogs in functional immune assays. We revealed this enhancement was in fact due to the increased kinetic stability and not concentration, of ternary complexes. This finding was recapitulated using analogous CIR modalities that integrate peptidic or carbohydrate binding ligands with Sulfur(VI) Fluoride Exchange (SuFEx) electrophiles to induce cell-cell proximity. Mechanistic studies in a distinct model system that uses T cells engineered with receptors that recognize covalent chimeras or ARMs, revealed covalent receptor engagement uniquely enforces downstream activation signaling. Finally, this Account discusses potential challenges and future directions for adapting and optimizing covalent chimeric/bifunctional molecules for diverse applications in cell-cell induced proximity.
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Affiliation(s)
- Karolina Krygier
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Anjalee N Wijetunge
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Arthur Srayeddin
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Harrison Mccann
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Anthony F Rullo
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
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23
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Sakamoto KM. Can PROTACs cure Leukemia? Leukemia 2024:10.1038/s41375-024-02427-z. [PMID: 39327464 DOI: 10.1038/s41375-024-02427-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 09/18/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
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24
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Tam DY, Li P, Liu LS, Wang F, Leung HM, Lo PK. Versatility of threose nucleic acids: synthesis, properties, and applications in chemical biology and biomedical advancements. Chem Commun (Camb) 2024. [PMID: 39318271 DOI: 10.1039/d4cc04443f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
This feature article delves into the realm of α-L-threose nucleic acid (TNA), an artificial nucleic acid analog characterized by a backbone comprising an unconventional four-carbon sugar, α-L-threose, with phosphodiester linkages connecting at the 2' and 3' vicinal positions of the sugar ring. Within this article, we encapsulate the potential, progress, current state of the art, and persisting challenges within TNA research. Kicking off with a historical overview of xeno nucleic acids (XNAs), the discussion transitions to the compelling attributes and structure-property relationships of TNAs as advanced tools when contrasted with natural nucleic acids. Noteworthy aspects such as their advantageous spatial arrangements of functional groups around the sugar ring, stable Watson-Crick base pairing, high binding affinity, biostability, biocompatibility, and in vivo bio-safety are highlighted. Moreover, the narrative unfolds the latest advancements in chemical and biological methodologies for TNA synthesis, spanning from monomer and oligomer synthesis to polymerization, alongside cutting-edge developments in enzyme engineering aimed at bolstering large-scale TNA synthesis for in vitro selection initiatives. The article sheds light on the evolution of TNA aptamers over time, expounding on the tools and selection techniques engineered to unearth superior binding aptamers and TNA catalysts. Furthermore, the article accentuates the recent applications of TNAs across diverse domains such as molecular detection, immunotherapy, gene therapy, synthetic biology, and molecular computing. In conclusion, we summarize the key aspects of recent TNA research, address persisting gaps and challenges, and provide crucial insights and future perspectives in the dynamic domain of TNA research.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Pan Li
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Ling Sum Liu
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Fei Wang
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China
| | - Hoi Man Leung
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Pik Kwan Lo
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
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25
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Huang J, Su J, Wang H, Chen J, Tian Y, Zhang J, Feng T, Di L, Lu X, Sheng H, Zhu Q, Chen X, Wang J, He X, Yerkinkazhina Y, Xie Z, Shu Y, Kang T, Tang H, Qian J, Zhu WG. Discovery of Novel PROTAC SIRT6 Degraders with Potent Efficacy against Hepatocellular Carcinoma. J Med Chem 2024. [PMID: 39323022 DOI: 10.1021/acs.jmedchem.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Sirtuin 6 (SIRT6), a member of the SIRT family, plays essential roles in the regulation of metabolism, inflammation, aging, DNA repair, and cancer development, making it a promising anticancer drug target. Herein, we present our use of proteolysis-targeting chimera (PROTAC) technology to formulate a series of highly potent and selective SIRT6 degraders. One of the degraders, SZU-B6, induced the near-complete degradation of SIRT6 in both SK-HEP-1 and Huh-7 cell lines and more potently inhibited hepatocellular carcinoma (HCC) cell proliferation than the parental inhibitors. In preliminary mechanistic studies, SZU-B6 hampered DNA damage repair, promoting the cellular radiosensitization of cancer cells. Our SIRT6 degrader SZU-B6 displayed promising antitumor activity, particularly when combined with the well-known kinase inhibitor sorafenib or irradiation in an SK-HEP-1 xenograft mouse model. Our results suggest that these PROTACs might constitute a potent therapeutic strategy for HCC.
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Affiliation(s)
- Jinbo Huang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
- National Engineering Research Centrer for Biotechnology, Shenzhen 518055, China
| | - Jiajie Su
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Haiyu Wang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jiayi Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Tingting Feng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Longjiang Di
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hao Sheng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xinyun Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Jingchao Wang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Xingkai He
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Yerkezhan Yerkinkazhina
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Zhongyi Xie
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Tianshu Kang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Huangqi Tang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Jinqin Qian
- Department of Urology, Peking University First Hospital, Beijing 100035, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
- Shenzhen University School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
- School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China
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26
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Teng X, Zhao X, Dai Y, Zhang X, Zhang Q, Wu Y, Hu D, Li J. ClickRNA-PROTAC for Tumor-Selective Protein Degradation and Targeted Cancer Therapy. J Am Chem Soc 2024. [PMID: 39320981 DOI: 10.1021/jacs.4c06402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) show promise in tumor treatment. However, the E3 ligases VHL and CRBN, commonly used in PROTAC, are highly expressed in only a few tumors, thus limiting the application scope and efficacy of PROTAC drugs. Furthermore, the lack of tumor specificity in PROTAC drugs can result in toxic side effects. Therefore, there is an urgent need to develop tumor-selective PROTAC drugs that do not rely on endogenous E3 ligases. In this study, we introduce the ClickRNA-PROTAC system, which involves the expression of a fusion protein of the E3 ubiquitin ligase SIAH1 and SNAPTag through mRNA transfection and recruits the protein of interest (POI) using bio-orthogonal click chemistry. ClickRNA-PROTAC can effectively degrade various proteins such as BRD4, KRAS, and NFκB simply by replacing the warhead molecules. By employing a tumor-specific mRNA-responsive translation strategy, ClickRNA-PROTAC can selectively degrade POIs in tumor cells. Furthermore, ClickRNA-PROTAC demonstrated strong efficacy in targeted cancer therapy in a xenograft mouse model of adrenocortical carcinoma. In conclusion, this approach offers several advantages, including independence from endogenous E3 ubiquitin ligases, tumor specificity, and programmability, thereby paving the way for the development of PROTAC drugs.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Life Science Academy, Beijing 102209, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Xuan Zhao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xiangdong Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Qiushuang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yuncong Wu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Difei Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Life Science Academy, Beijing 102209, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
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27
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Zhang SH, Su Y, Zheng M, Zeng N, Sun JX, Xu JZ, Liu CQ, Wang SG, Zhou Y, Xia QD. Design, synthesis and biological evaluation of dual inhibitors targeting AR/AR-Vs and PARP1 in castration resistant prostate cancer therapy. Biomed Pharmacother 2024; 180:117485. [PMID: 39326103 DOI: 10.1016/j.biopha.2024.117485] [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: 07/15/2024] [Revised: 08/30/2024] [Accepted: 09/20/2024] [Indexed: 09/28/2024] Open
Abstract
The combination of androgen signaling inhibitors and PARP inhibitors has shown promising results in clinical trials for the treatment of castration-resistant prostate cancer (CRPC). Multi-target inhibitors can inhibit tumors through different pathways, addressing the limitations of traditional single target inhibitors. We designed and synthesized dual inhibitors targeting AR/AR-Vs and PARP1 using a pharmacophore hybridization strategy. The most potent compound, II-3, inhibits AR/AR-Vs signaling and induces DNA damage by inhibiting PARP1. The IC50 values of II-3 in the castration-resistant prostate cancer cell lines 22RV1 and C4-2 are 4.38 ± 0.56 µM, and 3.44 ± 0.63 µM, respectively. II-3 not only suppresses the proliferation and migration of 22RV1 and C4-2 cells, but also promotes their apoptosis. Intraperitoneal injection of II-3 effectively inhibits tumor growth in 22RV1 xenograft nude mice without evident drug-induced toxicity. Overall, a series of novel dual inhibitors targeting AR/AR-Vs and PARP1 were designed and synthesized, and meanwhile the in vivo and in vitro effects were comprehensively explored, which provided a potential new therapeutic strategy for CRPC.
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Affiliation(s)
- Si-Han Zhang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Yaowu Su
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Na Zeng
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Jian-Xuan Sun
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Jin-Zhou Xu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Chen-Qian Liu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Shao-Gang Wang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China.
| | - Yirong Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China.
| | - Qi-Dong Xia
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China.
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28
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Venkatesan J, Murugan D, Lakshminarayanan K, Smith AR, Thirumalaiswamy HV, Kandhasamy H, Zender B, Zheng G, Rangasamy L. Powering up targeted protein degradation through active and passive tumour-targeting strategies: Current and future scopes. Pharmacol Ther 2024:108725. [PMID: 39322067 DOI: 10.1016/j.pharmthera.2024.108725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 08/31/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024]
Abstract
Targeted protein degradation (TPD) has emerged as a prominent and vital strategy for therapeutic intervention of cancers and other diseases. One such approach involves the exploration of proteolysis targeting chimeras (PROTACs) for the selective elimination of disease-causing proteins through the innate ubiquitin-proteasome pathway. Due to the unprecedented achievements of various PROTAC molecules in clinical trials, researchers have moved towards other physiological protein degradation approaches for the targeted degradation of abnormal proteins, including lysosome-targeting chimeras (LYTACs), autophagy-targeting chimeras (AUTACs), autophagosome-tethering compounds (ATTECs), molecular glue degraders, and other derivatives for their precise mode of action. Despite numerous advantages, these molecules face challenges in solubility, permeability, bioavailability, and potential off-target or on-target off-tissue effects. Thus, an urgent need arises to direct the action of these degrader molecules specifically against cancer cells, leaving the proteins of non-cancerous cells intact. Recent advancements in TPD have led to innovative delivery methods that ensure the degraders are delivered in a cell- or tissue-specific manner to achieve cell/tissue-selective degradation of target proteins. Such receptor-specific active delivery or nano-based passive delivery of the PROTACs could be achieved by conjugating them with targeting ligands (antibodies, aptamers, peptides, or small molecule ligands) or nano-based carriers. These techniques help to achieve precise delivery of PROTAC payloads to the target sites. Notably, the successful entry of a Degrader Antibody Conjugate (DAC), ORM-5029, into a phase 1 clinical trial underscores the therapeutic potential of these conjugates, including LYTAC-antibody conjugates (LACs) and aptamer-based targeted protein degraders. Further, using bispecific antibody-based degraders (AbTACs) and delivering the PROTAC pre-fused with E3 ligases provides a solution for cell type-specific protein degradation. Here, we highlighted the current advancements and challenges associated with developing new tumour-specific protein degrader approaches and summarized their potential as single agents or combination therapeutics for cancer.
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Affiliation(s)
- Janarthanan Venkatesan
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Dhanashree Murugan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India; School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Kalaiarasu Lakshminarayanan
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Alexis R Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Harashkumar Vasanthakumari Thirumalaiswamy
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Hariprasath Kandhasamy
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Boutheina Zender
- Department of Biomedical Engineering, Bahçeşehir University, Istanbul 34353, Turkey
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
| | - Loganathan Rangasamy
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India.
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29
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Cheng-Sánchez I, Gosselé K, Palaferri L, Laul E, Riccabella G, Bedi RK, Li Y, Müller A, Corbeski I, Caflisch A, Nevado C. Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity. JACS AU 2024; 4:3466-3474. [PMID: 39328757 PMCID: PMC11423305 DOI: 10.1021/jacsau.4c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 09/28/2024]
Abstract
We present the development of dCE-2, a structurally novel PROTAC targeting the CREB-binding protein (CBP) and E1A-associated protein (EP300)-two homologous multidomain enzymes crucial for enhancer-mediated transcription. The design of dCE-2 was based on the crystal structure of an in-house bromodomain (BRD) inhibitor featuring a 3-methyl-cinnoline acetyl-lysine mimic acetyl-lysine mimic discovered by high-throughput fragment docking. Our study shows that, despite its modest binding affinity to CBP/EP300-BRD, dCE-2's remarkable protein degradation activity stems from its good cooperativity, which we demonstrate by the characterization of its ternary complex formation both in vitro and in cellulo. Molecular dynamics simulations indicate that in aqueous solvents, this active degrader populates both folded and extended conformations, which are likely to promote cell permeability and ternary complex formation, respectively.
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Affiliation(s)
- Iván Cheng-Sánchez
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Katherine Gosselé
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Leonardo Palaferri
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Eleen Laul
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Gionata Riccabella
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Rajiv K Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Anna Müller
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Ivan Corbeski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Cristina Nevado
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
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30
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Bhat SA, Vasi Z, Jiang L, Selvaraj S, Ferguson R, Salarvand S, Gudur A, Adhikari R, Castillo V, Ismail H, Dhabaria A, Ueberheide B, Kuchay S. Geranylgeranylated SCF FBXO10 regulates selective outer mitochondrial membrane proteostasis and function. Cell Rep 2024; 43:114783. [PMID: 39306844 DOI: 10.1016/j.celrep.2024.114783] [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: 03/26/2024] [Revised: 07/21/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
Compartment-specific cellular membrane protein turnover is not well understood. We show that FBXO10, the interchangeable component of the cullin-RING-ligase 1 complex, undergoes lipid modification with geranylgeranyl isoprenoid at cysteine953, facilitating its dynamic trafficking to the outer mitochondrial membrane (OMM). FBXO10 polypeptide lacks a canonical mitochondrial targeting sequence (MTS); instead, its geranylgeranylation at C953 and interaction with two cytosolic factors, cytosolic factor-like δ subunit of type 6 phosphodiesterase (PDE6δ; a prenyl-group-binding protein) and heat shock protein 90 (HSP90; a chaperone), orchestrate specific OMM targeting of prenyl-FBXO10. The FBXO10(C953S) mutant redistributes away from the OMM, impairs mitochondrial ATP production and membrane potential, and increases fragmentation. Phosphoglycerate mutase-5 (PGAM5) was identified as a potential substrate of FBXO10 at the OMM using comparative quantitative proteomics of enriched mitochondria. FBXO10 loss or expression of prenylation-deficient FBXO10(C953S) inhibited PGAM5 degradation, disrupted mitochondrial homeostasis, and impaired myogenic differentiation of human induced pluripotent stem cells (iPSCs) and murine myoblasts. Our studies identify a mechanism for FBXO10-mediated regulation of selective mitochondrial proteostasis potentially amenable to therapeutic intervention.
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Affiliation(s)
- Sameer Ahmed Bhat
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Zahra Vasi
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Liping Jiang
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Shruthi Selvaraj
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Rachel Ferguson
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Sanaz Salarvand
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Anish Gudur
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Ritika Adhikari
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Veronica Castillo
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Hagar Ismail
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10013, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10013, USA
| | - Shafi Kuchay
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1252, Chicago, IL 60607, USA; Cancer Center, University of Illinois at Chicago, Chicago, IL, USA.
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31
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Tan X, Huang Z, Pei H, Jia Z, Zheng J. Molecular glue-mediated targeted protein degradation: A novel strategy in small-molecule drug development. iScience 2024; 27:110712. [PMID: 39297173 PMCID: PMC11409024 DOI: 10.1016/j.isci.2024.110712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024] Open
Abstract
Small-molecule drugs are effective and thus most widely used. However, their applications are limited by their reliance on active high-affinity binding sites, restricting their target options. A breakthrough approach involves molecular glues, a novel class of small-molecule compounds capable of inducing protein-protein interactions (PPIs). This opens avenues to target conventionally undruggable proteins, overcoming limitations seen in conventional small-molecule drugs. Molecular glues play a key role in targeted protein degradation (TPD) techniques, including ubiquitin-proteasome system-based approaches such as proteolysis targeting chimeras (PROTACs) and molecular glue degraders and recently emergent lysosome system-based techniques like molecular degraders of extracellular proteins through the asialoglycoprotein receptors (MoDE-As) and macroautophagy degradation targeting chimeras (MADTACs). These techniques enable an innovative targeted degradation strategy for prolonged inhibition of pathology-associated proteins. This review provides an overview of them, emphasizing the clinical potential of molecular glues and guiding the development of molecular-glue-mediated TPD techniques.
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Affiliation(s)
- Xueqiang Tan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zuyi Huang
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hairun Pei
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology & Business University, Beijing 100048, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Jimin Zheng
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
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32
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Chen LY, Singha Roy SJ, Jadhav AM, Wang WW, Chen PH, Bishop T, Erb MA, Parker CG. Functional Investigations of p53 Acetylation Enabled by Heterobifunctional Molecules. ACS Chem Biol 2024; 19:1918-1929. [PMID: 39250704 PMCID: PMC11421428 DOI: 10.1021/acschembio.4c00438] [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: 06/20/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/11/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate the critical stress response and tumor suppressive functions of p53. Among these, acetylation events mediated by multiple acetyltransferases lead to differential target gene activation and subsequent cell fate. However, our understanding of these events is incomplete due to, in part, the inability to selectively and dynamically control p53 acetylation. We recently developed a heterobifunctional small molecule system, AceTAG, to direct the acetyltransferase p300/CBP for targeted protein acetylation in cells. Here, we expand AceTAG to leverage the acetyltransferase PCAF/GCN5 and apply these tools to investigate the functional consequences of targeted p53 acetylation in human cancer cells. We demonstrate that the recruitment of p300/CBP or PCAF/GCN5 to p53 results in distinct acetylation events and differentiated transcriptional activities. Further, we show that chemically induced acetylation of multiple hotspot p53 mutants results in increased stabilization and enhancement of transcriptional activity. Collectively, these studies demonstrate the utility of AceTAG for functional investigations of protein acetylation.
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Affiliation(s)
- Li-Yun Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Soumya Jyoti Singha Roy
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Appaso M. Jadhav
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Wesley W. Wang
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pei-Hsin Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Timothy Bishop
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael A. Erb
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher G. Parker
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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33
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Cox AD, Der CJ. KRAS takes the road to destruction. Science 2024; 385:1274-1275. [PMID: 39298611 DOI: 10.1126/science.ads2150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
A single small molecule degrades numerous KRAS variants involved in cancer.
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Affiliation(s)
- Adrienne D Cox
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Channing J Der
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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34
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Taylor JD, Barrett N, Martinez Cuesta S, Cassidy K, Pachl F, Dodgson J, Patel R, Eriksson TM, Riley A, Burrell M, Bauer C, Rees DG, Cimbro R, Zhang AX, Minter RR, Hunt J, Legg S. Targeted protein degradation using chimeric human E2 ubiquitin-conjugating enzymes. Commun Biol 2024; 7:1179. [PMID: 39300128 DOI: 10.1038/s42003-024-06803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Proteins can be targeted for degradation by engineering biomolecules that direct them to the eukaryotic ubiquitination machinery. For instance, the fusion of an E3 ubiquitin ligase to a suitable target binding domain creates a 'biological Proteolysis-Targeting Chimera' (bioPROTAC). Here we employ an analogous approach where the target protein is recruited directly to a human E2 ubiquitin-conjugating enzyme via an attached target binding domain. Through rational design and screening we develop E2 bioPROTACs that induce the degradation of the human intracellular proteins SHP2 and KRAS. Using global proteomics, we characterise the target-specific and wider effects of E2 vs. VHL-based fusions. Taking SHP2 as a model target, we also employ a route to bioPROTAC discovery based on protein display libraries, yielding a degrader with comparatively weak affinity capable of suppressing SHP2-mediated signalling.
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Affiliation(s)
- Jonathan D Taylor
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Nathalie Barrett
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Katelyn Cassidy
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Fiona Pachl
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - James Dodgson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Radhika Patel
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tuula M Eriksson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Aidan Riley
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Matthew Burrell
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Christin Bauer
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - D Gareth Rees
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Raffaello Cimbro
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Andrew X Zhang
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Ralph R Minter
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - James Hunt
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Sandrine Legg
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
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35
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Sauvé V, Stefan E, Croteau N, Goiran T, Fakih R, Bansal N, Hadzipasic A, Fang J, Murugan P, Chen S, Fon EA, Hirst WD, Silvian LF, Trempe JF, Gehring K. Activation of parkin by a molecular glue. Nat Commun 2024; 15:7707. [PMID: 39300082 PMCID: PMC11412986 DOI: 10.1038/s41467-024-51889-3] [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: 04/03/2024] [Accepted: 08/16/2024] [Indexed: 09/22/2024] Open
Abstract
Mutations in parkin and PINK1 cause early-onset Parkinson's disease (EOPD). The ubiquitin ligase parkin is recruited to damaged mitochondria and activated by PINK1, a kinase that phosphorylates ubiquitin and the ubiquitin-like domain of parkin. Activated phospho-parkin then ubiquitinates mitochondrial proteins to target the damaged organelle for degradation. Here, we present the mechanism of activation of a new class of small molecule allosteric modulators that enhance parkin activity. The compounds act as molecular glues to enhance the ability of phospho-ubiquitin (pUb) to activate parkin. Ubiquitination assays and isothermal titration calorimetry with the most active compound (BIO-2007817) identify the mechanism of action. We present the crystal structure of a closely related compound (BIO-1975900) bound to a complex of parkin and two pUb molecules. The compound binds next to pUb on RING0 and contacts both proteins. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments confirm that activation occurs through release of the catalytic Rcat domain. In organello and mitophagy assays demonstrate that BIO-2007817 partially rescues the activity of parkin EOPD mutants, R42P and V56E, offering a basis for the design of activators as therapeutics for Parkinson's disease.
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Affiliation(s)
- Véronique Sauvé
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Eric Stefan
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
| | - Nathalie Croteau
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- Brain Repair and Integrative Neuroscience (BRaIN) Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Thomas Goiran
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Rayan Fakih
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Nupur Bansal
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
| | - Adelajda Hadzipasic
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jing Fang
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Aura Biosciences, Boston, MA, USA
| | - Paramasivam Murugan
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Bristol-Myers Squibb, New York, NY, USA
| | - Shimin Chen
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Edward A Fon
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Warren D Hirst
- Neurodegenerative Disease Research Unit, Biogen, Cambridge, MA, USA
- DaCapo Brainscience, North Cambridge, MA, USA
| | - Laura F Silvian
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA.
| | - Jean-François Trempe
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- Brain Repair and Integrative Neuroscience (BRaIN) Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada.
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36
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Gregory JA, Hickey CM, Chavez J, Cacace AM. New therapies on the horizon: Targeted protein degradation in neuroscience. Cell Chem Biol 2024; 31:1688-1698. [PMID: 39303702 DOI: 10.1016/j.chembiol.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024]
Abstract
This minireview explores the burgeoning field of targeted protein degradation (TPD) and its promising applications in neuroscience and clinical development. TPD offers innovative strategies for modulating protein levels, presenting a paradigm shift in small-molecule drug discovery and therapeutic interventions. Importantly, small-molecule protein degraders specifically target and remove pathogenic proteins from central nervous system cells without the drug delivery challenges of genomic and antibody-based modalities. Here, we review recent advancements in TPD technologies, highlight proteolysis targeting chimera (PROTAC) protein degrader molecules with proximity-induced degradation event-driven and iterative pharmacology, provide applications in neuroscience research, and discuss the high potential for translation of TPD into clinical settings.
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Affiliation(s)
| | | | - Juan Chavez
- Arvinas, Inc., 5 Science Park, New Haven, CT 06511, USA
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37
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Wu J, Li D, Wang L. Overview of PRMT1 modulators: Inhibitors and degraders. Eur J Med Chem 2024; 279:116887. [PMID: 39316844 DOI: 10.1016/j.ejmech.2024.116887] [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: 07/12/2024] [Revised: 08/26/2024] [Accepted: 09/14/2024] [Indexed: 09/26/2024]
Abstract
Protein arginine methyltransferase 1 (PRMT1) is pivotal in executing normal cellular functions through its catalytic action on the methylation of arginine side chains on protein substrates. Emerging research has revealed a correlation between the dysregulation of PRMT1 expression and the initiation and progression of tumors, significantly influence on patient prognostication, attributed to the essential role played by PRMT1 in a number of biological processes, including transcriptional regulation, signal transduction or DNA repair. Therefore, PRMT1 emerged as a promising therapeutic target for anticancer drug discovery in the past decade. In this review, we first summarize the structure and biological functions of PRMT1 and its association with cancer. Next, we focus on the recent advances in the design and development of PRMT1 modulators, including isoform-selective PRMT1 inhibitors, pan type I PRMT inhibitors, PRMT1-based dual-target inhibitors, and PRMT1-targeting PROTAC degraders, from the perspectives of rational design, pharmacodynamics, pharmacokinetics, and clinical status. Finally, we discuss the challenges and future directions for PRMT1-based drug discovery for cancer therapy.
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Affiliation(s)
- Junwei Wu
- Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, 341000, China
| | - Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
| | - Lifang Wang
- Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, 341000, China.
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38
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Koszela J, Pham NT, Shave S, St-Cyr D, Ceccarelli DF, Orlicky S, Marinier A, Sicheri F, Tyers M, Auer M. A Novel Confocal Scanning Protein-Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin. Bioconjug Chem 2024; 35:1441-1449. [PMID: 39167708 PMCID: PMC11417995 DOI: 10.1021/acs.bioconjchem.4c00345] [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: 07/28/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
Protein-protein interactions (PPIs) are some of the most challenging target classes in drug discovery. Highly sensitive detection techniques are required for the identification of chemical modulators of PPIs. Here, we introduce PPI confocal nanoscanning (PPI-CONA), a miniaturized, microbead based high-resolution fluorescence imaging assay. We demonstrate the capabilities of PPI-CONA by detecting low affinity ternary complex formation between the human CDC34A ubiquitin-conjugating (E2) enzyme, ubiquitin, and CC0651, a small molecule enhancer of the CDC34A-ubiquitin interaction. We further exemplify PPI-CONA with an E2 enzyme binding study on CC0651 and a CDC34A binding specificity study of a series of CC0651 analogues. Our results indicate that CC0651 is highly selective toward CDC34A. We further demonstrate how PPI-CONA can be applied to screening very low affinity interactions. PPI-CONA holds potential for high-throughput screening for modulators of PPI targets and characterization of their affinity, specificity, and selectivity.
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Affiliation(s)
- Joanna Koszela
- School
of Molecular Biosciences, University of
Glasgow, Glasgow G12 8QQ, U.K.
| | - Nhan T. Pham
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- College
of Medicine and Veterinary Medicine, Institute for Regeneration and
Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, U.K.
| | - Steven Shave
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- Edinburgh
Cancer Research, Cancer Research UK Scotland Centre, Institute of
Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K.
| | - Daniel St-Cyr
- X-Chem
Inc., Montréal, Québec H4S 1Z9, Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Steven Orlicky
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anne Marinier
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Frank Sicheri
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Mike Tyers
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Manfred Auer
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
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39
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Taylor SJ, Stauber J, Bohorquez O, Tatsumi G, Kumari R, Chakraborty J, Bartholdy BA, Schwenger E, Sundaravel S, Farahat AA, Wheat JC, Goldfinger M, Verma A, Kumar A, Boykin DW, Stengel KR, Poon GMK, Steidl U. Pharmacological restriction of genomic binding sites redirects PU.1 pioneer transcription factor activity. Nat Genet 2024:10.1038/s41588-024-01911-7. [PMID: 39294495 DOI: 10.1038/s41588-024-01911-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/14/2024] [Indexed: 09/20/2024]
Abstract
Transcription factor (TF) DNA-binding dynamics govern cell fate and identity. However, our ability to pharmacologically control TF localization is limited. Here we leverage chemically driven binding site restriction leading to robust and DNA-sequence-specific redistribution of PU.1, a pioneer TF pertinent to many hematopoietic malignancies. Through an innovative technique, 'CLICK-on-CUT&Tag', we characterize the hierarchy of de novo PU.1 motifs, predicting occupancy in the PU.1 cistrome under binding site restriction. Temporal and single-molecule studies of binding site restriction uncover the pioneering dynamics of native PU.1 and identify the paradoxical activation of an alternate target gene set driven by PU.1 localization to second-tier binding sites. These transcriptional changes were corroborated by genetic blockade and site-specific reporter assays. Binding site restriction and subsequent PU.1 network rewiring causes primary human leukemia cells to differentiate. In summary, pharmacologically induced TF redistribution can be harnessed to govern TF localization, actuate alternate gene networks and direct cell fate.
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Affiliation(s)
- Samuel J Taylor
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jacob Stauber
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Oliver Bohorquez
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Goichi Tatsumi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joyeeta Chakraborty
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emily Schwenger
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Abdelbasset A Farahat
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Master of Pharmaceutical Sciences Program, California Northstate University, Elk Grove, CA, USA
| | - Justin C Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mendel Goldfinger
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
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40
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Wu Y, Meibohm B, Zhang T, Hou X, Wang H, Sun X, Jiang M, Zhang B, Zhang W, Liu Y, Jin W, Wang F. Translational modelling to predict human pharmacokinetics and pharmacodynamics of a Bruton's tyrosine kinase-targeted protein degrader BGB-16673. Br J Pharmacol 2024. [PMID: 39289908 DOI: 10.1111/bph.17332] [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: 01/12/2024] [Revised: 07/27/2024] [Accepted: 08/08/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND AND PURPOSE Bifunctional small molecule degraders, which link the target protein with E3 ubiquitin ligase, could lead to the efficient degradation of the target protein. BGB-16673 is a Bruton's tyrosine kinase (BTK) degrader. A translational PK/PD modelling approach was used to predict the human BTK degradation of BGB-16673 from preclinical in vitro and in vivo data. EXPERIMENTAL APPROACH A simplified mechanistic PK/PD model was used to establish the correlation between the in vitro and in vivo BTK degradation by BGB-16673 in a mouse model. Human and mouse species differences were compared using the parameters generated from in vitro human or mouse blood, and human or mouse serum spiked TMD-8 cells. Human PD was then predicted using the simplified mechanistic PK/PD model. KEY RESULTS BGB-16673 showed potent BTK degradation in mouse whole blood, human whole blood, and TMD-8 tumour cells in vitro. Furthermore, BGB-16673 showed BTK degradation in a murine TMD-8 xenograft model in vivo. The PK/PD model predicted human PD and the observed BTK degradation in clinical studies both showed robust BTK degradation in blood and tumour at clinical dose range. CONCLUSION AND IMPLICATIONS The presented simplified mechanistic model with reduced number of model parameters is practically easier to be applied to research projects compared with the full mechanistic model. It can be used as a tool to better understand the PK/PD behaviour for targeted protein degraders and increase the confidence when moving to the clinical stage.
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Affiliation(s)
- Yue Wu
- Department of DMPK-BA, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Bernd Meibohm
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Taichang Zhang
- Department of DMPK-BA, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Xinfeng Hou
- Department of Translational Science, BeiGene (Beijing) Co., Ltd., Beijing, China
- Migrasome Therapeutics Co. Ltd., Beijing, China
| | - Haitao Wang
- Department of Translational Science, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Xiaona Sun
- Department of Discovery Biology, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Ming Jiang
- Department of Discovery Biology, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Bo Zhang
- Department of Molecular Science, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Wenjing Zhang
- Department of Translational Science, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Ye Liu
- Department of Molecular Science, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Wei Jin
- Department of Translational Science, BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Fan Wang
- Department of DMPK-BA, BeiGene (Beijing) Co., Ltd., Beijing, China
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41
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Chi Y, Lu X, Li S, Wang J, Xi J, Zhou X, Tang C, Chen M, Yuan H, Lin S, Xiao Y, Lai L, Zou Q. A compact, versatile drug-induced splicing switch system with minimal background expression. CELL REPORTS METHODS 2024; 4:100842. [PMID: 39236714 DOI: 10.1016/j.crmeth.2024.100842] [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: 03/08/2024] [Revised: 07/01/2024] [Accepted: 08/06/2024] [Indexed: 09/07/2024]
Abstract
Gene-switch techniques hold promising applications in contemporary genetics research, particularly in disease treatment and genetic engineering. Here, we developed a compact drug-induced splicing system that maintains low background using a human ubiquitin C (hUBC) promoter and optimized drug (LMI070) binding sequences based on the Xon switch system. To ensure precise subcellular localization of the protein of interest (POI), we inserted a 2A self-cleaving peptide between the extra N-terminal peptide and POI. This streamlined and optimized switch system, named miniXon2G, effectively regulated POIs in different subcellular localizations both in vitro and in vivo. Furthermore, miniXon2G could be integrated into endogenous gene loci, resulting in precise, reversible regulation of target genes by both endogenous regulators and drugs. Overall, these findings highlight the performance of miniXon2G in controlling protein expression with great potential for general applicability to diverse biological scenarios requiring precise and delicate regulation.
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Affiliation(s)
- Yue Chi
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Xuan Lu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Shuangpeng Li
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Jinling Wang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Jiahui Xi
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Hui Yuan
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Shuo Lin
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China
| | - Yingying Xiao
- Jiangmen Wuyi Traditional Chinese Medicine Hospital, Jiangmen 529000, China
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China; CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen 529020, China.
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Baek K, Metivier RJ, Roy Burman SS, Bushman JW, Lumpkin RJ, Abeja DM, Lakshminarayan M, Yue H, Ojeda S, Verano AL, Gray NS, Donovan KA, Fischer ES. Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612438. [PMID: 39314457 PMCID: PMC11419069 DOI: 10.1101/2024.09.11.612438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
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43
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Pierri M, Liu X, Kroupova A, Rutter Z, Hallatt AJ, Ciulli A. Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity. Bioorg Med Chem Lett 2024; 110:129861. [PMID: 38942127 DOI: 10.1016/j.bmcl.2024.129861] [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: 03/24/2024] [Revised: 06/16/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional small-molecule degraders made of a linker connecting a target-binding moiety to a ubiquitin E3 ligase-binding moiety. The linker unit is known to influence the physicochemical and pharmacokinetic properties of PROTACs, as well as the properties of ternary complexes, in turn impacting on their degradation activity in cells and in vivo. Our LRRK2 PROTAC XL01126, bearing a trans-cyclohexyl group in the linker, is a better and more cooperative degrader than its corresponding cis- analogue despite its much weaker binary binding affinities. Here, we investigate how this subtle stereocenter alteration in the linker affects the ligand binding affinity to the E3 ligase VHL. We designed a series of molecular matched pairs, truncating from the full PROTACs down to the VHL ligand, and find that across the series the trans-cyclohexyl compounds showed consistently weaker VHL-binding affinity compared to the cis- counterparts. High-resolution co-crystal structures revealed that the trans linker exhibits a rigid stick-out conformation, while the cis linker collapses into a folded-back conformation featuring a network of intramolecular contacts and long-range interactions with VHL. These observations are noteworthy as they reveal how a single stereochemical inversion within a PROTAC linker impacts conformational rigidity and binding mode, in turn fine-tuning differentiated propensity to binary and ternary complex formation, and ultimately cellular degradation activity.
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Affiliation(s)
- Martina Pierri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Xingui Liu
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alena Kroupova
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Zoe Rutter
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alex J Hallatt
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom.
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44
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Zaman SU, Pagare PP, Ma H, Hoyle RG, Zhang Y, Li J. Novel PROTAC probes targeting KDM3 degradation to eliminate colorectal cancer stem cells through inhibition of Wnt/β-catenin signaling. RSC Med Chem 2024:d4md00122b. [PMID: 39281802 PMCID: PMC11393732 DOI: 10.1039/d4md00122b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/20/2024] [Indexed: 09/18/2024] Open
Abstract
It has been demonstrated that the KDM3 family of histone demethylases (KDM3A and KDM3B) epigenetically control the functional properties of colorectal cancer stem cells (CSCs) through Wnt/β-catenin signaling. Meanwhile, a broad-spectrum histone demethylase inhibitor, IOX1, suppresses Wnt-induced colorectal tumorigenesis predominantly through inhibiting the enzymatic activity of KDM3. In this work, several cereblon (CRBN)-recruiting PROTACs with various linker lengths were designed and synthesized using IOX1 as a warhead to target KDM3 proteins for degradation. Two of the synthesized PROTACs demonstrated favorable degradation profile and selectivity towards KDM3A and KDM3B. Compound 4 demonstrated favorable in vitro metabolic profile in liver enzymes as well as no hERG-associated cardiotoxicity. Compound 4 also showed dramatic ability in suppressing oncogenic Wnt signaling to eliminate colorectal CSCs and inhibit tumor growth, with around 10- to 35-fold increased potency over IOX1. In summary, this study suggests that PROTACs provide a unique molecular tool for the development of novel small molecules from the IOX1 skeleton for selective degradation of KDM3 to eliminate colorectal CSCs via suppressing oncogenic Wnt signaling.
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Affiliation(s)
- Shadid U Zaman
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Piyusha P Pagare
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Hongguang Ma
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Rosalie G Hoyle
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
- Department of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
- Massey Cancer Center, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
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45
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Wu B, Koehler AN, Westcott PMK. New opportunities to overcome T cell dysfunction: the role of transcription factors and how to target them. Trends Biochem Sci 2024:S0968-0004(24)00189-0. [PMID: 39277450 DOI: 10.1016/j.tibs.2024.08.002] [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: 12/20/2023] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/17/2024]
Abstract
Immune checkpoint blockade (ICB) therapies, which block inhibitory receptors on T cells, can be efficacious in reinvigorating dysfunctional T cell responses. However, most cancers do not respond to these therapies and even in those that respond, tumors can acquire resistance. New strategies are needed to rescue and recruit T cell responses across patient populations and disease states. In this review, we define mechanisms of T cell dysfunction, focusing on key transcription factor (TF) networks. We discuss the complex and sometimes contradictory roles of core TFs in both T cell function and dysfunction. Finally, we review strategies to target TFs using small molecule modulators, which represent a challenging but highly promising opportunity to tune the T cell response toward sustained immunity.
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Affiliation(s)
- Bocheng Wu
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Angela N Koehler
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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46
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Preston SEJ, Dahabieh MS, Flores González RE, Gonçalves C, Richard VR, Leibovitch M, Dakin E, Papadopoulos T, Lopez Naranjo C, McCallum PA, Huang F, Gagnon N, Perrino S, Zahedi RP, Borchers CH, Jones RG, Brodt P, Miller WH, Del Rincón SV. Blocking tumor-intrinsic MNK1 kinase restricts metabolic adaptation and diminishes liver metastasis. SCIENCE ADVANCES 2024; 10:eadi7673. [PMID: 39270021 PMCID: PMC11397505 DOI: 10.1126/sciadv.adi7673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/07/2024] [Indexed: 09/15/2024]
Abstract
Dysregulation of the mitogen-activated protein kinase interacting kinases 1/2 (MNK1/2)-eukaryotic initiation factor 4E (eIF4E) signaling axis promotes breast cancer progression. MNK1 is known to influence cancer stem cells (CSCs); self-renewing populations that support metastasis, recurrence, and chemotherapeutic resistance, making them a clinically relevant target. The precise function of MNK1 in regulating CSCs, however, remains unexplored. Here, we generated MNK1 knockout cancer cell lines, resulting in diminished CSC properties in vitro and slowed tumor growth in vivo. Using a multiomics approach, we functionally demonstrated that loss of MNK1 restricts tumor cell metabolic adaptation by reducing glycolysis and increasing dependence on oxidative phosphorylation. Furthermore, MNK1-null breast and pancreatic tumor cells demonstrated suppressed metastasis to the liver, but not the lung. Analysis of The Cancer Genome Atlas (TCGA) data from breast cancer patients validated the positive correlation between MNK1 and glycolytic enzyme protein expression. This study defines metabolic perturbations as a previously unknown consequence of targeting MNK1/2, which may be therapeutically exploited.
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Affiliation(s)
- Samuel E J Preston
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Michael S Dahabieh
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Raúl Ernesto Flores González
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Christophe Gonçalves
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Matthew Leibovitch
- MUHC Research Institute, McGill University Health Centre, Montréal, QC, Canada
| | - Eleanor Dakin
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Theodore Papadopoulos
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Carolina Lopez Naranjo
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Paige A McCallum
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Fan Huang
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Natascha Gagnon
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Stephanie Perrino
- MUHC Research Institute, McGill University Health Centre, Montréal, QC, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba, Winnipeg, MB, Canada
| | - Christoph H Borchers
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
- Department of Pathology, McGill University, Montréal, QC, Canada
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Pnina Brodt
- MUHC Research Institute, McGill University Health Centre, Montréal, QC, Canada
- Departments of Surgery, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Wilson H Miller
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Sonia V Del Rincón
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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47
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Malarvannan M, Ravichandiran V, Paul D. Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems. J Chromatogr A 2024; 1732:465226. [PMID: 39111181 DOI: 10.1016/j.chroma.2024.465226] [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: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024]
Abstract
The last few years have seen a rise in the identification and development of bio-therapeutics through the use of cutting-edge delivery methods or bio-formulations, which has created bio-analytical difficulties. Every year, new bio-pharmaceutical product innovations come out, but the analytical development of these products is challenging. Quantifying the products and components of conjugated molecular structures is essential for preclinical and clinical research in order to guide therapeutic development, given their intrinsic complexity. Furthermore, a significant amount of information is needed for the measurement of these unique modalities by LC-MS techniques. Numerous LC-MS based methods have been developed, including AEX-HPLC-MS, RP-IP-LCMS, HILIC-MS, LCHRMS, Microflow-LC-MS, ASMS, Hybrid LBA/LC-MS, and more. However, these methods continue to face problems, prompting the development of alternative approaches. Therefore, developing bio-molecules that are this complicated and, low in concentration requires a skilled LC-MS based approach and knowledgeable personnel. This review covers general novel modalities classifications, sample preparation techniques, current status and bio-analytical strategies for analyzing various novel modalities, including gene bio-therapeutics, oligonucleotides, antibody-drug conjugates, monoclonal antibodies and PROTACs. It also covers how these strategies have been used in the past and how they are being used now to address challenges in the development of LC-MS based methods, as well as improvement strategies, current advancements and recent developed methods. We additionally covered on the benefits and drawbacks of different LC-MS based techniques for the examination of bio-pharmaceutical products and the future perspectives.
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Affiliation(s)
- M Malarvannan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - V Ravichandiran
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - David Paul
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India.
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48
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Peng J, Ni B, Li D, Cheng B, Yang R. Overview of the PRMT6 modulators in cancer treatment: Current progress and emerged opportunity. Eur J Med Chem 2024; 279:116857. [PMID: 39276585 DOI: 10.1016/j.ejmech.2024.116857] [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: 07/31/2024] [Revised: 08/29/2024] [Accepted: 09/04/2024] [Indexed: 09/17/2024]
Abstract
Protein Arginine Methyltransferase 6 (PRMT6) is a Type I PRMT enzyme that plays a role in the epigenetic regulation of gene expression by methylating histone and non-histone proteins. It is also involved in various cellular processes, including alternative splicing, DNA repair, and cell signaling. Furthermore, PRMT6 exerts multiple effects on cellular processes such as growth, migration, invasion, apoptosis, and drug resistance in various cancers, positioning it as a promising target for anti-tumor therapeutics. In this review, we initially provide an overview of the structure and biological functions of PRMT6, along with its association with cancer. Subsequently, we focus on recent progress in the design and development of modulators targeting PRMT6. This includes a comprehensive review of PRMT6 inhibitors (isoform-selective and non-selective), dual-target inhibitors based on PRMT6, PRMT6 covalent inhibitors, and PRMT6-targeting hydrophobic tagging (HyT) degraders, from the perspectives of rational design, pharmacodynamics, pharmacokinetics, and the clinical status of these modulators. Finally, we also provided the challenges and prospective directions for PRMT6 targeting drug discovery in cancer therapy.
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Affiliation(s)
- Jinjin Peng
- Department of Pharmacy, First Affinity Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Bin Ni
- Department of Pharmacy, First Affinity Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Deping Li
- Department of Pharmacy, First Affinity Hospital of Gannan Medical University, Ganzhou 341000, China.
| | - Binbin Cheng
- School of Medicine, Hubei Polytechnic University, Huangshi 435003, China.
| | - Renze Yang
- Department of Pharmacy, First Affinity Hospital of Gannan Medical University, Ganzhou 341000, China.
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49
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Pliatsika D, Blatter C, Riedl R. Targeted protein degradation: current molecular targets, localization, and strategies. Drug Discov Today 2024:104178. [PMID: 39276920 DOI: 10.1016/j.drudis.2024.104178] [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: 05/31/2024] [Revised: 08/23/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
Targeted protein degradation (TPD) has revolutionized drug discovery by selectively eliminating specific proteins within and outside the cellular context. Over the past two decades, TPD has expanded its focus beyond well-established targets, exploring diverse proteins beyond cancer-related ones. This evolution extends the potential of TPD to various diseases. Notably, TPD can target proteins at demanding locations, such as the extracellular matrix (ECM) and cellular membranes, presenting both opportunities and challenges for future research. In this review, we comprehensively examine the exciting opportunities in the burgeoning field of TPD, highlighting different targets, their cellular environment, and innovative strategies for modern drug discovery.
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Affiliation(s)
- Dimanthi Pliatsika
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Cindy Blatter
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland.
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Winter GE. Extrapolating Lessons from Targeted Protein Degradation to Other Proximity-Inducing Drugs. ACS Chem Biol 2024. [PMID: 39264973 DOI: 10.1021/acschembio.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Targeted protein degradation (TPD) is an emerging pharmacologic strategy. It relies on small-molecule "degraders" that induce proximity of a component of an E3 ubiquitin ligase complex and a target protein to induce target ubiquitination and subsequent proteasomal degradation. Essentially, degraders thus expand the function of E3 ligases, allowing them to degrade proteins they would not recognize in the absence of the small molecule. Over the past decade, insights gained from identifying, designing, and characterizing various degraders have significantly enhanced our understanding of TPD mechanisms, precipitating in rational degrader discovery strategies. In this Account, I aim to explore how these insights can be extrapolated to anticipate both opportunities and challenges of utilizing the overarching concept of proximity-inducing pharmacology to manipulate other cellular circuits for the dissection of biological mechanisms and for therapeutic purposes.
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Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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